[gentoo-commits] repo/gentoo:master commit in: sci-mathematics/rstudio/, sci-mathematics/rstudio/files/

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* [gentoo-commits] repo/gentoo:master commit in: sci-mathematics/rstudio/, sci-mathematics/rstudio/files/
@ 2016-02-20  7:48 Mark Wright
  0 siblings, 0 replies; 12+ messages in thread
From: Mark Wright @ 2016-02-20  7:48 UTC (permalink / raw
  To: gentoo-commits

commit:     6fc8257f0c1be1c4ebd2f7db5486d43ab0749006
Author:     Mark Wright <gienah <AT> gentoo <DOT> org>
AuthorDate: Sat Feb 20 07:46:56 2016 +0000
Commit:     Mark Wright <gienah <AT> gentoo <DOT> org>
CommitDate: Sat Feb 20 07:47:53 2016 +0000
URL:        https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=6fc8257f

sci-mathematics/rstudio: Bump to 0.99.879

Package-Manager: portage-2.2.27

 sci-mathematics/rstudio/Manifest                   |   1 +
 .../files/rstudio-0.99.879-clang-pandoc.patch      |  77 +++++++
 .../rstudio/files/rstudio-0.99.879-paths.patch     | 130 +++++++++++
 .../rstudio/files/rstudio-0.99.879-prefs.patch     |  45 ++++
 sci-mathematics/rstudio/rstudio-0.99.879.ebuild    | 250 +++++++++++++++++++++
 5 files changed, 503 insertions(+)

diff --git a/sci-mathematics/rstudio/Manifest b/sci-mathematics/rstudio/Manifest
index cc582ca..d84f721 100644
--- a/sci-mathematics/rstudio/Manifest
+++ b/sci-mathematics/rstudio/Manifest
@@ -23,6 +23,7 @@ DIST rstudio-0.99.483.tar.gz 16993049 SHA256 85ce1a2f40690e4ed0338b153a1b3279ce9
 DIST rstudio-0.99.484.tar.gz 16993033 SHA256 8ca4abccb9b554713077cf1057ac13abadfd7606f22ac3386b2a88a38ae8a427 SHA512 407f50747bca749ef2c512e727cbe062abdd99c1eb76af09761e6bdfb4208f30117e1ee55b485447f64f6cf249bc939ef1fb4f8ce0199595e241a3cc617b4b8b WHIRLPOOL 8cc16553ea2703f005908c69803b64da4172092cb0b3ff9015e7ec354340fcd1cfa82a218ac890adffafe3565ead94bee6f7bd239b1c56ee38cbeb5896f556b0
 DIST rstudio-0.99.486.tar.gz 16992775 SHA256 4057195465e5032625bad0304bfbd9d123a78c3e4d6d5d41abcc6ef6ccd18a6f SHA512 bb88d12f8ae2f79779532371d03a698a2c2897c212c42c8438d5223c14e1033098dbd7c278a929958fa4bbc764a3ceb101abe03634f0e33192de44cf97128a1f WHIRLPOOL 13c35a69e525d90c6694d068526a2aede76a086427539294e46db67d0fc92759fb9cb0a1169cf88745ae1e121fdd7ba2e46bd2d2fb3fa17dc7fcc65848820941
 DIST rstudio-0.99.491.tar.gz 16992702 SHA256 e8c21e2262b610a7ccf39283b97d114bee33c6840a060067b8019404ff44b03f SHA512 2658694d6154f4b91b2dc07a7ec653edb7f593c4d9829a06a5e600e4db465ca6059418be6812d5ba2529fd6202dd136f0f58d74576f856fdcf6f81032d74f3c2 WHIRLPOOL e71650a07cc010ab3c25955c7fa9e90eee68577c1ef78e02a5f81a0160c688908ec5ec4fd89c89e5a9bc49b926623cd5de976fb249aa2d472354d23f5fad76de
+DIST rstudio-0.99.879.tar.gz 17406999 SHA256 73fa59be34eb63d9ed194642a93ad529d2c67cdcbcd2f291952fdef8e999a097 SHA512 c2bbe598a4a9c2abc69e39807af70be5729a06bbcb73bac5249f74f3c3daddb2909bf4a46d988f0d4bfeabe308f0c31d2a75aa28a52f11c1343dfcead07e2c45 WHIRLPOOL 5c9c75a7891ac53eb80a36eff518d77a0c281b16bff383526ac1ede07ee57486d7b00be4e400a0cad48dfea92729becf25c67f18782af7930f9b4218592afe5c
 DIST selenium-java-2.37.0.zip 24625928 SHA256 0eebba65d8edb01c1f46e462907c58f5d6e1cb0ddf63660a9985c8432bdffbb7 SHA512 68624e82dbc751a25c50fad72702a98eb30d77fd4337d2a969f8e06bcc49e5f8c835cd27ec53772f3375014ddde1d5636936e966b75f3594a9f86aa18ba4e779 WHIRLPOOL eb6659aae26f3c78b6f998546b23d0636c9d00ed8a7f985db1463ac4bd483ccb3e643d84e2ca0f59e0636a8de79eb552ff1d68eb6f9c06907029f7552d8f7777
 DIST selenium-server-standalone-2.37.0.jar 34730734 SHA256 97bc8c699037fb6e99ba7af570fb60dbb1b7ce30cde2448287a44ef65b13023e SHA512 b215446d42d2d1f69664349b6ae6dc53a532d3624c91254f0f4183d0ad764648792e5cc1126a55a1e60d9687d55200fed01d6d2f46cc3d853b1fa6ee38111018 WHIRLPOOL 20640591534f31f24825a9ed139589b182e8b60d86541bf0be104d3cc0280983f6566bd0459f2253ac3875b48a2798b205bac8f815a119fff6db625ce9bbc29e
 DIST shinyapps-0.98.1000.tar.gz 910095 SHA256 b95c512ae0a0fb4335878d9cfcf9073e2cb3ccfed73543abe27ea8878ed36d57 SHA512 3162317c4c20cfc1497e952a8235867084d629ae88407e6c465b3e208adb1dc97abfe6b9922e0374ddf4c8e38a76e112942bd312c54a66f74e6f2a3fe4c0a07c WHIRLPOOL ecc2bce78387cb42e9989163d8fca29220e66f085acde3323417058aebb624dafa8c0e1873c7d79e67324cbd5aad250ef9fcdbbc8f659d64482233b95d898a15

diff --git a/sci-mathematics/rstudio/files/rstudio-0.99.879-clang-pandoc.patch b/sci-mathematics/rstudio/files/rstudio-0.99.879-clang-pandoc.patch
new file mode 100644
index 0000000..c3af2b7
--- /dev/null
+++ b/sci-mathematics/rstudio/files/rstudio-0.99.879-clang-pandoc.patch
@@ -0,0 +1,77 @@
+--- rstudio-0.99.879-orig/src/cpp/session/CMakeLists.txt	2016-02-12 09:24:39.000000000 +1100
++++ rstudio-0.99.879/src/cpp/session/CMakeLists.txt	2016-02-19 23:04:57.266186448 +1100
+@@ -25,30 +25,11 @@
+ if(NOT EXISTS "${RSTUDIO_DEPENDENCIES_DIR}/common/mathjax-23")
+   message(FATAL_ERROR "Mathjax 2.3 not found (re-run install-dependencies script to install)")
+ endif()
+-if(NOT EXISTS "${RSTUDIO_DEPENDENCIES_DIR}/common/pandoc")
+-  message(FATAL_ERROR "pandoc not found (re-run install-dependencies script to install)")
+-endif()
+ if(NOT EXISTS "${RSTUDIO_DEPENDENCIES_DIR}/common/rsconnect")
+   message(FATAL_ERROR "rsconnect package not found (re-run install-dependencies script to install)")
+ endif()
+ 
+ 
+-# verify libclang is installed
+-if(WIN32)
+-   set(LIBCLANG_VERSION "3.4")
+-else()
+-   set(LIBCLANG_VERSION "3.5")
+-endif()
+-set(LIBCLANG_DIR "${RSTUDIO_DEPENDENCIES_DIR}/common/libclang/${LIBCLANG_VERSION}")
+-if(NOT EXISTS "${LIBCLANG_DIR}")
+-  message(FATAL_ERROR "libclang ${LIBCLANG_VERSION} not found  (re-run install-dependencies script to install)")
+-endif()
+-set(LIBCLANG_HEADERS_DIR "${RSTUDIO_DEPENDENCIES_DIR}/common/libclang/builtin-headers")
+-if(NOT EXISTS "${LIBCLANG_HEADERS_DIR}")
+-  message(FATAL_ERROR "libclang builtin-headers not found  (re-run install-dependencies script to install)")
+-endif()
+-
+-
+ # include files
+ file(GLOB_RECURSE SESSION_HEADER_FILES "*.h*")
+ 
+@@ -399,18 +380,6 @@
+    install(DIRECTORY "${RSTUDIO_DEPENDENCIES_DIR}/common/mathjax-23"
+            DESTINATION "${RSTUDIO_INSTALL_SUPPORTING}/resources")
+ 
+-   # install pandoc
+-   if(RSTUDIO_PACKAGE_BUILD_SLES)
+-      # when producing a SUSE Linux Enterpise build, we want to install the 
+-      # static Pandoc binaries (see dependencies/common/install-pandoc)
+-      set(PANDOC_EXTENSION_DIR "/static")
+-   endif()
+-   set(PANDOC_BIN "${RSTUDIO_DEPENDENCIES_DIR}/common/pandoc/1.15.2${PANDOC_EXTENSION_DIR}")
+-   file(GLOB PANDOC_FILES "${PANDOC_BIN}/pandoc*")
+-   install(FILES ${PANDOC_FILES}
+-           PERMISSIONS OWNER_READ OWNER_WRITE OWNER_EXECUTE GROUP_READ GROUP_EXECUTE WORLD_READ WORLD_EXECUTE
+-           DESTINATION  ${RSTUDIO_INSTALL_BIN}/pandoc)
+-
+    # install rsconnect package
+    file(GLOB RSCONNECT_PACKAGE "${RSTUDIO_DEPENDENCIES_DIR}/common/rsconnect*.tar.gz")
+    install(FILES ${RSCONNECT_PACKAGE}
+@@ -428,24 +397,6 @@
+    install(DIRECTORY "resources/help_resources"
+            DESTINATION ${RSTUDIO_INSTALL_SUPPORTING}/resources)
+ 
+-   # install libclang
+-   if(WIN32)
+-      file(GLOB LIBCLANG_32_FILES "${LIBCLANG_DIR}/x86/libclang.*")
+-      install(PROGRAMS ${LIBCLANG_32_FILES}
+-              DESTINATION  ${RSTUDIO_INSTALL_BIN}/rsclang/x86)
+-      file(GLOB LIBCLANG_64_FILES "${LIBCLANG_DIR}/x86_64/libclang.*")
+-      install(PROGRAMS ${LIBCLANG_64_FILES}
+-              DESTINATION  ${RSTUDIO_INSTALL_BIN}/rsclang/x86_64)
+-   else()
+-      file(GLOB_RECURSE LIBCLANG_FILES "${LIBCLANG_DIR}/libclang.*")
+-      install(PROGRAMS ${LIBCLANG_FILES}
+-              DESTINATION  ${RSTUDIO_INSTALL_BIN}/rsclang)
+-   endif()
+-
+-   # install libclang builtin-headers
+-   install(DIRECTORY "${RSTUDIO_DEPENDENCIES_DIR}/common/libclang/builtin-headers"
+-           DESTINATION "${RSTUDIO_INSTALL_SUPPORTING}/resources/libclang")
+-
+    # install 64 bit binaries if we are on win64
+    if(WIN32)
+       if(NOT ("$ENV{PROGRAMW6432}" STREQUAL ""))

diff --git a/sci-mathematics/rstudio/files/rstudio-0.99.879-paths.patch b/sci-mathematics/rstudio/files/rstudio-0.99.879-paths.patch
new file mode 100644
index 0000000..a8b48f2
--- /dev/null
+++ b/sci-mathematics/rstudio/files/rstudio-0.99.879-paths.patch
@@ -0,0 +1,130 @@
+--- rstudio-0.99.879-orig/CMakeGlobals.txt	2016-02-12 09:24:39.000000000 +1100
++++ rstudio-0.99.879/CMakeGlobals.txt	2016-02-19 22:58:41.396818474 +1100
+@@ -120,7 +120,7 @@
+    else()
+      set(RSTUDIO_INSTALL_BIN bin)
+    endif()
+-   set(RSTUDIO_INSTALL_SUPPORTING .)
++   set(RSTUDIO_INSTALL_SUPPORTING ${DISTRO_SHARE})
+ endif()
+ 
+ # if the install prefix is /usr/local then tweak as appropriate
+--- rstudio-0.99.879-orig/src/cpp/server/CMakeLists.txt	2016-02-12 09:24:39.000000000 +1100
++++ rstudio-0.99.879/src/cpp/server/CMakeLists.txt	2016-02-19 22:58:41.397818478 +1100
+@@ -155,7 +155,7 @@
+    configure_file(${CMAKE_CURRENT_SOURCE_DIR}/${RSERVER_INITD_DEBIAN_SCRIPT}.in
+                   ${CMAKE_CURRENT_BINARY_DIR}/${RSERVER_INITD_DEBIAN_SCRIPT})
+    install(PROGRAMS ${CMAKE_CURRENT_BINARY_DIR}/${RSERVER_INITD_DEBIAN_SCRIPT}
+-           DESTINATION ${RSERVER_INITD_DEBIAN_DIR})
++           DESTINATION ${DISTRO_SHARE}/${RSERVER_INITD_DEBIAN_DIR})
+ 
+    # install configured redhat init.d script
+    set(RSERVER_INITD_REDHAT_DIR "extras/init.d/redhat")
+@@ -163,7 +163,7 @@
+    configure_file(${CMAKE_CURRENT_SOURCE_DIR}/${RSERVER_INITD_REDHAT_SCRIPT}.in
+                   ${CMAKE_CURRENT_BINARY_DIR}/${RSERVER_INITD_REDHAT_SCRIPT})
+    install(PROGRAMS ${CMAKE_CURRENT_BINARY_DIR}/${RSERVER_INITD_REDHAT_SCRIPT}
+-           DESTINATION ${RSERVER_INITD_REDHAT_DIR})
++           DESTINATION ${DISTRO_SHARE}/${RSERVER_INITD_REDHAT_DIR})
+ 
+    # install configured suse init.d script
+    set(RSERVER_INITD_SUSE_DIR "extras/init.d/suse")
+@@ -171,13 +171,13 @@
+    configure_file(${CMAKE_CURRENT_SOURCE_DIR}/${RSERVER_INITD_SUSE_SCRIPT}.in
+                   ${CMAKE_CURRENT_BINARY_DIR}/${RSERVER_INITD_SUSE_SCRIPT})
+    install(PROGRAMS ${CMAKE_CURRENT_BINARY_DIR}/${RSERVER_INITD_SUSE_SCRIPT}
+-           DESTINATION ${RSERVER_INITD_SUSE_DIR})
++           DESTINATION ${DISTRO_SHARE}/${RSERVER_INITD_SUSE_DIR})
+ 
+    # install pam profile
+    set(RSERVER_PAM_DIR "extras/pam")
+    set(RSERVER_PAM_PROFILE "${RSERVER_PAM_DIR}/rstudio")
+    install(FILES ${CMAKE_CURRENT_SOURCE_DIR}/${RSERVER_PAM_PROFILE}
+-           DESTINATION ${RSERVER_PAM_DIR})
++           DESTINATION ${DISTRO_SHARE}/${RSERVER_PAM_DIR})
+ 
+    # install configured apparmor profile
+    set(RSERVER_APPARMOR_DIR "extras/apparmor")
+@@ -185,9 +185,9 @@
+    configure_file(${CMAKE_CURRENT_SOURCE_DIR}/${RSERVER_APPARMOR_PROFILE}.in
+                   ${CMAKE_CURRENT_BINARY_DIR}/${RSERVER_APPARMOR_PROFILE})
+    install(FILES ${CMAKE_CURRENT_BINARY_DIR}/${RSERVER_APPARMOR_PROFILE}
+-           DESTINATION ${RSERVER_APPARMOR_DIR})
++           DESTINATION ${DISTRO_SHARE}/${RSERVER_APPARMOR_DIR})
+    install(PROGRAMS ${CMAKE_CURRENT_SOURCE_DIR}/${RSERVER_APPARMOR_DIR}/apparmor-profile-load
+-           DESTINATION ${RSERVER_APPARMOR_DIR})
++           DESTINATION ${DISTRO_SHARE}/${RSERVER_APPARMOR_DIR})
+ 
+    # install configured upstart profile
+    set(RSERVER_UPSTART_DIR "extras/upstart")
+@@ -195,12 +195,12 @@
+    configure_file(${CMAKE_CURRENT_SOURCE_DIR}/${RSERVER_UPSTART_PROFILE}.in
+                   ${CMAKE_CURRENT_BINARY_DIR}/${RSERVER_UPSTART_PROFILE})
+    install(FILES ${CMAKE_CURRENT_BINARY_DIR}/${RSERVER_UPSTART_PROFILE}
+-           DESTINATION ${RSERVER_UPSTART_DIR})
++           DESTINATION ${DISTRO_SHARE}/${RSERVER_UPSTART_DIR})
+    set(RSERVER_UPSTART_PROFILE_REDHAT "${RSERVER_UPSTART_DIR}/rstudio-server.redhat.conf")
+    configure_file(${CMAKE_CURRENT_SOURCE_DIR}/${RSERVER_UPSTART_PROFILE_REDHAT}.in
+                   ${CMAKE_CURRENT_BINARY_DIR}/${RSERVER_UPSTART_PROFILE_REDHAT})
+    install(FILES ${CMAKE_CURRENT_BINARY_DIR}/${RSERVER_UPSTART_PROFILE_REDHAT}
+-           DESTINATION ${RSERVER_UPSTART_DIR})
++           DESTINATION ${DISTRO_SHARE}/${RSERVER_UPSTART_DIR})
+            
+     # install configured systemd profile
+    set(RSERVER_SYSTEMD_DIR "extras/systemd")
+--- rstudio-0.99.879-orig/src/cpp/server/ServerOptions.cpp	2016-02-12 09:24:39.000000000 +1100
++++ rstudio-0.99.879/src/cpp/server/ServerOptions.cpp	2016-02-19 22:58:41.397818478 +1100
+@@ -382,8 +382,8 @@
+ 
+    // convert relative paths by completing from the system installation
+    // path (this allows us to be relocatable)
+-   resolvePath(resourcePath, &wwwLocalPath_);
+-   resolvePath(resourcePath, &wwwSymbolMapsPath_);
++   resolvePath(resourcePath.childPath(DISTRO_SHARE), &wwwLocalPath_);
++   resolvePath(resourcePath.childPath(DISTRO_SHARE), &wwwSymbolMapsPath_);
+    resolvePath(binaryPath, &authPamHelperPath_);
+    resolvePath(binaryPath, &rsessionPath_);
+    resolvePath(binaryPath, &rldpathPath_);
+--- rstudio-0.99.879-orig/src/cpp/session/SessionOptions.cpp	2016-02-12 09:24:39.000000000 +1100
++++ rstudio-0.99.879/src/cpp/session/SessionOptions.cpp	2016-02-20 18:13:34.807771539 +1100
+@@ -49,7 +49,7 @@
+ namespace session {  
+ 
+ namespace {
+-const char* const kDefaultPandocPath = "bin/pandoc";
++const char* const kDefaultPandocPath = "bin";
+ const char* const kDefaultPostbackPath = "bin/postback/rpostback";
+ const char* const kDefaultRsclangPath = "bin/rsclang";
+ } // anonymous namespace
+@@ -451,14 +451,14 @@
+    }
+    
+    // convert relative paths by completing from the app resource path
+-   resolvePath(resourcePath_, &rResourcesPath_);
+-   resolvePath(resourcePath_, &agreementFilePath_);
+-   resolvePath(resourcePath_, &wwwLocalPath_);
+-   resolvePath(resourcePath_, &wwwSymbolMapsPath_);
+-   resolvePath(resourcePath_, &coreRSourcePath_);
+-   resolvePath(resourcePath_, &modulesRSourcePath_);
+-   resolvePath(resourcePath_, &sessionLibraryPath_);
+-   resolvePath(resourcePath_, &sessionPackageArchivesPath_);
++   resolvePath(resourcePath_.childPath(DISTRO_SHARE), &rResourcesPath_);
++   resolvePath(resourcePath_.childPath(DISTRO_SHARE), &agreementFilePath_);
++   resolvePath(resourcePath_.childPath(DISTRO_SHARE), &wwwLocalPath_);
++   resolvePath(resourcePath_.childPath(DISTRO_SHARE), &wwwSymbolMapsPath_);
++   resolvePath(resourcePath_.childPath(DISTRO_SHARE), &coreRSourcePath_);
++   resolvePath(resourcePath_.childPath(DISTRO_SHARE), &modulesRSourcePath_);
++   resolvePath(resourcePath_.childPath(DISTRO_SHARE), &sessionLibraryPath_);
++   resolvePath(resourcePath_.childPath(DISTRO_SHARE), &sessionPackageArchivesPath_);
+    resolvePostbackPath(resourcePath_, &rpostbackPath_);
+ #ifdef _WIN32
+    resolvePath(resourcePath_, &consoleIoPath_);
+@@ -467,7 +467,7 @@
+    resolvePath(resourcePath_, &msysSshPath_);
+    resolvePath(resourcePath_, &sumatraPath_);
+ #endif
+-   resolvePath(resourcePath_, &hunspellDictionariesPath_);
++   resolvePath(resourcePath_.childPath(DISTRO_SHARE), &hunspellDictionariesPath_);
+    resolvePath(resourcePath_, &mathjaxPath_);
+    resolvePath(resourcePath_, &libclangHeadersPath_);
+    resolvePandocPath(resourcePath_, &pandocPath_);

diff --git a/sci-mathematics/rstudio/files/rstudio-0.99.879-prefs.patch b/sci-mathematics/rstudio/files/rstudio-0.99.879-prefs.patch
new file mode 100644
index 0000000..483613c
--- /dev/null
+++ b/sci-mathematics/rstudio/files/rstudio-0.99.879-prefs.patch
@@ -0,0 +1,45 @@
+--- rstudio-0.99.879-orig/src/gwt/build.xml	2016-02-12 09:24:39.000000000 +1100
++++ rstudio-0.99.879/src/gwt/build.xml	2016-02-20 00:25:39.458756693 +1100
+@@ -25,6 +25,7 @@
+    <property name="gwt.extra.args" value=""/>
+    <property name="gwt.main.module" value="org.rstudio.studio.RStudio"/>
+    <property name="ace.bin" value="src/org/rstudio/studio/client/workbench/views/source/editors/text/ace"/>
++   <property environment="env"/>
+ 
+    <path id="project.class.path">
+       <pathelement location="bin"/>
+@@ -101,8 +102,10 @@
+             <pathelement location="src"/>
+             <path refid="project.class.path"/>
+          </classpath>
++         <jvmarg value="-Duser.home=${env.T}"/>
+          <!-- add jvmarg -Xss16M or similar if you see a StackOverflowError -->
+          <jvmarg value="-Xmx1536M"/>
++         <jvmarg value="-Djava.util.prefs.userRoot=${env.T}"/>
+          <arg value="-war"/>
+          <arg value="www"/>
+          <arg value="-localWorkers"/>
+@@ -142,6 +145,7 @@
+             <pathelement location="src"/>
+             <path refid="project.class.path"/>
+          </classpath>
++         <jvmarg value="-Duser.home=${env.T}"/>
+          <jvmarg value="-Xmx2048M"/>
+          <arg value="-war"/>
+          <arg value="www"/>
+@@ -163,6 +167,7 @@
+             <pathelement location="src"/>
+             <path refid="project.class.path"/>
+          </classpath>
++         <jvmarg value="-Duser.home=${env.T}"/>
+          <jvmarg value="-Xmx2048M"/>
+       	<arg value="-src"/>
+       	<arg value = "src"/>
+@@ -194,6 +199,7 @@
+                   <pathelement location="src"/>
+                   <path refid="test.class.path"/>
+                </classpath>
++               <jvmarg value="-Duser.home=${env.T}"/>
+                <arg value="org.rstudio.studio.selenium.RStudioTestSuite"/>
+             </java>
+          </sequential>

diff --git a/sci-mathematics/rstudio/rstudio-0.99.879.ebuild b/sci-mathematics/rstudio/rstudio-0.99.879.ebuild
new file mode 100644
index 0000000..35a886b
--- /dev/null
+++ b/sci-mathematics/rstudio/rstudio-0.99.879.ebuild
@@ -0,0 +1,250 @@
+# Copyright 1999-2016 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=5
+
+inherit eutils user cmake-utils gnome2-utils pam versionator fdo-mime java-pkg-2 pax-utils
+
+# TODO
+# * package gin and gwt
+# * use dict from tree, linguas
+# * do src_test (use junit from tree?)
+
+# update from scripts in dependencies/common
+# egrep '(GWT_SDK_VER=|GIN_VER=|SELENIUM_VER=|CHROMEDRIVER_VER=)' dependencies/common/install-gwt
+GWT_VER=2.7.0
+GIN_VER=1.5
+SELENIUM_VER=2.37.0
+CHROMEDRIVER_VER=2.7
+# grep 'PANDOC_VERSION=' dependencies/common/update-pandoc
+PANDOC_VER=1.13.1
+# ls dependencies/common/*.tar.gz
+PACKRAT_VER=0.98.1000
+RMARKDOWN_VER=0.98.1000
+SHINYAPPS_VER=0.98.1000
+RSCONNECT_VER=0.4.1.4_fcac892a69817febd7b655b189bf57193260cda0
+
+DESCRIPTION="IDE for the R language"
+HOMEPAGE="
+	http://www.rstudio.org
+	https://github.com/rstudio/rstudio/"
+SRC_URI="
+	https://github.com/rstudio/rstudio/archive/v${PV}.tar.gz -> ${P}.tar.gz
+	https://s3.amazonaws.com/rstudio-buildtools/gin-${GIN_VER}.zip
+	https://s3.amazonaws.com/rstudio-buildtools/gwt-${GWT_VER}.zip
+	https://s3.amazonaws.com/rstudio-buildtools/selenium-java-${SELENIUM_VER}.zip
+	https://s3.amazonaws.com/rstudio-buildtools/selenium-server-standalone-${SELENIUM_VER}.jar
+	https://s3.amazonaws.com/rstudio-buildtools/chromedriver-linux
+	https://s3.amazonaws.com/rstudio-dictionaries/core-dictionaries.zip
+	https://dev.gentoo.org/~gienah/distfiles/packrat-${PACKRAT_VER}.tar.gz
+	https://dev.gentoo.org/~gienah/distfiles/rmarkdown-${RMARKDOWN_VER}.tar.gz
+	https://dev.gentoo.org/~gienah/distfiles/shinyapps-${SHINYAPPS_VER}.tar.gz
+	https://dev.gentoo.org/~gienah/distfiles/rsconnect_${RSCONNECT_VER}.tar.gz
+"
+
+LICENSE="AGPL-3"
+SLOT="0"
+KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
+IUSE="dedicated server"
+
+QT_VER=5.4
+QT_SLOT=5
+RDEPEND="
+	app-text/pandoc
+	dev-haskell/pandoc-citeproc
+	>=dev-lang/R-2.11.1
+	>=dev-libs/boost-1.50:=
+	>=dev-libs/mathjax-2.3
+	dev-libs/openssl:0
+	sys-apps/util-linux
+	>=sys-devel/clang-3.5.0
+	sys-libs/zlib
+	|| ( =virtual/jre-1.7*:= =virtual/jre-1.8*:= )
+	x11-libs/pango
+	!dedicated? (
+		>=dev-qt/qtcore-${QT_VER}:${QT_SLOT}
+		>=dev-qt/qtdeclarative-${QT_VER}:${QT_SLOT}
+		>=dev-qt/qtdbus-${QT_VER}:${QT_SLOT}
+		>=dev-qt/qtgui-${QT_VER}:${QT_SLOT}
+		>=dev-qt/qtnetwork-${QT_VER}:${QT_SLOT}
+		>=dev-qt/qtopengl-${QT_VER}:${QT_SLOT}
+		>=dev-qt/qtpositioning-${QT_VER}:${QT_SLOT}
+		>=dev-qt/qtprintsupport-${QT_VER}:${QT_SLOT}
+		>=dev-qt/qtsingleapplication-2.6.1_p20150629[qt5]
+		>=dev-qt/qtsensors-${QT_VER}:${QT_SLOT}
+		>=dev-qt/qtsql-${QT_VER}:${QT_SLOT}
+		>=dev-qt/qtsvg-${QT_VER}:${QT_SLOT}
+		>=dev-qt/qtwebkit-${QT_VER}:${QT_SLOT}
+		>=dev-qt/qtwidgets-${QT_VER}:${QT_SLOT}
+		>=dev-qt/qtxml-${QT_VER}:${QT_SLOT}
+		>=dev-qt/qtxmlpatterns-${QT_VER}:${QT_SLOT}
+		server? ( virtual/pam )
+	)
+	dedicated? ( virtual/pam )"
+DEPEND="${RDEPEND}
+	app-arch/unzip
+	dev-java/ant-core
+	|| ( =virtual/jdk-1.7*:= =virtual/jdk-1.8*:= )
+	virtual/pkgconfig"
+#	test? ( dev-java/junit:4 )
+
+PATCHES=(
+		"${FILESDIR}/${PN}-0.99.879-prefs.patch"
+		"${FILESDIR}/${PN}-0.99.879-paths.patch"
+		"${FILESDIR}/${PN}-0.99.879-clang-pandoc.patch"
+		"${FILESDIR}/${PN}-0.98.490-linker_flags.patch"
+		"${FILESDIR}/${PN}-0.98.1091-boost-1.57.patch"
+		"${FILESDIR}/${PN}-0.99.473-qtsingleapplication.patch"
+		"${FILESDIR}/${PN}-0.99.486-systemd.patch"
+)
+
+src_unpack() {
+	unpack ${P}.tar.gz gwt-${GWT_VER}.zip
+	cd "${S}" || die
+	mkdir -p src/gwt/lib/{gin,gwt} \
+		dependencies/common/dictionaries \
+		src/gwt/lib/selenium/${SELENIUM_VER} \
+		src/gwt/lib/selenium/chromedriver/${CHROMEDRIVER_VER} || die
+	mv ../gwt-${GWT_VER} src/gwt/lib/gwt/${GWT_VER} || die
+	unzip -qd src/gwt/lib/gin/${GIN_VER} \
+		"${DISTDIR}"/gin-${GIN_VER}.zip || die
+	unzip -qd dependencies/common/dictionaries \
+		"${DISTDIR}"/core-dictionaries.zip || die
+	unzip -qd src/gwt/lib/selenium/${SELENIUM_VER} \
+		"${DISTDIR}"/selenium-java-${SELENIUM_VER}.zip || die
+	cp "${DISTDIR}"/selenium-server-standalone-${SELENIUM_VER}.jar \
+		src/gwt/lib/selenium/${SELENIUM_VER}/ || die
+	cp "${DISTDIR}"/chromedriver-linux \
+		src/gwt/lib/selenium/chromedriver/${CHROMEDRIVER_VER}/ || die
+	cd dependencies/common || die
+	unpack packrat-${PACKRAT_VER}.tar.gz
+	unpack rmarkdown-${RMARKDOWN_VER}.tar.gz
+	unpack shinyapps-${SHINYAPPS_VER}.tar.gz
+	unpack rsconnect_${RSCONNECT_VER}.tar.gz
+	cp "${DISTDIR}"/rmarkdown-${RMARKDOWN_VER}.tar.gz \
+		. || die
+	cp "${DISTDIR}"/packrat-${PACKRAT_VER}.tar.gz \
+		. || die
+	cp "${DISTDIR}"/shinyapps-${SHINYAPPS_VER}.tar.gz \
+		. || die
+	cp "${DISTDIR}"/rsconnect_${RSCONNECT_VER}.tar.gz \
+		. || die
+}
+
+src_prepare() {
+	java-pkg-2_src_prepare
+
+	egit_clean
+
+	epatch "${PATCHES[@]}"
+
+	# Enable CMake to install our .service file for systemd usage
+	mkdir -vp "${S}/src/cpp/server/lib/systemd/system" || die
+	cp -v "${FILESDIR}/rstudio-server.service.in" "${S}/src/cpp/server/lib/systemd/system/" || die
+
+	# Adding -DDISTRO_SHARE=... to append-flags breaks cmake so using
+	# this sed hack for now. ~RMH
+	sed -i \
+		-e "s|DISTRO_SHARE|\"share/${PN}\"|g" \
+		src/cpp/server/ServerOptions.cpp \
+		src/cpp/session/SessionOptions.cpp || die
+
+	# use mathjax from system
+	ln -sf "${EPREFIX}"/usr/share/mathjax dependencies/common/mathjax-23 || die
+
+	# make sure icons and mime stuff are with prefix
+	sed -i \
+		-e "s:/usr:${EPREFIX}/usr:g" \
+		CMakeGlobals.txt src/cpp/desktop/CMakeLists.txt || die
+
+	# On Gentoo the rstudio-server configuration file is /etc/conf.d/rstudio-server.conf
+	sed -e "s@/etc/rstudio/rserver.conf@${EROOT}etc/conf.d/rstudio-server.conf@" \
+		-i src/cpp/server/ServerOptions.cpp \
+		|| die
+
+	# Set the rsession.conf file location for Gentoo prefix
+	sed -e "s@/etc/rstudio/rsession.conf@${EROOT}etc/rstudio/rsession.conf@" \
+		-i src/cpp/session/SessionOptions.cpp \
+		|| die
+
+	# dev-qt/qtsingleapplication-2.6.1_p20150629 does not provide a cmake module.
+	# It provides a library that has its version number appended to the end,
+	# which is difficult to handle in cmake, as find_library does not support
+	# searching for wildcard library names. So I find the library name from the
+	# qmake spec, and then sed this into the patched src/cpp/desktop/CMakeLists.txt.
+	rm -rf "${S}"/src/cpp/desktop/3rdparty || die
+	local s=$(grep '\-lQt$${QT_MAJOR_VERSION}Solutions_SingleApplication' \
+				   "${EROOT}"/usr/lib64/qt5/mkspecs/features/qtsingleapplication.prf \
+					 | sed -e 's@\$\${QT_MAJOR_VERSION}@5@' \
+						   -e 's@LIBS \*= -l@@')
+	sed -e "s@Qt5Solutions_SingleApplication-2.6@${s}@g" \
+		-i "${S}"/src/cpp/desktop/CMakeLists.txt \
+		|| die
+
+	# The git commit for tag v0.99.879
+	sed -e 's@git ARGS rev-parse HEAD@echo ARGS 9ac918338d6f9d6dd25807d6d746b470f1cfcf6d@'\
+		-i "${S}"/CMakeLists.txt \
+		"${S}"/CMakeGlobals.txt \
+		|| die
+}
+
+src_configure() {
+	export RSTUDIO_VERSION_MAJOR=$(get_version_component_range 1)
+	export RSTUDIO_VERSION_MINOR=$(get_version_component_range 2)
+	export RSTUDIO_VERSION_PATCH=$(get_version_component_range 3)
+
+	local mycmakeargs=(
+		-DDISTRO_SHARE=share/${PN}
+		$(cmake-utils_use !dedicated RSTUDIO_INSTALL_FREEDESKTOP)
+		-DRSTUDIO_TARGET=$(usex dedicated "Server" "$(usex server "Development" "Desktop")")
+		-DQT_QMAKE_EXECUTABLE="${EROOT}"usr/lib64/qt5/bin/qmake
+		-DRSTUDIO_VERIFY_R_VERSION=FALSE
+		)
+
+	cmake-utils_src_configure
+}
+
+src_compile() {
+	# Avoid the rest of the oracle-jdk-bin-1.8.0.60 sandbox violations F: mkdir S: deny
+	# P: /root/.oracle_jre_usage.
+	export ANT_OPTS="-Duser.home=${T}"
+	cmake-utils_src_compile
+}
+
+src_install() {
+	export ANT_OPTS="-Duser.home=${T}"
+	cmake-utils_src_install
+	pax-mark m "${ED}usr/bin/rstudio"
+	doconfd "${FILESDIR}"/rstudio-server.conf
+	dodir /etc/rstudio
+	insinto /etc/rstudio
+	doins "${FILESDIR}"/rsession.conf
+	dosym /etc/conf.d/rstudio-server.conf /etc/rstudio/rserver.conf
+	if use dedicated || use server; then
+		dopamd src/cpp/server/extras/pam/rstudio
+		newinitd "${FILESDIR}"/rstudio-server.initd rstudio-server
+	fi
+}
+
+pkg_preinst() {
+	use dedicated || gnome2_icon_savelist
+	java-pkg-2_pkg_preinst
+}
+
+pkg_postinst() {
+	use dedicated || { fdo-mime_desktop_database_update
+		fdo-mime_mime_database_update
+		gnome2_icon_cache_update ;}
+
+	if use dedicated || use server; then
+		enewgroup rstudio-server
+		enewuser rstudio-server -1 -1 -1 rstudio-server
+	fi
+}
+
+pkg_postrm() {
+	use dedicated || { fdo-mime_desktop_database_update
+		fdo-mime_mime_database_update
+		gnome2_icon_cache_update ;}
+}


^ permalink raw reply related	[flat|nested] 12+ messages in thread

* [gentoo-commits] repo/gentoo:master commit in: sci-mathematics/rstudio/, sci-mathematics/rstudio/files/
@ 2016-12-02  1:07 Mark Wright
  0 siblings, 0 replies; 12+ messages in thread
From: Mark Wright @ 2016-12-02  1:07 UTC (permalink / raw
  To: gentoo-commits

commit:     9b2645061cdbc30b2a6bfaab0937083c91655070
Author:     Mark Wright <gienah <AT> gentoo <DOT> org>
AuthorDate: Fri Dec  2 01:06:31 2016 +0000
Commit:     Mark Wright <gienah <AT> gentoo <DOT> org>
CommitDate: Fri Dec  2 01:07:09 2016 +0000
URL:        https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=9b264506

sci-mathematics/rstudio: Bump to 1.0.44, thanks to David Luna for reporting.

Gentoo-Bug: 599282

Package-Manager: portage-2.3.2

 sci-mathematics/rstudio/Manifest                   |   1 +
 .../files/rstudio-1.0.44-clang-pandoc.patch        |  71 ++++++
 .../rstudio/files/rstudio-1.0.44-paths.patch       | 130 +++++++++++
 .../rstudio/files/rstudio-1.0.44-systemd.patch     |  21 ++
 sci-mathematics/rstudio/rstudio-1.0.44.ebuild      | 248 +++++++++++++++++++++
 5 files changed, 471 insertions(+)

diff --git a/sci-mathematics/rstudio/Manifest b/sci-mathematics/rstudio/Manifest
index 8ff2707..26d0c77 100644
--- a/sci-mathematics/rstudio/Manifest
+++ b/sci-mathematics/rstudio/Manifest
@@ -28,6 +28,7 @@ DIST rstudio-0.99.893.tar.gz 17407634 SHA256 90a657b1fa16cfc575ca884789bac47f178
 DIST rstudio-0.99.896.tar.gz 17409121 SHA256 05fc7546ad1d21d7e6219538056ec2ee1b86d09b731a588198ce137d3fe25bae SHA512 c62df2a1c54f8c6d14b1239dd746b88693c11c48ec56aa5ae89023e98901793b0e65df44526cbc8c71036c0f73a512767cae086ed3777540b1ceda05e3398e17 WHIRLPOOL 7f4d0ebc8db509f09ccc15da02a4a426de431312f2dc65126bda76e11de0e106671fc7a83e9ea8e66b88f81268d0db8b44014a70744b30641bb58bedda73427d
 DIST rstudio-0.99.902.tar.gz 17408815 SHA256 703a3ebedbb4bb44d2cacffed2615b4f65156fcd4115029931eb5fd99950c689 SHA512 23db68f05900666287901d75f02006f7edacafab057d82a312b4e5aac639ef4b5db702420632f2768e509411bbfc73c32a533aa0f1b33379c10df82e009b974e WHIRLPOOL e7ef3cf0d9a414257c4c0c68809c674721f9513917bd450c9946133ee69dd735374417483c7dc380ee4d387119558c961d4ea815aac5bcd3fa22ee863556e0a4
 DIST rstudio-0.99.903.tar.gz 17409865 SHA256 8902fe7a6f7f6e0d6e8fae2472e479bb9cbe9cbb2e0747e5f01a093d31993a3c SHA512 9ddcfdab187c907dfa3cbf386ee902b43ba35c242b44a4190c58d1e3bad590ca428209423739768b57f759c4bde61ef2b5958fb3cba366d7740753c3c5dbf739 WHIRLPOOL 82ca64883d02aacc0c1081779f769c3ea2bbac3c370f1e62fba18465547742114df18d431f30c3fe449c0ae2ac212cd7dd98a72bb2e5810eb1fc6cdbb3c82a69
+DIST rstudio-1.0.44.tar.gz 17774065 SHA256 43ece6cfdd1a13ac0e17f2a50154a30a1a14ad6c1b3cf381cc6007988ce44a0f SHA512 a8b975dc517125a257e5f61db5bb137e133b02d738d55553770aa65e388cd112ce646b53b77dc069d1ca95ccd95979f4a57ad60b99fc3b91543cf61e737e8169 WHIRLPOOL 4ad472aed130451e81d8d8e3251d3bbd701a8b8e2fbddf17dc357f39335e33c75505f9443c2c7208e60a19c2767b9328134433e5d4fd22504813020712c658ef
 DIST selenium-java-2.37.0.zip 24625928 SHA256 0eebba65d8edb01c1f46e462907c58f5d6e1cb0ddf63660a9985c8432bdffbb7 SHA512 68624e82dbc751a25c50fad72702a98eb30d77fd4337d2a969f8e06bcc49e5f8c835cd27ec53772f3375014ddde1d5636936e966b75f3594a9f86aa18ba4e779 WHIRLPOOL eb6659aae26f3c78b6f998546b23d0636c9d00ed8a7f985db1463ac4bd483ccb3e643d84e2ca0f59e0636a8de79eb552ff1d68eb6f9c06907029f7552d8f7777
 DIST selenium-server-standalone-2.37.0.jar 34730734 SHA256 97bc8c699037fb6e99ba7af570fb60dbb1b7ce30cde2448287a44ef65b13023e SHA512 b215446d42d2d1f69664349b6ae6dc53a532d3624c91254f0f4183d0ad764648792e5cc1126a55a1e60d9687d55200fed01d6d2f46cc3d853b1fa6ee38111018 WHIRLPOOL 20640591534f31f24825a9ed139589b182e8b60d86541bf0be104d3cc0280983f6566bd0459f2253ac3875b48a2798b205bac8f815a119fff6db625ce9bbc29e
 DIST shinyapps-0.98.1000.tar.gz 910095 SHA256 b95c512ae0a0fb4335878d9cfcf9073e2cb3ccfed73543abe27ea8878ed36d57 SHA512 3162317c4c20cfc1497e952a8235867084d629ae88407e6c465b3e208adb1dc97abfe6b9922e0374ddf4c8e38a76e112942bd312c54a66f74e6f2a3fe4c0a07c WHIRLPOOL ecc2bce78387cb42e9989163d8fca29220e66f085acde3323417058aebb624dafa8c0e1873c7d79e67324cbd5aad250ef9fcdbbc8f659d64482233b95d898a15

diff --git a/sci-mathematics/rstudio/files/rstudio-1.0.44-clang-pandoc.patch b/sci-mathematics/rstudio/files/rstudio-1.0.44-clang-pandoc.patch
new file mode 100644
index 00000000..ed0fc8e
--- /dev/null
+++ b/sci-mathematics/rstudio/files/rstudio-1.0.44-clang-pandoc.patch
@@ -0,0 +1,71 @@
+--- rstudio-1.0.44-orig/src/cpp/session/CMakeLists.txt	2016-10-19 08:32:41.000000000 +1100
++++ rstudio-1.0.44/src/cpp/session/CMakeLists.txt	2016-12-01 23:44:30.130725331 +1100
+@@ -25,24 +25,6 @@
+ if(NOT EXISTS "${RSTUDIO_DEPENDENCIES_DIR}/common/mathjax-26")
+   message(FATAL_ERROR "Mathjax 2.6 not found (re-run install-dependencies script to install)")
+ endif()
+-if(NOT EXISTS "${RSTUDIO_DEPENDENCIES_DIR}/common/pandoc")
+-  message(FATAL_ERROR "pandoc not found (re-run install-dependencies script to install)")
+-endif()
+-
+-# verify libclang is installed
+-if(WIN32)
+-   set(LIBCLANG_VERSION "3.4")
+-else()
+-   set(LIBCLANG_VERSION "3.5")
+-endif()
+-set(LIBCLANG_DIR "${RSTUDIO_DEPENDENCIES_DIR}/common/libclang/${LIBCLANG_VERSION}")
+-if(NOT EXISTS "${LIBCLANG_DIR}")
+-  message(FATAL_ERROR "libclang ${LIBCLANG_VERSION} not found  (re-run install-dependencies script to install)")
+-endif()
+-set(LIBCLANG_HEADERS_DIR "${RSTUDIO_DEPENDENCIES_DIR}/common/libclang/builtin-headers")
+-if(NOT EXISTS "${LIBCLANG_HEADERS_DIR}")
+-  message(FATAL_ERROR "libclang builtin-headers not found  (re-run install-dependencies script to install)")
+-endif()
+ 
+ 
+ # include files
+@@ -420,18 +402,6 @@
+    install(DIRECTORY "${RSTUDIO_DEPENDENCIES_DIR}/common/mathjax-26"
+            DESTINATION "${RSTUDIO_INSTALL_SUPPORTING}/resources")
+ 
+-   # install pandoc
+-   if(RSTUDIO_PACKAGE_BUILD_SLES)
+-      # when producing a SUSE Linux Enterpise build, we want to install the 
+-      # static Pandoc binaries (see dependencies/common/install-pandoc)
+-      set(PANDOC_EXTENSION_DIR "/static")
+-   endif()
+-   set(PANDOC_BIN "${RSTUDIO_DEPENDENCIES_DIR}/common/pandoc/1.17.2${PANDOC_EXTENSION_DIR}")
+-   file(GLOB PANDOC_FILES "${PANDOC_BIN}/pandoc*")
+-   install(FILES ${PANDOC_FILES}
+-           PERMISSIONS OWNER_READ OWNER_WRITE OWNER_EXECUTE GROUP_READ GROUP_EXECUTE WORLD_READ WORLD_EXECUTE
+-           DESTINATION  ${RSTUDIO_INSTALL_BIN}/pandoc)
+-
+    # install PDF.js
+    install(DIRECTORY "resources/pdfjs"
+            DESTINATION ${RSTUDIO_INSTALL_SUPPORTING}/resources)
+@@ -452,24 +422,6 @@
+    install(DIRECTORY "resources/pagedtable"
+            DESTINATION ${RSTUDIO_INSTALL_SUPPORTING}/resources)
+ 
+-   # install libclang
+-   if(WIN32)
+-      file(GLOB LIBCLANG_32_FILES "${LIBCLANG_DIR}/x86/libclang.*")
+-      install(PROGRAMS ${LIBCLANG_32_FILES}
+-              DESTINATION  ${RSTUDIO_INSTALL_BIN}/rsclang/x86)
+-      file(GLOB LIBCLANG_64_FILES "${LIBCLANG_DIR}/x86_64/libclang.*")
+-      install(PROGRAMS ${LIBCLANG_64_FILES}
+-              DESTINATION  ${RSTUDIO_INSTALL_BIN}/rsclang/x86_64)
+-   else()
+-      file(GLOB_RECURSE LIBCLANG_FILES "${LIBCLANG_DIR}/libclang.*")
+-      install(PROGRAMS ${LIBCLANG_FILES}
+-              DESTINATION  ${RSTUDIO_INSTALL_BIN}/rsclang)
+-   endif()
+-
+-   # install libclang builtin-headers
+-   install(DIRECTORY "${RSTUDIO_DEPENDENCIES_DIR}/common/libclang/builtin-headers"
+-           DESTINATION "${RSTUDIO_INSTALL_SUPPORTING}/resources/libclang")
+-
+    # install 64 bit binaries if we are on win64
+    if(WIN32)
+       if(NOT ("$ENV{PROGRAMW6432}" STREQUAL ""))

diff --git a/sci-mathematics/rstudio/files/rstudio-1.0.44-paths.patch b/sci-mathematics/rstudio/files/rstudio-1.0.44-paths.patch
new file mode 100644
index 00000000..b2a1a33
--- /dev/null
+++ b/sci-mathematics/rstudio/files/rstudio-1.0.44-paths.patch
@@ -0,0 +1,130 @@
+--- rstudio-1.0.44-orig/CMakeGlobals.txt	2016-10-19 08:32:41.000000000 +1100
++++ rstudio-1.0.44/CMakeGlobals.txt	2016-12-01 23:33:04.149326324 +1100
+@@ -123,7 +123,7 @@
+    else()
+      set(RSTUDIO_INSTALL_BIN bin)
+    endif()
+-   set(RSTUDIO_INSTALL_SUPPORTING .)
++   set(RSTUDIO_INSTALL_SUPPORTING ${DISTRO_SHARE})
+ endif()
+ 
+ # if the install prefix is /usr/local then tweak as appropriate
+--- rstudio-1.0.44-orig/src/cpp/server/CMakeLists.txt	2016-10-19 08:32:41.000000000 +1100
++++ rstudio-1.0.44/src/cpp/server/CMakeLists.txt	2016-12-01 23:35:51.634862018 +1100
+@@ -155,7 +155,7 @@
+    configure_file(${CMAKE_CURRENT_SOURCE_DIR}/${RSERVER_INITD_DEBIAN_SCRIPT}.in
+                   ${CMAKE_CURRENT_BINARY_DIR}/${RSERVER_INITD_DEBIAN_SCRIPT})
+    install(PROGRAMS ${CMAKE_CURRENT_BINARY_DIR}/${RSERVER_INITD_DEBIAN_SCRIPT}
+-           DESTINATION ${RSERVER_INITD_DEBIAN_DIR})
++           DESTINATION ${DISTRO_SHARE}/${RSERVER_INITD_DEBIAN_DIR})
+ 
+    # install configured redhat init.d script
+    set(RSERVER_INITD_REDHAT_DIR "extras/init.d/redhat")
+@@ -163,7 +163,7 @@
+    configure_file(${CMAKE_CURRENT_SOURCE_DIR}/${RSERVER_INITD_REDHAT_SCRIPT}.in
+                   ${CMAKE_CURRENT_BINARY_DIR}/${RSERVER_INITD_REDHAT_SCRIPT})
+    install(PROGRAMS ${CMAKE_CURRENT_BINARY_DIR}/${RSERVER_INITD_REDHAT_SCRIPT}
+-           DESTINATION ${RSERVER_INITD_REDHAT_DIR})
++           DESTINATION ${DISTRO_SHARE}/${RSERVER_INITD_REDHAT_DIR})
+ 
+    # install configured suse init.d script
+    set(RSERVER_INITD_SUSE_DIR "extras/init.d/suse")
+@@ -171,13 +171,13 @@
+    configure_file(${CMAKE_CURRENT_SOURCE_DIR}/${RSERVER_INITD_SUSE_SCRIPT}.in
+                   ${CMAKE_CURRENT_BINARY_DIR}/${RSERVER_INITD_SUSE_SCRIPT})
+    install(PROGRAMS ${CMAKE_CURRENT_BINARY_DIR}/${RSERVER_INITD_SUSE_SCRIPT}
+-           DESTINATION ${RSERVER_INITD_SUSE_DIR})
++           DESTINATION ${DISTRO_SHARE}/${RSERVER_INITD_SUSE_DIR})
+ 
+    # install pam profile
+    set(RSERVER_PAM_DIR "extras/pam")
+    set(RSERVER_PAM_PROFILE "${RSERVER_PAM_DIR}/rstudio")
+    install(FILES ${CMAKE_CURRENT_SOURCE_DIR}/${RSERVER_PAM_PROFILE}
+-           DESTINATION ${RSERVER_PAM_DIR})
++           DESTINATION ${DISTRO_SHARE}/${RSERVER_PAM_DIR})
+ 
+    # install configured apparmor profile
+    set(RSERVER_APPARMOR_DIR "extras/apparmor")
+@@ -185,9 +185,9 @@
+    configure_file(${CMAKE_CURRENT_SOURCE_DIR}/${RSERVER_APPARMOR_PROFILE}.in
+                   ${CMAKE_CURRENT_BINARY_DIR}/${RSERVER_APPARMOR_PROFILE})
+    install(FILES ${CMAKE_CURRENT_BINARY_DIR}/${RSERVER_APPARMOR_PROFILE}
+-           DESTINATION ${RSERVER_APPARMOR_DIR})
++           DESTINATION ${DISTRO_SHARE}/${RSERVER_APPARMOR_DIR})
+    install(PROGRAMS ${CMAKE_CURRENT_SOURCE_DIR}/${RSERVER_APPARMOR_DIR}/apparmor-profile-load
+-           DESTINATION ${RSERVER_APPARMOR_DIR})
++           DESTINATION ${DISTRO_SHARE}/${RSERVER_APPARMOR_DIR})
+ 
+    # install configured upstart profile
+    set(RSERVER_UPSTART_DIR "extras/upstart")
+@@ -195,12 +195,12 @@
+    configure_file(${CMAKE_CURRENT_SOURCE_DIR}/${RSERVER_UPSTART_PROFILE}.in
+                   ${CMAKE_CURRENT_BINARY_DIR}/${RSERVER_UPSTART_PROFILE})
+    install(FILES ${CMAKE_CURRENT_BINARY_DIR}/${RSERVER_UPSTART_PROFILE}
+-           DESTINATION ${RSERVER_UPSTART_DIR})
++           DESTINATION ${DISTRO_SHARE}/${RSERVER_UPSTART_DIR})
+    set(RSERVER_UPSTART_PROFILE_REDHAT "${RSERVER_UPSTART_DIR}/rstudio-server.redhat.conf")
+    configure_file(${CMAKE_CURRENT_SOURCE_DIR}/${RSERVER_UPSTART_PROFILE_REDHAT}.in
+                   ${CMAKE_CURRENT_BINARY_DIR}/${RSERVER_UPSTART_PROFILE_REDHAT})
+    install(FILES ${CMAKE_CURRENT_BINARY_DIR}/${RSERVER_UPSTART_PROFILE_REDHAT}
+-           DESTINATION ${RSERVER_UPSTART_DIR})
++           DESTINATION ${DISTRO_SHARE}/${RSERVER_UPSTART_DIR})
+ 
+     # install configured systemd profile
+    set(RSERVER_SYSTEMD_DIR "extras/systemd")
+--- rstudio-1.0.44-orig/src/cpp/server/ServerOptions.cpp	2016-10-19 08:32:41.000000000 +1100
++++ rstudio-1.0.44/src/cpp/server/ServerOptions.cpp	2016-12-01 23:33:04.151326331 +1100
+@@ -386,8 +386,8 @@
+ 
+    // convert relative paths by completing from the system installation
+    // path (this allows us to be relocatable)
+-   resolvePath(resourcePath, &wwwLocalPath_);
+-   resolvePath(resourcePath, &wwwSymbolMapsPath_);
++   resolvePath(resourcePath.childPath(DISTRO_SHARE), &wwwLocalPath_);
++   resolvePath(resourcePath.childPath(DISTRO_SHARE), &wwwSymbolMapsPath_);
+    resolvePath(binaryPath, &authPamHelperPath_);
+    resolvePath(binaryPath, &rsessionPath_);
+    resolvePath(binaryPath, &rldpathPath_);
+--- rstudio-1.0.44-orig/src/cpp/session/SessionOptions.cpp	2016-10-19 08:32:41.000000000 +1100
++++ rstudio-1.0.44/src/cpp/session/SessionOptions.cpp	2016-12-01 23:33:04.151326331 +1100
+@@ -49,7 +49,7 @@
+ namespace session {  
+ 
+ namespace {
+-const char* const kDefaultPandocPath = "bin/pandoc";
++const char* const kDefaultPandocPath = "bin";
+ const char* const kDefaultPostbackPath = "bin/postback/rpostback";
+ const char* const kDefaultRsclangPath = "bin/rsclang";
+ 
+@@ -481,14 +481,14 @@
+    }
+    
+    // convert relative paths by completing from the app resource path
+-   resolvePath(resourcePath_, &rResourcesPath_);
+-   resolvePath(resourcePath_, &agreementFilePath_);
+-   resolvePath(resourcePath_, &wwwLocalPath_);
+-   resolvePath(resourcePath_, &wwwSymbolMapsPath_);
+-   resolvePath(resourcePath_, &coreRSourcePath_);
+-   resolvePath(resourcePath_, &modulesRSourcePath_);
+-   resolvePath(resourcePath_, &sessionLibraryPath_);
+-   resolvePath(resourcePath_, &sessionPackageArchivesPath_);
++   resolvePath(resourcePath_.childPath(DISTRO_SHARE), &rResourcesPath_);
++   resolvePath(resourcePath_.childPath(DISTRO_SHARE), &agreementFilePath_);
++   resolvePath(resourcePath_.childPath(DISTRO_SHARE), &wwwLocalPath_);
++   resolvePath(resourcePath_.childPath(DISTRO_SHARE), &wwwSymbolMapsPath_);
++   resolvePath(resourcePath_.childPath(DISTRO_SHARE), &coreRSourcePath_);
++   resolvePath(resourcePath_.childPath(DISTRO_SHARE), &modulesRSourcePath_);
++   resolvePath(resourcePath_.childPath(DISTRO_SHARE), &sessionLibraryPath_);
++   resolvePath(resourcePath_.childPath(DISTRO_SHARE), &sessionPackageArchivesPath_);
+    resolvePostbackPath(resourcePath_, &rpostbackPath_);
+ #ifdef _WIN32
+    resolvePath(resourcePath_, &consoleIoPath_);
+@@ -498,7 +498,7 @@
+    resolvePath(resourcePath_, &sumatraPath_);
+    resolvePath(resourcePath_, &winutilsPath_);
+ #endif
+-   resolvePath(resourcePath_, &hunspellDictionariesPath_);
++   resolvePath(resourcePath_.childPath(DISTRO_SHARE), &hunspellDictionariesPath_);
+    resolvePath(resourcePath_, &mathjaxPath_);
+    resolvePath(resourcePath_, &libclangHeadersPath_);
+    resolvePandocPath(resourcePath_, &pandocPath_);

diff --git a/sci-mathematics/rstudio/files/rstudio-1.0.44-systemd.patch b/sci-mathematics/rstudio/files/rstudio-1.0.44-systemd.patch
new file mode 100644
index 00000000..7eafd43
--- /dev/null
+++ b/sci-mathematics/rstudio/files/rstudio-1.0.44-systemd.patch
@@ -0,0 +1,21 @@
+--- rstudio-1.0.44-orig/src/cpp/server/CMakeLists.txt	2016-10-19 08:32:41.000000000 +1100
++++ rstudio-1.0.44/src/cpp/server/CMakeLists.txt	2016-12-02 11:11:45.259050839 +1100
+@@ -203,17 +203,12 @@
+            DESTINATION ${RSERVER_UPSTART_DIR})
+ 
+     # install configured systemd profile
+-   set(RSERVER_SYSTEMD_DIR "extras/systemd")
++   set(RSERVER_SYSTEMD_DIR "lib/systemd/system")
+    set(RSERVER_SYSTEMD_PROFILE "${RSERVER_SYSTEMD_DIR}/rstudio-server.service")
+    configure_file(${CMAKE_CURRENT_SOURCE_DIR}/${RSERVER_SYSTEMD_PROFILE}.in
+                   ${CMAKE_CURRENT_BINARY_DIR}/${RSERVER_SYSTEMD_PROFILE})
+    install(FILES ${CMAKE_CURRENT_BINARY_DIR}/${RSERVER_SYSTEMD_PROFILE}
+            DESTINATION ${RSERVER_SYSTEMD_DIR})
+-   set(RSERVER_SYSTEMD_PROFILE_REDHAT "${RSERVER_SYSTEMD_DIR}/rstudio-server.redhat.service")
+-   configure_file(${CMAKE_CURRENT_SOURCE_DIR}/${RSERVER_SYSTEMD_PROFILE_REDHAT}.in
+-                  ${CMAKE_CURRENT_BINARY_DIR}/${RSERVER_SYSTEMD_PROFILE_REDHAT})
+-   install(FILES ${CMAKE_CURRENT_BINARY_DIR}/${RSERVER_SYSTEMD_PROFILE_REDHAT}
+-           DESTINATION ${RSERVER_SYSTEMD_DIR})
+ 
+ elseif(APPLE)
+ 

diff --git a/sci-mathematics/rstudio/rstudio-1.0.44.ebuild b/sci-mathematics/rstudio/rstudio-1.0.44.ebuild
new file mode 100644
index 00000000..884e05d
--- /dev/null
+++ b/sci-mathematics/rstudio/rstudio-1.0.44.ebuild
@@ -0,0 +1,248 @@
+# Copyright 1999-2016 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=6
+
+inherit eutils user cmake-utils gnome2-utils pam versionator fdo-mime java-pkg-2 pax-utils
+
+# TODO
+# * package gin and gwt
+# * use dict from tree, linguas
+# * do src_test (use junit from tree?)
+
+# update from scripts in dependencies/common
+# egrep '(GWT_SDK_VER=|GIN_VER=|SELENIUM_VER=|CHROMEDRIVER_VER=)' dependencies/common/install-gwt
+GWT_VER=2.7.0
+GIN_VER=1.5
+SELENIUM_VER=2.37.0
+CHROMEDRIVER_VER=2.7
+# grep 'PANDOC_VERSION=' dependencies/common/update-pandoc
+PANDOC_VER=1.13.1
+# ls dependencies/common/*.tar.gz
+PACKRAT_VER=0.98.1000
+RMARKDOWN_VER=0.98.1000
+SHINYAPPS_VER=0.98.1000
+RSCONNECT_VER=0.4.1.4_fcac892a69817febd7b655b189bf57193260cda0
+
+DESCRIPTION="IDE for the R language"
+HOMEPAGE="
+	http://www.rstudio.org
+	https://github.com/rstudio/rstudio/"
+SRC_URI="
+	https://github.com/rstudio/rstudio/archive/v${PV}.tar.gz -> ${P}.tar.gz
+	https://s3.amazonaws.com/rstudio-buildtools/gin-${GIN_VER}.zip
+	https://s3.amazonaws.com/rstudio-buildtools/gwt-${GWT_VER}.zip
+	https://s3.amazonaws.com/rstudio-buildtools/selenium-java-${SELENIUM_VER}.zip
+	https://s3.amazonaws.com/rstudio-buildtools/selenium-server-standalone-${SELENIUM_VER}.jar
+	https://s3.amazonaws.com/rstudio-buildtools/chromedriver-linux
+	https://s3.amazonaws.com/rstudio-dictionaries/core-dictionaries.zip
+	https://dev.gentoo.org/~gienah/distfiles/packrat-${PACKRAT_VER}.tar.gz
+	https://dev.gentoo.org/~gienah/distfiles/rmarkdown-${RMARKDOWN_VER}.tar.gz
+	https://dev.gentoo.org/~gienah/distfiles/shinyapps-${SHINYAPPS_VER}.tar.gz
+	https://dev.gentoo.org/~gienah/distfiles/rsconnect_${RSCONNECT_VER}.tar.gz
+"
+
+LICENSE="AGPL-3"
+SLOT="0"
+KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
+IUSE="dedicated server"
+
+QT_VER=5.4
+QT_SLOT=5
+RDEPEND="
+	app-text/pandoc
+	dev-haskell/pandoc-citeproc
+	>=dev-lang/R-2.11.1
+	>=dev-libs/boost-1.50:=
+	>=dev-libs/mathjax-2.7.0
+	dev-libs/openssl:0
+	sys-apps/util-linux
+	>=sys-devel/clang-3.5.0
+	sys-libs/zlib
+	>=virtual/jre-1.8:=
+	x11-libs/pango
+	!dedicated? (
+		>=dev-qt/qtcore-${QT_VER}:${QT_SLOT}
+		>=dev-qt/qtdeclarative-${QT_VER}:${QT_SLOT}
+		>=dev-qt/qtdbus-${QT_VER}:${QT_SLOT}
+		>=dev-qt/qtgui-${QT_VER}:${QT_SLOT}
+		>=dev-qt/qtnetwork-${QT_VER}:${QT_SLOT}
+		>=dev-qt/qtopengl-${QT_VER}:${QT_SLOT}
+		>=dev-qt/qtpositioning-${QT_VER}:${QT_SLOT}
+		>=dev-qt/qtprintsupport-${QT_VER}:${QT_SLOT}
+		>=dev-qt/qtsingleapplication-2.6.1_p20150629[qt5]
+		>=dev-qt/qtsensors-${QT_VER}:${QT_SLOT}
+		>=dev-qt/qtsql-${QT_VER}:${QT_SLOT}
+		>=dev-qt/qtsvg-${QT_VER}:${QT_SLOT}
+		>=dev-qt/qtwebkit-${QT_VER}:${QT_SLOT}
+		>=dev-qt/qtwidgets-${QT_VER}:${QT_SLOT}
+		>=dev-qt/qtxml-${QT_VER}:${QT_SLOT}
+		>=dev-qt/qtxmlpatterns-${QT_VER}:${QT_SLOT}
+		server? ( virtual/pam )
+	)
+	dedicated? ( virtual/pam )"
+DEPEND="${RDEPEND}
+	app-arch/unzip
+	dev-java/ant-core
+	>=virtual/jdk-1.8:=
+	virtual/pkgconfig"
+#	test? ( dev-java/junit:4 )
+
+PATCHES=(
+		"${FILESDIR}/${PN}-0.99.879-prefs.patch"
+		"${FILESDIR}/${PN}-1.0.44-paths.patch"
+		"${FILESDIR}/${PN}-1.0.44-clang-pandoc.patch"
+		"${FILESDIR}/${PN}-0.98.490-linker_flags.patch"
+		"${FILESDIR}/${PN}-0.98.1091-boost-1.57.patch"
+		"${FILESDIR}/${PN}-0.99.473-qtsingleapplication.patch"
+		"${FILESDIR}/${PN}-1.0.44-systemd.patch"
+)
+
+src_unpack() {
+	unpack ${P}.tar.gz gwt-${GWT_VER}.zip
+	cd "${S}" || die
+	mkdir -p src/gwt/lib/{gin,gwt} \
+		dependencies/common/dictionaries \
+		src/gwt/lib/selenium/${SELENIUM_VER} \
+		src/gwt/lib/selenium/chromedriver/${CHROMEDRIVER_VER} || die
+	mv ../gwt-${GWT_VER} src/gwt/lib/gwt/${GWT_VER} || die
+	unzip -qd src/gwt/lib/gin/${GIN_VER} \
+		"${DISTDIR}"/gin-${GIN_VER}.zip || die
+	unzip -qd dependencies/common/dictionaries \
+		"${DISTDIR}"/core-dictionaries.zip || die
+	unzip -qd src/gwt/lib/selenium/${SELENIUM_VER} \
+		"${DISTDIR}"/selenium-java-${SELENIUM_VER}.zip || die
+	cp "${DISTDIR}"/selenium-server-standalone-${SELENIUM_VER}.jar \
+		src/gwt/lib/selenium/${SELENIUM_VER}/ || die
+	cp "${DISTDIR}"/chromedriver-linux \
+		src/gwt/lib/selenium/chromedriver/${CHROMEDRIVER_VER}/ || die
+	cd dependencies/common || die
+	unpack packrat-${PACKRAT_VER}.tar.gz
+	unpack rmarkdown-${RMARKDOWN_VER}.tar.gz
+	unpack shinyapps-${SHINYAPPS_VER}.tar.gz
+	unpack rsconnect_${RSCONNECT_VER}.tar.gz
+	cp "${DISTDIR}"/rmarkdown-${RMARKDOWN_VER}.tar.gz \
+		. || die
+	cp "${DISTDIR}"/packrat-${PACKRAT_VER}.tar.gz \
+		. || die
+	cp "${DISTDIR}"/shinyapps-${SHINYAPPS_VER}.tar.gz \
+		. || die
+	cp "${DISTDIR}"/rsconnect_${RSCONNECT_VER}.tar.gz \
+		. || die
+}
+
+src_prepare() {
+	default
+	java-pkg-2_src_prepare
+	egit_clean
+
+	# Enable CMake to install our .service file for systemd usage
+	mkdir -vp "${S}/src/cpp/server/lib/systemd/system" || die
+	cp -v "${FILESDIR}/rstudio-server.service.in" "${S}/src/cpp/server/lib/systemd/system/" || die
+
+	# Adding -DDISTRO_SHARE=... to append-flags breaks cmake so using
+	# this sed hack for now. ~RMH
+	sed -i \
+		-e "s|DISTRO_SHARE|\"share/${PN}\"|g" \
+		src/cpp/server/ServerOptions.cpp \
+		src/cpp/session/SessionOptions.cpp || die
+
+	# use mathjax from system
+	ln -sf "${EPREFIX}"/usr/share/mathjax dependencies/common/mathjax-26 || die
+
+	# make sure icons and mime stuff are with prefix
+	sed -i \
+		-e "s:/usr:${EPREFIX}/usr:g" \
+		CMakeGlobals.txt src/cpp/desktop/CMakeLists.txt || die
+
+	# On Gentoo the rstudio-server configuration file is /etc/conf.d/rstudio-server.conf
+	sed -e "s@/etc/rstudio/rserver.conf@${EROOT}etc/conf.d/rstudio-server.conf@" \
+		-i src/cpp/server/ServerOptions.cpp \
+		|| die
+
+	# Set the rsession.conf file location for Gentoo prefix
+	sed -e "s@/etc/rstudio/rsession.conf@${EROOT}etc/rstudio/rsession.conf@" \
+		-i src/cpp/session/SessionOptions.cpp \
+		|| die
+
+	# dev-qt/qtsingleapplication-2.6.1_p20150629 does not provide a cmake module.
+	# It provides a library that has its version number appended to the end,
+	# which is difficult to handle in cmake, as find_library does not support
+	# searching for wildcard library names. So I find the library name from the
+	# qmake spec, and then sed this into the patched src/cpp/desktop/CMakeLists.txt.
+	rm -rf "${S}"/src/cpp/desktop/3rdparty || die
+	local s=$(grep '\-lQt$${QT_MAJOR_VERSION}Solutions_SingleApplication' \
+				   "${EROOT}"/usr/lib64/qt5/mkspecs/features/qtsingleapplication.prf \
+					 | sed -e 's@\$\${QT_MAJOR_VERSION}@5@' \
+						   -e 's@LIBS \*= -l@@')
+	sed -e "s@Qt5Solutions_SingleApplication-2.6@${s}@g" \
+		-i "${S}"/src/cpp/desktop/CMakeLists.txt \
+		|| die
+
+	# The git commit for tag: git rev-list -n 1 v0.99.903
+	sed -e 's@git ARGS rev-parse HEAD@echo ARGS 0eb2d8ea28ebc1ac6ac327e023becb6133b679c4@'\
+		-i "${S}"/CMakeLists.txt \
+		"${S}"/CMakeGlobals.txt \
+		|| die
+}
+
+src_configure() {
+	export RSTUDIO_VERSION_MAJOR=$(get_version_component_range 1)
+	export RSTUDIO_VERSION_MINOR=$(get_version_component_range 2)
+	export RSTUDIO_VERSION_PATCH=$(get_version_component_range 3)
+
+	local mycmakeargs=(
+		-DDISTRO_SHARE=share/${PN}
+		-DRSTUDIO_INSTALL_FREEDESKTOP="$(usex !dedicated "ON" "OFF")"
+		-DRSTUDIO_TARGET=$(usex dedicated "Server" "$(usex server "Development" "Desktop")")
+		-DQT_QMAKE_EXECUTABLE="${EROOT}"usr/lib64/qt5/bin/qmake
+		-DRSTUDIO_VERIFY_R_VERSION=FALSE
+		)
+
+	cmake-utils_src_configure
+}
+
+src_compile() {
+	# Avoid the rest of the oracle-jdk-bin-1.8.0.60 sandbox violations F: mkdir S: deny
+	# P: /root/.oracle_jre_usage.
+	export ANT_OPTS="-Duser.home=${T}"
+	cmake-utils_src_compile
+}
+
+src_install() {
+	export ANT_OPTS="-Duser.home=${T}"
+	cmake-utils_src_install
+	pax-mark m "${ED}usr/bin/rstudio"
+	doconfd "${FILESDIR}"/rstudio-server.conf
+	dodir /etc/rstudio
+	insinto /etc/rstudio
+	doins "${FILESDIR}"/rsession.conf
+	dosym /etc/conf.d/rstudio-server.conf /etc/rstudio/rserver.conf
+	if use dedicated || use server; then
+		dopamd src/cpp/server/extras/pam/rstudio
+		newinitd "${FILESDIR}"/rstudio-server.initd rstudio-server
+	fi
+}
+
+pkg_preinst() {
+	use dedicated || gnome2_icon_savelist
+	java-pkg-2_pkg_preinst
+}
+
+pkg_postinst() {
+	use dedicated || { fdo-mime_desktop_database_update
+		fdo-mime_mime_database_update
+		gnome2_icon_cache_update ;}
+
+	if use dedicated || use server; then
+		enewgroup rstudio-server
+		enewuser rstudio-server -1 -1 -1 rstudio-server
+	fi
+}
+
+pkg_postrm() {
+	use dedicated || { fdo-mime_desktop_database_update
+		fdo-mime_mime_database_update
+		gnome2_icon_cache_update ;}
+}


^ permalink raw reply related	[flat|nested] 12+ messages in thread

* [gentoo-commits] repo/gentoo:master commit in: sci-mathematics/rstudio/, sci-mathematics/rstudio/files/
@ 2017-10-15 12:23 Andreas Sturmlechner
  0 siblings, 0 replies; 12+ messages in thread
From: Andreas Sturmlechner @ 2017-10-15 12:23 UTC (permalink / raw
  To: gentoo-commits

commit:     679cc5c1a355784caac199f88a5dcfb84c6d6b06
Author:     Andreas Sturmlechner <asturm <AT> gentoo <DOT> org>
AuthorDate: Sat Oct 14 21:16:37 2017 +0000
Commit:     Andreas Sturmlechner <asturm <AT> gentoo <DOT> org>
CommitDate: Sun Oct 15 12:22:41 2017 +0000
URL:        https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=679cc5c1

sci-mathematics/rstudio: Drop old, Qt4WebKit rdeps

Gentoo-bug: 526660, 583100, 608134, 634280
Package-Manager: Portage-2.3.11, Repoman-2.3.3

 sci-mathematics/rstudio/Manifest                   |  12 --
 .../files/rstudio-0.97.336-boost-1.53.patch        |  64 -------
 .../files/rstudio-0.97.336-linker_flags.patch      |  18 --
 .../rstudio/files/rstudio-0.97.336-paths.patch     | 112 ------------
 .../rstudio/files/rstudio-0.97.336-prefs.patch     |  24 ---
 .../files/rstudio-0.97.551-boost-1.53.patch        |  64 -------
 .../files/rstudio-0.97.551-linker_flags.patch      |  18 --
 .../rstudio/files/rstudio-0.97.551-paths.patch     | 112 ------------
 .../rstudio/files/rstudio-0.97.551-prefs.patch     |  24 ---
 sci-mathematics/rstudio/rstudio-0.97.336.ebuild    | 143 ---------------
 sci-mathematics/rstudio/rstudio-0.97.551.ebuild    | 143 ---------------
 sci-mathematics/rstudio/rstudio-0.98.1028.ebuild   | 164 -----------------
 sci-mathematics/rstudio/rstudio-0.98.1091.ebuild   | 198 ---------------------
 sci-mathematics/rstudio/rstudio-0.98.490-r1.ebuild | 129 --------------
 sci-mathematics/rstudio/rstudio-0.98.490.ebuild    | 142 ---------------
 sci-mathematics/rstudio/rstudio-0.98.932.ebuild    | 173 ------------------
 sci-mathematics/rstudio/rstudio-0.98.953.ebuild    | 174 ------------------
 17 files changed, 1714 deletions(-)

diff --git a/sci-mathematics/rstudio/Manifest b/sci-mathematics/rstudio/Manifest
index f742b19bb98..728e003ec65 100644
--- a/sci-mathematics/rstudio/Manifest
+++ b/sci-mathematics/rstudio/Manifest
@@ -1,22 +1,10 @@
 DIST chromedriver-linux 19303552 SHA256 1ff3e9fc17e456571c440ab160f25ee451b2a4d36e61c8e297737cff7433f48c SHA512 18774ede961dec222058dd0e3f128d63732cd444ee310136b44d5bf508a4f2f2c164a2c8d195d80bce8b5fb6303559e167f82f384e4a58e30f48b151a4206ee8 WHIRLPOOL 06534c131d3a8ade4fb12ad94955f430f23d86654342357d223e78e210cc401416361a847934bccb3957702bbe8fc8a6dd7f18416461edf486145bde96c7091e
 DIST core-dictionaries.zip 876339 SHA256 4341a9630efb9dcf7f215c324136407f3b3d6003e1c96f2e5e1f9f14d5787494 SHA512 9c5830cc9fed575e223f1c61f02e48c5aea6801bb0cd2586f02437c17fdffdb1d36c396d5a8ecbe02ba01196e73458304345b1f6b92c052bc7a7d05961fac2c9 WHIRLPOOL 316dced8ac46e4216613b0b850c33d4c1e10ef0ecd954d786eb131ea80b34e66ba3d39a0ef25b45230b64ded415737ddabef8f7d68f4d42caea98679cff44ee0
 DIST gin-1.5.zip 1055663 SHA256 f561f4eb5d5fe1cff95c881e6aed53a86e9f0de8a52863295a8600375f96ab94 SHA512 3f6649565f9600daaca6ddf3fb431925b5a1ce1ada38e6389de64cef617abba9d3f49c555d0a20053fb06f17ccbe4e1141b39966fbe4b2975d7b120377504897 WHIRLPOOL e66d348ed275eb20518369c39592a5a03ee4257422e2947520385377939de65a54d131332818362a47597392026db48ed1332f11ae218e336798498ae5d5b196
-DIST gwt-2.5.0.rc1.zip 104156555 SHA256 83a6dec583d1b7f3bf3fd2e321d89c1d95881eed1f81c7ea4056201fc105258b SHA512 c0c4f502b4ca191537eada53eb0458c0d33282661423f6d2648e6107ed8e38465b189377fcd0d9babcbf2c688e16080d33cbd7165ed20dafda7fedc39a74e163 WHIRLPOOL b37f12d1937b6479b97e274a59a1856dcf0c5cc3b767b6a19f65d7807e1f32cc2483358f1414c4c9e427d890eb1e0617fe8af84c6f0dca4a9ded64ae5ffde129
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 DIST rmarkdown-0.98.1000.tar.gz 1423820 SHA256 56e9f964f805627f6d6face9bf09e6435be4cc48321447ad4041fee86d6f88b4 SHA512 df3540c24c87930fe55bff2ffe67c86c219800cb00ed72ba9451ecd0d0cad411548a78c1a04b9a2e301e853616dcb77e09129c4e48ade6f16d3f14b7ea7e4852 WHIRLPOOL 51098cd48a12a61da312fc1cc96927626db4a19cc069c88f615dd20abe40f52a7b1ac1325b52b1922110ffa76a7f255d9ff2a75cd05d3de01d1b96f0c8286790
-DIST rmarkdown_0.2.49.tar.gz 3846795 SHA256 56b9a032b07d62c6af2a4a2d04007cccf379a9c8e91426c59f265c8b7fd992ee SHA512 46d15c354c9a90ae75a7dc3660b1ea82d097aaceb3dd220a4a8c6f4b22751ad2d63fd5ef3d56821160716ab6552529cef6513b5cd7043368d13513f537511fef WHIRLPOOL d658a091d1b4508ea38fbf2f3691517dc2b814aa3ffaec25483263266106756a89712d7c8a2ec3de8d6d45234d5f8b11340c287509bd836be5875527077f7fcd
 DIST rsconnect_0.4.1.4_fcac892a69817febd7b655b189bf57193260cda0.tar.gz 197051 SHA256 e1e3e1f799eb8be679be9a2ed5aad7e9ce6cd603e3cb43fdc242490f0c311113 SHA512 208dc349f4aa7613ecf94939aba60d22d3a06972344b526c9b6c951015571f5922927bca08db571a7b8a268e42609a4f558f01278c9685f6da2ffc66a1f95ade WHIRLPOOL 4e3d64de00a98190c435d76f12a401d30950fdc7590b6bcc886ae50d4771825d39f93ea2bdcb4a9db026361c522f16f11297ff89dcb15c35f9471c1abf4f4e2c
-DIST rstudio-0.97.336.tar.gz 12598580 SHA256 e6c24d6a865827d3a39e64508976a825bba705efe0921eb06f9a95ba58aefcd1 SHA512 bfaf6218cb400e83a97a320cf633e4656f1552e27bb9843fda1837945a3823fb0df20a2c86e0b6d76608d98806b0acf163aaba10783c923ef900b3eaf03b7569 WHIRLPOOL eca7b837ccff6cc6595298c3137f8663c0754256763a1d049e44a11e10daf53914234c426e004cc1f0158d7b4a38319f61653f78785c7189a64413fc196848c2
-DIST rstudio-0.97.551.tar.gz 12602738 SHA256 caed5f6b6ec57139ddf550dc2f51c1f9a74b39b81b878863b97e1a12edecf498 SHA512 f855a5ba3a86e44c870a4843e94678a1f6eeedc49934d8ad42f202815f93d282913a0be739435be63e510a6ec81b7a1436e4c911acbff955f5fb28b78b00fd10 WHIRLPOOL d8cd3d2978b690fc8c83696cb2017748e74b38309174ac85d6d35d5a1dd91d8e0d8ea06177b349754b3be9eb5e78e04b1d23b82f9e7940d062b262c1eb7eb58e
-DIST rstudio-0.98.1028.tar.gz 15555649 SHA256 19827c3d05b4817530fb07f235fe38ec5e391324acd1d5d8ab6711d0db4757ef SHA512 db1be9f91263386ad0fb8addc80421434695d2c8dd53101af268e878fd59c59b9349cc9456d7096d2c660ee2681cd0172d8f4d8432ccf7322a1a2b473ce291fd WHIRLPOOL ab2974d2e529fea03fe641569d4b74a6eb1d86179be47de46531a970d5f70624824e08573835d531a5033d20f800117174926b83aee290f784ac31f7a9627d7d
-DIST rstudio-0.98.1091.tar.gz 15551758 SHA256 61745708096b5feb3d88befab65adf67dd386262cde1ef2b351f56695f5b9ac2 SHA512 6b2fcd7418118b8845266dc12ff4680623a68a8fdfda2bdc523e8cd30139e99fa29063438fbb441f23d04e57715eec1ee21763baf0ab77d313b763d8b3d9e3a0 WHIRLPOOL 356297217bdc70954b79695755fb873127e9b7c5a8ff2be18e237b559638aa1ec3c0349d8606598bd81e4057914e518748c236dc4a701d9a1f27805c2a4c7327
-DIST rstudio-0.98.490.tar.gz 14989329 SHA256 e38296a10b12c9e769a8be0545c36745999b9ba90942f7ffb6d27f05192a7f93 SHA512 b167083eb4adf1203da63299e61c9e3f40b8aeb4728d25c9d840f8a22659aad8de442dbba3a68e7d11f6157680d3a3636f6d5fecbabab82fd8d1a8278e3f1cb1 WHIRLPOOL d7c07aea3aef424aa9fa05f74b8222cae69b9ce287ba67d80591dc2a433471e7127d975119667560bf6667190d128b0ffcf82f641792075dacf826f4d76df568
-DIST rstudio-0.98.932.tar.gz 15515025 SHA256 e4a69a2f746cb7cfcacd3811f15e41a9d156175607da334f412614cc4cb70728 SHA512 beeb8c035d4f8524bd3e497162e3a218e92fbd1c1704ff3bc99a70a1248244155e3998272a6aa985b59cfa67c640adec877465f5d50acb9e47abca2657f2a06f WHIRLPOOL e422a2cef857aa9d094dd11e62b6c762a2a7477e7d84fd66456152c6521aebd94d4c365980ed6c06fc1c90d5a62426376d978de0ed23186d4732c0b148cc62bc
-DIST rstudio-0.98.953.tar.gz 15518231 SHA256 944f5882a0d61f551cd6f6cbe7882b5a5ea5be12d2c6d5ec9e79cee65869dbb7 SHA512 38a17d1abf91f4e775c4d735152fe6c8030b2df771bd7333fb3c9408fe14ac0b6180d7eaad7ac09ce2d50e5dcaa5a3b828909b30f507fd7c35fe27f7bd96866c WHIRLPOOL e2135f425b48b952282d8c44bd121517098521715c70537a6ac1a3be1732928666c5cb40fbc20b9f394a606e0e116723190790a202cbf62986ffbca528646058
 DIST rstudio-0.99.473.tar.gz 16993092 SHA256 a402995251393d50fa70e2e02188a8b32dc34e067f2f8461f087bf71f643585c SHA512 5615840501f7629e82100fee78c35b8d4dc78d78932d65c2e91a6472bc94726389566f5853a99e3d0631fd260e59acea5a40acf82f72709741b89a1ed3c901af WHIRLPOOL 809549c76efee8b29452584ab4295bcbbf533f8100c8caf4dd3b4a3c8843dc54a0d8f3178a6aecab5c188f2498a74daa6c6677fc6d43bd7dd861487c557e48df
 DIST rstudio-0.99.482.tar.gz 16992873 SHA256 1185d6ce5d3872e134f3255668d8f082370c760f06ec409c7b84c0936f52c4bf SHA512 bdb845cceae851d27323448a3570621bcb2aba7742e9e1669c88f3ebeaaade8c8371eb38f2ad348d7e2b740778c34f73e59013502ae3cebafba84e5d249c3e52 WHIRLPOOL 743440227c8d7e56000b1ff0b1a12def50e006b4f34d2067587274e2bae0eda42656787fc0cf6c51ffdbfcca08fc6eab0d042891bd77e4446b6fe26c6d19cc05
 DIST rstudio-0.99.483.tar.gz 16993049 SHA256 85ce1a2f40690e4ed0338b153a1b3279ce9564396d8c6d6201a0ad39297d4a9a SHA512 7d9cc8b471a4d799f286193da5f6f950f85e82949ede0f1ffe3626a429a49204878fb731250e5f54164a48e1d6e9cbb19a04a38ff83e35fd46c0ba05ef78a9bc WHIRLPOOL 0c5c1d86b0bafe9d5ca02397793f902b4dca7edc3f507a472b8b235f91965d8a769a7873cc87d834fbb121792b52eb6908018ce6579acdf3d285b6ec986abc20

diff --git a/sci-mathematics/rstudio/files/rstudio-0.97.336-boost-1.53.patch b/sci-mathematics/rstudio/files/rstudio-0.97.336-boost-1.53.patch
deleted file mode 100644
index 38bb63a8ab6..00000000000
--- a/sci-mathematics/rstudio/files/rstudio-0.97.336-boost-1.53.patch
+++ /dev/null
@@ -1,64 +0,0 @@
-=== modified file 'src/cpp/core/include/core/http/AsyncServer.hpp'
---- src/cpp/core/include/core/http/AsyncServer.hpp	2013-07-09 12:02:58 +0000
-+++ src/cpp/core/include/core/http/AsyncServer.hpp	2013-07-09 12:03:34 +0000
-@@ -264,7 +264,7 @@
-          
-          // convert to cannonical HttpConnection
-          boost::shared_ptr<AsyncConnection> pAsyncConnection =
--             boost::shared_static_cast<AsyncConnection>(pConnection);
-+             boost::static_pointer_cast<AsyncConnection>(pConnection);
- 
-          // call the appropriate handler to generate a response
-          std::string uri = pRequest->uri();
-
-=== modified file 'src/cpp/core/include/core/http/LocalStreamAsyncClient.hpp'
---- src/cpp/core/include/core/http/LocalStreamAsyncClient.hpp	2013-07-09 12:02:58 +0000
-+++ src/cpp/core/include/core/http/LocalStreamAsyncClient.hpp	2013-07-09 12:03:36 +0000
-@@ -87,7 +87,7 @@
-       boost::shared_ptr<AsyncClient<boost::asio::local::stream_protocol::socket> >
-                                     ptrShared = shared_from_this();
- 
--      return boost::shared_static_cast<LocalStreamAsyncClient>(ptrShared);
-+      return boost::static_pointer_cast<LocalStreamAsyncClient>(ptrShared);
-    }
- 
- private:
-
-=== modified file 'src/cpp/core/include/core/http/TcpIpAsyncClient.hpp'
---- src/cpp/core/include/core/http/TcpIpAsyncClient.hpp	2013-07-09 12:02:58 +0000
-+++ src/cpp/core/include/core/http/TcpIpAsyncClient.hpp	2013-07-09 12:03:32 +0000
-@@ -74,7 +74,7 @@
-       boost::shared_ptr<AsyncClient<boost::asio::ip::tcp::socket> > ptrShared
-                                                 = shared_from_this();
- 
--      return boost::shared_static_cast<TcpIpAsyncClient>(ptrShared);
-+      return boost::static_pointer_cast<TcpIpAsyncClient>(ptrShared);
-    }
- 
- private:
-
-=== modified file 'src/cpp/core/include/core/http/TcpIpAsyncClientSsl.hpp'
---- src/cpp/core/include/core/http/TcpIpAsyncClientSsl.hpp	2013-07-09 12:02:58 +0000
-+++ src/cpp/core/include/core/http/TcpIpAsyncClientSsl.hpp	2013-07-09 12:03:39 +0000
-@@ -109,7 +109,7 @@
-       boost::shared_ptr<AsyncClient<boost::asio::ssl::stream<boost::asio::ip::tcp::socket> > > ptrShared
-                                                  = shared_from_this();
- 
--      return boost::shared_static_cast<TcpIpAsyncClientSsl>(ptrShared);
-+      return boost::static_pointer_cast<TcpIpAsyncClientSsl>(ptrShared);
-    }
- 
-    virtual bool isShutdownError(const boost::system::error_code& ec)
-
-=== modified file 'src/cpp/session/http/SessionHttpConnectionListenerImpl.hpp'
---- src/cpp/session/http/SessionHttpConnectionListenerImpl.hpp	2013-07-09 12:02:58 +0000
-+++ src/cpp/session/http/SessionHttpConnectionListenerImpl.hpp	2013-07-09 12:03:29 +0000
-@@ -256,7 +256,7 @@
-    {
-       // convert to cannonical HttpConnection
-       boost::shared_ptr<HttpConnection> ptrHttpConnection =
--            boost::shared_static_cast<HttpConnection>(ptrConnection);
-+            boost::static_pointer_cast<HttpConnection>(ptrConnection);
- 
-       if (!authenticate(ptrHttpConnection))
-       {

diff --git a/sci-mathematics/rstudio/files/rstudio-0.97.336-linker_flags.patch b/sci-mathematics/rstudio/files/rstudio-0.97.336-linker_flags.patch
deleted file mode 100644
index a336fccbc98..00000000000
--- a/sci-mathematics/rstudio/files/rstudio-0.97.336-linker_flags.patch
+++ /dev/null
@@ -1,18 +0,0 @@
-Some gcc hardening options were added, however since we add
-"-Wl,--as-needed" we end up with "-Wl,--as-needed;-Wl,-z,relro" which
-leads to linker errors about unknown options, if we make it so the
-as-needed option is the last option on the line, everything is fine.
-
-diff --git a/src/cpp/CMakeLists.txt b/src/cpp/CMakeLists.txt
-index 0589ca0..fe5bd5f 100644
---- a/src/cpp/CMakeLists.txt
-+++ b/src/cpp/CMakeLists.txt
-@@ -57,7 +57,7 @@ if(UNIX)
-       add_definitions(-D_FORTIFY_SOURCE=2)
-       add_definitions(-fstack-protector --param ssp-buffer-size=4)
-       add_definitions(-pie -fPIE)
--      set(CMAKE_EXE_LINKER_FLAGS "${CMAKE_EXE_LINKER_FLAGS} -Wl,-z,relro,-z,now")
-+      set(CMAKE_EXE_LINKER_FLAGS "-Wl,-z,relro,-z,now ${CMAKE_EXE_LINKER_FLAGS}")
-    endif()
- 
- # Win32 specific global directives

diff --git a/sci-mathematics/rstudio/files/rstudio-0.97.336-paths.patch b/sci-mathematics/rstudio/files/rstudio-0.97.336-paths.patch
deleted file mode 100644
index 7b44374a72d..00000000000
--- a/sci-mathematics/rstudio/files/rstudio-0.97.336-paths.patch
+++ /dev/null
@@ -1,112 +0,0 @@
-change the install path, as by default everything is dumped right under
-the prefix. After fixing install paths, now fix the source so the
-program can find the moved resources.
-	
-diff --git a/CMakeGlobals.txt b/CMakeGlobals.txt
-index da74970..1537bff 100644
---- a/CMakeGlobals.txt
-+++ b/CMakeGlobals.txt
-@@ -103,7 +103,7 @@ else()
-    else()
-      set(RSTUDIO_INSTALL_BIN bin)
-    endif()
--   set(RSTUDIO_INSTALL_SUPPORTING .)
-+   set(RSTUDIO_INSTALL_SUPPORTING ${DISTRO_SHARE})
- endif()
- 
- # if the install prefix is /usr/local then tweak as appropriate
-diff --git a/src/cpp/server/CMakeLists.txt b/src/cpp/server/CMakeLists.txt
-index af4db1c..96b767e 100644
---- a/src/cpp/server/CMakeLists.txt
-+++ b/src/cpp/server/CMakeLists.txt
-@@ -142,7 +142,7 @@ if (UNIX AND NOT APPLE)
-    configure_file(${CMAKE_CURRENT_SOURCE_DIR}/${RSERVER_INITD_DEBIAN_SCRIPT}.in
-                   ${CMAKE_CURRENT_BINARY_DIR}/${RSERVER_INITD_DEBIAN_SCRIPT})
-    install(PROGRAMS ${CMAKE_CURRENT_BINARY_DIR}/${RSERVER_INITD_DEBIAN_SCRIPT}
--           DESTINATION ${RSERVER_INITD_DEBIAN_DIR})
-+           DESTINATION ${DISTRO_SHARE}/${RSERVER_INITD_DEBIAN_DIR})
- 
-    # install configured redhat init.d script
-    set(RSERVER_INITD_REDHAT_DIR "extras/init.d/redhat")
-@@ -150,7 +150,7 @@ if (UNIX AND NOT APPLE)
-    configure_file(${CMAKE_CURRENT_SOURCE_DIR}/${RSERVER_INITD_REDHAT_SCRIPT}.in
-                   ${CMAKE_CURRENT_BINARY_DIR}/${RSERVER_INITD_REDHAT_SCRIPT})
-    install(PROGRAMS ${CMAKE_CURRENT_BINARY_DIR}/${RSERVER_INITD_REDHAT_SCRIPT}
--           DESTINATION ${RSERVER_INITD_REDHAT_DIR})
-+           DESTINATION ${DISTRO_SHARE}/${RSERVER_INITD_REDHAT_DIR})
- 
-    # install configured suse init.d script
-    set(RSERVER_INITD_SUSE_DIR "extras/init.d/suse")
-@@ -158,13 +158,13 @@ if (UNIX AND NOT APPLE)
-    configure_file(${CMAKE_CURRENT_SOURCE_DIR}/${RSERVER_INITD_SUSE_SCRIPT}.in
-                   ${CMAKE_CURRENT_BINARY_DIR}/${RSERVER_INITD_SUSE_SCRIPT})
-    install(PROGRAMS ${CMAKE_CURRENT_BINARY_DIR}/${RSERVER_INITD_SUSE_SCRIPT}
--           DESTINATION ${RSERVER_INITD_SUSE_DIR})
-+           DESTINATION ${DISTRO_SHARE}/${RSERVER_INITD_SUSE_DIR})
- 
-    # install pam profile
-    set(RSERVER_PAM_DIR "extras/pam")
-    set(RSERVER_PAM_PROFILE "${RSERVER_PAM_DIR}/rstudio")
-    install(FILES ${CMAKE_CURRENT_SOURCE_DIR}/${RSERVER_PAM_PROFILE}
--           DESTINATION ${RSERVER_PAM_DIR})
-+           DESTINATION ${DISTRO_SHARE}/${RSERVER_PAM_DIR})
- 
-    # install configured apparmor profile
-    set(RSERVER_APPARMOR_DIR "extras/apparmor")
-@@ -172,9 +172,9 @@ if (UNIX AND NOT APPLE)
-    configure_file(${CMAKE_CURRENT_SOURCE_DIR}/${RSERVER_APPARMOR_PROFILE}.in
-                   ${CMAKE_CURRENT_BINARY_DIR}/${RSERVER_APPARMOR_PROFILE})
-    install(FILES ${CMAKE_CURRENT_BINARY_DIR}/${RSERVER_APPARMOR_PROFILE}
--           DESTINATION ${RSERVER_APPARMOR_DIR})
-+           DESTINATION ${DISTRO_SHARE}/${RSERVER_APPARMOR_DIR})
-    install(PROGRAMS ${CMAKE_CURRENT_SOURCE_DIR}/${RSERVER_APPARMOR_DIR}/apparmor-profile-load
--           DESTINATION ${RSERVER_APPARMOR_DIR})
-+           DESTINATION ${DISTRO_SHARE}/${RSERVER_APPARMOR_DIR})
- 
-    # install configured upstart profile
-    set(RSERVER_UPSTART_DIR "extras/upstart")
-@@ -182,6 +182,6 @@ if (UNIX AND NOT APPLE)
-    configure_file(${CMAKE_CURRENT_SOURCE_DIR}/${RSERVER_UPSTART_PROFILE}.in
-                   ${CMAKE_CURRENT_BINARY_DIR}/${RSERVER_UPSTART_PROFILE})
-    install(FILES ${CMAKE_CURRENT_BINARY_DIR}/${RSERVER_UPSTART_PROFILE}
--           DESTINATION ${RSERVER_UPSTART_DIR})
-+           DESTINATION ${DISTRO_SHARE}/${RSERVER_UPSTART_DIR})
- 
- endif()
-diff --git a/src/cpp/server/ServerOptions.cpp b/src/cpp/server/ServerOptions.cpp
-index 77a63f1..f0d25f0 100644
---- a/src/cpp/server/ServerOptions.cpp
-+++ b/src/cpp/server/ServerOptions.cpp
-@@ -201,7 +201,7 @@ ProgramStatus Options::read(int argc, char * const argv[])
- 
-    // convert relative paths by completing from the system installation
-    // path (this allows us to be relocatable)
--   resolvePath(installPath, &wwwLocalPath_);
-+   resolvePath(installPath.childPath(DISTRO_SHARE), &wwwLocalPath_);
-    resolvePath(installPath, &authPamHelperPath_);
-    resolvePath(installPath, &rsessionPath_);
-    resolvePath(installPath, &rldpathPath_);
-diff --git a/src/cpp/session/SessionOptions.cpp b/src/cpp/session/SessionOptions.cpp
-index 0df1081..777cc6a 100644
---- a/src/cpp/session/SessionOptions.cpp
-+++ b/src/cpp/session/SessionOptions.cpp
-@@ -333,12 +333,12 @@ core::ProgramStatus Options::read(int argc, char * const argv[])
- 
-    // convert relative paths by completing from the app resource path
--   resolvePath(resourcePath, &rResourcesPath_);
-+   resolvePath(resourcePath.childPath(DISTRO_SHARE), &rResourcesPath_);
-    resolvePath(resourcePath, &agreementFilePath_);
--   resolvePath(resourcePath, &wwwLocalPath_);
--   resolvePath(resourcePath, &coreRSourcePath_);
--   resolvePath(resourcePath, &modulesRSourcePath_);
--   resolvePath(resourcePath, &sessionLibraryPath_);
--   resolvePath(resourcePath, &sessionPackagesPath_);
-+   resolvePath(resourcePath.childPath(DISTRO_SHARE), &wwwLocalPath_);
-+   resolvePath(resourcePath.childPath(DISTRO_SHARE), &coreRSourcePath_);
-+   resolvePath(resourcePath.childPath(DISTRO_SHARE), &modulesRSourcePath_);
-+   resolvePath(resourcePath.childPath(DISTRO_SHARE), &sessionLibraryPath_);
-+   resolvePath(resourcePath.childPath(DISTRO_SHARE), &sessionPackagesPath_);
-    resolvePostbackPath(resourcePath, &rpostbackPath_);
- #ifdef _WIN32
-    resolvePath(resourcePath, &consoleIoPath_);
-

diff --git a/sci-mathematics/rstudio/files/rstudio-0.97.336-prefs.patch b/sci-mathematics/rstudio/files/rstudio-0.97.336-prefs.patch
deleted file mode 100644
index 3175d47235a..00000000000
--- a/sci-mathematics/rstudio/files/rstudio-0.97.336-prefs.patch
+++ /dev/null
@@ -1,24 +0,0 @@
-And now we fix src/gwt/build.xml since java's user preference class is
-braindead and insists on writing where it is not allowed.
-much thanks to http://www.allaboutbalance.com/articles/disableprefs/
-
-diff --git a/src/gwt/build.xml b/src/gwt/build.xml
-index e7d2418..ae3a331 100644
---- a/src/gwt/build.xml
-+++ b/src/gwt/build.xml
-@@ -25,6 +25,7 @@
-    <property name="gwt.extra.args" value=""/>
-    <property name="gwt.main.module" value="org.rstudio.studio.RStudio"/>
-    <property name="ace.bin" value="src/org/rstudio/studio/client/workbench/views/source/editors/text/ace"/>
-+   <property environment="env"/>
- 
-    <path id="project.class.path">
-       <pathelement location="bin"/>
-@@ -109,6 +110,7 @@
-          </classpath>
-          <!-- add jvmarg -Xss16M or similar if you see a StackOverflowError -->
-          <jvmarg value="-Xmx1024M"/>
-+         <jvmarg value="-Djava.util.prefs.userRoot=${env.T}"/>
-          <arg value="-war"/>
-          <arg value="www"/>
-          <arg value="-localWorkers"/>

diff --git a/sci-mathematics/rstudio/files/rstudio-0.97.551-boost-1.53.patch b/sci-mathematics/rstudio/files/rstudio-0.97.551-boost-1.53.patch
deleted file mode 100644
index 38bb63a8ab6..00000000000
--- a/sci-mathematics/rstudio/files/rstudio-0.97.551-boost-1.53.patch
+++ /dev/null
@@ -1,64 +0,0 @@
-=== modified file 'src/cpp/core/include/core/http/AsyncServer.hpp'
---- src/cpp/core/include/core/http/AsyncServer.hpp	2013-07-09 12:02:58 +0000
-+++ src/cpp/core/include/core/http/AsyncServer.hpp	2013-07-09 12:03:34 +0000
-@@ -264,7 +264,7 @@
-          
-          // convert to cannonical HttpConnection
-          boost::shared_ptr<AsyncConnection> pAsyncConnection =
--             boost::shared_static_cast<AsyncConnection>(pConnection);
-+             boost::static_pointer_cast<AsyncConnection>(pConnection);
- 
-          // call the appropriate handler to generate a response
-          std::string uri = pRequest->uri();
-
-=== modified file 'src/cpp/core/include/core/http/LocalStreamAsyncClient.hpp'
---- src/cpp/core/include/core/http/LocalStreamAsyncClient.hpp	2013-07-09 12:02:58 +0000
-+++ src/cpp/core/include/core/http/LocalStreamAsyncClient.hpp	2013-07-09 12:03:36 +0000
-@@ -87,7 +87,7 @@
-       boost::shared_ptr<AsyncClient<boost::asio::local::stream_protocol::socket> >
-                                     ptrShared = shared_from_this();
- 
--      return boost::shared_static_cast<LocalStreamAsyncClient>(ptrShared);
-+      return boost::static_pointer_cast<LocalStreamAsyncClient>(ptrShared);
-    }
- 
- private:
-
-=== modified file 'src/cpp/core/include/core/http/TcpIpAsyncClient.hpp'
---- src/cpp/core/include/core/http/TcpIpAsyncClient.hpp	2013-07-09 12:02:58 +0000
-+++ src/cpp/core/include/core/http/TcpIpAsyncClient.hpp	2013-07-09 12:03:32 +0000
-@@ -74,7 +74,7 @@
-       boost::shared_ptr<AsyncClient<boost::asio::ip::tcp::socket> > ptrShared
-                                                 = shared_from_this();
- 
--      return boost::shared_static_cast<TcpIpAsyncClient>(ptrShared);
-+      return boost::static_pointer_cast<TcpIpAsyncClient>(ptrShared);
-    }
- 
- private:
-
-=== modified file 'src/cpp/core/include/core/http/TcpIpAsyncClientSsl.hpp'
---- src/cpp/core/include/core/http/TcpIpAsyncClientSsl.hpp	2013-07-09 12:02:58 +0000
-+++ src/cpp/core/include/core/http/TcpIpAsyncClientSsl.hpp	2013-07-09 12:03:39 +0000
-@@ -109,7 +109,7 @@
-       boost::shared_ptr<AsyncClient<boost::asio::ssl::stream<boost::asio::ip::tcp::socket> > > ptrShared
-                                                  = shared_from_this();
- 
--      return boost::shared_static_cast<TcpIpAsyncClientSsl>(ptrShared);
-+      return boost::static_pointer_cast<TcpIpAsyncClientSsl>(ptrShared);
-    }
- 
-    virtual bool isShutdownError(const boost::system::error_code& ec)
-
-=== modified file 'src/cpp/session/http/SessionHttpConnectionListenerImpl.hpp'
---- src/cpp/session/http/SessionHttpConnectionListenerImpl.hpp	2013-07-09 12:02:58 +0000
-+++ src/cpp/session/http/SessionHttpConnectionListenerImpl.hpp	2013-07-09 12:03:29 +0000
-@@ -256,7 +256,7 @@
-    {
-       // convert to cannonical HttpConnection
-       boost::shared_ptr<HttpConnection> ptrHttpConnection =
--            boost::shared_static_cast<HttpConnection>(ptrConnection);
-+            boost::static_pointer_cast<HttpConnection>(ptrConnection);
- 
-       if (!authenticate(ptrHttpConnection))
-       {

diff --git a/sci-mathematics/rstudio/files/rstudio-0.97.551-linker_flags.patch b/sci-mathematics/rstudio/files/rstudio-0.97.551-linker_flags.patch
deleted file mode 100644
index a336fccbc98..00000000000
--- a/sci-mathematics/rstudio/files/rstudio-0.97.551-linker_flags.patch
+++ /dev/null
@@ -1,18 +0,0 @@
-Some gcc hardening options were added, however since we add
-"-Wl,--as-needed" we end up with "-Wl,--as-needed;-Wl,-z,relro" which
-leads to linker errors about unknown options, if we make it so the
-as-needed option is the last option on the line, everything is fine.
-
-diff --git a/src/cpp/CMakeLists.txt b/src/cpp/CMakeLists.txt
-index 0589ca0..fe5bd5f 100644
---- a/src/cpp/CMakeLists.txt
-+++ b/src/cpp/CMakeLists.txt
-@@ -57,7 +57,7 @@ if(UNIX)
-       add_definitions(-D_FORTIFY_SOURCE=2)
-       add_definitions(-fstack-protector --param ssp-buffer-size=4)
-       add_definitions(-pie -fPIE)
--      set(CMAKE_EXE_LINKER_FLAGS "${CMAKE_EXE_LINKER_FLAGS} -Wl,-z,relro,-z,now")
-+      set(CMAKE_EXE_LINKER_FLAGS "-Wl,-z,relro,-z,now ${CMAKE_EXE_LINKER_FLAGS}")
-    endif()
- 
- # Win32 specific global directives

diff --git a/sci-mathematics/rstudio/files/rstudio-0.97.551-paths.patch b/sci-mathematics/rstudio/files/rstudio-0.97.551-paths.patch
deleted file mode 100644
index 7b44374a72d..00000000000
--- a/sci-mathematics/rstudio/files/rstudio-0.97.551-paths.patch
+++ /dev/null
@@ -1,112 +0,0 @@
-change the install path, as by default everything is dumped right under
-the prefix. After fixing install paths, now fix the source so the
-program can find the moved resources.
-	
-diff --git a/CMakeGlobals.txt b/CMakeGlobals.txt
-index da74970..1537bff 100644
---- a/CMakeGlobals.txt
-+++ b/CMakeGlobals.txt
-@@ -103,7 +103,7 @@ else()
-    else()
-      set(RSTUDIO_INSTALL_BIN bin)
-    endif()
--   set(RSTUDIO_INSTALL_SUPPORTING .)
-+   set(RSTUDIO_INSTALL_SUPPORTING ${DISTRO_SHARE})
- endif()
- 
- # if the install prefix is /usr/local then tweak as appropriate
-diff --git a/src/cpp/server/CMakeLists.txt b/src/cpp/server/CMakeLists.txt
-index af4db1c..96b767e 100644
---- a/src/cpp/server/CMakeLists.txt
-+++ b/src/cpp/server/CMakeLists.txt
-@@ -142,7 +142,7 @@ if (UNIX AND NOT APPLE)
-    configure_file(${CMAKE_CURRENT_SOURCE_DIR}/${RSERVER_INITD_DEBIAN_SCRIPT}.in
-                   ${CMAKE_CURRENT_BINARY_DIR}/${RSERVER_INITD_DEBIAN_SCRIPT})
-    install(PROGRAMS ${CMAKE_CURRENT_BINARY_DIR}/${RSERVER_INITD_DEBIAN_SCRIPT}
--           DESTINATION ${RSERVER_INITD_DEBIAN_DIR})
-+           DESTINATION ${DISTRO_SHARE}/${RSERVER_INITD_DEBIAN_DIR})
- 
-    # install configured redhat init.d script
-    set(RSERVER_INITD_REDHAT_DIR "extras/init.d/redhat")
-@@ -150,7 +150,7 @@ if (UNIX AND NOT APPLE)
-    configure_file(${CMAKE_CURRENT_SOURCE_DIR}/${RSERVER_INITD_REDHAT_SCRIPT}.in
-                   ${CMAKE_CURRENT_BINARY_DIR}/${RSERVER_INITD_REDHAT_SCRIPT})
-    install(PROGRAMS ${CMAKE_CURRENT_BINARY_DIR}/${RSERVER_INITD_REDHAT_SCRIPT}
--           DESTINATION ${RSERVER_INITD_REDHAT_DIR})
-+           DESTINATION ${DISTRO_SHARE}/${RSERVER_INITD_REDHAT_DIR})
- 
-    # install configured suse init.d script
-    set(RSERVER_INITD_SUSE_DIR "extras/init.d/suse")
-@@ -158,13 +158,13 @@ if (UNIX AND NOT APPLE)
-    configure_file(${CMAKE_CURRENT_SOURCE_DIR}/${RSERVER_INITD_SUSE_SCRIPT}.in
-                   ${CMAKE_CURRENT_BINARY_DIR}/${RSERVER_INITD_SUSE_SCRIPT})
-    install(PROGRAMS ${CMAKE_CURRENT_BINARY_DIR}/${RSERVER_INITD_SUSE_SCRIPT}
--           DESTINATION ${RSERVER_INITD_SUSE_DIR})
-+           DESTINATION ${DISTRO_SHARE}/${RSERVER_INITD_SUSE_DIR})
- 
-    # install pam profile
-    set(RSERVER_PAM_DIR "extras/pam")
-    set(RSERVER_PAM_PROFILE "${RSERVER_PAM_DIR}/rstudio")
-    install(FILES ${CMAKE_CURRENT_SOURCE_DIR}/${RSERVER_PAM_PROFILE}
--           DESTINATION ${RSERVER_PAM_DIR})
-+           DESTINATION ${DISTRO_SHARE}/${RSERVER_PAM_DIR})
- 
-    # install configured apparmor profile
-    set(RSERVER_APPARMOR_DIR "extras/apparmor")
-@@ -172,9 +172,9 @@ if (UNIX AND NOT APPLE)
-    configure_file(${CMAKE_CURRENT_SOURCE_DIR}/${RSERVER_APPARMOR_PROFILE}.in
-                   ${CMAKE_CURRENT_BINARY_DIR}/${RSERVER_APPARMOR_PROFILE})
-    install(FILES ${CMAKE_CURRENT_BINARY_DIR}/${RSERVER_APPARMOR_PROFILE}
--           DESTINATION ${RSERVER_APPARMOR_DIR})
-+           DESTINATION ${DISTRO_SHARE}/${RSERVER_APPARMOR_DIR})
-    install(PROGRAMS ${CMAKE_CURRENT_SOURCE_DIR}/${RSERVER_APPARMOR_DIR}/apparmor-profile-load
--           DESTINATION ${RSERVER_APPARMOR_DIR})
-+           DESTINATION ${DISTRO_SHARE}/${RSERVER_APPARMOR_DIR})
- 
-    # install configured upstart profile
-    set(RSERVER_UPSTART_DIR "extras/upstart")
-@@ -182,6 +182,6 @@ if (UNIX AND NOT APPLE)
-    configure_file(${CMAKE_CURRENT_SOURCE_DIR}/${RSERVER_UPSTART_PROFILE}.in
-                   ${CMAKE_CURRENT_BINARY_DIR}/${RSERVER_UPSTART_PROFILE})
-    install(FILES ${CMAKE_CURRENT_BINARY_DIR}/${RSERVER_UPSTART_PROFILE}
--           DESTINATION ${RSERVER_UPSTART_DIR})
-+           DESTINATION ${DISTRO_SHARE}/${RSERVER_UPSTART_DIR})
- 
- endif()
-diff --git a/src/cpp/server/ServerOptions.cpp b/src/cpp/server/ServerOptions.cpp
-index 77a63f1..f0d25f0 100644
---- a/src/cpp/server/ServerOptions.cpp
-+++ b/src/cpp/server/ServerOptions.cpp
-@@ -201,7 +201,7 @@ ProgramStatus Options::read(int argc, char * const argv[])
- 
-    // convert relative paths by completing from the system installation
-    // path (this allows us to be relocatable)
--   resolvePath(installPath, &wwwLocalPath_);
-+   resolvePath(installPath.childPath(DISTRO_SHARE), &wwwLocalPath_);
-    resolvePath(installPath, &authPamHelperPath_);
-    resolvePath(installPath, &rsessionPath_);
-    resolvePath(installPath, &rldpathPath_);
-diff --git a/src/cpp/session/SessionOptions.cpp b/src/cpp/session/SessionOptions.cpp
-index 0df1081..777cc6a 100644
---- a/src/cpp/session/SessionOptions.cpp
-+++ b/src/cpp/session/SessionOptions.cpp
-@@ -333,12 +333,12 @@ core::ProgramStatus Options::read(int argc, char * const argv[])
- 
-    // convert relative paths by completing from the app resource path
--   resolvePath(resourcePath, &rResourcesPath_);
-+   resolvePath(resourcePath.childPath(DISTRO_SHARE), &rResourcesPath_);
-    resolvePath(resourcePath, &agreementFilePath_);
--   resolvePath(resourcePath, &wwwLocalPath_);
--   resolvePath(resourcePath, &coreRSourcePath_);
--   resolvePath(resourcePath, &modulesRSourcePath_);
--   resolvePath(resourcePath, &sessionLibraryPath_);
--   resolvePath(resourcePath, &sessionPackagesPath_);
-+   resolvePath(resourcePath.childPath(DISTRO_SHARE), &wwwLocalPath_);
-+   resolvePath(resourcePath.childPath(DISTRO_SHARE), &coreRSourcePath_);
-+   resolvePath(resourcePath.childPath(DISTRO_SHARE), &modulesRSourcePath_);
-+   resolvePath(resourcePath.childPath(DISTRO_SHARE), &sessionLibraryPath_);
-+   resolvePath(resourcePath.childPath(DISTRO_SHARE), &sessionPackagesPath_);
-    resolvePostbackPath(resourcePath, &rpostbackPath_);
- #ifdef _WIN32
-    resolvePath(resourcePath, &consoleIoPath_);
-

diff --git a/sci-mathematics/rstudio/files/rstudio-0.97.551-prefs.patch b/sci-mathematics/rstudio/files/rstudio-0.97.551-prefs.patch
deleted file mode 100644
index 3175d47235a..00000000000
--- a/sci-mathematics/rstudio/files/rstudio-0.97.551-prefs.patch
+++ /dev/null
@@ -1,24 +0,0 @@
-And now we fix src/gwt/build.xml since java's user preference class is
-braindead and insists on writing where it is not allowed.
-much thanks to http://www.allaboutbalance.com/articles/disableprefs/
-
-diff --git a/src/gwt/build.xml b/src/gwt/build.xml
-index e7d2418..ae3a331 100644
---- a/src/gwt/build.xml
-+++ b/src/gwt/build.xml
-@@ -25,6 +25,7 @@
-    <property name="gwt.extra.args" value=""/>
-    <property name="gwt.main.module" value="org.rstudio.studio.RStudio"/>
-    <property name="ace.bin" value="src/org/rstudio/studio/client/workbench/views/source/editors/text/ace"/>
-+   <property environment="env"/>
- 
-    <path id="project.class.path">
-       <pathelement location="bin"/>
-@@ -109,6 +110,7 @@
-          </classpath>
-          <!-- add jvmarg -Xss16M or similar if you see a StackOverflowError -->
-          <jvmarg value="-Xmx1024M"/>
-+         <jvmarg value="-Djava.util.prefs.userRoot=${env.T}"/>
-          <arg value="-war"/>
-          <arg value="www"/>
-          <arg value="-localWorkers"/>

diff --git a/sci-mathematics/rstudio/rstudio-0.97.336.ebuild b/sci-mathematics/rstudio/rstudio-0.97.336.ebuild
deleted file mode 100644
index e10f30a21ca..00000000000
--- a/sci-mathematics/rstudio/rstudio-0.97.336.ebuild
+++ /dev/null
@@ -1,143 +0,0 @@
-# Copyright 1999-2016 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-inherit eutils user cmake-utils gnome2-utils pam versionator fdo-mime java-pkg-2 pax-utils
-
-# TODO
-# * package gin and gwt
-# * use dict from tree, linguas
-# * do src_test (use junit from tree?)
-# * fix the about/help/menu and get rid of license
-
-GWTVER=2.5.0.rc1
-GINVER=1.5
-
-DESCRIPTION="IDE for the R language"
-HOMEPAGE="http://www.rstudio.org"
-SRC_URI="
-	https://github.com/rstudio/rstudio/archive/v${PV}.tar.gz -> ${P}.tar.gz
-	https://s3.amazonaws.com/rstudio-buildtools/gin-${GINVER}.zip
-	https://s3.amazonaws.com/rstudio-buildtools/gwt-${GWTVER}.zip
-	https://s3.amazonaws.com/rstudio-dictionaries/core-dictionaries.zip"
-
-LICENSE="AGPL-3"
-SLOT="0"
-KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
-IUSE="dedicated server"
-
-QTVER=4.8
-QTSLOT=4
-RDEPEND="
-	>=dev-lang/R-2.11.1
-	>=dev-libs/boost-1.50:=
-	dev-libs/mathjax
-	dev-libs/openssl:0
-	>=virtual/jre-1.5:=
-	x11-libs/pango
-	!dedicated? (
-		>=dev-qt/qtcore-${QTVER}:${QTSLOT}
-		>=dev-qt/qtdbus-${QTVER}:${QTSLOT}
-		>=dev-qt/qtgui-${QTVER}:${QTSLOT}
-		>=dev-qt/qtwebkit-${QTVER}:${QTSLOT}
-		>=dev-qt/qtxmlpatterns-${QTVER}:${QTSLOT}
-		server? ( virtual/pam )
-	)
-	dedicated? ( virtual/pam )"
-DEPEND="${RDEPEND}
-	app-arch/unzip
-	dev-java/ant-core
-	>=virtual/jdk-1.5
-	virtual/pkgconfig"
-#	test? ( dev-java/junit:4 )
-
-src_unpack() {
-	unpack ${P}.tar.gz gwt-${GWTVER}.zip
-	cd "${S}" || die
-	mkdir -p src/gwt/lib/{gin,gwt} dependencies/common/dictionaries || die
-	mv ../gwt-${GWTVER} src/gwt/lib/gwt/${GWTVER} || die
-	unzip -qd src/gwt/lib/gin/${GINVER} "${DISTDIR}"/gin-${GINVER}.zip || die
-	unzip -qd dependencies/common/dictionaries "${DISTDIR}"/core-dictionaries.zip || die
-}
-
-src_prepare() {
-	java-pkg-2_src_prepare
-
-	egit_clean
-
-	epatch \
-		"${FILESDIR}"/${P}-prefs.patch \
-		"${FILESDIR}"/${P}-paths.patch \
-		"${FILESDIR}"/${P}-linker_flags.patch \
-		"${FILESDIR}"/${P}-boost-1.53.patch
-
-	# Adding -DDISTRO_SHARE=... to append-flags breaks cmake so using
-	# this sed hack for now. ~RMH
-	sed -i \
-		-e "s|DISTRO_SHARE|\"share/${PN}\"|g" \
-		src/cpp/server/ServerOptions.cpp \
-		src/cpp/session/SessionOptions.cpp || die
-
-	# use mathjax from system
-	ln -sf "${EPREFIX}"/usr/share/mathjax dependencies/common/mathjax || die
-
-	# make sure icons and mime stuff are with prefix
-	sed -i \
-		-e "s:/usr:${EPREFIX}/usr:g" \
-		CMakeGlobals.txt src/cpp/desktop/CMakeLists.txt || die
-
-	# specify that namespace core the is in the global namespace and not
-	# relative to some other namespace (like its ::core not ::boost::core)
-	find . \( -name *.cpp -or -name *.hpp \) -exec sed \
-		-e 's@<core::@< ::core::@g' -e 's@\([^:]\)core::@\1::core::@g' -i {} \;
-}
-
-src_configure() {
-	export RSTUDIO_VERSION_MAJOR=$(get_version_component_range 1)
-	export RSTUDIO_VERSION_MINOR=$(get_version_component_range 2)
-	export RSTUDIO_VERSION_PATCH=$(get_version_component_range 3)
-
-	local mycmakeargs=(
-		-DDISTRO_SHARE=share/${PN}
-		$(cmake-utils_use !dedicated RSTUDIO_INSTALL_FREEDESKTOP)
-		-DRSTUDIO_TARGET=$(usex dedicated "Server" "$(usex server "All" "Desktop")")
-		)
-
-	cmake-utils_src_configure
-}
-
-src_compile() {
-	cmake-utils_src_compile
-}
-
-src_install() {
-	cmake-utils_src_install
-	pax-mark m "${ED}usr/bin/rstudio"
-	if use dedicated || use server; then
-		dopamd src/cpp/server/extras/pam/rstudio
-		newinitd "${FILESDIR}"/rstudio-server.initd rstudio-server
-	fi
-}
-
-pkg_preinst() {
-	use dedicated || gnome2_icon_savelist
-	java-pkg-2_pkg_preinst
-}
-
-pkg_postinst() {
-	use dedicated || { fdo-mime_desktop_database_update
-		fdo-mime_mime_database_update
-		gnome2_icon_cache_update ;}
-
-	if use dedicated || use server; then
-		enewgroup rstudio-server
-		enewuser rstudio-server -1 -1 -1 rstudio-server
-	fi
-}
-
-pkg_postrm() {
-	use dedicated || { fdo-mime_desktop_database_update
-		fdo-mime_mime_database_update
-		gnome2_icon_cache_update ;}
-}

diff --git a/sci-mathematics/rstudio/rstudio-0.97.551.ebuild b/sci-mathematics/rstudio/rstudio-0.97.551.ebuild
deleted file mode 100644
index e10f30a21ca..00000000000
--- a/sci-mathematics/rstudio/rstudio-0.97.551.ebuild
+++ /dev/null
@@ -1,143 +0,0 @@
-# Copyright 1999-2016 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-inherit eutils user cmake-utils gnome2-utils pam versionator fdo-mime java-pkg-2 pax-utils
-
-# TODO
-# * package gin and gwt
-# * use dict from tree, linguas
-# * do src_test (use junit from tree?)
-# * fix the about/help/menu and get rid of license
-
-GWTVER=2.5.0.rc1
-GINVER=1.5
-
-DESCRIPTION="IDE for the R language"
-HOMEPAGE="http://www.rstudio.org"
-SRC_URI="
-	https://github.com/rstudio/rstudio/archive/v${PV}.tar.gz -> ${P}.tar.gz
-	https://s3.amazonaws.com/rstudio-buildtools/gin-${GINVER}.zip
-	https://s3.amazonaws.com/rstudio-buildtools/gwt-${GWTVER}.zip
-	https://s3.amazonaws.com/rstudio-dictionaries/core-dictionaries.zip"
-
-LICENSE="AGPL-3"
-SLOT="0"
-KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
-IUSE="dedicated server"
-
-QTVER=4.8
-QTSLOT=4
-RDEPEND="
-	>=dev-lang/R-2.11.1
-	>=dev-libs/boost-1.50:=
-	dev-libs/mathjax
-	dev-libs/openssl:0
-	>=virtual/jre-1.5:=
-	x11-libs/pango
-	!dedicated? (
-		>=dev-qt/qtcore-${QTVER}:${QTSLOT}
-		>=dev-qt/qtdbus-${QTVER}:${QTSLOT}
-		>=dev-qt/qtgui-${QTVER}:${QTSLOT}
-		>=dev-qt/qtwebkit-${QTVER}:${QTSLOT}
-		>=dev-qt/qtxmlpatterns-${QTVER}:${QTSLOT}
-		server? ( virtual/pam )
-	)
-	dedicated? ( virtual/pam )"
-DEPEND="${RDEPEND}
-	app-arch/unzip
-	dev-java/ant-core
-	>=virtual/jdk-1.5
-	virtual/pkgconfig"
-#	test? ( dev-java/junit:4 )
-
-src_unpack() {
-	unpack ${P}.tar.gz gwt-${GWTVER}.zip
-	cd "${S}" || die
-	mkdir -p src/gwt/lib/{gin,gwt} dependencies/common/dictionaries || die
-	mv ../gwt-${GWTVER} src/gwt/lib/gwt/${GWTVER} || die
-	unzip -qd src/gwt/lib/gin/${GINVER} "${DISTDIR}"/gin-${GINVER}.zip || die
-	unzip -qd dependencies/common/dictionaries "${DISTDIR}"/core-dictionaries.zip || die
-}
-
-src_prepare() {
-	java-pkg-2_src_prepare
-
-	egit_clean
-
-	epatch \
-		"${FILESDIR}"/${P}-prefs.patch \
-		"${FILESDIR}"/${P}-paths.patch \
-		"${FILESDIR}"/${P}-linker_flags.patch \
-		"${FILESDIR}"/${P}-boost-1.53.patch
-
-	# Adding -DDISTRO_SHARE=... to append-flags breaks cmake so using
-	# this sed hack for now. ~RMH
-	sed -i \
-		-e "s|DISTRO_SHARE|\"share/${PN}\"|g" \
-		src/cpp/server/ServerOptions.cpp \
-		src/cpp/session/SessionOptions.cpp || die
-
-	# use mathjax from system
-	ln -sf "${EPREFIX}"/usr/share/mathjax dependencies/common/mathjax || die
-
-	# make sure icons and mime stuff are with prefix
-	sed -i \
-		-e "s:/usr:${EPREFIX}/usr:g" \
-		CMakeGlobals.txt src/cpp/desktop/CMakeLists.txt || die
-
-	# specify that namespace core the is in the global namespace and not
-	# relative to some other namespace (like its ::core not ::boost::core)
-	find . \( -name *.cpp -or -name *.hpp \) -exec sed \
-		-e 's@<core::@< ::core::@g' -e 's@\([^:]\)core::@\1::core::@g' -i {} \;
-}
-
-src_configure() {
-	export RSTUDIO_VERSION_MAJOR=$(get_version_component_range 1)
-	export RSTUDIO_VERSION_MINOR=$(get_version_component_range 2)
-	export RSTUDIO_VERSION_PATCH=$(get_version_component_range 3)
-
-	local mycmakeargs=(
-		-DDISTRO_SHARE=share/${PN}
-		$(cmake-utils_use !dedicated RSTUDIO_INSTALL_FREEDESKTOP)
-		-DRSTUDIO_TARGET=$(usex dedicated "Server" "$(usex server "All" "Desktop")")
-		)
-
-	cmake-utils_src_configure
-}
-
-src_compile() {
-	cmake-utils_src_compile
-}
-
-src_install() {
-	cmake-utils_src_install
-	pax-mark m "${ED}usr/bin/rstudio"
-	if use dedicated || use server; then
-		dopamd src/cpp/server/extras/pam/rstudio
-		newinitd "${FILESDIR}"/rstudio-server.initd rstudio-server
-	fi
-}
-
-pkg_preinst() {
-	use dedicated || gnome2_icon_savelist
-	java-pkg-2_pkg_preinst
-}
-
-pkg_postinst() {
-	use dedicated || { fdo-mime_desktop_database_update
-		fdo-mime_mime_database_update
-		gnome2_icon_cache_update ;}
-
-	if use dedicated || use server; then
-		enewgroup rstudio-server
-		enewuser rstudio-server -1 -1 -1 rstudio-server
-	fi
-}
-
-pkg_postrm() {
-	use dedicated || { fdo-mime_desktop_database_update
-		fdo-mime_mime_database_update
-		gnome2_icon_cache_update ;}
-}

diff --git a/sci-mathematics/rstudio/rstudio-0.98.1028.ebuild b/sci-mathematics/rstudio/rstudio-0.98.1028.ebuild
deleted file mode 100644
index ebaf1bd04ec..00000000000
--- a/sci-mathematics/rstudio/rstudio-0.98.1028.ebuild
+++ /dev/null
@@ -1,164 +0,0 @@
-# Copyright 1999-2016 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-inherit eutils cmake-utils gnome2-utils versionator fdo-mime java-pkg-2 pax-utils
-
-# TODO
-# * package gin and gwt
-# * use dict from tree, linguas
-# * do src_test (use junit from tree?)
-
-# update from scripts in dependencies/common
-GWTVER=2.6.0
-GINVER=1.5
-SELENIUMVER=2.37.0
-CHROMEDRIVER_VER=2.7
-PANDOC_VER=1.12.3
-PACKRAT_VER=0.3.0
-RMARKDOWN_VER=0.2.49
-
-DESCRIPTION="IDE for the R language"
-HOMEPAGE="
-	http://www.rstudio.org
-	https://github.com/rstudio/rstudio/"
-SRC_URI="
-	https://github.com/rstudio/rstudio/archive/v${PV}.tar.gz -> ${P}.tar.gz
-	https://s3.amazonaws.com/rstudio-buildtools/gin-${GINVER}.zip
-	https://s3.amazonaws.com/rstudio-buildtools/gwt-${GWTVER}.zip
-	https://s3.amazonaws.com/rstudio-buildtools/selenium-java-${SELENIUMVER}.zip
-	https://s3.amazonaws.com/rstudio-buildtools/selenium-server-standalone-${SELENIUMVER}.jar
-	https://s3.amazonaws.com/rstudio-buildtools/chromedriver-linux
-	https://s3.amazonaws.com/rstudio-dictionaries/core-dictionaries.zip
-	https://dev.gentoo.org/~hasufell/distfiles/packrat_${PACKRAT_VER}.tar.gz
-	https://dev.gentoo.org/~hasufell/distfiles/rmarkdown_${RMARKDOWN_VER}.tar.gz"
-
-LICENSE="AGPL-3"
-SLOT="0"
-KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
-IUSE=""
-
-QTVER=4.8
-QTSLOT=4
-RDEPEND="
-	app-text/pandoc
-	dev-haskell/pandoc-citeproc
-	>=dev-lang/R-2.11.1
-	>=dev-libs/boost-1.50
-	dev-libs/mathjax
-	dev-libs/openssl:0
-	sys-apps/util-linux
-	sys-libs/zlib
-	>=virtual/jre-1.5:=
-	x11-libs/pango
-	>=dev-qt/qtcore-${QTVER}:${QTSLOT}
-	>=dev-qt/qtdbus-${QTVER}:${QTSLOT}
-	>=dev-qt/qtgui-${QTVER}:${QTSLOT}
-	>=dev-qt/qtwebkit-${QTVER}:${QTSLOT}
-	>=dev-qt/qtxmlpatterns-${QTVER}:${QTSLOT}"
-DEPEND="${RDEPEND}
-	app-arch/unzip
-	dev-java/ant-core
-	>=virtual/jdk-1.5
-	virtual/pkgconfig"
-#	test? ( dev-java/junit:4 )
-
-src_unpack() {
-	unpack ${P}.tar.gz gwt-${GWTVER}.zip
-	cd "${S}" || die
-	mkdir -p src/gwt/lib/{gin,gwt} \
-		dependencies/common/dictionaries \
-		src/gwt/lib/selenium/${SELENIUMVER} \
-		src/gwt/lib/selenium/chromedriver/${CHROMEDRIVER_VER} || die
-	mv ../gwt-${GWTVER} src/gwt/lib/gwt/${GWTVER} || die
-	unzip -qd src/gwt/lib/gin/${GINVER} \
-		"${DISTDIR}"/gin-${GINVER}.zip || die
-	unzip -qd dependencies/common/dictionaries \
-		"${DISTDIR}"/core-dictionaries.zip || die
-	unzip -qd src/gwt/lib/selenium/${SELENIUMVER} \
-		"${DISTDIR}"/selenium-java-${SELENIUMVER}.zip || die
-	cp "${DISTDIR}"/selenium-server-standalone-${SELENIUMVER}.jar \
-		src/gwt/lib/selenium/${SELENIUMVER}/ || die
-	cp "${DISTDIR}"/chromedriver-linux \
-		src/gwt/lib/selenium/chromedriver/${CHROMEDRIVER_VER}/ || die
-	cd dependencies/common || die
-	unpack packrat_${PACKRAT_VER}.tar.gz
-	unpack rmarkdown_${RMARKDOWN_VER}.tar.gz
-	cp "${DISTDIR}"/rmarkdown_${RMARKDOWN_VER}.tar.gz \
-		. || die
-	cp "${DISTDIR}"/packrat_${PACKRAT_VER}.tar.gz \
-		. || die
-}
-
-src_prepare() {
-	java-pkg-2_src_prepare
-
-	egit_clean
-
-	epatch \
-		"${FILESDIR}"/${PN}-0.98.490-prefs.patch \
-		"${FILESDIR}"/${PN}-0.98.932-paths.patch \
-		"${FILESDIR}"/${PN}-0.98.932-pandoc.patch \
-		"${FILESDIR}"/${PN}-0.98.490-linker_flags.patch
-
-	# Adding -DDISTRO_SHARE=... to append-flags breaks cmake so using
-	# this sed hack for now. ~RMH
-	sed -i \
-		-e "s|DISTRO_SHARE|\"share/${PN}\"|g" \
-		src/cpp/server/ServerOptions.cpp \
-		src/cpp/session/SessionOptions.cpp || die
-
-	# use mathjax from system
-	ln -sf "${EPREFIX}"/usr/share/mathjax dependencies/common/mathjax || die
-
-	# make sure icons and mime stuff are with prefix
-	sed -i \
-		-e "s:/usr:${EPREFIX}/usr:g" \
-		CMakeGlobals.txt src/cpp/desktop/CMakeLists.txt || die
-
-	# specify that namespace core the is in the global namespace and not
-	# relative to some other namespace (like its ::core not ::boost::core)
-	find . \( -name *.cpp -or -name *.hpp \) -exec sed \
-		-e 's@<core::@< ::core::@g' -e 's@\([^:]\)core::@\1::core::@g' -i {} \;
-}
-
-src_configure() {
-	export RSTUDIO_VERSION_MAJOR=$(get_version_component_range 1)
-	export RSTUDIO_VERSION_MINOR=$(get_version_component_range 2)
-	export RSTUDIO_VERSION_PATCH=$(get_version_component_range 3)
-
-	local mycmakeargs=(
-		-DDISTRO_SHARE=share/${PN}
-		-DRSTUDIO_INSTALL_FREEDESKTOP=ON
-		-DRSTUDIO_TARGET=Desktop
-		)
-
-	cmake-utils_src_configure
-}
-
-src_compile() {
-	cmake-utils_src_compile
-}
-
-src_install() {
-	cmake-utils_src_install
-	pax-mark m "${ED}usr/bin/rstudio"
-}
-
-pkg_preinst() {
-	gnome2_icon_savelist
-	java-pkg-2_pkg_preinst
-}
-
-pkg_postinst() {
-	fdo-mime_desktop_database_update
-	fdo-mime_mime_database_update
-	gnome2_icon_cache_update
-}
-
-pkg_postrm() {
-	fdo-mime_desktop_database_update
-	fdo-mime_mime_database_update
-	gnome2_icon_cache_update
-}

diff --git a/sci-mathematics/rstudio/rstudio-0.98.1091.ebuild b/sci-mathematics/rstudio/rstudio-0.98.1091.ebuild
deleted file mode 100644
index eeda0fd3c15..00000000000
--- a/sci-mathematics/rstudio/rstudio-0.98.1091.ebuild
+++ /dev/null
@@ -1,198 +0,0 @@
-# Copyright 1999-2016 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-inherit eutils user cmake-utils gnome2-utils pam versionator fdo-mime java-pkg-2 pax-utils
-
-# TODO
-# * package gin and gwt
-# * use dict from tree, linguas
-# * do src_test (use junit from tree?)
-
-# update from scripts in dependencies/common
-GWTVER=2.6.0
-GINVER=1.5
-SELENIUMVER=2.37.0
-CHROMEDRIVER_VER=2.7
-PANDOC_VER=1.12.4.2
-PACKRAT_VER=0.98.1000
-RMARKDOWN_VER=0.98.1000
-SHINYAPPS_VER=0.98.1000
-
-DESCRIPTION="IDE for the R language"
-HOMEPAGE="
-	http://www.rstudio.org
-	https://github.com/rstudio/rstudio/"
-SRC_URI="
-	https://github.com/rstudio/rstudio/archive/v${PV}.tar.gz -> ${P}.tar.gz
-	https://s3.amazonaws.com/rstudio-buildtools/gin-${GINVER}.zip
-	https://s3.amazonaws.com/rstudio-buildtools/gwt-${GWTVER}.zip
-	https://s3.amazonaws.com/rstudio-buildtools/selenium-java-${SELENIUMVER}.zip
-	https://s3.amazonaws.com/rstudio-buildtools/selenium-server-standalone-${SELENIUMVER}.jar
-	https://s3.amazonaws.com/rstudio-buildtools/chromedriver-linux
-	https://s3.amazonaws.com/rstudio-dictionaries/core-dictionaries.zip
-	https://dev.gentoo.org/~gienah/distfiles/packrat-${PACKRAT_VER}.tar.gz
-	https://dev.gentoo.org/~gienah/distfiles/rmarkdown-${RMARKDOWN_VER}.tar.gz
-	https://dev.gentoo.org/~gienah/distfiles/shinyapps-${SHINYAPPS_VER}.tar.gz"
-
-LICENSE="AGPL-3"
-SLOT="0"
-KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
-IUSE="dedicated server"
-
-QTVER=4.8
-QTSLOT=4
-RDEPEND="
-	app-text/pandoc
-	dev-haskell/pandoc-citeproc
-	>=dev-lang/R-2.11.1
-	>=dev-libs/boost-1.50:=
-	>=dev-libs/mathjax-2.3
-	dev-libs/openssl:0
-	sys-apps/util-linux
-	sys-libs/zlib
-	>=virtual/jre-1.5:=
-	x11-libs/pango
-	!dedicated? (
-		>=dev-qt/qtcore-${QTVER}:${QTSLOT}
-		>=dev-qt/qtdbus-${QTVER}:${QTSLOT}
-		>=dev-qt/qtgui-${QTVER}:${QTSLOT}
-		>=dev-qt/qtwebkit-${QTVER}:${QTSLOT}
-		>=dev-qt/qtxmlpatterns-${QTVER}:${QTSLOT}
-		server? ( virtual/pam )
-	)
-	dedicated? ( virtual/pam )"
-DEPEND="${RDEPEND}
-	app-arch/unzip
-	dev-java/ant-core
-	>=virtual/jdk-1.5
-	virtual/pkgconfig"
-#	test? ( dev-java/junit:4 )
-
-src_unpack() {
-	unpack ${P}.tar.gz gwt-${GWTVER}.zip
-	cd "${S}" || die
-	mkdir -p src/gwt/lib/{gin,gwt} \
-		dependencies/common/dictionaries \
-		src/gwt/lib/selenium/${SELENIUMVER} \
-		src/gwt/lib/selenium/chromedriver/${CHROMEDRIVER_VER} || die
-	mv ../gwt-${GWTVER} src/gwt/lib/gwt/${GWTVER} || die
-	unzip -qd src/gwt/lib/gin/${GINVER} \
-		"${DISTDIR}"/gin-${GINVER}.zip || die
-	unzip -qd dependencies/common/dictionaries \
-		"${DISTDIR}"/core-dictionaries.zip || die
-	unzip -qd src/gwt/lib/selenium/${SELENIUMVER} \
-		"${DISTDIR}"/selenium-java-${SELENIUMVER}.zip || die
-	cp "${DISTDIR}"/selenium-server-standalone-${SELENIUMVER}.jar \
-		src/gwt/lib/selenium/${SELENIUMVER}/ || die
-	cp "${DISTDIR}"/chromedriver-linux \
-		src/gwt/lib/selenium/chromedriver/${CHROMEDRIVER_VER}/ || die
-	cd dependencies/common || die
-	unpack packrat-${PACKRAT_VER}.tar.gz
-	unpack rmarkdown-${RMARKDOWN_VER}.tar.gz
-	unpack shinyapps-${RMARKDOWN_VER}.tar.gz
-	cp "${DISTDIR}"/rmarkdown-${RMARKDOWN_VER}.tar.gz \
-		. || die
-	cp "${DISTDIR}"/packrat-${PACKRAT_VER}.tar.gz \
-		. || die
-	cp "${DISTDIR}"/shinyapps-${SHINYAPPS_VER}.tar.gz \
-		. || die
-}
-
-src_prepare() {
-	java-pkg-2_src_prepare
-
-	egit_clean
-
-	epatch \
-		"${FILESDIR}"/${PN}-0.98.490-prefs.patch \
-		"${FILESDIR}"/${PN}-0.98.932-paths.patch \
-		"${FILESDIR}"/${PN}-0.98.1091-pandoc.patch \
-		"${FILESDIR}"/${PN}-0.98.490-linker_flags.patch \
-		"${FILESDIR}"/${PN}-0.98.1091-boost-1.57.patch
-
-	# Adding -DDISTRO_SHARE=... to append-flags breaks cmake so using
-	# this sed hack for now. ~RMH
-	sed -i \
-		-e "s|DISTRO_SHARE|\"share/${PN}\"|g" \
-		src/cpp/server/ServerOptions.cpp \
-		src/cpp/session/SessionOptions.cpp || die
-
-	# use mathjax from system
-	ln -sf "${EPREFIX}"/usr/share/mathjax dependencies/common/mathjax-23 || die
-
-	# make sure icons and mime stuff are with prefix
-	sed -i \
-		-e "s:/usr:${EPREFIX}/usr:g" \
-		CMakeGlobals.txt src/cpp/desktop/CMakeLists.txt || die
-
-	# specify that namespace core the is in the global namespace and not
-	# relative to some other namespace (like its ::core not ::boost::core)
-	find . \( -name *.cpp -or -name *.hpp \) -exec sed \
-		 -e 's@<core::@< ::core::@g' -e 's@\([^:]\)core::@\1::core::@g' -i {} \;
-
-	# On Gentoo the rstudio-server configuration file is /etc/conf.d/rstudio-server.conf
-	sed -e "s@/etc/rstudio/rserver.conf@${EROOT}etc/conf.d/rstudio-server.conf@" \
-		-i src/cpp/server/ServerOptions.cpp \
-		|| die
-
-	# Set the rsession.conf file location for Gentoo prefix
-	sed -e "s@/etc/rstudio/rsession.conf@${EROOT}etc/rstudio/rsession.conf@" \
-		-i src/cpp/session/SessionOptions.cpp \
-		|| die
-}
-
-src_configure() {
-	export RSTUDIO_VERSION_MAJOR=$(get_version_component_range 1)
-	export RSTUDIO_VERSION_MINOR=$(get_version_component_range 2)
-	export RSTUDIO_VERSION_PATCH=$(get_version_component_range 3)
-
-	local mycmakeargs=(
-		-DDISTRO_SHARE=share/${PN}
-		$(cmake-utils_use !dedicated RSTUDIO_INSTALL_FREEDESKTOP)
-		-DRSTUDIO_TARGET=$(usex dedicated "Server" "$(usex server "Development" "Desktop")")
-		)
-
-	cmake-utils_src_configure
-}
-
-src_compile() {
-	cmake-utils_src_compile
-}
-
-src_install() {
-	cmake-utils_src_install
-	pax-mark m "${ED}usr/bin/rstudio"
-	doconfd "${FILESDIR}"/rstudio-server.conf
-	dodir /etc/rstudio
-	insinto /etc/rstudio
-	doins "${FILESDIR}"/rsession.conf
-	dosym /etc/conf.d/rstudio-server.conf /etc/rstudio/rserver.conf
-	if use dedicated || use server; then
-		dopamd src/cpp/server/extras/pam/rstudio
-		newinitd "${FILESDIR}"/rstudio-server.initd rstudio-server
-	fi
-}
-
-pkg_preinst() {
-	use dedicated || gnome2_icon_savelist
-	java-pkg-2_pkg_preinst
-}
-
-pkg_postinst() {
-	use dedicated || { fdo-mime_desktop_database_update
-		fdo-mime_mime_database_update
-		gnome2_icon_cache_update ;}
-
-	if use dedicated || use server; then
-		enewgroup rstudio-server
-		enewuser rstudio-server -1 -1 -1 rstudio-server
-	fi
-}
-
-pkg_postrm() {
-	use dedicated || { fdo-mime_desktop_database_update
-		fdo-mime_mime_database_update
-		gnome2_icon_cache_update ;}
-}

diff --git a/sci-mathematics/rstudio/rstudio-0.98.490-r1.ebuild b/sci-mathematics/rstudio/rstudio-0.98.490-r1.ebuild
deleted file mode 100644
index cb0e8c0ef94..00000000000
--- a/sci-mathematics/rstudio/rstudio-0.98.490-r1.ebuild
+++ /dev/null
@@ -1,129 +0,0 @@
-# Copyright 1999-2016 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-inherit eutils cmake-utils gnome2-utils versionator fdo-mime java-pkg-2 pax-utils
-
-# TODO
-# * package gin and gwt
-# * use dict from tree, linguas
-# * do src_test (use junit from tree?)
-
-GWTVER=2.5.1
-GINVER=1.5
-
-DESCRIPTION="IDE for the R language"
-HOMEPAGE="http://www.rstudio.org"
-SRC_URI="
-	https://github.com/rstudio/rstudio/archive/v${PV}.tar.gz -> ${P}.tar.gz
-	https://s3.amazonaws.com/rstudio-buildtools/gin-${GINVER}.zip
-	https://s3.amazonaws.com/rstudio-buildtools/gwt-${GWTVER}.zip
-	https://s3.amazonaws.com/rstudio-dictionaries/core-dictionaries.zip"
-
-LICENSE="AGPL-3"
-SLOT="0"
-KEYWORDS="amd64 x86 ~amd64-linux ~x86-linux"
-IUSE=""
-
-QTVER=4.8
-QTSLOT=4
-RDEPEND="
-	>=dev-lang/R-2.11.1
-	>=dev-libs/boost-1.50:=
-	dev-libs/mathjax
-	dev-libs/openssl:0
-	sys-libs/zlib
-	>=virtual/jre-1.5:=
-	x11-libs/pango
-	>=dev-qt/qtcore-${QTVER}:${QTSLOT}
-	>=dev-qt/qtdbus-${QTVER}:${QTSLOT}
-	>=dev-qt/qtgui-${QTVER}:${QTSLOT}
-	>=dev-qt/qtwebkit-${QTVER}:${QTSLOT}
-	>=dev-qt/qtxmlpatterns-${QTVER}:${QTSLOT}"
-DEPEND="${RDEPEND}
-	app-arch/unzip
-	dev-java/ant-core
-	>=virtual/jdk-1.5
-	virtual/pkgconfig"
-#	test? ( dev-java/junit:4 )
-
-src_unpack() {
-	unpack ${P}.tar.gz gwt-${GWTVER}.zip
-	cd "${S}" || die
-	mkdir -p src/gwt/lib/{gin,gwt} dependencies/common/dictionaries || die
-	mv ../gwt-${GWTVER} src/gwt/lib/gwt/${GWTVER} || die
-	unzip -qd src/gwt/lib/gin/${GINVER} "${DISTDIR}"/gin-${GINVER}.zip || die
-	unzip -qd dependencies/common/dictionaries "${DISTDIR}"/core-dictionaries.zip || die
-}
-
-src_prepare() {
-	java-pkg-2_src_prepare
-
-	egit_clean
-
-	epatch \
-		"${FILESDIR}"/${P}-prefs.patch \
-		"${FILESDIR}"/${P}-paths.patch \
-		"${FILESDIR}"/${P}-linker_flags.patch
-
-	# Adding -DDISTRO_SHARE=... to append-flags breaks cmake so using
-	# this sed hack for now. ~RMH
-	sed -i \
-		-e "s|DISTRO_SHARE|\"share/${PN}\"|g" \
-		src/cpp/server/ServerOptions.cpp \
-		src/cpp/session/SessionOptions.cpp || die
-
-	# use mathjax from system
-	ln -sf "${EPREFIX}"/usr/share/mathjax dependencies/common/mathjax || die
-
-	# make sure icons and mime stuff are with prefix
-	sed -i \
-		-e "s:/usr:${EPREFIX}/usr:g" \
-		CMakeGlobals.txt src/cpp/desktop/CMakeLists.txt || die
-
-	# specify that namespace core the is in the global namespace and not
-	# relative to some other namespace (like its ::core not ::boost::core)
-	find . \( -name *.cpp -or -name *.hpp \) -exec sed \
-		-e 's@<core::@< ::core::@g' -e 's@\([^:]\)core::@\1::core::@g' -i {} \;
-}
-
-src_configure() {
-	export RSTUDIO_VERSION_MAJOR=$(get_version_component_range 1)
-	export RSTUDIO_VERSION_MINOR=$(get_version_component_range 2)
-	export RSTUDIO_VERSION_PATCH=$(get_version_component_range 3)
-
-	local mycmakeargs=(
-		-DDISTRO_SHARE=share/${PN}
-		-DRSTUDIO_INSTALL_FREEDESKTOP=ON
-		-DRSTUDIO_TARGET=Desktop
-		)
-
-	cmake-utils_src_configure
-}
-
-src_compile() {
-	cmake-utils_src_compile
-}
-
-src_install() {
-	cmake-utils_src_install
-	pax-mark m "${ED}usr/bin/rstudio"
-}
-
-pkg_preinst() {
-	gnome2_icon_savelist
-	java-pkg-2_pkg_preinst
-}
-
-pkg_postinst() {
-	fdo-mime_desktop_database_update
-	fdo-mime_mime_database_update
-	gnome2_icon_cache_update
-}
-
-pkg_postrm() {
-	fdo-mime_desktop_database_update
-	fdo-mime_mime_database_update
-	gnome2_icon_cache_update
-}

diff --git a/sci-mathematics/rstudio/rstudio-0.98.490.ebuild b/sci-mathematics/rstudio/rstudio-0.98.490.ebuild
deleted file mode 100644
index 59f506a074b..00000000000
--- a/sci-mathematics/rstudio/rstudio-0.98.490.ebuild
+++ /dev/null
@@ -1,142 +0,0 @@
-# Copyright 1999-2016 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-inherit eutils user cmake-utils gnome2-utils pam versionator fdo-mime java-pkg-2 pax-utils
-
-# TODO
-# * package gin and gwt
-# * use dict from tree, linguas
-# * do src_test (use junit from tree?)
-
-GWTVER=2.5.1
-GINVER=1.5
-
-DESCRIPTION="IDE for the R language"
-HOMEPAGE="http://www.rstudio.org"
-SRC_URI="
-	https://github.com/rstudio/rstudio/archive/v${PV}.tar.gz -> ${P}.tar.gz
-	https://s3.amazonaws.com/rstudio-buildtools/gin-${GINVER}.zip
-	https://s3.amazonaws.com/rstudio-buildtools/gwt-${GWTVER}.zip
-	https://s3.amazonaws.com/rstudio-dictionaries/core-dictionaries.zip"
-
-LICENSE="AGPL-3"
-SLOT="0"
-KEYWORDS="~amd64 x86 ~amd64-linux ~x86-linux"
-IUSE="dedicated server"
-
-QTVER=4.8
-QTSLOT=4
-RDEPEND="
-	>=dev-lang/R-2.11.1
-	>=dev-libs/boost-1.50:=
-	dev-libs/mathjax
-	dev-libs/openssl:0
-	sys-libs/zlib
-	>=virtual/jre-1.5:=
-	x11-libs/pango
-	!dedicated? (
-		>=dev-qt/qtcore-${QTVER}:${QTSLOT}
-		>=dev-qt/qtdbus-${QTVER}:${QTSLOT}
-		>=dev-qt/qtgui-${QTVER}:${QTSLOT}
-		>=dev-qt/qtwebkit-${QTVER}:${QTSLOT}
-		>=dev-qt/qtxmlpatterns-${QTVER}:${QTSLOT}
-		server? ( virtual/pam )
-	)
-	dedicated? ( virtual/pam )"
-DEPEND="${RDEPEND}
-	app-arch/unzip
-	dev-java/ant-core
-	>=virtual/jdk-1.5
-	virtual/pkgconfig"
-#	test? ( dev-java/junit:4 )
-
-src_unpack() {
-	unpack ${P}.tar.gz gwt-${GWTVER}.zip
-	cd "${S}" || die
-	mkdir -p src/gwt/lib/{gin,gwt} dependencies/common/dictionaries || die
-	mv ../gwt-${GWTVER} src/gwt/lib/gwt/${GWTVER} || die
-	unzip -qd src/gwt/lib/gin/${GINVER} "${DISTDIR}"/gin-${GINVER}.zip || die
-	unzip -qd dependencies/common/dictionaries "${DISTDIR}"/core-dictionaries.zip || die
-}
-
-src_prepare() {
-	java-pkg-2_src_prepare
-
-	egit_clean
-
-	epatch \
-		"${FILESDIR}"/${P}-prefs.patch \
-		"${FILESDIR}"/${P}-paths.patch \
-		"${FILESDIR}"/${P}-linker_flags.patch
-
-	# Adding -DDISTRO_SHARE=... to append-flags breaks cmake so using
-	# this sed hack for now. ~RMH
-	sed -i \
-		-e "s|DISTRO_SHARE|\"share/${PN}\"|g" \
-		src/cpp/server/ServerOptions.cpp \
-		src/cpp/session/SessionOptions.cpp || die
-
-	# use mathjax from system
-	ln -sf "${EPREFIX}"/usr/share/mathjax dependencies/common/mathjax || die
-
-	# make sure icons and mime stuff are with prefix
-	sed -i \
-		-e "s:/usr:${EPREFIX}/usr:g" \
-		CMakeGlobals.txt src/cpp/desktop/CMakeLists.txt || die
-
-	# specify that namespace core the is in the global namespace and not
-	# relative to some other namespace (like its ::core not ::boost::core)
-	find . \( -name *.cpp -or -name *.hpp \) -exec sed \
-		-e 's@<core::@< ::core::@g' -e 's@\([^:]\)core::@\1::core::@g' -i {} \;
-}
-
-src_configure() {
-	export RSTUDIO_VERSION_MAJOR=$(get_version_component_range 1)
-	export RSTUDIO_VERSION_MINOR=$(get_version_component_range 2)
-	export RSTUDIO_VERSION_PATCH=$(get_version_component_range 3)
-
-	local mycmakeargs=(
-		-DDISTRO_SHARE=share/${PN}
-		$(cmake-utils_use !dedicated RSTUDIO_INSTALL_FREEDESKTOP)
-		-DRSTUDIO_TARGET=$(usex dedicated "Server" "$(usex server "Development" "Desktop")")
-		)
-
-	cmake-utils_src_configure
-}
-
-src_compile() {
-	cmake-utils_src_compile
-}
-
-src_install() {
-	cmake-utils_src_install
-	pax-mark m "${ED}usr/bin/rstudio"
-	if use dedicated || use server; then
-		dopamd src/cpp/server/extras/pam/rstudio
-		newinitd "${FILESDIR}"/rstudio-server.initd rstudio-server
-	fi
-}
-
-pkg_preinst() {
-	use dedicated || gnome2_icon_savelist
-	java-pkg-2_pkg_preinst
-}
-
-pkg_postinst() {
-	use dedicated || { fdo-mime_desktop_database_update
-		fdo-mime_mime_database_update
-		gnome2_icon_cache_update ;}
-
-	if use dedicated || use server; then
-		enewgroup rstudio-server
-		enewuser rstudio-server -1 -1 -1 rstudio-server
-	fi
-}
-
-pkg_postrm() {
-	use dedicated || { fdo-mime_desktop_database_update
-		fdo-mime_mime_database_update
-		gnome2_icon_cache_update ;}
-}

diff --git a/sci-mathematics/rstudio/rstudio-0.98.932.ebuild b/sci-mathematics/rstudio/rstudio-0.98.932.ebuild
deleted file mode 100644
index f52c74fdfd9..00000000000
--- a/sci-mathematics/rstudio/rstudio-0.98.932.ebuild
+++ /dev/null
@@ -1,173 +0,0 @@
-# Copyright 1999-2016 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-inherit eutils user cmake-utils gnome2-utils pam versionator fdo-mime java-pkg-2 pax-utils
-
-# TODO
-# * package gin and gwt
-# * use dict from tree, linguas
-# * do src_test (use junit from tree?)
-
-GWTVER=2.6.0
-GINVER=1.5
-SELENIUMVER=2.37.0
-CHROMEDRIVER_VER=2.7
-PANDOC_VER=1.12.3
-PACKRAT_VER=0.3.0
-RMARKDOWN_VER=0.2.49
-
-DESCRIPTION="IDE for the R language"
-HOMEPAGE="http://www.rstudio.org"
-SRC_URI="
-	https://github.com/rstudio/rstudio/archive/v${PV}.tar.gz -> ${P}.tar.gz
-	https://s3.amazonaws.com/rstudio-buildtools/gin-${GINVER}.zip
-	https://s3.amazonaws.com/rstudio-buildtools/gwt-${GWTVER}.zip
-	https://s3.amazonaws.com/rstudio-buildtools/selenium-java-${SELENIUMVER}.zip
-	https://s3.amazonaws.com/rstudio-buildtools/selenium-server-standalone-${SELENIUMVER}.jar
-	https://s3.amazonaws.com/rstudio-buildtools/chromedriver-linux
-	https://s3.amazonaws.com/rstudio-dictionaries/core-dictionaries.zip
-	https://dev.gentoo.org/~hasufell/distfiles/packrat_${PACKRAT_VER}.tar.gz
-	https://dev.gentoo.org/~hasufell/distfiles/rmarkdown_${RMARKDOWN_VER}.tar.gz"
-
-LICENSE="AGPL-3"
-SLOT="0"
-KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
-IUSE="dedicated server"
-
-QTVER=4.8
-QTSLOT=4
-RDEPEND="
-	app-text/pandoc
-	dev-haskell/pandoc-citeproc
-	>=dev-lang/R-2.11.1
-	>=dev-libs/boost-1.50:=
-	dev-libs/mathjax
-	dev-libs/openssl:0
-	sys-libs/zlib
-	>=virtual/jre-1.5:=
-	x11-libs/pango
-	!dedicated? (
-		>=dev-qt/qtcore-${QTVER}:${QTSLOT}
-		>=dev-qt/qtdbus-${QTVER}:${QTSLOT}
-		>=dev-qt/qtgui-${QTVER}:${QTSLOT}
-		>=dev-qt/qtwebkit-${QTVER}:${QTSLOT}
-		>=dev-qt/qtxmlpatterns-${QTVER}:${QTSLOT}
-		server? ( virtual/pam )
-	)
-	dedicated? ( virtual/pam )"
-DEPEND="${RDEPEND}
-	app-arch/unzip
-	dev-java/ant-core
-	>=virtual/jdk-1.5
-	virtual/pkgconfig"
-#	test? ( dev-java/junit:4 )
-
-src_unpack() {
-	unpack ${P}.tar.gz gwt-${GWTVER}.zip
-	cd "${S}" || die
-	mkdir -p src/gwt/lib/{gin,gwt} \
-		dependencies/common/dictionaries \
-		src/gwt/lib/selenium/${SELENIUMVER} \
-		src/gwt/lib/selenium/chromedriver/${CHROMEDRIVER_VER} || die
-	mv ../gwt-${GWTVER} src/gwt/lib/gwt/${GWTVER} || die
-	unzip -qd src/gwt/lib/gin/${GINVER} \
-		"${DISTDIR}"/gin-${GINVER}.zip || die
-	unzip -qd dependencies/common/dictionaries \
-		"${DISTDIR}"/core-dictionaries.zip || die
-	unzip -qd src/gwt/lib/selenium/${SELENIUMVER} \
-		"${DISTDIR}"/selenium-java-${SELENIUMVER}.zip || die
-	cp "${DISTDIR}"/selenium-server-standalone-${SELENIUMVER}.jar \
-		src/gwt/lib/selenium/${SELENIUMVER}/ || die
-	cp "${DISTDIR}"/chromedriver-linux \
-		src/gwt/lib/selenium/chromedriver/${CHROMEDRIVER_VER}/ || die
-	cd dependencies/common || die
-	unpack packrat_${PACKRAT_VER}.tar.gz
-	unpack rmarkdown_${RMARKDOWN_VER}.tar.gz
-	cp "${DISTDIR}"/rmarkdown_${RMARKDOWN_VER}.tar.gz \
-		. || die
-	cp "${DISTDIR}"/packrat_${PACKRAT_VER}.tar.gz \
-		. || die
-}
-
-src_prepare() {
-	java-pkg-2_src_prepare
-
-	egit_clean
-
-	epatch \
-		"${FILESDIR}"/${PN}-0.98.490-prefs.patch \
-		"${FILESDIR}"/${P}-paths.patch \
-		"${FILESDIR}"/${P}-pandoc.patch \
-		"${FILESDIR}"/${PN}-0.98.490-linker_flags.patch
-
-	# Adding -DDISTRO_SHARE=... to append-flags breaks cmake so using
-	# this sed hack for now. ~RMH
-	sed -i \
-		-e "s|DISTRO_SHARE|\"share/${PN}\"|g" \
-		src/cpp/server/ServerOptions.cpp \
-		src/cpp/session/SessionOptions.cpp || die
-
-	# use mathjax from system
-	ln -sf "${EPREFIX}"/usr/share/mathjax dependencies/common/mathjax || die
-
-	# make sure icons and mime stuff are with prefix
-	sed -i \
-		-e "s:/usr:${EPREFIX}/usr:g" \
-		CMakeGlobals.txt src/cpp/desktop/CMakeLists.txt || die
-
-	# specify that namespace core the is in the global namespace and not
-	# relative to some other namespace (like its ::core not ::boost::core)
-	find . \( -name *.cpp -or -name *.hpp \) -exec sed \
-		-e 's@<core::@< ::core::@g' -e 's@\([^:]\)core::@\1::core::@g' -i {} \;
-}
-
-src_configure() {
-	export RSTUDIO_VERSION_MAJOR=$(get_version_component_range 1)
-	export RSTUDIO_VERSION_MINOR=$(get_version_component_range 2)
-	export RSTUDIO_VERSION_PATCH=$(get_version_component_range 3)
-
-	local mycmakeargs=(
-		-DDISTRO_SHARE=share/${PN}
-		$(cmake-utils_use !dedicated RSTUDIO_INSTALL_FREEDESKTOP)
-		-DRSTUDIO_TARGET=$(usex dedicated "Server" "$(usex server "Development" "Desktop")")
-		)
-
-	cmake-utils_src_configure
-}
-
-src_compile() {
-	cmake-utils_src_compile
-}
-
-src_install() {
-	cmake-utils_src_install
-	pax-mark m "${ED}usr/bin/rstudio"
-	if use dedicated || use server; then
-		dopamd src/cpp/server/extras/pam/rstudio
-		newinitd "${FILESDIR}"/rstudio-server.initd rstudio-server
-	fi
-}
-
-pkg_preinst() {
-	use dedicated || gnome2_icon_savelist
-	java-pkg-2_pkg_preinst
-}
-
-pkg_postinst() {
-	use dedicated || { fdo-mime_desktop_database_update
-		fdo-mime_mime_database_update
-		gnome2_icon_cache_update ;}
-
-	if use dedicated || use server; then
-		enewgroup rstudio-server
-		enewuser rstudio-server -1 -1 -1 rstudio-server
-	fi
-}
-
-pkg_postrm() {
-	use dedicated || { fdo-mime_desktop_database_update
-		fdo-mime_mime_database_update
-		gnome2_icon_cache_update ;}
-}

diff --git a/sci-mathematics/rstudio/rstudio-0.98.953.ebuild b/sci-mathematics/rstudio/rstudio-0.98.953.ebuild
deleted file mode 100644
index 9b56c4790ed..00000000000
--- a/sci-mathematics/rstudio/rstudio-0.98.953.ebuild
+++ /dev/null
@@ -1,174 +0,0 @@
-# Copyright 1999-2016 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-inherit eutils user cmake-utils gnome2-utils pam versionator fdo-mime java-pkg-2 pax-utils
-
-# TODO
-# * package gin and gwt
-# * use dict from tree, linguas
-# * do src_test (use junit from tree?)
-
-GWTVER=2.6.0
-GINVER=1.5
-SELENIUMVER=2.37.0
-CHROMEDRIVER_VER=2.7
-PANDOC_VER=1.12.3
-PACKRAT_VER=0.3.0
-RMARKDOWN_VER=0.2.49
-
-DESCRIPTION="IDE for the R language"
-HOMEPAGE="http://www.rstudio.org"
-SRC_URI="
-	https://github.com/rstudio/rstudio/archive/v${PV}.tar.gz -> ${P}.tar.gz
-	https://s3.amazonaws.com/rstudio-buildtools/gin-${GINVER}.zip
-	https://s3.amazonaws.com/rstudio-buildtools/gwt-${GWTVER}.zip
-	https://s3.amazonaws.com/rstudio-buildtools/selenium-java-${SELENIUMVER}.zip
-	https://s3.amazonaws.com/rstudio-buildtools/selenium-server-standalone-${SELENIUMVER}.jar
-	https://s3.amazonaws.com/rstudio-buildtools/chromedriver-linux
-	https://s3.amazonaws.com/rstudio-dictionaries/core-dictionaries.zip
-	https://dev.gentoo.org/~hasufell/distfiles/packrat_${PACKRAT_VER}.tar.gz
-	https://dev.gentoo.org/~hasufell/distfiles/rmarkdown_${RMARKDOWN_VER}.tar.gz"
-
-LICENSE="AGPL-3"
-SLOT="0"
-KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
-IUSE="dedicated server"
-
-QTVER=4.8
-QTSLOT=4
-RDEPEND="
-	app-text/pandoc
-	dev-haskell/pandoc-citeproc
-	>=dev-lang/R-2.11.1
-	>=dev-libs/boost-1.50:=
-	dev-libs/mathjax
-	dev-libs/openssl:0
-	sys-apps/util-linux
-	sys-libs/zlib
-	>=virtual/jre-1.5:=
-	x11-libs/pango
-	!dedicated? (
-		>=dev-qt/qtcore-${QTVER}:${QTSLOT}
-		>=dev-qt/qtdbus-${QTVER}:${QTSLOT}
-		>=dev-qt/qtgui-${QTVER}:${QTSLOT}
-		>=dev-qt/qtwebkit-${QTVER}:${QTSLOT}
-		>=dev-qt/qtxmlpatterns-${QTVER}:${QTSLOT}
-		server? ( virtual/pam )
-	)
-	dedicated? ( virtual/pam )"
-DEPEND="${RDEPEND}
-	app-arch/unzip
-	dev-java/ant-core
-	>=virtual/jdk-1.5
-	virtual/pkgconfig"
-#	test? ( dev-java/junit:4 )
-
-src_unpack() {
-	unpack ${P}.tar.gz gwt-${GWTVER}.zip
-	cd "${S}" || die
-	mkdir -p src/gwt/lib/{gin,gwt} \
-		dependencies/common/dictionaries \
-		src/gwt/lib/selenium/${SELENIUMVER} \
-		src/gwt/lib/selenium/chromedriver/${CHROMEDRIVER_VER} || die
-	mv ../gwt-${GWTVER} src/gwt/lib/gwt/${GWTVER} || die
-	unzip -qd src/gwt/lib/gin/${GINVER} \
-		"${DISTDIR}"/gin-${GINVER}.zip || die
-	unzip -qd dependencies/common/dictionaries \
-		"${DISTDIR}"/core-dictionaries.zip || die
-	unzip -qd src/gwt/lib/selenium/${SELENIUMVER} \
-		"${DISTDIR}"/selenium-java-${SELENIUMVER}.zip || die
-	cp "${DISTDIR}"/selenium-server-standalone-${SELENIUMVER}.jar \
-		src/gwt/lib/selenium/${SELENIUMVER}/ || die
-	cp "${DISTDIR}"/chromedriver-linux \
-		src/gwt/lib/selenium/chromedriver/${CHROMEDRIVER_VER}/ || die
-	cd dependencies/common || die
-	unpack packrat_${PACKRAT_VER}.tar.gz
-	unpack rmarkdown_${RMARKDOWN_VER}.tar.gz
-	cp "${DISTDIR}"/rmarkdown_${RMARKDOWN_VER}.tar.gz \
-		. || die
-	cp "${DISTDIR}"/packrat_${PACKRAT_VER}.tar.gz \
-		. || die
-}
-
-src_prepare() {
-	java-pkg-2_src_prepare
-
-	egit_clean
-
-	epatch \
-		"${FILESDIR}"/${PN}-0.98.490-prefs.patch \
-		"${FILESDIR}"/${PN}-0.98.932-paths.patch \
-		"${FILESDIR}"/${PN}-0.98.932-pandoc.patch \
-		"${FILESDIR}"/${PN}-0.98.490-linker_flags.patch
-
-	# Adding -DDISTRO_SHARE=... to append-flags breaks cmake so using
-	# this sed hack for now. ~RMH
-	sed -i \
-		-e "s|DISTRO_SHARE|\"share/${PN}\"|g" \
-		src/cpp/server/ServerOptions.cpp \
-		src/cpp/session/SessionOptions.cpp || die
-
-	# use mathjax from system
-	ln -sf "${EPREFIX}"/usr/share/mathjax dependencies/common/mathjax || die
-
-	# make sure icons and mime stuff are with prefix
-	sed -i \
-		-e "s:/usr:${EPREFIX}/usr:g" \
-		CMakeGlobals.txt src/cpp/desktop/CMakeLists.txt || die
-
-	# specify that namespace core the is in the global namespace and not
-	# relative to some other namespace (like its ::core not ::boost::core)
-	find . \( -name *.cpp -or -name *.hpp \) -exec sed \
-		-e 's@<core::@< ::core::@g' -e 's@\([^:]\)core::@\1::core::@g' -i {} \;
-}
-
-src_configure() {
-	export RSTUDIO_VERSION_MAJOR=$(get_version_component_range 1)
-	export RSTUDIO_VERSION_MINOR=$(get_version_component_range 2)
-	export RSTUDIO_VERSION_PATCH=$(get_version_component_range 3)
-
-	local mycmakeargs=(
-		-DDISTRO_SHARE=share/${PN}
-		$(cmake-utils_use !dedicated RSTUDIO_INSTALL_FREEDESKTOP)
-		-DRSTUDIO_TARGET=$(usex dedicated "Server" "$(usex server "Development" "Desktop")")
-		)
-
-	cmake-utils_src_configure
-}
-
-src_compile() {
-	cmake-utils_src_compile
-}
-
-src_install() {
-	cmake-utils_src_install
-	pax-mark m "${ED}usr/bin/rstudio"
-	if use dedicated || use server; then
-		dopamd src/cpp/server/extras/pam/rstudio
-		newinitd "${FILESDIR}"/rstudio-server.initd rstudio-server
-	fi
-}
-
-pkg_preinst() {
-	use dedicated || gnome2_icon_savelist
-	java-pkg-2_pkg_preinst
-}
-
-pkg_postinst() {
-	use dedicated || { fdo-mime_desktop_database_update
-		fdo-mime_mime_database_update
-		gnome2_icon_cache_update ;}
-
-	if use dedicated || use server; then
-		enewgroup rstudio-server
-		enewuser rstudio-server -1 -1 -1 rstudio-server
-	fi
-}
-
-pkg_postrm() {
-	use dedicated || { fdo-mime_desktop_database_update
-		fdo-mime_mime_database_update
-		gnome2_icon_cache_update ;}
-}


^ permalink raw reply related	[flat|nested] 12+ messages in thread

* [gentoo-commits] repo/gentoo:master commit in: sci-mathematics/rstudio/, sci-mathematics/rstudio/files/
@ 2017-10-24  6:48 Mark Wright
  0 siblings, 0 replies; 12+ messages in thread
From: Mark Wright @ 2017-10-24  6:48 UTC (permalink / raw
  To: gentoo-commits

commit:     a36219a050e6d671f2c796191b1273153b640a35
Author:     Sobhan Mohammadpour <www.sobhan.mohammadpour <AT> gmail <DOT> com>
AuthorDate: Mon Oct 23 12:28:39 2017 +0000
Commit:     Mark Wright <gienah <AT> gentoo <DOT> org>
CommitDate: Tue Oct 24 06:46:05 2017 +0000
URL:        https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=a36219a0

sci-mathematics/rstudio: version bump to 1.1.368

Bump to 1.1.368. This also updates the clang pandoc patch
Fixes bug 626056, thanks to Harris Landgarten for reporting, Sobhan
Mohammadpour for adding the missing dependency in 1.1.383.
Fixes bug 626062 by bumping rstudio to version 1.1.383 that builds with R 3.4.
Thanks to Harris Landgarten for reporting, jstein, Volkmar Glauche, Bernd
Feige and yuri for testing and helping, Sobhan Mohammadpour for bumping
rstudio in PR #6003.
Fixes bug 622254, thanks to jstein for reporting, Volkmar Glauche, Bernd Feige,
Carl W. Harlow, Rolf S. Arvidson, Oleg, Alex and Sobhan Mohammadpour for
testing and helping.
Fixes bug 633936, thanks to Neil for reporting, François Valenduc and Bernd
for helping.

Suggested-by: Bernd Feige <Bernd.Feige <AT> gmx.net>
Gentoo-bug: 626056, 626062. 622254, 633936

 sci-mathematics/rstudio/Manifest                   |   1 +
 .../files/rstudio-1.1.357-clang-pandoc.patch       |  76 +++++++
 sci-mathematics/rstudio/rstudio-1.1.368.ebuild     | 248 +++++++++++++++++++++
 3 files changed, 325 insertions(+)

diff --git a/sci-mathematics/rstudio/Manifest b/sci-mathematics/rstudio/Manifest
index 728e003ec65..5d4b2fdc369 100644
--- a/sci-mathematics/rstudio/Manifest
+++ b/sci-mathematics/rstudio/Manifest
@@ -20,6 +20,7 @@ DIST rstudio-1.0.136.tar.gz 17786389 SHA256 bb6a8aa475e09dd090cd2b5ea505f578d270
 DIST rstudio-1.0.143.tar.gz 17791067 SHA256 8ae88731b4474e5e2ff9030aa14e168903fe3a7ffc4fa716f497084a86801062 SHA512 46eaa88dd8332f18bb3a43de6e262d8a365860d9add78aea6a2d345784b239972c9c73bf0b56f1736b2981b8f688dbaf5a83c6848d170c0cf61d0e51dd636a82 WHIRLPOOL db1c11be240db3528e46d359c7d40d64068dfe5f7d915c4a6b690444f7f7fbc11f3898a6e262fa625bfab906f0cbfb2a8e3288a4fd20470423a99d992972fcda
 DIST rstudio-1.0.153.tar.gz 17790922 SHA256 79b90e21e56b114e28b03fd8543a208c55bb9d5f47a87fd29143d08b9a06f7a0 SHA512 d970a9bde88845e3fc6cdaff5233ffb65c03939c685c3fca0dd052246e065c7580b3f9bc4e053a79d2ecbb5f8c283d3fce7b97cc69e43176bd49587c736dab86 WHIRLPOOL c1f4c7bdc8e5a85af53411a35d736278b83f4732d2e273378fecc77cb075dff507147d56012682564edd58041c91cc051189eb38a7348d0827b76c7ac37bd54d
 DIST rstudio-1.0.44.tar.gz 17774065 SHA256 43ece6cfdd1a13ac0e17f2a50154a30a1a14ad6c1b3cf381cc6007988ce44a0f SHA512 a8b975dc517125a257e5f61db5bb137e133b02d738d55553770aa65e388cd112ce646b53b77dc069d1ca95ccd95979f4a57ad60b99fc3b91543cf61e737e8169 WHIRLPOOL 4ad472aed130451e81d8d8e3251d3bbd701a8b8e2fbddf17dc357f39335e33c75505f9443c2c7208e60a19c2767b9328134433e5d4fd22504813020712c658ef
+DIST rstudio-1.1.368.tar.gz 20197144 SHA256 586573707a488b5f528680b932ba5f8ea6d07667cc5ae6426104e2abf5ddab75 SHA512 39cdf583d7dcd22338916cc0ea4f90681580e41663b2d3e04b2e650759c6b030c85ee111cdfe1f717f931932a9b7ca423a21585d69a785f056f754f6d50399a1 WHIRLPOOL e18ff21823638d458179819e0b0b234b80be2f095f5b7bf5b9ac0190b078f0d7acb51e8896cbfcf1ce33cd203ed4e9fbe097aac6eee62515cace1d2f08c08219
 DIST selenium-java-2.37.0.zip 24625928 SHA256 0eebba65d8edb01c1f46e462907c58f5d6e1cb0ddf63660a9985c8432bdffbb7 SHA512 68624e82dbc751a25c50fad72702a98eb30d77fd4337d2a969f8e06bcc49e5f8c835cd27ec53772f3375014ddde1d5636936e966b75f3594a9f86aa18ba4e779 WHIRLPOOL eb6659aae26f3c78b6f998546b23d0636c9d00ed8a7f985db1463ac4bd483ccb3e643d84e2ca0f59e0636a8de79eb552ff1d68eb6f9c06907029f7552d8f7777
 DIST selenium-server-standalone-2.37.0.jar 34730734 SHA256 97bc8c699037fb6e99ba7af570fb60dbb1b7ce30cde2448287a44ef65b13023e SHA512 b215446d42d2d1f69664349b6ae6dc53a532d3624c91254f0f4183d0ad764648792e5cc1126a55a1e60d9687d55200fed01d6d2f46cc3d853b1fa6ee38111018 WHIRLPOOL 20640591534f31f24825a9ed139589b182e8b60d86541bf0be104d3cc0280983f6566bd0459f2253ac3875b48a2798b205bac8f815a119fff6db625ce9bbc29e
 DIST shinyapps-0.98.1000.tar.gz 910095 SHA256 b95c512ae0a0fb4335878d9cfcf9073e2cb3ccfed73543abe27ea8878ed36d57 SHA512 3162317c4c20cfc1497e952a8235867084d629ae88407e6c465b3e208adb1dc97abfe6b9922e0374ddf4c8e38a76e112942bd312c54a66f74e6f2a3fe4c0a07c WHIRLPOOL ecc2bce78387cb42e9989163d8fca29220e66f085acde3323417058aebb624dafa8c0e1873c7d79e67324cbd5aad250ef9fcdbbc8f659d64482233b95d898a15

diff --git a/sci-mathematics/rstudio/files/rstudio-1.1.357-clang-pandoc.patch b/sci-mathematics/rstudio/files/rstudio-1.1.357-clang-pandoc.patch
new file mode 100644
index 00000000000..28b0220912a
--- /dev/null
+++ b/sci-mathematics/rstudio/files/rstudio-1.1.357-clang-pandoc.patch
@@ -0,0 +1,76 @@
+Index: rstudio-1.1.357/src/cpp/session/CMakeLists.txt
+===================================================================
+--- rstudio-1.1.357.orig/src/cpp/session/CMakeLists.txt
++++ rstudio-1.1.357/src/cpp/session/CMakeLists.txt
+@@ -25,9 +25,6 @@ endif()
+ if(NOT EXISTS "${RSTUDIO_DEPENDENCIES_DIR}/common/mathjax-26")
+   message(FATAL_ERROR "Mathjax 2.6 not found (re-run install-dependencies script to install)")
+ endif()
+-if(NOT EXISTS "${RSTUDIO_DEPENDENCIES_DIR}/common/pandoc")
+-  message(FATAL_ERROR "pandoc not found (re-run install-dependencies script to install)")
+-endif()
+ 
+ # we often install embedded versions of these packages but don't do so currently
+ 
+@@ -38,22 +35,6 @@ endif()
+ #   message(FATAL_ERROR "rsconnect package not found (re-run install-dependencies script to install)")
+ # endif()
+ 
+-# verify libclang is installed
+-if(WIN32)
+-   set(LIBCLANG_VERSION "3.4")
+-else()
+-   set(LIBCLANG_VERSION "3.5")
+-endif()
+-set(LIBCLANG_DIR "${RSTUDIO_DEPENDENCIES_DIR}/common/libclang/${LIBCLANG_VERSION}")
+-if(NOT EXISTS "${LIBCLANG_DIR}")
+-  message(FATAL_ERROR "libclang ${LIBCLANG_VERSION} not found  (re-run install-dependencies script to install)")
+-endif()
+-set(LIBCLANG_HEADERS_DIR "${RSTUDIO_DEPENDENCIES_DIR}/common/libclang/builtin-headers")
+-if(NOT EXISTS "${LIBCLANG_HEADERS_DIR}")
+-  message(FATAL_ERROR "libclang builtin-headers not found  (re-run install-dependencies script to install)")
+-endif()
+-
+-
+ # include files
+ file(GLOB_RECURSE SESSION_HEADER_FILES "*.h*")
+ 
+@@ -465,13 +446,6 @@ if (NOT RSTUDIO_SESSION_WIN64)
+    install(DIRECTORY "resources/connections"
+            DESTINATION ${RSTUDIO_INSTALL_SUPPORTING}/resources)
+ 
+-   # install pandoc
+-   set(PANDOC_BIN "${RSTUDIO_DEPENDENCIES_DIR}/common/pandoc/1.19.2.1")
+-   file(GLOB PANDOC_FILES "${PANDOC_BIN}/pandoc*")
+-   install(FILES ${PANDOC_FILES}
+-           PERMISSIONS OWNER_READ OWNER_WRITE OWNER_EXECUTE GROUP_READ GROUP_EXECUTE WORLD_READ WORLD_EXECUTE
+-           DESTINATION  ${RSTUDIO_INSTALL_BIN}/pandoc)
+-
+    # install rmarkdown package
+    # file(GLOB RMARKDOWN_PACKAGE "${RSTUDIO_DEPENDENCIES_DIR}/common/rmarkdown*.tar.gz")
+    # install(FILES ${RMARKDOWN_PACKAGE}
+@@ -502,24 +476,6 @@ if (NOT RSTUDIO_SESSION_WIN64)
+    install(DIRECTORY "resources/profiler"
+            DESTINATION ${RSTUDIO_INSTALL_SUPPORTING}/resources)
+ 
+-   # install libclang
+-   if(WIN32)
+-      file(GLOB LIBCLANG_32_FILES "${LIBCLANG_DIR}/x86/libclang.*")
+-      install(PROGRAMS ${LIBCLANG_32_FILES}
+-              DESTINATION  ${RSTUDIO_INSTALL_BIN}/rsclang/x86)
+-      file(GLOB LIBCLANG_64_FILES "${LIBCLANG_DIR}/x86_64/libclang.*")
+-      install(PROGRAMS ${LIBCLANG_64_FILES}
+-              DESTINATION  ${RSTUDIO_INSTALL_BIN}/rsclang/x86_64)
+-   else()
+-      file(GLOB_RECURSE LIBCLANG_FILES "${LIBCLANG_DIR}/libclang.*")
+-      install(PROGRAMS ${LIBCLANG_FILES}
+-              DESTINATION  ${RSTUDIO_INSTALL_BIN}/rsclang)
+-   endif()
+-
+-   # install libclang builtin-headers
+-   install(DIRECTORY "${RSTUDIO_DEPENDENCIES_DIR}/common/libclang/builtin-headers"
+-           DESTINATION "${RSTUDIO_INSTALL_SUPPORTING}/resources/libclang")
+-
+    # install winpty on windows
+    if(WIN32)
+       install(PROGRAMS "${WINPTY_BINDIR_32}/winpty.dll"

diff --git a/sci-mathematics/rstudio/rstudio-1.1.368.ebuild b/sci-mathematics/rstudio/rstudio-1.1.368.ebuild
new file mode 100644
index 00000000000..38ac6d8ddf2
--- /dev/null
+++ b/sci-mathematics/rstudio/rstudio-1.1.368.ebuild
@@ -0,0 +1,248 @@
+# Copyright 1999-2017 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=6
+
+inherit eutils user cmake-utils gnome2-utils pam versionator xdg-utils java-pkg-2 pax-utils qmake-utils
+
+# TODO
+# * package gin and gwt
+# * use dict from tree, linguas
+# * do src_test (use junit from tree?)
+
+# update from scripts in dependencies/common
+# egrep '(GWT_SDK_VER=|GIN_VER=|SELENIUM_VER=|CHROMEDRIVER_VER=)' dependencies/common/install-gwt
+GWT_VER=2.7.0
+GIN_VER=1.5
+SELENIUM_VER=2.37.0
+CHROMEDRIVER_VER=2.7
+# grep 'PANDOC_VERSION=' dependencies/common/update-pandoc
+PANDOC_VER=1.13.1
+# ls dependencies/common/*.tar.gz
+PACKRAT_VER=0.98.1000
+RMARKDOWN_VER=0.98.1000
+SHINYAPPS_VER=0.98.1000
+RSCONNECT_VER=0.4.1.4_fcac892a69817febd7b655b189bf57193260cda0
+
+DESCRIPTION="IDE for the R language"
+HOMEPAGE="
+	http://www.rstudio.org
+	https://github.com/rstudio/rstudio/"
+SRC_URI="
+	https://github.com/rstudio/rstudio/archive/v${PV}.tar.gz -> ${P}.tar.gz
+	https://s3.amazonaws.com/rstudio-buildtools/gin-${GIN_VER}.zip
+	https://s3.amazonaws.com/rstudio-buildtools/gwt-${GWT_VER}.zip
+	https://s3.amazonaws.com/rstudio-buildtools/selenium-java-${SELENIUM_VER}.zip
+	https://s3.amazonaws.com/rstudio-buildtools/selenium-server-standalone-${SELENIUM_VER}.jar
+	https://s3.amazonaws.com/rstudio-buildtools/chromedriver-linux
+	https://s3.amazonaws.com/rstudio-dictionaries/core-dictionaries.zip
+	https://dev.gentoo.org/~gienah/distfiles/packrat-${PACKRAT_VER}.tar.gz
+	https://dev.gentoo.org/~gienah/distfiles/rmarkdown-${RMARKDOWN_VER}.tar.gz
+	https://dev.gentoo.org/~gienah/distfiles/shinyapps-${SHINYAPPS_VER}.tar.gz
+	https://dev.gentoo.org/~gienah/distfiles/rsconnect_${RSCONNECT_VER}.tar.gz
+"
+
+LICENSE="AGPL-3"
+SLOT="0"
+KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
+IUSE="dedicated server"
+
+QT_VER=5.4
+QT_SLOT=5
+RDEPEND="
+	app-text/pandoc
+	dev-haskell/pandoc-citeproc
+	>=dev-lang/R-2.11.1
+	>=dev-libs/boost-1.63:=
+	>=dev-libs/mathjax-2.7.0
+	dev-libs/openssl:0
+	sys-apps/util-linux
+	>=sys-devel/clang-3.5.0:*
+	sys-libs/zlib
+	>=virtual/jre-1.8:=
+	x11-libs/pango
+	!dedicated? (
+		>=dev-qt/qtcore-${QT_VER}:${QT_SLOT}
+		>=dev-qt/qtdeclarative-${QT_VER}:${QT_SLOT}
+		>=dev-qt/qtdbus-${QT_VER}:${QT_SLOT}
+		>=dev-qt/qtgui-${QT_VER}:${QT_SLOT}
+		>=dev-qt/qtnetwork-${QT_VER}:${QT_SLOT}
+		>=dev-qt/qtopengl-${QT_VER}:${QT_SLOT}
+		>=dev-qt/qtpositioning-${QT_VER}:${QT_SLOT}
+		>=dev-qt/qtprintsupport-${QT_VER}:${QT_SLOT}
+		>=dev-qt/qtsingleapplication-2.6.1_p20150629[X,qt5]
+		>=dev-qt/qtsensors-${QT_VER}:${QT_SLOT}
+		>=dev-qt/qtsql-${QT_VER}:${QT_SLOT}
+		>=dev-qt/qtsvg-${QT_VER}:${QT_SLOT}
+		>=dev-qt/qtwebchannel-${QT_VER}:${QT_SLOT}
+		>=dev-qt/qtwebkit-${QT_VER}:${QT_SLOT}
+		>=dev-qt/qtwidgets-${QT_VER}:${QT_SLOT}
+		>=dev-qt/qtxml-${QT_VER}:${QT_SLOT}
+		>=dev-qt/qtxmlpatterns-${QT_VER}:${QT_SLOT}
+		server? ( virtual/pam )
+	)
+	dedicated? ( virtual/pam )"
+DEPEND="${RDEPEND}
+	app-arch/unzip
+	dev-java/ant-core
+	>=virtual/jdk-1.8:=
+	virtual/pkgconfig"
+#	test? ( dev-java/junit:4 )
+
+PATCHES=(
+		"${FILESDIR}/${PN}-0.99.879-prefs.patch"
+		"${FILESDIR}/${PN}-1.0.44-paths.patch"
+		"${FILESDIR}/${PN}-1.1.357-clang-pandoc.patch"
+		"${FILESDIR}/${PN}-0.98.490-linker_flags.patch"
+		"${FILESDIR}/${PN}-0.98.1091-boost-1.57.patch"
+		"${FILESDIR}/${PN}-0.99.473-qtsingleapplication.patch"
+		"${FILESDIR}/${PN}-1.0.44-systemd.patch"
+)
+
+src_unpack() {
+	unpack ${P}.tar.gz gwt-${GWT_VER}.zip
+	cd "${S}" || die
+	mkdir -p src/gwt/lib/{gin,gwt} \
+		dependencies/common/dictionaries \
+		src/gwt/lib/selenium/${SELENIUM_VER} \
+		src/gwt/lib/selenium/chromedriver/${CHROMEDRIVER_VER} || die
+	mv ../gwt-${GWT_VER} src/gwt/lib/gwt/${GWT_VER} || die
+	unzip -qd src/gwt/lib/gin/${GIN_VER} \
+		"${DISTDIR}"/gin-${GIN_VER}.zip || die
+	unzip -qd dependencies/common/dictionaries \
+		"${DISTDIR}"/core-dictionaries.zip || die
+	unzip -qd src/gwt/lib/selenium/${SELENIUM_VER} \
+		"${DISTDIR}"/selenium-java-${SELENIUM_VER}.zip || die
+	cp "${DISTDIR}"/selenium-server-standalone-${SELENIUM_VER}.jar \
+		src/gwt/lib/selenium/${SELENIUM_VER}/ || die
+	cp "${DISTDIR}"/chromedriver-linux \
+		src/gwt/lib/selenium/chromedriver/${CHROMEDRIVER_VER}/ || die
+	cd dependencies/common || die
+	unpack packrat-${PACKRAT_VER}.tar.gz
+	unpack rmarkdown-${RMARKDOWN_VER}.tar.gz
+	unpack shinyapps-${SHINYAPPS_VER}.tar.gz
+	unpack rsconnect_${RSCONNECT_VER}.tar.gz
+	cp "${DISTDIR}"/rmarkdown-${RMARKDOWN_VER}.tar.gz \
+		. || die
+	cp "${DISTDIR}"/packrat-${PACKRAT_VER}.tar.gz \
+		. || die
+	cp "${DISTDIR}"/shinyapps-${SHINYAPPS_VER}.tar.gz \
+		. || die
+	cp "${DISTDIR}"/rsconnect_${RSCONNECT_VER}.tar.gz \
+		. || die
+}
+
+src_prepare() {
+	default
+	java-pkg-2_src_prepare
+	egit_clean
+
+	# Enable CMake to install our .service file for systemd usage
+	mkdir -vp "${S}/src/cpp/server/lib/systemd/system" || die
+	cp -v "${FILESDIR}/rstudio-server.service.in" "${S}/src/cpp/server/lib/systemd/system/" || die
+
+	# Adding -DDISTRO_SHARE=... to append-flags breaks cmake so using
+	# this sed hack for now. ~RMH
+	sed -i \
+		-e "s|DISTRO_SHARE|\"share/${PN}\"|g" \
+		src/cpp/server/ServerOptions.cpp \
+		src/cpp/session/SessionOptions.cpp || die
+
+	# use mathjax from system
+	ln -sf "${EPREFIX}"/usr/share/mathjax dependencies/common/mathjax-26 || die
+
+	# make sure icons and mime stuff are with prefix
+	sed -i \
+		-e "s:/usr:${EPREFIX}/usr:g" \
+		CMakeGlobals.txt src/cpp/desktop/CMakeLists.txt || die
+
+	# On Gentoo the rstudio-server configuration file is /etc/conf.d/rstudio-server.conf
+	sed -e "s@/etc/rstudio/rserver.conf@${EROOT}etc/conf.d/rstudio-server.conf@" \
+		-i src/cpp/server/ServerOptions.cpp \
+		|| die
+
+	# Set the rsession.conf file location for Gentoo prefix
+	sed -e "s@/etc/rstudio/rsession.conf@${EROOT}etc/rstudio/rsession.conf@" \
+		-i src/cpp/session/SessionOptions.cpp \
+		|| die
+
+	# dev-qt/qtsingleapplication-2.6.1_p20150629 does not provide a cmake module.
+	# It provides a library that has its version number appended to the end,
+	# which is difficult to handle in cmake, as find_library does not support
+	# searching for wildcard library names. So I find the library name from the
+	# qmake spec, and then sed this into the patched src/cpp/desktop/CMakeLists.txt.
+	rm -rf "${S}"/src/cpp/desktop/3rdparty || die
+	local s=$(grep '\-lQt$${QT_MAJOR_VERSION}Solutions_SingleApplication' \
+				   $(qt5_get_mkspecsdir)/features/qtsingleapplication.prf \
+					 | sed -e 's@\$\${QT_MAJOR_VERSION}@5@' \
+						   -e 's@LIBS \*= -l@@')
+	sed -e "s@Qt5Solutions_SingleApplication-2.6@${s}@g" \
+		-i "${S}"/src/cpp/desktop/CMakeLists.txt \
+		|| die
+
+	# The git commit for tag: git rev-list -n 1 v0.99.903
+	sed -e 's@git ARGS rev-parse HEAD@echo ARGS 0eb2d8ea28ebc1ac6ac327e023becb6133b679c4@'\
+		-i "${S}"/CMakeLists.txt \
+		"${S}"/CMakeGlobals.txt \
+		|| die
+}
+
+src_configure() {
+	export RSTUDIO_VERSION_MAJOR=$(get_version_component_range 1)
+	export RSTUDIO_VERSION_MINOR=$(get_version_component_range 2)
+	export RSTUDIO_VERSION_PATCH=$(get_version_component_range 3)
+
+	local mycmakeargs=(
+		-DDISTRO_SHARE=share/${PN}
+		-DRSTUDIO_INSTALL_FREEDESKTOP="$(usex !dedicated "ON" "OFF")"
+		-DRSTUDIO_TARGET=$(usex dedicated "Server" "$(usex server "Development" "Desktop")")
+		-DQT_QMAKE_EXECUTABLE=$(qt5_get_bindir)/qmake
+		-DRSTUDIO_VERIFY_R_VERSION=FALSE
+		)
+
+	cmake-utils_src_configure
+}
+
+src_compile() {
+	# Avoid the rest of the oracle-jdk-bin-1.8.0.60 sandbox violations F: mkdir S: deny
+	# P: /root/.oracle_jre_usage.
+	export ANT_OPTS="-Duser.home=${T}"
+	cmake-utils_src_compile
+}
+
+src_install() {
+	export ANT_OPTS="-Duser.home=${T}"
+	cmake-utils_src_install
+	pax-mark m "${ED}usr/bin/rstudio"
+	doconfd "${FILESDIR}"/rstudio-server.conf
+	dodir /etc/rstudio
+	insinto /etc/rstudio
+	doins "${FILESDIR}"/rsession.conf
+	dosym "${ROOT}etc/conf.d/rstudio-server.conf" "${ROOT}etc/rstudio/rserver.conf"
+	if use dedicated || use server; then
+		dopamd src/cpp/server/extras/pam/rstudio
+		newinitd "${FILESDIR}"/rstudio-server.initd rstudio-server
+	fi
+}
+
+pkg_preinst() {
+	use dedicated || gnome2_icon_savelist
+	java-pkg-2_pkg_preinst
+}
+
+pkg_postinst() {
+	use dedicated || { xdg_desktop_database_update
+		xdg_mimeinfo_database_update
+		gnome2_icon_cache_update ;}
+
+	if use dedicated || use server; then
+		enewgroup rstudio-server
+		enewuser rstudio-server -1 -1 -1 rstudio-server
+	fi
+}
+
+pkg_postrm() {
+	use dedicated || { xdg_desktop_database_update
+		xdg_mimeinfo_database_update
+		gnome2_icon_cache_update ;}
+}


^ permalink raw reply related	[flat|nested] 12+ messages in thread

* [gentoo-commits] repo/gentoo:master commit in: sci-mathematics/rstudio/, sci-mathematics/rstudio/files/
@ 2017-11-19 12:52 David Seifert
  0 siblings, 0 replies; 12+ messages in thread
From: David Seifert @ 2017-11-19 12:52 UTC (permalink / raw
  To: gentoo-commits

commit:     13286961d7bff3782a86321066e83cd944a22466
Author:     David Seifert <soap <AT> gentoo <DOT> org>
AuthorDate: Sun Nov 19 12:49:48 2017 +0000
Commit:     David Seifert <soap <AT> gentoo <DOT> org>
CommitDate: Sun Nov 19 12:52:27 2017 +0000
URL:        https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=13286961

sci-mathematics/rstudio: Remove old

Package-Manager: Portage-2.3.14, Repoman-2.3.6

 sci-mathematics/rstudio/Manifest                   |  15 --
 .../rstudio/files/rstudio-0.98.1091-pandoc.patch   |  26 ---
 .../rstudio/files/rstudio-0.98.490-paths.patch     | 120 ----------
 .../rstudio/files/rstudio-0.98.490-prefs.patch     |  24 --
 .../rstudio/files/rstudio-0.98.932-pandoc.patch    |  25 ---
 .../rstudio/files/rstudio-0.98.932-paths.patch     | 140 ------------
 .../files/rstudio-0.99.473-clang-pandoc.patch      |  77 -------
 .../rstudio/files/rstudio-0.99.473-paths.patch     | 130 -----------
 .../rstudio/files/rstudio-0.99.486-systemd.patch   |  22 --
 .../files/rstudio-0.99.879-clang-pandoc.patch      |  77 -------
 .../rstudio/files/rstudio-0.99.879-paths.patch     | 130 -----------
 .../files/rstudio-1.0.44-clang-pandoc.patch        |  71 ------
 sci-mathematics/rstudio/rstudio-0.99.473-r1.ebuild | 240 --------------------
 sci-mathematics/rstudio/rstudio-0.99.482.ebuild    | 240 --------------------
 sci-mathematics/rstudio/rstudio-0.99.483.ebuild    | 240 --------------------
 sci-mathematics/rstudio/rstudio-0.99.484.ebuild    | 240 --------------------
 sci-mathematics/rstudio/rstudio-0.99.486-r1.ebuild | 248 --------------------
 sci-mathematics/rstudio/rstudio-0.99.491.ebuild    | 248 --------------------
 sci-mathematics/rstudio/rstudio-0.99.879.ebuild    | 249 ---------------------
 sci-mathematics/rstudio/rstudio-0.99.893.ebuild    | 249 ---------------------
 sci-mathematics/rstudio/rstudio-0.99.896.ebuild    | 249 ---------------------
 sci-mathematics/rstudio/rstudio-0.99.902.ebuild    | 249 ---------------------
 sci-mathematics/rstudio/rstudio-0.99.903.ebuild    | 249 ---------------------
 sci-mathematics/rstudio/rstudio-1.0.136.ebuild     | 247 --------------------
 sci-mathematics/rstudio/rstudio-1.0.143.ebuild     | 247 --------------------
 sci-mathematics/rstudio/rstudio-1.0.153.ebuild     | 247 --------------------
 sci-mathematics/rstudio/rstudio-1.0.44.ebuild      | 247 --------------------
 27 files changed, 4546 deletions(-)

diff --git a/sci-mathematics/rstudio/Manifest b/sci-mathematics/rstudio/Manifest
index 5d4b2fdc369..76c18739074 100644
--- a/sci-mathematics/rstudio/Manifest
+++ b/sci-mathematics/rstudio/Manifest
@@ -5,21 +5,6 @@ DIST gwt-2.7.0.zip 108818328 SHA256 aa65061b73836190410720bea422eb8e787680d7bc0c
 DIST packrat-0.98.1000.tar.gz 97677 SHA256 c2da99ea6b62fd460f36b76f6c9b91865c42851545d61817c181bf6109e2df6b SHA512 2290c768ecf27a037e73c3f8336b9fd71c68ff19d071b4a8fbc469550d29007cacacdb75f854f73b5db2139a5104f129b85a3612e2ee47bd6118ee13f7d103a6 WHIRLPOOL a2d0c3c3e04cbc496f59abbf1065fcd0b7ae25433ce0b7ca8e75ab59362f320508537b2a62ed1028dd5baad6cbab5ef2e91dd9d3af327bbd04c08a96c57d80f4
 DIST rmarkdown-0.98.1000.tar.gz 1423820 SHA256 56e9f964f805627f6d6face9bf09e6435be4cc48321447ad4041fee86d6f88b4 SHA512 df3540c24c87930fe55bff2ffe67c86c219800cb00ed72ba9451ecd0d0cad411548a78c1a04b9a2e301e853616dcb77e09129c4e48ade6f16d3f14b7ea7e4852 WHIRLPOOL 51098cd48a12a61da312fc1cc96927626db4a19cc069c88f615dd20abe40f52a7b1ac1325b52b1922110ffa76a7f255d9ff2a75cd05d3de01d1b96f0c8286790
 DIST rsconnect_0.4.1.4_fcac892a69817febd7b655b189bf57193260cda0.tar.gz 197051 SHA256 e1e3e1f799eb8be679be9a2ed5aad7e9ce6cd603e3cb43fdc242490f0c311113 SHA512 208dc349f4aa7613ecf94939aba60d22d3a06972344b526c9b6c951015571f5922927bca08db571a7b8a268e42609a4f558f01278c9685f6da2ffc66a1f95ade WHIRLPOOL 4e3d64de00a98190c435d76f12a401d30950fdc7590b6bcc886ae50d4771825d39f93ea2bdcb4a9db026361c522f16f11297ff89dcb15c35f9471c1abf4f4e2c
-DIST rstudio-0.99.473.tar.gz 16993092 SHA256 a402995251393d50fa70e2e02188a8b32dc34e067f2f8461f087bf71f643585c SHA512 5615840501f7629e82100fee78c35b8d4dc78d78932d65c2e91a6472bc94726389566f5853a99e3d0631fd260e59acea5a40acf82f72709741b89a1ed3c901af WHIRLPOOL 809549c76efee8b29452584ab4295bcbbf533f8100c8caf4dd3b4a3c8843dc54a0d8f3178a6aecab5c188f2498a74daa6c6677fc6d43bd7dd861487c557e48df
-DIST rstudio-0.99.482.tar.gz 16992873 SHA256 1185d6ce5d3872e134f3255668d8f082370c760f06ec409c7b84c0936f52c4bf SHA512 bdb845cceae851d27323448a3570621bcb2aba7742e9e1669c88f3ebeaaade8c8371eb38f2ad348d7e2b740778c34f73e59013502ae3cebafba84e5d249c3e52 WHIRLPOOL 743440227c8d7e56000b1ff0b1a12def50e006b4f34d2067587274e2bae0eda42656787fc0cf6c51ffdbfcca08fc6eab0d042891bd77e4446b6fe26c6d19cc05
-DIST rstudio-0.99.483.tar.gz 16993049 SHA256 85ce1a2f40690e4ed0338b153a1b3279ce9564396d8c6d6201a0ad39297d4a9a SHA512 7d9cc8b471a4d799f286193da5f6f950f85e82949ede0f1ffe3626a429a49204878fb731250e5f54164a48e1d6e9cbb19a04a38ff83e35fd46c0ba05ef78a9bc WHIRLPOOL 0c5c1d86b0bafe9d5ca02397793f902b4dca7edc3f507a472b8b235f91965d8a769a7873cc87d834fbb121792b52eb6908018ce6579acdf3d285b6ec986abc20
-DIST rstudio-0.99.484.tar.gz 16993033 SHA256 8ca4abccb9b554713077cf1057ac13abadfd7606f22ac3386b2a88a38ae8a427 SHA512 407f50747bca749ef2c512e727cbe062abdd99c1eb76af09761e6bdfb4208f30117e1ee55b485447f64f6cf249bc939ef1fb4f8ce0199595e241a3cc617b4b8b WHIRLPOOL 8cc16553ea2703f005908c69803b64da4172092cb0b3ff9015e7ec354340fcd1cfa82a218ac890adffafe3565ead94bee6f7bd239b1c56ee38cbeb5896f556b0
-DIST rstudio-0.99.486.tar.gz 16992775 SHA256 4057195465e5032625bad0304bfbd9d123a78c3e4d6d5d41abcc6ef6ccd18a6f SHA512 bb88d12f8ae2f79779532371d03a698a2c2897c212c42c8438d5223c14e1033098dbd7c278a929958fa4bbc764a3ceb101abe03634f0e33192de44cf97128a1f WHIRLPOOL 13c35a69e525d90c6694d068526a2aede76a086427539294e46db67d0fc92759fb9cb0a1169cf88745ae1e121fdd7ba2e46bd2d2fb3fa17dc7fcc65848820941
-DIST rstudio-0.99.491.tar.gz 16992702 SHA256 e8c21e2262b610a7ccf39283b97d114bee33c6840a060067b8019404ff44b03f SHA512 2658694d6154f4b91b2dc07a7ec653edb7f593c4d9829a06a5e600e4db465ca6059418be6812d5ba2529fd6202dd136f0f58d74576f856fdcf6f81032d74f3c2 WHIRLPOOL e71650a07cc010ab3c25955c7fa9e90eee68577c1ef78e02a5f81a0160c688908ec5ec4fd89c89e5a9bc49b926623cd5de976fb249aa2d472354d23f5fad76de
-DIST rstudio-0.99.879.tar.gz 17406999 SHA256 73fa59be34eb63d9ed194642a93ad529d2c67cdcbcd2f291952fdef8e999a097 SHA512 c2bbe598a4a9c2abc69e39807af70be5729a06bbcb73bac5249f74f3c3daddb2909bf4a46d988f0d4bfeabe308f0c31d2a75aa28a52f11c1343dfcead07e2c45 WHIRLPOOL 5c9c75a7891ac53eb80a36eff518d77a0c281b16bff383526ac1ede07ee57486d7b00be4e400a0cad48dfea92729becf25c67f18782af7930f9b4218592afe5c
-DIST rstudio-0.99.893.tar.gz 17407634 SHA256 90a657b1fa16cfc575ca884789bac47f17832eb8b92496d044da3c5d79b0b874 SHA512 baa2a8c27e101e74b8a3f3b1cd290c90031881ae11fb44606b9af1efa4114c4c6fe68298f554d8b83f96418159477579414ddb99d49d2942c021aa0697947222 WHIRLPOOL a81ed5ee17a730e9674b2a98b95f87e70c532df95fda15402952901f7def24cc673db724841579e5dbf184a3e9fc16cfada93284b40014edf74863a61e0798a5
-DIST rstudio-0.99.896.tar.gz 17409121 SHA256 05fc7546ad1d21d7e6219538056ec2ee1b86d09b731a588198ce137d3fe25bae SHA512 c62df2a1c54f8c6d14b1239dd746b88693c11c48ec56aa5ae89023e98901793b0e65df44526cbc8c71036c0f73a512767cae086ed3777540b1ceda05e3398e17 WHIRLPOOL 7f4d0ebc8db509f09ccc15da02a4a426de431312f2dc65126bda76e11de0e106671fc7a83e9ea8e66b88f81268d0db8b44014a70744b30641bb58bedda73427d
-DIST rstudio-0.99.902.tar.gz 17408815 SHA256 703a3ebedbb4bb44d2cacffed2615b4f65156fcd4115029931eb5fd99950c689 SHA512 23db68f05900666287901d75f02006f7edacafab057d82a312b4e5aac639ef4b5db702420632f2768e509411bbfc73c32a533aa0f1b33379c10df82e009b974e WHIRLPOOL e7ef3cf0d9a414257c4c0c68809c674721f9513917bd450c9946133ee69dd735374417483c7dc380ee4d387119558c961d4ea815aac5bcd3fa22ee863556e0a4
-DIST rstudio-0.99.903.tar.gz 17409865 SHA256 8902fe7a6f7f6e0d6e8fae2472e479bb9cbe9cbb2e0747e5f01a093d31993a3c SHA512 9ddcfdab187c907dfa3cbf386ee902b43ba35c242b44a4190c58d1e3bad590ca428209423739768b57f759c4bde61ef2b5958fb3cba366d7740753c3c5dbf739 WHIRLPOOL 82ca64883d02aacc0c1081779f769c3ea2bbac3c370f1e62fba18465547742114df18d431f30c3fe449c0ae2ac212cd7dd98a72bb2e5810eb1fc6cdbb3c82a69
-DIST rstudio-1.0.136.tar.gz 17786389 SHA256 bb6a8aa475e09dd090cd2b5ea505f578d270858784120599aee5c10bd8ca58e8 SHA512 cb4f98834f287267925169c8141bd0f95fd23cefdba8f407f76a24617bc40da56430745f112774838345330b9f99b9cac86d5b99517346a019e8e2cb3b01f713 WHIRLPOOL 5932ef2572670951a094f79e8805215fd50c3643b4a4654cb469d7181708a3327763531cb68e968e64ebdb7b44df03da0c18f9a06a12d968e908bedc43dac52f
-DIST rstudio-1.0.143.tar.gz 17791067 SHA256 8ae88731b4474e5e2ff9030aa14e168903fe3a7ffc4fa716f497084a86801062 SHA512 46eaa88dd8332f18bb3a43de6e262d8a365860d9add78aea6a2d345784b239972c9c73bf0b56f1736b2981b8f688dbaf5a83c6848d170c0cf61d0e51dd636a82 WHIRLPOOL db1c11be240db3528e46d359c7d40d64068dfe5f7d915c4a6b690444f7f7fbc11f3898a6e262fa625bfab906f0cbfb2a8e3288a4fd20470423a99d992972fcda
-DIST rstudio-1.0.153.tar.gz 17790922 SHA256 79b90e21e56b114e28b03fd8543a208c55bb9d5f47a87fd29143d08b9a06f7a0 SHA512 d970a9bde88845e3fc6cdaff5233ffb65c03939c685c3fca0dd052246e065c7580b3f9bc4e053a79d2ecbb5f8c283d3fce7b97cc69e43176bd49587c736dab86 WHIRLPOOL c1f4c7bdc8e5a85af53411a35d736278b83f4732d2e273378fecc77cb075dff507147d56012682564edd58041c91cc051189eb38a7348d0827b76c7ac37bd54d
-DIST rstudio-1.0.44.tar.gz 17774065 SHA256 43ece6cfdd1a13ac0e17f2a50154a30a1a14ad6c1b3cf381cc6007988ce44a0f SHA512 a8b975dc517125a257e5f61db5bb137e133b02d738d55553770aa65e388cd112ce646b53b77dc069d1ca95ccd95979f4a57ad60b99fc3b91543cf61e737e8169 WHIRLPOOL 4ad472aed130451e81d8d8e3251d3bbd701a8b8e2fbddf17dc357f39335e33c75505f9443c2c7208e60a19c2767b9328134433e5d4fd22504813020712c658ef
 DIST rstudio-1.1.368.tar.gz 20197144 SHA256 586573707a488b5f528680b932ba5f8ea6d07667cc5ae6426104e2abf5ddab75 SHA512 39cdf583d7dcd22338916cc0ea4f90681580e41663b2d3e04b2e650759c6b030c85ee111cdfe1f717f931932a9b7ca423a21585d69a785f056f754f6d50399a1 WHIRLPOOL e18ff21823638d458179819e0b0b234b80be2f095f5b7bf5b9ac0190b078f0d7acb51e8896cbfcf1ce33cd203ed4e9fbe097aac6eee62515cace1d2f08c08219
 DIST selenium-java-2.37.0.zip 24625928 SHA256 0eebba65d8edb01c1f46e462907c58f5d6e1cb0ddf63660a9985c8432bdffbb7 SHA512 68624e82dbc751a25c50fad72702a98eb30d77fd4337d2a969f8e06bcc49e5f8c835cd27ec53772f3375014ddde1d5636936e966b75f3594a9f86aa18ba4e779 WHIRLPOOL eb6659aae26f3c78b6f998546b23d0636c9d00ed8a7f985db1463ac4bd483ccb3e643d84e2ca0f59e0636a8de79eb552ff1d68eb6f9c06907029f7552d8f7777
 DIST selenium-server-standalone-2.37.0.jar 34730734 SHA256 97bc8c699037fb6e99ba7af570fb60dbb1b7ce30cde2448287a44ef65b13023e SHA512 b215446d42d2d1f69664349b6ae6dc53a532d3624c91254f0f4183d0ad764648792e5cc1126a55a1e60d9687d55200fed01d6d2f46cc3d853b1fa6ee38111018 WHIRLPOOL 20640591534f31f24825a9ed139589b182e8b60d86541bf0be104d3cc0280983f6566bd0459f2253ac3875b48a2798b205bac8f815a119fff6db625ce9bbc29e

diff --git a/sci-mathematics/rstudio/files/rstudio-0.98.1091-pandoc.patch b/sci-mathematics/rstudio/files/rstudio-0.98.1091-pandoc.patch
deleted file mode 100644
index 3df8d1a986a..00000000000
--- a/sci-mathematics/rstudio/files/rstudio-0.98.1091-pandoc.patch
+++ /dev/null
@@ -1,26 +0,0 @@
---- rstudio-0.98.1091-orig/src/cpp/session/CMakeLists.txt	2014-11-06 23:15:47.000000000 +1100
-+++ rstudio-0.98.1091/src/cpp/session/CMakeLists.txt	2014-11-26 17:12:42.699712510 +1100
-@@ -25,9 +25,6 @@
- if(NOT EXISTS "${RSTUDIO_DEPENDENCIES_DIR}/common/mathjax-23")
-   message(FATAL_ERROR "Mathjax 2.3 not found (re-run install-dependencies script to install)")
- endif()
--if(NOT EXISTS "${RSTUDIO_DEPENDENCIES_DIR}/common/pandoc")
--  message(FATAL_ERROR "pandoc not found (re-run install-dependencies script to install)")
--endif()
- if(NOT EXISTS "${RSTUDIO_DEPENDENCIES_DIR}/common/rmarkdown")
-   message(FATAL_ERROR "rmarkdown package not found (re-run install-dependencies script to install)")
- endif()
-@@ -343,13 +340,6 @@
-    install(DIRECTORY "${RSTUDIO_DEPENDENCIES_DIR}/common/mathjax-23"
-            DESTINATION "${RSTUDIO_INSTALL_SUPPORTING}/resources")
- 
--   # install pandoc
--   set(PANDOC_BIN "${RSTUDIO_DEPENDENCIES_DIR}/common/pandoc/1.12.4.2")
--   file(GLOB PANDOC_FILES "${PANDOC_BIN}/pandoc*")
--   install(FILES ${PANDOC_FILES}
--           PERMISSIONS OWNER_READ OWNER_WRITE OWNER_EXECUTE GROUP_READ GROUP_EXECUTE WORLD_READ WORLD_EXECUTE
--           DESTINATION  ${RSTUDIO_INSTALL_BIN}/pandoc)
--
-    # install rmarkdown package
-    file(GLOB RMARKDOWN_PACKAGE "${RSTUDIO_DEPENDENCIES_DIR}/common/rmarkdown*.tar.gz")
-    install(FILES ${RMARKDOWN_PACKAGE}

diff --git a/sci-mathematics/rstudio/files/rstudio-0.98.490-paths.patch b/sci-mathematics/rstudio/files/rstudio-0.98.490-paths.patch
deleted file mode 100644
index d28ad5cb075..00000000000
--- a/sci-mathematics/rstudio/files/rstudio-0.98.490-paths.patch
+++ /dev/null
@@ -1,120 +0,0 @@
-diff --git a/CMakeGlobals.txt b/CMakeGlobals.txt
-index cc10191..f75b85a 100644
---- a/CMakeGlobals.txt
-+++ b/CMakeGlobals.txt
-@@ -105,7 +105,7 @@ else()
-    else()
-      set(RSTUDIO_INSTALL_BIN bin)
-    endif()
--   set(RSTUDIO_INSTALL_SUPPORTING .)
-+   set(RSTUDIO_INSTALL_SUPPORTING ${DISTRO_SHARE})
- endif()
- 
- # if the install prefix is /usr/local then tweak as appropriate
-diff --git a/src/cpp/server/CMakeLists.txt b/src/cpp/server/CMakeLists.txt
-index 184e514..d09aac5 100644
---- a/src/cpp/server/CMakeLists.txt
-+++ b/src/cpp/server/CMakeLists.txt
-@@ -145,7 +145,7 @@ if (UNIX AND NOT APPLE)
-    configure_file(${CMAKE_CURRENT_SOURCE_DIR}/${RSERVER_INITD_DEBIAN_SCRIPT}.in
-                   ${CMAKE_CURRENT_BINARY_DIR}/${RSERVER_INITD_DEBIAN_SCRIPT})
-    install(PROGRAMS ${CMAKE_CURRENT_BINARY_DIR}/${RSERVER_INITD_DEBIAN_SCRIPT}
--           DESTINATION ${RSERVER_INITD_DEBIAN_DIR})
-+           DESTINATION ${DISTRO_SHARE}/${RSERVER_INITD_DEBIAN_DIR})
- 
-    # install configured redhat init.d script
-    set(RSERVER_INITD_REDHAT_DIR "extras/init.d/redhat")
-@@ -153,7 +153,7 @@ if (UNIX AND NOT APPLE)
-    configure_file(${CMAKE_CURRENT_SOURCE_DIR}/${RSERVER_INITD_REDHAT_SCRIPT}.in
-                   ${CMAKE_CURRENT_BINARY_DIR}/${RSERVER_INITD_REDHAT_SCRIPT})
-    install(PROGRAMS ${CMAKE_CURRENT_BINARY_DIR}/${RSERVER_INITD_REDHAT_SCRIPT}
--           DESTINATION ${RSERVER_INITD_REDHAT_DIR})
-+           DESTINATION ${DISTRO_SHARE}/${RSERVER_INITD_REDHAT_DIR})
- 
-    # install configured suse init.d script
-    set(RSERVER_INITD_SUSE_DIR "extras/init.d/suse")
-@@ -161,13 +161,13 @@ if (UNIX AND NOT APPLE)
-    configure_file(${CMAKE_CURRENT_SOURCE_DIR}/${RSERVER_INITD_SUSE_SCRIPT}.in
-                   ${CMAKE_CURRENT_BINARY_DIR}/${RSERVER_INITD_SUSE_SCRIPT})
-    install(PROGRAMS ${CMAKE_CURRENT_BINARY_DIR}/${RSERVER_INITD_SUSE_SCRIPT}
--           DESTINATION ${RSERVER_INITD_SUSE_DIR})
-+           DESTINATION ${DISTRO_SHARE}/${RSERVER_INITD_SUSE_DIR})
- 
-    # install pam profile
-    set(RSERVER_PAM_DIR "extras/pam")
-    set(RSERVER_PAM_PROFILE "${RSERVER_PAM_DIR}/rstudio")
-    install(FILES ${CMAKE_CURRENT_SOURCE_DIR}/${RSERVER_PAM_PROFILE}
--           DESTINATION ${RSERVER_PAM_DIR})
-+           DESTINATION ${DISTRO_SHARE}/${RSERVER_PAM_DIR})
- 
-    # install configured apparmor profile
-    set(RSERVER_APPARMOR_DIR "extras/apparmor")
-@@ -175,9 +175,9 @@ if (UNIX AND NOT APPLE)
-    configure_file(${CMAKE_CURRENT_SOURCE_DIR}/${RSERVER_APPARMOR_PROFILE}.in
-                   ${CMAKE_CURRENT_BINARY_DIR}/${RSERVER_APPARMOR_PROFILE})
-    install(FILES ${CMAKE_CURRENT_BINARY_DIR}/${RSERVER_APPARMOR_PROFILE}
--           DESTINATION ${RSERVER_APPARMOR_DIR})
-+           DESTINATION ${DISTRO_SHARE}/${RSERVER_APPARMOR_DIR})
-    install(PROGRAMS ${CMAKE_CURRENT_SOURCE_DIR}/${RSERVER_APPARMOR_DIR}/apparmor-profile-load
--           DESTINATION ${RSERVER_APPARMOR_DIR})
-+           DESTINATION ${DISTRO_SHARE}/${RSERVER_APPARMOR_DIR})
- 
-    # install configured upstart profile
-    set(RSERVER_UPSTART_DIR "extras/upstart")
-@@ -185,12 +185,12 @@ if (UNIX AND NOT APPLE)
-    configure_file(${CMAKE_CURRENT_SOURCE_DIR}/${RSERVER_UPSTART_PROFILE}.in
-                   ${CMAKE_CURRENT_BINARY_DIR}/${RSERVER_UPSTART_PROFILE})
-    install(FILES ${CMAKE_CURRENT_BINARY_DIR}/${RSERVER_UPSTART_PROFILE}
--           DESTINATION ${RSERVER_UPSTART_DIR})
-+           DESTINATION ${DISTRO_SHARE}/${RSERVER_UPSTART_DIR})
-    set(RSERVER_UPSTART_PROFILE_REDHAT "${RSERVER_UPSTART_DIR}/rstudio-server.redhat.conf")
-    configure_file(${CMAKE_CURRENT_SOURCE_DIR}/${RSERVER_UPSTART_PROFILE_REDHAT}.in
-                   ${CMAKE_CURRENT_BINARY_DIR}/${RSERVER_UPSTART_PROFILE_REDHAT})
-    install(FILES ${CMAKE_CURRENT_BINARY_DIR}/${RSERVER_UPSTART_PROFILE_REDHAT}
--           DESTINATION ${RSERVER_UPSTART_DIR})
-+           DESTINATION ${DISTRO_SHARE}/${RSERVER_UPSTART_DIR})
- 
- endif()
- 
-diff --git a/src/cpp/server/ServerOptions.cpp b/src/cpp/server/ServerOptions.cpp
-index 1eaf7c0..4b25fa1 100644
---- a/src/cpp/server/ServerOptions.cpp
-+++ b/src/cpp/server/ServerOptions.cpp
-@@ -307,8 +307,8 @@ ProgramStatus Options::read(int argc,
- 
-    // convert relative paths by completing from the system installation
-    // path (this allows us to be relocatable)
--   resolvePath(resourcePath, &wwwLocalPath_);
--   resolvePath(resourcePath, &wwwSymbolMapsPath_);
-+   resolvePath(resourcePath.childPath(DISTRO_SHARE), &wwwLocalPath_);
-+   resolvePath(resourcePath.childPath(DISTRO_SHARE), &wwwSymbolMapsPath_);
-    resolvePath(binaryPath, &authPamHelperPath_);
-    resolvePath(binaryPath, &rsessionPath_);
-    resolvePath(binaryPath, &rldpathPath_);
-diff --git a/src/cpp/session/SessionOptions.cpp b/src/cpp/session/SessionOptions.cpp
-index 44b3d55..a48cdb6 100644
---- a/src/cpp/session/SessionOptions.cpp
-+++ b/src/cpp/session/SessionOptions.cpp
-@@ -357,14 +357,14 @@ core::ProgramStatus Options::read(int argc, char * const argv[])
-       timeoutMinutes_ = 0;
- 
-    // convert relative paths by completing from the app resource path
--   resolvePath(resourcePath, &rResourcesPath_);
--   resolvePath(resourcePath, &agreementFilePath_);
--   resolvePath(resourcePath, &wwwLocalPath_);
--   resolvePath(resourcePath, &wwwSymbolMapsPath_);
--   resolvePath(resourcePath, &coreRSourcePath_);
--   resolvePath(resourcePath, &modulesRSourcePath_);
--   resolvePath(resourcePath, &sessionLibraryPath_);
--   resolvePath(resourcePath, &sessionPackagesPath_);
-+   resolvePath(resourcePath.childPath(DISTRO_SHARE), &rResourcesPath_);
-+   resolvePath(resourcePath.childPath(DISTRO_SHARE), &agreementFilePath_);
-+   resolvePath(resourcePath.childPath(DISTRO_SHARE), &wwwLocalPath_);
-+   resolvePath(resourcePath.childPath(DISTRO_SHARE), &coreRSourcePath_);
-+   resolvePath(resourcePath.childPath(DISTRO_SHARE), &modulesRSourcePath_);
-+   resolvePath(resourcePath.childPath(DISTRO_SHARE), &sessionLibraryPath_);
-+   resolvePath(resourcePath.childPath(DISTRO_SHARE), &sessionPackagesPath_);
-+   resolvePath(resourcePath.childPath(DISTRO_SHARE), &wwwSymbolMapsPath_);
-    resolvePostbackPath(resourcePath, &rpostbackPath_);
- #ifdef _WIN32
-    resolvePath(resourcePath, &consoleIoPath_);

diff --git a/sci-mathematics/rstudio/files/rstudio-0.98.490-prefs.patch b/sci-mathematics/rstudio/files/rstudio-0.98.490-prefs.patch
deleted file mode 100644
index 3175d47235a..00000000000
--- a/sci-mathematics/rstudio/files/rstudio-0.98.490-prefs.patch
+++ /dev/null
@@ -1,24 +0,0 @@
-And now we fix src/gwt/build.xml since java's user preference class is
-braindead and insists on writing where it is not allowed.
-much thanks to http://www.allaboutbalance.com/articles/disableprefs/
-
-diff --git a/src/gwt/build.xml b/src/gwt/build.xml
-index e7d2418..ae3a331 100644
---- a/src/gwt/build.xml
-+++ b/src/gwt/build.xml
-@@ -25,6 +25,7 @@
-    <property name="gwt.extra.args" value=""/>
-    <property name="gwt.main.module" value="org.rstudio.studio.RStudio"/>
-    <property name="ace.bin" value="src/org/rstudio/studio/client/workbench/views/source/editors/text/ace"/>
-+   <property environment="env"/>
- 
-    <path id="project.class.path">
-       <pathelement location="bin"/>
-@@ -109,6 +110,7 @@
-          </classpath>
-          <!-- add jvmarg -Xss16M or similar if you see a StackOverflowError -->
-          <jvmarg value="-Xmx1024M"/>
-+         <jvmarg value="-Djava.util.prefs.userRoot=${env.T}"/>
-          <arg value="-war"/>
-          <arg value="www"/>
-          <arg value="-localWorkers"/>

diff --git a/sci-mathematics/rstudio/files/rstudio-0.98.932-pandoc.patch b/sci-mathematics/rstudio/files/rstudio-0.98.932-pandoc.patch
deleted file mode 100644
index d2b6911eabb..00000000000
--- a/sci-mathematics/rstudio/files/rstudio-0.98.932-pandoc.patch
+++ /dev/null
@@ -1,25 +0,0 @@
---- a/src/cpp/session/CMakeLists.txt
-+++ b/src/cpp/session/CMakeLists.txt
-@@ -25,9 +25,6 @@
- if(NOT EXISTS "${RSTUDIO_DEPENDENCIES_DIR}/common/mathjax")
-   message(FATAL_ERROR "Mathjax not found (re-run install-dependencies script to install)")
- endif()
--if(NOT EXISTS "${RSTUDIO_DEPENDENCIES_DIR}/common/pandoc")
--  message(FATAL_ERROR "pandoc not found (re-run install-dependencies script to install)")
--endif()
- if(NOT EXISTS "${RSTUDIO_DEPENDENCIES_DIR}/common/rmarkdown")
-   message(FATAL_ERROR "rmarkdown package not found (re-run install-dependencies script to install)")
- endif()
-@@ -337,12 +334,6 @@
-    install(DIRECTORY "${RSTUDIO_DEPENDENCIES_DIR}/common/mathjax"
-            DESTINATION "${RSTUDIO_INSTALL_SUPPORTING}/resources")
- 
--   # install pandoc
--   set(PANDOC_BIN "${RSTUDIO_DEPENDENCIES_DIR}/common/pandoc/1.12.3")
--   file(GLOB PANDOC_FILES "${PANDOC_BIN}/pandoc*")
--   install(PROGRAMS ${PANDOC_FILES}
--           DESTINATION  ${RSTUDIO_INSTALL_BIN}/pandoc)
--
-    # install rmarkdown package
-    file(GLOB RMARKDOWN_PACKAGE "${RSTUDIO_DEPENDENCIES_DIR}/common/rmarkdown*.tar.gz")
-    install(FILES ${RMARKDOWN_PACKAGE}

diff --git a/sci-mathematics/rstudio/files/rstudio-0.98.932-paths.patch b/sci-mathematics/rstudio/files/rstudio-0.98.932-paths.patch
deleted file mode 100644
index d4bb4249f1a..00000000000
--- a/sci-mathematics/rstudio/files/rstudio-0.98.932-paths.patch
+++ /dev/null
@@ -1,140 +0,0 @@
-diff --git a/CMakeGlobals.txt b/CMakeGlobals.txt
-index cc10191..f75b85a 100644
---- a/CMakeGlobals.txt
-+++ b/CMakeGlobals.txt
-@@ -105,7 +105,7 @@ else()
-    else()
-      set(RSTUDIO_INSTALL_BIN bin)
-    endif()
--   set(RSTUDIO_INSTALL_SUPPORTING .)
-+   set(RSTUDIO_INSTALL_SUPPORTING ${DISTRO_SHARE})
- endif()
- 
- # if the install prefix is /usr/local then tweak as appropriate
-diff --git a/src/cpp/server/CMakeLists.txt b/src/cpp/server/CMakeLists.txt
-index 184e514..d09aac5 100644
---- a/src/cpp/server/CMakeLists.txt
-+++ b/src/cpp/server/CMakeLists.txt
-@@ -145,7 +145,7 @@ if (UNIX AND NOT APPLE)
-    configure_file(${CMAKE_CURRENT_SOURCE_DIR}/${RSERVER_INITD_DEBIAN_SCRIPT}.in
-                   ${CMAKE_CURRENT_BINARY_DIR}/${RSERVER_INITD_DEBIAN_SCRIPT})
-    install(PROGRAMS ${CMAKE_CURRENT_BINARY_DIR}/${RSERVER_INITD_DEBIAN_SCRIPT}
--           DESTINATION ${RSERVER_INITD_DEBIAN_DIR})
-+           DESTINATION ${DISTRO_SHARE}/${RSERVER_INITD_DEBIAN_DIR})
- 
-    # install configured redhat init.d script
-    set(RSERVER_INITD_REDHAT_DIR "extras/init.d/redhat")
-@@ -153,7 +153,7 @@ if (UNIX AND NOT APPLE)
-    configure_file(${CMAKE_CURRENT_SOURCE_DIR}/${RSERVER_INITD_REDHAT_SCRIPT}.in
-                   ${CMAKE_CURRENT_BINARY_DIR}/${RSERVER_INITD_REDHAT_SCRIPT})
-    install(PROGRAMS ${CMAKE_CURRENT_BINARY_DIR}/${RSERVER_INITD_REDHAT_SCRIPT}
--           DESTINATION ${RSERVER_INITD_REDHAT_DIR})
-+           DESTINATION ${DISTRO_SHARE}/${RSERVER_INITD_REDHAT_DIR})
- 
-    # install configured suse init.d script
-    set(RSERVER_INITD_SUSE_DIR "extras/init.d/suse")
-@@ -161,13 +161,13 @@ if (UNIX AND NOT APPLE)
-    configure_file(${CMAKE_CURRENT_SOURCE_DIR}/${RSERVER_INITD_SUSE_SCRIPT}.in
-                   ${CMAKE_CURRENT_BINARY_DIR}/${RSERVER_INITD_SUSE_SCRIPT})
-    install(PROGRAMS ${CMAKE_CURRENT_BINARY_DIR}/${RSERVER_INITD_SUSE_SCRIPT}
--           DESTINATION ${RSERVER_INITD_SUSE_DIR})
-+           DESTINATION ${DISTRO_SHARE}/${RSERVER_INITD_SUSE_DIR})
- 
-    # install pam profile
-    set(RSERVER_PAM_DIR "extras/pam")
-    set(RSERVER_PAM_PROFILE "${RSERVER_PAM_DIR}/rstudio")
-    install(FILES ${CMAKE_CURRENT_SOURCE_DIR}/${RSERVER_PAM_PROFILE}
--           DESTINATION ${RSERVER_PAM_DIR})
-+           DESTINATION ${DISTRO_SHARE}/${RSERVER_PAM_DIR})
- 
-    # install configured apparmor profile
-    set(RSERVER_APPARMOR_DIR "extras/apparmor")
-@@ -175,9 +175,9 @@ if (UNIX AND NOT APPLE)
-    configure_file(${CMAKE_CURRENT_SOURCE_DIR}/${RSERVER_APPARMOR_PROFILE}.in
-                   ${CMAKE_CURRENT_BINARY_DIR}/${RSERVER_APPARMOR_PROFILE})
-    install(FILES ${CMAKE_CURRENT_BINARY_DIR}/${RSERVER_APPARMOR_PROFILE}
--           DESTINATION ${RSERVER_APPARMOR_DIR})
-+           DESTINATION ${DISTRO_SHARE}/${RSERVER_APPARMOR_DIR})
-    install(PROGRAMS ${CMAKE_CURRENT_SOURCE_DIR}/${RSERVER_APPARMOR_DIR}/apparmor-profile-load
--           DESTINATION ${RSERVER_APPARMOR_DIR})
-+           DESTINATION ${DISTRO_SHARE}/${RSERVER_APPARMOR_DIR})
- 
-    # install configured upstart profile
-    set(RSERVER_UPSTART_DIR "extras/upstart")
-@@ -185,12 +185,12 @@ if (UNIX AND NOT APPLE)
-    configure_file(${CMAKE_CURRENT_SOURCE_DIR}/${RSERVER_UPSTART_PROFILE}.in
-                   ${CMAKE_CURRENT_BINARY_DIR}/${RSERVER_UPSTART_PROFILE})
-    install(FILES ${CMAKE_CURRENT_BINARY_DIR}/${RSERVER_UPSTART_PROFILE}
--           DESTINATION ${RSERVER_UPSTART_DIR})
-+           DESTINATION ${DISTRO_SHARE}/${RSERVER_UPSTART_DIR})
-    set(RSERVER_UPSTART_PROFILE_REDHAT "${RSERVER_UPSTART_DIR}/rstudio-server.redhat.conf")
-    configure_file(${CMAKE_CURRENT_SOURCE_DIR}/${RSERVER_UPSTART_PROFILE_REDHAT}.in
-                   ${CMAKE_CURRENT_BINARY_DIR}/${RSERVER_UPSTART_PROFILE_REDHAT})
-    install(FILES ${CMAKE_CURRENT_BINARY_DIR}/${RSERVER_UPSTART_PROFILE_REDHAT}
--           DESTINATION ${RSERVER_UPSTART_DIR})
-+           DESTINATION ${DISTRO_SHARE}/${RSERVER_UPSTART_DIR})
- 
- endif()
- 
-diff --git a/src/cpp/server/ServerOptions.cpp b/src/cpp/server/ServerOptions.cpp
-index 1eaf7c0..4b25fa1 100644
---- a/src/cpp/server/ServerOptions.cpp
-+++ b/src/cpp/server/ServerOptions.cpp
-@@ -307,8 +307,8 @@ ProgramStatus Options::read(int argc,
- 
-    // convert relative paths by completing from the system installation
-    // path (this allows us to be relocatable)
--   resolvePath(resourcePath, &wwwLocalPath_);
--   resolvePath(resourcePath, &wwwSymbolMapsPath_);
-+   resolvePath(resourcePath.childPath(DISTRO_SHARE), &wwwLocalPath_);
-+   resolvePath(resourcePath.childPath(DISTRO_SHARE), &wwwSymbolMapsPath_);
-    resolvePath(binaryPath, &authPamHelperPath_);
-    resolvePath(binaryPath, &rsessionPath_);
-    resolvePath(binaryPath, &rldpathPath_);
-diff --git a/src/cpp/session/SessionOptions.cpp b/src/cpp/session/SessionOptions.cpp
-index 44b3d55..a48cdb6 100644
---- a/src/cpp/session/SessionOptions.cpp
-+++ b/src/cpp/session/SessionOptions.cpp
-@@ -40,7 +40,7 @@
- namespace session {  
- 
- namespace {
--const char* const kDefaultPandocPath = "bin/pandoc";
-+const char* const kDefaultPandocPath = "bin";
- const char* const kDefaultPostbackPath = "bin/postback/rpostback";
- } // anonymous namespace
- 
-@@ -392,15 +392,15 @@
-    }
- 
-    // convert relative paths by completing from the app resource path
--   resolvePath(resourcePath, &rResourcesPath_);
--   resolvePath(resourcePath, &agreementFilePath_);
--   resolvePath(resourcePath, &wwwLocalPath_);
--   resolvePath(resourcePath, &wwwSymbolMapsPath_);
--   resolvePath(resourcePath, &coreRSourcePath_);
--   resolvePath(resourcePath, &modulesRSourcePath_);
--   resolvePath(resourcePath, &sessionLibraryPath_);
--   resolvePath(resourcePath, &sessionPackagesPath_);
--   resolvePath(resourcePath, &sessionPackageArchivesPath_);
-+   resolvePath(resourcePath.childPath(DISTRO_SHARE), &rResourcesPath_);
-+   resolvePath(resourcePath.childPath(DISTRO_SHARE), &agreementFilePath_);
-+   resolvePath(resourcePath.childPath(DISTRO_SHARE), &wwwLocalPath_);
-+   resolvePath(resourcePath.childPath(DISTRO_SHARE), &coreRSourcePath_);
-+   resolvePath(resourcePath.childPath(DISTRO_SHARE), &modulesRSourcePath_);
-+   resolvePath(resourcePath.childPath(DISTRO_SHARE), &sessionLibraryPath_);
-+   resolvePath(resourcePath.childPath(DISTRO_SHARE), &sessionPackagesPath_);
-+   resolvePath(resourcePath.childPath(DISTRO_SHARE), &sessionPackageArchivesPath_);
-+   resolvePath(resourcePath.childPath(DISTRO_SHARE), &wwwSymbolMapsPath_);
-    resolvePostbackPath(resourcePath, &rpostbackPath_);
- #ifdef _WIN32
-    resolvePath(resourcePath, &consoleIoPath_);
-@@ -409,7 +409,7 @@
-    resolvePath(resourcePath, &msysSshPath_);
-    resolvePath(resourcePath, &sumatraPath_);
- #endif
--   resolvePath(resourcePath, &hunspellDictionariesPath_);
-+   resolvePath(resourcePath.childPath(DISTRO_SHARE), &hunspellDictionariesPath_);
-    resolvePath(resourcePath, &mathjaxPath_);
-    resolvePandocPath(resourcePath, &pandocPath_);
- 

diff --git a/sci-mathematics/rstudio/files/rstudio-0.99.473-clang-pandoc.patch b/sci-mathematics/rstudio/files/rstudio-0.99.473-clang-pandoc.patch
deleted file mode 100644
index b37a9192957..00000000000
--- a/sci-mathematics/rstudio/files/rstudio-0.99.473-clang-pandoc.patch
+++ /dev/null
@@ -1,77 +0,0 @@
---- rstudio-0.99.473-orig/src/cpp/session/CMakeLists.txt	2015-08-12 09:58:43.000000000 +1000
-+++ rstudio-0.99.473/src/cpp/session/CMakeLists.txt	2015-08-27 00:51:48.395751378 +1000
-@@ -25,30 +25,11 @@
- if(NOT EXISTS "${RSTUDIO_DEPENDENCIES_DIR}/common/mathjax-23")
-   message(FATAL_ERROR "Mathjax 2.3 not found (re-run install-dependencies script to install)")
- endif()
--if(NOT EXISTS "${RSTUDIO_DEPENDENCIES_DIR}/common/pandoc")
--  message(FATAL_ERROR "pandoc not found (re-run install-dependencies script to install)")
--endif()
- if(NOT EXISTS "${RSTUDIO_DEPENDENCIES_DIR}/common/rsconnect")
-   message(FATAL_ERROR "rsconnect package not found (re-run install-dependencies script to install)")
- endif()
- 
- 
--# verify libclang is installed
--if(WIN32)
--   set(LIBCLANG_VERSION "3.4")
--else()
--   set(LIBCLANG_VERSION "3.5")
--endif()
--set(LIBCLANG_DIR "${RSTUDIO_DEPENDENCIES_DIR}/common/libclang/${LIBCLANG_VERSION}")
--if(NOT EXISTS "${LIBCLANG_DIR}")
--  message(FATAL_ERROR "libclang ${LIBCLANG_VERSION} not found  (re-run install-dependencies script to install)")
--endif()
--set(LIBCLANG_HEADERS_DIR "${RSTUDIO_DEPENDENCIES_DIR}/common/libclang/builtin-headers")
--if(NOT EXISTS "${LIBCLANG_HEADERS_DIR}")
--  message(FATAL_ERROR "libclang builtin-headers not found  (re-run install-dependencies script to install)")
--endif()
--
--
- # include files
- file(GLOB_RECURSE SESSION_HEADER_FILES "*.h*")
- 
-@@ -391,18 +372,6 @@
-    install(DIRECTORY "${RSTUDIO_DEPENDENCIES_DIR}/common/mathjax-23"
-            DESTINATION "${RSTUDIO_INSTALL_SUPPORTING}/resources")
- 
--   # install pandoc
--   if(RSTUDIO_PACKAGE_BUILD_SLES)
--      # when producing a SUSE Linux Enterpise build, we want to install the 
--      # static Pandoc binaries (see dependencies/common/install-pandoc)
--      set(PANDOC_EXTENSION_DIR "/static")
--   endif()
--   set(PANDOC_BIN "${RSTUDIO_DEPENDENCIES_DIR}/common/pandoc/1.13.1${PANDOC_EXTENSION_DIR}")
--   file(GLOB PANDOC_FILES "${PANDOC_BIN}/pandoc*")
--   install(FILES ${PANDOC_FILES}
--           PERMISSIONS OWNER_READ OWNER_WRITE OWNER_EXECUTE GROUP_READ GROUP_EXECUTE WORLD_READ WORLD_EXECUTE
--           DESTINATION  ${RSTUDIO_INSTALL_BIN}/pandoc)
--
-    # install rsconnect package
-    file(GLOB RSCONNECT_PACKAGE "${RSTUDIO_DEPENDENCIES_DIR}/common/rsconnect*.tar.gz")
-    install(FILES ${RSCONNECT_PACKAGE}
-@@ -420,24 +389,6 @@
-    install(DIRECTORY "resources/help_resources"
-            DESTINATION ${RSTUDIO_INSTALL_SUPPORTING}/resources)
- 
--   # install libclang
--   if(WIN32)
--      file(GLOB LIBCLANG_32_FILES "${LIBCLANG_DIR}/x86/libclang.*")
--      install(PROGRAMS ${LIBCLANG_32_FILES}
--              DESTINATION  ${RSTUDIO_INSTALL_BIN}/rsclang/x86)
--      file(GLOB LIBCLANG_64_FILES "${LIBCLANG_DIR}/x86_64/libclang.*")
--      install(PROGRAMS ${LIBCLANG_64_FILES}
--              DESTINATION  ${RSTUDIO_INSTALL_BIN}/rsclang/x86_64)
--   else()
--      file(GLOB_RECURSE LIBCLANG_FILES "${LIBCLANG_DIR}/libclang.*")
--      install(PROGRAMS ${LIBCLANG_FILES}
--              DESTINATION  ${RSTUDIO_INSTALL_BIN}/rsclang)
--   endif()
--
--   # install libclang builtin-headers
--   install(DIRECTORY "${RSTUDIO_DEPENDENCIES_DIR}/common/libclang/builtin-headers"
--           DESTINATION "${RSTUDIO_INSTALL_SUPPORTING}/resources/libclang")
--
-    # install 64 bit binaries if we are on win64
-    if(WIN32)
-       if(NOT ("$ENV{PROGRAMW6432}" STREQUAL ""))

diff --git a/sci-mathematics/rstudio/files/rstudio-0.99.473-paths.patch b/sci-mathematics/rstudio/files/rstudio-0.99.473-paths.patch
deleted file mode 100644
index 6b8d8886e21..00000000000
--- a/sci-mathematics/rstudio/files/rstudio-0.99.473-paths.patch
+++ /dev/null
@@ -1,130 +0,0 @@
---- rstudio-0.99.473-orig/CMakeGlobals.txt	2015-08-12 09:58:43.000000000 +1000
-+++ rstudio-0.99.473/CMakeGlobals.txt	2015-08-26 22:12:43.614346285 +1000
-@@ -111,7 +111,7 @@
-    else()
-      set(RSTUDIO_INSTALL_BIN bin)
-    endif()
--   set(RSTUDIO_INSTALL_SUPPORTING .)
-+   set(RSTUDIO_INSTALL_SUPPORTING ${DISTRO_SHARE})
- endif()
- 
- # if the install prefix is /usr/local then tweak as appropriate
---- rstudio-0.99.473-orig/src/cpp/server/CMakeLists.txt	2015-08-12 09:58:43.000000000 +1000
-+++ rstudio-0.99.473/src/cpp/server/CMakeLists.txt	2015-08-26 22:15:30.988353389 +1000
-@@ -160,7 +160,7 @@
-    configure_file(${CMAKE_CURRENT_SOURCE_DIR}/${RSERVER_INITD_DEBIAN_SCRIPT}.in
-                   ${CMAKE_CURRENT_BINARY_DIR}/${RSERVER_INITD_DEBIAN_SCRIPT})
-    install(PROGRAMS ${CMAKE_CURRENT_BINARY_DIR}/${RSERVER_INITD_DEBIAN_SCRIPT}
--           DESTINATION ${RSERVER_INITD_DEBIAN_DIR})
-+           DESTINATION ${DISTRO_SHARE}/${RSERVER_INITD_DEBIAN_DIR})
- 
-    # install configured redhat init.d script
-    set(RSERVER_INITD_REDHAT_DIR "extras/init.d/redhat")
-@@ -168,7 +168,7 @@
-    configure_file(${CMAKE_CURRENT_SOURCE_DIR}/${RSERVER_INITD_REDHAT_SCRIPT}.in
-                   ${CMAKE_CURRENT_BINARY_DIR}/${RSERVER_INITD_REDHAT_SCRIPT})
-    install(PROGRAMS ${CMAKE_CURRENT_BINARY_DIR}/${RSERVER_INITD_REDHAT_SCRIPT}
--           DESTINATION ${RSERVER_INITD_REDHAT_DIR})
-+           DESTINATION ${DISTRO_SHARE}/${RSERVER_INITD_REDHAT_DIR})
- 
-    # install configured suse init.d script
-    set(RSERVER_INITD_SUSE_DIR "extras/init.d/suse")
-@@ -176,13 +176,13 @@
-    configure_file(${CMAKE_CURRENT_SOURCE_DIR}/${RSERVER_INITD_SUSE_SCRIPT}.in
-                   ${CMAKE_CURRENT_BINARY_DIR}/${RSERVER_INITD_SUSE_SCRIPT})
-    install(PROGRAMS ${CMAKE_CURRENT_BINARY_DIR}/${RSERVER_INITD_SUSE_SCRIPT}
--           DESTINATION ${RSERVER_INITD_SUSE_DIR})
-+           DESTINATION ${DISTRO_SHARE}/${RSERVER_INITD_SUSE_DIR})
- 
-    # install pam profile
-    set(RSERVER_PAM_DIR "extras/pam")
-    set(RSERVER_PAM_PROFILE "${RSERVER_PAM_DIR}/rstudio")
-    install(FILES ${CMAKE_CURRENT_SOURCE_DIR}/${RSERVER_PAM_PROFILE}
--           DESTINATION ${RSERVER_PAM_DIR})
-+           DESTINATION ${DISTRO_SHARE}/${RSERVER_PAM_DIR})
- 
-    # install configured apparmor profile
-    set(RSERVER_APPARMOR_DIR "extras/apparmor")
-@@ -190,9 +190,9 @@
-    configure_file(${CMAKE_CURRENT_SOURCE_DIR}/${RSERVER_APPARMOR_PROFILE}.in
-                   ${CMAKE_CURRENT_BINARY_DIR}/${RSERVER_APPARMOR_PROFILE})
-    install(FILES ${CMAKE_CURRENT_BINARY_DIR}/${RSERVER_APPARMOR_PROFILE}
--           DESTINATION ${RSERVER_APPARMOR_DIR})
-+           DESTINATION ${DISTRO_SHARE}/${RSERVER_APPARMOR_DIR})
-    install(PROGRAMS ${CMAKE_CURRENT_SOURCE_DIR}/${RSERVER_APPARMOR_DIR}/apparmor-profile-load
--           DESTINATION ${RSERVER_APPARMOR_DIR})
-+           DESTINATION ${DISTRO_SHARE}/${RSERVER_APPARMOR_DIR})
- 
-    # install configured upstart profile
-    set(RSERVER_UPSTART_DIR "extras/upstart")
-@@ -200,12 +200,12 @@
-    configure_file(${CMAKE_CURRENT_SOURCE_DIR}/${RSERVER_UPSTART_PROFILE}.in
-                   ${CMAKE_CURRENT_BINARY_DIR}/${RSERVER_UPSTART_PROFILE})
-    install(FILES ${CMAKE_CURRENT_BINARY_DIR}/${RSERVER_UPSTART_PROFILE}
--           DESTINATION ${RSERVER_UPSTART_DIR})
-+           DESTINATION ${DISTRO_SHARE}/${RSERVER_UPSTART_DIR})
-    set(RSERVER_UPSTART_PROFILE_REDHAT "${RSERVER_UPSTART_DIR}/rstudio-server.redhat.conf")
-    configure_file(${CMAKE_CURRENT_SOURCE_DIR}/${RSERVER_UPSTART_PROFILE_REDHAT}.in
-                   ${CMAKE_CURRENT_BINARY_DIR}/${RSERVER_UPSTART_PROFILE_REDHAT})
-    install(FILES ${CMAKE_CURRENT_BINARY_DIR}/${RSERVER_UPSTART_PROFILE_REDHAT}
--           DESTINATION ${RSERVER_UPSTART_DIR})
-+           DESTINATION ${DISTRO_SHARE}/${RSERVER_UPSTART_DIR})
-            
-     # install configured systemd profile
-    set(RSERVER_SYSTEMD_DIR "extras/systemd")
---- rstudio-0.99.473-orig/src/cpp/server/ServerOptions.cpp	2015-08-12 09:58:43.000000000 +1000
-+++ rstudio-0.99.473/src/cpp/server/ServerOptions.cpp	2015-08-26 22:12:43.615346286 +1000
-@@ -314,8 +314,8 @@
- 
-    // convert relative paths by completing from the system installation
-    // path (this allows us to be relocatable)
--   resolvePath(resourcePath, &wwwLocalPath_);
--   resolvePath(resourcePath, &wwwSymbolMapsPath_);
-+   resolvePath(resourcePath.childPath(DISTRO_SHARE), &wwwLocalPath_);
-+   resolvePath(resourcePath.childPath(DISTRO_SHARE), &wwwSymbolMapsPath_);
-    resolvePath(binaryPath, &authPamHelperPath_);
-    resolvePath(binaryPath, &rsessionPath_);
-    resolvePath(binaryPath, &rldpathPath_);
---- rstudio-0.99.473-orig/src/cpp/session/SessionOptions.cpp	2015-08-12 09:58:43.000000000 +1000
-+++ rstudio-0.99.473/src/cpp/session/SessionOptions.cpp	2015-08-26 22:17:40.594358890 +1000
-@@ -43,7 +43,7 @@
- namespace session {  
- 
- namespace {
--const char* const kDefaultPandocPath = "bin/pandoc";
-+const char* const kDefaultPandocPath = "bin";
- const char* const kDefaultPostbackPath = "bin/postback/rpostback";
- const char* const kDefaultRsclangPath = "bin/rsclang";
- } // anonymous namespace
-@@ -431,14 +431,14 @@
-    }
-    
-    // convert relative paths by completing from the app resource path
--   resolvePath(resourcePath, &rResourcesPath_);
--   resolvePath(resourcePath, &agreementFilePath_);
--   resolvePath(resourcePath, &wwwLocalPath_);
--   resolvePath(resourcePath, &wwwSymbolMapsPath_);
--   resolvePath(resourcePath, &coreRSourcePath_);
--   resolvePath(resourcePath, &modulesRSourcePath_);
--   resolvePath(resourcePath, &sessionLibraryPath_);
--   resolvePath(resourcePath, &sessionPackageArchivesPath_);
-+   resolvePath(resourcePath.childPath(DISTRO_SHARE), &rResourcesPath_);
-+   resolvePath(resourcePath.childPath(DISTRO_SHARE), &agreementFilePath_);
-+   resolvePath(resourcePath.childPath(DISTRO_SHARE), &wwwLocalPath_);
-+   resolvePath(resourcePath.childPath(DISTRO_SHARE), &wwwSymbolMapsPath_);
-+   resolvePath(resourcePath.childPath(DISTRO_SHARE), &coreRSourcePath_);
-+   resolvePath(resourcePath.childPath(DISTRO_SHARE), &modulesRSourcePath_);
-+   resolvePath(resourcePath.childPath(DISTRO_SHARE), &sessionLibraryPath_);
-+   resolvePath(resourcePath.childPath(DISTRO_SHARE), &sessionPackageArchivesPath_);
-    resolvePostbackPath(resourcePath, &rpostbackPath_);
- #ifdef _WIN32
-    resolvePath(resourcePath, &consoleIoPath_);
-@@ -447,7 +447,7 @@
-    resolvePath(resourcePath, &msysSshPath_);
-    resolvePath(resourcePath, &sumatraPath_);
- #endif
--   resolvePath(resourcePath, &hunspellDictionariesPath_);
-+   resolvePath(resourcePath.childPath(DISTRO_SHARE), &hunspellDictionariesPath_);
-    resolvePath(resourcePath, &mathjaxPath_);
-    resolvePath(resourcePath, &libclangHeadersPath_);
-    resolvePandocPath(resourcePath, &pandocPath_);

diff --git a/sci-mathematics/rstudio/files/rstudio-0.99.486-systemd.patch b/sci-mathematics/rstudio/files/rstudio-0.99.486-systemd.patch
deleted file mode 100644
index 4c7eda39cc2..00000000000
--- a/sci-mathematics/rstudio/files/rstudio-0.99.486-systemd.patch
+++ /dev/null
@@ -1,22 +0,0 @@
-diff -Naur /tmp/rstudio.org/work/rstudio-0.99.486/src/cpp/server/CMakeLists.txt ./work/rstudio-0.99.486/src/cpp/server/CMakeLists.txt
---- /tmp/rstudio.org/work/rstudio-0.99.486/src/cpp/server/CMakeLists.txt	2015-12-10 19:29:24.408267862 +0100
-+++ ./work/rstudio-0.99.486/src/cpp/server/CMakeLists.txt	2015-12-10 19:35:24.660194216 +0100
-@@ -208,17 +208,12 @@
-            DESTINATION ${DISTRO_SHARE}/${RSERVER_UPSTART_DIR})
-            
-     # install configured systemd profile
--   set(RSERVER_SYSTEMD_DIR "extras/systemd")
-+   set(RSERVER_SYSTEMD_DIR "lib/systemd/system")
-    set(RSERVER_SYSTEMD_PROFILE "${RSERVER_SYSTEMD_DIR}/rstudio-server.service")
-    configure_file(${CMAKE_CURRENT_SOURCE_DIR}/${RSERVER_SYSTEMD_PROFILE}.in
-                   ${CMAKE_CURRENT_BINARY_DIR}/${RSERVER_SYSTEMD_PROFILE})
-    install(FILES ${CMAKE_CURRENT_BINARY_DIR}/${RSERVER_SYSTEMD_PROFILE}
-            DESTINATION ${RSERVER_SYSTEMD_DIR})
--   set(RSERVER_SYSTEMD_PROFILE_REDHAT "${RSERVER_SYSTEMD_DIR}/rstudio-server.redhat.service")
--   configure_file(${CMAKE_CURRENT_SOURCE_DIR}/${RSERVER_SYSTEMD_PROFILE_REDHAT}.in
--                  ${CMAKE_CURRENT_BINARY_DIR}/${RSERVER_SYSTEMD_PROFILE_REDHAT})
--   install(FILES ${CMAKE_CURRENT_BINARY_DIR}/${RSERVER_SYSTEMD_PROFILE_REDHAT}
--           DESTINATION ${RSERVER_SYSTEMD_DIR})
- 
- endif()
- 

diff --git a/sci-mathematics/rstudio/files/rstudio-0.99.879-clang-pandoc.patch b/sci-mathematics/rstudio/files/rstudio-0.99.879-clang-pandoc.patch
deleted file mode 100644
index c3af2b7a6f5..00000000000
--- a/sci-mathematics/rstudio/files/rstudio-0.99.879-clang-pandoc.patch
+++ /dev/null
@@ -1,77 +0,0 @@
---- rstudio-0.99.879-orig/src/cpp/session/CMakeLists.txt	2016-02-12 09:24:39.000000000 +1100
-+++ rstudio-0.99.879/src/cpp/session/CMakeLists.txt	2016-02-19 23:04:57.266186448 +1100
-@@ -25,30 +25,11 @@
- if(NOT EXISTS "${RSTUDIO_DEPENDENCIES_DIR}/common/mathjax-23")
-   message(FATAL_ERROR "Mathjax 2.3 not found (re-run install-dependencies script to install)")
- endif()
--if(NOT EXISTS "${RSTUDIO_DEPENDENCIES_DIR}/common/pandoc")
--  message(FATAL_ERROR "pandoc not found (re-run install-dependencies script to install)")
--endif()
- if(NOT EXISTS "${RSTUDIO_DEPENDENCIES_DIR}/common/rsconnect")
-   message(FATAL_ERROR "rsconnect package not found (re-run install-dependencies script to install)")
- endif()
- 
- 
--# verify libclang is installed
--if(WIN32)
--   set(LIBCLANG_VERSION "3.4")
--else()
--   set(LIBCLANG_VERSION "3.5")
--endif()
--set(LIBCLANG_DIR "${RSTUDIO_DEPENDENCIES_DIR}/common/libclang/${LIBCLANG_VERSION}")
--if(NOT EXISTS "${LIBCLANG_DIR}")
--  message(FATAL_ERROR "libclang ${LIBCLANG_VERSION} not found  (re-run install-dependencies script to install)")
--endif()
--set(LIBCLANG_HEADERS_DIR "${RSTUDIO_DEPENDENCIES_DIR}/common/libclang/builtin-headers")
--if(NOT EXISTS "${LIBCLANG_HEADERS_DIR}")
--  message(FATAL_ERROR "libclang builtin-headers not found  (re-run install-dependencies script to install)")
--endif()
--
--
- # include files
- file(GLOB_RECURSE SESSION_HEADER_FILES "*.h*")
- 
-@@ -399,18 +380,6 @@
-    install(DIRECTORY "${RSTUDIO_DEPENDENCIES_DIR}/common/mathjax-23"
-            DESTINATION "${RSTUDIO_INSTALL_SUPPORTING}/resources")
- 
--   # install pandoc
--   if(RSTUDIO_PACKAGE_BUILD_SLES)
--      # when producing a SUSE Linux Enterpise build, we want to install the 
--      # static Pandoc binaries (see dependencies/common/install-pandoc)
--      set(PANDOC_EXTENSION_DIR "/static")
--   endif()
--   set(PANDOC_BIN "${RSTUDIO_DEPENDENCIES_DIR}/common/pandoc/1.15.2${PANDOC_EXTENSION_DIR}")
--   file(GLOB PANDOC_FILES "${PANDOC_BIN}/pandoc*")
--   install(FILES ${PANDOC_FILES}
--           PERMISSIONS OWNER_READ OWNER_WRITE OWNER_EXECUTE GROUP_READ GROUP_EXECUTE WORLD_READ WORLD_EXECUTE
--           DESTINATION  ${RSTUDIO_INSTALL_BIN}/pandoc)
--
-    # install rsconnect package
-    file(GLOB RSCONNECT_PACKAGE "${RSTUDIO_DEPENDENCIES_DIR}/common/rsconnect*.tar.gz")
-    install(FILES ${RSCONNECT_PACKAGE}
-@@ -428,24 +397,6 @@
-    install(DIRECTORY "resources/help_resources"
-            DESTINATION ${RSTUDIO_INSTALL_SUPPORTING}/resources)
- 
--   # install libclang
--   if(WIN32)
--      file(GLOB LIBCLANG_32_FILES "${LIBCLANG_DIR}/x86/libclang.*")
--      install(PROGRAMS ${LIBCLANG_32_FILES}
--              DESTINATION  ${RSTUDIO_INSTALL_BIN}/rsclang/x86)
--      file(GLOB LIBCLANG_64_FILES "${LIBCLANG_DIR}/x86_64/libclang.*")
--      install(PROGRAMS ${LIBCLANG_64_FILES}
--              DESTINATION  ${RSTUDIO_INSTALL_BIN}/rsclang/x86_64)
--   else()
--      file(GLOB_RECURSE LIBCLANG_FILES "${LIBCLANG_DIR}/libclang.*")
--      install(PROGRAMS ${LIBCLANG_FILES}
--              DESTINATION  ${RSTUDIO_INSTALL_BIN}/rsclang)
--   endif()
--
--   # install libclang builtin-headers
--   install(DIRECTORY "${RSTUDIO_DEPENDENCIES_DIR}/common/libclang/builtin-headers"
--           DESTINATION "${RSTUDIO_INSTALL_SUPPORTING}/resources/libclang")
--
-    # install 64 bit binaries if we are on win64
-    if(WIN32)
-       if(NOT ("$ENV{PROGRAMW6432}" STREQUAL ""))

diff --git a/sci-mathematics/rstudio/files/rstudio-0.99.879-paths.patch b/sci-mathematics/rstudio/files/rstudio-0.99.879-paths.patch
deleted file mode 100644
index a8b48f24968..00000000000
--- a/sci-mathematics/rstudio/files/rstudio-0.99.879-paths.patch
+++ /dev/null
@@ -1,130 +0,0 @@
---- rstudio-0.99.879-orig/CMakeGlobals.txt	2016-02-12 09:24:39.000000000 +1100
-+++ rstudio-0.99.879/CMakeGlobals.txt	2016-02-19 22:58:41.396818474 +1100
-@@ -120,7 +120,7 @@
-    else()
-      set(RSTUDIO_INSTALL_BIN bin)
-    endif()
--   set(RSTUDIO_INSTALL_SUPPORTING .)
-+   set(RSTUDIO_INSTALL_SUPPORTING ${DISTRO_SHARE})
- endif()
- 
- # if the install prefix is /usr/local then tweak as appropriate
---- rstudio-0.99.879-orig/src/cpp/server/CMakeLists.txt	2016-02-12 09:24:39.000000000 +1100
-+++ rstudio-0.99.879/src/cpp/server/CMakeLists.txt	2016-02-19 22:58:41.397818478 +1100
-@@ -155,7 +155,7 @@
-    configure_file(${CMAKE_CURRENT_SOURCE_DIR}/${RSERVER_INITD_DEBIAN_SCRIPT}.in
-                   ${CMAKE_CURRENT_BINARY_DIR}/${RSERVER_INITD_DEBIAN_SCRIPT})
-    install(PROGRAMS ${CMAKE_CURRENT_BINARY_DIR}/${RSERVER_INITD_DEBIAN_SCRIPT}
--           DESTINATION ${RSERVER_INITD_DEBIAN_DIR})
-+           DESTINATION ${DISTRO_SHARE}/${RSERVER_INITD_DEBIAN_DIR})
- 
-    # install configured redhat init.d script
-    set(RSERVER_INITD_REDHAT_DIR "extras/init.d/redhat")
-@@ -163,7 +163,7 @@
-    configure_file(${CMAKE_CURRENT_SOURCE_DIR}/${RSERVER_INITD_REDHAT_SCRIPT}.in
-                   ${CMAKE_CURRENT_BINARY_DIR}/${RSERVER_INITD_REDHAT_SCRIPT})
-    install(PROGRAMS ${CMAKE_CURRENT_BINARY_DIR}/${RSERVER_INITD_REDHAT_SCRIPT}
--           DESTINATION ${RSERVER_INITD_REDHAT_DIR})
-+           DESTINATION ${DISTRO_SHARE}/${RSERVER_INITD_REDHAT_DIR})
- 
-    # install configured suse init.d script
-    set(RSERVER_INITD_SUSE_DIR "extras/init.d/suse")
-@@ -171,13 +171,13 @@
-    configure_file(${CMAKE_CURRENT_SOURCE_DIR}/${RSERVER_INITD_SUSE_SCRIPT}.in
-                   ${CMAKE_CURRENT_BINARY_DIR}/${RSERVER_INITD_SUSE_SCRIPT})
-    install(PROGRAMS ${CMAKE_CURRENT_BINARY_DIR}/${RSERVER_INITD_SUSE_SCRIPT}
--           DESTINATION ${RSERVER_INITD_SUSE_DIR})
-+           DESTINATION ${DISTRO_SHARE}/${RSERVER_INITD_SUSE_DIR})
- 
-    # install pam profile
-    set(RSERVER_PAM_DIR "extras/pam")
-    set(RSERVER_PAM_PROFILE "${RSERVER_PAM_DIR}/rstudio")
-    install(FILES ${CMAKE_CURRENT_SOURCE_DIR}/${RSERVER_PAM_PROFILE}
--           DESTINATION ${RSERVER_PAM_DIR})
-+           DESTINATION ${DISTRO_SHARE}/${RSERVER_PAM_DIR})
- 
-    # install configured apparmor profile
-    set(RSERVER_APPARMOR_DIR "extras/apparmor")
-@@ -185,9 +185,9 @@
-    configure_file(${CMAKE_CURRENT_SOURCE_DIR}/${RSERVER_APPARMOR_PROFILE}.in
-                   ${CMAKE_CURRENT_BINARY_DIR}/${RSERVER_APPARMOR_PROFILE})
-    install(FILES ${CMAKE_CURRENT_BINARY_DIR}/${RSERVER_APPARMOR_PROFILE}
--           DESTINATION ${RSERVER_APPARMOR_DIR})
-+           DESTINATION ${DISTRO_SHARE}/${RSERVER_APPARMOR_DIR})
-    install(PROGRAMS ${CMAKE_CURRENT_SOURCE_DIR}/${RSERVER_APPARMOR_DIR}/apparmor-profile-load
--           DESTINATION ${RSERVER_APPARMOR_DIR})
-+           DESTINATION ${DISTRO_SHARE}/${RSERVER_APPARMOR_DIR})
- 
-    # install configured upstart profile
-    set(RSERVER_UPSTART_DIR "extras/upstart")
-@@ -195,12 +195,12 @@
-    configure_file(${CMAKE_CURRENT_SOURCE_DIR}/${RSERVER_UPSTART_PROFILE}.in
-                   ${CMAKE_CURRENT_BINARY_DIR}/${RSERVER_UPSTART_PROFILE})
-    install(FILES ${CMAKE_CURRENT_BINARY_DIR}/${RSERVER_UPSTART_PROFILE}
--           DESTINATION ${RSERVER_UPSTART_DIR})
-+           DESTINATION ${DISTRO_SHARE}/${RSERVER_UPSTART_DIR})
-    set(RSERVER_UPSTART_PROFILE_REDHAT "${RSERVER_UPSTART_DIR}/rstudio-server.redhat.conf")
-    configure_file(${CMAKE_CURRENT_SOURCE_DIR}/${RSERVER_UPSTART_PROFILE_REDHAT}.in
-                   ${CMAKE_CURRENT_BINARY_DIR}/${RSERVER_UPSTART_PROFILE_REDHAT})
-    install(FILES ${CMAKE_CURRENT_BINARY_DIR}/${RSERVER_UPSTART_PROFILE_REDHAT}
--           DESTINATION ${RSERVER_UPSTART_DIR})
-+           DESTINATION ${DISTRO_SHARE}/${RSERVER_UPSTART_DIR})
-            
-     # install configured systemd profile
-    set(RSERVER_SYSTEMD_DIR "extras/systemd")
---- rstudio-0.99.879-orig/src/cpp/server/ServerOptions.cpp	2016-02-12 09:24:39.000000000 +1100
-+++ rstudio-0.99.879/src/cpp/server/ServerOptions.cpp	2016-02-19 22:58:41.397818478 +1100
-@@ -382,8 +382,8 @@
- 
-    // convert relative paths by completing from the system installation
-    // path (this allows us to be relocatable)
--   resolvePath(resourcePath, &wwwLocalPath_);
--   resolvePath(resourcePath, &wwwSymbolMapsPath_);
-+   resolvePath(resourcePath.childPath(DISTRO_SHARE), &wwwLocalPath_);
-+   resolvePath(resourcePath.childPath(DISTRO_SHARE), &wwwSymbolMapsPath_);
-    resolvePath(binaryPath, &authPamHelperPath_);
-    resolvePath(binaryPath, &rsessionPath_);
-    resolvePath(binaryPath, &rldpathPath_);
---- rstudio-0.99.879-orig/src/cpp/session/SessionOptions.cpp	2016-02-12 09:24:39.000000000 +1100
-+++ rstudio-0.99.879/src/cpp/session/SessionOptions.cpp	2016-02-20 18:13:34.807771539 +1100
-@@ -49,7 +49,7 @@
- namespace session {  
- 
- namespace {
--const char* const kDefaultPandocPath = "bin/pandoc";
-+const char* const kDefaultPandocPath = "bin";
- const char* const kDefaultPostbackPath = "bin/postback/rpostback";
- const char* const kDefaultRsclangPath = "bin/rsclang";
- } // anonymous namespace
-@@ -451,14 +451,14 @@
-    }
-    
-    // convert relative paths by completing from the app resource path
--   resolvePath(resourcePath_, &rResourcesPath_);
--   resolvePath(resourcePath_, &agreementFilePath_);
--   resolvePath(resourcePath_, &wwwLocalPath_);
--   resolvePath(resourcePath_, &wwwSymbolMapsPath_);
--   resolvePath(resourcePath_, &coreRSourcePath_);
--   resolvePath(resourcePath_, &modulesRSourcePath_);
--   resolvePath(resourcePath_, &sessionLibraryPath_);
--   resolvePath(resourcePath_, &sessionPackageArchivesPath_);
-+   resolvePath(resourcePath_.childPath(DISTRO_SHARE), &rResourcesPath_);
-+   resolvePath(resourcePath_.childPath(DISTRO_SHARE), &agreementFilePath_);
-+   resolvePath(resourcePath_.childPath(DISTRO_SHARE), &wwwLocalPath_);
-+   resolvePath(resourcePath_.childPath(DISTRO_SHARE), &wwwSymbolMapsPath_);
-+   resolvePath(resourcePath_.childPath(DISTRO_SHARE), &coreRSourcePath_);
-+   resolvePath(resourcePath_.childPath(DISTRO_SHARE), &modulesRSourcePath_);
-+   resolvePath(resourcePath_.childPath(DISTRO_SHARE), &sessionLibraryPath_);
-+   resolvePath(resourcePath_.childPath(DISTRO_SHARE), &sessionPackageArchivesPath_);
-    resolvePostbackPath(resourcePath_, &rpostbackPath_);
- #ifdef _WIN32
-    resolvePath(resourcePath_, &consoleIoPath_);
-@@ -467,7 +467,7 @@
-    resolvePath(resourcePath_, &msysSshPath_);
-    resolvePath(resourcePath_, &sumatraPath_);
- #endif
--   resolvePath(resourcePath_, &hunspellDictionariesPath_);
-+   resolvePath(resourcePath_.childPath(DISTRO_SHARE), &hunspellDictionariesPath_);
-    resolvePath(resourcePath_, &mathjaxPath_);
-    resolvePath(resourcePath_, &libclangHeadersPath_);
-    resolvePandocPath(resourcePath_, &pandocPath_);

diff --git a/sci-mathematics/rstudio/files/rstudio-1.0.44-clang-pandoc.patch b/sci-mathematics/rstudio/files/rstudio-1.0.44-clang-pandoc.patch
deleted file mode 100644
index ed0fc8ebce4..00000000000
--- a/sci-mathematics/rstudio/files/rstudio-1.0.44-clang-pandoc.patch
+++ /dev/null
@@ -1,71 +0,0 @@
---- rstudio-1.0.44-orig/src/cpp/session/CMakeLists.txt	2016-10-19 08:32:41.000000000 +1100
-+++ rstudio-1.0.44/src/cpp/session/CMakeLists.txt	2016-12-01 23:44:30.130725331 +1100
-@@ -25,24 +25,6 @@
- if(NOT EXISTS "${RSTUDIO_DEPENDENCIES_DIR}/common/mathjax-26")
-   message(FATAL_ERROR "Mathjax 2.6 not found (re-run install-dependencies script to install)")
- endif()
--if(NOT EXISTS "${RSTUDIO_DEPENDENCIES_DIR}/common/pandoc")
--  message(FATAL_ERROR "pandoc not found (re-run install-dependencies script to install)")
--endif()
--
--# verify libclang is installed
--if(WIN32)
--   set(LIBCLANG_VERSION "3.4")
--else()
--   set(LIBCLANG_VERSION "3.5")
--endif()
--set(LIBCLANG_DIR "${RSTUDIO_DEPENDENCIES_DIR}/common/libclang/${LIBCLANG_VERSION}")
--if(NOT EXISTS "${LIBCLANG_DIR}")
--  message(FATAL_ERROR "libclang ${LIBCLANG_VERSION} not found  (re-run install-dependencies script to install)")
--endif()
--set(LIBCLANG_HEADERS_DIR "${RSTUDIO_DEPENDENCIES_DIR}/common/libclang/builtin-headers")
--if(NOT EXISTS "${LIBCLANG_HEADERS_DIR}")
--  message(FATAL_ERROR "libclang builtin-headers not found  (re-run install-dependencies script to install)")
--endif()
- 
- 
- # include files
-@@ -420,18 +402,6 @@
-    install(DIRECTORY "${RSTUDIO_DEPENDENCIES_DIR}/common/mathjax-26"
-            DESTINATION "${RSTUDIO_INSTALL_SUPPORTING}/resources")
- 
--   # install pandoc
--   if(RSTUDIO_PACKAGE_BUILD_SLES)
--      # when producing a SUSE Linux Enterpise build, we want to install the 
--      # static Pandoc binaries (see dependencies/common/install-pandoc)
--      set(PANDOC_EXTENSION_DIR "/static")
--   endif()
--   set(PANDOC_BIN "${RSTUDIO_DEPENDENCIES_DIR}/common/pandoc/1.17.2${PANDOC_EXTENSION_DIR}")
--   file(GLOB PANDOC_FILES "${PANDOC_BIN}/pandoc*")
--   install(FILES ${PANDOC_FILES}
--           PERMISSIONS OWNER_READ OWNER_WRITE OWNER_EXECUTE GROUP_READ GROUP_EXECUTE WORLD_READ WORLD_EXECUTE
--           DESTINATION  ${RSTUDIO_INSTALL_BIN}/pandoc)
--
-    # install PDF.js
-    install(DIRECTORY "resources/pdfjs"
-            DESTINATION ${RSTUDIO_INSTALL_SUPPORTING}/resources)
-@@ -452,24 +422,6 @@
-    install(DIRECTORY "resources/pagedtable"
-            DESTINATION ${RSTUDIO_INSTALL_SUPPORTING}/resources)
- 
--   # install libclang
--   if(WIN32)
--      file(GLOB LIBCLANG_32_FILES "${LIBCLANG_DIR}/x86/libclang.*")
--      install(PROGRAMS ${LIBCLANG_32_FILES}
--              DESTINATION  ${RSTUDIO_INSTALL_BIN}/rsclang/x86)
--      file(GLOB LIBCLANG_64_FILES "${LIBCLANG_DIR}/x86_64/libclang.*")
--      install(PROGRAMS ${LIBCLANG_64_FILES}
--              DESTINATION  ${RSTUDIO_INSTALL_BIN}/rsclang/x86_64)
--   else()
--      file(GLOB_RECURSE LIBCLANG_FILES "${LIBCLANG_DIR}/libclang.*")
--      install(PROGRAMS ${LIBCLANG_FILES}
--              DESTINATION  ${RSTUDIO_INSTALL_BIN}/rsclang)
--   endif()
--
--   # install libclang builtin-headers
--   install(DIRECTORY "${RSTUDIO_DEPENDENCIES_DIR}/common/libclang/builtin-headers"
--           DESTINATION "${RSTUDIO_INSTALL_SUPPORTING}/resources/libclang")
--
-    # install 64 bit binaries if we are on win64
-    if(WIN32)
-       if(NOT ("$ENV{PROGRAMW6432}" STREQUAL ""))

diff --git a/sci-mathematics/rstudio/rstudio-0.99.473-r1.ebuild b/sci-mathematics/rstudio/rstudio-0.99.473-r1.ebuild
deleted file mode 100644
index cd4815f5d33..00000000000
--- a/sci-mathematics/rstudio/rstudio-0.99.473-r1.ebuild
+++ /dev/null
@@ -1,240 +0,0 @@
-# Copyright 1999-2017 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-inherit eutils user cmake-utils gnome2-utils pam versionator fdo-mime java-pkg-2 pax-utils qmake-utils
-
-# TODO
-# * package gin and gwt
-# * use dict from tree, linguas
-# * do src_test (use junit from tree?)
-
-# update from scripts in dependencies/common
-# egrep '(GWT_SDK_VER=|GIN_VER=|SELENIUM_VER=|CHROMEDRIVER_VER=)' dependencies/common/install-gwt
-GWT_VER=2.7.0
-GIN_VER=1.5
-SELENIUM_VER=2.37.0
-CHROMEDRIVER_VER=2.7
-# grep 'PANDOC_VERSION=' dependencies/common/update-pandoc
-PANDOC_VER=1.13.1
-# ls dependencies/common/*.tar.gz
-PACKRAT_VER=0.98.1000
-RMARKDOWN_VER=0.98.1000
-SHINYAPPS_VER=0.98.1000
-RSCONNECT_VER=0.4.1.4_fcac892a69817febd7b655b189bf57193260cda0
-
-DESCRIPTION="IDE for the R language"
-HOMEPAGE="
-	http://www.rstudio.org
-	https://github.com/rstudio/rstudio/"
-SRC_URI="
-	https://github.com/rstudio/rstudio/archive/v${PV}.tar.gz -> ${P}.tar.gz
-	https://s3.amazonaws.com/rstudio-buildtools/gin-${GIN_VER}.zip
-	https://s3.amazonaws.com/rstudio-buildtools/gwt-${GWT_VER}.zip
-	https://s3.amazonaws.com/rstudio-buildtools/selenium-java-${SELENIUM_VER}.zip
-	https://s3.amazonaws.com/rstudio-buildtools/selenium-server-standalone-${SELENIUM_VER}.jar
-	https://s3.amazonaws.com/rstudio-buildtools/chromedriver-linux
-	https://s3.amazonaws.com/rstudio-dictionaries/core-dictionaries.zip
-	https://dev.gentoo.org/~gienah/distfiles/packrat-${PACKRAT_VER}.tar.gz
-	https://dev.gentoo.org/~gienah/distfiles/rmarkdown-${RMARKDOWN_VER}.tar.gz
-	https://dev.gentoo.org/~gienah/distfiles/shinyapps-${SHINYAPPS_VER}.tar.gz
-	https://dev.gentoo.org/~gienah/distfiles/rsconnect_${RSCONNECT_VER}.tar.gz
-"
-
-LICENSE="AGPL-3"
-SLOT="0"
-KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
-IUSE="dedicated server"
-
-QT_VER=5.4
-QT_SLOT=5
-RDEPEND="
-	app-text/pandoc
-	dev-haskell/pandoc-citeproc
-	>=dev-lang/R-2.11.1
-	>=dev-libs/boost-1.50:=
-	>=dev-libs/mathjax-2.3
-	dev-libs/openssl:0
-	sys-apps/util-linux
-	>=sys-devel/clang-3.5.0:*
-	sys-libs/zlib
-	>=virtual/jre-1.7:=
-	x11-libs/pango
-	!dedicated? (
-		>=dev-qt/qtcore-${QT_VER}:${QT_SLOT}
-		>=dev-qt/qtdeclarative-${QT_VER}:${QT_SLOT}
-		>=dev-qt/qtdbus-${QT_VER}:${QT_SLOT}
-		>=dev-qt/qtgui-${QT_VER}:${QT_SLOT}
-		>=dev-qt/qtnetwork-${QT_VER}:${QT_SLOT}
-		>=dev-qt/qtopengl-${QT_VER}:${QT_SLOT}
-		>=dev-qt/qtpositioning-${QT_VER}:${QT_SLOT}
-		>=dev-qt/qtprintsupport-${QT_VER}:${QT_SLOT}
-		>=dev-qt/qtsingleapplication-2.6.1_p20150629[X,qt5]
-		>=dev-qt/qtsensors-${QT_VER}:${QT_SLOT}
-		>=dev-qt/qtsql-${QT_VER}:${QT_SLOT}
-		>=dev-qt/qtsvg-${QT_VER}:${QT_SLOT}
-		>=dev-qt/qtwebkit-${QT_VER}:${QT_SLOT}
-		>=dev-qt/qtwidgets-${QT_VER}:${QT_SLOT}
-		>=dev-qt/qtxml-${QT_VER}:${QT_SLOT}
-		>=dev-qt/qtxmlpatterns-${QT_VER}:${QT_SLOT}
-		server? ( virtual/pam )
-	)
-	dedicated? ( virtual/pam )"
-DEPEND="${RDEPEND}
-	app-arch/unzip
-	dev-java/ant-core
-	>=virtual/jdk-1.7:=
-	virtual/pkgconfig"
-#	test? ( dev-java/junit:4 )
-
-src_unpack() {
-	unpack ${P}.tar.gz gwt-${GWT_VER}.zip
-	cd "${S}" || die
-	mkdir -p src/gwt/lib/{gin,gwt} \
-		dependencies/common/dictionaries \
-		src/gwt/lib/selenium/${SELENIUM_VER} \
-		src/gwt/lib/selenium/chromedriver/${CHROMEDRIVER_VER} || die
-	mv ../gwt-${GWT_VER} src/gwt/lib/gwt/${GWT_VER} || die
-	unzip -qd src/gwt/lib/gin/${GIN_VER} \
-		"${DISTDIR}"/gin-${GIN_VER}.zip || die
-	unzip -qd dependencies/common/dictionaries \
-		"${DISTDIR}"/core-dictionaries.zip || die
-	unzip -qd src/gwt/lib/selenium/${SELENIUM_VER} \
-		"${DISTDIR}"/selenium-java-${SELENIUM_VER}.zip || die
-	cp "${DISTDIR}"/selenium-server-standalone-${SELENIUM_VER}.jar \
-		src/gwt/lib/selenium/${SELENIUM_VER}/ || die
-	cp "${DISTDIR}"/chromedriver-linux \
-		src/gwt/lib/selenium/chromedriver/${CHROMEDRIVER_VER}/ || die
-	cd dependencies/common || die
-	unpack packrat-${PACKRAT_VER}.tar.gz
-	unpack rmarkdown-${RMARKDOWN_VER}.tar.gz
-	unpack shinyapps-${SHINYAPPS_VER}.tar.gz
-	unpack rsconnect_${RSCONNECT_VER}.tar.gz
-	cp "${DISTDIR}"/rmarkdown-${RMARKDOWN_VER}.tar.gz \
-		. || die
-	cp "${DISTDIR}"/packrat-${PACKRAT_VER}.tar.gz \
-		. || die
-	cp "${DISTDIR}"/shinyapps-${SHINYAPPS_VER}.tar.gz \
-		. || die
-	cp "${DISTDIR}"/rsconnect_${RSCONNECT_VER}.tar.gz \
-		. || die
-}
-
-src_prepare() {
-	java-pkg-2_src_prepare
-
-	egit_clean
-
-	epatch \
-		"${FILESDIR}"/${PN}-0.98.490-prefs.patch \
-		"${FILESDIR}"/${PN}-0.99.473-paths.patch \
-		"${FILESDIR}"/${PN}-0.99.473-clang-pandoc.patch \
-		"${FILESDIR}"/${PN}-0.98.490-linker_flags.patch \
-		"${FILESDIR}"/${PN}-0.98.1091-boost-1.57.patch \
-		"${FILESDIR}"/${PN}-0.99.473-qtsingleapplication.patch
-
-	# Adding -DDISTRO_SHARE=... to append-flags breaks cmake so using
-	# this sed hack for now. ~RMH
-	sed -i \
-		-e "s|DISTRO_SHARE|\"share/${PN}\"|g" \
-		src/cpp/server/ServerOptions.cpp \
-		src/cpp/session/SessionOptions.cpp || die
-
-	# use mathjax from system
-	ln -sf "${EPREFIX}"/usr/share/mathjax dependencies/common/mathjax-23 || die
-
-	# make sure icons and mime stuff are with prefix
-	sed -i \
-		-e "s:/usr:${EPREFIX}/usr:g" \
-		CMakeGlobals.txt src/cpp/desktop/CMakeLists.txt || die
-
-	# On Gentoo the rstudio-server configuration file is /etc/conf.d/rstudio-server.conf
-	sed -e "s@/etc/rstudio/rserver.conf@${EROOT}etc/conf.d/rstudio-server.conf@" \
-		-i src/cpp/server/ServerOptions.cpp \
-		|| die
-
-	# Set the rsession.conf file location for Gentoo prefix
-	sed -e "s@/etc/rstudio/rsession.conf@${EROOT}etc/rstudio/rsession.conf@" \
-		-i src/cpp/session/SessionOptions.cpp \
-		|| die
-
-	# dev-qt/qtsingleapplication-2.6.1_p20150629 does not provide a cmake module.
-	# It provides a library that has its version number appended to the end,
-	# which is difficult to handle in cmake, as find_library does not support
-	# searching for wildcard library names. So I find the library name from the
-	# qmake spec, and then sed this into the patched src/cpp/desktop/CMakeLists.txt.
-	rm -rf "${S}"/src/cpp/desktop/3rdparty || die
-	local s=$(grep '\-lQt$${QT_MAJOR_VERSION}Solutions_SingleApplication' \
-				   $(qt5_get_mkspecsdir)/features/qtsingleapplication.prf \
-					 | sed -e 's@\$\${QT_MAJOR_VERSION}@5@' \
-						   -e 's@LIBS \*= -l@@')
-	sed -e "s@Qt5Solutions_SingleApplication-2.6@${s}@g" \
-		-i "${S}"/src/cpp/desktop/CMakeLists.txt \
-		|| die
-
-	# Avoid some of the oracle-jdk-bin-1.8.0.60 sandbox violations F: mkdir S: deny
-	# P: /root/.oracle_jre_usage.
-	sed -e 's@\(\s*\)\(</classpath>\)@\1\2\n\1\<jvmarg value="-Duser.home=${env.T}"/>@g' \
-		-i "${S}"/src/gwt/build.xml \
-		|| die
-}
-
-src_configure() {
-	export RSTUDIO_VERSION_MAJOR=$(get_version_component_range 1)
-	export RSTUDIO_VERSION_MINOR=$(get_version_component_range 2)
-	export RSTUDIO_VERSION_PATCH=$(get_version_component_range 3)
-
-	local mycmakeargs=(
-		-DDISTRO_SHARE=share/${PN}
-		$(cmake-utils_use !dedicated RSTUDIO_INSTALL_FREEDESKTOP)
-		-DRSTUDIO_TARGET=$(usex dedicated "Server" "$(usex server "Development" "Desktop")")
-		-DQT_QMAKE_EXECUTABLE=$(qt5_get_bindir)/qmake
-		)
-
-	cmake-utils_src_configure
-}
-
-src_compile() {
-	# Avoid the rest of the oracle-jdk-bin-1.8.0.60 sandbox violations F: mkdir S: deny
-	# P: /root/.oracle_jre_usage.
-	export ANT_OPTS="-Duser.home=${T}"
-	cmake-utils_src_compile
-}
-
-src_install() {
-	export ANT_OPTS="-Duser.home=${T}"
-	cmake-utils_src_install
-	pax-mark m "${ED}usr/bin/rstudio"
-	doconfd "${FILESDIR}"/rstudio-server.conf
-	dodir /etc/rstudio
-	insinto /etc/rstudio
-	doins "${FILESDIR}"/rsession.conf
-	dosym /etc/conf.d/rstudio-server.conf /etc/rstudio/rserver.conf
-	if use dedicated || use server; then
-		dopamd src/cpp/server/extras/pam/rstudio
-		newinitd "${FILESDIR}"/rstudio-server.initd rstudio-server
-	fi
-}
-
-pkg_preinst() {
-	use dedicated || gnome2_icon_savelist
-	java-pkg-2_pkg_preinst
-}
-
-pkg_postinst() {
-	use dedicated || { fdo-mime_desktop_database_update
-		fdo-mime_mime_database_update
-		gnome2_icon_cache_update ;}
-
-	if use dedicated || use server; then
-		enewgroup rstudio-server
-		enewuser rstudio-server -1 -1 -1 rstudio-server
-	fi
-}
-
-pkg_postrm() {
-	use dedicated || { fdo-mime_desktop_database_update
-		fdo-mime_mime_database_update
-		gnome2_icon_cache_update ;}
-}

diff --git a/sci-mathematics/rstudio/rstudio-0.99.482.ebuild b/sci-mathematics/rstudio/rstudio-0.99.482.ebuild
deleted file mode 100644
index cd4815f5d33..00000000000
--- a/sci-mathematics/rstudio/rstudio-0.99.482.ebuild
+++ /dev/null
@@ -1,240 +0,0 @@
-# Copyright 1999-2017 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-inherit eutils user cmake-utils gnome2-utils pam versionator fdo-mime java-pkg-2 pax-utils qmake-utils
-
-# TODO
-# * package gin and gwt
-# * use dict from tree, linguas
-# * do src_test (use junit from tree?)
-
-# update from scripts in dependencies/common
-# egrep '(GWT_SDK_VER=|GIN_VER=|SELENIUM_VER=|CHROMEDRIVER_VER=)' dependencies/common/install-gwt
-GWT_VER=2.7.0
-GIN_VER=1.5
-SELENIUM_VER=2.37.0
-CHROMEDRIVER_VER=2.7
-# grep 'PANDOC_VERSION=' dependencies/common/update-pandoc
-PANDOC_VER=1.13.1
-# ls dependencies/common/*.tar.gz
-PACKRAT_VER=0.98.1000
-RMARKDOWN_VER=0.98.1000
-SHINYAPPS_VER=0.98.1000
-RSCONNECT_VER=0.4.1.4_fcac892a69817febd7b655b189bf57193260cda0
-
-DESCRIPTION="IDE for the R language"
-HOMEPAGE="
-	http://www.rstudio.org
-	https://github.com/rstudio/rstudio/"
-SRC_URI="
-	https://github.com/rstudio/rstudio/archive/v${PV}.tar.gz -> ${P}.tar.gz
-	https://s3.amazonaws.com/rstudio-buildtools/gin-${GIN_VER}.zip
-	https://s3.amazonaws.com/rstudio-buildtools/gwt-${GWT_VER}.zip
-	https://s3.amazonaws.com/rstudio-buildtools/selenium-java-${SELENIUM_VER}.zip
-	https://s3.amazonaws.com/rstudio-buildtools/selenium-server-standalone-${SELENIUM_VER}.jar
-	https://s3.amazonaws.com/rstudio-buildtools/chromedriver-linux
-	https://s3.amazonaws.com/rstudio-dictionaries/core-dictionaries.zip
-	https://dev.gentoo.org/~gienah/distfiles/packrat-${PACKRAT_VER}.tar.gz
-	https://dev.gentoo.org/~gienah/distfiles/rmarkdown-${RMARKDOWN_VER}.tar.gz
-	https://dev.gentoo.org/~gienah/distfiles/shinyapps-${SHINYAPPS_VER}.tar.gz
-	https://dev.gentoo.org/~gienah/distfiles/rsconnect_${RSCONNECT_VER}.tar.gz
-"
-
-LICENSE="AGPL-3"
-SLOT="0"
-KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
-IUSE="dedicated server"
-
-QT_VER=5.4
-QT_SLOT=5
-RDEPEND="
-	app-text/pandoc
-	dev-haskell/pandoc-citeproc
-	>=dev-lang/R-2.11.1
-	>=dev-libs/boost-1.50:=
-	>=dev-libs/mathjax-2.3
-	dev-libs/openssl:0
-	sys-apps/util-linux
-	>=sys-devel/clang-3.5.0:*
-	sys-libs/zlib
-	>=virtual/jre-1.7:=
-	x11-libs/pango
-	!dedicated? (
-		>=dev-qt/qtcore-${QT_VER}:${QT_SLOT}
-		>=dev-qt/qtdeclarative-${QT_VER}:${QT_SLOT}
-		>=dev-qt/qtdbus-${QT_VER}:${QT_SLOT}
-		>=dev-qt/qtgui-${QT_VER}:${QT_SLOT}
-		>=dev-qt/qtnetwork-${QT_VER}:${QT_SLOT}
-		>=dev-qt/qtopengl-${QT_VER}:${QT_SLOT}
-		>=dev-qt/qtpositioning-${QT_VER}:${QT_SLOT}
-		>=dev-qt/qtprintsupport-${QT_VER}:${QT_SLOT}
-		>=dev-qt/qtsingleapplication-2.6.1_p20150629[X,qt5]
-		>=dev-qt/qtsensors-${QT_VER}:${QT_SLOT}
-		>=dev-qt/qtsql-${QT_VER}:${QT_SLOT}
-		>=dev-qt/qtsvg-${QT_VER}:${QT_SLOT}
-		>=dev-qt/qtwebkit-${QT_VER}:${QT_SLOT}
-		>=dev-qt/qtwidgets-${QT_VER}:${QT_SLOT}
-		>=dev-qt/qtxml-${QT_VER}:${QT_SLOT}
-		>=dev-qt/qtxmlpatterns-${QT_VER}:${QT_SLOT}
-		server? ( virtual/pam )
-	)
-	dedicated? ( virtual/pam )"
-DEPEND="${RDEPEND}
-	app-arch/unzip
-	dev-java/ant-core
-	>=virtual/jdk-1.7:=
-	virtual/pkgconfig"
-#	test? ( dev-java/junit:4 )
-
-src_unpack() {
-	unpack ${P}.tar.gz gwt-${GWT_VER}.zip
-	cd "${S}" || die
-	mkdir -p src/gwt/lib/{gin,gwt} \
-		dependencies/common/dictionaries \
-		src/gwt/lib/selenium/${SELENIUM_VER} \
-		src/gwt/lib/selenium/chromedriver/${CHROMEDRIVER_VER} || die
-	mv ../gwt-${GWT_VER} src/gwt/lib/gwt/${GWT_VER} || die
-	unzip -qd src/gwt/lib/gin/${GIN_VER} \
-		"${DISTDIR}"/gin-${GIN_VER}.zip || die
-	unzip -qd dependencies/common/dictionaries \
-		"${DISTDIR}"/core-dictionaries.zip || die
-	unzip -qd src/gwt/lib/selenium/${SELENIUM_VER} \
-		"${DISTDIR}"/selenium-java-${SELENIUM_VER}.zip || die
-	cp "${DISTDIR}"/selenium-server-standalone-${SELENIUM_VER}.jar \
-		src/gwt/lib/selenium/${SELENIUM_VER}/ || die
-	cp "${DISTDIR}"/chromedriver-linux \
-		src/gwt/lib/selenium/chromedriver/${CHROMEDRIVER_VER}/ || die
-	cd dependencies/common || die
-	unpack packrat-${PACKRAT_VER}.tar.gz
-	unpack rmarkdown-${RMARKDOWN_VER}.tar.gz
-	unpack shinyapps-${SHINYAPPS_VER}.tar.gz
-	unpack rsconnect_${RSCONNECT_VER}.tar.gz
-	cp "${DISTDIR}"/rmarkdown-${RMARKDOWN_VER}.tar.gz \
-		. || die
-	cp "${DISTDIR}"/packrat-${PACKRAT_VER}.tar.gz \
-		. || die
-	cp "${DISTDIR}"/shinyapps-${SHINYAPPS_VER}.tar.gz \
-		. || die
-	cp "${DISTDIR}"/rsconnect_${RSCONNECT_VER}.tar.gz \
-		. || die
-}
-
-src_prepare() {
-	java-pkg-2_src_prepare
-
-	egit_clean
-
-	epatch \
-		"${FILESDIR}"/${PN}-0.98.490-prefs.patch \
-		"${FILESDIR}"/${PN}-0.99.473-paths.patch \
-		"${FILESDIR}"/${PN}-0.99.473-clang-pandoc.patch \
-		"${FILESDIR}"/${PN}-0.98.490-linker_flags.patch \
-		"${FILESDIR}"/${PN}-0.98.1091-boost-1.57.patch \
-		"${FILESDIR}"/${PN}-0.99.473-qtsingleapplication.patch
-
-	# Adding -DDISTRO_SHARE=... to append-flags breaks cmake so using
-	# this sed hack for now. ~RMH
-	sed -i \
-		-e "s|DISTRO_SHARE|\"share/${PN}\"|g" \
-		src/cpp/server/ServerOptions.cpp \
-		src/cpp/session/SessionOptions.cpp || die
-
-	# use mathjax from system
-	ln -sf "${EPREFIX}"/usr/share/mathjax dependencies/common/mathjax-23 || die
-
-	# make sure icons and mime stuff are with prefix
-	sed -i \
-		-e "s:/usr:${EPREFIX}/usr:g" \
-		CMakeGlobals.txt src/cpp/desktop/CMakeLists.txt || die
-
-	# On Gentoo the rstudio-server configuration file is /etc/conf.d/rstudio-server.conf
-	sed -e "s@/etc/rstudio/rserver.conf@${EROOT}etc/conf.d/rstudio-server.conf@" \
-		-i src/cpp/server/ServerOptions.cpp \
-		|| die
-
-	# Set the rsession.conf file location for Gentoo prefix
-	sed -e "s@/etc/rstudio/rsession.conf@${EROOT}etc/rstudio/rsession.conf@" \
-		-i src/cpp/session/SessionOptions.cpp \
-		|| die
-
-	# dev-qt/qtsingleapplication-2.6.1_p20150629 does not provide a cmake module.
-	# It provides a library that has its version number appended to the end,
-	# which is difficult to handle in cmake, as find_library does not support
-	# searching for wildcard library names. So I find the library name from the
-	# qmake spec, and then sed this into the patched src/cpp/desktop/CMakeLists.txt.
-	rm -rf "${S}"/src/cpp/desktop/3rdparty || die
-	local s=$(grep '\-lQt$${QT_MAJOR_VERSION}Solutions_SingleApplication' \
-				   $(qt5_get_mkspecsdir)/features/qtsingleapplication.prf \
-					 | sed -e 's@\$\${QT_MAJOR_VERSION}@5@' \
-						   -e 's@LIBS \*= -l@@')
-	sed -e "s@Qt5Solutions_SingleApplication-2.6@${s}@g" \
-		-i "${S}"/src/cpp/desktop/CMakeLists.txt \
-		|| die
-
-	# Avoid some of the oracle-jdk-bin-1.8.0.60 sandbox violations F: mkdir S: deny
-	# P: /root/.oracle_jre_usage.
-	sed -e 's@\(\s*\)\(</classpath>\)@\1\2\n\1\<jvmarg value="-Duser.home=${env.T}"/>@g' \
-		-i "${S}"/src/gwt/build.xml \
-		|| die
-}
-
-src_configure() {
-	export RSTUDIO_VERSION_MAJOR=$(get_version_component_range 1)
-	export RSTUDIO_VERSION_MINOR=$(get_version_component_range 2)
-	export RSTUDIO_VERSION_PATCH=$(get_version_component_range 3)
-
-	local mycmakeargs=(
-		-DDISTRO_SHARE=share/${PN}
-		$(cmake-utils_use !dedicated RSTUDIO_INSTALL_FREEDESKTOP)
-		-DRSTUDIO_TARGET=$(usex dedicated "Server" "$(usex server "Development" "Desktop")")
-		-DQT_QMAKE_EXECUTABLE=$(qt5_get_bindir)/qmake
-		)
-
-	cmake-utils_src_configure
-}
-
-src_compile() {
-	# Avoid the rest of the oracle-jdk-bin-1.8.0.60 sandbox violations F: mkdir S: deny
-	# P: /root/.oracle_jre_usage.
-	export ANT_OPTS="-Duser.home=${T}"
-	cmake-utils_src_compile
-}
-
-src_install() {
-	export ANT_OPTS="-Duser.home=${T}"
-	cmake-utils_src_install
-	pax-mark m "${ED}usr/bin/rstudio"
-	doconfd "${FILESDIR}"/rstudio-server.conf
-	dodir /etc/rstudio
-	insinto /etc/rstudio
-	doins "${FILESDIR}"/rsession.conf
-	dosym /etc/conf.d/rstudio-server.conf /etc/rstudio/rserver.conf
-	if use dedicated || use server; then
-		dopamd src/cpp/server/extras/pam/rstudio
-		newinitd "${FILESDIR}"/rstudio-server.initd rstudio-server
-	fi
-}
-
-pkg_preinst() {
-	use dedicated || gnome2_icon_savelist
-	java-pkg-2_pkg_preinst
-}
-
-pkg_postinst() {
-	use dedicated || { fdo-mime_desktop_database_update
-		fdo-mime_mime_database_update
-		gnome2_icon_cache_update ;}
-
-	if use dedicated || use server; then
-		enewgroup rstudio-server
-		enewuser rstudio-server -1 -1 -1 rstudio-server
-	fi
-}
-
-pkg_postrm() {
-	use dedicated || { fdo-mime_desktop_database_update
-		fdo-mime_mime_database_update
-		gnome2_icon_cache_update ;}
-}

diff --git a/sci-mathematics/rstudio/rstudio-0.99.483.ebuild b/sci-mathematics/rstudio/rstudio-0.99.483.ebuild
deleted file mode 100644
index cd4815f5d33..00000000000
--- a/sci-mathematics/rstudio/rstudio-0.99.483.ebuild
+++ /dev/null
@@ -1,240 +0,0 @@
-# Copyright 1999-2017 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-inherit eutils user cmake-utils gnome2-utils pam versionator fdo-mime java-pkg-2 pax-utils qmake-utils
-
-# TODO
-# * package gin and gwt
-# * use dict from tree, linguas
-# * do src_test (use junit from tree?)
-
-# update from scripts in dependencies/common
-# egrep '(GWT_SDK_VER=|GIN_VER=|SELENIUM_VER=|CHROMEDRIVER_VER=)' dependencies/common/install-gwt
-GWT_VER=2.7.0
-GIN_VER=1.5
-SELENIUM_VER=2.37.0
-CHROMEDRIVER_VER=2.7
-# grep 'PANDOC_VERSION=' dependencies/common/update-pandoc
-PANDOC_VER=1.13.1
-# ls dependencies/common/*.tar.gz
-PACKRAT_VER=0.98.1000
-RMARKDOWN_VER=0.98.1000
-SHINYAPPS_VER=0.98.1000
-RSCONNECT_VER=0.4.1.4_fcac892a69817febd7b655b189bf57193260cda0
-
-DESCRIPTION="IDE for the R language"
-HOMEPAGE="
-	http://www.rstudio.org
-	https://github.com/rstudio/rstudio/"
-SRC_URI="
-	https://github.com/rstudio/rstudio/archive/v${PV}.tar.gz -> ${P}.tar.gz
-	https://s3.amazonaws.com/rstudio-buildtools/gin-${GIN_VER}.zip
-	https://s3.amazonaws.com/rstudio-buildtools/gwt-${GWT_VER}.zip
-	https://s3.amazonaws.com/rstudio-buildtools/selenium-java-${SELENIUM_VER}.zip
-	https://s3.amazonaws.com/rstudio-buildtools/selenium-server-standalone-${SELENIUM_VER}.jar
-	https://s3.amazonaws.com/rstudio-buildtools/chromedriver-linux
-	https://s3.amazonaws.com/rstudio-dictionaries/core-dictionaries.zip
-	https://dev.gentoo.org/~gienah/distfiles/packrat-${PACKRAT_VER}.tar.gz
-	https://dev.gentoo.org/~gienah/distfiles/rmarkdown-${RMARKDOWN_VER}.tar.gz
-	https://dev.gentoo.org/~gienah/distfiles/shinyapps-${SHINYAPPS_VER}.tar.gz
-	https://dev.gentoo.org/~gienah/distfiles/rsconnect_${RSCONNECT_VER}.tar.gz
-"
-
-LICENSE="AGPL-3"
-SLOT="0"
-KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
-IUSE="dedicated server"
-
-QT_VER=5.4
-QT_SLOT=5
-RDEPEND="
-	app-text/pandoc
-	dev-haskell/pandoc-citeproc
-	>=dev-lang/R-2.11.1
-	>=dev-libs/boost-1.50:=
-	>=dev-libs/mathjax-2.3
-	dev-libs/openssl:0
-	sys-apps/util-linux
-	>=sys-devel/clang-3.5.0:*
-	sys-libs/zlib
-	>=virtual/jre-1.7:=
-	x11-libs/pango
-	!dedicated? (
-		>=dev-qt/qtcore-${QT_VER}:${QT_SLOT}
-		>=dev-qt/qtdeclarative-${QT_VER}:${QT_SLOT}
-		>=dev-qt/qtdbus-${QT_VER}:${QT_SLOT}
-		>=dev-qt/qtgui-${QT_VER}:${QT_SLOT}
-		>=dev-qt/qtnetwork-${QT_VER}:${QT_SLOT}
-		>=dev-qt/qtopengl-${QT_VER}:${QT_SLOT}
-		>=dev-qt/qtpositioning-${QT_VER}:${QT_SLOT}
-		>=dev-qt/qtprintsupport-${QT_VER}:${QT_SLOT}
-		>=dev-qt/qtsingleapplication-2.6.1_p20150629[X,qt5]
-		>=dev-qt/qtsensors-${QT_VER}:${QT_SLOT}
-		>=dev-qt/qtsql-${QT_VER}:${QT_SLOT}
-		>=dev-qt/qtsvg-${QT_VER}:${QT_SLOT}
-		>=dev-qt/qtwebkit-${QT_VER}:${QT_SLOT}
-		>=dev-qt/qtwidgets-${QT_VER}:${QT_SLOT}
-		>=dev-qt/qtxml-${QT_VER}:${QT_SLOT}
-		>=dev-qt/qtxmlpatterns-${QT_VER}:${QT_SLOT}
-		server? ( virtual/pam )
-	)
-	dedicated? ( virtual/pam )"
-DEPEND="${RDEPEND}
-	app-arch/unzip
-	dev-java/ant-core
-	>=virtual/jdk-1.7:=
-	virtual/pkgconfig"
-#	test? ( dev-java/junit:4 )
-
-src_unpack() {
-	unpack ${P}.tar.gz gwt-${GWT_VER}.zip
-	cd "${S}" || die
-	mkdir -p src/gwt/lib/{gin,gwt} \
-		dependencies/common/dictionaries \
-		src/gwt/lib/selenium/${SELENIUM_VER} \
-		src/gwt/lib/selenium/chromedriver/${CHROMEDRIVER_VER} || die
-	mv ../gwt-${GWT_VER} src/gwt/lib/gwt/${GWT_VER} || die
-	unzip -qd src/gwt/lib/gin/${GIN_VER} \
-		"${DISTDIR}"/gin-${GIN_VER}.zip || die
-	unzip -qd dependencies/common/dictionaries \
-		"${DISTDIR}"/core-dictionaries.zip || die
-	unzip -qd src/gwt/lib/selenium/${SELENIUM_VER} \
-		"${DISTDIR}"/selenium-java-${SELENIUM_VER}.zip || die
-	cp "${DISTDIR}"/selenium-server-standalone-${SELENIUM_VER}.jar \
-		src/gwt/lib/selenium/${SELENIUM_VER}/ || die
-	cp "${DISTDIR}"/chromedriver-linux \
-		src/gwt/lib/selenium/chromedriver/${CHROMEDRIVER_VER}/ || die
-	cd dependencies/common || die
-	unpack packrat-${PACKRAT_VER}.tar.gz
-	unpack rmarkdown-${RMARKDOWN_VER}.tar.gz
-	unpack shinyapps-${SHINYAPPS_VER}.tar.gz
-	unpack rsconnect_${RSCONNECT_VER}.tar.gz
-	cp "${DISTDIR}"/rmarkdown-${RMARKDOWN_VER}.tar.gz \
-		. || die
-	cp "${DISTDIR}"/packrat-${PACKRAT_VER}.tar.gz \
-		. || die
-	cp "${DISTDIR}"/shinyapps-${SHINYAPPS_VER}.tar.gz \
-		. || die
-	cp "${DISTDIR}"/rsconnect_${RSCONNECT_VER}.tar.gz \
-		. || die
-}
-
-src_prepare() {
-	java-pkg-2_src_prepare
-
-	egit_clean
-
-	epatch \
-		"${FILESDIR}"/${PN}-0.98.490-prefs.patch \
-		"${FILESDIR}"/${PN}-0.99.473-paths.patch \
-		"${FILESDIR}"/${PN}-0.99.473-clang-pandoc.patch \
-		"${FILESDIR}"/${PN}-0.98.490-linker_flags.patch \
-		"${FILESDIR}"/${PN}-0.98.1091-boost-1.57.patch \
-		"${FILESDIR}"/${PN}-0.99.473-qtsingleapplication.patch
-
-	# Adding -DDISTRO_SHARE=... to append-flags breaks cmake so using
-	# this sed hack for now. ~RMH
-	sed -i \
-		-e "s|DISTRO_SHARE|\"share/${PN}\"|g" \
-		src/cpp/server/ServerOptions.cpp \
-		src/cpp/session/SessionOptions.cpp || die
-
-	# use mathjax from system
-	ln -sf "${EPREFIX}"/usr/share/mathjax dependencies/common/mathjax-23 || die
-
-	# make sure icons and mime stuff are with prefix
-	sed -i \
-		-e "s:/usr:${EPREFIX}/usr:g" \
-		CMakeGlobals.txt src/cpp/desktop/CMakeLists.txt || die
-
-	# On Gentoo the rstudio-server configuration file is /etc/conf.d/rstudio-server.conf
-	sed -e "s@/etc/rstudio/rserver.conf@${EROOT}etc/conf.d/rstudio-server.conf@" \
-		-i src/cpp/server/ServerOptions.cpp \
-		|| die
-
-	# Set the rsession.conf file location for Gentoo prefix
-	sed -e "s@/etc/rstudio/rsession.conf@${EROOT}etc/rstudio/rsession.conf@" \
-		-i src/cpp/session/SessionOptions.cpp \
-		|| die
-
-	# dev-qt/qtsingleapplication-2.6.1_p20150629 does not provide a cmake module.
-	# It provides a library that has its version number appended to the end,
-	# which is difficult to handle in cmake, as find_library does not support
-	# searching for wildcard library names. So I find the library name from the
-	# qmake spec, and then sed this into the patched src/cpp/desktop/CMakeLists.txt.
-	rm -rf "${S}"/src/cpp/desktop/3rdparty || die
-	local s=$(grep '\-lQt$${QT_MAJOR_VERSION}Solutions_SingleApplication' \
-				   $(qt5_get_mkspecsdir)/features/qtsingleapplication.prf \
-					 | sed -e 's@\$\${QT_MAJOR_VERSION}@5@' \
-						   -e 's@LIBS \*= -l@@')
-	sed -e "s@Qt5Solutions_SingleApplication-2.6@${s}@g" \
-		-i "${S}"/src/cpp/desktop/CMakeLists.txt \
-		|| die
-
-	# Avoid some of the oracle-jdk-bin-1.8.0.60 sandbox violations F: mkdir S: deny
-	# P: /root/.oracle_jre_usage.
-	sed -e 's@\(\s*\)\(</classpath>\)@\1\2\n\1\<jvmarg value="-Duser.home=${env.T}"/>@g' \
-		-i "${S}"/src/gwt/build.xml \
-		|| die
-}
-
-src_configure() {
-	export RSTUDIO_VERSION_MAJOR=$(get_version_component_range 1)
-	export RSTUDIO_VERSION_MINOR=$(get_version_component_range 2)
-	export RSTUDIO_VERSION_PATCH=$(get_version_component_range 3)
-
-	local mycmakeargs=(
-		-DDISTRO_SHARE=share/${PN}
-		$(cmake-utils_use !dedicated RSTUDIO_INSTALL_FREEDESKTOP)
-		-DRSTUDIO_TARGET=$(usex dedicated "Server" "$(usex server "Development" "Desktop")")
-		-DQT_QMAKE_EXECUTABLE=$(qt5_get_bindir)/qmake
-		)
-
-	cmake-utils_src_configure
-}
-
-src_compile() {
-	# Avoid the rest of the oracle-jdk-bin-1.8.0.60 sandbox violations F: mkdir S: deny
-	# P: /root/.oracle_jre_usage.
-	export ANT_OPTS="-Duser.home=${T}"
-	cmake-utils_src_compile
-}
-
-src_install() {
-	export ANT_OPTS="-Duser.home=${T}"
-	cmake-utils_src_install
-	pax-mark m "${ED}usr/bin/rstudio"
-	doconfd "${FILESDIR}"/rstudio-server.conf
-	dodir /etc/rstudio
-	insinto /etc/rstudio
-	doins "${FILESDIR}"/rsession.conf
-	dosym /etc/conf.d/rstudio-server.conf /etc/rstudio/rserver.conf
-	if use dedicated || use server; then
-		dopamd src/cpp/server/extras/pam/rstudio
-		newinitd "${FILESDIR}"/rstudio-server.initd rstudio-server
-	fi
-}
-
-pkg_preinst() {
-	use dedicated || gnome2_icon_savelist
-	java-pkg-2_pkg_preinst
-}
-
-pkg_postinst() {
-	use dedicated || { fdo-mime_desktop_database_update
-		fdo-mime_mime_database_update
-		gnome2_icon_cache_update ;}
-
-	if use dedicated || use server; then
-		enewgroup rstudio-server
-		enewuser rstudio-server -1 -1 -1 rstudio-server
-	fi
-}
-
-pkg_postrm() {
-	use dedicated || { fdo-mime_desktop_database_update
-		fdo-mime_mime_database_update
-		gnome2_icon_cache_update ;}
-}

diff --git a/sci-mathematics/rstudio/rstudio-0.99.484.ebuild b/sci-mathematics/rstudio/rstudio-0.99.484.ebuild
deleted file mode 100644
index cd4815f5d33..00000000000
--- a/sci-mathematics/rstudio/rstudio-0.99.484.ebuild
+++ /dev/null
@@ -1,240 +0,0 @@
-# Copyright 1999-2017 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-inherit eutils user cmake-utils gnome2-utils pam versionator fdo-mime java-pkg-2 pax-utils qmake-utils
-
-# TODO
-# * package gin and gwt
-# * use dict from tree, linguas
-# * do src_test (use junit from tree?)
-
-# update from scripts in dependencies/common
-# egrep '(GWT_SDK_VER=|GIN_VER=|SELENIUM_VER=|CHROMEDRIVER_VER=)' dependencies/common/install-gwt
-GWT_VER=2.7.0
-GIN_VER=1.5
-SELENIUM_VER=2.37.0
-CHROMEDRIVER_VER=2.7
-# grep 'PANDOC_VERSION=' dependencies/common/update-pandoc
-PANDOC_VER=1.13.1
-# ls dependencies/common/*.tar.gz
-PACKRAT_VER=0.98.1000
-RMARKDOWN_VER=0.98.1000
-SHINYAPPS_VER=0.98.1000
-RSCONNECT_VER=0.4.1.4_fcac892a69817febd7b655b189bf57193260cda0
-
-DESCRIPTION="IDE for the R language"
-HOMEPAGE="
-	http://www.rstudio.org
-	https://github.com/rstudio/rstudio/"
-SRC_URI="
-	https://github.com/rstudio/rstudio/archive/v${PV}.tar.gz -> ${P}.tar.gz
-	https://s3.amazonaws.com/rstudio-buildtools/gin-${GIN_VER}.zip
-	https://s3.amazonaws.com/rstudio-buildtools/gwt-${GWT_VER}.zip
-	https://s3.amazonaws.com/rstudio-buildtools/selenium-java-${SELENIUM_VER}.zip
-	https://s3.amazonaws.com/rstudio-buildtools/selenium-server-standalone-${SELENIUM_VER}.jar
-	https://s3.amazonaws.com/rstudio-buildtools/chromedriver-linux
-	https://s3.amazonaws.com/rstudio-dictionaries/core-dictionaries.zip
-	https://dev.gentoo.org/~gienah/distfiles/packrat-${PACKRAT_VER}.tar.gz
-	https://dev.gentoo.org/~gienah/distfiles/rmarkdown-${RMARKDOWN_VER}.tar.gz
-	https://dev.gentoo.org/~gienah/distfiles/shinyapps-${SHINYAPPS_VER}.tar.gz
-	https://dev.gentoo.org/~gienah/distfiles/rsconnect_${RSCONNECT_VER}.tar.gz
-"
-
-LICENSE="AGPL-3"
-SLOT="0"
-KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
-IUSE="dedicated server"
-
-QT_VER=5.4
-QT_SLOT=5
-RDEPEND="
-	app-text/pandoc
-	dev-haskell/pandoc-citeproc
-	>=dev-lang/R-2.11.1
-	>=dev-libs/boost-1.50:=
-	>=dev-libs/mathjax-2.3
-	dev-libs/openssl:0
-	sys-apps/util-linux
-	>=sys-devel/clang-3.5.0:*
-	sys-libs/zlib
-	>=virtual/jre-1.7:=
-	x11-libs/pango
-	!dedicated? (
-		>=dev-qt/qtcore-${QT_VER}:${QT_SLOT}
-		>=dev-qt/qtdeclarative-${QT_VER}:${QT_SLOT}
-		>=dev-qt/qtdbus-${QT_VER}:${QT_SLOT}
-		>=dev-qt/qtgui-${QT_VER}:${QT_SLOT}
-		>=dev-qt/qtnetwork-${QT_VER}:${QT_SLOT}
-		>=dev-qt/qtopengl-${QT_VER}:${QT_SLOT}
-		>=dev-qt/qtpositioning-${QT_VER}:${QT_SLOT}
-		>=dev-qt/qtprintsupport-${QT_VER}:${QT_SLOT}
-		>=dev-qt/qtsingleapplication-2.6.1_p20150629[X,qt5]
-		>=dev-qt/qtsensors-${QT_VER}:${QT_SLOT}
-		>=dev-qt/qtsql-${QT_VER}:${QT_SLOT}
-		>=dev-qt/qtsvg-${QT_VER}:${QT_SLOT}
-		>=dev-qt/qtwebkit-${QT_VER}:${QT_SLOT}
-		>=dev-qt/qtwidgets-${QT_VER}:${QT_SLOT}
-		>=dev-qt/qtxml-${QT_VER}:${QT_SLOT}
-		>=dev-qt/qtxmlpatterns-${QT_VER}:${QT_SLOT}
-		server? ( virtual/pam )
-	)
-	dedicated? ( virtual/pam )"
-DEPEND="${RDEPEND}
-	app-arch/unzip
-	dev-java/ant-core
-	>=virtual/jdk-1.7:=
-	virtual/pkgconfig"
-#	test? ( dev-java/junit:4 )
-
-src_unpack() {
-	unpack ${P}.tar.gz gwt-${GWT_VER}.zip
-	cd "${S}" || die
-	mkdir -p src/gwt/lib/{gin,gwt} \
-		dependencies/common/dictionaries \
-		src/gwt/lib/selenium/${SELENIUM_VER} \
-		src/gwt/lib/selenium/chromedriver/${CHROMEDRIVER_VER} || die
-	mv ../gwt-${GWT_VER} src/gwt/lib/gwt/${GWT_VER} || die
-	unzip -qd src/gwt/lib/gin/${GIN_VER} \
-		"${DISTDIR}"/gin-${GIN_VER}.zip || die
-	unzip -qd dependencies/common/dictionaries \
-		"${DISTDIR}"/core-dictionaries.zip || die
-	unzip -qd src/gwt/lib/selenium/${SELENIUM_VER} \
-		"${DISTDIR}"/selenium-java-${SELENIUM_VER}.zip || die
-	cp "${DISTDIR}"/selenium-server-standalone-${SELENIUM_VER}.jar \
-		src/gwt/lib/selenium/${SELENIUM_VER}/ || die
-	cp "${DISTDIR}"/chromedriver-linux \
-		src/gwt/lib/selenium/chromedriver/${CHROMEDRIVER_VER}/ || die
-	cd dependencies/common || die
-	unpack packrat-${PACKRAT_VER}.tar.gz
-	unpack rmarkdown-${RMARKDOWN_VER}.tar.gz
-	unpack shinyapps-${SHINYAPPS_VER}.tar.gz
-	unpack rsconnect_${RSCONNECT_VER}.tar.gz
-	cp "${DISTDIR}"/rmarkdown-${RMARKDOWN_VER}.tar.gz \
-		. || die
-	cp "${DISTDIR}"/packrat-${PACKRAT_VER}.tar.gz \
-		. || die
-	cp "${DISTDIR}"/shinyapps-${SHINYAPPS_VER}.tar.gz \
-		. || die
-	cp "${DISTDIR}"/rsconnect_${RSCONNECT_VER}.tar.gz \
-		. || die
-}
-
-src_prepare() {
-	java-pkg-2_src_prepare
-
-	egit_clean
-
-	epatch \
-		"${FILESDIR}"/${PN}-0.98.490-prefs.patch \
-		"${FILESDIR}"/${PN}-0.99.473-paths.patch \
-		"${FILESDIR}"/${PN}-0.99.473-clang-pandoc.patch \
-		"${FILESDIR}"/${PN}-0.98.490-linker_flags.patch \
-		"${FILESDIR}"/${PN}-0.98.1091-boost-1.57.patch \
-		"${FILESDIR}"/${PN}-0.99.473-qtsingleapplication.patch
-
-	# Adding -DDISTRO_SHARE=... to append-flags breaks cmake so using
-	# this sed hack for now. ~RMH
-	sed -i \
-		-e "s|DISTRO_SHARE|\"share/${PN}\"|g" \
-		src/cpp/server/ServerOptions.cpp \
-		src/cpp/session/SessionOptions.cpp || die
-
-	# use mathjax from system
-	ln -sf "${EPREFIX}"/usr/share/mathjax dependencies/common/mathjax-23 || die
-
-	# make sure icons and mime stuff are with prefix
-	sed -i \
-		-e "s:/usr:${EPREFIX}/usr:g" \
-		CMakeGlobals.txt src/cpp/desktop/CMakeLists.txt || die
-
-	# On Gentoo the rstudio-server configuration file is /etc/conf.d/rstudio-server.conf
-	sed -e "s@/etc/rstudio/rserver.conf@${EROOT}etc/conf.d/rstudio-server.conf@" \
-		-i src/cpp/server/ServerOptions.cpp \
-		|| die
-
-	# Set the rsession.conf file location for Gentoo prefix
-	sed -e "s@/etc/rstudio/rsession.conf@${EROOT}etc/rstudio/rsession.conf@" \
-		-i src/cpp/session/SessionOptions.cpp \
-		|| die
-
-	# dev-qt/qtsingleapplication-2.6.1_p20150629 does not provide a cmake module.
-	# It provides a library that has its version number appended to the end,
-	# which is difficult to handle in cmake, as find_library does not support
-	# searching for wildcard library names. So I find the library name from the
-	# qmake spec, and then sed this into the patched src/cpp/desktop/CMakeLists.txt.
-	rm -rf "${S}"/src/cpp/desktop/3rdparty || die
-	local s=$(grep '\-lQt$${QT_MAJOR_VERSION}Solutions_SingleApplication' \
-				   $(qt5_get_mkspecsdir)/features/qtsingleapplication.prf \
-					 | sed -e 's@\$\${QT_MAJOR_VERSION}@5@' \
-						   -e 's@LIBS \*= -l@@')
-	sed -e "s@Qt5Solutions_SingleApplication-2.6@${s}@g" \
-		-i "${S}"/src/cpp/desktop/CMakeLists.txt \
-		|| die
-
-	# Avoid some of the oracle-jdk-bin-1.8.0.60 sandbox violations F: mkdir S: deny
-	# P: /root/.oracle_jre_usage.
-	sed -e 's@\(\s*\)\(</classpath>\)@\1\2\n\1\<jvmarg value="-Duser.home=${env.T}"/>@g' \
-		-i "${S}"/src/gwt/build.xml \
-		|| die
-}
-
-src_configure() {
-	export RSTUDIO_VERSION_MAJOR=$(get_version_component_range 1)
-	export RSTUDIO_VERSION_MINOR=$(get_version_component_range 2)
-	export RSTUDIO_VERSION_PATCH=$(get_version_component_range 3)
-
-	local mycmakeargs=(
-		-DDISTRO_SHARE=share/${PN}
-		$(cmake-utils_use !dedicated RSTUDIO_INSTALL_FREEDESKTOP)
-		-DRSTUDIO_TARGET=$(usex dedicated "Server" "$(usex server "Development" "Desktop")")
-		-DQT_QMAKE_EXECUTABLE=$(qt5_get_bindir)/qmake
-		)
-
-	cmake-utils_src_configure
-}
-
-src_compile() {
-	# Avoid the rest of the oracle-jdk-bin-1.8.0.60 sandbox violations F: mkdir S: deny
-	# P: /root/.oracle_jre_usage.
-	export ANT_OPTS="-Duser.home=${T}"
-	cmake-utils_src_compile
-}
-
-src_install() {
-	export ANT_OPTS="-Duser.home=${T}"
-	cmake-utils_src_install
-	pax-mark m "${ED}usr/bin/rstudio"
-	doconfd "${FILESDIR}"/rstudio-server.conf
-	dodir /etc/rstudio
-	insinto /etc/rstudio
-	doins "${FILESDIR}"/rsession.conf
-	dosym /etc/conf.d/rstudio-server.conf /etc/rstudio/rserver.conf
-	if use dedicated || use server; then
-		dopamd src/cpp/server/extras/pam/rstudio
-		newinitd "${FILESDIR}"/rstudio-server.initd rstudio-server
-	fi
-}
-
-pkg_preinst() {
-	use dedicated || gnome2_icon_savelist
-	java-pkg-2_pkg_preinst
-}
-
-pkg_postinst() {
-	use dedicated || { fdo-mime_desktop_database_update
-		fdo-mime_mime_database_update
-		gnome2_icon_cache_update ;}
-
-	if use dedicated || use server; then
-		enewgroup rstudio-server
-		enewuser rstudio-server -1 -1 -1 rstudio-server
-	fi
-}
-
-pkg_postrm() {
-	use dedicated || { fdo-mime_desktop_database_update
-		fdo-mime_mime_database_update
-		gnome2_icon_cache_update ;}
-}

diff --git a/sci-mathematics/rstudio/rstudio-0.99.486-r1.ebuild b/sci-mathematics/rstudio/rstudio-0.99.486-r1.ebuild
deleted file mode 100644
index a0c4907f68f..00000000000
--- a/sci-mathematics/rstudio/rstudio-0.99.486-r1.ebuild
+++ /dev/null
@@ -1,248 +0,0 @@
-# Copyright 1999-2017 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-inherit eutils user cmake-utils gnome2-utils pam versionator fdo-mime java-pkg-2 pax-utils qmake-utils
-
-# TODO
-# * package gin and gwt
-# * use dict from tree, linguas
-# * do src_test (use junit from tree?)
-
-# update from scripts in dependencies/common
-# egrep '(GWT_SDK_VER=|GIN_VER=|SELENIUM_VER=|CHROMEDRIVER_VER=)' dependencies/common/install-gwt
-GWT_VER=2.7.0
-GIN_VER=1.5
-SELENIUM_VER=2.37.0
-CHROMEDRIVER_VER=2.7
-# grep 'PANDOC_VERSION=' dependencies/common/update-pandoc
-PANDOC_VER=1.13.1
-# ls dependencies/common/*.tar.gz
-PACKRAT_VER=0.98.1000
-RMARKDOWN_VER=0.98.1000
-SHINYAPPS_VER=0.98.1000
-RSCONNECT_VER=0.4.1.4_fcac892a69817febd7b655b189bf57193260cda0
-
-DESCRIPTION="IDE for the R language"
-HOMEPAGE="
-	http://www.rstudio.org
-	https://github.com/rstudio/rstudio/"
-SRC_URI="
-	https://github.com/rstudio/rstudio/archive/v${PV}.tar.gz -> ${P}.tar.gz
-	https://s3.amazonaws.com/rstudio-buildtools/gin-${GIN_VER}.zip
-	https://s3.amazonaws.com/rstudio-buildtools/gwt-${GWT_VER}.zip
-	https://s3.amazonaws.com/rstudio-buildtools/selenium-java-${SELENIUM_VER}.zip
-	https://s3.amazonaws.com/rstudio-buildtools/selenium-server-standalone-${SELENIUM_VER}.jar
-	https://s3.amazonaws.com/rstudio-buildtools/chromedriver-linux
-	https://s3.amazonaws.com/rstudio-dictionaries/core-dictionaries.zip
-	https://dev.gentoo.org/~gienah/distfiles/packrat-${PACKRAT_VER}.tar.gz
-	https://dev.gentoo.org/~gienah/distfiles/rmarkdown-${RMARKDOWN_VER}.tar.gz
-	https://dev.gentoo.org/~gienah/distfiles/shinyapps-${SHINYAPPS_VER}.tar.gz
-	https://dev.gentoo.org/~gienah/distfiles/rsconnect_${RSCONNECT_VER}.tar.gz
-"
-
-LICENSE="AGPL-3"
-SLOT="0"
-KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
-IUSE="dedicated server"
-
-QT_VER=5.4
-QT_SLOT=5
-RDEPEND="
-	app-text/pandoc
-	dev-haskell/pandoc-citeproc
-	>=dev-lang/R-2.11.1
-	>=dev-libs/boost-1.50:=
-	>=dev-libs/mathjax-2.3
-	dev-libs/openssl:0
-	sys-apps/util-linux
-	>=sys-devel/clang-3.5.0:*
-	sys-libs/zlib
-	>=virtual/jre-1.7:=
-	x11-libs/pango
-	!dedicated? (
-		>=dev-qt/qtcore-${QT_VER}:${QT_SLOT}
-		>=dev-qt/qtdeclarative-${QT_VER}:${QT_SLOT}
-		>=dev-qt/qtdbus-${QT_VER}:${QT_SLOT}
-		>=dev-qt/qtgui-${QT_VER}:${QT_SLOT}
-		>=dev-qt/qtnetwork-${QT_VER}:${QT_SLOT}
-		>=dev-qt/qtopengl-${QT_VER}:${QT_SLOT}
-		>=dev-qt/qtpositioning-${QT_VER}:${QT_SLOT}
-		>=dev-qt/qtprintsupport-${QT_VER}:${QT_SLOT}
-		>=dev-qt/qtsingleapplication-2.6.1_p20150629[X,qt5]
-		>=dev-qt/qtsensors-${QT_VER}:${QT_SLOT}
-		>=dev-qt/qtsql-${QT_VER}:${QT_SLOT}
-		>=dev-qt/qtsvg-${QT_VER}:${QT_SLOT}
-		>=dev-qt/qtwebkit-${QT_VER}:${QT_SLOT}
-		>=dev-qt/qtwidgets-${QT_VER}:${QT_SLOT}
-		>=dev-qt/qtxml-${QT_VER}:${QT_SLOT}
-		>=dev-qt/qtxmlpatterns-${QT_VER}:${QT_SLOT}
-		server? ( virtual/pam )
-	)
-	dedicated? ( virtual/pam )"
-DEPEND="${RDEPEND}
-	app-arch/unzip
-	dev-java/ant-core
-	>=virtual/jdk-1.7:=
-	virtual/pkgconfig"
-#	test? ( dev-java/junit:4 )
-
-PATCHES=(
-		"${FILESDIR}/${PN}-0.98.490-prefs.patch"
-		"${FILESDIR}/${PN}-0.99.473-paths.patch"
-		"${FILESDIR}/${PN}-0.99.473-clang-pandoc.patch"
-		"${FILESDIR}/${PN}-0.98.490-linker_flags.patch"
-		"${FILESDIR}/${PN}-0.98.1091-boost-1.57.patch"
-		"${FILESDIR}/${PN}-0.99.473-qtsingleapplication.patch"
-		"${FILESDIR}/${PN}-0.99.486-systemd.patch"
-)
-
-src_unpack() {
-	unpack ${P}.tar.gz gwt-${GWT_VER}.zip
-	cd "${S}" || die
-	mkdir -p src/gwt/lib/{gin,gwt} \
-		dependencies/common/dictionaries \
-		src/gwt/lib/selenium/${SELENIUM_VER} \
-		src/gwt/lib/selenium/chromedriver/${CHROMEDRIVER_VER} || die
-	mv ../gwt-${GWT_VER} src/gwt/lib/gwt/${GWT_VER} || die
-	unzip -qd src/gwt/lib/gin/${GIN_VER} \
-		"${DISTDIR}"/gin-${GIN_VER}.zip || die
-	unzip -qd dependencies/common/dictionaries \
-		"${DISTDIR}"/core-dictionaries.zip || die
-	unzip -qd src/gwt/lib/selenium/${SELENIUM_VER} \
-		"${DISTDIR}"/selenium-java-${SELENIUM_VER}.zip || die
-	cp "${DISTDIR}"/selenium-server-standalone-${SELENIUM_VER}.jar \
-		src/gwt/lib/selenium/${SELENIUM_VER}/ || die
-	cp "${DISTDIR}"/chromedriver-linux \
-		src/gwt/lib/selenium/chromedriver/${CHROMEDRIVER_VER}/ || die
-	cd dependencies/common || die
-	unpack packrat-${PACKRAT_VER}.tar.gz
-	unpack rmarkdown-${RMARKDOWN_VER}.tar.gz
-	unpack shinyapps-${SHINYAPPS_VER}.tar.gz
-	unpack rsconnect_${RSCONNECT_VER}.tar.gz
-	cp "${DISTDIR}"/rmarkdown-${RMARKDOWN_VER}.tar.gz \
-		. || die
-	cp "${DISTDIR}"/packrat-${PACKRAT_VER}.tar.gz \
-		. || die
-	cp "${DISTDIR}"/shinyapps-${SHINYAPPS_VER}.tar.gz \
-		. || die
-	cp "${DISTDIR}"/rsconnect_${RSCONNECT_VER}.tar.gz \
-		. || die
-}
-
-src_prepare() {
-	java-pkg-2_src_prepare
-
-	egit_clean
-
-	epatch "${PATCHES[@]}"
-
-	# Enable CMake to install our .service file for systemd usage
-	mkdir -vp "${S}/src/cpp/server/lib/systemd/system" || die
-	cp -v "${FILESDIR}/rstudio-server.service.in" "${S}/src/cpp/server/lib/systemd/system/" || die
-
-	# Adding -DDISTRO_SHARE=... to append-flags breaks cmake so using
-	# this sed hack for now. ~RMH
-	sed -i \
-		-e "s|DISTRO_SHARE|\"share/${PN}\"|g" \
-		src/cpp/server/ServerOptions.cpp \
-		src/cpp/session/SessionOptions.cpp || die
-
-	# use mathjax from system
-	ln -sf "${EPREFIX}"/usr/share/mathjax dependencies/common/mathjax-23 || die
-
-	# make sure icons and mime stuff are with prefix
-	sed -i \
-		-e "s:/usr:${EPREFIX}/usr:g" \
-		CMakeGlobals.txt src/cpp/desktop/CMakeLists.txt || die
-
-	# On Gentoo the rstudio-server configuration file is /etc/conf.d/rstudio-server.conf
-	sed -e "s@/etc/rstudio/rserver.conf@${EROOT}etc/conf.d/rstudio-server.conf@" \
-		-i src/cpp/server/ServerOptions.cpp \
-		|| die
-
-	# Set the rsession.conf file location for Gentoo prefix
-	sed -e "s@/etc/rstudio/rsession.conf@${EROOT}etc/rstudio/rsession.conf@" \
-		-i src/cpp/session/SessionOptions.cpp \
-		|| die
-
-	# dev-qt/qtsingleapplication-2.6.1_p20150629 does not provide a cmake module.
-	# It provides a library that has its version number appended to the end,
-	# which is difficult to handle in cmake, as find_library does not support
-	# searching for wildcard library names. So I find the library name from the
-	# qmake spec, and then sed this into the patched src/cpp/desktop/CMakeLists.txt.
-	rm -rf "${S}"/src/cpp/desktop/3rdparty || die
-	local s=$(grep '\-lQt$${QT_MAJOR_VERSION}Solutions_SingleApplication' \
-				   $(qt5_get_mkspecsdir)/features/qtsingleapplication.prf \
-					 | sed -e 's@\$\${QT_MAJOR_VERSION}@5@' \
-						   -e 's@LIBS \*= -l@@')
-	sed -e "s@Qt5Solutions_SingleApplication-2.6@${s}@g" \
-		-i "${S}"/src/cpp/desktop/CMakeLists.txt \
-		|| die
-
-	# Avoid some of the oracle-jdk-bin-1.8.0.60 sandbox violations F: mkdir S: deny
-	# P: /root/.oracle_jre_usage.
-	sed -e 's@\(\s*\)\(</classpath>\)@\1\2\n\1\<jvmarg value="-Duser.home=${env.T}"/>@g' \
-		-i "${S}"/src/gwt/build.xml \
-		|| die
-}
-
-src_configure() {
-	export RSTUDIO_VERSION_MAJOR=$(get_version_component_range 1)
-	export RSTUDIO_VERSION_MINOR=$(get_version_component_range 2)
-	export RSTUDIO_VERSION_PATCH=$(get_version_component_range 3)
-
-	local mycmakeargs=(
-		-DDISTRO_SHARE=share/${PN}
-		$(cmake-utils_use !dedicated RSTUDIO_INSTALL_FREEDESKTOP)
-		-DRSTUDIO_TARGET=$(usex dedicated "Server" "$(usex server "Development" "Desktop")")
-		-DQT_QMAKE_EXECUTABLE=$(qt5_get_bindir)/qmake
-		)
-
-	cmake-utils_src_configure
-}
-
-src_compile() {
-	# Avoid the rest of the oracle-jdk-bin-1.8.0.60 sandbox violations F: mkdir S: deny
-	# P: /root/.oracle_jre_usage.
-	export ANT_OPTS="-Duser.home=${T}"
-	cmake-utils_src_compile
-}
-
-src_install() {
-	export ANT_OPTS="-Duser.home=${T}"
-	cmake-utils_src_install
-	pax-mark m "${ED}usr/bin/rstudio"
-	doconfd "${FILESDIR}"/rstudio-server.conf
-	dodir /etc/rstudio
-	insinto /etc/rstudio
-	doins "${FILESDIR}"/rsession.conf
-	dosym /etc/conf.d/rstudio-server.conf /etc/rstudio/rserver.conf
-	if use dedicated || use server; then
-		dopamd src/cpp/server/extras/pam/rstudio
-		newinitd "${FILESDIR}"/rstudio-server.initd rstudio-server
-	fi
-}
-
-pkg_preinst() {
-	use dedicated || gnome2_icon_savelist
-	java-pkg-2_pkg_preinst
-}
-
-pkg_postinst() {
-	use dedicated || { fdo-mime_desktop_database_update
-		fdo-mime_mime_database_update
-		gnome2_icon_cache_update ;}
-
-	if use dedicated || use server; then
-		enewgroup rstudio-server
-		enewuser rstudio-server -1 -1 -1 rstudio-server
-	fi
-}
-
-pkg_postrm() {
-	use dedicated || { fdo-mime_desktop_database_update
-		fdo-mime_mime_database_update
-		gnome2_icon_cache_update ;}
-}

diff --git a/sci-mathematics/rstudio/rstudio-0.99.491.ebuild b/sci-mathematics/rstudio/rstudio-0.99.491.ebuild
deleted file mode 100644
index a0c4907f68f..00000000000
--- a/sci-mathematics/rstudio/rstudio-0.99.491.ebuild
+++ /dev/null
@@ -1,248 +0,0 @@
-# Copyright 1999-2017 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-inherit eutils user cmake-utils gnome2-utils pam versionator fdo-mime java-pkg-2 pax-utils qmake-utils
-
-# TODO
-# * package gin and gwt
-# * use dict from tree, linguas
-# * do src_test (use junit from tree?)
-
-# update from scripts in dependencies/common
-# egrep '(GWT_SDK_VER=|GIN_VER=|SELENIUM_VER=|CHROMEDRIVER_VER=)' dependencies/common/install-gwt
-GWT_VER=2.7.0
-GIN_VER=1.5
-SELENIUM_VER=2.37.0
-CHROMEDRIVER_VER=2.7
-# grep 'PANDOC_VERSION=' dependencies/common/update-pandoc
-PANDOC_VER=1.13.1
-# ls dependencies/common/*.tar.gz
-PACKRAT_VER=0.98.1000
-RMARKDOWN_VER=0.98.1000
-SHINYAPPS_VER=0.98.1000
-RSCONNECT_VER=0.4.1.4_fcac892a69817febd7b655b189bf57193260cda0
-
-DESCRIPTION="IDE for the R language"
-HOMEPAGE="
-	http://www.rstudio.org
-	https://github.com/rstudio/rstudio/"
-SRC_URI="
-	https://github.com/rstudio/rstudio/archive/v${PV}.tar.gz -> ${P}.tar.gz
-	https://s3.amazonaws.com/rstudio-buildtools/gin-${GIN_VER}.zip
-	https://s3.amazonaws.com/rstudio-buildtools/gwt-${GWT_VER}.zip
-	https://s3.amazonaws.com/rstudio-buildtools/selenium-java-${SELENIUM_VER}.zip
-	https://s3.amazonaws.com/rstudio-buildtools/selenium-server-standalone-${SELENIUM_VER}.jar
-	https://s3.amazonaws.com/rstudio-buildtools/chromedriver-linux
-	https://s3.amazonaws.com/rstudio-dictionaries/core-dictionaries.zip
-	https://dev.gentoo.org/~gienah/distfiles/packrat-${PACKRAT_VER}.tar.gz
-	https://dev.gentoo.org/~gienah/distfiles/rmarkdown-${RMARKDOWN_VER}.tar.gz
-	https://dev.gentoo.org/~gienah/distfiles/shinyapps-${SHINYAPPS_VER}.tar.gz
-	https://dev.gentoo.org/~gienah/distfiles/rsconnect_${RSCONNECT_VER}.tar.gz
-"
-
-LICENSE="AGPL-3"
-SLOT="0"
-KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
-IUSE="dedicated server"
-
-QT_VER=5.4
-QT_SLOT=5
-RDEPEND="
-	app-text/pandoc
-	dev-haskell/pandoc-citeproc
-	>=dev-lang/R-2.11.1
-	>=dev-libs/boost-1.50:=
-	>=dev-libs/mathjax-2.3
-	dev-libs/openssl:0
-	sys-apps/util-linux
-	>=sys-devel/clang-3.5.0:*
-	sys-libs/zlib
-	>=virtual/jre-1.7:=
-	x11-libs/pango
-	!dedicated? (
-		>=dev-qt/qtcore-${QT_VER}:${QT_SLOT}
-		>=dev-qt/qtdeclarative-${QT_VER}:${QT_SLOT}
-		>=dev-qt/qtdbus-${QT_VER}:${QT_SLOT}
-		>=dev-qt/qtgui-${QT_VER}:${QT_SLOT}
-		>=dev-qt/qtnetwork-${QT_VER}:${QT_SLOT}
-		>=dev-qt/qtopengl-${QT_VER}:${QT_SLOT}
-		>=dev-qt/qtpositioning-${QT_VER}:${QT_SLOT}
-		>=dev-qt/qtprintsupport-${QT_VER}:${QT_SLOT}
-		>=dev-qt/qtsingleapplication-2.6.1_p20150629[X,qt5]
-		>=dev-qt/qtsensors-${QT_VER}:${QT_SLOT}
-		>=dev-qt/qtsql-${QT_VER}:${QT_SLOT}
-		>=dev-qt/qtsvg-${QT_VER}:${QT_SLOT}
-		>=dev-qt/qtwebkit-${QT_VER}:${QT_SLOT}
-		>=dev-qt/qtwidgets-${QT_VER}:${QT_SLOT}
-		>=dev-qt/qtxml-${QT_VER}:${QT_SLOT}
-		>=dev-qt/qtxmlpatterns-${QT_VER}:${QT_SLOT}
-		server? ( virtual/pam )
-	)
-	dedicated? ( virtual/pam )"
-DEPEND="${RDEPEND}
-	app-arch/unzip
-	dev-java/ant-core
-	>=virtual/jdk-1.7:=
-	virtual/pkgconfig"
-#	test? ( dev-java/junit:4 )
-
-PATCHES=(
-		"${FILESDIR}/${PN}-0.98.490-prefs.patch"
-		"${FILESDIR}/${PN}-0.99.473-paths.patch"
-		"${FILESDIR}/${PN}-0.99.473-clang-pandoc.patch"
-		"${FILESDIR}/${PN}-0.98.490-linker_flags.patch"
-		"${FILESDIR}/${PN}-0.98.1091-boost-1.57.patch"
-		"${FILESDIR}/${PN}-0.99.473-qtsingleapplication.patch"
-		"${FILESDIR}/${PN}-0.99.486-systemd.patch"
-)
-
-src_unpack() {
-	unpack ${P}.tar.gz gwt-${GWT_VER}.zip
-	cd "${S}" || die
-	mkdir -p src/gwt/lib/{gin,gwt} \
-		dependencies/common/dictionaries \
-		src/gwt/lib/selenium/${SELENIUM_VER} \
-		src/gwt/lib/selenium/chromedriver/${CHROMEDRIVER_VER} || die
-	mv ../gwt-${GWT_VER} src/gwt/lib/gwt/${GWT_VER} || die
-	unzip -qd src/gwt/lib/gin/${GIN_VER} \
-		"${DISTDIR}"/gin-${GIN_VER}.zip || die
-	unzip -qd dependencies/common/dictionaries \
-		"${DISTDIR}"/core-dictionaries.zip || die
-	unzip -qd src/gwt/lib/selenium/${SELENIUM_VER} \
-		"${DISTDIR}"/selenium-java-${SELENIUM_VER}.zip || die
-	cp "${DISTDIR}"/selenium-server-standalone-${SELENIUM_VER}.jar \
-		src/gwt/lib/selenium/${SELENIUM_VER}/ || die
-	cp "${DISTDIR}"/chromedriver-linux \
-		src/gwt/lib/selenium/chromedriver/${CHROMEDRIVER_VER}/ || die
-	cd dependencies/common || die
-	unpack packrat-${PACKRAT_VER}.tar.gz
-	unpack rmarkdown-${RMARKDOWN_VER}.tar.gz
-	unpack shinyapps-${SHINYAPPS_VER}.tar.gz
-	unpack rsconnect_${RSCONNECT_VER}.tar.gz
-	cp "${DISTDIR}"/rmarkdown-${RMARKDOWN_VER}.tar.gz \
-		. || die
-	cp "${DISTDIR}"/packrat-${PACKRAT_VER}.tar.gz \
-		. || die
-	cp "${DISTDIR}"/shinyapps-${SHINYAPPS_VER}.tar.gz \
-		. || die
-	cp "${DISTDIR}"/rsconnect_${RSCONNECT_VER}.tar.gz \
-		. || die
-}
-
-src_prepare() {
-	java-pkg-2_src_prepare
-
-	egit_clean
-
-	epatch "${PATCHES[@]}"
-
-	# Enable CMake to install our .service file for systemd usage
-	mkdir -vp "${S}/src/cpp/server/lib/systemd/system" || die
-	cp -v "${FILESDIR}/rstudio-server.service.in" "${S}/src/cpp/server/lib/systemd/system/" || die
-
-	# Adding -DDISTRO_SHARE=... to append-flags breaks cmake so using
-	# this sed hack for now. ~RMH
-	sed -i \
-		-e "s|DISTRO_SHARE|\"share/${PN}\"|g" \
-		src/cpp/server/ServerOptions.cpp \
-		src/cpp/session/SessionOptions.cpp || die
-
-	# use mathjax from system
-	ln -sf "${EPREFIX}"/usr/share/mathjax dependencies/common/mathjax-23 || die
-
-	# make sure icons and mime stuff are with prefix
-	sed -i \
-		-e "s:/usr:${EPREFIX}/usr:g" \
-		CMakeGlobals.txt src/cpp/desktop/CMakeLists.txt || die
-
-	# On Gentoo the rstudio-server configuration file is /etc/conf.d/rstudio-server.conf
-	sed -e "s@/etc/rstudio/rserver.conf@${EROOT}etc/conf.d/rstudio-server.conf@" \
-		-i src/cpp/server/ServerOptions.cpp \
-		|| die
-
-	# Set the rsession.conf file location for Gentoo prefix
-	sed -e "s@/etc/rstudio/rsession.conf@${EROOT}etc/rstudio/rsession.conf@" \
-		-i src/cpp/session/SessionOptions.cpp \
-		|| die
-
-	# dev-qt/qtsingleapplication-2.6.1_p20150629 does not provide a cmake module.
-	# It provides a library that has its version number appended to the end,
-	# which is difficult to handle in cmake, as find_library does not support
-	# searching for wildcard library names. So I find the library name from the
-	# qmake spec, and then sed this into the patched src/cpp/desktop/CMakeLists.txt.
-	rm -rf "${S}"/src/cpp/desktop/3rdparty || die
-	local s=$(grep '\-lQt$${QT_MAJOR_VERSION}Solutions_SingleApplication' \
-				   $(qt5_get_mkspecsdir)/features/qtsingleapplication.prf \
-					 | sed -e 's@\$\${QT_MAJOR_VERSION}@5@' \
-						   -e 's@LIBS \*= -l@@')
-	sed -e "s@Qt5Solutions_SingleApplication-2.6@${s}@g" \
-		-i "${S}"/src/cpp/desktop/CMakeLists.txt \
-		|| die
-
-	# Avoid some of the oracle-jdk-bin-1.8.0.60 sandbox violations F: mkdir S: deny
-	# P: /root/.oracle_jre_usage.
-	sed -e 's@\(\s*\)\(</classpath>\)@\1\2\n\1\<jvmarg value="-Duser.home=${env.T}"/>@g' \
-		-i "${S}"/src/gwt/build.xml \
-		|| die
-}
-
-src_configure() {
-	export RSTUDIO_VERSION_MAJOR=$(get_version_component_range 1)
-	export RSTUDIO_VERSION_MINOR=$(get_version_component_range 2)
-	export RSTUDIO_VERSION_PATCH=$(get_version_component_range 3)
-
-	local mycmakeargs=(
-		-DDISTRO_SHARE=share/${PN}
-		$(cmake-utils_use !dedicated RSTUDIO_INSTALL_FREEDESKTOP)
-		-DRSTUDIO_TARGET=$(usex dedicated "Server" "$(usex server "Development" "Desktop")")
-		-DQT_QMAKE_EXECUTABLE=$(qt5_get_bindir)/qmake
-		)
-
-	cmake-utils_src_configure
-}
-
-src_compile() {
-	# Avoid the rest of the oracle-jdk-bin-1.8.0.60 sandbox violations F: mkdir S: deny
-	# P: /root/.oracle_jre_usage.
-	export ANT_OPTS="-Duser.home=${T}"
-	cmake-utils_src_compile
-}
-
-src_install() {
-	export ANT_OPTS="-Duser.home=${T}"
-	cmake-utils_src_install
-	pax-mark m "${ED}usr/bin/rstudio"
-	doconfd "${FILESDIR}"/rstudio-server.conf
-	dodir /etc/rstudio
-	insinto /etc/rstudio
-	doins "${FILESDIR}"/rsession.conf
-	dosym /etc/conf.d/rstudio-server.conf /etc/rstudio/rserver.conf
-	if use dedicated || use server; then
-		dopamd src/cpp/server/extras/pam/rstudio
-		newinitd "${FILESDIR}"/rstudio-server.initd rstudio-server
-	fi
-}
-
-pkg_preinst() {
-	use dedicated || gnome2_icon_savelist
-	java-pkg-2_pkg_preinst
-}
-
-pkg_postinst() {
-	use dedicated || { fdo-mime_desktop_database_update
-		fdo-mime_mime_database_update
-		gnome2_icon_cache_update ;}
-
-	if use dedicated || use server; then
-		enewgroup rstudio-server
-		enewuser rstudio-server -1 -1 -1 rstudio-server
-	fi
-}
-
-pkg_postrm() {
-	use dedicated || { fdo-mime_desktop_database_update
-		fdo-mime_mime_database_update
-		gnome2_icon_cache_update ;}
-}

diff --git a/sci-mathematics/rstudio/rstudio-0.99.879.ebuild b/sci-mathematics/rstudio/rstudio-0.99.879.ebuild
deleted file mode 100644
index 6adb372e5cd..00000000000
--- a/sci-mathematics/rstudio/rstudio-0.99.879.ebuild
+++ /dev/null
@@ -1,249 +0,0 @@
-# Copyright 1999-2017 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-inherit eutils user cmake-utils gnome2-utils pam versionator fdo-mime java-pkg-2 pax-utils qmake-utils
-
-# TODO
-# * package gin and gwt
-# * use dict from tree, linguas
-# * do src_test (use junit from tree?)
-
-# update from scripts in dependencies/common
-# egrep '(GWT_SDK_VER=|GIN_VER=|SELENIUM_VER=|CHROMEDRIVER_VER=)' dependencies/common/install-gwt
-GWT_VER=2.7.0
-GIN_VER=1.5
-SELENIUM_VER=2.37.0
-CHROMEDRIVER_VER=2.7
-# grep 'PANDOC_VERSION=' dependencies/common/update-pandoc
-PANDOC_VER=1.13.1
-# ls dependencies/common/*.tar.gz
-PACKRAT_VER=0.98.1000
-RMARKDOWN_VER=0.98.1000
-SHINYAPPS_VER=0.98.1000
-RSCONNECT_VER=0.4.1.4_fcac892a69817febd7b655b189bf57193260cda0
-
-DESCRIPTION="IDE for the R language"
-HOMEPAGE="
-	http://www.rstudio.org
-	https://github.com/rstudio/rstudio/"
-SRC_URI="
-	https://github.com/rstudio/rstudio/archive/v${PV}.tar.gz -> ${P}.tar.gz
-	https://s3.amazonaws.com/rstudio-buildtools/gin-${GIN_VER}.zip
-	https://s3.amazonaws.com/rstudio-buildtools/gwt-${GWT_VER}.zip
-	https://s3.amazonaws.com/rstudio-buildtools/selenium-java-${SELENIUM_VER}.zip
-	https://s3.amazonaws.com/rstudio-buildtools/selenium-server-standalone-${SELENIUM_VER}.jar
-	https://s3.amazonaws.com/rstudio-buildtools/chromedriver-linux
-	https://s3.amazonaws.com/rstudio-dictionaries/core-dictionaries.zip
-	https://dev.gentoo.org/~gienah/distfiles/packrat-${PACKRAT_VER}.tar.gz
-	https://dev.gentoo.org/~gienah/distfiles/rmarkdown-${RMARKDOWN_VER}.tar.gz
-	https://dev.gentoo.org/~gienah/distfiles/shinyapps-${SHINYAPPS_VER}.tar.gz
-	https://dev.gentoo.org/~gienah/distfiles/rsconnect_${RSCONNECT_VER}.tar.gz
-"
-
-LICENSE="AGPL-3"
-SLOT="0"
-KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
-IUSE="dedicated server"
-
-QT_VER=5.4
-QT_SLOT=5
-RDEPEND="
-	app-text/pandoc
-	dev-haskell/pandoc-citeproc
-	>=dev-lang/R-2.11.1
-	>=dev-libs/boost-1.50:=
-	>=dev-libs/mathjax-2.3
-	dev-libs/openssl:0
-	sys-apps/util-linux
-	>=sys-devel/clang-3.5.0:*
-	sys-libs/zlib
-	>=virtual/jre-1.7:=
-	x11-libs/pango
-	!dedicated? (
-		>=dev-qt/qtcore-${QT_VER}:${QT_SLOT}
-		>=dev-qt/qtdeclarative-${QT_VER}:${QT_SLOT}
-		>=dev-qt/qtdbus-${QT_VER}:${QT_SLOT}
-		>=dev-qt/qtgui-${QT_VER}:${QT_SLOT}
-		>=dev-qt/qtnetwork-${QT_VER}:${QT_SLOT}
-		>=dev-qt/qtopengl-${QT_VER}:${QT_SLOT}
-		>=dev-qt/qtpositioning-${QT_VER}:${QT_SLOT}
-		>=dev-qt/qtprintsupport-${QT_VER}:${QT_SLOT}
-		>=dev-qt/qtsingleapplication-2.6.1_p20150629[X,qt5]
-		>=dev-qt/qtsensors-${QT_VER}:${QT_SLOT}
-		>=dev-qt/qtsql-${QT_VER}:${QT_SLOT}
-		>=dev-qt/qtsvg-${QT_VER}:${QT_SLOT}
-		>=dev-qt/qtwebkit-${QT_VER}:${QT_SLOT}
-		>=dev-qt/qtwidgets-${QT_VER}:${QT_SLOT}
-		>=dev-qt/qtxml-${QT_VER}:${QT_SLOT}
-		>=dev-qt/qtxmlpatterns-${QT_VER}:${QT_SLOT}
-		server? ( virtual/pam )
-	)
-	dedicated? ( virtual/pam )"
-DEPEND="${RDEPEND}
-	app-arch/unzip
-	dev-java/ant-core
-	>=virtual/jdk-1.7:=
-	virtual/pkgconfig"
-#	test? ( dev-java/junit:4 )
-
-PATCHES=(
-		"${FILESDIR}/${PN}-0.99.879-prefs.patch"
-		"${FILESDIR}/${PN}-0.99.879-paths.patch"
-		"${FILESDIR}/${PN}-0.99.879-clang-pandoc.patch"
-		"${FILESDIR}/${PN}-0.98.490-linker_flags.patch"
-		"${FILESDIR}/${PN}-0.98.1091-boost-1.57.patch"
-		"${FILESDIR}/${PN}-0.99.473-qtsingleapplication.patch"
-		"${FILESDIR}/${PN}-0.99.486-systemd.patch"
-)
-
-src_unpack() {
-	unpack ${P}.tar.gz gwt-${GWT_VER}.zip
-	cd "${S}" || die
-	mkdir -p src/gwt/lib/{gin,gwt} \
-		dependencies/common/dictionaries \
-		src/gwt/lib/selenium/${SELENIUM_VER} \
-		src/gwt/lib/selenium/chromedriver/${CHROMEDRIVER_VER} || die
-	mv ../gwt-${GWT_VER} src/gwt/lib/gwt/${GWT_VER} || die
-	unzip -qd src/gwt/lib/gin/${GIN_VER} \
-		"${DISTDIR}"/gin-${GIN_VER}.zip || die
-	unzip -qd dependencies/common/dictionaries \
-		"${DISTDIR}"/core-dictionaries.zip || die
-	unzip -qd src/gwt/lib/selenium/${SELENIUM_VER} \
-		"${DISTDIR}"/selenium-java-${SELENIUM_VER}.zip || die
-	cp "${DISTDIR}"/selenium-server-standalone-${SELENIUM_VER}.jar \
-		src/gwt/lib/selenium/${SELENIUM_VER}/ || die
-	cp "${DISTDIR}"/chromedriver-linux \
-		src/gwt/lib/selenium/chromedriver/${CHROMEDRIVER_VER}/ || die
-	cd dependencies/common || die
-	unpack packrat-${PACKRAT_VER}.tar.gz
-	unpack rmarkdown-${RMARKDOWN_VER}.tar.gz
-	unpack shinyapps-${SHINYAPPS_VER}.tar.gz
-	unpack rsconnect_${RSCONNECT_VER}.tar.gz
-	cp "${DISTDIR}"/rmarkdown-${RMARKDOWN_VER}.tar.gz \
-		. || die
-	cp "${DISTDIR}"/packrat-${PACKRAT_VER}.tar.gz \
-		. || die
-	cp "${DISTDIR}"/shinyapps-${SHINYAPPS_VER}.tar.gz \
-		. || die
-	cp "${DISTDIR}"/rsconnect_${RSCONNECT_VER}.tar.gz \
-		. || die
-}
-
-src_prepare() {
-	java-pkg-2_src_prepare
-
-	egit_clean
-
-	epatch "${PATCHES[@]}"
-
-	# Enable CMake to install our .service file for systemd usage
-	mkdir -vp "${S}/src/cpp/server/lib/systemd/system" || die
-	cp -v "${FILESDIR}/rstudio-server.service.in" "${S}/src/cpp/server/lib/systemd/system/" || die
-
-	# Adding -DDISTRO_SHARE=... to append-flags breaks cmake so using
-	# this sed hack for now. ~RMH
-	sed -i \
-		-e "s|DISTRO_SHARE|\"share/${PN}\"|g" \
-		src/cpp/server/ServerOptions.cpp \
-		src/cpp/session/SessionOptions.cpp || die
-
-	# use mathjax from system
-	ln -sf "${EPREFIX}"/usr/share/mathjax dependencies/common/mathjax-23 || die
-
-	# make sure icons and mime stuff are with prefix
-	sed -i \
-		-e "s:/usr:${EPREFIX}/usr:g" \
-		CMakeGlobals.txt src/cpp/desktop/CMakeLists.txt || die
-
-	# On Gentoo the rstudio-server configuration file is /etc/conf.d/rstudio-server.conf
-	sed -e "s@/etc/rstudio/rserver.conf@${EROOT}etc/conf.d/rstudio-server.conf@" \
-		-i src/cpp/server/ServerOptions.cpp \
-		|| die
-
-	# Set the rsession.conf file location for Gentoo prefix
-	sed -e "s@/etc/rstudio/rsession.conf@${EROOT}etc/rstudio/rsession.conf@" \
-		-i src/cpp/session/SessionOptions.cpp \
-		|| die
-
-	# dev-qt/qtsingleapplication-2.6.1_p20150629 does not provide a cmake module.
-	# It provides a library that has its version number appended to the end,
-	# which is difficult to handle in cmake, as find_library does not support
-	# searching for wildcard library names. So I find the library name from the
-	# qmake spec, and then sed this into the patched src/cpp/desktop/CMakeLists.txt.
-	rm -rf "${S}"/src/cpp/desktop/3rdparty || die
-	local s=$(grep '\-lQt$${QT_MAJOR_VERSION}Solutions_SingleApplication' \
-				   $(qt5_get_mkspecsdir)/features/qtsingleapplication.prf \
-					 | sed -e 's@\$\${QT_MAJOR_VERSION}@5@' \
-						   -e 's@LIBS \*= -l@@')
-	sed -e "s@Qt5Solutions_SingleApplication-2.6@${s}@g" \
-		-i "${S}"/src/cpp/desktop/CMakeLists.txt \
-		|| die
-
-	# The git commit for tag v0.99.879
-	sed -e 's@git ARGS rev-parse HEAD@echo ARGS 9ac918338d6f9d6dd25807d6d746b470f1cfcf6d@'\
-		-i "${S}"/CMakeLists.txt \
-		"${S}"/CMakeGlobals.txt \
-		|| die
-}
-
-src_configure() {
-	export RSTUDIO_VERSION_MAJOR=$(get_version_component_range 1)
-	export RSTUDIO_VERSION_MINOR=$(get_version_component_range 2)
-	export RSTUDIO_VERSION_PATCH=$(get_version_component_range 3)
-
-	local mycmakeargs=(
-		-DDISTRO_SHARE=share/${PN}
-		$(cmake-utils_use !dedicated RSTUDIO_INSTALL_FREEDESKTOP)
-		-DRSTUDIO_TARGET=$(usex dedicated "Server" "$(usex server "Development" "Desktop")")
-		-DQT_QMAKE_EXECUTABLE=$(qt5_get_bindir)/qmake
-		-DRSTUDIO_VERIFY_R_VERSION=FALSE
-		)
-
-	cmake-utils_src_configure
-}
-
-src_compile() {
-	# Avoid the rest of the oracle-jdk-bin-1.8.0.60 sandbox violations F: mkdir S: deny
-	# P: /root/.oracle_jre_usage.
-	export ANT_OPTS="-Duser.home=${T}"
-	cmake-utils_src_compile
-}
-
-src_install() {
-	export ANT_OPTS="-Duser.home=${T}"
-	cmake-utils_src_install
-	pax-mark m "${ED}usr/bin/rstudio"
-	doconfd "${FILESDIR}"/rstudio-server.conf
-	dodir /etc/rstudio
-	insinto /etc/rstudio
-	doins "${FILESDIR}"/rsession.conf
-	dosym /etc/conf.d/rstudio-server.conf /etc/rstudio/rserver.conf
-	if use dedicated || use server; then
-		dopamd src/cpp/server/extras/pam/rstudio
-		newinitd "${FILESDIR}"/rstudio-server.initd rstudio-server
-	fi
-}
-
-pkg_preinst() {
-	use dedicated || gnome2_icon_savelist
-	java-pkg-2_pkg_preinst
-}
-
-pkg_postinst() {
-	use dedicated || { fdo-mime_desktop_database_update
-		fdo-mime_mime_database_update
-		gnome2_icon_cache_update ;}
-
-	if use dedicated || use server; then
-		enewgroup rstudio-server
-		enewuser rstudio-server -1 -1 -1 rstudio-server
-	fi
-}
-
-pkg_postrm() {
-	use dedicated || { fdo-mime_desktop_database_update
-		fdo-mime_mime_database_update
-		gnome2_icon_cache_update ;}
-}

diff --git a/sci-mathematics/rstudio/rstudio-0.99.893.ebuild b/sci-mathematics/rstudio/rstudio-0.99.893.ebuild
deleted file mode 100644
index c3bc93830dd..00000000000
--- a/sci-mathematics/rstudio/rstudio-0.99.893.ebuild
+++ /dev/null
@@ -1,249 +0,0 @@
-# Copyright 1999-2017 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-inherit eutils user cmake-utils gnome2-utils pam versionator fdo-mime java-pkg-2 pax-utils qmake-utils
-
-# TODO
-# * package gin and gwt
-# * use dict from tree, linguas
-# * do src_test (use junit from tree?)
-
-# update from scripts in dependencies/common
-# egrep '(GWT_SDK_VER=|GIN_VER=|SELENIUM_VER=|CHROMEDRIVER_VER=)' dependencies/common/install-gwt
-GWT_VER=2.7.0
-GIN_VER=1.5
-SELENIUM_VER=2.37.0
-CHROMEDRIVER_VER=2.7
-# grep 'PANDOC_VERSION=' dependencies/common/update-pandoc
-PANDOC_VER=1.13.1
-# ls dependencies/common/*.tar.gz
-PACKRAT_VER=0.98.1000
-RMARKDOWN_VER=0.98.1000
-SHINYAPPS_VER=0.98.1000
-RSCONNECT_VER=0.4.1.4_fcac892a69817febd7b655b189bf57193260cda0
-
-DESCRIPTION="IDE for the R language"
-HOMEPAGE="
-	http://www.rstudio.org
-	https://github.com/rstudio/rstudio/"
-SRC_URI="
-	https://github.com/rstudio/rstudio/archive/v${PV}.tar.gz -> ${P}.tar.gz
-	https://s3.amazonaws.com/rstudio-buildtools/gin-${GIN_VER}.zip
-	https://s3.amazonaws.com/rstudio-buildtools/gwt-${GWT_VER}.zip
-	https://s3.amazonaws.com/rstudio-buildtools/selenium-java-${SELENIUM_VER}.zip
-	https://s3.amazonaws.com/rstudio-buildtools/selenium-server-standalone-${SELENIUM_VER}.jar
-	https://s3.amazonaws.com/rstudio-buildtools/chromedriver-linux
-	https://s3.amazonaws.com/rstudio-dictionaries/core-dictionaries.zip
-	https://dev.gentoo.org/~gienah/distfiles/packrat-${PACKRAT_VER}.tar.gz
-	https://dev.gentoo.org/~gienah/distfiles/rmarkdown-${RMARKDOWN_VER}.tar.gz
-	https://dev.gentoo.org/~gienah/distfiles/shinyapps-${SHINYAPPS_VER}.tar.gz
-	https://dev.gentoo.org/~gienah/distfiles/rsconnect_${RSCONNECT_VER}.tar.gz
-"
-
-LICENSE="AGPL-3"
-SLOT="0"
-KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
-IUSE="dedicated server"
-
-QT_VER=5.4
-QT_SLOT=5
-RDEPEND="
-	app-text/pandoc
-	dev-haskell/pandoc-citeproc
-	>=dev-lang/R-2.11.1
-	>=dev-libs/boost-1.50:=
-	>=dev-libs/mathjax-2.3
-	dev-libs/openssl:0
-	sys-apps/util-linux
-	>=sys-devel/clang-3.5.0:*
-	sys-libs/zlib
-	>=virtual/jre-1.7:=
-	x11-libs/pango
-	!dedicated? (
-		>=dev-qt/qtcore-${QT_VER}:${QT_SLOT}
-		>=dev-qt/qtdeclarative-${QT_VER}:${QT_SLOT}
-		>=dev-qt/qtdbus-${QT_VER}:${QT_SLOT}
-		>=dev-qt/qtgui-${QT_VER}:${QT_SLOT}
-		>=dev-qt/qtnetwork-${QT_VER}:${QT_SLOT}
-		>=dev-qt/qtopengl-${QT_VER}:${QT_SLOT}
-		>=dev-qt/qtpositioning-${QT_VER}:${QT_SLOT}
-		>=dev-qt/qtprintsupport-${QT_VER}:${QT_SLOT}
-		>=dev-qt/qtsingleapplication-2.6.1_p20150629[X,qt5]
-		>=dev-qt/qtsensors-${QT_VER}:${QT_SLOT}
-		>=dev-qt/qtsql-${QT_VER}:${QT_SLOT}
-		>=dev-qt/qtsvg-${QT_VER}:${QT_SLOT}
-		>=dev-qt/qtwebkit-${QT_VER}:${QT_SLOT}
-		>=dev-qt/qtwidgets-${QT_VER}:${QT_SLOT}
-		>=dev-qt/qtxml-${QT_VER}:${QT_SLOT}
-		>=dev-qt/qtxmlpatterns-${QT_VER}:${QT_SLOT}
-		server? ( virtual/pam )
-	)
-	dedicated? ( virtual/pam )"
-DEPEND="${RDEPEND}
-	app-arch/unzip
-	dev-java/ant-core
-	>=virtual/jdk-1.7:=
-	virtual/pkgconfig"
-#	test? ( dev-java/junit:4 )
-
-PATCHES=(
-		"${FILESDIR}/${PN}-0.99.879-prefs.patch"
-		"${FILESDIR}/${PN}-0.99.879-paths.patch"
-		"${FILESDIR}/${PN}-0.99.879-clang-pandoc.patch"
-		"${FILESDIR}/${PN}-0.98.490-linker_flags.patch"
-		"${FILESDIR}/${PN}-0.98.1091-boost-1.57.patch"
-		"${FILESDIR}/${PN}-0.99.473-qtsingleapplication.patch"
-		"${FILESDIR}/${PN}-0.99.486-systemd.patch"
-)
-
-src_unpack() {
-	unpack ${P}.tar.gz gwt-${GWT_VER}.zip
-	cd "${S}" || die
-	mkdir -p src/gwt/lib/{gin,gwt} \
-		dependencies/common/dictionaries \
-		src/gwt/lib/selenium/${SELENIUM_VER} \
-		src/gwt/lib/selenium/chromedriver/${CHROMEDRIVER_VER} || die
-	mv ../gwt-${GWT_VER} src/gwt/lib/gwt/${GWT_VER} || die
-	unzip -qd src/gwt/lib/gin/${GIN_VER} \
-		"${DISTDIR}"/gin-${GIN_VER}.zip || die
-	unzip -qd dependencies/common/dictionaries \
-		"${DISTDIR}"/core-dictionaries.zip || die
-	unzip -qd src/gwt/lib/selenium/${SELENIUM_VER} \
-		"${DISTDIR}"/selenium-java-${SELENIUM_VER}.zip || die
-	cp "${DISTDIR}"/selenium-server-standalone-${SELENIUM_VER}.jar \
-		src/gwt/lib/selenium/${SELENIUM_VER}/ || die
-	cp "${DISTDIR}"/chromedriver-linux \
-		src/gwt/lib/selenium/chromedriver/${CHROMEDRIVER_VER}/ || die
-	cd dependencies/common || die
-	unpack packrat-${PACKRAT_VER}.tar.gz
-	unpack rmarkdown-${RMARKDOWN_VER}.tar.gz
-	unpack shinyapps-${SHINYAPPS_VER}.tar.gz
-	unpack rsconnect_${RSCONNECT_VER}.tar.gz
-	cp "${DISTDIR}"/rmarkdown-${RMARKDOWN_VER}.tar.gz \
-		. || die
-	cp "${DISTDIR}"/packrat-${PACKRAT_VER}.tar.gz \
-		. || die
-	cp "${DISTDIR}"/shinyapps-${SHINYAPPS_VER}.tar.gz \
-		. || die
-	cp "${DISTDIR}"/rsconnect_${RSCONNECT_VER}.tar.gz \
-		. || die
-}
-
-src_prepare() {
-	java-pkg-2_src_prepare
-
-	egit_clean
-
-	epatch "${PATCHES[@]}"
-
-	# Enable CMake to install our .service file for systemd usage
-	mkdir -vp "${S}/src/cpp/server/lib/systemd/system" || die
-	cp -v "${FILESDIR}/rstudio-server.service.in" "${S}/src/cpp/server/lib/systemd/system/" || die
-
-	# Adding -DDISTRO_SHARE=... to append-flags breaks cmake so using
-	# this sed hack for now. ~RMH
-	sed -i \
-		-e "s|DISTRO_SHARE|\"share/${PN}\"|g" \
-		src/cpp/server/ServerOptions.cpp \
-		src/cpp/session/SessionOptions.cpp || die
-
-	# use mathjax from system
-	ln -sf "${EPREFIX}"/usr/share/mathjax dependencies/common/mathjax-23 || die
-
-	# make sure icons and mime stuff are with prefix
-	sed -i \
-		-e "s:/usr:${EPREFIX}/usr:g" \
-		CMakeGlobals.txt src/cpp/desktop/CMakeLists.txt || die
-
-	# On Gentoo the rstudio-server configuration file is /etc/conf.d/rstudio-server.conf
-	sed -e "s@/etc/rstudio/rserver.conf@${EROOT}etc/conf.d/rstudio-server.conf@" \
-		-i src/cpp/server/ServerOptions.cpp \
-		|| die
-
-	# Set the rsession.conf file location for Gentoo prefix
-	sed -e "s@/etc/rstudio/rsession.conf@${EROOT}etc/rstudio/rsession.conf@" \
-		-i src/cpp/session/SessionOptions.cpp \
-		|| die
-
-	# dev-qt/qtsingleapplication-2.6.1_p20150629 does not provide a cmake module.
-	# It provides a library that has its version number appended to the end,
-	# which is difficult to handle in cmake, as find_library does not support
-	# searching for wildcard library names. So I find the library name from the
-	# qmake spec, and then sed this into the patched src/cpp/desktop/CMakeLists.txt.
-	rm -rf "${S}"/src/cpp/desktop/3rdparty || die
-	local s=$(grep '\-lQt$${QT_MAJOR_VERSION}Solutions_SingleApplication' \
-				   $(qt5_get_mkspecsdir)/features/qtsingleapplication.prf \
-					 | sed -e 's@\$\${QT_MAJOR_VERSION}@5@' \
-						   -e 's@LIBS \*= -l@@')
-	sed -e "s@Qt5Solutions_SingleApplication-2.6@${s}@g" \
-		-i "${S}"/src/cpp/desktop/CMakeLists.txt \
-		|| die
-
-	# The git commit for tag v0.99.893
-	sed -e 's@git ARGS rev-parse HEAD@echo ARGS 7510856081e5b1b577bcc230fc2c8ac62eafa62e@'\
-		-i "${S}"/CMakeLists.txt \
-		"${S}"/CMakeGlobals.txt \
-		|| die
-}
-
-src_configure() {
-	export RSTUDIO_VERSION_MAJOR=$(get_version_component_range 1)
-	export RSTUDIO_VERSION_MINOR=$(get_version_component_range 2)
-	export RSTUDIO_VERSION_PATCH=$(get_version_component_range 3)
-
-	local mycmakeargs=(
-		-DDISTRO_SHARE=share/${PN}
-		$(cmake-utils_use !dedicated RSTUDIO_INSTALL_FREEDESKTOP)
-		-DRSTUDIO_TARGET=$(usex dedicated "Server" "$(usex server "Development" "Desktop")")
-		-DQT_QMAKE_EXECUTABLE=$(qt5_get_bindir)/qmake
-		-DRSTUDIO_VERIFY_R_VERSION=FALSE
-		)
-
-	cmake-utils_src_configure
-}
-
-src_compile() {
-	# Avoid the rest of the oracle-jdk-bin-1.8.0.60 sandbox violations F: mkdir S: deny
-	# P: /root/.oracle_jre_usage.
-	export ANT_OPTS="-Duser.home=${T}"
-	cmake-utils_src_compile
-}
-
-src_install() {
-	export ANT_OPTS="-Duser.home=${T}"
-	cmake-utils_src_install
-	pax-mark m "${ED}usr/bin/rstudio"
-	doconfd "${FILESDIR}"/rstudio-server.conf
-	dodir /etc/rstudio
-	insinto /etc/rstudio
-	doins "${FILESDIR}"/rsession.conf
-	dosym /etc/conf.d/rstudio-server.conf /etc/rstudio/rserver.conf
-	if use dedicated || use server; then
-		dopamd src/cpp/server/extras/pam/rstudio
-		newinitd "${FILESDIR}"/rstudio-server.initd rstudio-server
-	fi
-}
-
-pkg_preinst() {
-	use dedicated || gnome2_icon_savelist
-	java-pkg-2_pkg_preinst
-}
-
-pkg_postinst() {
-	use dedicated || { fdo-mime_desktop_database_update
-		fdo-mime_mime_database_update
-		gnome2_icon_cache_update ;}
-
-	if use dedicated || use server; then
-		enewgroup rstudio-server
-		enewuser rstudio-server -1 -1 -1 rstudio-server
-	fi
-}
-
-pkg_postrm() {
-	use dedicated || { fdo-mime_desktop_database_update
-		fdo-mime_mime_database_update
-		gnome2_icon_cache_update ;}
-}

diff --git a/sci-mathematics/rstudio/rstudio-0.99.896.ebuild b/sci-mathematics/rstudio/rstudio-0.99.896.ebuild
deleted file mode 100644
index 134838bcf65..00000000000
--- a/sci-mathematics/rstudio/rstudio-0.99.896.ebuild
+++ /dev/null
@@ -1,249 +0,0 @@
-# Copyright 1999-2017 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-inherit eutils user cmake-utils gnome2-utils pam versionator fdo-mime java-pkg-2 pax-utils qmake-utils
-
-# TODO
-# * package gin and gwt
-# * use dict from tree, linguas
-# * do src_test (use junit from tree?)
-
-# update from scripts in dependencies/common
-# egrep '(GWT_SDK_VER=|GIN_VER=|SELENIUM_VER=|CHROMEDRIVER_VER=)' dependencies/common/install-gwt
-GWT_VER=2.7.0
-GIN_VER=1.5
-SELENIUM_VER=2.37.0
-CHROMEDRIVER_VER=2.7
-# grep 'PANDOC_VERSION=' dependencies/common/update-pandoc
-PANDOC_VER=1.13.1
-# ls dependencies/common/*.tar.gz
-PACKRAT_VER=0.98.1000
-RMARKDOWN_VER=0.98.1000
-SHINYAPPS_VER=0.98.1000
-RSCONNECT_VER=0.4.1.4_fcac892a69817febd7b655b189bf57193260cda0
-
-DESCRIPTION="IDE for the R language"
-HOMEPAGE="
-	http://www.rstudio.org
-	https://github.com/rstudio/rstudio/"
-SRC_URI="
-	https://github.com/rstudio/rstudio/archive/v${PV}.tar.gz -> ${P}.tar.gz
-	https://s3.amazonaws.com/rstudio-buildtools/gin-${GIN_VER}.zip
-	https://s3.amazonaws.com/rstudio-buildtools/gwt-${GWT_VER}.zip
-	https://s3.amazonaws.com/rstudio-buildtools/selenium-java-${SELENIUM_VER}.zip
-	https://s3.amazonaws.com/rstudio-buildtools/selenium-server-standalone-${SELENIUM_VER}.jar
-	https://s3.amazonaws.com/rstudio-buildtools/chromedriver-linux
-	https://s3.amazonaws.com/rstudio-dictionaries/core-dictionaries.zip
-	https://dev.gentoo.org/~gienah/distfiles/packrat-${PACKRAT_VER}.tar.gz
-	https://dev.gentoo.org/~gienah/distfiles/rmarkdown-${RMARKDOWN_VER}.tar.gz
-	https://dev.gentoo.org/~gienah/distfiles/shinyapps-${SHINYAPPS_VER}.tar.gz
-	https://dev.gentoo.org/~gienah/distfiles/rsconnect_${RSCONNECT_VER}.tar.gz
-"
-
-LICENSE="AGPL-3"
-SLOT="0"
-KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
-IUSE="dedicated server"
-
-QT_VER=5.4
-QT_SLOT=5
-RDEPEND="
-	app-text/pandoc
-	dev-haskell/pandoc-citeproc
-	>=dev-lang/R-2.11.1
-	>=dev-libs/boost-1.50:=
-	>=dev-libs/mathjax-2.3
-	dev-libs/openssl:0
-	sys-apps/util-linux
-	>=sys-devel/clang-3.5.0:*
-	sys-libs/zlib
-	>=virtual/jre-1.7:=
-	x11-libs/pango
-	!dedicated? (
-		>=dev-qt/qtcore-${QT_VER}:${QT_SLOT}
-		>=dev-qt/qtdeclarative-${QT_VER}:${QT_SLOT}
-		>=dev-qt/qtdbus-${QT_VER}:${QT_SLOT}
-		>=dev-qt/qtgui-${QT_VER}:${QT_SLOT}
-		>=dev-qt/qtnetwork-${QT_VER}:${QT_SLOT}
-		>=dev-qt/qtopengl-${QT_VER}:${QT_SLOT}
-		>=dev-qt/qtpositioning-${QT_VER}:${QT_SLOT}
-		>=dev-qt/qtprintsupport-${QT_VER}:${QT_SLOT}
-		>=dev-qt/qtsingleapplication-2.6.1_p20150629[X,qt5]
-		>=dev-qt/qtsensors-${QT_VER}:${QT_SLOT}
-		>=dev-qt/qtsql-${QT_VER}:${QT_SLOT}
-		>=dev-qt/qtsvg-${QT_VER}:${QT_SLOT}
-		>=dev-qt/qtwebkit-${QT_VER}:${QT_SLOT}
-		>=dev-qt/qtwidgets-${QT_VER}:${QT_SLOT}
-		>=dev-qt/qtxml-${QT_VER}:${QT_SLOT}
-		>=dev-qt/qtxmlpatterns-${QT_VER}:${QT_SLOT}
-		server? ( virtual/pam )
-	)
-	dedicated? ( virtual/pam )"
-DEPEND="${RDEPEND}
-	app-arch/unzip
-	dev-java/ant-core
-	>=virtual/jdk-1.7:=
-	virtual/pkgconfig"
-#	test? ( dev-java/junit:4 )
-
-PATCHES=(
-		"${FILESDIR}/${PN}-0.99.879-prefs.patch"
-		"${FILESDIR}/${PN}-0.99.879-paths.patch"
-		"${FILESDIR}/${PN}-0.99.879-clang-pandoc.patch"
-		"${FILESDIR}/${PN}-0.98.490-linker_flags.patch"
-		"${FILESDIR}/${PN}-0.98.1091-boost-1.57.patch"
-		"${FILESDIR}/${PN}-0.99.473-qtsingleapplication.patch"
-		"${FILESDIR}/${PN}-0.99.486-systemd.patch"
-)
-
-src_unpack() {
-	unpack ${P}.tar.gz gwt-${GWT_VER}.zip
-	cd "${S}" || die
-	mkdir -p src/gwt/lib/{gin,gwt} \
-		dependencies/common/dictionaries \
-		src/gwt/lib/selenium/${SELENIUM_VER} \
-		src/gwt/lib/selenium/chromedriver/${CHROMEDRIVER_VER} || die
-	mv ../gwt-${GWT_VER} src/gwt/lib/gwt/${GWT_VER} || die
-	unzip -qd src/gwt/lib/gin/${GIN_VER} \
-		"${DISTDIR}"/gin-${GIN_VER}.zip || die
-	unzip -qd dependencies/common/dictionaries \
-		"${DISTDIR}"/core-dictionaries.zip || die
-	unzip -qd src/gwt/lib/selenium/${SELENIUM_VER} \
-		"${DISTDIR}"/selenium-java-${SELENIUM_VER}.zip || die
-	cp "${DISTDIR}"/selenium-server-standalone-${SELENIUM_VER}.jar \
-		src/gwt/lib/selenium/${SELENIUM_VER}/ || die
-	cp "${DISTDIR}"/chromedriver-linux \
-		src/gwt/lib/selenium/chromedriver/${CHROMEDRIVER_VER}/ || die
-	cd dependencies/common || die
-	unpack packrat-${PACKRAT_VER}.tar.gz
-	unpack rmarkdown-${RMARKDOWN_VER}.tar.gz
-	unpack shinyapps-${SHINYAPPS_VER}.tar.gz
-	unpack rsconnect_${RSCONNECT_VER}.tar.gz
-	cp "${DISTDIR}"/rmarkdown-${RMARKDOWN_VER}.tar.gz \
-		. || die
-	cp "${DISTDIR}"/packrat-${PACKRAT_VER}.tar.gz \
-		. || die
-	cp "${DISTDIR}"/shinyapps-${SHINYAPPS_VER}.tar.gz \
-		. || die
-	cp "${DISTDIR}"/rsconnect_${RSCONNECT_VER}.tar.gz \
-		. || die
-}
-
-src_prepare() {
-	java-pkg-2_src_prepare
-
-	egit_clean
-
-	epatch "${PATCHES[@]}"
-
-	# Enable CMake to install our .service file for systemd usage
-	mkdir -vp "${S}/src/cpp/server/lib/systemd/system" || die
-	cp -v "${FILESDIR}/rstudio-server.service.in" "${S}/src/cpp/server/lib/systemd/system/" || die
-
-	# Adding -DDISTRO_SHARE=... to append-flags breaks cmake so using
-	# this sed hack for now. ~RMH
-	sed -i \
-		-e "s|DISTRO_SHARE|\"share/${PN}\"|g" \
-		src/cpp/server/ServerOptions.cpp \
-		src/cpp/session/SessionOptions.cpp || die
-
-	# use mathjax from system
-	ln -sf "${EPREFIX}"/usr/share/mathjax dependencies/common/mathjax-23 || die
-
-	# make sure icons and mime stuff are with prefix
-	sed -i \
-		-e "s:/usr:${EPREFIX}/usr:g" \
-		CMakeGlobals.txt src/cpp/desktop/CMakeLists.txt || die
-
-	# On Gentoo the rstudio-server configuration file is /etc/conf.d/rstudio-server.conf
-	sed -e "s@/etc/rstudio/rserver.conf@${EROOT}etc/conf.d/rstudio-server.conf@" \
-		-i src/cpp/server/ServerOptions.cpp \
-		|| die
-
-	# Set the rsession.conf file location for Gentoo prefix
-	sed -e "s@/etc/rstudio/rsession.conf@${EROOT}etc/rstudio/rsession.conf@" \
-		-i src/cpp/session/SessionOptions.cpp \
-		|| die
-
-	# dev-qt/qtsingleapplication-2.6.1_p20150629 does not provide a cmake module.
-	# It provides a library that has its version number appended to the end,
-	# which is difficult to handle in cmake, as find_library does not support
-	# searching for wildcard library names. So I find the library name from the
-	# qmake spec, and then sed this into the patched src/cpp/desktop/CMakeLists.txt.
-	rm -rf "${S}"/src/cpp/desktop/3rdparty || die
-	local s=$(grep '\-lQt$${QT_MAJOR_VERSION}Solutions_SingleApplication' \
-				   $(qt5_get_mkspecsdir)/features/qtsingleapplication.prf \
-					 | sed -e 's@\$\${QT_MAJOR_VERSION}@5@' \
-						   -e 's@LIBS \*= -l@@')
-	sed -e "s@Qt5Solutions_SingleApplication-2.6@${s}@g" \
-		-i "${S}"/src/cpp/desktop/CMakeLists.txt \
-		|| die
-
-	# The git commit for tag v0.99.896
-	sed -e 's@git ARGS rev-parse HEAD@echo ARGS 5dbc604635bb296bc41fb7fa21e56f7195fbe1ca@'\
-		-i "${S}"/CMakeLists.txt \
-		"${S}"/CMakeGlobals.txt \
-		|| die
-}
-
-src_configure() {
-	export RSTUDIO_VERSION_MAJOR=$(get_version_component_range 1)
-	export RSTUDIO_VERSION_MINOR=$(get_version_component_range 2)
-	export RSTUDIO_VERSION_PATCH=$(get_version_component_range 3)
-
-	local mycmakeargs=(
-		-DDISTRO_SHARE=share/${PN}
-		$(cmake-utils_use !dedicated RSTUDIO_INSTALL_FREEDESKTOP)
-		-DRSTUDIO_TARGET=$(usex dedicated "Server" "$(usex server "Development" "Desktop")")
-		-DQT_QMAKE_EXECUTABLE=$(qt5_get_bindir)/qmake
-		-DRSTUDIO_VERIFY_R_VERSION=FALSE
-		)
-
-	cmake-utils_src_configure
-}
-
-src_compile() {
-	# Avoid the rest of the oracle-jdk-bin-1.8.0.60 sandbox violations F: mkdir S: deny
-	# P: /root/.oracle_jre_usage.
-	export ANT_OPTS="-Duser.home=${T}"
-	cmake-utils_src_compile
-}
-
-src_install() {
-	export ANT_OPTS="-Duser.home=${T}"
-	cmake-utils_src_install
-	pax-mark m "${ED}usr/bin/rstudio"
-	doconfd "${FILESDIR}"/rstudio-server.conf
-	dodir /etc/rstudio
-	insinto /etc/rstudio
-	doins "${FILESDIR}"/rsession.conf
-	dosym /etc/conf.d/rstudio-server.conf /etc/rstudio/rserver.conf
-	if use dedicated || use server; then
-		dopamd src/cpp/server/extras/pam/rstudio
-		newinitd "${FILESDIR}"/rstudio-server.initd rstudio-server
-	fi
-}
-
-pkg_preinst() {
-	use dedicated || gnome2_icon_savelist
-	java-pkg-2_pkg_preinst
-}
-
-pkg_postinst() {
-	use dedicated || { fdo-mime_desktop_database_update
-		fdo-mime_mime_database_update
-		gnome2_icon_cache_update ;}
-
-	if use dedicated || use server; then
-		enewgroup rstudio-server
-		enewuser rstudio-server -1 -1 -1 rstudio-server
-	fi
-}
-
-pkg_postrm() {
-	use dedicated || { fdo-mime_desktop_database_update
-		fdo-mime_mime_database_update
-		gnome2_icon_cache_update ;}
-}

diff --git a/sci-mathematics/rstudio/rstudio-0.99.902.ebuild b/sci-mathematics/rstudio/rstudio-0.99.902.ebuild
deleted file mode 100644
index bd0e219d50f..00000000000
--- a/sci-mathematics/rstudio/rstudio-0.99.902.ebuild
+++ /dev/null
@@ -1,249 +0,0 @@
-# Copyright 1999-2017 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-inherit eutils user cmake-utils gnome2-utils pam versionator fdo-mime java-pkg-2 pax-utils qmake-utils
-
-# TODO
-# * package gin and gwt
-# * use dict from tree, linguas
-# * do src_test (use junit from tree?)
-
-# update from scripts in dependencies/common
-# egrep '(GWT_SDK_VER=|GIN_VER=|SELENIUM_VER=|CHROMEDRIVER_VER=)' dependencies/common/install-gwt
-GWT_VER=2.7.0
-GIN_VER=1.5
-SELENIUM_VER=2.37.0
-CHROMEDRIVER_VER=2.7
-# grep 'PANDOC_VERSION=' dependencies/common/update-pandoc
-PANDOC_VER=1.13.1
-# ls dependencies/common/*.tar.gz
-PACKRAT_VER=0.98.1000
-RMARKDOWN_VER=0.98.1000
-SHINYAPPS_VER=0.98.1000
-RSCONNECT_VER=0.4.1.4_fcac892a69817febd7b655b189bf57193260cda0
-
-DESCRIPTION="IDE for the R language"
-HOMEPAGE="
-	http://www.rstudio.org
-	https://github.com/rstudio/rstudio/"
-SRC_URI="
-	https://github.com/rstudio/rstudio/archive/v${PV}.tar.gz -> ${P}.tar.gz
-	https://s3.amazonaws.com/rstudio-buildtools/gin-${GIN_VER}.zip
-	https://s3.amazonaws.com/rstudio-buildtools/gwt-${GWT_VER}.zip
-	https://s3.amazonaws.com/rstudio-buildtools/selenium-java-${SELENIUM_VER}.zip
-	https://s3.amazonaws.com/rstudio-buildtools/selenium-server-standalone-${SELENIUM_VER}.jar
-	https://s3.amazonaws.com/rstudio-buildtools/chromedriver-linux
-	https://s3.amazonaws.com/rstudio-dictionaries/core-dictionaries.zip
-	https://dev.gentoo.org/~gienah/distfiles/packrat-${PACKRAT_VER}.tar.gz
-	https://dev.gentoo.org/~gienah/distfiles/rmarkdown-${RMARKDOWN_VER}.tar.gz
-	https://dev.gentoo.org/~gienah/distfiles/shinyapps-${SHINYAPPS_VER}.tar.gz
-	https://dev.gentoo.org/~gienah/distfiles/rsconnect_${RSCONNECT_VER}.tar.gz
-"
-
-LICENSE="AGPL-3"
-SLOT="0"
-KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
-IUSE="dedicated server"
-
-QT_VER=5.4
-QT_SLOT=5
-RDEPEND="
-	app-text/pandoc
-	dev-haskell/pandoc-citeproc
-	>=dev-lang/R-2.11.1
-	>=dev-libs/boost-1.50:=
-	>=dev-libs/mathjax-2.3
-	dev-libs/openssl:0
-	sys-apps/util-linux
-	>=sys-devel/clang-3.5.0:*
-	sys-libs/zlib
-	>=virtual/jre-1.7:=
-	x11-libs/pango
-	!dedicated? (
-		>=dev-qt/qtcore-${QT_VER}:${QT_SLOT}
-		>=dev-qt/qtdeclarative-${QT_VER}:${QT_SLOT}
-		>=dev-qt/qtdbus-${QT_VER}:${QT_SLOT}
-		>=dev-qt/qtgui-${QT_VER}:${QT_SLOT}
-		>=dev-qt/qtnetwork-${QT_VER}:${QT_SLOT}
-		>=dev-qt/qtopengl-${QT_VER}:${QT_SLOT}
-		>=dev-qt/qtpositioning-${QT_VER}:${QT_SLOT}
-		>=dev-qt/qtprintsupport-${QT_VER}:${QT_SLOT}
-		>=dev-qt/qtsingleapplication-2.6.1_p20150629[X,qt5]
-		>=dev-qt/qtsensors-${QT_VER}:${QT_SLOT}
-		>=dev-qt/qtsql-${QT_VER}:${QT_SLOT}
-		>=dev-qt/qtsvg-${QT_VER}:${QT_SLOT}
-		>=dev-qt/qtwebkit-${QT_VER}:${QT_SLOT}
-		>=dev-qt/qtwidgets-${QT_VER}:${QT_SLOT}
-		>=dev-qt/qtxml-${QT_VER}:${QT_SLOT}
-		>=dev-qt/qtxmlpatterns-${QT_VER}:${QT_SLOT}
-		server? ( virtual/pam )
-	)
-	dedicated? ( virtual/pam )"
-DEPEND="${RDEPEND}
-	app-arch/unzip
-	dev-java/ant-core
-	>=virtual/jdk-1.7:=
-	virtual/pkgconfig"
-#	test? ( dev-java/junit:4 )
-
-PATCHES=(
-		"${FILESDIR}/${PN}-0.99.879-prefs.patch"
-		"${FILESDIR}/${PN}-0.99.879-paths.patch"
-		"${FILESDIR}/${PN}-0.99.879-clang-pandoc.patch"
-		"${FILESDIR}/${PN}-0.98.490-linker_flags.patch"
-		"${FILESDIR}/${PN}-0.98.1091-boost-1.57.patch"
-		"${FILESDIR}/${PN}-0.99.473-qtsingleapplication.patch"
-		"${FILESDIR}/${PN}-0.99.486-systemd.patch"
-)
-
-src_unpack() {
-	unpack ${P}.tar.gz gwt-${GWT_VER}.zip
-	cd "${S}" || die
-	mkdir -p src/gwt/lib/{gin,gwt} \
-		dependencies/common/dictionaries \
-		src/gwt/lib/selenium/${SELENIUM_VER} \
-		src/gwt/lib/selenium/chromedriver/${CHROMEDRIVER_VER} || die
-	mv ../gwt-${GWT_VER} src/gwt/lib/gwt/${GWT_VER} || die
-	unzip -qd src/gwt/lib/gin/${GIN_VER} \
-		"${DISTDIR}"/gin-${GIN_VER}.zip || die
-	unzip -qd dependencies/common/dictionaries \
-		"${DISTDIR}"/core-dictionaries.zip || die
-	unzip -qd src/gwt/lib/selenium/${SELENIUM_VER} \
-		"${DISTDIR}"/selenium-java-${SELENIUM_VER}.zip || die
-	cp "${DISTDIR}"/selenium-server-standalone-${SELENIUM_VER}.jar \
-		src/gwt/lib/selenium/${SELENIUM_VER}/ || die
-	cp "${DISTDIR}"/chromedriver-linux \
-		src/gwt/lib/selenium/chromedriver/${CHROMEDRIVER_VER}/ || die
-	cd dependencies/common || die
-	unpack packrat-${PACKRAT_VER}.tar.gz
-	unpack rmarkdown-${RMARKDOWN_VER}.tar.gz
-	unpack shinyapps-${SHINYAPPS_VER}.tar.gz
-	unpack rsconnect_${RSCONNECT_VER}.tar.gz
-	cp "${DISTDIR}"/rmarkdown-${RMARKDOWN_VER}.tar.gz \
-		. || die
-	cp "${DISTDIR}"/packrat-${PACKRAT_VER}.tar.gz \
-		. || die
-	cp "${DISTDIR}"/shinyapps-${SHINYAPPS_VER}.tar.gz \
-		. || die
-	cp "${DISTDIR}"/rsconnect_${RSCONNECT_VER}.tar.gz \
-		. || die
-}
-
-src_prepare() {
-	java-pkg-2_src_prepare
-
-	egit_clean
-
-	epatch "${PATCHES[@]}"
-
-	# Enable CMake to install our .service file for systemd usage
-	mkdir -vp "${S}/src/cpp/server/lib/systemd/system" || die
-	cp -v "${FILESDIR}/rstudio-server.service.in" "${S}/src/cpp/server/lib/systemd/system/" || die
-
-	# Adding -DDISTRO_SHARE=... to append-flags breaks cmake so using
-	# this sed hack for now. ~RMH
-	sed -i \
-		-e "s|DISTRO_SHARE|\"share/${PN}\"|g" \
-		src/cpp/server/ServerOptions.cpp \
-		src/cpp/session/SessionOptions.cpp || die
-
-	# use mathjax from system
-	ln -sf "${EPREFIX}"/usr/share/mathjax dependencies/common/mathjax-23 || die
-
-	# make sure icons and mime stuff are with prefix
-	sed -i \
-		-e "s:/usr:${EPREFIX}/usr:g" \
-		CMakeGlobals.txt src/cpp/desktop/CMakeLists.txt || die
-
-	# On Gentoo the rstudio-server configuration file is /etc/conf.d/rstudio-server.conf
-	sed -e "s@/etc/rstudio/rserver.conf@${EROOT}etc/conf.d/rstudio-server.conf@" \
-		-i src/cpp/server/ServerOptions.cpp \
-		|| die
-
-	# Set the rsession.conf file location for Gentoo prefix
-	sed -e "s@/etc/rstudio/rsession.conf@${EROOT}etc/rstudio/rsession.conf@" \
-		-i src/cpp/session/SessionOptions.cpp \
-		|| die
-
-	# dev-qt/qtsingleapplication-2.6.1_p20150629 does not provide a cmake module.
-	# It provides a library that has its version number appended to the end,
-	# which is difficult to handle in cmake, as find_library does not support
-	# searching for wildcard library names. So I find the library name from the
-	# qmake spec, and then sed this into the patched src/cpp/desktop/CMakeLists.txt.
-	rm -rf "${S}"/src/cpp/desktop/3rdparty || die
-	local s=$(grep '\-lQt$${QT_MAJOR_VERSION}Solutions_SingleApplication' \
-				   $(qt5_get_mkspecsdir)/features/qtsingleapplication.prf \
-					 | sed -e 's@\$\${QT_MAJOR_VERSION}@5@' \
-						   -e 's@LIBS \*= -l@@')
-	sed -e "s@Qt5Solutions_SingleApplication-2.6@${s}@g" \
-		-i "${S}"/src/cpp/desktop/CMakeLists.txt \
-		|| die
-
-	# The git commit for tag v0.99.902
-	sed -e 's@git ARGS rev-parse HEAD@echo ARGS 4daf125408b86eeba48a39f62df34eb81d934639@'\
-		-i "${S}"/CMakeLists.txt \
-		"${S}"/CMakeGlobals.txt \
-		|| die
-}
-
-src_configure() {
-	export RSTUDIO_VERSION_MAJOR=$(get_version_component_range 1)
-	export RSTUDIO_VERSION_MINOR=$(get_version_component_range 2)
-	export RSTUDIO_VERSION_PATCH=$(get_version_component_range 3)
-
-	local mycmakeargs=(
-		-DDISTRO_SHARE=share/${PN}
-		$(cmake-utils_use !dedicated RSTUDIO_INSTALL_FREEDESKTOP)
-		-DRSTUDIO_TARGET=$(usex dedicated "Server" "$(usex server "Development" "Desktop")")
-		-DQT_QMAKE_EXECUTABLE=$(qt5_get_bindir)/qmake
-		-DRSTUDIO_VERIFY_R_VERSION=FALSE
-		)
-
-	cmake-utils_src_configure
-}
-
-src_compile() {
-	# Avoid the rest of the oracle-jdk-bin-1.8.0.60 sandbox violations F: mkdir S: deny
-	# P: /root/.oracle_jre_usage.
-	export ANT_OPTS="-Duser.home=${T}"
-	cmake-utils_src_compile
-}
-
-src_install() {
-	export ANT_OPTS="-Duser.home=${T}"
-	cmake-utils_src_install
-	pax-mark m "${ED}usr/bin/rstudio"
-	doconfd "${FILESDIR}"/rstudio-server.conf
-	dodir /etc/rstudio
-	insinto /etc/rstudio
-	doins "${FILESDIR}"/rsession.conf
-	dosym /etc/conf.d/rstudio-server.conf /etc/rstudio/rserver.conf
-	if use dedicated || use server; then
-		dopamd src/cpp/server/extras/pam/rstudio
-		newinitd "${FILESDIR}"/rstudio-server.initd rstudio-server
-	fi
-}
-
-pkg_preinst() {
-	use dedicated || gnome2_icon_savelist
-	java-pkg-2_pkg_preinst
-}
-
-pkg_postinst() {
-	use dedicated || { fdo-mime_desktop_database_update
-		fdo-mime_mime_database_update
-		gnome2_icon_cache_update ;}
-
-	if use dedicated || use server; then
-		enewgroup rstudio-server
-		enewuser rstudio-server -1 -1 -1 rstudio-server
-	fi
-}
-
-pkg_postrm() {
-	use dedicated || { fdo-mime_desktop_database_update
-		fdo-mime_mime_database_update
-		gnome2_icon_cache_update ;}
-}

diff --git a/sci-mathematics/rstudio/rstudio-0.99.903.ebuild b/sci-mathematics/rstudio/rstudio-0.99.903.ebuild
deleted file mode 100644
index 60d0858c53c..00000000000
--- a/sci-mathematics/rstudio/rstudio-0.99.903.ebuild
+++ /dev/null
@@ -1,249 +0,0 @@
-# Copyright 1999-2017 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-inherit eutils user cmake-utils gnome2-utils pam versionator fdo-mime java-pkg-2 pax-utils qmake-utils
-
-# TODO
-# * package gin and gwt
-# * use dict from tree, linguas
-# * do src_test (use junit from tree?)
-
-# update from scripts in dependencies/common
-# egrep '(GWT_SDK_VER=|GIN_VER=|SELENIUM_VER=|CHROMEDRIVER_VER=)' dependencies/common/install-gwt
-GWT_VER=2.7.0
-GIN_VER=1.5
-SELENIUM_VER=2.37.0
-CHROMEDRIVER_VER=2.7
-# grep 'PANDOC_VERSION=' dependencies/common/update-pandoc
-PANDOC_VER=1.13.1
-# ls dependencies/common/*.tar.gz
-PACKRAT_VER=0.98.1000
-RMARKDOWN_VER=0.98.1000
-SHINYAPPS_VER=0.98.1000
-RSCONNECT_VER=0.4.1.4_fcac892a69817febd7b655b189bf57193260cda0
-
-DESCRIPTION="IDE for the R language"
-HOMEPAGE="
-	http://www.rstudio.org
-	https://github.com/rstudio/rstudio/"
-SRC_URI="
-	https://github.com/rstudio/rstudio/archive/v${PV}.tar.gz -> ${P}.tar.gz
-	https://s3.amazonaws.com/rstudio-buildtools/gin-${GIN_VER}.zip
-	https://s3.amazonaws.com/rstudio-buildtools/gwt-${GWT_VER}.zip
-	https://s3.amazonaws.com/rstudio-buildtools/selenium-java-${SELENIUM_VER}.zip
-	https://s3.amazonaws.com/rstudio-buildtools/selenium-server-standalone-${SELENIUM_VER}.jar
-	https://s3.amazonaws.com/rstudio-buildtools/chromedriver-linux
-	https://s3.amazonaws.com/rstudio-dictionaries/core-dictionaries.zip
-	https://dev.gentoo.org/~gienah/distfiles/packrat-${PACKRAT_VER}.tar.gz
-	https://dev.gentoo.org/~gienah/distfiles/rmarkdown-${RMARKDOWN_VER}.tar.gz
-	https://dev.gentoo.org/~gienah/distfiles/shinyapps-${SHINYAPPS_VER}.tar.gz
-	https://dev.gentoo.org/~gienah/distfiles/rsconnect_${RSCONNECT_VER}.tar.gz
-"
-
-LICENSE="AGPL-3"
-SLOT="0"
-KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
-IUSE="dedicated server"
-
-QT_VER=5.4
-QT_SLOT=5
-RDEPEND="
-	app-text/pandoc
-	dev-haskell/pandoc-citeproc
-	>=dev-lang/R-2.11.1
-	>=dev-libs/boost-1.50:=
-	>=dev-libs/mathjax-2.3
-	dev-libs/openssl:0
-	sys-apps/util-linux
-	>=sys-devel/clang-3.5.0:*
-	sys-libs/zlib
-	>=virtual/jre-1.7:=
-	x11-libs/pango
-	!dedicated? (
-		>=dev-qt/qtcore-${QT_VER}:${QT_SLOT}
-		>=dev-qt/qtdeclarative-${QT_VER}:${QT_SLOT}
-		>=dev-qt/qtdbus-${QT_VER}:${QT_SLOT}
-		>=dev-qt/qtgui-${QT_VER}:${QT_SLOT}
-		>=dev-qt/qtnetwork-${QT_VER}:${QT_SLOT}
-		>=dev-qt/qtopengl-${QT_VER}:${QT_SLOT}
-		>=dev-qt/qtpositioning-${QT_VER}:${QT_SLOT}
-		>=dev-qt/qtprintsupport-${QT_VER}:${QT_SLOT}
-		>=dev-qt/qtsingleapplication-2.6.1_p20150629[X,qt5]
-		>=dev-qt/qtsensors-${QT_VER}:${QT_SLOT}
-		>=dev-qt/qtsql-${QT_VER}:${QT_SLOT}
-		>=dev-qt/qtsvg-${QT_VER}:${QT_SLOT}
-		>=dev-qt/qtwebkit-${QT_VER}:${QT_SLOT}
-		>=dev-qt/qtwidgets-${QT_VER}:${QT_SLOT}
-		>=dev-qt/qtxml-${QT_VER}:${QT_SLOT}
-		>=dev-qt/qtxmlpatterns-${QT_VER}:${QT_SLOT}
-		server? ( virtual/pam )
-	)
-	dedicated? ( virtual/pam )"
-DEPEND="${RDEPEND}
-	app-arch/unzip
-	dev-java/ant-core
-	>=virtual/jdk-1.7:=
-	virtual/pkgconfig"
-#	test? ( dev-java/junit:4 )
-
-PATCHES=(
-		"${FILESDIR}/${PN}-0.99.879-prefs.patch"
-		"${FILESDIR}/${PN}-0.99.879-paths.patch"
-		"${FILESDIR}/${PN}-0.99.879-clang-pandoc.patch"
-		"${FILESDIR}/${PN}-0.98.490-linker_flags.patch"
-		"${FILESDIR}/${PN}-0.98.1091-boost-1.57.patch"
-		"${FILESDIR}/${PN}-0.99.473-qtsingleapplication.patch"
-		"${FILESDIR}/${PN}-0.99.486-systemd.patch"
-)
-
-src_unpack() {
-	unpack ${P}.tar.gz gwt-${GWT_VER}.zip
-	cd "${S}" || die
-	mkdir -p src/gwt/lib/{gin,gwt} \
-		dependencies/common/dictionaries \
-		src/gwt/lib/selenium/${SELENIUM_VER} \
-		src/gwt/lib/selenium/chromedriver/${CHROMEDRIVER_VER} || die
-	mv ../gwt-${GWT_VER} src/gwt/lib/gwt/${GWT_VER} || die
-	unzip -qd src/gwt/lib/gin/${GIN_VER} \
-		"${DISTDIR}"/gin-${GIN_VER}.zip || die
-	unzip -qd dependencies/common/dictionaries \
-		"${DISTDIR}"/core-dictionaries.zip || die
-	unzip -qd src/gwt/lib/selenium/${SELENIUM_VER} \
-		"${DISTDIR}"/selenium-java-${SELENIUM_VER}.zip || die
-	cp "${DISTDIR}"/selenium-server-standalone-${SELENIUM_VER}.jar \
-		src/gwt/lib/selenium/${SELENIUM_VER}/ || die
-	cp "${DISTDIR}"/chromedriver-linux \
-		src/gwt/lib/selenium/chromedriver/${CHROMEDRIVER_VER}/ || die
-	cd dependencies/common || die
-	unpack packrat-${PACKRAT_VER}.tar.gz
-	unpack rmarkdown-${RMARKDOWN_VER}.tar.gz
-	unpack shinyapps-${SHINYAPPS_VER}.tar.gz
-	unpack rsconnect_${RSCONNECT_VER}.tar.gz
-	cp "${DISTDIR}"/rmarkdown-${RMARKDOWN_VER}.tar.gz \
-		. || die
-	cp "${DISTDIR}"/packrat-${PACKRAT_VER}.tar.gz \
-		. || die
-	cp "${DISTDIR}"/shinyapps-${SHINYAPPS_VER}.tar.gz \
-		. || die
-	cp "${DISTDIR}"/rsconnect_${RSCONNECT_VER}.tar.gz \
-		. || die
-}
-
-src_prepare() {
-	java-pkg-2_src_prepare
-
-	egit_clean
-
-	epatch "${PATCHES[@]}"
-
-	# Enable CMake to install our .service file for systemd usage
-	mkdir -vp "${S}/src/cpp/server/lib/systemd/system" || die
-	cp -v "${FILESDIR}/rstudio-server.service.in" "${S}/src/cpp/server/lib/systemd/system/" || die
-
-	# Adding -DDISTRO_SHARE=... to append-flags breaks cmake so using
-	# this sed hack for now. ~RMH
-	sed -i \
-		-e "s|DISTRO_SHARE|\"share/${PN}\"|g" \
-		src/cpp/server/ServerOptions.cpp \
-		src/cpp/session/SessionOptions.cpp || die
-
-	# use mathjax from system
-	ln -sf "${EPREFIX}"/usr/share/mathjax dependencies/common/mathjax-23 || die
-
-	# make sure icons and mime stuff are with prefix
-	sed -i \
-		-e "s:/usr:${EPREFIX}/usr:g" \
-		CMakeGlobals.txt src/cpp/desktop/CMakeLists.txt || die
-
-	# On Gentoo the rstudio-server configuration file is /etc/conf.d/rstudio-server.conf
-	sed -e "s@/etc/rstudio/rserver.conf@${EROOT}etc/conf.d/rstudio-server.conf@" \
-		-i src/cpp/server/ServerOptions.cpp \
-		|| die
-
-	# Set the rsession.conf file location for Gentoo prefix
-	sed -e "s@/etc/rstudio/rsession.conf@${EROOT}etc/rstudio/rsession.conf@" \
-		-i src/cpp/session/SessionOptions.cpp \
-		|| die
-
-	# dev-qt/qtsingleapplication-2.6.1_p20150629 does not provide a cmake module.
-	# It provides a library that has its version number appended to the end,
-	# which is difficult to handle in cmake, as find_library does not support
-	# searching for wildcard library names. So I find the library name from the
-	# qmake spec, and then sed this into the patched src/cpp/desktop/CMakeLists.txt.
-	rm -rf "${S}"/src/cpp/desktop/3rdparty || die
-	local s=$(grep '\-lQt$${QT_MAJOR_VERSION}Solutions_SingleApplication' \
-				   $(qt5_get_mkspecsdir)/features/qtsingleapplication.prf \
-					 | sed -e 's@\$\${QT_MAJOR_VERSION}@5@' \
-						   -e 's@LIBS \*= -l@@')
-	sed -e "s@Qt5Solutions_SingleApplication-2.6@${s}@g" \
-		-i "${S}"/src/cpp/desktop/CMakeLists.txt \
-		|| die
-
-	# The git commit for tag: git rev-list -n 1 v0.99.903
-	sed -e 's@git ARGS rev-parse HEAD@echo ARGS 0eb2d8ea28ebc1ac6ac327e023becb6133b679c4@'\
-		-i "${S}"/CMakeLists.txt \
-		"${S}"/CMakeGlobals.txt \
-		|| die
-}
-
-src_configure() {
-	export RSTUDIO_VERSION_MAJOR=$(get_version_component_range 1)
-	export RSTUDIO_VERSION_MINOR=$(get_version_component_range 2)
-	export RSTUDIO_VERSION_PATCH=$(get_version_component_range 3)
-
-	local mycmakeargs=(
-		-DDISTRO_SHARE=share/${PN}
-		$(cmake-utils_use !dedicated RSTUDIO_INSTALL_FREEDESKTOP)
-		-DRSTUDIO_TARGET=$(usex dedicated "Server" "$(usex server "Development" "Desktop")")
-		-DQT_QMAKE_EXECUTABLE=$(qt5_get_bindir)/qmake
-		-DRSTUDIO_VERIFY_R_VERSION=FALSE
-		)
-
-	cmake-utils_src_configure
-}
-
-src_compile() {
-	# Avoid the rest of the oracle-jdk-bin-1.8.0.60 sandbox violations F: mkdir S: deny
-	# P: /root/.oracle_jre_usage.
-	export ANT_OPTS="-Duser.home=${T}"
-	cmake-utils_src_compile
-}
-
-src_install() {
-	export ANT_OPTS="-Duser.home=${T}"
-	cmake-utils_src_install
-	pax-mark m "${ED}usr/bin/rstudio"
-	doconfd "${FILESDIR}"/rstudio-server.conf
-	dodir /etc/rstudio
-	insinto /etc/rstudio
-	doins "${FILESDIR}"/rsession.conf
-	dosym /etc/conf.d/rstudio-server.conf /etc/rstudio/rserver.conf
-	if use dedicated || use server; then
-		dopamd src/cpp/server/extras/pam/rstudio
-		newinitd "${FILESDIR}"/rstudio-server.initd rstudio-server
-	fi
-}
-
-pkg_preinst() {
-	use dedicated || gnome2_icon_savelist
-	java-pkg-2_pkg_preinst
-}
-
-pkg_postinst() {
-	use dedicated || { fdo-mime_desktop_database_update
-		fdo-mime_mime_database_update
-		gnome2_icon_cache_update ;}
-
-	if use dedicated || use server; then
-		enewgroup rstudio-server
-		enewuser rstudio-server -1 -1 -1 rstudio-server
-	fi
-}
-
-pkg_postrm() {
-	use dedicated || { fdo-mime_desktop_database_update
-		fdo-mime_mime_database_update
-		gnome2_icon_cache_update ;}
-}

diff --git a/sci-mathematics/rstudio/rstudio-1.0.136.ebuild b/sci-mathematics/rstudio/rstudio-1.0.136.ebuild
deleted file mode 100644
index dcb101cac4e..00000000000
--- a/sci-mathematics/rstudio/rstudio-1.0.136.ebuild
+++ /dev/null
@@ -1,247 +0,0 @@
-# Copyright 1999-2017 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-inherit eutils user cmake-utils gnome2-utils pam versionator fdo-mime java-pkg-2 pax-utils qmake-utils
-
-# TODO
-# * package gin and gwt
-# * use dict from tree, linguas
-# * do src_test (use junit from tree?)
-
-# update from scripts in dependencies/common
-# egrep '(GWT_SDK_VER=|GIN_VER=|SELENIUM_VER=|CHROMEDRIVER_VER=)' dependencies/common/install-gwt
-GWT_VER=2.7.0
-GIN_VER=1.5
-SELENIUM_VER=2.37.0
-CHROMEDRIVER_VER=2.7
-# grep 'PANDOC_VERSION=' dependencies/common/update-pandoc
-PANDOC_VER=1.13.1
-# ls dependencies/common/*.tar.gz
-PACKRAT_VER=0.98.1000
-RMARKDOWN_VER=0.98.1000
-SHINYAPPS_VER=0.98.1000
-RSCONNECT_VER=0.4.1.4_fcac892a69817febd7b655b189bf57193260cda0
-
-DESCRIPTION="IDE for the R language"
-HOMEPAGE="
-	http://www.rstudio.org
-	https://github.com/rstudio/rstudio/"
-SRC_URI="
-	https://github.com/rstudio/rstudio/archive/v${PV}.tar.gz -> ${P}.tar.gz
-	https://s3.amazonaws.com/rstudio-buildtools/gin-${GIN_VER}.zip
-	https://s3.amazonaws.com/rstudio-buildtools/gwt-${GWT_VER}.zip
-	https://s3.amazonaws.com/rstudio-buildtools/selenium-java-${SELENIUM_VER}.zip
-	https://s3.amazonaws.com/rstudio-buildtools/selenium-server-standalone-${SELENIUM_VER}.jar
-	https://s3.amazonaws.com/rstudio-buildtools/chromedriver-linux
-	https://s3.amazonaws.com/rstudio-dictionaries/core-dictionaries.zip
-	https://dev.gentoo.org/~gienah/distfiles/packrat-${PACKRAT_VER}.tar.gz
-	https://dev.gentoo.org/~gienah/distfiles/rmarkdown-${RMARKDOWN_VER}.tar.gz
-	https://dev.gentoo.org/~gienah/distfiles/shinyapps-${SHINYAPPS_VER}.tar.gz
-	https://dev.gentoo.org/~gienah/distfiles/rsconnect_${RSCONNECT_VER}.tar.gz
-"
-
-LICENSE="AGPL-3"
-SLOT="0"
-KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
-IUSE="dedicated server"
-
-QT_VER=5.4
-QT_SLOT=5
-RDEPEND="
-	app-text/pandoc
-	dev-haskell/pandoc-citeproc
-	>=dev-lang/R-2.11.1
-	>=dev-libs/boost-1.50:=
-	>=dev-libs/mathjax-2.7.0
-	dev-libs/openssl:0
-	sys-apps/util-linux
-	>=sys-devel/clang-3.5.0:*
-	sys-libs/zlib
-	>=virtual/jre-1.8:=
-	x11-libs/pango
-	!dedicated? (
-		>=dev-qt/qtcore-${QT_VER}:${QT_SLOT}
-		>=dev-qt/qtdeclarative-${QT_VER}:${QT_SLOT}
-		>=dev-qt/qtdbus-${QT_VER}:${QT_SLOT}
-		>=dev-qt/qtgui-${QT_VER}:${QT_SLOT}
-		>=dev-qt/qtnetwork-${QT_VER}:${QT_SLOT}
-		>=dev-qt/qtopengl-${QT_VER}:${QT_SLOT}
-		>=dev-qt/qtpositioning-${QT_VER}:${QT_SLOT}
-		>=dev-qt/qtprintsupport-${QT_VER}:${QT_SLOT}
-		>=dev-qt/qtsingleapplication-2.6.1_p20150629[X,qt5]
-		>=dev-qt/qtsensors-${QT_VER}:${QT_SLOT}
-		>=dev-qt/qtsql-${QT_VER}:${QT_SLOT}
-		>=dev-qt/qtsvg-${QT_VER}:${QT_SLOT}
-		>=dev-qt/qtwebkit-${QT_VER}:${QT_SLOT}
-		>=dev-qt/qtwidgets-${QT_VER}:${QT_SLOT}
-		>=dev-qt/qtxml-${QT_VER}:${QT_SLOT}
-		>=dev-qt/qtxmlpatterns-${QT_VER}:${QT_SLOT}
-		server? ( virtual/pam )
-	)
-	dedicated? ( virtual/pam )"
-DEPEND="${RDEPEND}
-	app-arch/unzip
-	dev-java/ant-core
-	>=virtual/jdk-1.8:=
-	virtual/pkgconfig"
-#	test? ( dev-java/junit:4 )
-
-PATCHES=(
-		"${FILESDIR}/${PN}-0.99.879-prefs.patch"
-		"${FILESDIR}/${PN}-1.0.44-paths.patch"
-		"${FILESDIR}/${PN}-1.0.44-clang-pandoc.patch"
-		"${FILESDIR}/${PN}-0.98.490-linker_flags.patch"
-		"${FILESDIR}/${PN}-0.98.1091-boost-1.57.patch"
-		"${FILESDIR}/${PN}-0.99.473-qtsingleapplication.patch"
-		"${FILESDIR}/${PN}-1.0.44-systemd.patch"
-)
-
-src_unpack() {
-	unpack ${P}.tar.gz gwt-${GWT_VER}.zip
-	cd "${S}" || die
-	mkdir -p src/gwt/lib/{gin,gwt} \
-		dependencies/common/dictionaries \
-		src/gwt/lib/selenium/${SELENIUM_VER} \
-		src/gwt/lib/selenium/chromedriver/${CHROMEDRIVER_VER} || die
-	mv ../gwt-${GWT_VER} src/gwt/lib/gwt/${GWT_VER} || die
-	unzip -qd src/gwt/lib/gin/${GIN_VER} \
-		"${DISTDIR}"/gin-${GIN_VER}.zip || die
-	unzip -qd dependencies/common/dictionaries \
-		"${DISTDIR}"/core-dictionaries.zip || die
-	unzip -qd src/gwt/lib/selenium/${SELENIUM_VER} \
-		"${DISTDIR}"/selenium-java-${SELENIUM_VER}.zip || die
-	cp "${DISTDIR}"/selenium-server-standalone-${SELENIUM_VER}.jar \
-		src/gwt/lib/selenium/${SELENIUM_VER}/ || die
-	cp "${DISTDIR}"/chromedriver-linux \
-		src/gwt/lib/selenium/chromedriver/${CHROMEDRIVER_VER}/ || die
-	cd dependencies/common || die
-	unpack packrat-${PACKRAT_VER}.tar.gz
-	unpack rmarkdown-${RMARKDOWN_VER}.tar.gz
-	unpack shinyapps-${SHINYAPPS_VER}.tar.gz
-	unpack rsconnect_${RSCONNECT_VER}.tar.gz
-	cp "${DISTDIR}"/rmarkdown-${RMARKDOWN_VER}.tar.gz \
-		. || die
-	cp "${DISTDIR}"/packrat-${PACKRAT_VER}.tar.gz \
-		. || die
-	cp "${DISTDIR}"/shinyapps-${SHINYAPPS_VER}.tar.gz \
-		. || die
-	cp "${DISTDIR}"/rsconnect_${RSCONNECT_VER}.tar.gz \
-		. || die
-}
-
-src_prepare() {
-	default
-	java-pkg-2_src_prepare
-	egit_clean
-
-	# Enable CMake to install our .service file for systemd usage
-	mkdir -vp "${S}/src/cpp/server/lib/systemd/system" || die
-	cp -v "${FILESDIR}/rstudio-server.service.in" "${S}/src/cpp/server/lib/systemd/system/" || die
-
-	# Adding -DDISTRO_SHARE=... to append-flags breaks cmake so using
-	# this sed hack for now. ~RMH
-	sed -i \
-		-e "s|DISTRO_SHARE|\"share/${PN}\"|g" \
-		src/cpp/server/ServerOptions.cpp \
-		src/cpp/session/SessionOptions.cpp || die
-
-	# use mathjax from system
-	ln -sf "${EPREFIX}"/usr/share/mathjax dependencies/common/mathjax-26 || die
-
-	# make sure icons and mime stuff are with prefix
-	sed -i \
-		-e "s:/usr:${EPREFIX}/usr:g" \
-		CMakeGlobals.txt src/cpp/desktop/CMakeLists.txt || die
-
-	# On Gentoo the rstudio-server configuration file is /etc/conf.d/rstudio-server.conf
-	sed -e "s@/etc/rstudio/rserver.conf@${EROOT}etc/conf.d/rstudio-server.conf@" \
-		-i src/cpp/server/ServerOptions.cpp \
-		|| die
-
-	# Set the rsession.conf file location for Gentoo prefix
-	sed -e "s@/etc/rstudio/rsession.conf@${EROOT}etc/rstudio/rsession.conf@" \
-		-i src/cpp/session/SessionOptions.cpp \
-		|| die
-
-	# dev-qt/qtsingleapplication-2.6.1_p20150629 does not provide a cmake module.
-	# It provides a library that has its version number appended to the end,
-	# which is difficult to handle in cmake, as find_library does not support
-	# searching for wildcard library names. So I find the library name from the
-	# qmake spec, and then sed this into the patched src/cpp/desktop/CMakeLists.txt.
-	rm -rf "${S}"/src/cpp/desktop/3rdparty || die
-	local s=$(grep '\-lQt$${QT_MAJOR_VERSION}Solutions_SingleApplication' \
-				   $(qt5_get_mkspecsdir)/features/qtsingleapplication.prf \
-					 | sed -e 's@\$\${QT_MAJOR_VERSION}@5@' \
-						   -e 's@LIBS \*= -l@@')
-	sed -e "s@Qt5Solutions_SingleApplication-2.6@${s}@g" \
-		-i "${S}"/src/cpp/desktop/CMakeLists.txt \
-		|| die
-
-	# The git commit for tag: git rev-list -n 1 v0.99.903
-	sed -e 's@git ARGS rev-parse HEAD@echo ARGS 0eb2d8ea28ebc1ac6ac327e023becb6133b679c4@'\
-		-i "${S}"/CMakeLists.txt \
-		"${S}"/CMakeGlobals.txt \
-		|| die
-}
-
-src_configure() {
-	export RSTUDIO_VERSION_MAJOR=$(get_version_component_range 1)
-	export RSTUDIO_VERSION_MINOR=$(get_version_component_range 2)
-	export RSTUDIO_VERSION_PATCH=$(get_version_component_range 3)
-
-	local mycmakeargs=(
-		-DDISTRO_SHARE=share/${PN}
-		-DRSTUDIO_INSTALL_FREEDESKTOP="$(usex !dedicated "ON" "OFF")"
-		-DRSTUDIO_TARGET=$(usex dedicated "Server" "$(usex server "Development" "Desktop")")
-		-DQT_QMAKE_EXECUTABLE=$(qt5_get_bindir)/qmake
-		-DRSTUDIO_VERIFY_R_VERSION=FALSE
-		)
-
-	cmake-utils_src_configure
-}
-
-src_compile() {
-	# Avoid the rest of the oracle-jdk-bin-1.8.0.60 sandbox violations F: mkdir S: deny
-	# P: /root/.oracle_jre_usage.
-	export ANT_OPTS="-Duser.home=${T}"
-	cmake-utils_src_compile
-}
-
-src_install() {
-	export ANT_OPTS="-Duser.home=${T}"
-	cmake-utils_src_install
-	pax-mark m "${ED}usr/bin/rstudio"
-	doconfd "${FILESDIR}"/rstudio-server.conf
-	dodir /etc/rstudio
-	insinto /etc/rstudio
-	doins "${FILESDIR}"/rsession.conf
-	dosym /etc/conf.d/rstudio-server.conf /etc/rstudio/rserver.conf
-	if use dedicated || use server; then
-		dopamd src/cpp/server/extras/pam/rstudio
-		newinitd "${FILESDIR}"/rstudio-server.initd rstudio-server
-	fi
-}
-
-pkg_preinst() {
-	use dedicated || gnome2_icon_savelist
-	java-pkg-2_pkg_preinst
-}
-
-pkg_postinst() {
-	use dedicated || { fdo-mime_desktop_database_update
-		fdo-mime_mime_database_update
-		gnome2_icon_cache_update ;}
-
-	if use dedicated || use server; then
-		enewgroup rstudio-server
-		enewuser rstudio-server -1 -1 -1 rstudio-server
-	fi
-}
-
-pkg_postrm() {
-	use dedicated || { fdo-mime_desktop_database_update
-		fdo-mime_mime_database_update
-		gnome2_icon_cache_update ;}
-}

diff --git a/sci-mathematics/rstudio/rstudio-1.0.143.ebuild b/sci-mathematics/rstudio/rstudio-1.0.143.ebuild
deleted file mode 100644
index dcb101cac4e..00000000000
--- a/sci-mathematics/rstudio/rstudio-1.0.143.ebuild
+++ /dev/null
@@ -1,247 +0,0 @@
-# Copyright 1999-2017 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-inherit eutils user cmake-utils gnome2-utils pam versionator fdo-mime java-pkg-2 pax-utils qmake-utils
-
-# TODO
-# * package gin and gwt
-# * use dict from tree, linguas
-# * do src_test (use junit from tree?)
-
-# update from scripts in dependencies/common
-# egrep '(GWT_SDK_VER=|GIN_VER=|SELENIUM_VER=|CHROMEDRIVER_VER=)' dependencies/common/install-gwt
-GWT_VER=2.7.0
-GIN_VER=1.5
-SELENIUM_VER=2.37.0
-CHROMEDRIVER_VER=2.7
-# grep 'PANDOC_VERSION=' dependencies/common/update-pandoc
-PANDOC_VER=1.13.1
-# ls dependencies/common/*.tar.gz
-PACKRAT_VER=0.98.1000
-RMARKDOWN_VER=0.98.1000
-SHINYAPPS_VER=0.98.1000
-RSCONNECT_VER=0.4.1.4_fcac892a69817febd7b655b189bf57193260cda0
-
-DESCRIPTION="IDE for the R language"
-HOMEPAGE="
-	http://www.rstudio.org
-	https://github.com/rstudio/rstudio/"
-SRC_URI="
-	https://github.com/rstudio/rstudio/archive/v${PV}.tar.gz -> ${P}.tar.gz
-	https://s3.amazonaws.com/rstudio-buildtools/gin-${GIN_VER}.zip
-	https://s3.amazonaws.com/rstudio-buildtools/gwt-${GWT_VER}.zip
-	https://s3.amazonaws.com/rstudio-buildtools/selenium-java-${SELENIUM_VER}.zip
-	https://s3.amazonaws.com/rstudio-buildtools/selenium-server-standalone-${SELENIUM_VER}.jar
-	https://s3.amazonaws.com/rstudio-buildtools/chromedriver-linux
-	https://s3.amazonaws.com/rstudio-dictionaries/core-dictionaries.zip
-	https://dev.gentoo.org/~gienah/distfiles/packrat-${PACKRAT_VER}.tar.gz
-	https://dev.gentoo.org/~gienah/distfiles/rmarkdown-${RMARKDOWN_VER}.tar.gz
-	https://dev.gentoo.org/~gienah/distfiles/shinyapps-${SHINYAPPS_VER}.tar.gz
-	https://dev.gentoo.org/~gienah/distfiles/rsconnect_${RSCONNECT_VER}.tar.gz
-"
-
-LICENSE="AGPL-3"
-SLOT="0"
-KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
-IUSE="dedicated server"
-
-QT_VER=5.4
-QT_SLOT=5
-RDEPEND="
-	app-text/pandoc
-	dev-haskell/pandoc-citeproc
-	>=dev-lang/R-2.11.1
-	>=dev-libs/boost-1.50:=
-	>=dev-libs/mathjax-2.7.0
-	dev-libs/openssl:0
-	sys-apps/util-linux
-	>=sys-devel/clang-3.5.0:*
-	sys-libs/zlib
-	>=virtual/jre-1.8:=
-	x11-libs/pango
-	!dedicated? (
-		>=dev-qt/qtcore-${QT_VER}:${QT_SLOT}
-		>=dev-qt/qtdeclarative-${QT_VER}:${QT_SLOT}
-		>=dev-qt/qtdbus-${QT_VER}:${QT_SLOT}
-		>=dev-qt/qtgui-${QT_VER}:${QT_SLOT}
-		>=dev-qt/qtnetwork-${QT_VER}:${QT_SLOT}
-		>=dev-qt/qtopengl-${QT_VER}:${QT_SLOT}
-		>=dev-qt/qtpositioning-${QT_VER}:${QT_SLOT}
-		>=dev-qt/qtprintsupport-${QT_VER}:${QT_SLOT}
-		>=dev-qt/qtsingleapplication-2.6.1_p20150629[X,qt5]
-		>=dev-qt/qtsensors-${QT_VER}:${QT_SLOT}
-		>=dev-qt/qtsql-${QT_VER}:${QT_SLOT}
-		>=dev-qt/qtsvg-${QT_VER}:${QT_SLOT}
-		>=dev-qt/qtwebkit-${QT_VER}:${QT_SLOT}
-		>=dev-qt/qtwidgets-${QT_VER}:${QT_SLOT}
-		>=dev-qt/qtxml-${QT_VER}:${QT_SLOT}
-		>=dev-qt/qtxmlpatterns-${QT_VER}:${QT_SLOT}
-		server? ( virtual/pam )
-	)
-	dedicated? ( virtual/pam )"
-DEPEND="${RDEPEND}
-	app-arch/unzip
-	dev-java/ant-core
-	>=virtual/jdk-1.8:=
-	virtual/pkgconfig"
-#	test? ( dev-java/junit:4 )
-
-PATCHES=(
-		"${FILESDIR}/${PN}-0.99.879-prefs.patch"
-		"${FILESDIR}/${PN}-1.0.44-paths.patch"
-		"${FILESDIR}/${PN}-1.0.44-clang-pandoc.patch"
-		"${FILESDIR}/${PN}-0.98.490-linker_flags.patch"
-		"${FILESDIR}/${PN}-0.98.1091-boost-1.57.patch"
-		"${FILESDIR}/${PN}-0.99.473-qtsingleapplication.patch"
-		"${FILESDIR}/${PN}-1.0.44-systemd.patch"
-)
-
-src_unpack() {
-	unpack ${P}.tar.gz gwt-${GWT_VER}.zip
-	cd "${S}" || die
-	mkdir -p src/gwt/lib/{gin,gwt} \
-		dependencies/common/dictionaries \
-		src/gwt/lib/selenium/${SELENIUM_VER} \
-		src/gwt/lib/selenium/chromedriver/${CHROMEDRIVER_VER} || die
-	mv ../gwt-${GWT_VER} src/gwt/lib/gwt/${GWT_VER} || die
-	unzip -qd src/gwt/lib/gin/${GIN_VER} \
-		"${DISTDIR}"/gin-${GIN_VER}.zip || die
-	unzip -qd dependencies/common/dictionaries \
-		"${DISTDIR}"/core-dictionaries.zip || die
-	unzip -qd src/gwt/lib/selenium/${SELENIUM_VER} \
-		"${DISTDIR}"/selenium-java-${SELENIUM_VER}.zip || die
-	cp "${DISTDIR}"/selenium-server-standalone-${SELENIUM_VER}.jar \
-		src/gwt/lib/selenium/${SELENIUM_VER}/ || die
-	cp "${DISTDIR}"/chromedriver-linux \
-		src/gwt/lib/selenium/chromedriver/${CHROMEDRIVER_VER}/ || die
-	cd dependencies/common || die
-	unpack packrat-${PACKRAT_VER}.tar.gz
-	unpack rmarkdown-${RMARKDOWN_VER}.tar.gz
-	unpack shinyapps-${SHINYAPPS_VER}.tar.gz
-	unpack rsconnect_${RSCONNECT_VER}.tar.gz
-	cp "${DISTDIR}"/rmarkdown-${RMARKDOWN_VER}.tar.gz \
-		. || die
-	cp "${DISTDIR}"/packrat-${PACKRAT_VER}.tar.gz \
-		. || die
-	cp "${DISTDIR}"/shinyapps-${SHINYAPPS_VER}.tar.gz \
-		. || die
-	cp "${DISTDIR}"/rsconnect_${RSCONNECT_VER}.tar.gz \
-		. || die
-}
-
-src_prepare() {
-	default
-	java-pkg-2_src_prepare
-	egit_clean
-
-	# Enable CMake to install our .service file for systemd usage
-	mkdir -vp "${S}/src/cpp/server/lib/systemd/system" || die
-	cp -v "${FILESDIR}/rstudio-server.service.in" "${S}/src/cpp/server/lib/systemd/system/" || die
-
-	# Adding -DDISTRO_SHARE=... to append-flags breaks cmake so using
-	# this sed hack for now. ~RMH
-	sed -i \
-		-e "s|DISTRO_SHARE|\"share/${PN}\"|g" \
-		src/cpp/server/ServerOptions.cpp \
-		src/cpp/session/SessionOptions.cpp || die
-
-	# use mathjax from system
-	ln -sf "${EPREFIX}"/usr/share/mathjax dependencies/common/mathjax-26 || die
-
-	# make sure icons and mime stuff are with prefix
-	sed -i \
-		-e "s:/usr:${EPREFIX}/usr:g" \
-		CMakeGlobals.txt src/cpp/desktop/CMakeLists.txt || die
-
-	# On Gentoo the rstudio-server configuration file is /etc/conf.d/rstudio-server.conf
-	sed -e "s@/etc/rstudio/rserver.conf@${EROOT}etc/conf.d/rstudio-server.conf@" \
-		-i src/cpp/server/ServerOptions.cpp \
-		|| die
-
-	# Set the rsession.conf file location for Gentoo prefix
-	sed -e "s@/etc/rstudio/rsession.conf@${EROOT}etc/rstudio/rsession.conf@" \
-		-i src/cpp/session/SessionOptions.cpp \
-		|| die
-
-	# dev-qt/qtsingleapplication-2.6.1_p20150629 does not provide a cmake module.
-	# It provides a library that has its version number appended to the end,
-	# which is difficult to handle in cmake, as find_library does not support
-	# searching for wildcard library names. So I find the library name from the
-	# qmake spec, and then sed this into the patched src/cpp/desktop/CMakeLists.txt.
-	rm -rf "${S}"/src/cpp/desktop/3rdparty || die
-	local s=$(grep '\-lQt$${QT_MAJOR_VERSION}Solutions_SingleApplication' \
-				   $(qt5_get_mkspecsdir)/features/qtsingleapplication.prf \
-					 | sed -e 's@\$\${QT_MAJOR_VERSION}@5@' \
-						   -e 's@LIBS \*= -l@@')
-	sed -e "s@Qt5Solutions_SingleApplication-2.6@${s}@g" \
-		-i "${S}"/src/cpp/desktop/CMakeLists.txt \
-		|| die
-
-	# The git commit for tag: git rev-list -n 1 v0.99.903
-	sed -e 's@git ARGS rev-parse HEAD@echo ARGS 0eb2d8ea28ebc1ac6ac327e023becb6133b679c4@'\
-		-i "${S}"/CMakeLists.txt \
-		"${S}"/CMakeGlobals.txt \
-		|| die
-}
-
-src_configure() {
-	export RSTUDIO_VERSION_MAJOR=$(get_version_component_range 1)
-	export RSTUDIO_VERSION_MINOR=$(get_version_component_range 2)
-	export RSTUDIO_VERSION_PATCH=$(get_version_component_range 3)
-
-	local mycmakeargs=(
-		-DDISTRO_SHARE=share/${PN}
-		-DRSTUDIO_INSTALL_FREEDESKTOP="$(usex !dedicated "ON" "OFF")"
-		-DRSTUDIO_TARGET=$(usex dedicated "Server" "$(usex server "Development" "Desktop")")
-		-DQT_QMAKE_EXECUTABLE=$(qt5_get_bindir)/qmake
-		-DRSTUDIO_VERIFY_R_VERSION=FALSE
-		)
-
-	cmake-utils_src_configure
-}
-
-src_compile() {
-	# Avoid the rest of the oracle-jdk-bin-1.8.0.60 sandbox violations F: mkdir S: deny
-	# P: /root/.oracle_jre_usage.
-	export ANT_OPTS="-Duser.home=${T}"
-	cmake-utils_src_compile
-}
-
-src_install() {
-	export ANT_OPTS="-Duser.home=${T}"
-	cmake-utils_src_install
-	pax-mark m "${ED}usr/bin/rstudio"
-	doconfd "${FILESDIR}"/rstudio-server.conf
-	dodir /etc/rstudio
-	insinto /etc/rstudio
-	doins "${FILESDIR}"/rsession.conf
-	dosym /etc/conf.d/rstudio-server.conf /etc/rstudio/rserver.conf
-	if use dedicated || use server; then
-		dopamd src/cpp/server/extras/pam/rstudio
-		newinitd "${FILESDIR}"/rstudio-server.initd rstudio-server
-	fi
-}
-
-pkg_preinst() {
-	use dedicated || gnome2_icon_savelist
-	java-pkg-2_pkg_preinst
-}
-
-pkg_postinst() {
-	use dedicated || { fdo-mime_desktop_database_update
-		fdo-mime_mime_database_update
-		gnome2_icon_cache_update ;}
-
-	if use dedicated || use server; then
-		enewgroup rstudio-server
-		enewuser rstudio-server -1 -1 -1 rstudio-server
-	fi
-}
-
-pkg_postrm() {
-	use dedicated || { fdo-mime_desktop_database_update
-		fdo-mime_mime_database_update
-		gnome2_icon_cache_update ;}
-}

diff --git a/sci-mathematics/rstudio/rstudio-1.0.153.ebuild b/sci-mathematics/rstudio/rstudio-1.0.153.ebuild
deleted file mode 100644
index dcb101cac4e..00000000000
--- a/sci-mathematics/rstudio/rstudio-1.0.153.ebuild
+++ /dev/null
@@ -1,247 +0,0 @@
-# Copyright 1999-2017 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-inherit eutils user cmake-utils gnome2-utils pam versionator fdo-mime java-pkg-2 pax-utils qmake-utils
-
-# TODO
-# * package gin and gwt
-# * use dict from tree, linguas
-# * do src_test (use junit from tree?)
-
-# update from scripts in dependencies/common
-# egrep '(GWT_SDK_VER=|GIN_VER=|SELENIUM_VER=|CHROMEDRIVER_VER=)' dependencies/common/install-gwt
-GWT_VER=2.7.0
-GIN_VER=1.5
-SELENIUM_VER=2.37.0
-CHROMEDRIVER_VER=2.7
-# grep 'PANDOC_VERSION=' dependencies/common/update-pandoc
-PANDOC_VER=1.13.1
-# ls dependencies/common/*.tar.gz
-PACKRAT_VER=0.98.1000
-RMARKDOWN_VER=0.98.1000
-SHINYAPPS_VER=0.98.1000
-RSCONNECT_VER=0.4.1.4_fcac892a69817febd7b655b189bf57193260cda0
-
-DESCRIPTION="IDE for the R language"
-HOMEPAGE="
-	http://www.rstudio.org
-	https://github.com/rstudio/rstudio/"
-SRC_URI="
-	https://github.com/rstudio/rstudio/archive/v${PV}.tar.gz -> ${P}.tar.gz
-	https://s3.amazonaws.com/rstudio-buildtools/gin-${GIN_VER}.zip
-	https://s3.amazonaws.com/rstudio-buildtools/gwt-${GWT_VER}.zip
-	https://s3.amazonaws.com/rstudio-buildtools/selenium-java-${SELENIUM_VER}.zip
-	https://s3.amazonaws.com/rstudio-buildtools/selenium-server-standalone-${SELENIUM_VER}.jar
-	https://s3.amazonaws.com/rstudio-buildtools/chromedriver-linux
-	https://s3.amazonaws.com/rstudio-dictionaries/core-dictionaries.zip
-	https://dev.gentoo.org/~gienah/distfiles/packrat-${PACKRAT_VER}.tar.gz
-	https://dev.gentoo.org/~gienah/distfiles/rmarkdown-${RMARKDOWN_VER}.tar.gz
-	https://dev.gentoo.org/~gienah/distfiles/shinyapps-${SHINYAPPS_VER}.tar.gz
-	https://dev.gentoo.org/~gienah/distfiles/rsconnect_${RSCONNECT_VER}.tar.gz
-"
-
-LICENSE="AGPL-3"
-SLOT="0"
-KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
-IUSE="dedicated server"
-
-QT_VER=5.4
-QT_SLOT=5
-RDEPEND="
-	app-text/pandoc
-	dev-haskell/pandoc-citeproc
-	>=dev-lang/R-2.11.1
-	>=dev-libs/boost-1.50:=
-	>=dev-libs/mathjax-2.7.0
-	dev-libs/openssl:0
-	sys-apps/util-linux
-	>=sys-devel/clang-3.5.0:*
-	sys-libs/zlib
-	>=virtual/jre-1.8:=
-	x11-libs/pango
-	!dedicated? (
-		>=dev-qt/qtcore-${QT_VER}:${QT_SLOT}
-		>=dev-qt/qtdeclarative-${QT_VER}:${QT_SLOT}
-		>=dev-qt/qtdbus-${QT_VER}:${QT_SLOT}
-		>=dev-qt/qtgui-${QT_VER}:${QT_SLOT}
-		>=dev-qt/qtnetwork-${QT_VER}:${QT_SLOT}
-		>=dev-qt/qtopengl-${QT_VER}:${QT_SLOT}
-		>=dev-qt/qtpositioning-${QT_VER}:${QT_SLOT}
-		>=dev-qt/qtprintsupport-${QT_VER}:${QT_SLOT}
-		>=dev-qt/qtsingleapplication-2.6.1_p20150629[X,qt5]
-		>=dev-qt/qtsensors-${QT_VER}:${QT_SLOT}
-		>=dev-qt/qtsql-${QT_VER}:${QT_SLOT}
-		>=dev-qt/qtsvg-${QT_VER}:${QT_SLOT}
-		>=dev-qt/qtwebkit-${QT_VER}:${QT_SLOT}
-		>=dev-qt/qtwidgets-${QT_VER}:${QT_SLOT}
-		>=dev-qt/qtxml-${QT_VER}:${QT_SLOT}
-		>=dev-qt/qtxmlpatterns-${QT_VER}:${QT_SLOT}
-		server? ( virtual/pam )
-	)
-	dedicated? ( virtual/pam )"
-DEPEND="${RDEPEND}
-	app-arch/unzip
-	dev-java/ant-core
-	>=virtual/jdk-1.8:=
-	virtual/pkgconfig"
-#	test? ( dev-java/junit:4 )
-
-PATCHES=(
-		"${FILESDIR}/${PN}-0.99.879-prefs.patch"
-		"${FILESDIR}/${PN}-1.0.44-paths.patch"
-		"${FILESDIR}/${PN}-1.0.44-clang-pandoc.patch"
-		"${FILESDIR}/${PN}-0.98.490-linker_flags.patch"
-		"${FILESDIR}/${PN}-0.98.1091-boost-1.57.patch"
-		"${FILESDIR}/${PN}-0.99.473-qtsingleapplication.patch"
-		"${FILESDIR}/${PN}-1.0.44-systemd.patch"
-)
-
-src_unpack() {
-	unpack ${P}.tar.gz gwt-${GWT_VER}.zip
-	cd "${S}" || die
-	mkdir -p src/gwt/lib/{gin,gwt} \
-		dependencies/common/dictionaries \
-		src/gwt/lib/selenium/${SELENIUM_VER} \
-		src/gwt/lib/selenium/chromedriver/${CHROMEDRIVER_VER} || die
-	mv ../gwt-${GWT_VER} src/gwt/lib/gwt/${GWT_VER} || die
-	unzip -qd src/gwt/lib/gin/${GIN_VER} \
-		"${DISTDIR}"/gin-${GIN_VER}.zip || die
-	unzip -qd dependencies/common/dictionaries \
-		"${DISTDIR}"/core-dictionaries.zip || die
-	unzip -qd src/gwt/lib/selenium/${SELENIUM_VER} \
-		"${DISTDIR}"/selenium-java-${SELENIUM_VER}.zip || die
-	cp "${DISTDIR}"/selenium-server-standalone-${SELENIUM_VER}.jar \
-		src/gwt/lib/selenium/${SELENIUM_VER}/ || die
-	cp "${DISTDIR}"/chromedriver-linux \
-		src/gwt/lib/selenium/chromedriver/${CHROMEDRIVER_VER}/ || die
-	cd dependencies/common || die
-	unpack packrat-${PACKRAT_VER}.tar.gz
-	unpack rmarkdown-${RMARKDOWN_VER}.tar.gz
-	unpack shinyapps-${SHINYAPPS_VER}.tar.gz
-	unpack rsconnect_${RSCONNECT_VER}.tar.gz
-	cp "${DISTDIR}"/rmarkdown-${RMARKDOWN_VER}.tar.gz \
-		. || die
-	cp "${DISTDIR}"/packrat-${PACKRAT_VER}.tar.gz \
-		. || die
-	cp "${DISTDIR}"/shinyapps-${SHINYAPPS_VER}.tar.gz \
-		. || die
-	cp "${DISTDIR}"/rsconnect_${RSCONNECT_VER}.tar.gz \
-		. || die
-}
-
-src_prepare() {
-	default
-	java-pkg-2_src_prepare
-	egit_clean
-
-	# Enable CMake to install our .service file for systemd usage
-	mkdir -vp "${S}/src/cpp/server/lib/systemd/system" || die
-	cp -v "${FILESDIR}/rstudio-server.service.in" "${S}/src/cpp/server/lib/systemd/system/" || die
-
-	# Adding -DDISTRO_SHARE=... to append-flags breaks cmake so using
-	# this sed hack for now. ~RMH
-	sed -i \
-		-e "s|DISTRO_SHARE|\"share/${PN}\"|g" \
-		src/cpp/server/ServerOptions.cpp \
-		src/cpp/session/SessionOptions.cpp || die
-
-	# use mathjax from system
-	ln -sf "${EPREFIX}"/usr/share/mathjax dependencies/common/mathjax-26 || die
-
-	# make sure icons and mime stuff are with prefix
-	sed -i \
-		-e "s:/usr:${EPREFIX}/usr:g" \
-		CMakeGlobals.txt src/cpp/desktop/CMakeLists.txt || die
-
-	# On Gentoo the rstudio-server configuration file is /etc/conf.d/rstudio-server.conf
-	sed -e "s@/etc/rstudio/rserver.conf@${EROOT}etc/conf.d/rstudio-server.conf@" \
-		-i src/cpp/server/ServerOptions.cpp \
-		|| die
-
-	# Set the rsession.conf file location for Gentoo prefix
-	sed -e "s@/etc/rstudio/rsession.conf@${EROOT}etc/rstudio/rsession.conf@" \
-		-i src/cpp/session/SessionOptions.cpp \
-		|| die
-
-	# dev-qt/qtsingleapplication-2.6.1_p20150629 does not provide a cmake module.
-	# It provides a library that has its version number appended to the end,
-	# which is difficult to handle in cmake, as find_library does not support
-	# searching for wildcard library names. So I find the library name from the
-	# qmake spec, and then sed this into the patched src/cpp/desktop/CMakeLists.txt.
-	rm -rf "${S}"/src/cpp/desktop/3rdparty || die
-	local s=$(grep '\-lQt$${QT_MAJOR_VERSION}Solutions_SingleApplication' \
-				   $(qt5_get_mkspecsdir)/features/qtsingleapplication.prf \
-					 | sed -e 's@\$\${QT_MAJOR_VERSION}@5@' \
-						   -e 's@LIBS \*= -l@@')
-	sed -e "s@Qt5Solutions_SingleApplication-2.6@${s}@g" \
-		-i "${S}"/src/cpp/desktop/CMakeLists.txt \
-		|| die
-
-	# The git commit for tag: git rev-list -n 1 v0.99.903
-	sed -e 's@git ARGS rev-parse HEAD@echo ARGS 0eb2d8ea28ebc1ac6ac327e023becb6133b679c4@'\
-		-i "${S}"/CMakeLists.txt \
-		"${S}"/CMakeGlobals.txt \
-		|| die
-}
-
-src_configure() {
-	export RSTUDIO_VERSION_MAJOR=$(get_version_component_range 1)
-	export RSTUDIO_VERSION_MINOR=$(get_version_component_range 2)
-	export RSTUDIO_VERSION_PATCH=$(get_version_component_range 3)
-
-	local mycmakeargs=(
-		-DDISTRO_SHARE=share/${PN}
-		-DRSTUDIO_INSTALL_FREEDESKTOP="$(usex !dedicated "ON" "OFF")"
-		-DRSTUDIO_TARGET=$(usex dedicated "Server" "$(usex server "Development" "Desktop")")
-		-DQT_QMAKE_EXECUTABLE=$(qt5_get_bindir)/qmake
-		-DRSTUDIO_VERIFY_R_VERSION=FALSE
-		)
-
-	cmake-utils_src_configure
-}
-
-src_compile() {
-	# Avoid the rest of the oracle-jdk-bin-1.8.0.60 sandbox violations F: mkdir S: deny
-	# P: /root/.oracle_jre_usage.
-	export ANT_OPTS="-Duser.home=${T}"
-	cmake-utils_src_compile
-}
-
-src_install() {
-	export ANT_OPTS="-Duser.home=${T}"
-	cmake-utils_src_install
-	pax-mark m "${ED}usr/bin/rstudio"
-	doconfd "${FILESDIR}"/rstudio-server.conf
-	dodir /etc/rstudio
-	insinto /etc/rstudio
-	doins "${FILESDIR}"/rsession.conf
-	dosym /etc/conf.d/rstudio-server.conf /etc/rstudio/rserver.conf
-	if use dedicated || use server; then
-		dopamd src/cpp/server/extras/pam/rstudio
-		newinitd "${FILESDIR}"/rstudio-server.initd rstudio-server
-	fi
-}
-
-pkg_preinst() {
-	use dedicated || gnome2_icon_savelist
-	java-pkg-2_pkg_preinst
-}
-
-pkg_postinst() {
-	use dedicated || { fdo-mime_desktop_database_update
-		fdo-mime_mime_database_update
-		gnome2_icon_cache_update ;}
-
-	if use dedicated || use server; then
-		enewgroup rstudio-server
-		enewuser rstudio-server -1 -1 -1 rstudio-server
-	fi
-}
-
-pkg_postrm() {
-	use dedicated || { fdo-mime_desktop_database_update
-		fdo-mime_mime_database_update
-		gnome2_icon_cache_update ;}
-}

diff --git a/sci-mathematics/rstudio/rstudio-1.0.44.ebuild b/sci-mathematics/rstudio/rstudio-1.0.44.ebuild
deleted file mode 100644
index dcb101cac4e..00000000000
--- a/sci-mathematics/rstudio/rstudio-1.0.44.ebuild
+++ /dev/null
@@ -1,247 +0,0 @@
-# Copyright 1999-2017 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-inherit eutils user cmake-utils gnome2-utils pam versionator fdo-mime java-pkg-2 pax-utils qmake-utils
-
-# TODO
-# * package gin and gwt
-# * use dict from tree, linguas
-# * do src_test (use junit from tree?)
-
-# update from scripts in dependencies/common
-# egrep '(GWT_SDK_VER=|GIN_VER=|SELENIUM_VER=|CHROMEDRIVER_VER=)' dependencies/common/install-gwt
-GWT_VER=2.7.0
-GIN_VER=1.5
-SELENIUM_VER=2.37.0
-CHROMEDRIVER_VER=2.7
-# grep 'PANDOC_VERSION=' dependencies/common/update-pandoc
-PANDOC_VER=1.13.1
-# ls dependencies/common/*.tar.gz
-PACKRAT_VER=0.98.1000
-RMARKDOWN_VER=0.98.1000
-SHINYAPPS_VER=0.98.1000
-RSCONNECT_VER=0.4.1.4_fcac892a69817febd7b655b189bf57193260cda0
-
-DESCRIPTION="IDE for the R language"
-HOMEPAGE="
-	http://www.rstudio.org
-	https://github.com/rstudio/rstudio/"
-SRC_URI="
-	https://github.com/rstudio/rstudio/archive/v${PV}.tar.gz -> ${P}.tar.gz
-	https://s3.amazonaws.com/rstudio-buildtools/gin-${GIN_VER}.zip
-	https://s3.amazonaws.com/rstudio-buildtools/gwt-${GWT_VER}.zip
-	https://s3.amazonaws.com/rstudio-buildtools/selenium-java-${SELENIUM_VER}.zip
-	https://s3.amazonaws.com/rstudio-buildtools/selenium-server-standalone-${SELENIUM_VER}.jar
-	https://s3.amazonaws.com/rstudio-buildtools/chromedriver-linux
-	https://s3.amazonaws.com/rstudio-dictionaries/core-dictionaries.zip
-	https://dev.gentoo.org/~gienah/distfiles/packrat-${PACKRAT_VER}.tar.gz
-	https://dev.gentoo.org/~gienah/distfiles/rmarkdown-${RMARKDOWN_VER}.tar.gz
-	https://dev.gentoo.org/~gienah/distfiles/shinyapps-${SHINYAPPS_VER}.tar.gz
-	https://dev.gentoo.org/~gienah/distfiles/rsconnect_${RSCONNECT_VER}.tar.gz
-"
-
-LICENSE="AGPL-3"
-SLOT="0"
-KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
-IUSE="dedicated server"
-
-QT_VER=5.4
-QT_SLOT=5
-RDEPEND="
-	app-text/pandoc
-	dev-haskell/pandoc-citeproc
-	>=dev-lang/R-2.11.1
-	>=dev-libs/boost-1.50:=
-	>=dev-libs/mathjax-2.7.0
-	dev-libs/openssl:0
-	sys-apps/util-linux
-	>=sys-devel/clang-3.5.0:*
-	sys-libs/zlib
-	>=virtual/jre-1.8:=
-	x11-libs/pango
-	!dedicated? (
-		>=dev-qt/qtcore-${QT_VER}:${QT_SLOT}
-		>=dev-qt/qtdeclarative-${QT_VER}:${QT_SLOT}
-		>=dev-qt/qtdbus-${QT_VER}:${QT_SLOT}
-		>=dev-qt/qtgui-${QT_VER}:${QT_SLOT}
-		>=dev-qt/qtnetwork-${QT_VER}:${QT_SLOT}
-		>=dev-qt/qtopengl-${QT_VER}:${QT_SLOT}
-		>=dev-qt/qtpositioning-${QT_VER}:${QT_SLOT}
-		>=dev-qt/qtprintsupport-${QT_VER}:${QT_SLOT}
-		>=dev-qt/qtsingleapplication-2.6.1_p20150629[X,qt5]
-		>=dev-qt/qtsensors-${QT_VER}:${QT_SLOT}
-		>=dev-qt/qtsql-${QT_VER}:${QT_SLOT}
-		>=dev-qt/qtsvg-${QT_VER}:${QT_SLOT}
-		>=dev-qt/qtwebkit-${QT_VER}:${QT_SLOT}
-		>=dev-qt/qtwidgets-${QT_VER}:${QT_SLOT}
-		>=dev-qt/qtxml-${QT_VER}:${QT_SLOT}
-		>=dev-qt/qtxmlpatterns-${QT_VER}:${QT_SLOT}
-		server? ( virtual/pam )
-	)
-	dedicated? ( virtual/pam )"
-DEPEND="${RDEPEND}
-	app-arch/unzip
-	dev-java/ant-core
-	>=virtual/jdk-1.8:=
-	virtual/pkgconfig"
-#	test? ( dev-java/junit:4 )
-
-PATCHES=(
-		"${FILESDIR}/${PN}-0.99.879-prefs.patch"
-		"${FILESDIR}/${PN}-1.0.44-paths.patch"
-		"${FILESDIR}/${PN}-1.0.44-clang-pandoc.patch"
-		"${FILESDIR}/${PN}-0.98.490-linker_flags.patch"
-		"${FILESDIR}/${PN}-0.98.1091-boost-1.57.patch"
-		"${FILESDIR}/${PN}-0.99.473-qtsingleapplication.patch"
-		"${FILESDIR}/${PN}-1.0.44-systemd.patch"
-)
-
-src_unpack() {
-	unpack ${P}.tar.gz gwt-${GWT_VER}.zip
-	cd "${S}" || die
-	mkdir -p src/gwt/lib/{gin,gwt} \
-		dependencies/common/dictionaries \
-		src/gwt/lib/selenium/${SELENIUM_VER} \
-		src/gwt/lib/selenium/chromedriver/${CHROMEDRIVER_VER} || die
-	mv ../gwt-${GWT_VER} src/gwt/lib/gwt/${GWT_VER} || die
-	unzip -qd src/gwt/lib/gin/${GIN_VER} \
-		"${DISTDIR}"/gin-${GIN_VER}.zip || die
-	unzip -qd dependencies/common/dictionaries \
-		"${DISTDIR}"/core-dictionaries.zip || die
-	unzip -qd src/gwt/lib/selenium/${SELENIUM_VER} \
-		"${DISTDIR}"/selenium-java-${SELENIUM_VER}.zip || die
-	cp "${DISTDIR}"/selenium-server-standalone-${SELENIUM_VER}.jar \
-		src/gwt/lib/selenium/${SELENIUM_VER}/ || die
-	cp "${DISTDIR}"/chromedriver-linux \
-		src/gwt/lib/selenium/chromedriver/${CHROMEDRIVER_VER}/ || die
-	cd dependencies/common || die
-	unpack packrat-${PACKRAT_VER}.tar.gz
-	unpack rmarkdown-${RMARKDOWN_VER}.tar.gz
-	unpack shinyapps-${SHINYAPPS_VER}.tar.gz
-	unpack rsconnect_${RSCONNECT_VER}.tar.gz
-	cp "${DISTDIR}"/rmarkdown-${RMARKDOWN_VER}.tar.gz \
-		. || die
-	cp "${DISTDIR}"/packrat-${PACKRAT_VER}.tar.gz \
-		. || die
-	cp "${DISTDIR}"/shinyapps-${SHINYAPPS_VER}.tar.gz \
-		. || die
-	cp "${DISTDIR}"/rsconnect_${RSCONNECT_VER}.tar.gz \
-		. || die
-}
-
-src_prepare() {
-	default
-	java-pkg-2_src_prepare
-	egit_clean
-
-	# Enable CMake to install our .service file for systemd usage
-	mkdir -vp "${S}/src/cpp/server/lib/systemd/system" || die
-	cp -v "${FILESDIR}/rstudio-server.service.in" "${S}/src/cpp/server/lib/systemd/system/" || die
-
-	# Adding -DDISTRO_SHARE=... to append-flags breaks cmake so using
-	# this sed hack for now. ~RMH
-	sed -i \
-		-e "s|DISTRO_SHARE|\"share/${PN}\"|g" \
-		src/cpp/server/ServerOptions.cpp \
-		src/cpp/session/SessionOptions.cpp || die
-
-	# use mathjax from system
-	ln -sf "${EPREFIX}"/usr/share/mathjax dependencies/common/mathjax-26 || die
-
-	# make sure icons and mime stuff are with prefix
-	sed -i \
-		-e "s:/usr:${EPREFIX}/usr:g" \
-		CMakeGlobals.txt src/cpp/desktop/CMakeLists.txt || die
-
-	# On Gentoo the rstudio-server configuration file is /etc/conf.d/rstudio-server.conf
-	sed -e "s@/etc/rstudio/rserver.conf@${EROOT}etc/conf.d/rstudio-server.conf@" \
-		-i src/cpp/server/ServerOptions.cpp \
-		|| die
-
-	# Set the rsession.conf file location for Gentoo prefix
-	sed -e "s@/etc/rstudio/rsession.conf@${EROOT}etc/rstudio/rsession.conf@" \
-		-i src/cpp/session/SessionOptions.cpp \
-		|| die
-
-	# dev-qt/qtsingleapplication-2.6.1_p20150629 does not provide a cmake module.
-	# It provides a library that has its version number appended to the end,
-	# which is difficult to handle in cmake, as find_library does not support
-	# searching for wildcard library names. So I find the library name from the
-	# qmake spec, and then sed this into the patched src/cpp/desktop/CMakeLists.txt.
-	rm -rf "${S}"/src/cpp/desktop/3rdparty || die
-	local s=$(grep '\-lQt$${QT_MAJOR_VERSION}Solutions_SingleApplication' \
-				   $(qt5_get_mkspecsdir)/features/qtsingleapplication.prf \
-					 | sed -e 's@\$\${QT_MAJOR_VERSION}@5@' \
-						   -e 's@LIBS \*= -l@@')
-	sed -e "s@Qt5Solutions_SingleApplication-2.6@${s}@g" \
-		-i "${S}"/src/cpp/desktop/CMakeLists.txt \
-		|| die
-
-	# The git commit for tag: git rev-list -n 1 v0.99.903
-	sed -e 's@git ARGS rev-parse HEAD@echo ARGS 0eb2d8ea28ebc1ac6ac327e023becb6133b679c4@'\
-		-i "${S}"/CMakeLists.txt \
-		"${S}"/CMakeGlobals.txt \
-		|| die
-}
-
-src_configure() {
-	export RSTUDIO_VERSION_MAJOR=$(get_version_component_range 1)
-	export RSTUDIO_VERSION_MINOR=$(get_version_component_range 2)
-	export RSTUDIO_VERSION_PATCH=$(get_version_component_range 3)
-
-	local mycmakeargs=(
-		-DDISTRO_SHARE=share/${PN}
-		-DRSTUDIO_INSTALL_FREEDESKTOP="$(usex !dedicated "ON" "OFF")"
-		-DRSTUDIO_TARGET=$(usex dedicated "Server" "$(usex server "Development" "Desktop")")
-		-DQT_QMAKE_EXECUTABLE=$(qt5_get_bindir)/qmake
-		-DRSTUDIO_VERIFY_R_VERSION=FALSE
-		)
-
-	cmake-utils_src_configure
-}
-
-src_compile() {
-	# Avoid the rest of the oracle-jdk-bin-1.8.0.60 sandbox violations F: mkdir S: deny
-	# P: /root/.oracle_jre_usage.
-	export ANT_OPTS="-Duser.home=${T}"
-	cmake-utils_src_compile
-}
-
-src_install() {
-	export ANT_OPTS="-Duser.home=${T}"
-	cmake-utils_src_install
-	pax-mark m "${ED}usr/bin/rstudio"
-	doconfd "${FILESDIR}"/rstudio-server.conf
-	dodir /etc/rstudio
-	insinto /etc/rstudio
-	doins "${FILESDIR}"/rsession.conf
-	dosym /etc/conf.d/rstudio-server.conf /etc/rstudio/rserver.conf
-	if use dedicated || use server; then
-		dopamd src/cpp/server/extras/pam/rstudio
-		newinitd "${FILESDIR}"/rstudio-server.initd rstudio-server
-	fi
-}
-
-pkg_preinst() {
-	use dedicated || gnome2_icon_savelist
-	java-pkg-2_pkg_preinst
-}
-
-pkg_postinst() {
-	use dedicated || { fdo-mime_desktop_database_update
-		fdo-mime_mime_database_update
-		gnome2_icon_cache_update ;}
-
-	if use dedicated || use server; then
-		enewgroup rstudio-server
-		enewuser rstudio-server -1 -1 -1 rstudio-server
-	fi
-}
-
-pkg_postrm() {
-	use dedicated || { fdo-mime_desktop_database_update
-		fdo-mime_mime_database_update
-		gnome2_icon_cache_update ;}
-}


^ permalink raw reply related	[flat|nested] 12+ messages in thread

* [gentoo-commits] repo/gentoo:master commit in: sci-mathematics/rstudio/, sci-mathematics/rstudio/files/
@ 2018-05-03 11:48 Andreas Sturmlechner
  0 siblings, 0 replies; 12+ messages in thread
From: Andreas Sturmlechner @ 2018-05-03 11:48 UTC (permalink / raw
  To: gentoo-commits

commit:     501d7bfb446a299cd64c67eec0ba789e79004ac9
Author:     Andreas Sturmlechner <asturm <AT> gentoo <DOT> org>
AuthorDate: Thu May  3 11:48:42 2018 +0000
Commit:     Andreas Sturmlechner <asturm <AT> gentoo <DOT> org>
CommitDate: Thu May  3 11:48:42 2018 +0000
URL:        https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=501d7bfb

sci-mathematics/rstudio: Drop old

Package-Manager: Portage-2.3.33, Repoman-2.3.9

 sci-mathematics/rstudio/Manifest                   |   1 -
 .../files/rstudio-0.98.1091-boost-1.57.patch       |  60 -----
 sci-mathematics/rstudio/rstudio-1.1.368.ebuild     | 248 ---------------------
 3 files changed, 309 deletions(-)

diff --git a/sci-mathematics/rstudio/Manifest b/sci-mathematics/rstudio/Manifest
index 41930c74cdf..68418950fa6 100644
--- a/sci-mathematics/rstudio/Manifest
+++ b/sci-mathematics/rstudio/Manifest
@@ -5,7 +5,6 @@ DIST gwt-2.7.0.zip 108818328 BLAKE2B 9af969f3f2577be041fcfb58f228fab4b5479fa0da5
 DIST packrat-0.98.1000.tar.gz 97677 BLAKE2B 282fe33dc5ba366ceea05a222ae2d018bc3ad8f35fad73c585a3d4901c3287e6902277a9c7ca087854f3944bd85ff1b1d1f02869ece686b10f946e2f1cb1296c SHA512 2290c768ecf27a037e73c3f8336b9fd71c68ff19d071b4a8fbc469550d29007cacacdb75f854f73b5db2139a5104f129b85a3612e2ee47bd6118ee13f7d103a6
 DIST rmarkdown-0.98.1000.tar.gz 1423820 BLAKE2B eac8c9cf438c9b44ddfe954602dd67a83764b0c988b3ba571877c986b0d5d237059ed6643a86bb404428857ec8c346bfecd12f7cd15cde301cb0ce331f842b7f SHA512 df3540c24c87930fe55bff2ffe67c86c219800cb00ed72ba9451ecd0d0cad411548a78c1a04b9a2e301e853616dcb77e09129c4e48ade6f16d3f14b7ea7e4852
 DIST rsconnect_0.4.1.4_fcac892a69817febd7b655b189bf57193260cda0.tar.gz 197051 BLAKE2B 1f3f9fe71d7b50ab5108dfdbd3cc0b882bcc935ee58e8a9145b07a18bb86c39bc45e321a13add24df99492bc30548df716775c339bcbf4efc2bfe158299ae55a SHA512 208dc349f4aa7613ecf94939aba60d22d3a06972344b526c9b6c951015571f5922927bca08db571a7b8a268e42609a4f558f01278c9685f6da2ffc66a1f95ade
-DIST rstudio-1.1.368.tar.gz 20197144 BLAKE2B c97a86faa28b40552539eebc4faeec8a4199df6972efc2b112a2af08e47982e41b7cd92a6f06d14411dd67c21efa632ab017d99d28c1521f90b6075ed0232ce0 SHA512 39cdf583d7dcd22338916cc0ea4f90681580e41663b2d3e04b2e650759c6b030c85ee111cdfe1f717f931932a9b7ca423a21585d69a785f056f754f6d50399a1
 DIST rstudio-1.1.383.tar.gz 20196702 BLAKE2B 5164230a92618e4252269ad0016b200294d1e7fa502cc49aa694486cda098ee7ffc65e6c74a87d891d0532f5cc15d1552aa86d04047d07b4f275cbc4d2758647 SHA512 3f637f9bce2c1ad1a4ed3e74287da722190a4e12b0cace6ffcca271977d49dcecca9365f2064366aad94e87851593cab83fa9361e9a9222a9f67fe9451f31ed2
 DIST selenium-java-2.37.0.zip 24625928 BLAKE2B b369a805ae96f0d0913c4be42888d9c2a1e213ff982f9daefe73fadb705baa80ab0186ab50ed52609e83697cffaf8d617d06d75405cb8e1c3fe8e7c5b81dba25 SHA512 68624e82dbc751a25c50fad72702a98eb30d77fd4337d2a969f8e06bcc49e5f8c835cd27ec53772f3375014ddde1d5636936e966b75f3594a9f86aa18ba4e779
 DIST selenium-server-standalone-2.37.0.jar 34730734 BLAKE2B 3899b1d4c5f9153c1f9f13bec66f7c1456ea2e0f34db7d8e54a1ce9063c33a05b3cf95216c2ae06bb40504f72f343a4b9ba6c8553fbbc340e7c18a5b612dde5c SHA512 b215446d42d2d1f69664349b6ae6dc53a532d3624c91254f0f4183d0ad764648792e5cc1126a55a1e60d9687d55200fed01d6d2f46cc3d853b1fa6ee38111018

diff --git a/sci-mathematics/rstudio/files/rstudio-0.98.1091-boost-1.57.patch b/sci-mathematics/rstudio/files/rstudio-0.98.1091-boost-1.57.patch
deleted file mode 100644
index 3a157183c22..00000000000
--- a/sci-mathematics/rstudio/files/rstudio-0.98.1091-boost-1.57.patch
+++ /dev/null
@@ -1,60 +0,0 @@
---- rstudio-0.98.1091-orig/src/cpp/desktop/DesktopApplicationLaunch.hpp	2014-11-06 23:15:47.000000000 +1100
-+++ rstudio-0.98.1091/src/cpp/desktop/DesktopApplicationLaunch.hpp	2015-02-28 14:01:51.970672316 +1100
-@@ -19,7 +19,10 @@
- #include <QObject>
- #include <QWidget>
- #include <QApplication>
-+// see https://bugreports.qt-project.org/browse/QTBUG-22829
-+#ifndef Q_MOC_RUN
- #include <boost/scoped_ptr.hpp>
-+#endif
- 
- namespace desktop {
- 
---- rstudio-0.98.1091-orig/src/cpp/desktop/DesktopSessionLauncher.hpp	2014-11-06 23:15:47.000000000 +1100
-+++ rstudio-0.98.1091/src/cpp/desktop/DesktopSessionLauncher.hpp	2015-02-28 14:01:51.972672316 +1100
-@@ -18,7 +18,10 @@
- 
- #include <string>
- 
-+// see https://bugreports.qt-project.org/browse/QTBUG-22829
-+#ifndef Q_MOC_RUN
- #include <boost/utility.hpp>
-+#endif
- 
- #include <core/Error.hpp>
- #include <core/FilePath.hpp>
---- rstudio-0.98.1091-orig/src/cpp/core/include/core/FilePath.hpp	2014-11-06 23:15:47.000000000 +1100
-+++ rstudio-0.98.1091/src/cpp/core/include/core/FilePath.hpp	2015-02-28 14:01:51.984672314 +1100
-@@ -23,11 +23,14 @@
- #include <vector>
- #include <iosfwd>
- 
-+// see https://bugreports.qt-project.org/browse/QTBUG-22829
-+#ifndef Q_MOC_RUN
- #include <boost/shared_ptr.hpp>
- #include <boost/scoped_ptr.hpp>
- #include <boost/function.hpp>
- 
- #include <boost/utility.hpp>
-+#endif
- 
- #include <core/Error.hpp>
- #include <core/Log.hpp>
---- rstudio-0.98.1091-orig/src/cpp/core/include/core/Error.hpp	2014-11-06 23:15:47.000000000 +1100
-+++ rstudio-0.98.1091/src/cpp/core/include/core/Error.hpp	2015-02-28 14:01:51.977672315 +1100
-@@ -20,11 +20,14 @@
- #include <string>
- #include <vector>
- 
-+// see https://bugreports.qt-project.org/browse/QTBUG-22829
-+#ifndef Q_MOC_RUN
- #include <boost/shared_ptr.hpp>
- 
- #include <boost/system/error_code.hpp>
- 
- #include <boost/current_function.hpp>
-+#endif
- 
- namespace core {
- 

diff --git a/sci-mathematics/rstudio/rstudio-1.1.368.ebuild b/sci-mathematics/rstudio/rstudio-1.1.368.ebuild
deleted file mode 100644
index 221887f8aa3..00000000000
--- a/sci-mathematics/rstudio/rstudio-1.1.368.ebuild
+++ /dev/null
@@ -1,248 +0,0 @@
-# Copyright 1999-2017 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-inherit eutils user cmake-utils gnome2-utils pam versionator xdg-utils java-pkg-2 pax-utils qmake-utils
-
-# TODO
-# * package gin and gwt
-# * use dict from tree, linguas
-# * do src_test (use junit from tree?)
-
-# update from scripts in dependencies/common
-# egrep '(GWT_SDK_VER=|GIN_VER=|SELENIUM_VER=|CHROMEDRIVER_VER=)' dependencies/common/install-gwt
-GWT_VER=2.7.0
-GIN_VER=1.5
-SELENIUM_VER=2.37.0
-CHROMEDRIVER_VER=2.7
-# grep 'PANDOC_VERSION=' dependencies/common/update-pandoc
-PANDOC_VER=1.13.1
-# ls dependencies/common/*.tar.gz
-PACKRAT_VER=0.98.1000
-RMARKDOWN_VER=0.98.1000
-SHINYAPPS_VER=0.98.1000
-RSCONNECT_VER=0.4.1.4_fcac892a69817febd7b655b189bf57193260cda0
-
-DESCRIPTION="IDE for the R language"
-HOMEPAGE="
-	http://www.rstudio.org
-	https://github.com/rstudio/rstudio/"
-SRC_URI="
-	https://github.com/rstudio/rstudio/archive/v${PV}.tar.gz -> ${P}.tar.gz
-	https://s3.amazonaws.com/rstudio-buildtools/gin-${GIN_VER}.zip
-	https://s3.amazonaws.com/rstudio-buildtools/gwt-${GWT_VER}.zip
-	https://s3.amazonaws.com/rstudio-buildtools/selenium-java-${SELENIUM_VER}.zip
-	https://s3.amazonaws.com/rstudio-buildtools/selenium-server-standalone-${SELENIUM_VER}.jar
-	https://s3.amazonaws.com/rstudio-buildtools/chromedriver-linux
-	https://s3.amazonaws.com/rstudio-dictionaries/core-dictionaries.zip
-	https://dev.gentoo.org/~gienah/distfiles/packrat-${PACKRAT_VER}.tar.gz
-	https://dev.gentoo.org/~gienah/distfiles/rmarkdown-${RMARKDOWN_VER}.tar.gz
-	https://dev.gentoo.org/~gienah/distfiles/shinyapps-${SHINYAPPS_VER}.tar.gz
-	https://dev.gentoo.org/~gienah/distfiles/rsconnect_${RSCONNECT_VER}.tar.gz
-"
-
-LICENSE="AGPL-3"
-SLOT="0"
-KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
-IUSE="dedicated server"
-
-QT_VER=5.4
-QT_SLOT=5
-RDEPEND="
-	app-text/pandoc
-	dev-haskell/pandoc-citeproc
-	>=dev-lang/R-2.11.1
-	>=dev-libs/boost-1.63:=
-	>=dev-libs/mathjax-2.7.0
-	dev-libs/openssl:0
-	sys-apps/util-linux
-	>=sys-devel/clang-3.5.0:*
-	sys-libs/zlib
-	>=virtual/jre-1.8:=
-	x11-libs/pango
-	!dedicated? (
-		>=dev-qt/qtcore-${QT_VER}:${QT_SLOT}
-		>=dev-qt/qtdeclarative-${QT_VER}:${QT_SLOT}
-		>=dev-qt/qtdbus-${QT_VER}:${QT_SLOT}
-		>=dev-qt/qtgui-${QT_VER}:${QT_SLOT}
-		>=dev-qt/qtnetwork-${QT_VER}:${QT_SLOT}
-		>=dev-qt/qtopengl-${QT_VER}:${QT_SLOT}
-		>=dev-qt/qtpositioning-${QT_VER}:${QT_SLOT}
-		>=dev-qt/qtprintsupport-${QT_VER}:${QT_SLOT}
-		>=dev-qt/qtsingleapplication-2.6.1_p20150629[X,qt5]
-		>=dev-qt/qtsensors-${QT_VER}:${QT_SLOT}
-		>=dev-qt/qtsql-${QT_VER}:${QT_SLOT}
-		>=dev-qt/qtsvg-${QT_VER}:${QT_SLOT}
-		>=dev-qt/qtwebchannel-${QT_VER}:${QT_SLOT}
-		>=dev-qt/qtwebkit-${QT_VER}:${QT_SLOT}
-		>=dev-qt/qtwidgets-${QT_VER}:${QT_SLOT}
-		>=dev-qt/qtxml-${QT_VER}:${QT_SLOT}
-		>=dev-qt/qtxmlpatterns-${QT_VER}:${QT_SLOT}
-		server? ( virtual/pam )
-	)
-	dedicated? ( virtual/pam )"
-DEPEND="${RDEPEND}
-	app-arch/unzip
-	dev-java/ant-core
-	>=virtual/jdk-1.8:=
-	virtual/pkgconfig"
-#	test? ( dev-java/junit:4 )
-
-PATCHES=(
-		"${FILESDIR}/${PN}-0.99.879-prefs.patch"
-		"${FILESDIR}/${PN}-1.0.44-paths.patch"
-		"${FILESDIR}/${PN}-1.1.357-clang-pandoc.patch"
-		"${FILESDIR}/${PN}-0.98.490-linker_flags.patch"
-		"${FILESDIR}/${PN}-0.98.1091-boost-1.57.patch"
-		"${FILESDIR}/${PN}-0.99.473-qtsingleapplication.patch"
-		"${FILESDIR}/${PN}-1.0.44-systemd.patch"
-)
-
-src_unpack() {
-	unpack ${P}.tar.gz gwt-${GWT_VER}.zip
-	cd "${S}" || die
-	mkdir -p src/gwt/lib/{gin,gwt} \
-		dependencies/common/dictionaries \
-		src/gwt/lib/selenium/${SELENIUM_VER} \
-		src/gwt/lib/selenium/chromedriver/${CHROMEDRIVER_VER} || die
-	mv ../gwt-${GWT_VER} src/gwt/lib/gwt/${GWT_VER} || die
-	unzip -qd src/gwt/lib/gin/${GIN_VER} \
-		"${DISTDIR}"/gin-${GIN_VER}.zip || die
-	unzip -qd dependencies/common/dictionaries \
-		"${DISTDIR}"/core-dictionaries.zip || die
-	unzip -qd src/gwt/lib/selenium/${SELENIUM_VER} \
-		"${DISTDIR}"/selenium-java-${SELENIUM_VER}.zip || die
-	cp "${DISTDIR}"/selenium-server-standalone-${SELENIUM_VER}.jar \
-		src/gwt/lib/selenium/${SELENIUM_VER}/ || die
-	cp "${DISTDIR}"/chromedriver-linux \
-		src/gwt/lib/selenium/chromedriver/${CHROMEDRIVER_VER}/ || die
-	cd dependencies/common || die
-	unpack packrat-${PACKRAT_VER}.tar.gz
-	unpack rmarkdown-${RMARKDOWN_VER}.tar.gz
-	unpack shinyapps-${SHINYAPPS_VER}.tar.gz
-	unpack rsconnect_${RSCONNECT_VER}.tar.gz
-	cp "${DISTDIR}"/rmarkdown-${RMARKDOWN_VER}.tar.gz \
-		. || die
-	cp "${DISTDIR}"/packrat-${PACKRAT_VER}.tar.gz \
-		. || die
-	cp "${DISTDIR}"/shinyapps-${SHINYAPPS_VER}.tar.gz \
-		. || die
-	cp "${DISTDIR}"/rsconnect_${RSCONNECT_VER}.tar.gz \
-		. || die
-}
-
-src_prepare() {
-	cmake-utils_src_prepare
-	java-pkg-2_src_prepare
-	egit_clean
-
-	# Enable CMake to install our .service file for systemd usage
-	mkdir -vp "${S}/src/cpp/server/lib/systemd/system" || die
-	cp -v "${FILESDIR}/rstudio-server.service.in" "${S}/src/cpp/server/lib/systemd/system/" || die
-
-	# Adding -DDISTRO_SHARE=... to append-flags breaks cmake so using
-	# this sed hack for now. ~RMH
-	sed -i \
-		-e "s|DISTRO_SHARE|\"share/${PN}\"|g" \
-		src/cpp/server/ServerOptions.cpp \
-		src/cpp/session/SessionOptions.cpp || die
-
-	# use mathjax from system
-	ln -sf "${EPREFIX}"/usr/share/mathjax dependencies/common/mathjax-26 || die
-
-	# make sure icons and mime stuff are with prefix
-	sed -i \
-		-e "s:/usr:${EPREFIX}/usr:g" \
-		CMakeGlobals.txt src/cpp/desktop/CMakeLists.txt || die
-
-	# On Gentoo the rstudio-server configuration file is /etc/conf.d/rstudio-server.conf
-	sed -e "s@/etc/rstudio/rserver.conf@${EROOT}etc/conf.d/rstudio-server.conf@" \
-		-i src/cpp/server/ServerOptions.cpp \
-		|| die
-
-	# Set the rsession.conf file location for Gentoo prefix
-	sed -e "s@/etc/rstudio/rsession.conf@${EROOT}etc/rstudio/rsession.conf@" \
-		-i src/cpp/session/SessionOptions.cpp \
-		|| die
-
-	# dev-qt/qtsingleapplication-2.6.1_p20150629 does not provide a cmake module.
-	# It provides a library that has its version number appended to the end,
-	# which is difficult to handle in cmake, as find_library does not support
-	# searching for wildcard library names. So I find the library name from the
-	# qmake spec, and then sed this into the patched src/cpp/desktop/CMakeLists.txt.
-	rm -rf "${S}"/src/cpp/desktop/3rdparty || die
-	local s=$(grep '\-lQt$${QT_MAJOR_VERSION}Solutions_SingleApplication' \
-				   $(qt5_get_mkspecsdir)/features/qtsingleapplication.prf \
-					 | sed -e 's@\$\${QT_MAJOR_VERSION}@5@' \
-						   -e 's@LIBS \*= -l@@')
-	sed -e "s@Qt5Solutions_SingleApplication-2.6@${s}@g" \
-		-i "${S}"/src/cpp/desktop/CMakeLists.txt \
-		|| die
-
-	# The git commit for tag: git rev-list -n 1 v0.99.903
-	sed -e 's@git ARGS rev-parse HEAD@echo ARGS 0eb2d8ea28ebc1ac6ac327e023becb6133b679c4@'\
-		-i "${S}"/CMakeLists.txt \
-		"${S}"/CMakeGlobals.txt \
-		|| die
-}
-
-src_configure() {
-	export RSTUDIO_VERSION_MAJOR=$(get_version_component_range 1)
-	export RSTUDIO_VERSION_MINOR=$(get_version_component_range 2)
-	export RSTUDIO_VERSION_PATCH=$(get_version_component_range 3)
-
-	local mycmakeargs=(
-		-DDISTRO_SHARE=share/${PN}
-		-DRSTUDIO_INSTALL_FREEDESKTOP="$(usex !dedicated "ON" "OFF")"
-		-DRSTUDIO_TARGET=$(usex dedicated "Server" "$(usex server "Development" "Desktop")")
-		-DQT_QMAKE_EXECUTABLE=$(qt5_get_bindir)/qmake
-		-DRSTUDIO_VERIFY_R_VERSION=FALSE
-		)
-
-	cmake-utils_src_configure
-}
-
-src_compile() {
-	# Avoid the rest of the oracle-jdk-bin-1.8.0.60 sandbox violations F: mkdir S: deny
-	# P: /root/.oracle_jre_usage.
-	export ANT_OPTS="-Duser.home=${T}"
-	cmake-utils_src_compile
-}
-
-src_install() {
-	export ANT_OPTS="-Duser.home=${T}"
-	cmake-utils_src_install
-	pax-mark m "${ED}usr/bin/rstudio"
-	doconfd "${FILESDIR}"/rstudio-server.conf
-	dodir /etc/rstudio
-	insinto /etc/rstudio
-	doins "${FILESDIR}"/rsession.conf
-	dosym "${ROOT}etc/conf.d/rstudio-server.conf" "${ROOT}etc/rstudio/rserver.conf"
-	if use dedicated || use server; then
-		dopamd src/cpp/server/extras/pam/rstudio
-		newinitd "${FILESDIR}"/rstudio-server.initd rstudio-server
-	fi
-}
-
-pkg_preinst() {
-	use dedicated || gnome2_icon_savelist
-	java-pkg-2_pkg_preinst
-}
-
-pkg_postinst() {
-	use dedicated || { xdg_desktop_database_update
-		xdg_mimeinfo_database_update
-		gnome2_icon_cache_update ;}
-
-	if use dedicated || use server; then
-		enewgroup rstudio-server
-		enewuser rstudio-server -1 -1 -1 rstudio-server
-	fi
-}
-
-pkg_postrm() {
-	use dedicated || { xdg_desktop_database_update
-		xdg_mimeinfo_database_update
-		gnome2_icon_cache_update ;}
-}


^ permalink raw reply related	[flat|nested] 12+ messages in thread

* [gentoo-commits] repo/gentoo:master commit in: sci-mathematics/rstudio/, sci-mathematics/rstudio/files/
@ 2018-07-03  2:39 Mark Wright
  0 siblings, 0 replies; 12+ messages in thread
From: Mark Wright @ 2018-07-03  2:39 UTC (permalink / raw
  To: gentoo-commits

commit:     07ba37d27c35a88152a5f413289892c47b8325c6
Author:     Mark Wright <gienah <AT> gentoo <DOT> org>
AuthorDate: Tue Jul  3 02:09:07 2018 +0000
Commit:     Mark Wright <gienah <AT> gentoo <DOT> org>
CommitDate: Tue Jul  3 02:38:40 2018 +0000
URL:        https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=07ba37d2

sci-mathematics/rstudio: Bump to 1.1.453

Thanks to John Dough for reporting 652116.
Thanks to Harris Landgarten for reporting 626056.
Closes https://bugs.gentoo.org/652116
Closes https://bugs.gentoo.org/626056

 sci-mathematics/rstudio/Manifest                   |   1 +
 .../files/rstudio-1.1.453-boost-1.67.0.patch       |  38 ++++
 .../rstudio/files/rstudio-1.1.453-core.patch       | 143 ++++++++++++
 sci-mathematics/rstudio/rstudio-1.1.453.ebuild     | 249 +++++++++++++++++++++
 4 files changed, 431 insertions(+)

diff --git a/sci-mathematics/rstudio/Manifest b/sci-mathematics/rstudio/Manifest
index 68418950fa6..77cc3217237 100644
--- a/sci-mathematics/rstudio/Manifest
+++ b/sci-mathematics/rstudio/Manifest
@@ -6,6 +6,7 @@ DIST packrat-0.98.1000.tar.gz 97677 BLAKE2B 282fe33dc5ba366ceea05a222ae2d018bc3a
 DIST rmarkdown-0.98.1000.tar.gz 1423820 BLAKE2B eac8c9cf438c9b44ddfe954602dd67a83764b0c988b3ba571877c986b0d5d237059ed6643a86bb404428857ec8c346bfecd12f7cd15cde301cb0ce331f842b7f SHA512 df3540c24c87930fe55bff2ffe67c86c219800cb00ed72ba9451ecd0d0cad411548a78c1a04b9a2e301e853616dcb77e09129c4e48ade6f16d3f14b7ea7e4852
 DIST rsconnect_0.4.1.4_fcac892a69817febd7b655b189bf57193260cda0.tar.gz 197051 BLAKE2B 1f3f9fe71d7b50ab5108dfdbd3cc0b882bcc935ee58e8a9145b07a18bb86c39bc45e321a13add24df99492bc30548df716775c339bcbf4efc2bfe158299ae55a SHA512 208dc349f4aa7613ecf94939aba60d22d3a06972344b526c9b6c951015571f5922927bca08db571a7b8a268e42609a4f558f01278c9685f6da2ffc66a1f95ade
 DIST rstudio-1.1.383.tar.gz 20196702 BLAKE2B 5164230a92618e4252269ad0016b200294d1e7fa502cc49aa694486cda098ee7ffc65e6c74a87d891d0532f5cc15d1552aa86d04047d07b4f275cbc4d2758647 SHA512 3f637f9bce2c1ad1a4ed3e74287da722190a4e12b0cace6ffcca271977d49dcecca9365f2064366aad94e87851593cab83fa9361e9a9222a9f67fe9451f31ed2
+DIST rstudio-1.1.453.tar.gz 20200360 BLAKE2B 560b89e53b04356ecf9a02dd8a7e72ad8d6c30bf406fbe7e22a82cc6d33d40e84bececf5ecda9cf086360b2bd2fa64d6b33c2dd675ef5f605f9e825d7ca2dc84 SHA512 f2be0866f645007a6f80959109928820c89480057c3660d23e790591797d4f4c371733f49290dae9c81bfc2715821528e2a105e7a66d4d9ffbfc7ee2a596976c
 DIST selenium-java-2.37.0.zip 24625928 BLAKE2B b369a805ae96f0d0913c4be42888d9c2a1e213ff982f9daefe73fadb705baa80ab0186ab50ed52609e83697cffaf8d617d06d75405cb8e1c3fe8e7c5b81dba25 SHA512 68624e82dbc751a25c50fad72702a98eb30d77fd4337d2a969f8e06bcc49e5f8c835cd27ec53772f3375014ddde1d5636936e966b75f3594a9f86aa18ba4e779
 DIST selenium-server-standalone-2.37.0.jar 34730734 BLAKE2B 3899b1d4c5f9153c1f9f13bec66f7c1456ea2e0f34db7d8e54a1ce9063c33a05b3cf95216c2ae06bb40504f72f343a4b9ba6c8553fbbc340e7c18a5b612dde5c SHA512 b215446d42d2d1f69664349b6ae6dc53a532d3624c91254f0f4183d0ad764648792e5cc1126a55a1e60d9687d55200fed01d6d2f46cc3d853b1fa6ee38111018
 DIST shinyapps-0.98.1000.tar.gz 910095 BLAKE2B 4f9364692348bb52cbd12cc6ee447841cb0c805327f2518b2a9545920b602b954a98dea68ccb3daf32d2c3bab6464fb15402844d93277193315f1ae7b3ca5190 SHA512 3162317c4c20cfc1497e952a8235867084d629ae88407e6c465b3e208adb1dc97abfe6b9922e0374ddf4c8e38a76e112942bd312c54a66f74e6f2a3fe4c0a07c

diff --git a/sci-mathematics/rstudio/files/rstudio-1.1.453-boost-1.67.0.patch b/sci-mathematics/rstudio/files/rstudio-1.1.453-boost-1.67.0.patch
new file mode 100644
index 00000000000..760c9b56105
--- /dev/null
+++ b/sci-mathematics/rstudio/files/rstudio-1.1.453-boost-1.67.0.patch
@@ -0,0 +1,38 @@
+--- rstudio-1.1.453-orig/src/cpp/core/DateTime.cpp	2018-05-15 04:19:30.000000000 +1000
++++ rstudio-1.1.453/src/cpp/core/DateTime.cpp	2018-07-02 16:19:21.335703471 +1000
+@@ -65,7 +65,7 @@
+    using namespace boost::posix_time;
+ 
+    ptime time_t_epoch(date(1970,1,1));
+-   return time_t_epoch + seconds(sec);
++   return time_t_epoch + seconds(static_cast<long>(sec));
+ }
+ 
+ boost::posix_time::ptime timeFromMillisecondsSinceEpoch(int64_t ms)
+--- rstudio-1.1.453-orig/src/cpp/core/file_lock/FileLock.cpp	2018-05-15 04:19:30.000000000 +1000
++++ rstudio-1.1.453/src/cpp/core/file_lock/FileLock.cpp	2018-07-02 17:00:35.915695201 +1000
+@@ -133,11 +133,11 @@
+ 
+    // timeout interval
+    double timeoutInterval = getFieldPositive(settings, "timeout-interval", kDefaultTimeoutInterval);
+-   FileLock::s_timeoutInterval = boost::posix_time::seconds(timeoutInterval);
++   FileLock::s_timeoutInterval = boost::posix_time::seconds(static_cast<long>(timeoutInterval));
+    
+    // refresh rate
+    double refreshRate = getFieldPositive(settings, "refresh-rate", kDefaultRefreshRate);
+-   FileLock::s_refreshRate = boost::posix_time::seconds(refreshRate);
++   FileLock::s_refreshRate = boost::posix_time::seconds(static_cast<long>(refreshRate));
+    
+    // logging
+    bool loggingEnabled = settings.getBool("enable-logging", false);
+@@ -212,8 +212,8 @@
+ 
+ // default values for static members
+ FileLock::LockType FileLock::s_defaultType(FileLock::LOCKTYPE_LINKBASED);
+-boost::posix_time::seconds FileLock::s_timeoutInterval(kDefaultTimeoutInterval);
+-boost::posix_time::seconds FileLock::s_refreshRate(kDefaultRefreshRate);
++boost::posix_time::seconds FileLock::s_timeoutInterval(static_cast<long>(kDefaultTimeoutInterval));
++boost::posix_time::seconds FileLock::s_refreshRate(static_cast<long>(kDefaultRefreshRate));
+ bool FileLock::s_loggingEnabled(false);
+ bool FileLock::s_isLoadBalanced(false);
+ FilePath FileLock::s_logFile;

diff --git a/sci-mathematics/rstudio/files/rstudio-1.1.453-core.patch b/sci-mathematics/rstudio/files/rstudio-1.1.453-core.patch
new file mode 100644
index 00000000000..641f7710167
--- /dev/null
+++ b/sci-mathematics/rstudio/files/rstudio-1.1.453-core.patch
@@ -0,0 +1,143 @@
+--- rstudio-1.1.453-orig/src/cpp/session/SessionClientInit.cpp	2018-05-15 04:19:30.000000000 +1000
++++ rstudio-1.1.453/src/cpp/session/SessionClientInit.cpp	2018-07-02 20:21:41.595654877 +1000
+@@ -105,7 +105,7 @@
+    }
+ 
+    // prepare session info 
+-   json::Object sessionInfo ;
++   core::json::Object sessionInfo ;
+    sessionInfo["clientId"] = clientId;
+    sessionInfo["mode"] = options.programMode();
+    
+@@ -119,8 +119,8 @@
+    }
+ 
+    // temp dir
+-   FilePath tempDir = rstudio::r::session::utils::tempDir();
+-   Error error = tempDir.ensureDirectory();
++   core::FilePath tempDir = rstudio::r::session::utils::tempDir();
++   core::Error error = tempDir.ensureDirectory();
+    if (error)
+       LOG_ERROR(error);
+    sessionInfo["temp_dir"] = tempDir.absolutePath();
+@@ -132,12 +132,12 @@
+    sessionInfo["prompt"] = rstudio::r::options::getOption<std::string>("prompt");
+ 
+    // client state
+-   json::Object clientStateObject;
++   core::json::Object clientStateObject;
+    rstudio::r::session::clientState().currentState(&clientStateObject);
+    sessionInfo["client_state"] = clientStateObject;
+    
+    // source documents
+-   json::Array jsonDocs;
++   core::json::Array jsonDocs;
+    error = modules::source::clientInitDocuments(&jsonDocs);
+    if (error)
+       LOG_ERROR(error);
+@@ -159,7 +159,7 @@
+    if (resumed)
+    {
+       // console actions
+-      json::Object actionsObject;
++     core::json::Object actionsObject;
+       consoleActions.asJson(&actionsObject);
+       sessionInfo["console_actions"] = actionsObject;
+    }
+@@ -211,12 +211,12 @@
+    }
+    else
+    {
+-      sessionInfo["active_project_file"] = json::Value();
+-      sessionInfo["project_ui_prefs"] = json::Value();
+-      sessionInfo["project_open_docs"] = json::Value();
++      sessionInfo["active_project_file"] = core::json::Value();
++      sessionInfo["project_ui_prefs"] = core::json::Value();
++      sessionInfo["project_open_docs"] = core::json::Value();
+       sessionInfo["project_supports_sharing"] = false;
+       sessionInfo["project_owned_by_user"] = false;
+-      sessionInfo["project_user_data_directory"] = json::Value();
++      sessionInfo["project_user_data_directory"] = core::json::Value();
+    }
+ 
+    sessionInfo["system_encoding"] = std::string(::locale2charset(NULL));
+@@ -253,20 +253,20 @@
+       sessionInfo["build_tools_bookdown_website"] =
+                               module_context::isBookdownWebsite();
+ 
+-      FilePath buildTargetDir = projects::projectContext().buildTargetPath();
++      core::FilePath buildTargetDir = projects::projectContext().buildTargetPath();
+       if (!buildTargetDir.empty())
+       {
+          sessionInfo["build_target_dir"] = module_context::createAliasedPath(
+                                                                 buildTargetDir);
+-         sessionInfo["has_pkg_src"] = (type == r_util::kBuildTypePackage) &&
++         sessionInfo["has_pkg_src"] = (type == core::r_util::kBuildTypePackage) &&
+                                       buildTargetDir.childPath("src").exists();
+          sessionInfo["has_pkg_vig"] =
+-               (type == r_util::kBuildTypePackage) &&
++               (type == core::r_util::kBuildTypePackage) &&
+                buildTargetDir.childPath("vignettes").exists();
+       }
+       else
+       {
+-         sessionInfo["build_target_dir"] = json::Value();
++         sessionInfo["build_target_dir"] = core::json::Value();
+          sessionInfo["has_pkg_src"] = false;
+          sessionInfo["has_pkg_vig"] = false;
+       }
+@@ -274,9 +274,9 @@
+    }
+    else
+    {
+-      sessionInfo["build_tools_type"] = r_util::kBuildTypeNone;
++      sessionInfo["build_tools_type"] = core::r_util::kBuildTypeNone;
+       sessionInfo["build_tools_bookdown_website"] = false;
+-      sessionInfo["build_target_dir"] = json::Value();
++      sessionInfo["build_target_dir"] = core::json::Value();
+       sessionInfo["has_pkg_src"] = false;
+       sessionInfo["has_pkg_vig"] = false;
+    }
+@@ -285,7 +285,7 @@
+    sessionInfo["presentation_commands"] = options.allowPresentationCommands();
+ 
+    sessionInfo["tutorial_api_available"] = false;
+-   sessionInfo["tutorial_api_client_origin"] = json::Value();
++   sessionInfo["tutorial_api_client_origin"] = core::json::Value();
+ 
+    sessionInfo["build_state"] = modules::build::buildStateAsJson();
+    sessionInfo["devtools_installed"] = module_context::isMinimumDevtoolsInstalled();
+@@ -296,7 +296,7 @@
+ 
+    // console history -- we do this at the end because
+    // restoreBuildRestartContext may have reset it
+-   json::Array historyArray;
++   core::json::Array historyArray;
+    rstudio::r::session::consoleHistory().asJson(&historyArray);
+    sessionInfo["console_history"] = historyArray;
+    sessionInfo["console_history_capacity"] =
+@@ -364,13 +364,13 @@
+ 
+    sessionInfo["multi_session"] = options.multiSession();
+ 
+-   json::Object rVersionsJson;
++   core::json::Object rVersionsJson;
+    rVersionsJson["r_version"] = module_context::rVersion();
+    rVersionsJson["r_home_dir"] = module_context::rHomeDir();
+    sessionInfo["r_versions_info"] = rVersionsJson;
+ 
+    sessionInfo["show_user_home_page"] = options.showUserHomePage();
+-   sessionInfo["user_home_page_url"] = json::Value();
++   sessionInfo["user_home_page_url"] = core::json::Value();
+    
+    sessionInfo["r_addins"] = modules::r_addins::addinRegistryAsJson();
+    sessionInfo["package_provided_extensions"] = modules::ppe::indexer().getPayload();
+@@ -394,7 +394,7 @@
+ 
+    // send response  (we always set kEventsPending to false so that the client
+    // won't poll for events until it is ready)
+-   json::JsonRpcResponse jsonRpcResponse ;
++   core::json::JsonRpcResponse jsonRpcResponse ;
+    jsonRpcResponse.setField(kEventsPending, "false");
+    jsonRpcResponse.setResult(sessionInfo) ;
+    ptrConnection->sendJsonRpcResponse(jsonRpcResponse);

diff --git a/sci-mathematics/rstudio/rstudio-1.1.453.ebuild b/sci-mathematics/rstudio/rstudio-1.1.453.ebuild
new file mode 100644
index 00000000000..35c991b9bd1
--- /dev/null
+++ b/sci-mathematics/rstudio/rstudio-1.1.453.ebuild
@@ -0,0 +1,249 @@
+# Copyright 1999-2018 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=6
+
+inherit eutils user cmake-utils gnome2-utils pam versionator xdg-utils java-pkg-2 pax-utils qmake-utils
+
+# TODO
+# * package gin and gwt
+# * use dict from tree, linguas
+# * do src_test (use junit from tree?)
+
+# update from scripts in dependencies/common
+# egrep '(GWT_SDK_VER=|GIN_VER=|SELENIUM_VER=|CHROMEDRIVER_VER=)' dependencies/common/install-gwt
+GWT_VER=2.7.0
+GIN_VER=1.5
+SELENIUM_VER=2.37.0
+CHROMEDRIVER_VER=2.7
+# grep 'PANDOC_VERSION=' dependencies/common/install-pandoc
+PANDOC_VER=1.19.2.1
+# ls dependencies/common/*.tar.gz
+PACKRAT_VER=0.98.1000
+RMARKDOWN_VER=0.98.1000
+SHINYAPPS_VER=0.98.1000
+RSCONNECT_VER=0.4.1.4_fcac892a69817febd7b655b189bf57193260cda0
+
+DESCRIPTION="IDE for the R language"
+HOMEPAGE="
+	http://www.rstudio.org
+	https://github.com/rstudio/rstudio/"
+SRC_URI="
+	https://github.com/rstudio/rstudio/archive/v${PV}.tar.gz -> ${P}.tar.gz
+	https://s3.amazonaws.com/rstudio-buildtools/gin-${GIN_VER}.zip
+	https://s3.amazonaws.com/rstudio-buildtools/gwt-${GWT_VER}.zip
+	https://s3.amazonaws.com/rstudio-buildtools/selenium-java-${SELENIUM_VER}.zip
+	https://s3.amazonaws.com/rstudio-buildtools/selenium-server-standalone-${SELENIUM_VER}.jar
+	https://s3.amazonaws.com/rstudio-buildtools/chromedriver-linux
+	https://s3.amazonaws.com/rstudio-dictionaries/core-dictionaries.zip
+	https://dev.gentoo.org/~gienah/distfiles/packrat-${PACKRAT_VER}.tar.gz
+	https://dev.gentoo.org/~gienah/distfiles/rmarkdown-${RMARKDOWN_VER}.tar.gz
+	https://dev.gentoo.org/~gienah/distfiles/shinyapps-${SHINYAPPS_VER}.tar.gz
+	https://dev.gentoo.org/~gienah/distfiles/rsconnect_${RSCONNECT_VER}.tar.gz
+"
+
+LICENSE="AGPL-3"
+SLOT="0"
+KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
+IUSE="dedicated server"
+
+QT_VER=5.4
+QT_SLOT=5
+RDEPEND="
+	>=app-text/pandoc-${PANDOC_VER}
+	dev-haskell/pandoc-citeproc
+	>=dev-lang/R-2.11.1
+	>=dev-libs/boost-1.63:=
+	>=dev-libs/mathjax-2.7.4
+	dev-libs/openssl:0
+	sys-apps/util-linux
+	>=sys-devel/clang-3.5.0:*
+	sys-libs/zlib
+	>=virtual/jre-1.8:=
+	x11-libs/pango
+	!dedicated? (
+		>=dev-qt/qtcore-${QT_VER}:${QT_SLOT}
+		>=dev-qt/qtdeclarative-${QT_VER}:${QT_SLOT}
+		>=dev-qt/qtdbus-${QT_VER}:${QT_SLOT}
+		>=dev-qt/qtgui-${QT_VER}:${QT_SLOT}
+		>=dev-qt/qtnetwork-${QT_VER}:${QT_SLOT}
+		>=dev-qt/qtopengl-${QT_VER}:${QT_SLOT}
+		>=dev-qt/qtpositioning-${QT_VER}:${QT_SLOT}
+		>=dev-qt/qtprintsupport-${QT_VER}:${QT_SLOT}
+		>=dev-qt/qtsingleapplication-2.6.1_p20150629[X,qt5(+)]
+		>=dev-qt/qtsensors-${QT_VER}:${QT_SLOT}
+		>=dev-qt/qtsql-${QT_VER}:${QT_SLOT}
+		>=dev-qt/qtsvg-${QT_VER}:${QT_SLOT}
+		>=dev-qt/qtwebchannel-${QT_VER}:${QT_SLOT}
+		>=dev-qt/qtwebkit-${QT_VER}:${QT_SLOT}
+		>=dev-qt/qtwidgets-${QT_VER}:${QT_SLOT}
+		>=dev-qt/qtxml-${QT_VER}:${QT_SLOT}
+		>=dev-qt/qtxmlpatterns-${QT_VER}:${QT_SLOT}
+		server? ( virtual/pam )
+	)
+	dedicated? ( virtual/pam )"
+DEPEND="${RDEPEND}
+	app-arch/unzip
+	dev-java/ant-core
+	>=virtual/jdk-1.8:=
+	virtual/pkgconfig"
+#	test? ( dev-java/junit:4 )
+
+PATCHES=(
+		"${FILESDIR}/${PN}-0.99.879-prefs.patch"
+		"${FILESDIR}/${PN}-1.0.44-paths.patch"
+		"${FILESDIR}/${PN}-1.1.357-clang-pandoc.patch"
+		"${FILESDIR}/${PN}-0.98.490-linker_flags.patch"
+		"${FILESDIR}/${PN}-0.99.473-qtsingleapplication.patch"
+		"${FILESDIR}/${PN}-1.0.44-systemd.patch"
+		"${FILESDIR}/${PN}-1.1.453-boost-1.67.0.patch"
+		"${FILESDIR}/${PN}-1.1.453-core.patch"
+)
+
+src_unpack() {
+	unpack ${P}.tar.gz gwt-${GWT_VER}.zip
+	cd "${S}" || die
+	mkdir -p src/gwt/lib/{gin,gwt} \
+		dependencies/common/dictionaries \
+		src/gwt/lib/selenium/${SELENIUM_VER} \
+		src/gwt/lib/selenium/chromedriver/${CHROMEDRIVER_VER} || die
+	mv ../gwt-${GWT_VER} src/gwt/lib/gwt/${GWT_VER} || die
+	unzip -qd src/gwt/lib/gin/${GIN_VER} \
+		"${DISTDIR}"/gin-${GIN_VER}.zip || die
+	unzip -qd dependencies/common/dictionaries \
+		"${DISTDIR}"/core-dictionaries.zip || die
+	unzip -qd src/gwt/lib/selenium/${SELENIUM_VER} \
+		"${DISTDIR}"/selenium-java-${SELENIUM_VER}.zip || die
+	cp "${DISTDIR}"/selenium-server-standalone-${SELENIUM_VER}.jar \
+		src/gwt/lib/selenium/${SELENIUM_VER}/ || die
+	cp "${DISTDIR}"/chromedriver-linux \
+		src/gwt/lib/selenium/chromedriver/${CHROMEDRIVER_VER}/ || die
+	cd dependencies/common || die
+	unpack packrat-${PACKRAT_VER}.tar.gz
+	unpack rmarkdown-${RMARKDOWN_VER}.tar.gz
+	unpack shinyapps-${SHINYAPPS_VER}.tar.gz
+	unpack rsconnect_${RSCONNECT_VER}.tar.gz
+	cp "${DISTDIR}"/rmarkdown-${RMARKDOWN_VER}.tar.gz \
+		. || die
+	cp "${DISTDIR}"/packrat-${PACKRAT_VER}.tar.gz \
+		. || die
+	cp "${DISTDIR}"/shinyapps-${SHINYAPPS_VER}.tar.gz \
+		. || die
+	cp "${DISTDIR}"/rsconnect_${RSCONNECT_VER}.tar.gz \
+		. || die
+}
+
+src_prepare() {
+	cmake-utils_src_prepare
+	java-pkg-2_src_prepare
+	egit_clean
+
+	# Enable CMake to install our .service file for systemd usage
+	mkdir -vp "${S}/src/cpp/server/lib/systemd/system" || die
+	cp -v "${FILESDIR}/rstudio-server.service.in" "${S}/src/cpp/server/lib/systemd/system/" || die
+
+	# Adding -DDISTRO_SHARE=... to append-flags breaks cmake so using
+	# this sed hack for now. ~RMH
+	sed -i \
+		-e "s|DISTRO_SHARE|\"share/${PN}\"|g" \
+		src/cpp/server/ServerOptions.cpp \
+		src/cpp/session/SessionOptions.cpp || die
+
+	# use mathjax from system
+	ln -sf "${EPREFIX}"/usr/share/mathjax dependencies/common/mathjax-26 || die
+
+	# make sure icons and mime stuff are with prefix
+	sed -i \
+		-e "s:/usr:${EPREFIX}/usr:g" \
+		CMakeGlobals.txt src/cpp/desktop/CMakeLists.txt || die
+
+	# On Gentoo the rstudio-server configuration file is /etc/conf.d/rstudio-server.conf
+	sed -e "s@/etc/rstudio/rserver.conf@${EROOT}etc/conf.d/rstudio-server.conf@" \
+		-i src/cpp/server/ServerOptions.cpp \
+		|| die
+
+	# Set the rsession.conf file location for Gentoo prefix
+	sed -e "s@/etc/rstudio/rsession.conf@${EROOT}etc/rstudio/rsession.conf@" \
+		-i src/cpp/session/SessionOptions.cpp \
+		|| die
+
+	# dev-qt/qtsingleapplication-2.6.1_p20150629 does not provide a cmake module.
+	# It provides a library that has its version number appended to the end,
+	# which is difficult to handle in cmake, as find_library does not support
+	# searching for wildcard library names. So I find the library name from the
+	# qmake spec, and then sed this into the patched src/cpp/desktop/CMakeLists.txt.
+	rm -rf "${S}"/src/cpp/desktop/3rdparty || die
+	local s=$(grep '\-lQt$${QT_MAJOR_VERSION}Solutions_SingleApplication' \
+				   $(qt5_get_mkspecsdir)/features/qtsingleapplication.prf \
+					 | sed -e 's@\$\${QT_MAJOR_VERSION}@5@' \
+						   -e 's@LIBS \*= -l@@')
+	sed -e "s@Qt5Solutions_SingleApplication-2.6@${s}@g" \
+		-i "${S}"/src/cpp/desktop/CMakeLists.txt \
+		|| die
+
+	# The git commit for tag: git rev-list -n 1 v${PV}
+	sed -e 's@git ARGS rev-parse HEAD@echo ARGS 6871a99b32add885fe6fa3d50fe15f62346142e7@'\
+		-i "${S}"/CMakeLists.txt \
+		"${S}"/CMakeGlobals.txt \
+		|| die
+}
+
+src_configure() {
+	export RSTUDIO_VERSION_MAJOR=$(get_version_component_range 1)
+	export RSTUDIO_VERSION_MINOR=$(get_version_component_range 2)
+	export RSTUDIO_VERSION_PATCH=$(get_version_component_range 3)
+
+	local mycmakeargs=(
+		-DDISTRO_SHARE=share/${PN}
+		-DRSTUDIO_INSTALL_FREEDESKTOP="$(usex !dedicated "ON" "OFF")"
+		-DRSTUDIO_TARGET=$(usex dedicated "Server" "$(usex server "Development" "Desktop")")
+		-DQT_QMAKE_EXECUTABLE=$(qt5_get_bindir)/qmake
+		-DRSTUDIO_VERIFY_R_VERSION=FALSE
+		)
+
+	cmake-utils_src_configure
+}
+
+src_compile() {
+	# Avoid the rest of the oracle-jdk-bin-1.8.0.60 sandbox violations F: mkdir S: deny
+	# P: /root/.oracle_jre_usage.
+	export ANT_OPTS="-Duser.home=${T}"
+	cmake-utils_src_compile
+}
+
+src_install() {
+	export ANT_OPTS="-Duser.home=${T}"
+	cmake-utils_src_install
+	pax-mark m "${ED}usr/bin/rstudio"
+	doconfd "${FILESDIR}"/rstudio-server.conf
+	dodir /etc/rstudio
+	insinto /etc/rstudio
+	doins "${FILESDIR}"/rsession.conf
+	dosym "${ROOT}etc/conf.d/rstudio-server.conf" "${ROOT}etc/rstudio/rserver.conf"
+	if use dedicated || use server; then
+		dopamd src/cpp/server/extras/pam/rstudio
+		newinitd "${FILESDIR}"/rstudio-server.initd rstudio-server
+	fi
+}
+
+pkg_preinst() {
+	use dedicated || gnome2_icon_savelist
+	java-pkg-2_pkg_preinst
+}
+
+pkg_postinst() {
+	use dedicated || { xdg_desktop_database_update
+		xdg_mimeinfo_database_update
+		gnome2_icon_cache_update ;}
+
+	if use dedicated || use server; then
+		enewgroup rstudio-server
+		enewuser rstudio-server -1 -1 -1 rstudio-server
+	fi
+}
+
+pkg_postrm() {
+	use dedicated || { xdg_desktop_database_update
+		xdg_mimeinfo_database_update
+		gnome2_icon_cache_update ;}
+}


^ permalink raw reply related	[flat|nested] 12+ messages in thread

* [gentoo-commits] repo/gentoo:master commit in: sci-mathematics/rstudio/, sci-mathematics/rstudio/files/
@ 2018-11-19 12:38 Mark Wright
  0 siblings, 0 replies; 12+ messages in thread
From: Mark Wright @ 2018-11-19 12:38 UTC (permalink / raw
  To: gentoo-commits

commit:     1ca93847092bdabc213f1631a295decdba82125c
Author:     Mark Wright <gienah <AT> gentoo <DOT> org>
AuthorDate: Mon Nov 19 12:25:51 2018 +0000
Commit:     Mark Wright <gienah <AT> gentoo <DOT> org>
CommitDate: Mon Nov 19 12:37:56 2018 +0000
URL:        https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=1ca93847

sci-mathematics/rstudio: Bump to 1.1.463

Signed-off-by: Mark Wright <gienah <AT> gentoo.org>

 sci-mathematics/rstudio/Manifest                   |   1 +
 .../files/rstudio-1.1.463-boost-1.69.0_p1.patch    | 680 +++++++++++++++++++++
 .../files/rstudio-1.1.463-boost-1.69.0_p2.patch    | 167 +++++
 .../rstudio-1.1.463-fix-ptr-int-compare.patch      |  13 +
 sci-mathematics/rstudio/rstudio-1.1.463.ebuild     | 253 ++++++++
 5 files changed, 1114 insertions(+)

diff --git a/sci-mathematics/rstudio/Manifest b/sci-mathematics/rstudio/Manifest
index 77cc3217237..79c6b60ad01 100644
--- a/sci-mathematics/rstudio/Manifest
+++ b/sci-mathematics/rstudio/Manifest
@@ -7,6 +7,7 @@ DIST rmarkdown-0.98.1000.tar.gz 1423820 BLAKE2B eac8c9cf438c9b44ddfe954602dd67a8
 DIST rsconnect_0.4.1.4_fcac892a69817febd7b655b189bf57193260cda0.tar.gz 197051 BLAKE2B 1f3f9fe71d7b50ab5108dfdbd3cc0b882bcc935ee58e8a9145b07a18bb86c39bc45e321a13add24df99492bc30548df716775c339bcbf4efc2bfe158299ae55a SHA512 208dc349f4aa7613ecf94939aba60d22d3a06972344b526c9b6c951015571f5922927bca08db571a7b8a268e42609a4f558f01278c9685f6da2ffc66a1f95ade
 DIST rstudio-1.1.383.tar.gz 20196702 BLAKE2B 5164230a92618e4252269ad0016b200294d1e7fa502cc49aa694486cda098ee7ffc65e6c74a87d891d0532f5cc15d1552aa86d04047d07b4f275cbc4d2758647 SHA512 3f637f9bce2c1ad1a4ed3e74287da722190a4e12b0cace6ffcca271977d49dcecca9365f2064366aad94e87851593cab83fa9361e9a9222a9f67fe9451f31ed2
 DIST rstudio-1.1.453.tar.gz 20200360 BLAKE2B 560b89e53b04356ecf9a02dd8a7e72ad8d6c30bf406fbe7e22a82cc6d33d40e84bececf5ecda9cf086360b2bd2fa64d6b33c2dd675ef5f605f9e825d7ca2dc84 SHA512 f2be0866f645007a6f80959109928820c89480057c3660d23e790591797d4f4c371733f49290dae9c81bfc2715821528e2a105e7a66d4d9ffbfc7ee2a596976c
+DIST rstudio-1.1.463.tar.gz 20203779 BLAKE2B 97f879539cbb7051af362a8469795a47feb42d18ff46dbbdffe36e0685d1cd5704848b3bf5a5611d482a09567722e35288527302cd521b18e2a48b347c919e17 SHA512 987347563a9726363c28d866e1372eae8eb19a5cbd0e33c7ee0e0c8f90471c4b69de0f559c00410523841b6c090b584652e01496f5db33c015a4554d2f4e179b
 DIST selenium-java-2.37.0.zip 24625928 BLAKE2B b369a805ae96f0d0913c4be42888d9c2a1e213ff982f9daefe73fadb705baa80ab0186ab50ed52609e83697cffaf8d617d06d75405cb8e1c3fe8e7c5b81dba25 SHA512 68624e82dbc751a25c50fad72702a98eb30d77fd4337d2a969f8e06bcc49e5f8c835cd27ec53772f3375014ddde1d5636936e966b75f3594a9f86aa18ba4e779
 DIST selenium-server-standalone-2.37.0.jar 34730734 BLAKE2B 3899b1d4c5f9153c1f9f13bec66f7c1456ea2e0f34db7d8e54a1ce9063c33a05b3cf95216c2ae06bb40504f72f343a4b9ba6c8553fbbc340e7c18a5b612dde5c SHA512 b215446d42d2d1f69664349b6ae6dc53a532d3624c91254f0f4183d0ad764648792e5cc1126a55a1e60d9687d55200fed01d6d2f46cc3d853b1fa6ee38111018
 DIST shinyapps-0.98.1000.tar.gz 910095 BLAKE2B 4f9364692348bb52cbd12cc6ee447841cb0c805327f2518b2a9545920b602b954a98dea68ccb3daf32d2c3bab6464fb15402844d93277193315f1ae7b3ca5190 SHA512 3162317c4c20cfc1497e952a8235867084d629ae88407e6c465b3e208adb1dc97abfe6b9922e0374ddf4c8e38a76e112942bd312c54a66f74e6f2a3fe4c0a07c

diff --git a/sci-mathematics/rstudio/files/rstudio-1.1.463-boost-1.69.0_p1.patch b/sci-mathematics/rstudio/files/rstudio-1.1.463-boost-1.69.0_p1.patch
new file mode 100644
index 00000000000..aa3db25f3c0
--- /dev/null
+++ b/sci-mathematics/rstudio/files/rstudio-1.1.463-boost-1.69.0_p1.patch
@@ -0,0 +1,680 @@
+--- /dev/null	2018-11-10 15:32:26.332997437 +1100
++++ rstudio-1.1.463/src/cpp/core/include/core/BoostSignals.hpp	2018-11-17 21:24:35.285976284 +1100
+@@ -0,0 +1,40 @@
++/*
++ * BoostSignals.hpp
++ *
++ * Copyright (C) 2009-18 by RStudio, Inc.
++ *
++ * Unless you have received this program directly from RStudio pursuant
++ * to the terms of a commercial license agreement with RStudio, then
++ * this program is licensed to you under the terms of version 3 of the
++ * GNU Affero General Public License. This program is distributed WITHOUT
++ * ANY EXPRESS OR IMPLIED WARRANTY, INCLUDING THOSE OF NON-INFRINGEMENT,
++ * MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. Please refer to the
++ * AGPL (http://www.gnu.org/licenses/agpl-3.0.txt) for more details.
++ *
++ */
++
++#ifndef CORE_RSTUDIO_BOOST_SIGNALS_HPP
++#define CORE_RSTUDIO_BOOST_SIGNALS_HPP
++
++#if RSTUDIO_BOOST_SIGNALS_VERSION == 1
++
++# include <boost/signals.hpp>
++# define RSTUDIO_BOOST_SIGNAL boost::signal
++# define RSTUDIO_BOOST_CONNECTION boost::signals::connection
++# define RSTUDIO_BOOST_SCOPED_CONNECTION boost::signals::scoped_connection
++# define RSTUDIO_BOOST_LAST_VALUE boost::last_value
++
++#elif RSTUDIO_BOOST_SIGNALS_VERSION == 2
++
++# include <boost/signals2.hpp>
++# define RSTUDIO_BOOST_SIGNAL boost::signals2::signal
++# define RSTUDIO_BOOST_CONNECTION boost::signals2::connection
++# define RSTUDIO_BOOST_SCOPED_CONNECTION boost::signals2::scoped_connection
++# define RSTUDIO_BOOST_LAST_VALUE boost::signals2::last_value
++
++#else
++# error "Unrecognized RSTUDIO_BOOST_SIGNALS_VERSION"
++#endif
++
++#endif // CORE_RSTUDIO_BOOST_SIGNALS_HPP
++
+--- rstudio-1.1.463-orig/src/cpp/CMakeLists.txt	2018-10-25 09:42:55.000000000 +1100
++++ rstudio-1.1.463/src/cpp/CMakeLists.txt	2018-11-17 21:24:35.285976284 +1100
+@@ -208,6 +208,18 @@
+    message(STATUS "Using RStudio-provided Boost ${BOOST_VERSION}")
+ endif()
+ 
++# allow opt-in to using Boost.Signals2
++# TODO: remove this in RStudio v1.3 and port to signals2
++if(NOT RSTUDIO_BOOST_SIGNALS_VERSION)
++   if (BOOST_VERSION VERSION_LESS 1.69.0)
++      set(RSTUDIO_BOOST_SIGNALS_VERSION 1)
++   else()
++      set(RSTUDIO_BOOST_SIGNALS_VERSION 2)
++   endif()
++endif()
++
++message(STATUS "Using Booost.Signals version ${RSTUDIO_BOOST_SIGNALS_VERSION}")
++add_definitions(-DRSTUDIO_BOOST_SIGNALS_VERSION=${RSTUDIO_BOOST_SIGNALS_VERSION})
+ 
+ # add boost as system include directory
+ include_directories(SYSTEM ${Boost_INCLUDE_DIRS})
+--- rstudio-1.1.463-orig/src/cpp/r/include/r/session/RConsoleHistory.hpp	2018-10-25 09:42:55.000000000 +1100
++++ rstudio-1.1.463/src/cpp/r/include/r/session/RConsoleHistory.hpp	2018-11-17 21:24:35.285976284 +1100
+@@ -20,8 +20,8 @@
+ 
+ #include <boost/utility.hpp>
+ #include <boost/circular_buffer.hpp>
+-#include <boost/signal.hpp>
+ 
++#include <core/BoostSignals.hpp>
+ #include <core/json/Json.hpp>
+ 
+ namespace rstudio {
+@@ -44,7 +44,7 @@
+ public:
+    typedef boost::circular_buffer<std::string>::value_type value_type;
+    typedef boost::circular_buffer<std::string>::const_iterator const_iterator;
+-   typedef boost::signal<void (const std::string&)> AddSignal;
++   typedef RSTUDIO_BOOST_SIGNAL<void (const std::string&)> AddSignal;
+ 
+ private:
+    ConsoleHistory();
+@@ -86,8 +86,7 @@
+    core::Error loadFromFile(const core::FilePath& filePath, bool verifyFile);
+    core::Error saveToFile(const core::FilePath& filePath) const;
+    
+-   boost::signals::connection connectOnAdd(
+-                                 const AddSignal::slot_function_type& slot)
++   RSTUDIO_BOOST_CONNECTION connectOnAdd(const AddSignal::slot_function_type& slot)
+    {
+       return onAdd_.connect(slot);
+    }
+--- rstudio-1.1.463-orig/src/cpp/r/include/r/session/RGraphics.hpp	2018-10-25 09:42:55.000000000 +1100
++++ rstudio-1.1.463/src/cpp/r/include/r/session/RGraphics.hpp	2018-11-17 21:24:35.286976293 +1100
+@@ -19,6 +19,8 @@
+ #include <boost/system/error_code.hpp>
+ #include <boost/date_time/posix_time/ptime.hpp>
+ 
++#include <core/BoostSignals.hpp>
++
+ namespace rstudio {
+ namespace r {
+ namespace session {
+@@ -56,8 +58,8 @@
+ #include <vector>
+ 
+ #include <boost/function.hpp>
+-#include <boost/signal.hpp>
+ 
++#include <core/BoostSignals.hpp>
+ #include <core/Error.hpp>
+ #include <core/json/Json.hpp>
+ 
+@@ -162,7 +164,7 @@
+    virtual void clear() = 0;
+ 
+    // subscribe to showManipulator event
+-   virtual boost::signal<void ()>& onShowManipulator() = 0;
++   virtual RSTUDIO_BOOST_SIGNAL<void ()>& onShowManipulator() = 0;
+ 
+    // set manipulator values
+    virtual void setPlotManipulatorValues(const core::json::Object& values) = 0;
+--- rstudio-1.1.463-orig/src/cpp/r/session/graphics/RGraphicsPlotManager.cpp	2018-10-25 09:42:55.000000000 +1100
++++ rstudio-1.1.463/src/cpp/r/session/graphics/RGraphicsPlotManager.cpp	2018-11-17 21:24:35.286976293 +1100
+@@ -540,7 +540,7 @@
+ 
+ 
+ 
+-boost::signal<void ()>& PlotManager::onShowManipulator()
++RSTUDIO_BOOST_SIGNAL<void ()>& PlotManager::onShowManipulator()
+ {
+    return plotManipulatorManager().onShowManipulator();
+ }
+--- rstudio-1.1.463-orig/src/cpp/r/session/graphics/RGraphicsPlotManager.hpp	2018-10-25 09:42:55.000000000 +1100
++++ rstudio-1.1.463/src/cpp/r/session/graphics/RGraphicsPlotManager.hpp	2018-11-17 21:24:35.287976303 +1100
+@@ -22,10 +22,10 @@
+ #include <boost/utility.hpp>
+ #include <boost/shared_ptr.hpp>
+ #include <boost/function.hpp>
+-#include <boost/signal.hpp>
+ #include <boost/regex.hpp>
+ #include <boost/circular_buffer.hpp>
+ 
++#include <core/BoostSignals.hpp>
+ #include <core/Error.hpp>
+ #include <core/FilePath.hpp>
+ 
+@@ -45,10 +45,10 @@
+ 
+ struct GraphicsDeviceEvents
+ {
+-   boost::signal<void (SEXP)> onNewPage; 
+-   boost::signal<void ()> onDrawing;
+-   boost::signal<void ()> onResized;
+-   boost::signal<void ()> onClosed;
++   RSTUDIO_BOOST_SIGNAL<void (SEXP)> onNewPage; 
++   RSTUDIO_BOOST_SIGNAL<void ()> onDrawing;
++   RSTUDIO_BOOST_SIGNAL<void ()> onResized;
++   RSTUDIO_BOOST_SIGNAL<void ()> onClosed;
+ };
+ 
+ class PlotManipulatorManager;
+@@ -110,7 +110,7 @@
+    
+    virtual void clear();
+ 
+-   virtual boost::signal<void ()>& onShowManipulator() ;
++   virtual RSTUDIO_BOOST_SIGNAL<void ()>& onShowManipulator() ;
+    virtual void setPlotManipulatorValues(const core::json::Object& values);
+    virtual void manipulatorPlotClicked(int x, int y);
+ 
+--- rstudio-1.1.463-orig/src/cpp/r/session/graphics/RGraphicsPlotManipulatorManager.cpp	2018-10-25 09:42:55.000000000 +1100
++++ rstudio-1.1.463/src/cpp/r/session/graphics/RGraphicsPlotManipulatorManager.cpp	2018-11-17 21:24:35.287976303 +1100
+@@ -184,7 +184,7 @@
+ }
+ 
+ 
+-boost::signal<void ()>& PlotManipulatorManager::onShowManipulator()
++RSTUDIO_BOOST_SIGNAL<void ()>& PlotManipulatorManager::onShowManipulator()
+ {
+    return onShowManipulator_;
+ }
+--- rstudio-1.1.463-orig/src/cpp/r/session/graphics/RGraphicsPlotManipulatorManager.hpp	2018-10-25 09:42:55.000000000 +1100
++++ rstudio-1.1.463/src/cpp/r/session/graphics/RGraphicsPlotManipulatorManager.hpp	2018-11-17 21:24:35.287976303 +1100
+@@ -16,8 +16,7 @@
+ #ifndef R_SESSION_GRAPHICS_PLOT_MANIPULATOR_MANAGER_HPP
+ #define R_SESSION_GRAPHICS_PLOT_MANIPULATOR_MANAGER_HPP
+ 
+-#include <boost/signal.hpp>
+-
++#include <core/BoostSignals.hpp>
+ #include <core/Error.hpp>
+ #include <core/json/Json.hpp>
+ 
+@@ -53,7 +52,7 @@
+ public:
+    core::Error initialize(const UnitConversionFunctions& convert);
+ 
+-   boost::signal<void ()>& onShowManipulator() ;
++   RSTUDIO_BOOST_SIGNAL<void ()>& onShowManipulator() ;
+    void setPlotManipulatorValues(const core::json::Object& values);
+    void manipulatorPlotClicked(int x, int y);
+    
+@@ -85,7 +84,7 @@
+    bool replayingManipulator_;
+ 
+    // manipulator event hook
+-   boost::signal<void ()> onShowManipulator_;
++   RSTUDIO_BOOST_SIGNAL<void ()> onShowManipulator_;
+ 
+    // unit conversion function
+    UnitConversionFunctions convert_;
+--- rstudio-1.1.463-orig/src/cpp/server/include/server/ServerSessionManager.hpp	2018-10-25 09:42:55.000000000 +1100
++++ rstudio-1.1.463/src/cpp/server/include/server/ServerSessionManager.hpp	2018-11-17 21:27:05.255436316 +1100
+@@ -20,9 +20,9 @@
+ #include <vector>
+ #include <map>
+ 
+-#include <boost/signals.hpp>
+ #include <boost/asio/io_service.hpp>
+ 
++#include <core/BoostSignals.hpp>
+ #include <core/Thread.hpp>
+ 
+ #include <core/system/PosixSystem.hpp>
+--- rstudio-1.1.463-orig/src/cpp/session/SessionMain.cpp	2018-10-25 09:42:55.000000000 +1100
++++ rstudio-1.1.463/src/cpp/session/SessionMain.cpp	2018-11-17 21:24:35.288976313 +1100
+@@ -33,12 +33,12 @@
+ #include <boost/lexical_cast.hpp>
+ #include <boost/format.hpp>
+ 
+-#include <boost/signals.hpp>
+ #include <boost/date_time/posix_time/posix_time.hpp>
+ #include <boost/algorithm/string/predicate.hpp>
+ #include <boost/algorithm/string/join.hpp>
+ 
+ #include <core/Error.hpp>
++#include <core/BoostSignals.hpp>
+ #include <core/BoostThread.hpp>
+ #include <core/ConfigUtils.hpp>
+ #include <core/FilePath.hpp>
+--- rstudio-1.1.463-orig/src/cpp/session/SessionModuleContext.cpp	2018-10-25 09:42:55.000000000 +1100
++++ rstudio-1.1.463/src/cpp/session/SessionModuleContext.cpp	2018-11-17 21:24:35.289976322 +1100
+@@ -19,10 +19,10 @@
+ 
+ #include <boost/assert.hpp>
+ #include <boost/utility.hpp>
+-#include <boost/signal.hpp>
+ #include <boost/format.hpp>
+ #include <boost/numeric/conversion/cast.hpp>
+ 
++#include <core/BoostSignals.hpp>
+ #include <core/BoostThread.hpp>
+ #include <core/Error.hpp>
+ #include <core/FilePath.hpp>
+@@ -586,13 +586,13 @@
+    
+    int nextGroup_; 
+    
+-   boost::signal<void(const r::session::RSuspendOptions&,Settings*),
+-                 boost::last_value<void>,
++   RSTUDIO_BOOST_SIGNAL<void(const r::session::RSuspendOptions&,Settings*),
++                 RSTUDIO_BOOST_LAST_VALUE<void>,
+                  int,
+                  std::less<int> > suspendSignal_;
+                   
+-   boost::signal<void(const Settings&),
+-                 boost::last_value<void>,
++   RSTUDIO_BOOST_SIGNAL<void(const Settings&),
++                 RSTUDIO_BOOST_LAST_VALUE<void>,
+                  int,
+                  std::greater<int> > resumeSignal_;
+ };
+--- rstudio-1.1.463-orig/src/cpp/session/include/session/SessionConsoleProcess.hpp	2018-10-25 09:42:55.000000000 +1100
++++ rstudio-1.1.463/src/cpp/session/include/session/SessionConsoleProcess.hpp	2018-11-17 21:24:35.290976332 +1100
+@@ -20,10 +20,10 @@
+ #include <deque>
+ 
+ #include <boost/regex.hpp>
+-#include <boost/signals.hpp>
+ #include <boost/circular_buffer.hpp>
+ #include <boost/enable_shared_from_this.hpp>
+ 
++#include <core/BoostSignals.hpp>
+ #include <core/system/Process.hpp>
+ #include <core/terminal/PrivateCommand.hpp>
+ 
+@@ -146,7 +146,7 @@
+    void setPromptHandler(
+          const boost::function<bool(const std::string&, Input*)>& onPrompt);
+ 
+-   boost::signal<void(int)>& onExit() { return onExit_; }
++   RSTUDIO_BOOST_SIGNAL<void(int)>& onExit() { return onExit_; }
+ 
+    std::string handle() const { return procInfo_->getHandle(); }
+    InteractionMode interactionMode() const { return procInfo_->getInteractionMode(); }
+@@ -264,7 +264,7 @@
+    boost::mutex inputOutputQueueMutex_;
+ 
+    boost::function<bool(const std::string&, Input*)> onPrompt_;
+-   boost::signal<void(int)> onExit_;
++   RSTUDIO_BOOST_SIGNAL<void(int)> onExit_;
+ 
+    // regex for prompt detection
+    boost::regex controlCharsPattern_;
+--- rstudio-1.1.463-orig/src/cpp/session/include/session/SessionModuleContext.hpp	2018-10-25 09:42:55.000000000 +1100
++++ rstudio-1.1.463/src/cpp/session/include/session/SessionModuleContext.hpp	2018-11-17 21:28:25.019212857 +1100
+@@ -21,9 +21,9 @@
+ 
+ #include <boost/utility.hpp>
+ #include <boost/function.hpp>
+-#include <boost/signals.hpp>
+ #include <boost/shared_ptr.hpp>
+ 
++#include <core/BoostSignals.hpp>
+ #include <core/HtmlUtils.hpp>
+ #include <core/system/System.hpp>
+ #include <core/system/ShellUtils.hpp>
+@@ -315,35 +315,35 @@
+ // session events
+ struct Events : boost::noncopyable
+ {
+-   boost::signal<void (core::json::Object*)> onSessionInfo;
+-   boost::signal<void ()>                    onClientInit;
+-   boost::signal<void ()>                    onBeforeExecute;
+-   boost::signal<void(const std::string&)>   onConsolePrompt;
+-   boost::signal<void(const std::string&)>   onConsoleInput;
+-   boost::signal<void(const std::string&, const std::string&)>  
++   RSTUDIO_BOOST_SIGNAL<void (core::json::Object*)> onSessionInfo;
++   RSTUDIO_BOOST_SIGNAL<void ()>                    onClientInit;
++   RSTUDIO_BOOST_SIGNAL<void ()>                    onBeforeExecute;
++   RSTUDIO_BOOST_SIGNAL<void(const std::string&)>   onConsolePrompt;
++   RSTUDIO_BOOST_SIGNAL<void(const std::string&)>   onConsoleInput;
++   RSTUDIO_BOOST_SIGNAL<void(const std::string&, const std::string&)>  
+                                              onActiveConsoleChanged;
+-   boost::signal<void (ConsoleOutputType, const std::string&)>
++   RSTUDIO_BOOST_SIGNAL<void (ConsoleOutputType, const std::string&)>
+                                              onConsoleOutput;
+-   boost::signal<void()>                     onUserInterrupt;
+-   boost::signal<void (ChangeSource)>        onDetectChanges;
+-   boost::signal<void (core::FilePath)>      onSourceEditorFileSaved;
+-   boost::signal<void(bool)>                 onDeferredInit;
+-   boost::signal<void(bool)>                 afterSessionInitHook;
+-   boost::signal<void(bool)>                 onBackgroundProcessing;
+-   boost::signal<void(bool)>                 onShutdown;
+-   boost::signal<void ()>                    onQuit;
+-   boost::signal<void ()>                    onDestroyed;
+-   boost::signal<void (const std::vector<std::string>&)>
++   RSTUDIO_BOOST_SIGNAL<void()>                     onUserInterrupt;
++   RSTUDIO_BOOST_SIGNAL<void (ChangeSource)>        onDetectChanges;
++   RSTUDIO_BOOST_SIGNAL<void (core::FilePath)>      onSourceEditorFileSaved;
++   RSTUDIO_BOOST_SIGNAL<void(bool)>                 onDeferredInit;
++   RSTUDIO_BOOST_SIGNAL<void(bool)>                 afterSessionInitHook;
++   RSTUDIO_BOOST_SIGNAL<void(bool)>                 onBackgroundProcessing;
++   RSTUDIO_BOOST_SIGNAL<void(bool)>                 onShutdown;
++   RSTUDIO_BOOST_SIGNAL<void ()>                    onQuit;
++   RSTUDIO_BOOST_SIGNAL<void ()>                    onDestroyed;
++   RSTUDIO_BOOST_SIGNAL<void (const std::vector<std::string>&)>
+                                              onLibPathsChanged;
+-   boost::signal<void (const std::string&)>  onPackageLoaded;
+-   boost::signal<void ()>                    onPackageLibraryMutated;
+-   boost::signal<void ()>                    onPreferencesSaved;
+-   boost::signal<void (const core::DistributedEvent&)>
++   RSTUDIO_BOOST_SIGNAL<void (const std::string&)>  onPackageLoaded;
++   RSTUDIO_BOOST_SIGNAL<void ()>                    onPackageLibraryMutated;
++   RSTUDIO_BOOST_SIGNAL<void ()>                    onPreferencesSaved;
++   RSTUDIO_BOOST_SIGNAL<void (const core::DistributedEvent&)>
+                                              onDistributedEvent;
+-   boost::signal<void (core::FilePath)>      onPermissionsChanged;
++   RSTUDIO_BOOST_SIGNAL<void (core::FilePath)>      onPermissionsChanged;
+ 
+    // signal for detecting extended type of documents
+-   boost::signal<std::string(boost::shared_ptr<source_database::SourceDocument>),
++   RSTUDIO_BOOST_SIGNAL<std::string(boost::shared_ptr<source_database::SourceDocument>),
+                  firstNonEmpty<std::string> > onDetectSourceExtendedType;
+ };
+ 
+--- rstudio-1.1.463-orig/src/cpp/session/include/session/SessionSourceDatabase.hpp	2018-10-25 09:42:55.000000000 +1100
++++ rstudio-1.1.463/src/cpp/session/include/session/SessionSourceDatabase.hpp	2018-11-17 21:24:35.291976342 +1100
+@@ -21,8 +21,8 @@
+ 
+ #include <boost/utility.hpp>
+ #include <boost/shared_ptr.hpp>
+-#include <boost/signals.hpp>
+ 
++#include <core/BoostSignals.hpp>
+ #include <core/FilePath.hpp>
+ #include <core/json/Json.hpp>
+ 
+@@ -204,14 +204,14 @@
+ // source database events
+ struct Events : boost::noncopyable
+ {
+-   boost::signal<void(boost::shared_ptr<SourceDocument>)>      onDocUpdated;
+-   boost::signal<void(const std::string&,
++   RSTUDIO_BOOST_SIGNAL<void(boost::shared_ptr<SourceDocument>)>      onDocUpdated;
++   RSTUDIO_BOOST_SIGNAL<void(const std::string&,
+                       boost::shared_ptr<SourceDocument>)>      onDocRenamed;
+-   boost::signal<void(const std::string&)>                     onDocAdded;
+-   boost::signal<void(
++   RSTUDIO_BOOST_SIGNAL<void(const std::string&)>                     onDocAdded;
++   RSTUDIO_BOOST_SIGNAL<void(
+       boost::shared_ptr<source_database::SourceDocument>)>     onDocPendingRemove;
+-   boost::signal<void(const std::string&, const std::string&)> onDocRemoved;
+-   boost::signal<void()>                                       onRemoveAll;
++   RSTUDIO_BOOST_SIGNAL<void(const std::string&, const std::string&)> onDocRemoved;
++   RSTUDIO_BOOST_SIGNAL<void()>                                       onRemoveAll;
+ };
+ 
+ Events& events();
+--- rstudio-1.1.463-orig/src/cpp/session/include/session/SessionUserSettings.hpp	2018-10-25 09:42:55.000000000 +1100
++++ rstudio-1.1.463/src/cpp/session/include/session/SessionUserSettings.hpp	2018-11-17 21:24:35.291976342 +1100
+@@ -20,8 +20,8 @@
+ 
+ #include <boost/utility.hpp>
+ #include <boost/scoped_ptr.hpp>
+-#include <boost/signal.hpp>
+ 
++#include <core/BoostSignals.hpp>
+ #include <core/Settings.hpp>
+ #include <core/FilePath.hpp>
+ #include <core/StringUtils.hpp>
+@@ -62,7 +62,7 @@
+    friend UserSettings& userSettings();
+ 
+ public:
+-   boost::signal<void()> onChanged;
++   RSTUDIO_BOOST_SIGNAL<void()> onChanged;
+ 
+ public:
+    // COPYING: boost::noncopyable
+--- rstudio-1.1.463-orig/src/cpp/session/include/session/projects/SessionProjects.hpp	2018-10-25 09:42:55.000000000 +1100
++++ rstudio-1.1.463/src/cpp/session/include/session/projects/SessionProjects.hpp	2018-11-17 21:24:35.291976342 +1100
+@@ -22,8 +22,8 @@
+ #include <boost/utility.hpp>
+ #include <boost/shared_ptr.hpp>
+ #include <boost/foreach.hpp>
+-#include <boost/signals.hpp>
+ 
++#include <core/BoostSignals.hpp>
+ #include <core/FileInfo.hpp>
+ #include <core/FilePath.hpp>
+ #include <core/Settings.hpp>
+@@ -220,10 +220,10 @@
+ 
+    bool hasFileMonitor_;
+    std::vector<std::string> monitorSubscribers_;
+-   boost::signal<void(const tree<core::FileInfo>&)> onMonitoringEnabled_;
+-   boost::signal<void(const std::vector<core::system::FileChangeEvent>&)>
++   RSTUDIO_BOOST_SIGNAL<void(const tree<core::FileInfo>&)> onMonitoringEnabled_;
++   RSTUDIO_BOOST_SIGNAL<void(const std::vector<core::system::FileChangeEvent>&)>
+                                                             onFilesChanged_;
+-   boost::signal<void()> onMonitoringDisabled_;
++   RSTUDIO_BOOST_SIGNAL<void()> onMonitoringDisabled_;
+ };
+ 
+ ProjectContext& projectContext();
+--- rstudio-1.1.463-orig/src/cpp/session/modules/SessionPlots.hpp	2018-10-25 09:42:55.000000000 +1100
++++ rstudio-1.1.463/src/cpp/session/modules/SessionPlots.hpp	2018-11-17 21:24:35.292976352 +1100
+@@ -16,7 +16,7 @@
+ #ifndef SESSION_PLOTS_HPP
+ #define SESSION_PLOTS_HPP
+ 
+-#include <boost/signals.hpp>
++#include <core/BoostSignals.hpp>
+ 
+ namespace rstudio {
+ namespace core {
+@@ -35,9 +35,9 @@
+ 
+ struct Events : boost::noncopyable
+ {
+-   boost::signal<void()> onBeforeNewPlot;
+-   boost::signal<void()> onBeforeNewGridPage;
+-   boost::signal<void()> onNewPlot;
++   RSTUDIO_BOOST_SIGNAL<void()> onBeforeNewPlot;
++   RSTUDIO_BOOST_SIGNAL<void()> onBeforeNewGridPage;
++   RSTUDIO_BOOST_SIGNAL<void()> onNewPlot;
+ };
+ 
+ Events& events();
+--- rstudio-1.1.463-orig/src/cpp/session/modules/build/SessionSourceCpp.cpp	2018-10-25 09:42:55.000000000 +1100
++++ rstudio-1.1.463/src/cpp/session/modules/build/SessionSourceCpp.cpp	2018-11-17 21:24:35.293976361 +1100
+@@ -15,11 +15,11 @@
+ 
+ #include "SessionSourceCpp.hpp"
+ 
+-#include <boost/signal.hpp>
+ #include <boost/algorithm/string/trim.hpp>
+ #include <boost/algorithm/string/predicate.hpp>
+ #include <boost/algorithm/string/join.hpp>
+ 
++#include <core/BoostSignals.hpp>
+ #include <core/Error.hpp>
+ #include <core/FilePath.hpp>
+ #include <core/StringUtils.hpp>
+--- rstudio-1.1.463-orig/src/cpp/session/modules/rmarkdown/NotebookAlternateEngines.cpp	2018-10-25 09:42:55.000000000 +1100
++++ rstudio-1.1.463/src/cpp/session/modules/rmarkdown/NotebookAlternateEngines.cpp	2018-11-17 21:24:35.294976371 +1100
+@@ -142,7 +142,7 @@
+       LOG_ERROR(error);
+    
+    // capture console output, error
+-   boost::signals::scoped_connection consoleHandler =
++   RSTUDIO_BOOST_SCOPED_CONNECTION consoleHandler =
+          module_context::events().onConsoleOutput.connect(
+             boost::bind(chunkConsoleOutputHandler,
+                         _1,
+@@ -219,7 +219,7 @@
+       LOG_ERROR(error);
+    
+    // capture console output, error
+-   boost::signals::scoped_connection consoleHandler =
++   RSTUDIO_BOOST_SCOPED_CONNECTION consoleHandler =
+          module_context::events().onConsoleOutput.connect(
+             boost::bind(chunkConsoleOutputHandler,
+                         _1,
+@@ -363,7 +363,7 @@
+       LOG_ERROR(error);
+    
+    // capture console output, error
+-   boost::signals::scoped_connection consoleHandler =
++   RSTUDIO_BOOST_SCOPED_CONNECTION consoleHandler =
+          module_context::events().onConsoleOutput.connect(
+             boost::bind(chunkConsoleOutputHandler,
+                         _1,
+--- rstudio-1.1.463-orig/src/cpp/session/modules/rmarkdown/NotebookCapture.cpp	2018-10-25 09:42:55.000000000 +1100
++++ rstudio-1.1.463/src/cpp/session/modules/rmarkdown/NotebookCapture.cpp	2018-11-17 21:24:35.294976371 +1100
+@@ -16,6 +16,8 @@
+ #include "SessionRmdNotebook.hpp"
+ #include "NotebookCapture.hpp"
+ 
++#include <boost/make_shared.hpp>
++
+ namespace rstudio {
+ namespace session {
+ namespace modules {
+--- rstudio-1.1.463-orig/src/cpp/session/modules/rmarkdown/NotebookExec.cpp	2018-10-25 09:42:55.000000000 +1100
++++ rstudio-1.1.463/src/cpp/session/modules/rmarkdown/NotebookExec.cpp	2018-11-17 21:24:35.295976381 +1100
+@@ -441,7 +441,7 @@
+    }
+ 
+    // unhook all our event handlers
+-   BOOST_FOREACH(const boost::signals::connection connection, connections_) 
++   BOOST_FOREACH(const RSTUDIO_BOOST_CONNECTION connection, connections_) 
+    {
+       connection.disconnect();
+    }
+--- rstudio-1.1.463-orig/src/cpp/session/modules/rmarkdown/NotebookExec.hpp	2018-10-25 09:42:55.000000000 +1100
++++ rstudio-1.1.463/src/cpp/session/modules/rmarkdown/NotebookExec.hpp	2018-11-17 21:24:35.295976381 +1100
+@@ -18,8 +18,7 @@
+ 
+ #include <session/SessionModuleContext.hpp>
+ 
+-#include <boost/signal.hpp>
+-
++#include <core/BoostSignals.hpp>
+ #include <core/json/Json.hpp>
+ 
+ #include <r/RSexp.hpp>
+@@ -99,7 +98,7 @@
+    bool hasErrors_;
+ 
+    std::vector<boost::shared_ptr<NotebookCapture> > captures_;
+-   std::vector<boost::signals::connection> connections_;
++   std::vector<RSTUDIO_BOOST_CONNECTION> connections_;
+ };
+ 
+ } // namespace notebook
+--- rstudio-1.1.463-orig/src/cpp/session/modules/rmarkdown/NotebookPlots.cpp	2018-10-25 09:42:55.000000000 +1100
++++ rstudio-1.1.463/src/cpp/session/modules/rmarkdown/NotebookPlots.cpp	2018-11-17 21:24:35.295976381 +1100
+@@ -20,11 +20,12 @@
+ 
+ #include <boost/format.hpp>
+ #include <boost/foreach.hpp>
+-#include <boost/signals/connection.hpp>
+ 
+-#include <core/system/FileMonitor.hpp>
+-#include <core/StringUtils.hpp>
++#include <core/BoostSignals.hpp>
+ #include <core/Exec.hpp>
++#include <core/StringUtils.hpp>
++
++#include <core/system/FileMonitor.hpp>
+ 
+ #include <session/SessionModuleContext.hpp>
+ 
+--- rstudio-1.1.463-orig/src/cpp/session/modules/rmarkdown/NotebookPlots.hpp	2018-10-25 09:42:55.000000000 +1100
++++ rstudio-1.1.463/src/cpp/session/modules/rmarkdown/NotebookPlots.hpp	2018-11-17 21:24:35.296976391 +1100
+@@ -18,8 +18,10 @@
+ #define SESSION_NOTEBOOK_PLOTS_HPP
+ 
+ #include <boost/function.hpp>
+-#include <boost/signals/connection.hpp>
++
++#include <core/BoostSignals.hpp>
+ #include <core/FilePath.hpp>
++
+ #include <r/RSexp.hpp>
+ 
+ #include "NotebookCapture.hpp"
+@@ -80,9 +82,9 @@
+ 
+    unsigned lastOrdinal_;
+ 
+-   boost::signals::connection onBeforeNewPlot_;
+-   boost::signals::connection onBeforeNewGridPage_;
+-   boost::signals::connection onNewPlot_;
++   RSTUDIO_BOOST_CONNECTION onBeforeNewPlot_;
++   RSTUDIO_BOOST_CONNECTION onBeforeNewGridPage_;
++   RSTUDIO_BOOST_CONNECTION onNewPlot_;
+ 
+    double width_;
+    double height_;
+--- rstudio-1.1.463-orig/src/cpp/session/modules/rmarkdown/NotebookQueue.cpp	2018-10-25 09:42:55.000000000 +1100
++++ rstudio-1.1.463/src/cpp/session/modules/rmarkdown/NotebookQueue.cpp	2018-11-17 21:24:35.296976391 +1100
+@@ -87,7 +87,7 @@
+       pInput_->enque(kThreadQuitCommand);
+ 
+       // unregister handlers
+-      BOOST_FOREACH(boost::signals::connection connection, handlers_)
++      BOOST_FOREACH(RSTUDIO_BOOST_CONNECTION connection, handlers_)
+       {
+          connection.disconnect();
+       }
+@@ -651,7 +651,7 @@
+    boost::shared_ptr<ChunkExecContext> execContext_;
+ 
+    // registered signal handlers
+-   std::vector<boost::signals::connection> handlers_;
++   std::vector<RSTUDIO_BOOST_CONNECTION> handlers_;
+ 
+    // the thread which submits console input, and the queue which feeds it
+    boost::thread console_;
+--- rstudio-1.1.463-orig/src/cpp/session/modules/rmarkdown/SessionRmdNotebook.hpp	2018-10-25 09:42:55.000000000 +1100
++++ rstudio-1.1.463/src/cpp/session/modules/rmarkdown/SessionRmdNotebook.hpp	2018-11-17 21:24:35.296976391 +1100
+@@ -18,7 +18,8 @@
+ #define SESSION_RMARKDOWN_NOTEBOOK_HPP
+ 
+ #include <ctime>
+-#include <boost/signals.hpp>
++
++#include <core/BoostSignals.hpp>
+ #include <core/json/Json.hpp>
+ 
+ #define kChunkLibDir "lib"
+@@ -76,24 +77,24 @@
+ struct Events : boost::noncopyable
+ {
+    // Document {0}, chunk {1} from context id {3} execution completed
+-   boost::signal<void(const std::string&, const std::string&,
++   RSTUDIO_BOOST_SIGNAL<void(const std::string&, const std::string&,
+                       const std::string&)> 
+                 onChunkExecCompleted;
+ 
+    // Document {0}, chunk {1} had console output of type {2} and text {3}
+-   boost::signal<void(const std::string&, const std::string&, int, 
++   RSTUDIO_BOOST_SIGNAL<void(const std::string&, const std::string&, int, 
+                 const std::string&)>
+                 onChunkConsoleOutput;
+ 
+-   boost::signal<void(const core::FilePath&, const core::FilePath&, 
++   RSTUDIO_BOOST_SIGNAL<void(const core::FilePath&, const core::FilePath&, 
+                       const core::json::Value& metadata, unsigned ordinal)> 
+                          onPlotOutput;
+-   boost::signal<void(const core::FilePath&, const core::FilePath&,
++   RSTUDIO_BOOST_SIGNAL<void(const core::FilePath&, const core::FilePath&,
+                       const core::json::Value& metadata)> onHtmlOutput;
+-   boost::signal<void(const core::json::Object&)> onErrorOutput;
+-   boost::signal<void(const core::FilePath&, const core::FilePath&,
++   RSTUDIO_BOOST_SIGNAL<void(const core::json::Object&)> onErrorOutput;
++   RSTUDIO_BOOST_SIGNAL<void(const core::FilePath&, const core::FilePath&,
+                       const core::json::Value& metadata)> onDataOutput;
+-   boost::signal<void(Condition condition, const std::string& message)> 
++   RSTUDIO_BOOST_SIGNAL<void(Condition condition, const std::string& message)> 
+                          onCondition;
+ };
+ 

diff --git a/sci-mathematics/rstudio/files/rstudio-1.1.463-boost-1.69.0_p2.patch b/sci-mathematics/rstudio/files/rstudio-1.1.463-boost-1.69.0_p2.patch
new file mode 100644
index 00000000000..961723fd224
--- /dev/null
+++ b/sci-mathematics/rstudio/files/rstudio-1.1.463-boost-1.69.0_p2.patch
@@ -0,0 +1,167 @@
+--- rstudio-1.1.463-orig/src/cpp/CMakeLists.txt	2018-11-17 21:24:35.285976284 +1100
++++ rstudio-1.1.463/src/cpp/CMakeLists.txt	2018-11-17 21:41:02.712507842 +1100
+@@ -175,6 +175,9 @@
+       set(Boost_USE_STATIC_LIBS ON)
+       set(BOOST_INCLUDEDIR  ${RSTUDIO_TOOLS_BOOST}/include)
+       find_package(Boost ${BOOST_VERSION} REQUIRED)
++      if(NOT Boost_VERSION VERSION_LESS 1.69.0)
++         list(REMOVE_ITEM BOOST_LIBS signals)
++      endif()
+ 
+       # define library list manually (find_package doesn't always pick them up)
+       set(BOOST_LIB_DIR ${RSTUDIO_TOOLS_BOOST}/lib)
+@@ -184,11 +187,15 @@
+       message(STATUS "Using RStudio-provided Boost ${BOOST_VERSION}")
+    else()
+       add_definitions(-DRSTUDIO_BOOST_NAMESPACE=boost)
++      find_package(Boost ${BOOST_VERSION} REQUIRED)
++      if(NOT Boost_VERSION VERSION_LESS 1.69.0)
++         list(REMOVE_ITEM BOOST_LIBS signals)
++      endif()
+       find_package(Boost ${BOOST_VERSION} REQUIRED COMPONENTS ${BOOST_LIBS})
+       message(STATUS "Using system Boost ${BOOST_VERSION}")
+    endif()
+ 
+-   # WIN32 BOOST
++# WIN32 BOOST
+ else()
+    # hard-code to our own prebuilt boost libs
+    add_definitions(-DRSTUDIO_BOOST_NAMESPACE=rstudio_boost)
+@@ -211,14 +218,14 @@
+ # allow opt-in to using Boost.Signals2
+ # TODO: remove this in RStudio v1.3 and port to signals2
+ if(NOT RSTUDIO_BOOST_SIGNALS_VERSION)
+-   if (BOOST_VERSION VERSION_LESS 1.69.0)
++   if (Boost_VERSION VERSION_LESS 1.69.0)
+       set(RSTUDIO_BOOST_SIGNALS_VERSION 1)
+    else()
+       set(RSTUDIO_BOOST_SIGNALS_VERSION 2)
+    endif()
+ endif()
+ 
+-message(STATUS "Using Booost.Signals version ${RSTUDIO_BOOST_SIGNALS_VERSION}")
++message(STATUS "Using Boost.Signals version ${RSTUDIO_BOOST_SIGNALS_VERSION}")
+ add_definitions(-DRSTUDIO_BOOST_SIGNALS_VERSION=${RSTUDIO_BOOST_SIGNALS_VERSION})
+ 
+ # add boost as system include directory
+--- rstudio-1.1.463-orig/src/cpp/core/include/core/r_util/RFunctionInformation.hpp	2018-10-25 09:42:55.000000000 +1100
++++ rstudio-1.1.463/src/cpp/core/include/core/r_util/RFunctionInformation.hpp	2018-11-17 21:41:02.713507852 +1100
+@@ -75,9 +75,9 @@
+    const std::string& name() const { return name_; }
+    const boost::optional<std::string>& defaultValue() const { return defaultValue_; }
+    boost::tribool hasDefault() const { return hasDefault_; }
+-   bool isUsed() const { return isUsed_; }
++   bool isUsed() const { return bool(isUsed_); }
+    void setIsUsed(bool value) { isUsed_ = value; }
+-   bool isMissingnessHandled() const { return isMissingnessHandled_; }
++   bool isMissingnessHandled() const { return bool(isMissingnessHandled_); }
+    void setMissingnessHandled(bool value) { isMissingnessHandled_ = value; }
+    
+ private:
+@@ -130,7 +130,7 @@
+    
+    bool isPrimitive()
+    {
+-      return isPrimitive_ == true;
++      return bool(isPrimitive_);
+    }
+    
+    void setIsPrimitive(bool isPrimitive)
+--- rstudio-1.1.463-orig/src/cpp/session/modules/SessionRParser.cpp	2018-10-25 09:42:55.000000000 +1100
++++ rstudio-1.1.463/src/cpp/session/modules/SessionRParser.cpp	2018-11-17 21:41:02.714507862 +1100
+@@ -390,7 +390,7 @@
+    if (!failed)
+    {
+       DEBUG("--- Found function in pkgInfo index: " << *fnInfo.binding());
+-      return fnInfo.performsNse();
++      return bool(fnInfo.performsNse());
+    }
+    
+    // Handle some special cases first.
+--- rstudio-1.1.463-orig/src/tools/clang-ubsan-build	2018-10-25 09:42:55.000000000 +1100
++++ rstudio-1.1.463/src/tools/clang-ubsan-build	2018-11-17 21:41:02.714507862 +1100
+@@ -10,19 +10,19 @@
+ 
+ : ${RSTUDIO_USE_LIBCXX="Yes"}
+ : ${RSTUDIO_USE_SYSTEM_BOOST="Yes"}
+-: ${RSTUDIO_BOOST_VERSION="1.56.0"}
++: ${RSTUDIO_BOOST_REQUESTED_VERSION="1.56.0"}
+ 
+ mkdir -p "${BUILD_DIR}"
+ cd "${BUILD_DIR}"
+-cmake ../cpp                                                 \
+-    -DLIBR_HOME="${R_HOME}"                                  \
+-    -DCMAKE_C_COMPILER="${CC}"                               \
+-    -DCMAKE_C_FLAGS="${ASANFLAGS} ${LDFLAGS}"                \
+-    -DCMAKE_CXX_COMPILER="${CXX}"                            \
+-    -DCMAKE_CXX_FLAGS="${ASANFLAGS} ${LDFLAGS}"              \
+-    -DRSTUDIO_USE_LIBCXX="${RSTUDIO_USE_LIBCXX}"             \
+-    -DRSTUDIO_USE_SYSTEM_BOOST="${RSTUDIO_USE_SYSTEM_BOOST}" \
+-    -DRSTUDIO_BOOST_VERSION="${RSTUDIO_BOOST_VERSION}"       \
++cmake ../cpp                                                               \
++    -DLIBR_HOME="${R_HOME}"                                                \
++    -DCMAKE_C_COMPILER="${CC}"                                             \
++    -DCMAKE_C_FLAGS="${ASANFLAGS} ${LDFLAGS}"                              \
++    -DCMAKE_CXX_COMPILER="${CXX}"                                          \
++    -DCMAKE_CXX_FLAGS="${ASANFLAGS} ${LDFLAGS}"                            \
++    -DRSTUDIO_USE_LIBCXX="${RSTUDIO_USE_LIBCXX}"                           \
++    -DRSTUDIO_USE_SYSTEM_BOOST="${RSTUDIO_USE_SYSTEM_BOOST}"               \
++    -DRSTUDIO_BOOST_REQUESTED_VERSION="${RSTUDIO_BOOST_REQUESTED_VERSION}" \
+     "$@"
+ cd ..
+ 
+--- rstudio-1.1.463-orig/src/tools/gcc-ubsan-build	2018-10-25 09:42:55.000000000 +1100
++++ rstudio-1.1.463/src/tools/gcc-ubsan-build	2018-11-17 21:41:02.715507871 +1100
+@@ -19,19 +19,19 @@
+ # NOTE: Boost 1.50.0 not compatible with gcc-6
+ : ${RSTUDIO_USE_LIBCXX="No"}
+ : ${RSTUDIO_USE_SYSTEM_BOOST="Yes"}
+-: ${RSTUDIO_BOOST_VERSION="1.54.0"}
++: ${RSTUDIO_BOOST_REQUESTED_VERSION="1.54.0"}
+ 
+ mkdir -p "${BUILD_DIR}"
+ cd "${BUILD_DIR}"
+-cmake ../cpp                                                 \
+-    -DLIBR_HOME="${R_HOME}"                                  \
+-    -DCMAKE_C_COMPILER="${CC}"                               \
+-    -DCMAKE_C_FLAGS="${ASANFLAGS} ${LDFLAGS}"                \
+-    -DCMAKE_CXX_COMPILER="${CXX}"                            \
+-    -DCMAKE_CXX_FLAGS="${ASANFLAGS} ${LDFLAGS}"              \
+-    -DRSTUDIO_USE_LIBCXX="${RSTUDIO_USE_LIBCXX}"             \
+-    -DRSTUDIO_USE_SYSTEM_BOOST="${RSTUDIO_USE_SYSTEM_BOOST}" \
+-    -DRSTUDIO_BOOST_VERSION="${RSTUDIO_BOOST_VERSION}"       \
++cmake ../cpp                                                               \
++    -DLIBR_HOME="${R_HOME}"                                                \
++    -DCMAKE_C_COMPILER="${CC}"                                             \
++    -DCMAKE_C_FLAGS="${ASANFLAGS} ${LDFLAGS}"                              \
++    -DCMAKE_CXX_COMPILER="${CXX}"                                          \
++    -DCMAKE_CXX_FLAGS="${ASANFLAGS} ${LDFLAGS}"                            \
++    -DRSTUDIO_USE_LIBCXX="${RSTUDIO_USE_LIBCXX}"                           \
++    -DRSTUDIO_USE_SYSTEM_BOOST="${RSTUDIO_USE_SYSTEM_BOOST}"               \
++    -DRSTUDIO_BOOST_REQUESTED_VERSION="${RSTUDIO_BOOST_REQUESTED_VERSION}" \
+     "$@"
+ cd ..
+ 
+--- rstudio-1.1.463-orig/src/tools/xcode-ubsan-build	2018-10-25 09:42:55.000000000 +1100
++++ rstudio-1.1.463/src/tools/xcode-ubsan-build	2018-11-17 21:41:02.715507871 +1100
+@@ -15,13 +15,13 @@
+ # sanitizers released with newer versions of clang)
+ mkdir -p "${BUILD_DIR}"
+ cd "${BUILD_DIR}"
+-cmake ../cpp -GXcode                 \
+-    -DLIBR_HOME="${R_HOME}"          \
+-    -DLIBR_INCLUDE_DIRS="${R_INCL}"  \
+-    -DLIBR_DOC_DIR="${R_DOCS}"       \
+-    -DRSTUDIO_USE_LIBCXX="Yes"       \
+-    -DRSTUDIO_USE_SYSTEM_BOOST="Yes" \
+-    -DRSTUDIO_BOOST_VERSION="1.56.0" \
++cmake ../cpp -GXcode                           \
++    -DLIBR_HOME="${R_HOME}"                    \
++    -DLIBR_INCLUDE_DIRS="${R_INCL}"            \
++    -DLIBR_DOC_DIR="${R_DOCS}"                 \
++    -DRSTUDIO_USE_LIBCXX="Yes"                 \
++    -DRSTUDIO_USE_SYSTEM_BOOST="Yes"           \
++    -DRSTUDIO_BOOST_REQUESTED_VERSION="1.56.0" \
+     "$@"
+ cmake ../cpp -DLIBR_LIBRARIES="${R_LIBS}/libR.dylib"
+ cd ..

diff --git a/sci-mathematics/rstudio/files/rstudio-1.1.463-fix-ptr-int-compare.patch b/sci-mathematics/rstudio/files/rstudio-1.1.463-fix-ptr-int-compare.patch
new file mode 100644
index 00000000000..914cd942e8f
--- /dev/null
+++ b/sci-mathematics/rstudio/files/rstudio-1.1.463-fix-ptr-int-compare.patch
@@ -0,0 +1,13 @@
+--- rstudio-1.1.463-orig/src/cpp/server/ServerSecureKeyFile.cpp	2018-10-25 09:42:55.000000000 +1100
++++ rstudio-1.1.463/src/cpp/server/ServerSecureKeyFile.cpp	2018-11-17 22:17:18.110012955 +1100
+@@ -79,8 +79,8 @@
+          return error;
+ 
+       // change mode it so it is only readable and writeable by this user
+-      if (changeFileMode(secureKeyPath,
+-                         core::system::UserReadWriteMode) < 0)
++      if (!!changeFileMode(secureKeyPath,
++                           core::system::UserReadWriteMode))
+       {
+          return systemError(errno, ERROR_LOCATION);
+       }

diff --git a/sci-mathematics/rstudio/rstudio-1.1.463.ebuild b/sci-mathematics/rstudio/rstudio-1.1.463.ebuild
new file mode 100644
index 00000000000..f2d6cf5a20f
--- /dev/null
+++ b/sci-mathematics/rstudio/rstudio-1.1.463.ebuild
@@ -0,0 +1,253 @@
+# Copyright 1999-2018 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=6
+
+inherit eutils user cmake-utils gnome2-utils pam versionator xdg-utils java-pkg-2 pax-utils qmake-utils
+
+# TODO
+# * package gin and gwt
+# * use dict from tree, linguas
+# * do src_test (use junit from tree?)
+
+# update from scripts in dependencies/common
+# egrep '(GWT_SDK_VER=|GIN_VER=|SELENIUM_VER=|CHROMEDRIVER_VER=)' dependencies/common/install-gwt
+GWT_VER=2.7.0
+GIN_VER=1.5
+SELENIUM_VER=2.37.0
+CHROMEDRIVER_VER=2.7
+# grep 'PANDOC_VERSION=' dependencies/common/install-pandoc
+PANDOC_VER=1.19.2.1
+# ls dependencies/common/*.tar.gz
+PACKRAT_VER=0.98.1000
+RMARKDOWN_VER=0.98.1000
+SHINYAPPS_VER=0.98.1000
+RSCONNECT_VER=0.4.1.4_fcac892a69817febd7b655b189bf57193260cda0
+
+DESCRIPTION="IDE for the R language"
+HOMEPAGE="
+	http://www.rstudio.org
+	https://github.com/rstudio/rstudio/"
+SRC_URI="
+	https://github.com/rstudio/rstudio/archive/v${PV}.tar.gz -> ${P}.tar.gz
+	https://s3.amazonaws.com/rstudio-buildtools/gin-${GIN_VER}.zip
+	https://s3.amazonaws.com/rstudio-buildtools/gwt-${GWT_VER}.zip
+	https://s3.amazonaws.com/rstudio-buildtools/selenium-java-${SELENIUM_VER}.zip
+	https://s3.amazonaws.com/rstudio-buildtools/selenium-server-standalone-${SELENIUM_VER}.jar
+	https://s3.amazonaws.com/rstudio-buildtools/chromedriver-linux
+	https://s3.amazonaws.com/rstudio-dictionaries/core-dictionaries.zip
+	https://dev.gentoo.org/~gienah/distfiles/packrat-${PACKRAT_VER}.tar.gz
+	https://dev.gentoo.org/~gienah/distfiles/rmarkdown-${RMARKDOWN_VER}.tar.gz
+	https://dev.gentoo.org/~gienah/distfiles/shinyapps-${SHINYAPPS_VER}.tar.gz
+	https://dev.gentoo.org/~gienah/distfiles/rsconnect_${RSCONNECT_VER}.tar.gz
+"
+
+LICENSE="AGPL-3"
+SLOT="0"
+KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
+IUSE="dedicated libressl server"
+
+QT_VER=5.4
+QT_SLOT=5
+RDEPEND="
+	>=app-text/pandoc-${PANDOC_VER}
+	dev-haskell/pandoc-citeproc
+	>=dev-lang/R-2.11.1
+	>=dev-libs/boost-1.63:=
+	>=dev-libs/mathjax-2.7.4
+	sys-apps/util-linux
+	>=sys-devel/clang-3.5.0:*
+	sys-libs/zlib
+	>=virtual/jre-1.8:=
+	x11-libs/pango
+	!dedicated? (
+		>=dev-qt/qtcore-${QT_VER}:${QT_SLOT}
+		>=dev-qt/qtdeclarative-${QT_VER}:${QT_SLOT}
+		>=dev-qt/qtdbus-${QT_VER}:${QT_SLOT}
+		>=dev-qt/qtgui-${QT_VER}:${QT_SLOT}
+		>=dev-qt/qtnetwork-${QT_VER}:${QT_SLOT}
+		>=dev-qt/qtopengl-${QT_VER}:${QT_SLOT}
+		>=dev-qt/qtpositioning-${QT_VER}:${QT_SLOT}
+		>=dev-qt/qtprintsupport-${QT_VER}:${QT_SLOT}
+		>=dev-qt/qtsingleapplication-2.6.1_p20150629[X,qt5(+)]
+		>=dev-qt/qtsensors-${QT_VER}:${QT_SLOT}
+		>=dev-qt/qtsql-${QT_VER}:${QT_SLOT}
+		>=dev-qt/qtsvg-${QT_VER}:${QT_SLOT}
+		>=dev-qt/qtwebchannel-${QT_VER}:${QT_SLOT}
+		>=dev-qt/qtwebkit-${QT_VER}:${QT_SLOT}
+		>=dev-qt/qtwidgets-${QT_VER}:${QT_SLOT}
+		>=dev-qt/qtxml-${QT_VER}:${QT_SLOT}
+		>=dev-qt/qtxmlpatterns-${QT_VER}:${QT_SLOT}
+		server? ( virtual/pam )
+	)
+	dedicated? ( virtual/pam )
+	!libressl? ( dev-libs/openssl:0 )
+	libressl? ( dev-libs/libressl:0 )"
+DEPEND="${RDEPEND}
+	app-arch/unzip
+	dev-java/ant-core
+	>=virtual/jdk-1.8:=
+	virtual/pkgconfig"
+#	test? ( dev-java/junit:4 )
+
+PATCHES=(
+		"${FILESDIR}/${PN}-0.99.879-prefs.patch"
+		"${FILESDIR}/${PN}-1.0.44-paths.patch"
+		"${FILESDIR}/${PN}-1.1.357-clang-pandoc.patch"
+		"${FILESDIR}/${PN}-0.98.490-linker_flags.patch"
+		"${FILESDIR}/${PN}-0.99.473-qtsingleapplication.patch"
+		"${FILESDIR}/${PN}-1.0.44-systemd.patch"
+		"${FILESDIR}/${PN}-1.1.453-boost-1.67.0.patch"
+		"${FILESDIR}/${PN}-1.1.453-core.patch"
+		"${FILESDIR}/${PN}-1.1.463-boost-1.69.0_p1.patch"
+		"${FILESDIR}/${PN}-1.1.463-boost-1.69.0_p2.patch"
+		"${FILESDIR}/${PN}-1.1.463-fix-ptr-int-compare.patch"
+)
+
+src_unpack() {
+	unpack ${P}.tar.gz gwt-${GWT_VER}.zip
+	cd "${S}" || die
+	mkdir -p src/gwt/lib/{gin,gwt} \
+		dependencies/common/dictionaries \
+		src/gwt/lib/selenium/${SELENIUM_VER} \
+		src/gwt/lib/selenium/chromedriver/${CHROMEDRIVER_VER} || die
+	mv ../gwt-${GWT_VER} src/gwt/lib/gwt/${GWT_VER} || die
+	unzip -qd src/gwt/lib/gin/${GIN_VER} \
+		"${DISTDIR}"/gin-${GIN_VER}.zip || die
+	unzip -qd dependencies/common/dictionaries \
+		"${DISTDIR}"/core-dictionaries.zip || die
+	unzip -qd src/gwt/lib/selenium/${SELENIUM_VER} \
+		"${DISTDIR}"/selenium-java-${SELENIUM_VER}.zip || die
+	cp "${DISTDIR}"/selenium-server-standalone-${SELENIUM_VER}.jar \
+		src/gwt/lib/selenium/${SELENIUM_VER}/ || die
+	cp "${DISTDIR}"/chromedriver-linux \
+		src/gwt/lib/selenium/chromedriver/${CHROMEDRIVER_VER}/ || die
+	cd dependencies/common || die
+	unpack packrat-${PACKRAT_VER}.tar.gz
+	unpack rmarkdown-${RMARKDOWN_VER}.tar.gz
+	unpack shinyapps-${SHINYAPPS_VER}.tar.gz
+	unpack rsconnect_${RSCONNECT_VER}.tar.gz
+	cp "${DISTDIR}"/rmarkdown-${RMARKDOWN_VER}.tar.gz \
+		. || die
+	cp "${DISTDIR}"/packrat-${PACKRAT_VER}.tar.gz \
+		. || die
+	cp "${DISTDIR}"/shinyapps-${SHINYAPPS_VER}.tar.gz \
+		. || die
+	cp "${DISTDIR}"/rsconnect_${RSCONNECT_VER}.tar.gz \
+		. || die
+}
+
+src_prepare() {
+	cmake-utils_src_prepare
+	java-pkg-2_src_prepare
+	egit_clean
+
+	# Enable CMake to install our .service file for systemd usage
+	mkdir -vp "${S}/src/cpp/server/lib/systemd/system" || die
+	cp -v "${FILESDIR}/rstudio-server.service.in" "${S}/src/cpp/server/lib/systemd/system/" || die
+
+	# Adding -DDISTRO_SHARE=... to append-flags breaks cmake so using
+	# this sed hack for now. ~RMH
+	sed -i \
+		-e "s|DISTRO_SHARE|\"share/${PN}\"|g" \
+		src/cpp/server/ServerOptions.cpp \
+		src/cpp/session/SessionOptions.cpp || die
+
+	# use mathjax from system
+	ln -sf "${EPREFIX}"/usr/share/mathjax dependencies/common/mathjax-26 || die
+
+	# make sure icons and mime stuff are with prefix
+	sed -i \
+		-e "s:/usr:${EPREFIX}/usr:g" \
+		CMakeGlobals.txt src/cpp/desktop/CMakeLists.txt || die
+
+	# On Gentoo the rstudio-server configuration file is /etc/conf.d/rstudio-server.conf
+	sed -e "s@/etc/rstudio/rserver.conf@${EROOT}etc/conf.d/rstudio-server.conf@" \
+		-i src/cpp/server/ServerOptions.cpp \
+		|| die
+
+	# Set the rsession.conf file location for Gentoo prefix
+	sed -e "s@/etc/rstudio/rsession.conf@${EROOT}etc/rstudio/rsession.conf@" \
+		-i src/cpp/session/SessionOptions.cpp \
+		|| die
+
+	# dev-qt/qtsingleapplication-2.6.1_p20150629 does not provide a cmake module.
+	# It provides a library that has its version number appended to the end,
+	# which is difficult to handle in cmake, as find_library does not support
+	# searching for wildcard library names. So I find the library name from the
+	# qmake spec, and then sed this into the patched src/cpp/desktop/CMakeLists.txt.
+	rm -rf "${S}"/src/cpp/desktop/3rdparty || die
+	local s=$(grep '\-lQt$${QT_MAJOR_VERSION}Solutions_SingleApplication' \
+				   $(qt5_get_mkspecsdir)/features/qtsingleapplication.prf \
+					 | sed -e 's@\$\${QT_MAJOR_VERSION}@5@' \
+						   -e 's@LIBS \*= -l@@')
+	sed -e "s@Qt5Solutions_SingleApplication-2.6@${s}@g" \
+		-i "${S}"/src/cpp/desktop/CMakeLists.txt \
+		|| die
+
+	# The git commit for tag: git rev-list -n 1 v${PV}
+	sed -e 's@git ARGS rev-parse HEAD@echo ARGS 6871a99b32add885fe6fa3d50fe15f62346142e7@'\
+		-i "${S}"/CMakeLists.txt \
+		"${S}"/CMakeGlobals.txt \
+		|| die
+}
+
+src_configure() {
+	export RSTUDIO_VERSION_MAJOR=$(get_version_component_range 1)
+	export RSTUDIO_VERSION_MINOR=$(get_version_component_range 2)
+	export RSTUDIO_VERSION_PATCH=$(get_version_component_range 3)
+
+	local mycmakeargs=(
+		-DDISTRO_SHARE=share/${PN}
+		-DRSTUDIO_INSTALL_FREEDESKTOP="$(usex !dedicated "ON" "OFF")"
+		-DRSTUDIO_TARGET=$(usex dedicated "Server" "$(usex server "Development" "Desktop")")
+		-DQT_QMAKE_EXECUTABLE=$(qt5_get_bindir)/qmake
+		-DRSTUDIO_VERIFY_R_VERSION=FALSE
+		)
+
+	cmake-utils_src_configure
+}
+
+src_compile() {
+	# Avoid the rest of the oracle-jdk-bin-1.8.0.60 sandbox violations F: mkdir S: deny
+	# P: /root/.oracle_jre_usage.
+	export ANT_OPTS="-Duser.home=${T}"
+	cmake-utils_src_compile
+}
+
+src_install() {
+	export ANT_OPTS="-Duser.home=${T}"
+	cmake-utils_src_install
+	pax-mark m "${ED}usr/bin/rstudio"
+	doconfd "${FILESDIR}"/rstudio-server.conf
+	dodir /etc/rstudio
+	insinto /etc/rstudio
+	doins "${FILESDIR}"/rsession.conf
+	dosym "${ROOT}etc/conf.d/rstudio-server.conf" "${ROOT}etc/rstudio/rserver.conf"
+	if use dedicated || use server; then
+		dopamd src/cpp/server/extras/pam/rstudio
+		newinitd "${FILESDIR}"/rstudio-server.initd rstudio-server
+	fi
+}
+
+pkg_preinst() {
+	use dedicated || gnome2_icon_savelist
+	java-pkg-2_pkg_preinst
+}
+
+pkg_postinst() {
+	use dedicated || { xdg_desktop_database_update
+		xdg_mimeinfo_database_update
+		gnome2_icon_cache_update ;}
+
+	if use dedicated || use server; then
+		enewgroup rstudio-server
+		enewuser rstudio-server -1 -1 -1 rstudio-server
+	fi
+}
+
+pkg_postrm() {
+	use dedicated || { xdg_desktop_database_update
+		xdg_mimeinfo_database_update
+		gnome2_icon_cache_update ;}
+}


^ permalink raw reply related	[flat|nested] 12+ messages in thread

* [gentoo-commits] repo/gentoo:master commit in: sci-mathematics/rstudio/, sci-mathematics/rstudio/files/
@ 2019-08-21 14:08 Mark Wright
  0 siblings, 0 replies; 12+ messages in thread
From: Mark Wright @ 2019-08-21 14:08 UTC (permalink / raw
  To: gentoo-commits

commit:     cdda9adf72b626d020a063419c1f376755d1b456
Author:     Mark Wright <gienah <AT> gentoo <DOT> org>
AuthorDate: Wed Aug 21 14:03:46 2019 +0000
Commit:     Mark Wright <gienah <AT> gentoo <DOT> org>
CommitDate: Wed Aug 21 14:03:46 2019 +0000
URL:        https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=cdda9adf

sci-mathematics/rstudio: Bump to 1.2.1335, fix compile with >=boost 1.70.0

Bump, thanks to Neil, Ulenrich, François Valenduc, Thomas Bettler,
Simon Maurer, Bernd Feige and asturm for helping.

Split the rstudio-1.1.463-boost-1.69.0_p?.patch patches into 3 patch files.

Closes: https://bugs.gentoo.org/683050
Closes: https://bugs.gentoo.org/686186
Package-Manager: Portage-2.3.71, Repoman-2.3.17
Signed-off-by: Mark Wright <gienah <AT> gentoo.org>

 sci-mathematics/rstudio/Manifest                   |   3 +
 .../files/rstudio-1.1.463-boost-1.69.0_p1.patch    | 222 +-----------
 .../files/rstudio-1.1.463-boost-1.69.0_p2.patch    | 377 ++++++++++++---------
 ...patch => rstudio-1.1.463-boost-1.69.0_p3.patch} |   0
 .../files/rstudio-1.1.463-boost-1.70.0.patch       |  46 +++
 .../files/rstudio-1.2.1335-boost-1.70.0_p1.patch   |  46 +++
 .../files/rstudio-1.2.1335-boost-1.70.0_p2.patch   |  17 +
 .../rstudio/files/rstudio-1.2.1335-core.patch      | 160 +++++++++
 .../rstudio-1.2.1335-fix-ptr-int-compare.patch     |  13 +
 .../files/rstudio-1.2.1335-linker_flags.patch      |  11 +
 .../rstudio/files/rstudio-1.2.1335-pandoc.patch    |  32 ++
 .../rstudio/files/rstudio-1.2.1335-paths.patch     | 118 +++++++
 .../rstudio/files/rstudio-1.2.1335-prefs.patch     |  53 +++
 .../rstudio-1.2.1335-qtsingleapplication.patch     |  60 ++++
 ...io-1.1.463.ebuild => rstudio-1.1.463-r1.ebuild} |  16 +-
 sci-mathematics/rstudio/rstudio-1.1.463.ebuild     |   1 +
 ...udio-1.1.463.ebuild => rstudio-1.2.1335.ebuild} |  38 +--
 17 files changed, 804 insertions(+), 409 deletions(-)

diff --git a/sci-mathematics/rstudio/Manifest b/sci-mathematics/rstudio/Manifest
index 79c6b60ad01..0b00d0f295a 100644
--- a/sci-mathematics/rstudio/Manifest
+++ b/sci-mathematics/rstudio/Manifest
@@ -1,13 +1,16 @@
 DIST chromedriver-linux 19303552 BLAKE2B 610396fd74f2adc4c249ca971a53a6dd4ab06145d0b37d59adf66180dfada52192b20203bf3d992c270bd4f787df5c85511ca325aed06cbd9318add3eccfde30 SHA512 18774ede961dec222058dd0e3f128d63732cd444ee310136b44d5bf508a4f2f2c164a2c8d195d80bce8b5fb6303559e167f82f384e4a58e30f48b151a4206ee8
 DIST core-dictionaries.zip 876339 BLAKE2B f29afcbf5a7f8ec635e5a5b248d978af286d18488f54c9a09a2b95fde19b796e4473e5846402a46dd24b71c6e4167512539aaa32ab6d99713d500a80aaf46796 SHA512 9c5830cc9fed575e223f1c61f02e48c5aea6801bb0cd2586f02437c17fdffdb1d36c396d5a8ecbe02ba01196e73458304345b1f6b92c052bc7a7d05961fac2c9
 DIST gin-1.5.zip 1055663 BLAKE2B 11b86245d54967f0c76f22f7460fb752c410db3c59a019bb538a48fd0de7e87552f2f5bb9ce604e6ed508136a6a2b0814f061161579429daae8ca55b1a448114 SHA512 3f6649565f9600daaca6ddf3fb431925b5a1ce1ada38e6389de64cef617abba9d3f49c555d0a20053fb06f17ccbe4e1141b39966fbe4b2975d7b120377504897
+DIST gin-2.1.2.zip 1341053 BLAKE2B 515338ba50ba2183c101b42183e42ebf15613aae8751a0dcedb4b047de4ca8fab85eb240f5f0c92955441dbb87e80b3edbdae8d83f1e74f74c7de067d18cf108 SHA512 03407b6318ffb0dd504ce520649ed90e845f13fbdbd0bfb4d7e3b127842f1735093e39674077c3a04a11d434aefdc3a734652c3f85e8ab00ff37ae760ccb8dbb
 DIST gwt-2.7.0.zip 108818328 BLAKE2B 9af969f3f2577be041fcfb58f228fab4b5479fa0da5ff054ab0a59cad751590a1b4ae8d7fabc8a50e3b0e5d7eb9b2896c485d929421f75e6a2f6513480438a31 SHA512 a1eed5cc25c888cf81d4f22b1f9494d5d8567b911f7aeb1d164a6359120543668280afe1a3ffc9ed87b139c7db67fbcaaabde2066e3279909d7cd6fc22eaf499
+DIST gwt-2.8.1.zip 95650299 BLAKE2B 3853d50d1346e313903b6f0c4b8405ce9e896e51652483e5c7e9d711daa213e1341c71765b4a3fb061b58f90d49420245963a0480db8b71fe7aed6cd43782c14 SHA512 feeb00cb0413c2703dfd6931f57ba669813bd65f814715f2c04dd6dc69e885a8048337272333d7504c48e9fa52cdab699f854ee13211228ab142a1f458ee33ae
 DIST packrat-0.98.1000.tar.gz 97677 BLAKE2B 282fe33dc5ba366ceea05a222ae2d018bc3ad8f35fad73c585a3d4901c3287e6902277a9c7ca087854f3944bd85ff1b1d1f02869ece686b10f946e2f1cb1296c SHA512 2290c768ecf27a037e73c3f8336b9fd71c68ff19d071b4a8fbc469550d29007cacacdb75f854f73b5db2139a5104f129b85a3612e2ee47bd6118ee13f7d103a6
 DIST rmarkdown-0.98.1000.tar.gz 1423820 BLAKE2B eac8c9cf438c9b44ddfe954602dd67a83764b0c988b3ba571877c986b0d5d237059ed6643a86bb404428857ec8c346bfecd12f7cd15cde301cb0ce331f842b7f SHA512 df3540c24c87930fe55bff2ffe67c86c219800cb00ed72ba9451ecd0d0cad411548a78c1a04b9a2e301e853616dcb77e09129c4e48ade6f16d3f14b7ea7e4852
 DIST rsconnect_0.4.1.4_fcac892a69817febd7b655b189bf57193260cda0.tar.gz 197051 BLAKE2B 1f3f9fe71d7b50ab5108dfdbd3cc0b882bcc935ee58e8a9145b07a18bb86c39bc45e321a13add24df99492bc30548df716775c339bcbf4efc2bfe158299ae55a SHA512 208dc349f4aa7613ecf94939aba60d22d3a06972344b526c9b6c951015571f5922927bca08db571a7b8a268e42609a4f558f01278c9685f6da2ffc66a1f95ade
 DIST rstudio-1.1.383.tar.gz 20196702 BLAKE2B 5164230a92618e4252269ad0016b200294d1e7fa502cc49aa694486cda098ee7ffc65e6c74a87d891d0532f5cc15d1552aa86d04047d07b4f275cbc4d2758647 SHA512 3f637f9bce2c1ad1a4ed3e74287da722190a4e12b0cace6ffcca271977d49dcecca9365f2064366aad94e87851593cab83fa9361e9a9222a9f67fe9451f31ed2
 DIST rstudio-1.1.453.tar.gz 20200360 BLAKE2B 560b89e53b04356ecf9a02dd8a7e72ad8d6c30bf406fbe7e22a82cc6d33d40e84bececf5ecda9cf086360b2bd2fa64d6b33c2dd675ef5f605f9e825d7ca2dc84 SHA512 f2be0866f645007a6f80959109928820c89480057c3660d23e790591797d4f4c371733f49290dae9c81bfc2715821528e2a105e7a66d4d9ffbfc7ee2a596976c
 DIST rstudio-1.1.463.tar.gz 20203779 BLAKE2B 97f879539cbb7051af362a8469795a47feb42d18ff46dbbdffe36e0685d1cd5704848b3bf5a5611d482a09567722e35288527302cd521b18e2a48b347c919e17 SHA512 987347563a9726363c28d866e1372eae8eb19a5cbd0e33c7ee0e0c8f90471c4b69de0f559c00410523841b6c090b584652e01496f5db33c015a4554d2f4e179b
+DIST rstudio-1.2.1335.tar.gz 20440199 BLAKE2B cdd54a7df5a234bcc6d440f4ba5b45e58ea469f8dac5a17d9088f9d65035495c86b5a308cde28a224648f96a74038299863291f3c516a1d567762ecc5bfb079c SHA512 90657effc55264bf3efa1a8a5d2bbe94a37727f0450202ade99b9fbb71ea75b6dd9fa798d17cd4d1a1a97a16f186de8004d1888b6ea43f36d5252508520d3cde
 DIST selenium-java-2.37.0.zip 24625928 BLAKE2B b369a805ae96f0d0913c4be42888d9c2a1e213ff982f9daefe73fadb705baa80ab0186ab50ed52609e83697cffaf8d617d06d75405cb8e1c3fe8e7c5b81dba25 SHA512 68624e82dbc751a25c50fad72702a98eb30d77fd4337d2a969f8e06bcc49e5f8c835cd27ec53772f3375014ddde1d5636936e966b75f3594a9f86aa18ba4e779
 DIST selenium-server-standalone-2.37.0.jar 34730734 BLAKE2B 3899b1d4c5f9153c1f9f13bec66f7c1456ea2e0f34db7d8e54a1ce9063c33a05b3cf95216c2ae06bb40504f72f343a4b9ba6c8553fbbc340e7c18a5b612dde5c SHA512 b215446d42d2d1f69664349b6ae6dc53a532d3624c91254f0f4183d0ad764648792e5cc1126a55a1e60d9687d55200fed01d6d2f46cc3d853b1fa6ee38111018
 DIST shinyapps-0.98.1000.tar.gz 910095 BLAKE2B 4f9364692348bb52cbd12cc6ee447841cb0c805327f2518b2a9545920b602b954a98dea68ccb3daf32d2c3bab6464fb15402844d93277193315f1ae7b3ca5190 SHA512 3162317c4c20cfc1497e952a8235867084d629ae88407e6c465b3e208adb1dc97abfe6b9922e0374ddf4c8e38a76e112942bd312c54a66f74e6f2a3fe4c0a07c

diff --git a/sci-mathematics/rstudio/files/rstudio-1.1.463-boost-1.69.0_p1.patch b/sci-mathematics/rstudio/files/rstudio-1.1.463-boost-1.69.0_p1.patch
index aa3db25f3c0..a7a48572de3 100644
--- a/sci-mathematics/rstudio/files/rstudio-1.1.463-boost-1.69.0_p1.patch
+++ b/sci-mathematics/rstudio/files/rstudio-1.1.463-boost-1.69.0_p1.patch
@@ -1,4 +1,4 @@
---- /dev/null	2018-11-10 15:32:26.332997437 +1100
+--- /dev/null	2019-03-19 11:03:33.121000004 +1100
 +++ rstudio-1.1.463/src/cpp/core/include/core/BoostSignals.hpp	2018-11-17 21:24:35.285976284 +1100
 @@ -0,0 +1,40 @@
 +/*
@@ -458,223 +458,3 @@
  };
  
  ProjectContext& projectContext();
---- rstudio-1.1.463-orig/src/cpp/session/modules/SessionPlots.hpp	2018-10-25 09:42:55.000000000 +1100
-+++ rstudio-1.1.463/src/cpp/session/modules/SessionPlots.hpp	2018-11-17 21:24:35.292976352 +1100
-@@ -16,7 +16,7 @@
- #ifndef SESSION_PLOTS_HPP
- #define SESSION_PLOTS_HPP
- 
--#include <boost/signals.hpp>
-+#include <core/BoostSignals.hpp>
- 
- namespace rstudio {
- namespace core {
-@@ -35,9 +35,9 @@
- 
- struct Events : boost::noncopyable
- {
--   boost::signal<void()> onBeforeNewPlot;
--   boost::signal<void()> onBeforeNewGridPage;
--   boost::signal<void()> onNewPlot;
-+   RSTUDIO_BOOST_SIGNAL<void()> onBeforeNewPlot;
-+   RSTUDIO_BOOST_SIGNAL<void()> onBeforeNewGridPage;
-+   RSTUDIO_BOOST_SIGNAL<void()> onNewPlot;
- };
- 
- Events& events();
---- rstudio-1.1.463-orig/src/cpp/session/modules/build/SessionSourceCpp.cpp	2018-10-25 09:42:55.000000000 +1100
-+++ rstudio-1.1.463/src/cpp/session/modules/build/SessionSourceCpp.cpp	2018-11-17 21:24:35.293976361 +1100
-@@ -15,11 +15,11 @@
- 
- #include "SessionSourceCpp.hpp"
- 
--#include <boost/signal.hpp>
- #include <boost/algorithm/string/trim.hpp>
- #include <boost/algorithm/string/predicate.hpp>
- #include <boost/algorithm/string/join.hpp>
- 
-+#include <core/BoostSignals.hpp>
- #include <core/Error.hpp>
- #include <core/FilePath.hpp>
- #include <core/StringUtils.hpp>
---- rstudio-1.1.463-orig/src/cpp/session/modules/rmarkdown/NotebookAlternateEngines.cpp	2018-10-25 09:42:55.000000000 +1100
-+++ rstudio-1.1.463/src/cpp/session/modules/rmarkdown/NotebookAlternateEngines.cpp	2018-11-17 21:24:35.294976371 +1100
-@@ -142,7 +142,7 @@
-       LOG_ERROR(error);
-    
-    // capture console output, error
--   boost::signals::scoped_connection consoleHandler =
-+   RSTUDIO_BOOST_SCOPED_CONNECTION consoleHandler =
-          module_context::events().onConsoleOutput.connect(
-             boost::bind(chunkConsoleOutputHandler,
-                         _1,
-@@ -219,7 +219,7 @@
-       LOG_ERROR(error);
-    
-    // capture console output, error
--   boost::signals::scoped_connection consoleHandler =
-+   RSTUDIO_BOOST_SCOPED_CONNECTION consoleHandler =
-          module_context::events().onConsoleOutput.connect(
-             boost::bind(chunkConsoleOutputHandler,
-                         _1,
-@@ -363,7 +363,7 @@
-       LOG_ERROR(error);
-    
-    // capture console output, error
--   boost::signals::scoped_connection consoleHandler =
-+   RSTUDIO_BOOST_SCOPED_CONNECTION consoleHandler =
-          module_context::events().onConsoleOutput.connect(
-             boost::bind(chunkConsoleOutputHandler,
-                         _1,
---- rstudio-1.1.463-orig/src/cpp/session/modules/rmarkdown/NotebookCapture.cpp	2018-10-25 09:42:55.000000000 +1100
-+++ rstudio-1.1.463/src/cpp/session/modules/rmarkdown/NotebookCapture.cpp	2018-11-17 21:24:35.294976371 +1100
-@@ -16,6 +16,8 @@
- #include "SessionRmdNotebook.hpp"
- #include "NotebookCapture.hpp"
- 
-+#include <boost/make_shared.hpp>
-+
- namespace rstudio {
- namespace session {
- namespace modules {
---- rstudio-1.1.463-orig/src/cpp/session/modules/rmarkdown/NotebookExec.cpp	2018-10-25 09:42:55.000000000 +1100
-+++ rstudio-1.1.463/src/cpp/session/modules/rmarkdown/NotebookExec.cpp	2018-11-17 21:24:35.295976381 +1100
-@@ -441,7 +441,7 @@
-    }
- 
-    // unhook all our event handlers
--   BOOST_FOREACH(const boost::signals::connection connection, connections_) 
-+   BOOST_FOREACH(const RSTUDIO_BOOST_CONNECTION connection, connections_) 
-    {
-       connection.disconnect();
-    }
---- rstudio-1.1.463-orig/src/cpp/session/modules/rmarkdown/NotebookExec.hpp	2018-10-25 09:42:55.000000000 +1100
-+++ rstudio-1.1.463/src/cpp/session/modules/rmarkdown/NotebookExec.hpp	2018-11-17 21:24:35.295976381 +1100
-@@ -18,8 +18,7 @@
- 
- #include <session/SessionModuleContext.hpp>
- 
--#include <boost/signal.hpp>
--
-+#include <core/BoostSignals.hpp>
- #include <core/json/Json.hpp>
- 
- #include <r/RSexp.hpp>
-@@ -99,7 +98,7 @@
-    bool hasErrors_;
- 
-    std::vector<boost::shared_ptr<NotebookCapture> > captures_;
--   std::vector<boost::signals::connection> connections_;
-+   std::vector<RSTUDIO_BOOST_CONNECTION> connections_;
- };
- 
- } // namespace notebook
---- rstudio-1.1.463-orig/src/cpp/session/modules/rmarkdown/NotebookPlots.cpp	2018-10-25 09:42:55.000000000 +1100
-+++ rstudio-1.1.463/src/cpp/session/modules/rmarkdown/NotebookPlots.cpp	2018-11-17 21:24:35.295976381 +1100
-@@ -20,11 +20,12 @@
- 
- #include <boost/format.hpp>
- #include <boost/foreach.hpp>
--#include <boost/signals/connection.hpp>
- 
--#include <core/system/FileMonitor.hpp>
--#include <core/StringUtils.hpp>
-+#include <core/BoostSignals.hpp>
- #include <core/Exec.hpp>
-+#include <core/StringUtils.hpp>
-+
-+#include <core/system/FileMonitor.hpp>
- 
- #include <session/SessionModuleContext.hpp>
- 
---- rstudio-1.1.463-orig/src/cpp/session/modules/rmarkdown/NotebookPlots.hpp	2018-10-25 09:42:55.000000000 +1100
-+++ rstudio-1.1.463/src/cpp/session/modules/rmarkdown/NotebookPlots.hpp	2018-11-17 21:24:35.296976391 +1100
-@@ -18,8 +18,10 @@
- #define SESSION_NOTEBOOK_PLOTS_HPP
- 
- #include <boost/function.hpp>
--#include <boost/signals/connection.hpp>
-+
-+#include <core/BoostSignals.hpp>
- #include <core/FilePath.hpp>
-+
- #include <r/RSexp.hpp>
- 
- #include "NotebookCapture.hpp"
-@@ -80,9 +82,9 @@
- 
-    unsigned lastOrdinal_;
- 
--   boost::signals::connection onBeforeNewPlot_;
--   boost::signals::connection onBeforeNewGridPage_;
--   boost::signals::connection onNewPlot_;
-+   RSTUDIO_BOOST_CONNECTION onBeforeNewPlot_;
-+   RSTUDIO_BOOST_CONNECTION onBeforeNewGridPage_;
-+   RSTUDIO_BOOST_CONNECTION onNewPlot_;
- 
-    double width_;
-    double height_;
---- rstudio-1.1.463-orig/src/cpp/session/modules/rmarkdown/NotebookQueue.cpp	2018-10-25 09:42:55.000000000 +1100
-+++ rstudio-1.1.463/src/cpp/session/modules/rmarkdown/NotebookQueue.cpp	2018-11-17 21:24:35.296976391 +1100
-@@ -87,7 +87,7 @@
-       pInput_->enque(kThreadQuitCommand);
- 
-       // unregister handlers
--      BOOST_FOREACH(boost::signals::connection connection, handlers_)
-+      BOOST_FOREACH(RSTUDIO_BOOST_CONNECTION connection, handlers_)
-       {
-          connection.disconnect();
-       }
-@@ -651,7 +651,7 @@
-    boost::shared_ptr<ChunkExecContext> execContext_;
- 
-    // registered signal handlers
--   std::vector<boost::signals::connection> handlers_;
-+   std::vector<RSTUDIO_BOOST_CONNECTION> handlers_;
- 
-    // the thread which submits console input, and the queue which feeds it
-    boost::thread console_;
---- rstudio-1.1.463-orig/src/cpp/session/modules/rmarkdown/SessionRmdNotebook.hpp	2018-10-25 09:42:55.000000000 +1100
-+++ rstudio-1.1.463/src/cpp/session/modules/rmarkdown/SessionRmdNotebook.hpp	2018-11-17 21:24:35.296976391 +1100
-@@ -18,7 +18,8 @@
- #define SESSION_RMARKDOWN_NOTEBOOK_HPP
- 
- #include <ctime>
--#include <boost/signals.hpp>
-+
-+#include <core/BoostSignals.hpp>
- #include <core/json/Json.hpp>
- 
- #define kChunkLibDir "lib"
-@@ -76,24 +77,24 @@
- struct Events : boost::noncopyable
- {
-    // Document {0}, chunk {1} from context id {3} execution completed
--   boost::signal<void(const std::string&, const std::string&,
-+   RSTUDIO_BOOST_SIGNAL<void(const std::string&, const std::string&,
-                       const std::string&)> 
-                 onChunkExecCompleted;
- 
-    // Document {0}, chunk {1} had console output of type {2} and text {3}
--   boost::signal<void(const std::string&, const std::string&, int, 
-+   RSTUDIO_BOOST_SIGNAL<void(const std::string&, const std::string&, int, 
-                 const std::string&)>
-                 onChunkConsoleOutput;
- 
--   boost::signal<void(const core::FilePath&, const core::FilePath&, 
-+   RSTUDIO_BOOST_SIGNAL<void(const core::FilePath&, const core::FilePath&, 
-                       const core::json::Value& metadata, unsigned ordinal)> 
-                          onPlotOutput;
--   boost::signal<void(const core::FilePath&, const core::FilePath&,
-+   RSTUDIO_BOOST_SIGNAL<void(const core::FilePath&, const core::FilePath&,
-                       const core::json::Value& metadata)> onHtmlOutput;
--   boost::signal<void(const core::json::Object&)> onErrorOutput;
--   boost::signal<void(const core::FilePath&, const core::FilePath&,
-+   RSTUDIO_BOOST_SIGNAL<void(const core::json::Object&)> onErrorOutput;
-+   RSTUDIO_BOOST_SIGNAL<void(const core::FilePath&, const core::FilePath&,
-                       const core::json::Value& metadata)> onDataOutput;
--   boost::signal<void(Condition condition, const std::string& message)> 
-+   RSTUDIO_BOOST_SIGNAL<void(Condition condition, const std::string& message)> 
-                          onCondition;
- };
- 

diff --git a/sci-mathematics/rstudio/files/rstudio-1.1.463-boost-1.69.0_p2.patch b/sci-mathematics/rstudio/files/rstudio-1.1.463-boost-1.69.0_p2.patch
index 961723fd224..d90ce005a1a 100644
--- a/sci-mathematics/rstudio/files/rstudio-1.1.463-boost-1.69.0_p2.patch
+++ b/sci-mathematics/rstudio/files/rstudio-1.1.463-boost-1.69.0_p2.patch
@@ -1,167 +1,220 @@
---- rstudio-1.1.463-orig/src/cpp/CMakeLists.txt	2018-11-17 21:24:35.285976284 +1100
-+++ rstudio-1.1.463/src/cpp/CMakeLists.txt	2018-11-17 21:41:02.712507842 +1100
-@@ -175,6 +175,9 @@
-       set(Boost_USE_STATIC_LIBS ON)
-       set(BOOST_INCLUDEDIR  ${RSTUDIO_TOOLS_BOOST}/include)
-       find_package(Boost ${BOOST_VERSION} REQUIRED)
-+      if(NOT Boost_VERSION VERSION_LESS 1.69.0)
-+         list(REMOVE_ITEM BOOST_LIBS signals)
-+      endif()
- 
-       # define library list manually (find_package doesn't always pick them up)
-       set(BOOST_LIB_DIR ${RSTUDIO_TOOLS_BOOST}/lib)
-@@ -184,11 +187,15 @@
-       message(STATUS "Using RStudio-provided Boost ${BOOST_VERSION}")
-    else()
-       add_definitions(-DRSTUDIO_BOOST_NAMESPACE=boost)
-+      find_package(Boost ${BOOST_VERSION} REQUIRED)
-+      if(NOT Boost_VERSION VERSION_LESS 1.69.0)
-+         list(REMOVE_ITEM BOOST_LIBS signals)
-+      endif()
-       find_package(Boost ${BOOST_VERSION} REQUIRED COMPONENTS ${BOOST_LIBS})
-       message(STATUS "Using system Boost ${BOOST_VERSION}")
-    endif()
- 
--   # WIN32 BOOST
-+# WIN32 BOOST
- else()
-    # hard-code to our own prebuilt boost libs
-    add_definitions(-DRSTUDIO_BOOST_NAMESPACE=rstudio_boost)
-@@ -211,14 +218,14 @@
- # allow opt-in to using Boost.Signals2
- # TODO: remove this in RStudio v1.3 and port to signals2
- if(NOT RSTUDIO_BOOST_SIGNALS_VERSION)
--   if (BOOST_VERSION VERSION_LESS 1.69.0)
-+   if (Boost_VERSION VERSION_LESS 1.69.0)
-       set(RSTUDIO_BOOST_SIGNALS_VERSION 1)
-    else()
-       set(RSTUDIO_BOOST_SIGNALS_VERSION 2)
-    endif()
- endif()
- 
--message(STATUS "Using Booost.Signals version ${RSTUDIO_BOOST_SIGNALS_VERSION}")
-+message(STATUS "Using Boost.Signals version ${RSTUDIO_BOOST_SIGNALS_VERSION}")
- add_definitions(-DRSTUDIO_BOOST_SIGNALS_VERSION=${RSTUDIO_BOOST_SIGNALS_VERSION})
- 
- # add boost as system include directory
---- rstudio-1.1.463-orig/src/cpp/core/include/core/r_util/RFunctionInformation.hpp	2018-10-25 09:42:55.000000000 +1100
-+++ rstudio-1.1.463/src/cpp/core/include/core/r_util/RFunctionInformation.hpp	2018-11-17 21:41:02.713507852 +1100
-@@ -75,9 +75,9 @@
-    const std::string& name() const { return name_; }
-    const boost::optional<std::string>& defaultValue() const { return defaultValue_; }
-    boost::tribool hasDefault() const { return hasDefault_; }
--   bool isUsed() const { return isUsed_; }
-+   bool isUsed() const { return bool(isUsed_); }
-    void setIsUsed(bool value) { isUsed_ = value; }
--   bool isMissingnessHandled() const { return isMissingnessHandled_; }
-+   bool isMissingnessHandled() const { return bool(isMissingnessHandled_); }
-    void setMissingnessHandled(bool value) { isMissingnessHandled_ = value; }
+--- rstudio-1.1.463-orig/src/cpp/session/modules/SessionPlots.hpp	2018-10-25 09:42:55.000000000 +1100
++++ rstudio-1.1.463/src/cpp/session/modules/SessionPlots.hpp	2018-11-17 21:24:35.292976352 +1100
+@@ -16,7 +16,7 @@
+ #ifndef SESSION_PLOTS_HPP
+ #define SESSION_PLOTS_HPP
+ 
+-#include <boost/signals.hpp>
++#include <core/BoostSignals.hpp>
+ 
+ namespace rstudio {
+ namespace core {
+@@ -35,9 +35,9 @@
+ 
+ struct Events : boost::noncopyable
+ {
+-   boost::signal<void()> onBeforeNewPlot;
+-   boost::signal<void()> onBeforeNewGridPage;
+-   boost::signal<void()> onNewPlot;
++   RSTUDIO_BOOST_SIGNAL<void()> onBeforeNewPlot;
++   RSTUDIO_BOOST_SIGNAL<void()> onBeforeNewGridPage;
++   RSTUDIO_BOOST_SIGNAL<void()> onNewPlot;
+ };
+ 
+ Events& events();
+--- rstudio-1.1.463-orig/src/cpp/session/modules/build/SessionSourceCpp.cpp	2018-10-25 09:42:55.000000000 +1100
++++ rstudio-1.1.463/src/cpp/session/modules/build/SessionSourceCpp.cpp	2018-11-17 21:24:35.293976361 +1100
+@@ -15,11 +15,11 @@
+ 
+ #include "SessionSourceCpp.hpp"
+ 
+-#include <boost/signal.hpp>
+ #include <boost/algorithm/string/trim.hpp>
+ #include <boost/algorithm/string/predicate.hpp>
+ #include <boost/algorithm/string/join.hpp>
+ 
++#include <core/BoostSignals.hpp>
+ #include <core/Error.hpp>
+ #include <core/FilePath.hpp>
+ #include <core/StringUtils.hpp>
+--- rstudio-1.1.463-orig/src/cpp/session/modules/rmarkdown/NotebookAlternateEngines.cpp	2018-10-25 09:42:55.000000000 +1100
++++ rstudio-1.1.463/src/cpp/session/modules/rmarkdown/NotebookAlternateEngines.cpp	2018-11-17 21:24:35.294976371 +1100
+@@ -142,7 +142,7 @@
+       LOG_ERROR(error);
     
- private:
-@@ -130,7 +130,7 @@
+    // capture console output, error
+-   boost::signals::scoped_connection consoleHandler =
++   RSTUDIO_BOOST_SCOPED_CONNECTION consoleHandler =
+          module_context::events().onConsoleOutput.connect(
+             boost::bind(chunkConsoleOutputHandler,
+                         _1,
+@@ -219,7 +219,7 @@
+       LOG_ERROR(error);
     
-    bool isPrimitive()
-    {
--      return isPrimitive_ == true;
-+      return bool(isPrimitive_);
-    }
+    // capture console output, error
+-   boost::signals::scoped_connection consoleHandler =
++   RSTUDIO_BOOST_SCOPED_CONNECTION consoleHandler =
+          module_context::events().onConsoleOutput.connect(
+             boost::bind(chunkConsoleOutputHandler,
+                         _1,
+@@ -363,7 +363,7 @@
+       LOG_ERROR(error);
     
-    void setIsPrimitive(bool isPrimitive)
---- rstudio-1.1.463-orig/src/cpp/session/modules/SessionRParser.cpp	2018-10-25 09:42:55.000000000 +1100
-+++ rstudio-1.1.463/src/cpp/session/modules/SessionRParser.cpp	2018-11-17 21:41:02.714507862 +1100
-@@ -390,7 +390,7 @@
-    if (!failed)
+    // capture console output, error
+-   boost::signals::scoped_connection consoleHandler =
++   RSTUDIO_BOOST_SCOPED_CONNECTION consoleHandler =
+          module_context::events().onConsoleOutput.connect(
+             boost::bind(chunkConsoleOutputHandler,
+                         _1,
+--- rstudio-1.1.463-orig/src/cpp/session/modules/rmarkdown/NotebookCapture.cpp	2018-10-25 09:42:55.000000000 +1100
++++ rstudio-1.1.463/src/cpp/session/modules/rmarkdown/NotebookCapture.cpp	2018-11-17 21:24:35.294976371 +1100
+@@ -16,6 +16,8 @@
+ #include "SessionRmdNotebook.hpp"
+ #include "NotebookCapture.hpp"
+ 
++#include <boost/make_shared.hpp>
++
+ namespace rstudio {
+ namespace session {
+ namespace modules {
+--- rstudio-1.1.463-orig/src/cpp/session/modules/rmarkdown/NotebookExec.cpp	2018-10-25 09:42:55.000000000 +1100
++++ rstudio-1.1.463/src/cpp/session/modules/rmarkdown/NotebookExec.cpp	2018-11-17 21:24:35.295976381 +1100
+@@ -441,7 +441,7 @@
+    }
+ 
+    // unhook all our event handlers
+-   BOOST_FOREACH(const boost::signals::connection connection, connections_) 
++   BOOST_FOREACH(const RSTUDIO_BOOST_CONNECTION connection, connections_) 
     {
-       DEBUG("--- Found function in pkgInfo index: " << *fnInfo.binding());
--      return fnInfo.performsNse();
-+      return bool(fnInfo.performsNse());
+       connection.disconnect();
     }
-    
-    // Handle some special cases first.
---- rstudio-1.1.463-orig/src/tools/clang-ubsan-build	2018-10-25 09:42:55.000000000 +1100
-+++ rstudio-1.1.463/src/tools/clang-ubsan-build	2018-11-17 21:41:02.714507862 +1100
-@@ -10,19 +10,19 @@
- 
- : ${RSTUDIO_USE_LIBCXX="Yes"}
- : ${RSTUDIO_USE_SYSTEM_BOOST="Yes"}
--: ${RSTUDIO_BOOST_VERSION="1.56.0"}
-+: ${RSTUDIO_BOOST_REQUESTED_VERSION="1.56.0"}
- 
- mkdir -p "${BUILD_DIR}"
- cd "${BUILD_DIR}"
--cmake ../cpp                                                 \
--    -DLIBR_HOME="${R_HOME}"                                  \
--    -DCMAKE_C_COMPILER="${CC}"                               \
--    -DCMAKE_C_FLAGS="${ASANFLAGS} ${LDFLAGS}"                \
--    -DCMAKE_CXX_COMPILER="${CXX}"                            \
--    -DCMAKE_CXX_FLAGS="${ASANFLAGS} ${LDFLAGS}"              \
--    -DRSTUDIO_USE_LIBCXX="${RSTUDIO_USE_LIBCXX}"             \
--    -DRSTUDIO_USE_SYSTEM_BOOST="${RSTUDIO_USE_SYSTEM_BOOST}" \
--    -DRSTUDIO_BOOST_VERSION="${RSTUDIO_BOOST_VERSION}"       \
-+cmake ../cpp                                                               \
-+    -DLIBR_HOME="${R_HOME}"                                                \
-+    -DCMAKE_C_COMPILER="${CC}"                                             \
-+    -DCMAKE_C_FLAGS="${ASANFLAGS} ${LDFLAGS}"                              \
-+    -DCMAKE_CXX_COMPILER="${CXX}"                                          \
-+    -DCMAKE_CXX_FLAGS="${ASANFLAGS} ${LDFLAGS}"                            \
-+    -DRSTUDIO_USE_LIBCXX="${RSTUDIO_USE_LIBCXX}"                           \
-+    -DRSTUDIO_USE_SYSTEM_BOOST="${RSTUDIO_USE_SYSTEM_BOOST}"               \
-+    -DRSTUDIO_BOOST_REQUESTED_VERSION="${RSTUDIO_BOOST_REQUESTED_VERSION}" \
-     "$@"
- cd ..
- 
---- rstudio-1.1.463-orig/src/tools/gcc-ubsan-build	2018-10-25 09:42:55.000000000 +1100
-+++ rstudio-1.1.463/src/tools/gcc-ubsan-build	2018-11-17 21:41:02.715507871 +1100
-@@ -19,19 +19,19 @@
- # NOTE: Boost 1.50.0 not compatible with gcc-6
- : ${RSTUDIO_USE_LIBCXX="No"}
- : ${RSTUDIO_USE_SYSTEM_BOOST="Yes"}
--: ${RSTUDIO_BOOST_VERSION="1.54.0"}
-+: ${RSTUDIO_BOOST_REQUESTED_VERSION="1.54.0"}
- 
- mkdir -p "${BUILD_DIR}"
- cd "${BUILD_DIR}"
--cmake ../cpp                                                 \
--    -DLIBR_HOME="${R_HOME}"                                  \
--    -DCMAKE_C_COMPILER="${CC}"                               \
--    -DCMAKE_C_FLAGS="${ASANFLAGS} ${LDFLAGS}"                \
--    -DCMAKE_CXX_COMPILER="${CXX}"                            \
--    -DCMAKE_CXX_FLAGS="${ASANFLAGS} ${LDFLAGS}"              \
--    -DRSTUDIO_USE_LIBCXX="${RSTUDIO_USE_LIBCXX}"             \
--    -DRSTUDIO_USE_SYSTEM_BOOST="${RSTUDIO_USE_SYSTEM_BOOST}" \
--    -DRSTUDIO_BOOST_VERSION="${RSTUDIO_BOOST_VERSION}"       \
-+cmake ../cpp                                                               \
-+    -DLIBR_HOME="${R_HOME}"                                                \
-+    -DCMAKE_C_COMPILER="${CC}"                                             \
-+    -DCMAKE_C_FLAGS="${ASANFLAGS} ${LDFLAGS}"                              \
-+    -DCMAKE_CXX_COMPILER="${CXX}"                                          \
-+    -DCMAKE_CXX_FLAGS="${ASANFLAGS} ${LDFLAGS}"                            \
-+    -DRSTUDIO_USE_LIBCXX="${RSTUDIO_USE_LIBCXX}"                           \
-+    -DRSTUDIO_USE_SYSTEM_BOOST="${RSTUDIO_USE_SYSTEM_BOOST}"               \
-+    -DRSTUDIO_BOOST_REQUESTED_VERSION="${RSTUDIO_BOOST_REQUESTED_VERSION}" \
-     "$@"
- cd ..
- 
---- rstudio-1.1.463-orig/src/tools/xcode-ubsan-build	2018-10-25 09:42:55.000000000 +1100
-+++ rstudio-1.1.463/src/tools/xcode-ubsan-build	2018-11-17 21:41:02.715507871 +1100
-@@ -15,13 +15,13 @@
- # sanitizers released with newer versions of clang)
- mkdir -p "${BUILD_DIR}"
- cd "${BUILD_DIR}"
--cmake ../cpp -GXcode                 \
--    -DLIBR_HOME="${R_HOME}"          \
--    -DLIBR_INCLUDE_DIRS="${R_INCL}"  \
--    -DLIBR_DOC_DIR="${R_DOCS}"       \
--    -DRSTUDIO_USE_LIBCXX="Yes"       \
--    -DRSTUDIO_USE_SYSTEM_BOOST="Yes" \
--    -DRSTUDIO_BOOST_VERSION="1.56.0" \
-+cmake ../cpp -GXcode                           \
-+    -DLIBR_HOME="${R_HOME}"                    \
-+    -DLIBR_INCLUDE_DIRS="${R_INCL}"            \
-+    -DLIBR_DOC_DIR="${R_DOCS}"                 \
-+    -DRSTUDIO_USE_LIBCXX="Yes"                 \
-+    -DRSTUDIO_USE_SYSTEM_BOOST="Yes"           \
-+    -DRSTUDIO_BOOST_REQUESTED_VERSION="1.56.0" \
-     "$@"
- cmake ../cpp -DLIBR_LIBRARIES="${R_LIBS}/libR.dylib"
- cd ..
+--- rstudio-1.1.463-orig/src/cpp/session/modules/rmarkdown/NotebookExec.hpp	2018-10-25 09:42:55.000000000 +1100
++++ rstudio-1.1.463/src/cpp/session/modules/rmarkdown/NotebookExec.hpp	2018-11-17 21:24:35.295976381 +1100
+@@ -18,8 +18,7 @@
+ 
+ #include <session/SessionModuleContext.hpp>
+ 
+-#include <boost/signal.hpp>
+-
++#include <core/BoostSignals.hpp>
+ #include <core/json/Json.hpp>
+ 
+ #include <r/RSexp.hpp>
+@@ -99,7 +98,7 @@
+    bool hasErrors_;
+ 
+    std::vector<boost::shared_ptr<NotebookCapture> > captures_;
+-   std::vector<boost::signals::connection> connections_;
++   std::vector<RSTUDIO_BOOST_CONNECTION> connections_;
+ };
+ 
+ } // namespace notebook
+--- rstudio-1.1.463-orig/src/cpp/session/modules/rmarkdown/NotebookPlots.cpp	2018-10-25 09:42:55.000000000 +1100
++++ rstudio-1.1.463/src/cpp/session/modules/rmarkdown/NotebookPlots.cpp	2018-11-17 21:24:35.295976381 +1100
+@@ -20,11 +20,12 @@
+ 
+ #include <boost/format.hpp>
+ #include <boost/foreach.hpp>
+-#include <boost/signals/connection.hpp>
+ 
+-#include <core/system/FileMonitor.hpp>
+-#include <core/StringUtils.hpp>
++#include <core/BoostSignals.hpp>
+ #include <core/Exec.hpp>
++#include <core/StringUtils.hpp>
++
++#include <core/system/FileMonitor.hpp>
+ 
+ #include <session/SessionModuleContext.hpp>
+ 
+--- rstudio-1.1.463-orig/src/cpp/session/modules/rmarkdown/NotebookPlots.hpp	2018-10-25 09:42:55.000000000 +1100
++++ rstudio-1.1.463/src/cpp/session/modules/rmarkdown/NotebookPlots.hpp	2018-11-17 21:24:35.296976391 +1100
+@@ -18,8 +18,10 @@
+ #define SESSION_NOTEBOOK_PLOTS_HPP
+ 
+ #include <boost/function.hpp>
+-#include <boost/signals/connection.hpp>
++
++#include <core/BoostSignals.hpp>
+ #include <core/FilePath.hpp>
++
+ #include <r/RSexp.hpp>
+ 
+ #include "NotebookCapture.hpp"
+@@ -80,9 +82,9 @@
+ 
+    unsigned lastOrdinal_;
+ 
+-   boost::signals::connection onBeforeNewPlot_;
+-   boost::signals::connection onBeforeNewGridPage_;
+-   boost::signals::connection onNewPlot_;
++   RSTUDIO_BOOST_CONNECTION onBeforeNewPlot_;
++   RSTUDIO_BOOST_CONNECTION onBeforeNewGridPage_;
++   RSTUDIO_BOOST_CONNECTION onNewPlot_;
+ 
+    double width_;
+    double height_;
+--- rstudio-1.1.463-orig/src/cpp/session/modules/rmarkdown/NotebookQueue.cpp	2018-10-25 09:42:55.000000000 +1100
++++ rstudio-1.1.463/src/cpp/session/modules/rmarkdown/NotebookQueue.cpp	2018-11-17 21:24:35.296976391 +1100
+@@ -87,7 +87,7 @@
+       pInput_->enque(kThreadQuitCommand);
+ 
+       // unregister handlers
+-      BOOST_FOREACH(boost::signals::connection connection, handlers_)
++      BOOST_FOREACH(RSTUDIO_BOOST_CONNECTION connection, handlers_)
+       {
+          connection.disconnect();
+       }
+@@ -651,7 +651,7 @@
+    boost::shared_ptr<ChunkExecContext> execContext_;
+ 
+    // registered signal handlers
+-   std::vector<boost::signals::connection> handlers_;
++   std::vector<RSTUDIO_BOOST_CONNECTION> handlers_;
+ 
+    // the thread which submits console input, and the queue which feeds it
+    boost::thread console_;
+--- rstudio-1.1.463-orig/src/cpp/session/modules/rmarkdown/SessionRmdNotebook.hpp	2018-10-25 09:42:55.000000000 +1100
++++ rstudio-1.1.463/src/cpp/session/modules/rmarkdown/SessionRmdNotebook.hpp	2018-11-17 21:24:35.296976391 +1100
+@@ -18,7 +18,8 @@
+ #define SESSION_RMARKDOWN_NOTEBOOK_HPP
+ 
+ #include <ctime>
+-#include <boost/signals.hpp>
++
++#include <core/BoostSignals.hpp>
+ #include <core/json/Json.hpp>
+ 
+ #define kChunkLibDir "lib"
+@@ -76,24 +77,24 @@
+ struct Events : boost::noncopyable
+ {
+    // Document {0}, chunk {1} from context id {3} execution completed
+-   boost::signal<void(const std::string&, const std::string&,
++   RSTUDIO_BOOST_SIGNAL<void(const std::string&, const std::string&,
+                       const std::string&)> 
+                 onChunkExecCompleted;
+ 
+    // Document {0}, chunk {1} had console output of type {2} and text {3}
+-   boost::signal<void(const std::string&, const std::string&, int, 
++   RSTUDIO_BOOST_SIGNAL<void(const std::string&, const std::string&, int, 
+                 const std::string&)>
+                 onChunkConsoleOutput;
+ 
+-   boost::signal<void(const core::FilePath&, const core::FilePath&, 
++   RSTUDIO_BOOST_SIGNAL<void(const core::FilePath&, const core::FilePath&, 
+                       const core::json::Value& metadata, unsigned ordinal)> 
+                          onPlotOutput;
+-   boost::signal<void(const core::FilePath&, const core::FilePath&,
++   RSTUDIO_BOOST_SIGNAL<void(const core::FilePath&, const core::FilePath&,
+                       const core::json::Value& metadata)> onHtmlOutput;
+-   boost::signal<void(const core::json::Object&)> onErrorOutput;
+-   boost::signal<void(const core::FilePath&, const core::FilePath&,
++   RSTUDIO_BOOST_SIGNAL<void(const core::json::Object&)> onErrorOutput;
++   RSTUDIO_BOOST_SIGNAL<void(const core::FilePath&, const core::FilePath&,
+                       const core::json::Value& metadata)> onDataOutput;
+-   boost::signal<void(Condition condition, const std::string& message)> 
++   RSTUDIO_BOOST_SIGNAL<void(Condition condition, const std::string& message)> 
+                          onCondition;
+ };
+ 

diff --git a/sci-mathematics/rstudio/files/rstudio-1.1.463-boost-1.69.0_p2.patch b/sci-mathematics/rstudio/files/rstudio-1.1.463-boost-1.69.0_p3.patch
similarity index 100%
copy from sci-mathematics/rstudio/files/rstudio-1.1.463-boost-1.69.0_p2.patch
copy to sci-mathematics/rstudio/files/rstudio-1.1.463-boost-1.69.0_p3.patch

diff --git a/sci-mathematics/rstudio/files/rstudio-1.1.463-boost-1.70.0.patch b/sci-mathematics/rstudio/files/rstudio-1.1.463-boost-1.70.0.patch
new file mode 100644
index 00000000000..320b823355a
--- /dev/null
+++ b/sci-mathematics/rstudio/files/rstudio-1.1.463-boost-1.70.0.patch
@@ -0,0 +1,46 @@
+--- rstudio-1.1.463-orig/src/cpp/ext/websocketpp/transport/asio/connection.hpp	2018-10-25 09:42:55.000000000 +1100
++++ rstudio-1.1.463/src/cpp/ext/websocketpp/transport/asio/connection.hpp	2019-03-30 20:14:40.634057634 +1100
+@@ -296,7 +296,11 @@
+      */
+     timer_ptr set_timer(long duration, timer_handler callback) {
+         timer_ptr new_timer = lib::make_shared<boost::asio::deadline_timer>(
++#if defined(BOOST_VERSION) && BOOST_VERSION >= 107000
++            *m_io_service,
++#else
+             lib::ref(*m_io_service),
++#endif
+             boost::posix_time::milliseconds(duration)
+         );
+ 
+--- rstudio-1.1.463-orig/src/cpp/ext/websocketpp/transport/asio/endpoint.hpp	2018-10-25 09:42:55.000000000 +1100
++++ rstudio-1.1.463/src/cpp/ext/websocketpp/transport/asio/endpoint.hpp	2019-03-30 20:14:36.319021594 +1100
+@@ -184,7 +184,12 @@
+         m_io_service = ptr;
+         m_external_io_service = true;
+         m_acceptor = lib::make_shared<boost::asio::ip::tcp::acceptor>(
+-            lib::ref(*m_io_service));
++#if defined(BOOST_VERSION) && BOOST_VERSION >= 107000
++            *m_io_service
++#else
++            lib::ref(*m_io_service)
++#endif
++        );
+ 
+         m_state = READY;
+         ec = lib::error_code();
+--- rstudio-1.1.463-orig/src/cpp/ext/websocketpp/transport/asio/security/none.hpp	2018-10-25 09:42:55.000000000 +1100
++++ rstudio-1.1.463/src/cpp/ext/websocketpp/transport/asio/security/none.hpp	2019-03-30 20:15:22.353406097 +1100
+@@ -167,7 +167,12 @@
+         }
+ 
+         m_socket = lib::make_shared<boost::asio::ip::tcp::socket>(
+-            lib::ref(*service));
++#if defined(BOOST_VERSION) && BOOST_VERSION >= 107000
++            *service
++#else
++            lib::ref(*service)
++#endif
++        );
+ 
+         m_state = READY;
+ 

diff --git a/sci-mathematics/rstudio/files/rstudio-1.2.1335-boost-1.70.0_p1.patch b/sci-mathematics/rstudio/files/rstudio-1.2.1335-boost-1.70.0_p1.patch
new file mode 100644
index 00000000000..1ec458bb869
--- /dev/null
+++ b/sci-mathematics/rstudio/files/rstudio-1.2.1335-boost-1.70.0_p1.patch
@@ -0,0 +1,46 @@
+--- rstudio-1.2.1335-orig/src/cpp/ext/websocketpp/transport/asio/connection.hpp	2019-03-28 16:08:20.000000000 +1100
++++ rstudio-1.2.1335/src/cpp/ext/websocketpp/transport/asio/connection.hpp	2019-08-20 22:38:53.808923305 +1000
+@@ -296,7 +296,11 @@
+      */
+     timer_ptr set_timer(long duration, timer_handler callback) {
+         timer_ptr new_timer = lib::make_shared<boost::asio::deadline_timer>(
++#if defined(BOOST_VERSION) && BOOST_VERSION >= 107000
++            *m_io_service,
++#else
+             lib::ref(*m_io_service),
++#endif
+             boost::posix_time::milliseconds(duration)
+         );
+ 
+--- rstudio-1.2.1335-orig/src/cpp/ext/websocketpp/transport/asio/endpoint.hpp	2019-03-28 16:08:20.000000000 +1100
++++ rstudio-1.2.1335/src/cpp/ext/websocketpp/transport/asio/endpoint.hpp	2019-08-20 22:38:53.822923358 +1000
+@@ -184,7 +184,12 @@
+         m_io_service = ptr;
+         m_external_io_service = true;
+         m_acceptor = lib::make_shared<boost::asio::ip::tcp::acceptor>(
+-            lib::ref(*m_io_service));
++#if defined(BOOST_VERSION) && BOOST_VERSION >= 107000
++            *m_io_service
++#else
++            lib::ref(*m_io_service)
++#endif
++        );
+ 
+         m_state = READY;
+         ec = lib::error_code();
+--- rstudio-1.2.1335-orig/src/cpp/ext/websocketpp/transport/asio/security/none.hpp	2019-03-28 16:08:20.000000000 +1100
++++ rstudio-1.2.1335/src/cpp/ext/websocketpp/transport/asio/security/none.hpp	2019-08-20 22:38:53.823923362 +1000
+@@ -167,7 +167,12 @@
+         }
+ 
+         m_socket = lib::make_shared<boost::asio::ip::tcp::socket>(
+-            lib::ref(*service));
++#if defined(BOOST_VERSION) && BOOST_VERSION >= 107000
++            *service
++#else
++            lib::ref(*service)
++#endif
++        );
+ 
+         m_state = READY;
+ 

diff --git a/sci-mathematics/rstudio/files/rstudio-1.2.1335-boost-1.70.0_p2.patch b/sci-mathematics/rstudio/files/rstudio-1.2.1335-boost-1.70.0_p2.patch
new file mode 100644
index 00000000000..eed2c5c955c
--- /dev/null
+++ b/sci-mathematics/rstudio/files/rstudio-1.2.1335-boost-1.70.0_p2.patch
@@ -0,0 +1,17 @@
+--- rstudio-1.2.1335-orig/src/cpp/core/include/core/http/TcpIpAsyncConnector.hpp	2019-03-28 16:08:20.000000000 +1100
++++ rstudio-1.2.1335/src/cpp/core/include/core/http/TcpIpAsyncConnector.hpp	2019-04-09 22:08:45.331273559 +1000
+@@ -77,7 +77,13 @@
+       {
+          // start a timer that will cancel any outstanding asynchronous operations
+          // when it elapses if the connection operation has not succeeded
+-         pConnectionTimer_.reset(new boost::asio::deadline_timer(resolver_.get_io_service(), timeout));
++         pConnectionTimer_.reset(new boost::asio::deadline_timer(
++#if BOOST_VERSION >= 107000
++                                   resolver_.get_executor(),
++#else
++                                   resolver_.get_io_service(),
++#endif
++                                   timeout));
+          pConnectionTimer_->async_wait(boost::bind(&TcpIpAsyncConnector::onConnectionTimeout,
+                                                    TcpIpAsyncConnector::shared_from_this(),
+                                                    boost::asio::placeholders::error));

diff --git a/sci-mathematics/rstudio/files/rstudio-1.2.1335-core.patch b/sci-mathematics/rstudio/files/rstudio-1.2.1335-core.patch
new file mode 100644
index 00000000000..2c4374bb804
--- /dev/null
+++ b/sci-mathematics/rstudio/files/rstudio-1.2.1335-core.patch
@@ -0,0 +1,160 @@
+--- rstudio-1.2.1335-orig/src/cpp/session/SessionClientInit.cpp	2019-03-28 16:08:20.000000000 +1100
++++ rstudio-1.2.1335/src/cpp/session/SessionClientInit.cpp	2019-04-09 18:15:37.746363789 +1000
+@@ -87,13 +87,13 @@
+       boost::shared_ptr<http::Cookie>* pCookie)
+ {
+    // extract the base URL
+-   json::JsonRpcRequest request;
++   core::json::JsonRpcRequest request;
+    Error error = parseJsonRpcRequest(ptrConnection->request().body(), &request);
+    if (error)
+       return error;
+    std::string baseURL;
+ 
+-   error = json::readParams(request.params, &baseURL);
++   error = core::json::readParams(request.params, &baseURL);
+    if (error)
+       return error;
+ 
+@@ -161,7 +161,7 @@
+    }
+ 
+    // prepare session info 
+-   json::Object sessionInfo ;
++   core::json::Object sessionInfo ;
+    sessionInfo["clientId"] = clientId;
+    sessionInfo["mode"] = options.programMode();
+    
+@@ -175,8 +175,8 @@
+    }
+ 
+    // temp dir
+-   FilePath tempDir = rstudio::r::session::utils::tempDir();
+-   Error error = tempDir.ensureDirectory();
++   core::FilePath tempDir = rstudio::r::session::utils::tempDir();
++   core::Error error = tempDir.ensureDirectory();
+    if (error)
+       LOG_ERROR(error);
+    sessionInfo["temp_dir"] = tempDir.absolutePath();
+@@ -194,12 +194,12 @@
+    sessionInfo["prompt"] = rstudio::r::options::getOption<std::string>("prompt");
+ 
+    // client state
+-   json::Object clientStateObject;
++   core::json::Object clientStateObject;
+    rstudio::r::session::clientState().currentState(&clientStateObject);
+    sessionInfo["client_state"] = clientStateObject;
+    
+    // source documents
+-   json::Array jsonDocs;
++   core::json::Array jsonDocs;
+    error = modules::source::clientInitDocuments(&jsonDocs);
+    if (error)
+       LOG_ERROR(error);
+@@ -224,7 +224,7 @@
+    if (resumed)
+    {
+       // console actions
+-      json::Object actionsObject;
++     core::json::Object actionsObject;
+       consoleActions.asJson(&actionsObject);
+       sessionInfo["console_actions"] = actionsObject;
+    }
+@@ -290,12 +290,12 @@
+    }
+    else
+    {
+-      sessionInfo["active_project_file"] = json::Value();
+-      sessionInfo["project_ui_prefs"] = json::Value();
+-      sessionInfo["project_open_docs"] = json::Value();
++      sessionInfo["active_project_file"] = core::json::Value();
++      sessionInfo["project_ui_prefs"] = core::json::Value();
++      sessionInfo["project_open_docs"] = core::json::Value();
+       sessionInfo["project_supports_sharing"] = false;
+       sessionInfo["project_owned_by_user"] = false;
+-      sessionInfo["project_user_data_directory"] = json::Value();
++      sessionInfo["project_user_data_directory"] = core::json::Value();
+    }
+ 
+    sessionInfo["system_encoding"] = std::string(::locale2charset(NULL));
+@@ -332,20 +332,20 @@
+       sessionInfo["build_tools_bookdown_website"] =
+                               module_context::isBookdownWebsite();
+ 
+-      FilePath buildTargetDir = projects::projectContext().buildTargetPath();
++      core::FilePath buildTargetDir = projects::projectContext().buildTargetPath();
+       if (!buildTargetDir.empty())
+       {
+          sessionInfo["build_target_dir"] = module_context::createAliasedPath(
+                                                                 buildTargetDir);
+-         sessionInfo["has_pkg_src"] = (type == r_util::kBuildTypePackage) &&
++         sessionInfo["has_pkg_src"] = (type == core::r_util::kBuildTypePackage) &&
+                                       buildTargetDir.childPath("src").exists();
+          sessionInfo["has_pkg_vig"] =
+-               (type == r_util::kBuildTypePackage) &&
++               (type == core::r_util::kBuildTypePackage) &&
+                buildTargetDir.childPath("vignettes").exists();
+       }
+       else
+       {
+-         sessionInfo["build_target_dir"] = json::Value();
++         sessionInfo["build_target_dir"] = core::json::Value();
+          sessionInfo["has_pkg_src"] = false;
+          sessionInfo["has_pkg_vig"] = false;
+       }
+@@ -353,9 +353,9 @@
+    }
+    else
+    {
+-      sessionInfo["build_tools_type"] = r_util::kBuildTypeNone;
++      sessionInfo["build_tools_type"] = core::r_util::kBuildTypeNone;
+       sessionInfo["build_tools_bookdown_website"] = false;
+-      sessionInfo["build_target_dir"] = json::Value();
++      sessionInfo["build_target_dir"] = core::json::Value();
+       sessionInfo["has_pkg_src"] = false;
+       sessionInfo["has_pkg_vig"] = false;
+    }
+@@ -364,7 +364,7 @@
+    sessionInfo["presentation_commands"] = options.allowPresentationCommands();
+ 
+    sessionInfo["tutorial_api_available"] = false;
+-   sessionInfo["tutorial_api_client_origin"] = json::Value();
++   sessionInfo["tutorial_api_client_origin"] = core::json::Value();
+ 
+    sessionInfo["build_state"] = modules::build::buildStateAsJson();
+    sessionInfo["devtools_installed"] = module_context::isMinimumDevtoolsInstalled();
+@@ -375,7 +375,7 @@
+ 
+    // console history -- we do this at the end because
+    // restoreBuildRestartContext may have reset it
+-   json::Array historyArray;
++   core::json::Array historyArray;
+    rstudio::r::session::consoleHistory().asJson(&historyArray);
+    sessionInfo["console_history"] = historyArray;
+    sessionInfo["console_history_capacity"] =
+@@ -447,14 +447,14 @@
+ 
+    sessionInfo["multi_session"] = options.multiSession();
+ 
+-   json::Object rVersionsJson;
++   core::json::Object rVersionsJson;
+    rVersionsJson["r_version"] = module_context::rVersion();
+    rVersionsJson["r_version_label"] = module_context::rVersionLabel();
+    rVersionsJson["r_home_dir"] = module_context::rHomeDir();
+    sessionInfo["r_versions_info"] = rVersionsJson;
+ 
+    sessionInfo["show_user_home_page"] = options.showUserHomePage();
+-   sessionInfo["user_home_page_url"] = json::Value();
++   sessionInfo["user_home_page_url"] = core::json::Value();
+    
+    sessionInfo["r_addins"] = modules::r_addins::addinRegistryAsJson();
+    sessionInfo["package_provided_extensions"] = modules::ppe::indexer().getPayload();
+@@ -491,7 +491,7 @@
+ 
+    // create response  (we always set kEventsPending to false so that the client
+    // won't poll for events until it is ready)
+-   json::JsonRpcResponse jsonRpcResponse;
++   core::json::JsonRpcResponse jsonRpcResponse;
+    jsonRpcResponse.setField(kEventsPending, "false");
+    jsonRpcResponse.setResult(sessionInfo);
+ 

diff --git a/sci-mathematics/rstudio/files/rstudio-1.2.1335-fix-ptr-int-compare.patch b/sci-mathematics/rstudio/files/rstudio-1.2.1335-fix-ptr-int-compare.patch
new file mode 100644
index 00000000000..e38f5e0c444
--- /dev/null
+++ b/sci-mathematics/rstudio/files/rstudio-1.2.1335-fix-ptr-int-compare.patch
@@ -0,0 +1,13 @@
+--- rstudio-1.2.1335-orig/src/cpp/server_core/SecureKeyFile.cpp	2019-03-28 16:08:20.000000000 +1100
++++ rstudio-1.2.1335/src/cpp/server_core/SecureKeyFile.cpp	2019-04-09 20:47:57.943317208 +1000
+@@ -68,8 +68,8 @@
+          return error;
+ 
+       // change mode it so it is only readable and writeable by this user
+-      if (changeFileMode(secureKeyPath,
+-                         core::system::UserReadWriteMode) < 0)
++      if (!!changeFileMode(secureKeyPath,
++                           core::system::UserReadWriteMode))
+       {
+          return systemError(errno, ERROR_LOCATION);
+       }

diff --git a/sci-mathematics/rstudio/files/rstudio-1.2.1335-linker_flags.patch b/sci-mathematics/rstudio/files/rstudio-1.2.1335-linker_flags.patch
new file mode 100644
index 00000000000..e07ead68969
--- /dev/null
+++ b/sci-mathematics/rstudio/files/rstudio-1.2.1335-linker_flags.patch
@@ -0,0 +1,11 @@
+--- rstudio-1.2.1335-orig/src/cpp/CMakeLists.txt	2019-03-28 16:08:20.000000000 +1100
++++ rstudio-1.2.1335/src/cpp/CMakeLists.txt	2019-04-09 17:58:59.926559001 +1000
+@@ -117,7 +117,7 @@
+          add_definitions(-O0)
+          add_definitions(-D_GLIBCXX_ASSERTIONS)
+       endif()
+-      set(CMAKE_EXE_LINKER_FLAGS "${CMAKE_EXE_LINKER_FLAGS} -pie -Wl,-z,relro,-z,now")
++      set(CMAKE_EXE_LINKER_FLAGS "-pie -Wl,-z,relro,-z,now ${CMAKE_EXE_LINKER_FLAGS}")
+    endif()
+ 
+    # other useful gcc diagnostics

diff --git a/sci-mathematics/rstudio/files/rstudio-1.2.1335-pandoc.patch b/sci-mathematics/rstudio/files/rstudio-1.2.1335-pandoc.patch
new file mode 100644
index 00000000000..e2fe83867bc
--- /dev/null
+++ b/sci-mathematics/rstudio/files/rstudio-1.2.1335-pandoc.patch
@@ -0,0 +1,32 @@
+--- rstudio-1.2.1335-orig/src/cpp/session/CMakeLists.txt	2019-03-28 16:08:20.000000000 +1100
++++ rstudio-1.2.1335/src/cpp/session/CMakeLists.txt	2019-04-09 17:22:59.210201624 +1000
+@@ -25,9 +25,6 @@
+ if(NOT EXISTS "${RSTUDIO_DEPENDENCIES_DIR}/common/mathjax-26")
+   message(FATAL_ERROR "Mathjax 2.6 not found (re-run install-dependencies script to install)")
+ endif()
+-if(NOT EXISTS "${RSTUDIO_DEPENDENCIES_DIR}/common/pandoc")
+-  message(FATAL_ERROR "pandoc not found (re-run install-dependencies script to install)")
+-endif()
+ 
+ # we often install embedded versions of these packages but don't do so currently
+ 
+@@ -479,19 +476,6 @@
+ install(DIRECTORY "resources/connections"
+         DESTINATION ${RSTUDIO_INSTALL_SUPPORTING}/resources)
+ 
+-# install pandoc
+-if(WIN32)
+-   set(PANDOC_VERSION "2.6" CACHE INTERNAL "Pandoc version")
+-else()
+-   set(PANDOC_VERSION "2.3.1" CACHE INTERNAL "Pandoc version")
+-endif()
+-
+-set(PANDOC_BIN "${RSTUDIO_DEPENDENCIES_DIR}/common/pandoc/${PANDOC_VERSION}")
+-file(GLOB PANDOC_FILES "${PANDOC_BIN}/pandoc*")
+-install(FILES ${PANDOC_FILES}
+-        PERMISSIONS OWNER_READ OWNER_WRITE OWNER_EXECUTE GROUP_READ GROUP_EXECUTE WORLD_READ WORLD_EXECUTE
+-        DESTINATION  ${RSTUDIO_INSTALL_BIN}/pandoc)
+-
+ # install rmarkdown package
+ # file(GLOB RMARKDOWN_PACKAGE "${RSTUDIO_DEPENDENCIES_DIR}/common/rmarkdown*.tar.gz")
+ # install(FILES ${RMARKDOWN_PACKAGE}

diff --git a/sci-mathematics/rstudio/files/rstudio-1.2.1335-paths.patch b/sci-mathematics/rstudio/files/rstudio-1.2.1335-paths.patch
new file mode 100644
index 00000000000..ba66ef9f0ea
--- /dev/null
+++ b/sci-mathematics/rstudio/files/rstudio-1.2.1335-paths.patch
@@ -0,0 +1,118 @@
+--- rstudio-1.2.1335-orig/CMakeGlobals.txt	2019-03-28 16:08:20.000000000 +1100
++++ rstudio-1.2.1335/CMakeGlobals.txt	2019-04-09 17:10:07.680657631 +1000
+@@ -161,7 +161,7 @@
+    set(RSTUDIO_INSTALL_SUPPORTING RStudio.app/Contents/Resources)
+ else()
+    set(RSTUDIO_INSTALL_BIN bin)
+-   set(RSTUDIO_INSTALL_SUPPORTING .)
++   set(RSTUDIO_INSTALL_SUPPORTING ${DISTRO_SHARE})
+ endif()
+ 
+ # if the install prefix is /usr/local then tweak as appropriate
+--- rstudio-1.2.1335-orig/src/cpp/server/CMakeLists.txt	2019-03-28 16:08:20.000000000 +1100
++++ rstudio-1.2.1335/src/cpp/server/CMakeLists.txt	2019-04-09 16:54:34.740739744 +1000
+@@ -194,7 +194,7 @@
+    configure_file(${CMAKE_CURRENT_SOURCE_DIR}/${RSERVER_INITD_DEBIAN_SCRIPT}.in
+                   ${CMAKE_CURRENT_BINARY_DIR}/${RSERVER_INITD_DEBIAN_SCRIPT})
+    install(PROGRAMS ${CMAKE_CURRENT_BINARY_DIR}/${RSERVER_INITD_DEBIAN_SCRIPT}
+-           DESTINATION ${RSERVER_INITD_DEBIAN_DIR})
++           DESTINATION ${DISTRO_SHARE}/${RSERVER_INITD_DEBIAN_DIR})
+ 
+    # install configured redhat init.d script
+    set(RSERVER_INITD_REDHAT_DIR "extras/init.d/redhat")
+@@ -202,7 +202,7 @@
+    configure_file(${CMAKE_CURRENT_SOURCE_DIR}/${RSERVER_INITD_REDHAT_SCRIPT}.in
+                   ${CMAKE_CURRENT_BINARY_DIR}/${RSERVER_INITD_REDHAT_SCRIPT})
+    install(PROGRAMS ${CMAKE_CURRENT_BINARY_DIR}/${RSERVER_INITD_REDHAT_SCRIPT}
+-           DESTINATION ${RSERVER_INITD_REDHAT_DIR})
++           DESTINATION ${DISTRO_SHARE}/${RSERVER_INITD_REDHAT_DIR})
+ 
+    # install configured suse init.d script
+    set(RSERVER_INITD_SUSE_DIR "extras/init.d/suse")
+@@ -210,13 +210,13 @@
+    configure_file(${CMAKE_CURRENT_SOURCE_DIR}/${RSERVER_INITD_SUSE_SCRIPT}.in
+                   ${CMAKE_CURRENT_BINARY_DIR}/${RSERVER_INITD_SUSE_SCRIPT})
+    install(PROGRAMS ${CMAKE_CURRENT_BINARY_DIR}/${RSERVER_INITD_SUSE_SCRIPT}
+-           DESTINATION ${RSERVER_INITD_SUSE_DIR})
++           DESTINATION ${DISTRO_SHARE}/${RSERVER_INITD_SUSE_DIR})
+ 
+    # install pam profile
+    set(RSERVER_PAM_DIR "extras/pam")
+    set(RSERVER_PAM_PROFILE "${RSERVER_PAM_DIR}/rstudio")
+    install(FILES ${CMAKE_CURRENT_SOURCE_DIR}/${RSERVER_PAM_PROFILE}
+-           DESTINATION ${RSERVER_PAM_DIR})
++           DESTINATION ${DISTRO_SHARE}/${RSERVER_PAM_DIR})
+ 
+    # install configured upstart profile
+    set(RSERVER_UPSTART_DIR "extras/upstart")
+@@ -224,12 +224,12 @@
+    configure_file(${CMAKE_CURRENT_SOURCE_DIR}/${RSERVER_UPSTART_PROFILE}.in
+                   ${CMAKE_CURRENT_BINARY_DIR}/${RSERVER_UPSTART_PROFILE})
+    install(FILES ${CMAKE_CURRENT_BINARY_DIR}/${RSERVER_UPSTART_PROFILE}
+-           DESTINATION ${RSERVER_UPSTART_DIR})
++           DESTINATION ${DISTRO_SHARE}/${RSERVER_UPSTART_DIR})
+    set(RSERVER_UPSTART_PROFILE_REDHAT "${RSERVER_UPSTART_DIR}/rstudio-server.redhat.conf")
+    configure_file(${CMAKE_CURRENT_SOURCE_DIR}/${RSERVER_UPSTART_PROFILE_REDHAT}.in
+                   ${CMAKE_CURRENT_BINARY_DIR}/${RSERVER_UPSTART_PROFILE_REDHAT})
+    install(FILES ${CMAKE_CURRENT_BINARY_DIR}/${RSERVER_UPSTART_PROFILE_REDHAT}
+-           DESTINATION ${RSERVER_UPSTART_DIR})
++           DESTINATION ${DISTRO_SHARE}/${RSERVER_UPSTART_DIR})
+ 
+     # install configured systemd profile
+    set(RSERVER_SYSTEMD_DIR "extras/systemd")
+--- rstudio-1.2.1335-orig/src/cpp/server/ServerOptions.cpp	2019-03-28 16:08:20.000000000 +1100
++++ rstudio-1.2.1335/src/cpp/server/ServerOptions.cpp	2019-04-09 16:54:34.740739744 +1000
+@@ -389,8 +389,8 @@
+ 
+    // convert relative paths by completing from the system installation
+    // path (this allows us to be relocatable)
+-   resolvePath(resourcePath, &wwwLocalPath_);
+-   resolvePath(resourcePath, &wwwSymbolMapsPath_);
++   resolvePath(resourcePath.childPath(DISTRO_SHARE), &wwwLocalPath_);
++   resolvePath(resourcePath.childPath(DISTRO_SHARE), &wwwSymbolMapsPath_);
+    resolvePath(binaryPath, &authPamHelperPath_);
+    resolvePath(binaryPath, &rsessionPath_);
+    resolvePath(binaryPath, &rldpathPath_);
+--- rstudio-1.2.1335-orig/src/cpp/session/SessionOptions.cpp	2019-03-28 16:08:20.000000000 +1100
++++ rstudio-1.2.1335/src/cpp/session/SessionOptions.cpp	2019-04-09 17:17:06.035206050 +1000
+@@ -53,7 +53,7 @@
+ namespace session {  
+ 
+ namespace {
+-const char* const kDefaultPandocPath = "bin/pandoc";
++const char* const kDefaultPandocPath = "bin";
+ const char* const kDefaultPostbackPath = "bin/postback/rpostback";
+ const char* const kDefaultRsclangPath = "bin/rsclang";
+ 
+@@ -569,14 +569,14 @@
+    }
+    
+    // convert relative paths by completing from the app resource path
+-   resolvePath(resourcePath_, &rResourcesPath_);
+-   resolvePath(resourcePath_, &agreementFilePath_);
+-   resolvePath(resourcePath_, &wwwLocalPath_);
+-   resolvePath(resourcePath_, &wwwSymbolMapsPath_);
+-   resolvePath(resourcePath_, &coreRSourcePath_);
+-   resolvePath(resourcePath_, &modulesRSourcePath_);
+-   resolvePath(resourcePath_, &sessionLibraryPath_);
+-   resolvePath(resourcePath_, &sessionPackageArchivesPath_);
++   resolvePath(resourcePath_.childPath(DISTRO_SHARE), &rResourcesPath_);
++   resolvePath(resourcePath_.childPath(DISTRO_SHARE), &agreementFilePath_);
++   resolvePath(resourcePath_.childPath(DISTRO_SHARE), &wwwLocalPath_);
++   resolvePath(resourcePath_.childPath(DISTRO_SHARE), &wwwSymbolMapsPath_);
++   resolvePath(resourcePath_.childPath(DISTRO_SHARE), &coreRSourcePath_);
++   resolvePath(resourcePath_.childPath(DISTRO_SHARE), &modulesRSourcePath_);
++   resolvePath(resourcePath_.childPath(DISTRO_SHARE), &sessionLibraryPath_);
++   resolvePath(resourcePath_.childPath(DISTRO_SHARE), &sessionPackageArchivesPath_);
+    resolvePostbackPath(resourcePath_, &rpostbackPath_);
+ #ifdef _WIN32
+    resolvePath(resourcePath_, &consoleIoPath_);
+@@ -601,7 +601,7 @@
+    }
+    winptyPath_ = pty.complete(completion).absolutePath();
+ #endif // _WIN32
+-   resolvePath(resourcePath_, &hunspellDictionariesPath_);
++   resolvePath(resourcePath_.childPath(DISTRO_SHARE), &hunspellDictionariesPath_);
+    resolvePath(resourcePath_, &mathjaxPath_);
+    resolvePath(resourcePath_, &libclangHeadersPath_);
+    resolvePandocPath(resourcePath_, &pandocPath_);

diff --git a/sci-mathematics/rstudio/files/rstudio-1.2.1335-prefs.patch b/sci-mathematics/rstudio/files/rstudio-1.2.1335-prefs.patch
new file mode 100644
index 00000000000..e72df553eeb
--- /dev/null
+++ b/sci-mathematics/rstudio/files/rstudio-1.2.1335-prefs.patch
@@ -0,0 +1,53 @@
+--- rstudio-1.2.1335-orig/src/gwt/build.xml	2019-03-28 16:08:20.000000000 +1100
++++ rstudio-1.2.1335/src/gwt/build.xml	2019-04-09 16:44:15.089471934 +1000
+@@ -34,6 +34,7 @@
+    <property name="gwt.extra.args" value=""/>
+    <property name="gwt.main.module" value="org.rstudio.studio.RStudio"/>
+    <property name="ace.bin" value="${src.dir}/org/rstudio/studio/client/workbench/views/source/editors/text/ace"/>
++   <property environment="env"/>
+ 
+    <path id="project.class.path">
+      <pathelement location="${build.dir}"/>
+@@ -112,8 +113,10 @@
+             <pathelement location="${src.dir}"/>
+             <path refid="project.class.path"/>
+          </classpath>
++         <jvmarg value="-Duser.home=${env.T}"/>
+          <!-- add jvmarg -Xss16M or similar if you see a StackOverflowError -->
+          <jvmarg value="-Xmx1536M"/>
++         <jvmarg value="-Djava.util.prefs.userRoot=${env.T}"/>
+          <arg value="-war"/>
+          <arg value="${www.dir}"/>
+          <arg value="-localWorkers"/>
+@@ -154,6 +157,7 @@
+             <pathelement location="${src.dir}"/>
+             <path refid="project.class.path"/>
+          </classpath>
++         <jvmarg value="-Duser.home=${env.T}"/>
+          <jvmarg value="-Xmx2048M"/>
+          <arg value="-style"/>
+          <arg value="PRETTY"/>
+@@ -176,6 +180,7 @@
+             <pathelement location="src"/>
+             <path refid="project.class.path"/>
+          </classpath>
++         <jvmarg value="-Duser.home=${env.T}"/>
+          <jvmarg value="-Xmx2048M"/>
+          <arg value="-style"/>
+          <arg value="PRETTY"/>
+@@ -202,6 +207,7 @@
+             <pathelement location="src"/>
+             <path refid="project.class.path"/>
+          </classpath>
++         <jvmarg value="-Duser.home=${env.T}"/>
+          <jvmarg value="-Xmx2048M"/>
+       	<arg value="-src"/>
+       	<arg value = "src"/>
+@@ -237,6 +243,7 @@
+             <pathelement location="${test.dir}"/>
+             <pathelement location="${src.dir}"/>
+         </classpath>
++        <jvmarg value="-Duser.home=${env.T}"/>
+         <classpath refid="project.class.path"/>
+         <classpath refid="unittest.class.path"/>
+         <arg value="org.rstudio.studio.client.RStudioUnitTestSuite"/>

diff --git a/sci-mathematics/rstudio/files/rstudio-1.2.1335-qtsingleapplication.patch b/sci-mathematics/rstudio/files/rstudio-1.2.1335-qtsingleapplication.patch
new file mode 100644
index 00000000000..a59fa02f1d2
--- /dev/null
+++ b/sci-mathematics/rstudio/files/rstudio-1.2.1335-qtsingleapplication.patch
@@ -0,0 +1,60 @@
+--- rstudio-1.2.1335-orig/src/cpp/desktop/CMakeLists.txt	2019-03-28 16:08:20.000000000 +1100
++++ rstudio-1.2.1335/src/cpp/desktop/CMakeLists.txt	2019-04-09 18:04:57.783616412 +1000
+@@ -140,6 +140,13 @@
+ get_filename_component(QT_LIBRARY_PATH "${QT_BIN_DIR}/../lib"     ABSOLUTE CACHE)
+ get_filename_component(QT_INSTALL_PATH "${QT_BIN_DIR}/.."         ABSOLUTE CACHE)
+ 
++find_path(QTSINGLEAPPLIB_INCLUDE_DIR NAMES QtSingleApplication
++  PATH_SUFFIXES QtSolutions
++  PATHS
++  /usr/include/qt5)
++find_library(QTSINGLEAPPLIB Qt5Solutions_SingleApplication-2.6
++  libQt5Solutions_SingleApplication-2.6)
++
+ # disable clang warnings for qt sources
+ if(APPLE)
+    add_definitions(-Wno-unused-private-field
+@@ -158,7 +165,6 @@
+ 
+ set(MOC_DESKTOP_HEADER_FILES ${DESKTOP_HEADER_FILES})
+ list(REMOVE_ITEM MOC_DESKTOP_HEADER_FILES
+-  ${CMAKE_CURRENT_SOURCE_DIR}/3rdparty/qtsingleapplication/qtlockedfile.h
+   ${CMAKE_CURRENT_SOURCE_DIR}/DesktopDetectRHome.hpp
+   ${CMAKE_CURRENT_SOURCE_DIR}/DesktopOptions.hpp
+   ${CMAKE_CURRENT_SOURCE_DIR}/DesktopRVersion.hpp
+@@ -224,8 +230,6 @@
+   DesktopSlotBinders.cpp
+   DesktopSubMenu.cpp
+   DesktopSynctex.cpp
+-  3rdparty/qtsingleapplication/qtsingleapplication.cpp
+-  3rdparty/qtsingleapplication/qtlocalpeer.cpp
+ )
+ 
+ if(WIN32)
+@@ -280,6 +284,7 @@
+   ${CORE_SOURCE_DIR}/include
+   ${CMAKE_CURRENT_SOURCE_DIR}
+   ${CMAKE_CURRENT_BINARY_DIR}
++  ${QTSINGLEAPPLIB_INCLUDE_DIR}
+   ${TESTS_INCLUDE_DIR}
+ )
+ 
+@@ -384,6 +389,7 @@
+    # set link dependencies
+    target_link_libraries(rstudio
+       ${RSTUDIO_QTMODULES}
++      ${QTSINGLEAPPLIB}
+       ${QT_LIBRARIES}
+       ${Boost_LIBRARIES}
+       rstudio-core
+--- rstudio-1.2.1335-orig/src/cpp/desktop/DesktopPosixApplication.hpp	2019-03-28 16:08:20.000000000 +1100
++++ rstudio-1.2.1335/src/cpp/desktop/DesktopPosixApplication.hpp	2019-04-09 18:01:39.333920927 +1000
+@@ -16,7 +16,7 @@
+ #ifndef DESKTOP_POSIX_APPLICATION_HPP
+ #define DESKTOP_POSIX_APPLICATION_HPP
+ 
+-#include "3rdparty/qtsingleapplication/QtSingleApplication"
++#include <QtSingleApplication>
+ 
+ #include "DesktopApplicationLaunch.hpp"
+ 

diff --git a/sci-mathematics/rstudio/rstudio-1.1.463.ebuild b/sci-mathematics/rstudio/rstudio-1.1.463-r1.ebuild
similarity index 95%
copy from sci-mathematics/rstudio/rstudio-1.1.463.ebuild
copy to sci-mathematics/rstudio/rstudio-1.1.463-r1.ebuild
index 271588e60b8..86b6db8da4b 100644
--- a/sci-mathematics/rstudio/rstudio-1.1.463.ebuild
+++ b/sci-mathematics/rstudio/rstudio-1.1.463-r1.ebuild
@@ -1,9 +1,9 @@
 # Copyright 1999-2019 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
-EAPI=6
+EAPI=7
 
-inherit eutils user cmake-utils gnome2-utils pam versionator xdg-utils java-pkg-2 pax-utils qmake-utils
+inherit eutils user cmake-utils gnome2-utils pam xdg-utils java-pkg-2 pax-utils qmake-utils
 
 # TODO
 # * package gin and gwt
@@ -53,7 +53,7 @@ RDEPEND="
 	>=app-text/pandoc-${PANDOC_VER}
 	dev-haskell/pandoc-citeproc
 	>=dev-lang/R-2.11.1
-	<dev-libs/boost-1.70:=
+	>=dev-libs/boost-1.63:=
 	>=dev-libs/mathjax-2.7.4
 	sys-apps/util-linux
 	>=sys-devel/clang-3.5.0:*
@@ -101,7 +101,9 @@ PATCHES=(
 		"${FILESDIR}/${PN}-1.1.453-core.patch"
 		"${FILESDIR}/${PN}-1.1.463-boost-1.69.0_p1.patch"
 		"${FILESDIR}/${PN}-1.1.463-boost-1.69.0_p2.patch"
+		"${FILESDIR}/${PN}-1.1.463-boost-1.69.0_p3.patch"
 		"${FILESDIR}/${PN}-1.1.463-fix-ptr-int-compare.patch"
+		"${FILESDIR}/${PN}-1.1.463-boost-1.70.0.patch"
 )
 
 src_unpack() {
@@ -193,9 +195,9 @@ src_prepare() {
 }
 
 src_configure() {
-	export RSTUDIO_VERSION_MAJOR=$(get_version_component_range 1)
-	export RSTUDIO_VERSION_MINOR=$(get_version_component_range 2)
-	export RSTUDIO_VERSION_PATCH=$(get_version_component_range 3)
+	export RSTUDIO_VERSION_MAJOR=$(ver_cut 1)
+	export RSTUDIO_VERSION_MINOR=$(ver_cut 2)
+	export RSTUDIO_VERSION_PATCH=$(ver_cut 3)
 
 	local mycmakeargs=(
 		-DDISTRO_SHARE=share/${PN}
@@ -218,7 +220,7 @@ src_compile() {
 src_install() {
 	export ANT_OPTS="-Duser.home=${T}"
 	cmake-utils_src_install
-	pax-mark m "${ED}usr/bin/rstudio"
+	pax-mark m "${ED}/usr/bin/rstudio"
 	doconfd "${FILESDIR}"/rstudio-server.conf
 	dodir /etc/rstudio
 	insinto /etc/rstudio

diff --git a/sci-mathematics/rstudio/rstudio-1.1.463.ebuild b/sci-mathematics/rstudio/rstudio-1.1.463.ebuild
index 271588e60b8..5c0511bb9a5 100644
--- a/sci-mathematics/rstudio/rstudio-1.1.463.ebuild
+++ b/sci-mathematics/rstudio/rstudio-1.1.463.ebuild
@@ -101,6 +101,7 @@ PATCHES=(
 		"${FILESDIR}/${PN}-1.1.453-core.patch"
 		"${FILESDIR}/${PN}-1.1.463-boost-1.69.0_p1.patch"
 		"${FILESDIR}/${PN}-1.1.463-boost-1.69.0_p2.patch"
+		"${FILESDIR}/${PN}-1.1.463-boost-1.69.0_p3.patch"
 		"${FILESDIR}/${PN}-1.1.463-fix-ptr-int-compare.patch"
 )
 

diff --git a/sci-mathematics/rstudio/rstudio-1.1.463.ebuild b/sci-mathematics/rstudio/rstudio-1.2.1335.ebuild
similarity index 89%
copy from sci-mathematics/rstudio/rstudio-1.1.463.ebuild
copy to sci-mathematics/rstudio/rstudio-1.2.1335.ebuild
index 271588e60b8..4ff5da66509 100644
--- a/sci-mathematics/rstudio/rstudio-1.1.463.ebuild
+++ b/sci-mathematics/rstudio/rstudio-1.2.1335.ebuild
@@ -1,9 +1,9 @@
 # Copyright 1999-2019 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
-EAPI=6
+EAPI=7
 
-inherit eutils user cmake-utils gnome2-utils pam versionator xdg-utils java-pkg-2 pax-utils qmake-utils
+inherit eutils user cmake-utils gnome2-utils pam xdg-utils java-pkg-2 pax-utils qmake-utils
 
 # TODO
 # * package gin and gwt
@@ -12,11 +12,12 @@ inherit eutils user cmake-utils gnome2-utils pam versionator xdg-utils java-pkg-
 
 # update from scripts in dependencies/common
 # egrep '(GWT_SDK_VER=|GIN_VER=|SELENIUM_VER=|CHROMEDRIVER_VER=)' dependencies/common/install-gwt
-GWT_VER=2.7.0
-GIN_VER=1.5
+GWT_VER=2.8.1
+GIN_VER=2.1.2
 SELENIUM_VER=2.37.0
 CHROMEDRIVER_VER=2.7
 # grep 'PANDOC_VERSION=' dependencies/common/install-pandoc
+# It should be PANDOC_VER=2.3.1 however >=app-text/pandoc-2.3.1 is not yet in portage
 PANDOC_VER=1.19.2.1
 # ls dependencies/common/*.tar.gz
 PACKRAT_VER=0.98.1000
@@ -53,7 +54,7 @@ RDEPEND="
 	>=app-text/pandoc-${PANDOC_VER}
 	dev-haskell/pandoc-citeproc
 	>=dev-lang/R-2.11.1
-	<dev-libs/boost-1.70:=
+	>=dev-libs/boost-1.63:=
 	>=dev-libs/mathjax-2.7.4
 	sys-apps/util-linux
 	>=sys-devel/clang-3.5.0:*
@@ -91,17 +92,16 @@ DEPEND="${RDEPEND}
 #	test? ( dev-java/junit:4 )
 
 PATCHES=(
-		"${FILESDIR}/${PN}-0.99.879-prefs.patch"
-		"${FILESDIR}/${PN}-1.0.44-paths.patch"
-		"${FILESDIR}/${PN}-1.1.357-clang-pandoc.patch"
-		"${FILESDIR}/${PN}-0.98.490-linker_flags.patch"
-		"${FILESDIR}/${PN}-0.99.473-qtsingleapplication.patch"
+		"${FILESDIR}/${PN}-1.2.1335-prefs.patch"
+		"${FILESDIR}/${PN}-1.2.1335-paths.patch"
+		"${FILESDIR}/${PN}-1.2.1335-pandoc.patch"
+		"${FILESDIR}/${PN}-1.2.1335-linker_flags.patch"
+		"${FILESDIR}/${PN}-1.2.1335-qtsingleapplication.patch"
 		"${FILESDIR}/${PN}-1.0.44-systemd.patch"
-		"${FILESDIR}/${PN}-1.1.453-boost-1.67.0.patch"
-		"${FILESDIR}/${PN}-1.1.453-core.patch"
-		"${FILESDIR}/${PN}-1.1.463-boost-1.69.0_p1.patch"
-		"${FILESDIR}/${PN}-1.1.463-boost-1.69.0_p2.patch"
-		"${FILESDIR}/${PN}-1.1.463-fix-ptr-int-compare.patch"
+		"${FILESDIR}/${PN}-1.2.1335-core.patch"
+		"${FILESDIR}/${PN}-1.2.1335-fix-ptr-int-compare.patch"
+		"${FILESDIR}/${PN}-1.2.1335-boost-1.70.0_p1.patch"
+		"${FILESDIR}/${PN}-1.2.1335-boost-1.70.0_p2.patch"
 )
 
 src_unpack() {
@@ -193,9 +193,9 @@ src_prepare() {
 }
 
 src_configure() {
-	export RSTUDIO_VERSION_MAJOR=$(get_version_component_range 1)
-	export RSTUDIO_VERSION_MINOR=$(get_version_component_range 2)
-	export RSTUDIO_VERSION_PATCH=$(get_version_component_range 3)
+	export RSTUDIO_VERSION_MAJOR=$(ver_cut 1)
+	export RSTUDIO_VERSION_MINOR=$(ver_cut 2)
+	export RSTUDIO_VERSION_PATCH=$(ver_cut 3)
 
 	local mycmakeargs=(
 		-DDISTRO_SHARE=share/${PN}
@@ -218,7 +218,7 @@ src_compile() {
 src_install() {
 	export ANT_OPTS="-Duser.home=${T}"
 	cmake-utils_src_install
-	pax-mark m "${ED}usr/bin/rstudio"
+	pax-mark m "${ED}/usr/bin/rstudio"
 	doconfd "${FILESDIR}"/rstudio-server.conf
 	dodir /etc/rstudio
 	insinto /etc/rstudio


^ permalink raw reply related	[flat|nested] 12+ messages in thread

* [gentoo-commits] repo/gentoo:master commit in: sci-mathematics/rstudio/, sci-mathematics/rstudio/files/
@ 2020-05-23 12:43 Mark Wright
  0 siblings, 0 replies; 12+ messages in thread
From: Mark Wright @ 2020-05-23 12:43 UTC (permalink / raw
  To: gentoo-commits

commit:     03406d4343f6bf8e63fcc86bfc6264cdb429fefb
Author:     Mark Wright <gienah <AT> gentoo <DOT> org>
AuthorDate: Sat May 23 12:34:01 2020 +0000
Commit:     Mark Wright <gienah <AT> gentoo <DOT> org>
CommitDate: Sat May 23 12:42:05 2020 +0000
URL:        https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=03406d43

sci-mathematics/rstudio: Remove old

Package-Manager: Portage-2.3.99, Repoman-2.3.22
Signed-off-by: Mark Wright <gienah <AT> gentoo.org>

 sci-mathematics/rstudio/Manifest                   |  13 -
 .../files/rstudio-0.98.490-linker_flags.patch      |  18 -
 .../rstudio-0.99.473-qtsingleapplication.patch     |  60 ---
 .../rstudio/files/rstudio-0.99.879-prefs.patch     |  45 --
 .../rstudio/files/rstudio-1.0.44-paths.patch       | 130 ------
 .../files/rstudio-1.1.357-clang-pandoc.patch       |  76 ----
 .../files/rstudio-1.1.453-boost-1.67.0.patch       |  38 --
 .../rstudio/files/rstudio-1.1.453-core.patch       | 143 -------
 .../files/rstudio-1.1.463-boost-1.69.0_p1.patch    | 460 ---------------------
 .../files/rstudio-1.1.463-boost-1.69.0_p2.patch    | 220 ----------
 .../files/rstudio-1.1.463-boost-1.69.0_p3.patch    | 167 --------
 .../files/rstudio-1.1.463-boost-1.70.0.patch       |  46 ---
 .../rstudio-1.1.463-fix-ptr-int-compare.patch      |  13 -
 .../rstudio-1.2.1335-boost-1.72-filesystem.patch   |  31 --
 .../rstudio-1.2.1335-fix-ptr-int-compare.patch     |  13 -
 .../rstudio/files/rstudio-1.2.1335-pandoc.patch    |  32 --
 .../rstudio/files/rstudio-1.2.1335-paths.patch     | 118 ------
 .../rstudio/files/rstudio-1.2.1335-prefs.patch     |  53 ---
 sci-mathematics/rstudio/rstudio-1.1.463-r1.ebuild  | 255 ------------
 sci-mathematics/rstudio/rstudio-1.2.1335.ebuild    | 254 ------------
 20 files changed, 2185 deletions(-)

diff --git a/sci-mathematics/rstudio/Manifest b/sci-mathematics/rstudio/Manifest
index 314a334a3e7..6821cacc59b 100644
--- a/sci-mathematics/rstudio/Manifest
+++ b/sci-mathematics/rstudio/Manifest
@@ -1,16 +1,3 @@
-DIST chromedriver-linux 19303552 BLAKE2B 610396fd74f2adc4c249ca971a53a6dd4ab06145d0b37d59adf66180dfada52192b20203bf3d992c270bd4f787df5c85511ca325aed06cbd9318add3eccfde30 SHA512 18774ede961dec222058dd0e3f128d63732cd444ee310136b44d5bf508a4f2f2c164a2c8d195d80bce8b5fb6303559e167f82f384e4a58e30f48b151a4206ee8
 DIST core-dictionaries.zip 876339 BLAKE2B f29afcbf5a7f8ec635e5a5b248d978af286d18488f54c9a09a2b95fde19b796e4473e5846402a46dd24b71c6e4167512539aaa32ab6d99713d500a80aaf46796 SHA512 9c5830cc9fed575e223f1c61f02e48c5aea6801bb0cd2586f02437c17fdffdb1d36c396d5a8ecbe02ba01196e73458304345b1f6b92c052bc7a7d05961fac2c9
-DIST gin-1.5.zip 1055663 BLAKE2B 11b86245d54967f0c76f22f7460fb752c410db3c59a019bb538a48fd0de7e87552f2f5bb9ce604e6ed508136a6a2b0814f061161579429daae8ca55b1a448114 SHA512 3f6649565f9600daaca6ddf3fb431925b5a1ce1ada38e6389de64cef617abba9d3f49c555d0a20053fb06f17ccbe4e1141b39966fbe4b2975d7b120377504897
-DIST gin-2.1.2.zip 1341053 BLAKE2B 515338ba50ba2183c101b42183e42ebf15613aae8751a0dcedb4b047de4ca8fab85eb240f5f0c92955441dbb87e80b3edbdae8d83f1e74f74c7de067d18cf108 SHA512 03407b6318ffb0dd504ce520649ed90e845f13fbdbd0bfb4d7e3b127842f1735093e39674077c3a04a11d434aefdc3a734652c3f85e8ab00ff37ae760ccb8dbb
-DIST gwt-2.7.0.zip 108818328 BLAKE2B 9af969f3f2577be041fcfb58f228fab4b5479fa0da5ff054ab0a59cad751590a1b4ae8d7fabc8a50e3b0e5d7eb9b2896c485d929421f75e6a2f6513480438a31 SHA512 a1eed5cc25c888cf81d4f22b1f9494d5d8567b911f7aeb1d164a6359120543668280afe1a3ffc9ed87b139c7db67fbcaaabde2066e3279909d7cd6fc22eaf499
-DIST gwt-2.8.1.zip 95650299 BLAKE2B 3853d50d1346e313903b6f0c4b8405ce9e896e51652483e5c7e9d711daa213e1341c71765b4a3fb061b58f90d49420245963a0480db8b71fe7aed6cd43782c14 SHA512 feeb00cb0413c2703dfd6931f57ba669813bd65f814715f2c04dd6dc69e885a8048337272333d7504c48e9fa52cdab699f854ee13211228ab142a1f458ee33ae
-DIST packrat-0.98.1000.tar.gz 97677 BLAKE2B 282fe33dc5ba366ceea05a222ae2d018bc3ad8f35fad73c585a3d4901c3287e6902277a9c7ca087854f3944bd85ff1b1d1f02869ece686b10f946e2f1cb1296c SHA512 2290c768ecf27a037e73c3f8336b9fd71c68ff19d071b4a8fbc469550d29007cacacdb75f854f73b5db2139a5104f129b85a3612e2ee47bd6118ee13f7d103a6
-DIST rmarkdown-0.98.1000.tar.gz 1423820 BLAKE2B eac8c9cf438c9b44ddfe954602dd67a83764b0c988b3ba571877c986b0d5d237059ed6643a86bb404428857ec8c346bfecd12f7cd15cde301cb0ce331f842b7f SHA512 df3540c24c87930fe55bff2ffe67c86c219800cb00ed72ba9451ecd0d0cad411548a78c1a04b9a2e301e853616dcb77e09129c4e48ade6f16d3f14b7ea7e4852
-DIST rsconnect_0.4.1.4_fcac892a69817febd7b655b189bf57193260cda0.tar.gz 197051 BLAKE2B 1f3f9fe71d7b50ab5108dfdbd3cc0b882bcc935ee58e8a9145b07a18bb86c39bc45e321a13add24df99492bc30548df716775c339bcbf4efc2bfe158299ae55a SHA512 208dc349f4aa7613ecf94939aba60d22d3a06972344b526c9b6c951015571f5922927bca08db571a7b8a268e42609a4f558f01278c9685f6da2ffc66a1f95ade
-DIST rstudio-1.1.463.tar.gz 20203779 BLAKE2B 97f879539cbb7051af362a8469795a47feb42d18ff46dbbdffe36e0685d1cd5704848b3bf5a5611d482a09567722e35288527302cd521b18e2a48b347c919e17 SHA512 987347563a9726363c28d866e1372eae8eb19a5cbd0e33c7ee0e0c8f90471c4b69de0f559c00410523841b6c090b584652e01496f5db33c015a4554d2f4e179b
-DIST rstudio-1.2.1335.tar.gz 20440199 BLAKE2B cdd54a7df5a234bcc6d440f4ba5b45e58ea469f8dac5a17d9088f9d65035495c86b5a308cde28a224648f96a74038299863291f3c516a1d567762ecc5bfb079c SHA512 90657effc55264bf3efa1a8a5d2bbe94a37727f0450202ade99b9fbb71ea75b6dd9fa798d17cd4d1a1a97a16f186de8004d1888b6ea43f36d5252508520d3cde
 DIST rstudio-1.2.5033.tar.gz 20456976 BLAKE2B 3cbca6a5180690104dddf1456168bd38708d4152ed9b7a167035dd66e270aeb6405169d34461cbd899738be1872607e3f3b6f81ff0b3c9e6a9ed965a889b1393 SHA512 3569d4fed342275a9905c87e4f97be63b6391d2c37f75397e06201a7c31f80d94799214f51ff8e57d458ef18d5e54afe1ec8a7c56ac05ed8b8225ecca72d1daf
 DIST rstudio-1.2.5042.tar.gz 20456999 BLAKE2B 3251ab2511daefefa395256fedb273ecc36dbc8118457474e3647f7616baea91301e597896582ad4b191195fc7baf17645c4c25b9a957a0c17a6251151b1dd87 SHA512 e09f2360abecde0c16e240e6838efb270a355bec3d3982ffde2b01b32b21e9281fef465734edbfeb5e05375529cc7f06d5b5d41304f367982f53ae7ad98e20f9
-DIST selenium-java-2.37.0.zip 24625928 BLAKE2B b369a805ae96f0d0913c4be42888d9c2a1e213ff982f9daefe73fadb705baa80ab0186ab50ed52609e83697cffaf8d617d06d75405cb8e1c3fe8e7c5b81dba25 SHA512 68624e82dbc751a25c50fad72702a98eb30d77fd4337d2a969f8e06bcc49e5f8c835cd27ec53772f3375014ddde1d5636936e966b75f3594a9f86aa18ba4e779
-DIST selenium-server-standalone-2.37.0.jar 34730734 BLAKE2B 3899b1d4c5f9153c1f9f13bec66f7c1456ea2e0f34db7d8e54a1ce9063c33a05b3cf95216c2ae06bb40504f72f343a4b9ba6c8553fbbc340e7c18a5b612dde5c SHA512 b215446d42d2d1f69664349b6ae6dc53a532d3624c91254f0f4183d0ad764648792e5cc1126a55a1e60d9687d55200fed01d6d2f46cc3d853b1fa6ee38111018
-DIST shinyapps-0.98.1000.tar.gz 910095 BLAKE2B 4f9364692348bb52cbd12cc6ee447841cb0c805327f2518b2a9545920b602b954a98dea68ccb3daf32d2c3bab6464fb15402844d93277193315f1ae7b3ca5190 SHA512 3162317c4c20cfc1497e952a8235867084d629ae88407e6c465b3e208adb1dc97abfe6b9922e0374ddf4c8e38a76e112942bd312c54a66f74e6f2a3fe4c0a07c

diff --git a/sci-mathematics/rstudio/files/rstudio-0.98.490-linker_flags.patch b/sci-mathematics/rstudio/files/rstudio-0.98.490-linker_flags.patch
deleted file mode 100644
index a336fccbc98..00000000000
--- a/sci-mathematics/rstudio/files/rstudio-0.98.490-linker_flags.patch
+++ /dev/null
@@ -1,18 +0,0 @@
-Some gcc hardening options were added, however since we add
-"-Wl,--as-needed" we end up with "-Wl,--as-needed;-Wl,-z,relro" which
-leads to linker errors about unknown options, if we make it so the
-as-needed option is the last option on the line, everything is fine.
-
-diff --git a/src/cpp/CMakeLists.txt b/src/cpp/CMakeLists.txt
-index 0589ca0..fe5bd5f 100644
---- a/src/cpp/CMakeLists.txt
-+++ b/src/cpp/CMakeLists.txt
-@@ -57,7 +57,7 @@ if(UNIX)
-       add_definitions(-D_FORTIFY_SOURCE=2)
-       add_definitions(-fstack-protector --param ssp-buffer-size=4)
-       add_definitions(-pie -fPIE)
--      set(CMAKE_EXE_LINKER_FLAGS "${CMAKE_EXE_LINKER_FLAGS} -Wl,-z,relro,-z,now")
-+      set(CMAKE_EXE_LINKER_FLAGS "-Wl,-z,relro,-z,now ${CMAKE_EXE_LINKER_FLAGS}")
-    endif()
- 
- # Win32 specific global directives

diff --git a/sci-mathematics/rstudio/files/rstudio-0.99.473-qtsingleapplication.patch b/sci-mathematics/rstudio/files/rstudio-0.99.473-qtsingleapplication.patch
deleted file mode 100644
index bf66bd23678..00000000000
--- a/sci-mathematics/rstudio/files/rstudio-0.99.473-qtsingleapplication.patch
+++ /dev/null
@@ -1,60 +0,0 @@
---- rstudio-0.99.473-orig/src/cpp/desktop/CMakeLists.txt	2015-08-12 09:58:43.000000000 +1000
-+++ rstudio-0.99.473/src/cpp/desktop/CMakeLists.txt	2015-08-30 23:16:11.396175587 +1000
-@@ -93,7 +93,12 @@
-    find_package(Qt5DBus REQUIRED)
- endif()
- 
--
-+find_path(QTSINGLEAPPLIB_INCLUDE_DIR NAMES QtSingleApplication
-+  PATH_SUFFIXES QtSolutions
-+  PATHS
-+  /usr/include/qt5)
-+find_library(QTSINGLEAPPLIB Qt5Solutions_SingleApplication-2.6
-+  libQt5Solutions_SingleApplication-2.6)
- 
- # disable clang warnings for qt sources
- if(APPLE)
-@@ -113,7 +118,6 @@
- 
- set(MOC_DESKTOP_HEADER_FILES ${DESKTOP_HEADER_FILES})
- list(REMOVE_ITEM MOC_DESKTOP_HEADER_FILES
--  ${CMAKE_CURRENT_SOURCE_DIR}/3rdparty/qtsingleapplication/qtlockedfile.h
-   ${CMAKE_CURRENT_SOURCE_DIR}/DesktopDetectRHome.hpp
-   ${CMAKE_CURRENT_SOURCE_DIR}/DesktopOptions.hpp
-   ${CMAKE_CURRENT_SOURCE_DIR}/DesktopRVersion.hpp
-@@ -175,8 +179,6 @@
-   DesktopSubMenu.cpp
-   DesktopSynctex.cpp
-   DesktopNetworkAccessManager.cpp
--  3rdparty/qtsingleapplication/qtsingleapplication.cpp
--  3rdparty/qtsingleapplication/qtlocalpeer.cpp
- )
- 
- if(WIN32)
-@@ -219,6 +221,7 @@
-   ${CORE_SOURCE_DIR}/include
-   ${CMAKE_CURRENT_SOURCE_DIR}
-   ${CMAKE_CURRENT_BINARY_DIR}
-+  ${QTSINGLEAPPLIB_INCLUDE_DIR}
-   ${TESTS_INCLUDE_DIR}
- )
- 
-@@ -332,6 +335,7 @@
- 
-    # set link dependencies
-    target_link_libraries(rstudio
-+      ${QTSINGLEAPPLIB}
-       ${QT_LIBRARIES}
-       rstudio-core
-       ${LINK_FLAGS}
---- rstudio-0.99.473-orig/src/cpp/desktop/DesktopPosixApplication.hpp	2015-08-12 09:58:43.000000000 +1000
-+++ rstudio-0.99.473/src/cpp/desktop/DesktopPosixApplication.hpp	2015-08-30 21:41:21.616934106 +1000
-@@ -16,7 +16,7 @@
- #ifndef DESKTOP_POSIX_APPLICATION_HPP
- #define DESKTOP_POSIX_APPLICATION_HPP
- 
--#include "3rdparty/qtsingleapplication/QtSingleApplication"
-+#include <QtSingleApplication>
- 
- namespace rstudio {
- namespace desktop {

diff --git a/sci-mathematics/rstudio/files/rstudio-0.99.879-prefs.patch b/sci-mathematics/rstudio/files/rstudio-0.99.879-prefs.patch
deleted file mode 100644
index 483613cc5c0..00000000000
--- a/sci-mathematics/rstudio/files/rstudio-0.99.879-prefs.patch
+++ /dev/null
@@ -1,45 +0,0 @@
---- rstudio-0.99.879-orig/src/gwt/build.xml	2016-02-12 09:24:39.000000000 +1100
-+++ rstudio-0.99.879/src/gwt/build.xml	2016-02-20 00:25:39.458756693 +1100
-@@ -25,6 +25,7 @@
-    <property name="gwt.extra.args" value=""/>
-    <property name="gwt.main.module" value="org.rstudio.studio.RStudio"/>
-    <property name="ace.bin" value="src/org/rstudio/studio/client/workbench/views/source/editors/text/ace"/>
-+   <property environment="env"/>
- 
-    <path id="project.class.path">
-       <pathelement location="bin"/>
-@@ -101,8 +102,10 @@
-             <pathelement location="src"/>
-             <path refid="project.class.path"/>
-          </classpath>
-+         <jvmarg value="-Duser.home=${env.T}"/>
-          <!-- add jvmarg -Xss16M or similar if you see a StackOverflowError -->
-          <jvmarg value="-Xmx1536M"/>
-+         <jvmarg value="-Djava.util.prefs.userRoot=${env.T}"/>
-          <arg value="-war"/>
-          <arg value="www"/>
-          <arg value="-localWorkers"/>
-@@ -142,6 +145,7 @@
-             <pathelement location="src"/>
-             <path refid="project.class.path"/>
-          </classpath>
-+         <jvmarg value="-Duser.home=${env.T}"/>
-          <jvmarg value="-Xmx2048M"/>
-          <arg value="-war"/>
-          <arg value="www"/>
-@@ -163,6 +167,7 @@
-             <pathelement location="src"/>
-             <path refid="project.class.path"/>
-          </classpath>
-+         <jvmarg value="-Duser.home=${env.T}"/>
-          <jvmarg value="-Xmx2048M"/>
-       	<arg value="-src"/>
-       	<arg value = "src"/>
-@@ -194,6 +199,7 @@
-                   <pathelement location="src"/>
-                   <path refid="test.class.path"/>
-                </classpath>
-+               <jvmarg value="-Duser.home=${env.T}"/>
-                <arg value="org.rstudio.studio.selenium.RStudioTestSuite"/>
-             </java>
-          </sequential>

diff --git a/sci-mathematics/rstudio/files/rstudio-1.0.44-paths.patch b/sci-mathematics/rstudio/files/rstudio-1.0.44-paths.patch
deleted file mode 100644
index b2a1a33b44c..00000000000
--- a/sci-mathematics/rstudio/files/rstudio-1.0.44-paths.patch
+++ /dev/null
@@ -1,130 +0,0 @@
---- rstudio-1.0.44-orig/CMakeGlobals.txt	2016-10-19 08:32:41.000000000 +1100
-+++ rstudio-1.0.44/CMakeGlobals.txt	2016-12-01 23:33:04.149326324 +1100
-@@ -123,7 +123,7 @@
-    else()
-      set(RSTUDIO_INSTALL_BIN bin)
-    endif()
--   set(RSTUDIO_INSTALL_SUPPORTING .)
-+   set(RSTUDIO_INSTALL_SUPPORTING ${DISTRO_SHARE})
- endif()
- 
- # if the install prefix is /usr/local then tweak as appropriate
---- rstudio-1.0.44-orig/src/cpp/server/CMakeLists.txt	2016-10-19 08:32:41.000000000 +1100
-+++ rstudio-1.0.44/src/cpp/server/CMakeLists.txt	2016-12-01 23:35:51.634862018 +1100
-@@ -155,7 +155,7 @@
-    configure_file(${CMAKE_CURRENT_SOURCE_DIR}/${RSERVER_INITD_DEBIAN_SCRIPT}.in
-                   ${CMAKE_CURRENT_BINARY_DIR}/${RSERVER_INITD_DEBIAN_SCRIPT})
-    install(PROGRAMS ${CMAKE_CURRENT_BINARY_DIR}/${RSERVER_INITD_DEBIAN_SCRIPT}
--           DESTINATION ${RSERVER_INITD_DEBIAN_DIR})
-+           DESTINATION ${DISTRO_SHARE}/${RSERVER_INITD_DEBIAN_DIR})
- 
-    # install configured redhat init.d script
-    set(RSERVER_INITD_REDHAT_DIR "extras/init.d/redhat")
-@@ -163,7 +163,7 @@
-    configure_file(${CMAKE_CURRENT_SOURCE_DIR}/${RSERVER_INITD_REDHAT_SCRIPT}.in
-                   ${CMAKE_CURRENT_BINARY_DIR}/${RSERVER_INITD_REDHAT_SCRIPT})
-    install(PROGRAMS ${CMAKE_CURRENT_BINARY_DIR}/${RSERVER_INITD_REDHAT_SCRIPT}
--           DESTINATION ${RSERVER_INITD_REDHAT_DIR})
-+           DESTINATION ${DISTRO_SHARE}/${RSERVER_INITD_REDHAT_DIR})
- 
-    # install configured suse init.d script
-    set(RSERVER_INITD_SUSE_DIR "extras/init.d/suse")
-@@ -171,13 +171,13 @@
-    configure_file(${CMAKE_CURRENT_SOURCE_DIR}/${RSERVER_INITD_SUSE_SCRIPT}.in
-                   ${CMAKE_CURRENT_BINARY_DIR}/${RSERVER_INITD_SUSE_SCRIPT})
-    install(PROGRAMS ${CMAKE_CURRENT_BINARY_DIR}/${RSERVER_INITD_SUSE_SCRIPT}
--           DESTINATION ${RSERVER_INITD_SUSE_DIR})
-+           DESTINATION ${DISTRO_SHARE}/${RSERVER_INITD_SUSE_DIR})
- 
-    # install pam profile
-    set(RSERVER_PAM_DIR "extras/pam")
-    set(RSERVER_PAM_PROFILE "${RSERVER_PAM_DIR}/rstudio")
-    install(FILES ${CMAKE_CURRENT_SOURCE_DIR}/${RSERVER_PAM_PROFILE}
--           DESTINATION ${RSERVER_PAM_DIR})
-+           DESTINATION ${DISTRO_SHARE}/${RSERVER_PAM_DIR})
- 
-    # install configured apparmor profile
-    set(RSERVER_APPARMOR_DIR "extras/apparmor")
-@@ -185,9 +185,9 @@
-    configure_file(${CMAKE_CURRENT_SOURCE_DIR}/${RSERVER_APPARMOR_PROFILE}.in
-                   ${CMAKE_CURRENT_BINARY_DIR}/${RSERVER_APPARMOR_PROFILE})
-    install(FILES ${CMAKE_CURRENT_BINARY_DIR}/${RSERVER_APPARMOR_PROFILE}
--           DESTINATION ${RSERVER_APPARMOR_DIR})
-+           DESTINATION ${DISTRO_SHARE}/${RSERVER_APPARMOR_DIR})
-    install(PROGRAMS ${CMAKE_CURRENT_SOURCE_DIR}/${RSERVER_APPARMOR_DIR}/apparmor-profile-load
--           DESTINATION ${RSERVER_APPARMOR_DIR})
-+           DESTINATION ${DISTRO_SHARE}/${RSERVER_APPARMOR_DIR})
- 
-    # install configured upstart profile
-    set(RSERVER_UPSTART_DIR "extras/upstart")
-@@ -195,12 +195,12 @@
-    configure_file(${CMAKE_CURRENT_SOURCE_DIR}/${RSERVER_UPSTART_PROFILE}.in
-                   ${CMAKE_CURRENT_BINARY_DIR}/${RSERVER_UPSTART_PROFILE})
-    install(FILES ${CMAKE_CURRENT_BINARY_DIR}/${RSERVER_UPSTART_PROFILE}
--           DESTINATION ${RSERVER_UPSTART_DIR})
-+           DESTINATION ${DISTRO_SHARE}/${RSERVER_UPSTART_DIR})
-    set(RSERVER_UPSTART_PROFILE_REDHAT "${RSERVER_UPSTART_DIR}/rstudio-server.redhat.conf")
-    configure_file(${CMAKE_CURRENT_SOURCE_DIR}/${RSERVER_UPSTART_PROFILE_REDHAT}.in
-                   ${CMAKE_CURRENT_BINARY_DIR}/${RSERVER_UPSTART_PROFILE_REDHAT})
-    install(FILES ${CMAKE_CURRENT_BINARY_DIR}/${RSERVER_UPSTART_PROFILE_REDHAT}
--           DESTINATION ${RSERVER_UPSTART_DIR})
-+           DESTINATION ${DISTRO_SHARE}/${RSERVER_UPSTART_DIR})
- 
-     # install configured systemd profile
-    set(RSERVER_SYSTEMD_DIR "extras/systemd")
---- rstudio-1.0.44-orig/src/cpp/server/ServerOptions.cpp	2016-10-19 08:32:41.000000000 +1100
-+++ rstudio-1.0.44/src/cpp/server/ServerOptions.cpp	2016-12-01 23:33:04.151326331 +1100
-@@ -386,8 +386,8 @@
- 
-    // convert relative paths by completing from the system installation
-    // path (this allows us to be relocatable)
--   resolvePath(resourcePath, &wwwLocalPath_);
--   resolvePath(resourcePath, &wwwSymbolMapsPath_);
-+   resolvePath(resourcePath.childPath(DISTRO_SHARE), &wwwLocalPath_);
-+   resolvePath(resourcePath.childPath(DISTRO_SHARE), &wwwSymbolMapsPath_);
-    resolvePath(binaryPath, &authPamHelperPath_);
-    resolvePath(binaryPath, &rsessionPath_);
-    resolvePath(binaryPath, &rldpathPath_);
---- rstudio-1.0.44-orig/src/cpp/session/SessionOptions.cpp	2016-10-19 08:32:41.000000000 +1100
-+++ rstudio-1.0.44/src/cpp/session/SessionOptions.cpp	2016-12-01 23:33:04.151326331 +1100
-@@ -49,7 +49,7 @@
- namespace session {  
- 
- namespace {
--const char* const kDefaultPandocPath = "bin/pandoc";
-+const char* const kDefaultPandocPath = "bin";
- const char* const kDefaultPostbackPath = "bin/postback/rpostback";
- const char* const kDefaultRsclangPath = "bin/rsclang";
- 
-@@ -481,14 +481,14 @@
-    }
-    
-    // convert relative paths by completing from the app resource path
--   resolvePath(resourcePath_, &rResourcesPath_);
--   resolvePath(resourcePath_, &agreementFilePath_);
--   resolvePath(resourcePath_, &wwwLocalPath_);
--   resolvePath(resourcePath_, &wwwSymbolMapsPath_);
--   resolvePath(resourcePath_, &coreRSourcePath_);
--   resolvePath(resourcePath_, &modulesRSourcePath_);
--   resolvePath(resourcePath_, &sessionLibraryPath_);
--   resolvePath(resourcePath_, &sessionPackageArchivesPath_);
-+   resolvePath(resourcePath_.childPath(DISTRO_SHARE), &rResourcesPath_);
-+   resolvePath(resourcePath_.childPath(DISTRO_SHARE), &agreementFilePath_);
-+   resolvePath(resourcePath_.childPath(DISTRO_SHARE), &wwwLocalPath_);
-+   resolvePath(resourcePath_.childPath(DISTRO_SHARE), &wwwSymbolMapsPath_);
-+   resolvePath(resourcePath_.childPath(DISTRO_SHARE), &coreRSourcePath_);
-+   resolvePath(resourcePath_.childPath(DISTRO_SHARE), &modulesRSourcePath_);
-+   resolvePath(resourcePath_.childPath(DISTRO_SHARE), &sessionLibraryPath_);
-+   resolvePath(resourcePath_.childPath(DISTRO_SHARE), &sessionPackageArchivesPath_);
-    resolvePostbackPath(resourcePath_, &rpostbackPath_);
- #ifdef _WIN32
-    resolvePath(resourcePath_, &consoleIoPath_);
-@@ -498,7 +498,7 @@
-    resolvePath(resourcePath_, &sumatraPath_);
-    resolvePath(resourcePath_, &winutilsPath_);
- #endif
--   resolvePath(resourcePath_, &hunspellDictionariesPath_);
-+   resolvePath(resourcePath_.childPath(DISTRO_SHARE), &hunspellDictionariesPath_);
-    resolvePath(resourcePath_, &mathjaxPath_);
-    resolvePath(resourcePath_, &libclangHeadersPath_);
-    resolvePandocPath(resourcePath_, &pandocPath_);

diff --git a/sci-mathematics/rstudio/files/rstudio-1.1.357-clang-pandoc.patch b/sci-mathematics/rstudio/files/rstudio-1.1.357-clang-pandoc.patch
deleted file mode 100644
index 28b0220912a..00000000000
--- a/sci-mathematics/rstudio/files/rstudio-1.1.357-clang-pandoc.patch
+++ /dev/null
@@ -1,76 +0,0 @@
-Index: rstudio-1.1.357/src/cpp/session/CMakeLists.txt
-===================================================================
---- rstudio-1.1.357.orig/src/cpp/session/CMakeLists.txt
-+++ rstudio-1.1.357/src/cpp/session/CMakeLists.txt
-@@ -25,9 +25,6 @@ endif()
- if(NOT EXISTS "${RSTUDIO_DEPENDENCIES_DIR}/common/mathjax-26")
-   message(FATAL_ERROR "Mathjax 2.6 not found (re-run install-dependencies script to install)")
- endif()
--if(NOT EXISTS "${RSTUDIO_DEPENDENCIES_DIR}/common/pandoc")
--  message(FATAL_ERROR "pandoc not found (re-run install-dependencies script to install)")
--endif()
- 
- # we often install embedded versions of these packages but don't do so currently
- 
-@@ -38,22 +35,6 @@ endif()
- #   message(FATAL_ERROR "rsconnect package not found (re-run install-dependencies script to install)")
- # endif()
- 
--# verify libclang is installed
--if(WIN32)
--   set(LIBCLANG_VERSION "3.4")
--else()
--   set(LIBCLANG_VERSION "3.5")
--endif()
--set(LIBCLANG_DIR "${RSTUDIO_DEPENDENCIES_DIR}/common/libclang/${LIBCLANG_VERSION}")
--if(NOT EXISTS "${LIBCLANG_DIR}")
--  message(FATAL_ERROR "libclang ${LIBCLANG_VERSION} not found  (re-run install-dependencies script to install)")
--endif()
--set(LIBCLANG_HEADERS_DIR "${RSTUDIO_DEPENDENCIES_DIR}/common/libclang/builtin-headers")
--if(NOT EXISTS "${LIBCLANG_HEADERS_DIR}")
--  message(FATAL_ERROR "libclang builtin-headers not found  (re-run install-dependencies script to install)")
--endif()
--
--
- # include files
- file(GLOB_RECURSE SESSION_HEADER_FILES "*.h*")
- 
-@@ -465,13 +446,6 @@ if (NOT RSTUDIO_SESSION_WIN64)
-    install(DIRECTORY "resources/connections"
-            DESTINATION ${RSTUDIO_INSTALL_SUPPORTING}/resources)
- 
--   # install pandoc
--   set(PANDOC_BIN "${RSTUDIO_DEPENDENCIES_DIR}/common/pandoc/1.19.2.1")
--   file(GLOB PANDOC_FILES "${PANDOC_BIN}/pandoc*")
--   install(FILES ${PANDOC_FILES}
--           PERMISSIONS OWNER_READ OWNER_WRITE OWNER_EXECUTE GROUP_READ GROUP_EXECUTE WORLD_READ WORLD_EXECUTE
--           DESTINATION  ${RSTUDIO_INSTALL_BIN}/pandoc)
--
-    # install rmarkdown package
-    # file(GLOB RMARKDOWN_PACKAGE "${RSTUDIO_DEPENDENCIES_DIR}/common/rmarkdown*.tar.gz")
-    # install(FILES ${RMARKDOWN_PACKAGE}
-@@ -502,24 +476,6 @@ if (NOT RSTUDIO_SESSION_WIN64)
-    install(DIRECTORY "resources/profiler"
-            DESTINATION ${RSTUDIO_INSTALL_SUPPORTING}/resources)
- 
--   # install libclang
--   if(WIN32)
--      file(GLOB LIBCLANG_32_FILES "${LIBCLANG_DIR}/x86/libclang.*")
--      install(PROGRAMS ${LIBCLANG_32_FILES}
--              DESTINATION  ${RSTUDIO_INSTALL_BIN}/rsclang/x86)
--      file(GLOB LIBCLANG_64_FILES "${LIBCLANG_DIR}/x86_64/libclang.*")
--      install(PROGRAMS ${LIBCLANG_64_FILES}
--              DESTINATION  ${RSTUDIO_INSTALL_BIN}/rsclang/x86_64)
--   else()
--      file(GLOB_RECURSE LIBCLANG_FILES "${LIBCLANG_DIR}/libclang.*")
--      install(PROGRAMS ${LIBCLANG_FILES}
--              DESTINATION  ${RSTUDIO_INSTALL_BIN}/rsclang)
--   endif()
--
--   # install libclang builtin-headers
--   install(DIRECTORY "${RSTUDIO_DEPENDENCIES_DIR}/common/libclang/builtin-headers"
--           DESTINATION "${RSTUDIO_INSTALL_SUPPORTING}/resources/libclang")
--
-    # install winpty on windows
-    if(WIN32)
-       install(PROGRAMS "${WINPTY_BINDIR_32}/winpty.dll"

diff --git a/sci-mathematics/rstudio/files/rstudio-1.1.453-boost-1.67.0.patch b/sci-mathematics/rstudio/files/rstudio-1.1.453-boost-1.67.0.patch
deleted file mode 100644
index 760c9b56105..00000000000
--- a/sci-mathematics/rstudio/files/rstudio-1.1.453-boost-1.67.0.patch
+++ /dev/null
@@ -1,38 +0,0 @@
---- rstudio-1.1.453-orig/src/cpp/core/DateTime.cpp	2018-05-15 04:19:30.000000000 +1000
-+++ rstudio-1.1.453/src/cpp/core/DateTime.cpp	2018-07-02 16:19:21.335703471 +1000
-@@ -65,7 +65,7 @@
-    using namespace boost::posix_time;
- 
-    ptime time_t_epoch(date(1970,1,1));
--   return time_t_epoch + seconds(sec);
-+   return time_t_epoch + seconds(static_cast<long>(sec));
- }
- 
- boost::posix_time::ptime timeFromMillisecondsSinceEpoch(int64_t ms)
---- rstudio-1.1.453-orig/src/cpp/core/file_lock/FileLock.cpp	2018-05-15 04:19:30.000000000 +1000
-+++ rstudio-1.1.453/src/cpp/core/file_lock/FileLock.cpp	2018-07-02 17:00:35.915695201 +1000
-@@ -133,11 +133,11 @@
- 
-    // timeout interval
-    double timeoutInterval = getFieldPositive(settings, "timeout-interval", kDefaultTimeoutInterval);
--   FileLock::s_timeoutInterval = boost::posix_time::seconds(timeoutInterval);
-+   FileLock::s_timeoutInterval = boost::posix_time::seconds(static_cast<long>(timeoutInterval));
-    
-    // refresh rate
-    double refreshRate = getFieldPositive(settings, "refresh-rate", kDefaultRefreshRate);
--   FileLock::s_refreshRate = boost::posix_time::seconds(refreshRate);
-+   FileLock::s_refreshRate = boost::posix_time::seconds(static_cast<long>(refreshRate));
-    
-    // logging
-    bool loggingEnabled = settings.getBool("enable-logging", false);
-@@ -212,8 +212,8 @@
- 
- // default values for static members
- FileLock::LockType FileLock::s_defaultType(FileLock::LOCKTYPE_LINKBASED);
--boost::posix_time::seconds FileLock::s_timeoutInterval(kDefaultTimeoutInterval);
--boost::posix_time::seconds FileLock::s_refreshRate(kDefaultRefreshRate);
-+boost::posix_time::seconds FileLock::s_timeoutInterval(static_cast<long>(kDefaultTimeoutInterval));
-+boost::posix_time::seconds FileLock::s_refreshRate(static_cast<long>(kDefaultRefreshRate));
- bool FileLock::s_loggingEnabled(false);
- bool FileLock::s_isLoadBalanced(false);
- FilePath FileLock::s_logFile;

diff --git a/sci-mathematics/rstudio/files/rstudio-1.1.453-core.patch b/sci-mathematics/rstudio/files/rstudio-1.1.453-core.patch
deleted file mode 100644
index 641f7710167..00000000000
--- a/sci-mathematics/rstudio/files/rstudio-1.1.453-core.patch
+++ /dev/null
@@ -1,143 +0,0 @@
---- rstudio-1.1.453-orig/src/cpp/session/SessionClientInit.cpp	2018-05-15 04:19:30.000000000 +1000
-+++ rstudio-1.1.453/src/cpp/session/SessionClientInit.cpp	2018-07-02 20:21:41.595654877 +1000
-@@ -105,7 +105,7 @@
-    }
- 
-    // prepare session info 
--   json::Object sessionInfo ;
-+   core::json::Object sessionInfo ;
-    sessionInfo["clientId"] = clientId;
-    sessionInfo["mode"] = options.programMode();
-    
-@@ -119,8 +119,8 @@
-    }
- 
-    // temp dir
--   FilePath tempDir = rstudio::r::session::utils::tempDir();
--   Error error = tempDir.ensureDirectory();
-+   core::FilePath tempDir = rstudio::r::session::utils::tempDir();
-+   core::Error error = tempDir.ensureDirectory();
-    if (error)
-       LOG_ERROR(error);
-    sessionInfo["temp_dir"] = tempDir.absolutePath();
-@@ -132,12 +132,12 @@
-    sessionInfo["prompt"] = rstudio::r::options::getOption<std::string>("prompt");
- 
-    // client state
--   json::Object clientStateObject;
-+   core::json::Object clientStateObject;
-    rstudio::r::session::clientState().currentState(&clientStateObject);
-    sessionInfo["client_state"] = clientStateObject;
-    
-    // source documents
--   json::Array jsonDocs;
-+   core::json::Array jsonDocs;
-    error = modules::source::clientInitDocuments(&jsonDocs);
-    if (error)
-       LOG_ERROR(error);
-@@ -159,7 +159,7 @@
-    if (resumed)
-    {
-       // console actions
--      json::Object actionsObject;
-+     core::json::Object actionsObject;
-       consoleActions.asJson(&actionsObject);
-       sessionInfo["console_actions"] = actionsObject;
-    }
-@@ -211,12 +211,12 @@
-    }
-    else
-    {
--      sessionInfo["active_project_file"] = json::Value();
--      sessionInfo["project_ui_prefs"] = json::Value();
--      sessionInfo["project_open_docs"] = json::Value();
-+      sessionInfo["active_project_file"] = core::json::Value();
-+      sessionInfo["project_ui_prefs"] = core::json::Value();
-+      sessionInfo["project_open_docs"] = core::json::Value();
-       sessionInfo["project_supports_sharing"] = false;
-       sessionInfo["project_owned_by_user"] = false;
--      sessionInfo["project_user_data_directory"] = json::Value();
-+      sessionInfo["project_user_data_directory"] = core::json::Value();
-    }
- 
-    sessionInfo["system_encoding"] = std::string(::locale2charset(NULL));
-@@ -253,20 +253,20 @@
-       sessionInfo["build_tools_bookdown_website"] =
-                               module_context::isBookdownWebsite();
- 
--      FilePath buildTargetDir = projects::projectContext().buildTargetPath();
-+      core::FilePath buildTargetDir = projects::projectContext().buildTargetPath();
-       if (!buildTargetDir.empty())
-       {
-          sessionInfo["build_target_dir"] = module_context::createAliasedPath(
-                                                                 buildTargetDir);
--         sessionInfo["has_pkg_src"] = (type == r_util::kBuildTypePackage) &&
-+         sessionInfo["has_pkg_src"] = (type == core::r_util::kBuildTypePackage) &&
-                                       buildTargetDir.childPath("src").exists();
-          sessionInfo["has_pkg_vig"] =
--               (type == r_util::kBuildTypePackage) &&
-+               (type == core::r_util::kBuildTypePackage) &&
-                buildTargetDir.childPath("vignettes").exists();
-       }
-       else
-       {
--         sessionInfo["build_target_dir"] = json::Value();
-+         sessionInfo["build_target_dir"] = core::json::Value();
-          sessionInfo["has_pkg_src"] = false;
-          sessionInfo["has_pkg_vig"] = false;
-       }
-@@ -274,9 +274,9 @@
-    }
-    else
-    {
--      sessionInfo["build_tools_type"] = r_util::kBuildTypeNone;
-+      sessionInfo["build_tools_type"] = core::r_util::kBuildTypeNone;
-       sessionInfo["build_tools_bookdown_website"] = false;
--      sessionInfo["build_target_dir"] = json::Value();
-+      sessionInfo["build_target_dir"] = core::json::Value();
-       sessionInfo["has_pkg_src"] = false;
-       sessionInfo["has_pkg_vig"] = false;
-    }
-@@ -285,7 +285,7 @@
-    sessionInfo["presentation_commands"] = options.allowPresentationCommands();
- 
-    sessionInfo["tutorial_api_available"] = false;
--   sessionInfo["tutorial_api_client_origin"] = json::Value();
-+   sessionInfo["tutorial_api_client_origin"] = core::json::Value();
- 
-    sessionInfo["build_state"] = modules::build::buildStateAsJson();
-    sessionInfo["devtools_installed"] = module_context::isMinimumDevtoolsInstalled();
-@@ -296,7 +296,7 @@
- 
-    // console history -- we do this at the end because
-    // restoreBuildRestartContext may have reset it
--   json::Array historyArray;
-+   core::json::Array historyArray;
-    rstudio::r::session::consoleHistory().asJson(&historyArray);
-    sessionInfo["console_history"] = historyArray;
-    sessionInfo["console_history_capacity"] =
-@@ -364,13 +364,13 @@
- 
-    sessionInfo["multi_session"] = options.multiSession();
- 
--   json::Object rVersionsJson;
-+   core::json::Object rVersionsJson;
-    rVersionsJson["r_version"] = module_context::rVersion();
-    rVersionsJson["r_home_dir"] = module_context::rHomeDir();
-    sessionInfo["r_versions_info"] = rVersionsJson;
- 
-    sessionInfo["show_user_home_page"] = options.showUserHomePage();
--   sessionInfo["user_home_page_url"] = json::Value();
-+   sessionInfo["user_home_page_url"] = core::json::Value();
-    
-    sessionInfo["r_addins"] = modules::r_addins::addinRegistryAsJson();
-    sessionInfo["package_provided_extensions"] = modules::ppe::indexer().getPayload();
-@@ -394,7 +394,7 @@
- 
-    // send response  (we always set kEventsPending to false so that the client
-    // won't poll for events until it is ready)
--   json::JsonRpcResponse jsonRpcResponse ;
-+   core::json::JsonRpcResponse jsonRpcResponse ;
-    jsonRpcResponse.setField(kEventsPending, "false");
-    jsonRpcResponse.setResult(sessionInfo) ;
-    ptrConnection->sendJsonRpcResponse(jsonRpcResponse);

diff --git a/sci-mathematics/rstudio/files/rstudio-1.1.463-boost-1.69.0_p1.patch b/sci-mathematics/rstudio/files/rstudio-1.1.463-boost-1.69.0_p1.patch
deleted file mode 100644
index a7a48572de3..00000000000
--- a/sci-mathematics/rstudio/files/rstudio-1.1.463-boost-1.69.0_p1.patch
+++ /dev/null
@@ -1,460 +0,0 @@
---- /dev/null	2019-03-19 11:03:33.121000004 +1100
-+++ rstudio-1.1.463/src/cpp/core/include/core/BoostSignals.hpp	2018-11-17 21:24:35.285976284 +1100
-@@ -0,0 +1,40 @@
-+/*
-+ * BoostSignals.hpp
-+ *
-+ * Copyright (C) 2009-18 by RStudio, Inc.
-+ *
-+ * Unless you have received this program directly from RStudio pursuant
-+ * to the terms of a commercial license agreement with RStudio, then
-+ * this program is licensed to you under the terms of version 3 of the
-+ * GNU Affero General Public License. This program is distributed WITHOUT
-+ * ANY EXPRESS OR IMPLIED WARRANTY, INCLUDING THOSE OF NON-INFRINGEMENT,
-+ * MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. Please refer to the
-+ * AGPL (http://www.gnu.org/licenses/agpl-3.0.txt) for more details.
-+ *
-+ */
-+
-+#ifndef CORE_RSTUDIO_BOOST_SIGNALS_HPP
-+#define CORE_RSTUDIO_BOOST_SIGNALS_HPP
-+
-+#if RSTUDIO_BOOST_SIGNALS_VERSION == 1
-+
-+# include <boost/signals.hpp>
-+# define RSTUDIO_BOOST_SIGNAL boost::signal
-+# define RSTUDIO_BOOST_CONNECTION boost::signals::connection
-+# define RSTUDIO_BOOST_SCOPED_CONNECTION boost::signals::scoped_connection
-+# define RSTUDIO_BOOST_LAST_VALUE boost::last_value
-+
-+#elif RSTUDIO_BOOST_SIGNALS_VERSION == 2
-+
-+# include <boost/signals2.hpp>
-+# define RSTUDIO_BOOST_SIGNAL boost::signals2::signal
-+# define RSTUDIO_BOOST_CONNECTION boost::signals2::connection
-+# define RSTUDIO_BOOST_SCOPED_CONNECTION boost::signals2::scoped_connection
-+# define RSTUDIO_BOOST_LAST_VALUE boost::signals2::last_value
-+
-+#else
-+# error "Unrecognized RSTUDIO_BOOST_SIGNALS_VERSION"
-+#endif
-+
-+#endif // CORE_RSTUDIO_BOOST_SIGNALS_HPP
-+
---- rstudio-1.1.463-orig/src/cpp/CMakeLists.txt	2018-10-25 09:42:55.000000000 +1100
-+++ rstudio-1.1.463/src/cpp/CMakeLists.txt	2018-11-17 21:24:35.285976284 +1100
-@@ -208,6 +208,18 @@
-    message(STATUS "Using RStudio-provided Boost ${BOOST_VERSION}")
- endif()
- 
-+# allow opt-in to using Boost.Signals2
-+# TODO: remove this in RStudio v1.3 and port to signals2
-+if(NOT RSTUDIO_BOOST_SIGNALS_VERSION)
-+   if (BOOST_VERSION VERSION_LESS 1.69.0)
-+      set(RSTUDIO_BOOST_SIGNALS_VERSION 1)
-+   else()
-+      set(RSTUDIO_BOOST_SIGNALS_VERSION 2)
-+   endif()
-+endif()
-+
-+message(STATUS "Using Booost.Signals version ${RSTUDIO_BOOST_SIGNALS_VERSION}")
-+add_definitions(-DRSTUDIO_BOOST_SIGNALS_VERSION=${RSTUDIO_BOOST_SIGNALS_VERSION})
- 
- # add boost as system include directory
- include_directories(SYSTEM ${Boost_INCLUDE_DIRS})
---- rstudio-1.1.463-orig/src/cpp/r/include/r/session/RConsoleHistory.hpp	2018-10-25 09:42:55.000000000 +1100
-+++ rstudio-1.1.463/src/cpp/r/include/r/session/RConsoleHistory.hpp	2018-11-17 21:24:35.285976284 +1100
-@@ -20,8 +20,8 @@
- 
- #include <boost/utility.hpp>
- #include <boost/circular_buffer.hpp>
--#include <boost/signal.hpp>
- 
-+#include <core/BoostSignals.hpp>
- #include <core/json/Json.hpp>
- 
- namespace rstudio {
-@@ -44,7 +44,7 @@
- public:
-    typedef boost::circular_buffer<std::string>::value_type value_type;
-    typedef boost::circular_buffer<std::string>::const_iterator const_iterator;
--   typedef boost::signal<void (const std::string&)> AddSignal;
-+   typedef RSTUDIO_BOOST_SIGNAL<void (const std::string&)> AddSignal;
- 
- private:
-    ConsoleHistory();
-@@ -86,8 +86,7 @@
-    core::Error loadFromFile(const core::FilePath& filePath, bool verifyFile);
-    core::Error saveToFile(const core::FilePath& filePath) const;
-    
--   boost::signals::connection connectOnAdd(
--                                 const AddSignal::slot_function_type& slot)
-+   RSTUDIO_BOOST_CONNECTION connectOnAdd(const AddSignal::slot_function_type& slot)
-    {
-       return onAdd_.connect(slot);
-    }
---- rstudio-1.1.463-orig/src/cpp/r/include/r/session/RGraphics.hpp	2018-10-25 09:42:55.000000000 +1100
-+++ rstudio-1.1.463/src/cpp/r/include/r/session/RGraphics.hpp	2018-11-17 21:24:35.286976293 +1100
-@@ -19,6 +19,8 @@
- #include <boost/system/error_code.hpp>
- #include <boost/date_time/posix_time/ptime.hpp>
- 
-+#include <core/BoostSignals.hpp>
-+
- namespace rstudio {
- namespace r {
- namespace session {
-@@ -56,8 +58,8 @@
- #include <vector>
- 
- #include <boost/function.hpp>
--#include <boost/signal.hpp>
- 
-+#include <core/BoostSignals.hpp>
- #include <core/Error.hpp>
- #include <core/json/Json.hpp>
- 
-@@ -162,7 +164,7 @@
-    virtual void clear() = 0;
- 
-    // subscribe to showManipulator event
--   virtual boost::signal<void ()>& onShowManipulator() = 0;
-+   virtual RSTUDIO_BOOST_SIGNAL<void ()>& onShowManipulator() = 0;
- 
-    // set manipulator values
-    virtual void setPlotManipulatorValues(const core::json::Object& values) = 0;
---- rstudio-1.1.463-orig/src/cpp/r/session/graphics/RGraphicsPlotManager.cpp	2018-10-25 09:42:55.000000000 +1100
-+++ rstudio-1.1.463/src/cpp/r/session/graphics/RGraphicsPlotManager.cpp	2018-11-17 21:24:35.286976293 +1100
-@@ -540,7 +540,7 @@
- 
- 
- 
--boost::signal<void ()>& PlotManager::onShowManipulator()
-+RSTUDIO_BOOST_SIGNAL<void ()>& PlotManager::onShowManipulator()
- {
-    return plotManipulatorManager().onShowManipulator();
- }
---- rstudio-1.1.463-orig/src/cpp/r/session/graphics/RGraphicsPlotManager.hpp	2018-10-25 09:42:55.000000000 +1100
-+++ rstudio-1.1.463/src/cpp/r/session/graphics/RGraphicsPlotManager.hpp	2018-11-17 21:24:35.287976303 +1100
-@@ -22,10 +22,10 @@
- #include <boost/utility.hpp>
- #include <boost/shared_ptr.hpp>
- #include <boost/function.hpp>
--#include <boost/signal.hpp>
- #include <boost/regex.hpp>
- #include <boost/circular_buffer.hpp>
- 
-+#include <core/BoostSignals.hpp>
- #include <core/Error.hpp>
- #include <core/FilePath.hpp>
- 
-@@ -45,10 +45,10 @@
- 
- struct GraphicsDeviceEvents
- {
--   boost::signal<void (SEXP)> onNewPage; 
--   boost::signal<void ()> onDrawing;
--   boost::signal<void ()> onResized;
--   boost::signal<void ()> onClosed;
-+   RSTUDIO_BOOST_SIGNAL<void (SEXP)> onNewPage; 
-+   RSTUDIO_BOOST_SIGNAL<void ()> onDrawing;
-+   RSTUDIO_BOOST_SIGNAL<void ()> onResized;
-+   RSTUDIO_BOOST_SIGNAL<void ()> onClosed;
- };
- 
- class PlotManipulatorManager;
-@@ -110,7 +110,7 @@
-    
-    virtual void clear();
- 
--   virtual boost::signal<void ()>& onShowManipulator() ;
-+   virtual RSTUDIO_BOOST_SIGNAL<void ()>& onShowManipulator() ;
-    virtual void setPlotManipulatorValues(const core::json::Object& values);
-    virtual void manipulatorPlotClicked(int x, int y);
- 
---- rstudio-1.1.463-orig/src/cpp/r/session/graphics/RGraphicsPlotManipulatorManager.cpp	2018-10-25 09:42:55.000000000 +1100
-+++ rstudio-1.1.463/src/cpp/r/session/graphics/RGraphicsPlotManipulatorManager.cpp	2018-11-17 21:24:35.287976303 +1100
-@@ -184,7 +184,7 @@
- }
- 
- 
--boost::signal<void ()>& PlotManipulatorManager::onShowManipulator()
-+RSTUDIO_BOOST_SIGNAL<void ()>& PlotManipulatorManager::onShowManipulator()
- {
-    return onShowManipulator_;
- }
---- rstudio-1.1.463-orig/src/cpp/r/session/graphics/RGraphicsPlotManipulatorManager.hpp	2018-10-25 09:42:55.000000000 +1100
-+++ rstudio-1.1.463/src/cpp/r/session/graphics/RGraphicsPlotManipulatorManager.hpp	2018-11-17 21:24:35.287976303 +1100
-@@ -16,8 +16,7 @@
- #ifndef R_SESSION_GRAPHICS_PLOT_MANIPULATOR_MANAGER_HPP
- #define R_SESSION_GRAPHICS_PLOT_MANIPULATOR_MANAGER_HPP
- 
--#include <boost/signal.hpp>
--
-+#include <core/BoostSignals.hpp>
- #include <core/Error.hpp>
- #include <core/json/Json.hpp>
- 
-@@ -53,7 +52,7 @@
- public:
-    core::Error initialize(const UnitConversionFunctions& convert);
- 
--   boost::signal<void ()>& onShowManipulator() ;
-+   RSTUDIO_BOOST_SIGNAL<void ()>& onShowManipulator() ;
-    void setPlotManipulatorValues(const core::json::Object& values);
-    void manipulatorPlotClicked(int x, int y);
-    
-@@ -85,7 +84,7 @@
-    bool replayingManipulator_;
- 
-    // manipulator event hook
--   boost::signal<void ()> onShowManipulator_;
-+   RSTUDIO_BOOST_SIGNAL<void ()> onShowManipulator_;
- 
-    // unit conversion function
-    UnitConversionFunctions convert_;
---- rstudio-1.1.463-orig/src/cpp/server/include/server/ServerSessionManager.hpp	2018-10-25 09:42:55.000000000 +1100
-+++ rstudio-1.1.463/src/cpp/server/include/server/ServerSessionManager.hpp	2018-11-17 21:27:05.255436316 +1100
-@@ -20,9 +20,9 @@
- #include <vector>
- #include <map>
- 
--#include <boost/signals.hpp>
- #include <boost/asio/io_service.hpp>
- 
-+#include <core/BoostSignals.hpp>
- #include <core/Thread.hpp>
- 
- #include <core/system/PosixSystem.hpp>
---- rstudio-1.1.463-orig/src/cpp/session/SessionMain.cpp	2018-10-25 09:42:55.000000000 +1100
-+++ rstudio-1.1.463/src/cpp/session/SessionMain.cpp	2018-11-17 21:24:35.288976313 +1100
-@@ -33,12 +33,12 @@
- #include <boost/lexical_cast.hpp>
- #include <boost/format.hpp>
- 
--#include <boost/signals.hpp>
- #include <boost/date_time/posix_time/posix_time.hpp>
- #include <boost/algorithm/string/predicate.hpp>
- #include <boost/algorithm/string/join.hpp>
- 
- #include <core/Error.hpp>
-+#include <core/BoostSignals.hpp>
- #include <core/BoostThread.hpp>
- #include <core/ConfigUtils.hpp>
- #include <core/FilePath.hpp>
---- rstudio-1.1.463-orig/src/cpp/session/SessionModuleContext.cpp	2018-10-25 09:42:55.000000000 +1100
-+++ rstudio-1.1.463/src/cpp/session/SessionModuleContext.cpp	2018-11-17 21:24:35.289976322 +1100
-@@ -19,10 +19,10 @@
- 
- #include <boost/assert.hpp>
- #include <boost/utility.hpp>
--#include <boost/signal.hpp>
- #include <boost/format.hpp>
- #include <boost/numeric/conversion/cast.hpp>
- 
-+#include <core/BoostSignals.hpp>
- #include <core/BoostThread.hpp>
- #include <core/Error.hpp>
- #include <core/FilePath.hpp>
-@@ -586,13 +586,13 @@
-    
-    int nextGroup_; 
-    
--   boost::signal<void(const r::session::RSuspendOptions&,Settings*),
--                 boost::last_value<void>,
-+   RSTUDIO_BOOST_SIGNAL<void(const r::session::RSuspendOptions&,Settings*),
-+                 RSTUDIO_BOOST_LAST_VALUE<void>,
-                  int,
-                  std::less<int> > suspendSignal_;
-                   
--   boost::signal<void(const Settings&),
--                 boost::last_value<void>,
-+   RSTUDIO_BOOST_SIGNAL<void(const Settings&),
-+                 RSTUDIO_BOOST_LAST_VALUE<void>,
-                  int,
-                  std::greater<int> > resumeSignal_;
- };
---- rstudio-1.1.463-orig/src/cpp/session/include/session/SessionConsoleProcess.hpp	2018-10-25 09:42:55.000000000 +1100
-+++ rstudio-1.1.463/src/cpp/session/include/session/SessionConsoleProcess.hpp	2018-11-17 21:24:35.290976332 +1100
-@@ -20,10 +20,10 @@
- #include <deque>
- 
- #include <boost/regex.hpp>
--#include <boost/signals.hpp>
- #include <boost/circular_buffer.hpp>
- #include <boost/enable_shared_from_this.hpp>
- 
-+#include <core/BoostSignals.hpp>
- #include <core/system/Process.hpp>
- #include <core/terminal/PrivateCommand.hpp>
- 
-@@ -146,7 +146,7 @@
-    void setPromptHandler(
-          const boost::function<bool(const std::string&, Input*)>& onPrompt);
- 
--   boost::signal<void(int)>& onExit() { return onExit_; }
-+   RSTUDIO_BOOST_SIGNAL<void(int)>& onExit() { return onExit_; }
- 
-    std::string handle() const { return procInfo_->getHandle(); }
-    InteractionMode interactionMode() const { return procInfo_->getInteractionMode(); }
-@@ -264,7 +264,7 @@
-    boost::mutex inputOutputQueueMutex_;
- 
-    boost::function<bool(const std::string&, Input*)> onPrompt_;
--   boost::signal<void(int)> onExit_;
-+   RSTUDIO_BOOST_SIGNAL<void(int)> onExit_;
- 
-    // regex for prompt detection
-    boost::regex controlCharsPattern_;
---- rstudio-1.1.463-orig/src/cpp/session/include/session/SessionModuleContext.hpp	2018-10-25 09:42:55.000000000 +1100
-+++ rstudio-1.1.463/src/cpp/session/include/session/SessionModuleContext.hpp	2018-11-17 21:28:25.019212857 +1100
-@@ -21,9 +21,9 @@
- 
- #include <boost/utility.hpp>
- #include <boost/function.hpp>
--#include <boost/signals.hpp>
- #include <boost/shared_ptr.hpp>
- 
-+#include <core/BoostSignals.hpp>
- #include <core/HtmlUtils.hpp>
- #include <core/system/System.hpp>
- #include <core/system/ShellUtils.hpp>
-@@ -315,35 +315,35 @@
- // session events
- struct Events : boost::noncopyable
- {
--   boost::signal<void (core::json::Object*)> onSessionInfo;
--   boost::signal<void ()>                    onClientInit;
--   boost::signal<void ()>                    onBeforeExecute;
--   boost::signal<void(const std::string&)>   onConsolePrompt;
--   boost::signal<void(const std::string&)>   onConsoleInput;
--   boost::signal<void(const std::string&, const std::string&)>  
-+   RSTUDIO_BOOST_SIGNAL<void (core::json::Object*)> onSessionInfo;
-+   RSTUDIO_BOOST_SIGNAL<void ()>                    onClientInit;
-+   RSTUDIO_BOOST_SIGNAL<void ()>                    onBeforeExecute;
-+   RSTUDIO_BOOST_SIGNAL<void(const std::string&)>   onConsolePrompt;
-+   RSTUDIO_BOOST_SIGNAL<void(const std::string&)>   onConsoleInput;
-+   RSTUDIO_BOOST_SIGNAL<void(const std::string&, const std::string&)>  
-                                              onActiveConsoleChanged;
--   boost::signal<void (ConsoleOutputType, const std::string&)>
-+   RSTUDIO_BOOST_SIGNAL<void (ConsoleOutputType, const std::string&)>
-                                              onConsoleOutput;
--   boost::signal<void()>                     onUserInterrupt;
--   boost::signal<void (ChangeSource)>        onDetectChanges;
--   boost::signal<void (core::FilePath)>      onSourceEditorFileSaved;
--   boost::signal<void(bool)>                 onDeferredInit;
--   boost::signal<void(bool)>                 afterSessionInitHook;
--   boost::signal<void(bool)>                 onBackgroundProcessing;
--   boost::signal<void(bool)>                 onShutdown;
--   boost::signal<void ()>                    onQuit;
--   boost::signal<void ()>                    onDestroyed;
--   boost::signal<void (const std::vector<std::string>&)>
-+   RSTUDIO_BOOST_SIGNAL<void()>                     onUserInterrupt;
-+   RSTUDIO_BOOST_SIGNAL<void (ChangeSource)>        onDetectChanges;
-+   RSTUDIO_BOOST_SIGNAL<void (core::FilePath)>      onSourceEditorFileSaved;
-+   RSTUDIO_BOOST_SIGNAL<void(bool)>                 onDeferredInit;
-+   RSTUDIO_BOOST_SIGNAL<void(bool)>                 afterSessionInitHook;
-+   RSTUDIO_BOOST_SIGNAL<void(bool)>                 onBackgroundProcessing;
-+   RSTUDIO_BOOST_SIGNAL<void(bool)>                 onShutdown;
-+   RSTUDIO_BOOST_SIGNAL<void ()>                    onQuit;
-+   RSTUDIO_BOOST_SIGNAL<void ()>                    onDestroyed;
-+   RSTUDIO_BOOST_SIGNAL<void (const std::vector<std::string>&)>
-                                              onLibPathsChanged;
--   boost::signal<void (const std::string&)>  onPackageLoaded;
--   boost::signal<void ()>                    onPackageLibraryMutated;
--   boost::signal<void ()>                    onPreferencesSaved;
--   boost::signal<void (const core::DistributedEvent&)>
-+   RSTUDIO_BOOST_SIGNAL<void (const std::string&)>  onPackageLoaded;
-+   RSTUDIO_BOOST_SIGNAL<void ()>                    onPackageLibraryMutated;
-+   RSTUDIO_BOOST_SIGNAL<void ()>                    onPreferencesSaved;
-+   RSTUDIO_BOOST_SIGNAL<void (const core::DistributedEvent&)>
-                                              onDistributedEvent;
--   boost::signal<void (core::FilePath)>      onPermissionsChanged;
-+   RSTUDIO_BOOST_SIGNAL<void (core::FilePath)>      onPermissionsChanged;
- 
-    // signal for detecting extended type of documents
--   boost::signal<std::string(boost::shared_ptr<source_database::SourceDocument>),
-+   RSTUDIO_BOOST_SIGNAL<std::string(boost::shared_ptr<source_database::SourceDocument>),
-                  firstNonEmpty<std::string> > onDetectSourceExtendedType;
- };
- 
---- rstudio-1.1.463-orig/src/cpp/session/include/session/SessionSourceDatabase.hpp	2018-10-25 09:42:55.000000000 +1100
-+++ rstudio-1.1.463/src/cpp/session/include/session/SessionSourceDatabase.hpp	2018-11-17 21:24:35.291976342 +1100
-@@ -21,8 +21,8 @@
- 
- #include <boost/utility.hpp>
- #include <boost/shared_ptr.hpp>
--#include <boost/signals.hpp>
- 
-+#include <core/BoostSignals.hpp>
- #include <core/FilePath.hpp>
- #include <core/json/Json.hpp>
- 
-@@ -204,14 +204,14 @@
- // source database events
- struct Events : boost::noncopyable
- {
--   boost::signal<void(boost::shared_ptr<SourceDocument>)>      onDocUpdated;
--   boost::signal<void(const std::string&,
-+   RSTUDIO_BOOST_SIGNAL<void(boost::shared_ptr<SourceDocument>)>      onDocUpdated;
-+   RSTUDIO_BOOST_SIGNAL<void(const std::string&,
-                       boost::shared_ptr<SourceDocument>)>      onDocRenamed;
--   boost::signal<void(const std::string&)>                     onDocAdded;
--   boost::signal<void(
-+   RSTUDIO_BOOST_SIGNAL<void(const std::string&)>                     onDocAdded;
-+   RSTUDIO_BOOST_SIGNAL<void(
-       boost::shared_ptr<source_database::SourceDocument>)>     onDocPendingRemove;
--   boost::signal<void(const std::string&, const std::string&)> onDocRemoved;
--   boost::signal<void()>                                       onRemoveAll;
-+   RSTUDIO_BOOST_SIGNAL<void(const std::string&, const std::string&)> onDocRemoved;
-+   RSTUDIO_BOOST_SIGNAL<void()>                                       onRemoveAll;
- };
- 
- Events& events();
---- rstudio-1.1.463-orig/src/cpp/session/include/session/SessionUserSettings.hpp	2018-10-25 09:42:55.000000000 +1100
-+++ rstudio-1.1.463/src/cpp/session/include/session/SessionUserSettings.hpp	2018-11-17 21:24:35.291976342 +1100
-@@ -20,8 +20,8 @@
- 
- #include <boost/utility.hpp>
- #include <boost/scoped_ptr.hpp>
--#include <boost/signal.hpp>
- 
-+#include <core/BoostSignals.hpp>
- #include <core/Settings.hpp>
- #include <core/FilePath.hpp>
- #include <core/StringUtils.hpp>
-@@ -62,7 +62,7 @@
-    friend UserSettings& userSettings();
- 
- public:
--   boost::signal<void()> onChanged;
-+   RSTUDIO_BOOST_SIGNAL<void()> onChanged;
- 
- public:
-    // COPYING: boost::noncopyable
---- rstudio-1.1.463-orig/src/cpp/session/include/session/projects/SessionProjects.hpp	2018-10-25 09:42:55.000000000 +1100
-+++ rstudio-1.1.463/src/cpp/session/include/session/projects/SessionProjects.hpp	2018-11-17 21:24:35.291976342 +1100
-@@ -22,8 +22,8 @@
- #include <boost/utility.hpp>
- #include <boost/shared_ptr.hpp>
- #include <boost/foreach.hpp>
--#include <boost/signals.hpp>
- 
-+#include <core/BoostSignals.hpp>
- #include <core/FileInfo.hpp>
- #include <core/FilePath.hpp>
- #include <core/Settings.hpp>
-@@ -220,10 +220,10 @@
- 
-    bool hasFileMonitor_;
-    std::vector<std::string> monitorSubscribers_;
--   boost::signal<void(const tree<core::FileInfo>&)> onMonitoringEnabled_;
--   boost::signal<void(const std::vector<core::system::FileChangeEvent>&)>
-+   RSTUDIO_BOOST_SIGNAL<void(const tree<core::FileInfo>&)> onMonitoringEnabled_;
-+   RSTUDIO_BOOST_SIGNAL<void(const std::vector<core::system::FileChangeEvent>&)>
-                                                             onFilesChanged_;
--   boost::signal<void()> onMonitoringDisabled_;
-+   RSTUDIO_BOOST_SIGNAL<void()> onMonitoringDisabled_;
- };
- 
- ProjectContext& projectContext();

diff --git a/sci-mathematics/rstudio/files/rstudio-1.1.463-boost-1.69.0_p2.patch b/sci-mathematics/rstudio/files/rstudio-1.1.463-boost-1.69.0_p2.patch
deleted file mode 100644
index d90ce005a1a..00000000000
--- a/sci-mathematics/rstudio/files/rstudio-1.1.463-boost-1.69.0_p2.patch
+++ /dev/null
@@ -1,220 +0,0 @@
---- rstudio-1.1.463-orig/src/cpp/session/modules/SessionPlots.hpp	2018-10-25 09:42:55.000000000 +1100
-+++ rstudio-1.1.463/src/cpp/session/modules/SessionPlots.hpp	2018-11-17 21:24:35.292976352 +1100
-@@ -16,7 +16,7 @@
- #ifndef SESSION_PLOTS_HPP
- #define SESSION_PLOTS_HPP
- 
--#include <boost/signals.hpp>
-+#include <core/BoostSignals.hpp>
- 
- namespace rstudio {
- namespace core {
-@@ -35,9 +35,9 @@
- 
- struct Events : boost::noncopyable
- {
--   boost::signal<void()> onBeforeNewPlot;
--   boost::signal<void()> onBeforeNewGridPage;
--   boost::signal<void()> onNewPlot;
-+   RSTUDIO_BOOST_SIGNAL<void()> onBeforeNewPlot;
-+   RSTUDIO_BOOST_SIGNAL<void()> onBeforeNewGridPage;
-+   RSTUDIO_BOOST_SIGNAL<void()> onNewPlot;
- };
- 
- Events& events();
---- rstudio-1.1.463-orig/src/cpp/session/modules/build/SessionSourceCpp.cpp	2018-10-25 09:42:55.000000000 +1100
-+++ rstudio-1.1.463/src/cpp/session/modules/build/SessionSourceCpp.cpp	2018-11-17 21:24:35.293976361 +1100
-@@ -15,11 +15,11 @@
- 
- #include "SessionSourceCpp.hpp"
- 
--#include <boost/signal.hpp>
- #include <boost/algorithm/string/trim.hpp>
- #include <boost/algorithm/string/predicate.hpp>
- #include <boost/algorithm/string/join.hpp>
- 
-+#include <core/BoostSignals.hpp>
- #include <core/Error.hpp>
- #include <core/FilePath.hpp>
- #include <core/StringUtils.hpp>
---- rstudio-1.1.463-orig/src/cpp/session/modules/rmarkdown/NotebookAlternateEngines.cpp	2018-10-25 09:42:55.000000000 +1100
-+++ rstudio-1.1.463/src/cpp/session/modules/rmarkdown/NotebookAlternateEngines.cpp	2018-11-17 21:24:35.294976371 +1100
-@@ -142,7 +142,7 @@
-       LOG_ERROR(error);
-    
-    // capture console output, error
--   boost::signals::scoped_connection consoleHandler =
-+   RSTUDIO_BOOST_SCOPED_CONNECTION consoleHandler =
-          module_context::events().onConsoleOutput.connect(
-             boost::bind(chunkConsoleOutputHandler,
-                         _1,
-@@ -219,7 +219,7 @@
-       LOG_ERROR(error);
-    
-    // capture console output, error
--   boost::signals::scoped_connection consoleHandler =
-+   RSTUDIO_BOOST_SCOPED_CONNECTION consoleHandler =
-          module_context::events().onConsoleOutput.connect(
-             boost::bind(chunkConsoleOutputHandler,
-                         _1,
-@@ -363,7 +363,7 @@
-       LOG_ERROR(error);
-    
-    // capture console output, error
--   boost::signals::scoped_connection consoleHandler =
-+   RSTUDIO_BOOST_SCOPED_CONNECTION consoleHandler =
-          module_context::events().onConsoleOutput.connect(
-             boost::bind(chunkConsoleOutputHandler,
-                         _1,
---- rstudio-1.1.463-orig/src/cpp/session/modules/rmarkdown/NotebookCapture.cpp	2018-10-25 09:42:55.000000000 +1100
-+++ rstudio-1.1.463/src/cpp/session/modules/rmarkdown/NotebookCapture.cpp	2018-11-17 21:24:35.294976371 +1100
-@@ -16,6 +16,8 @@
- #include "SessionRmdNotebook.hpp"
- #include "NotebookCapture.hpp"
- 
-+#include <boost/make_shared.hpp>
-+
- namespace rstudio {
- namespace session {
- namespace modules {
---- rstudio-1.1.463-orig/src/cpp/session/modules/rmarkdown/NotebookExec.cpp	2018-10-25 09:42:55.000000000 +1100
-+++ rstudio-1.1.463/src/cpp/session/modules/rmarkdown/NotebookExec.cpp	2018-11-17 21:24:35.295976381 +1100
-@@ -441,7 +441,7 @@
-    }
- 
-    // unhook all our event handlers
--   BOOST_FOREACH(const boost::signals::connection connection, connections_) 
-+   BOOST_FOREACH(const RSTUDIO_BOOST_CONNECTION connection, connections_) 
-    {
-       connection.disconnect();
-    }
---- rstudio-1.1.463-orig/src/cpp/session/modules/rmarkdown/NotebookExec.hpp	2018-10-25 09:42:55.000000000 +1100
-+++ rstudio-1.1.463/src/cpp/session/modules/rmarkdown/NotebookExec.hpp	2018-11-17 21:24:35.295976381 +1100
-@@ -18,8 +18,7 @@
- 
- #include <session/SessionModuleContext.hpp>
- 
--#include <boost/signal.hpp>
--
-+#include <core/BoostSignals.hpp>
- #include <core/json/Json.hpp>
- 
- #include <r/RSexp.hpp>
-@@ -99,7 +98,7 @@
-    bool hasErrors_;
- 
-    std::vector<boost::shared_ptr<NotebookCapture> > captures_;
--   std::vector<boost::signals::connection> connections_;
-+   std::vector<RSTUDIO_BOOST_CONNECTION> connections_;
- };
- 
- } // namespace notebook
---- rstudio-1.1.463-orig/src/cpp/session/modules/rmarkdown/NotebookPlots.cpp	2018-10-25 09:42:55.000000000 +1100
-+++ rstudio-1.1.463/src/cpp/session/modules/rmarkdown/NotebookPlots.cpp	2018-11-17 21:24:35.295976381 +1100
-@@ -20,11 +20,12 @@
- 
- #include <boost/format.hpp>
- #include <boost/foreach.hpp>
--#include <boost/signals/connection.hpp>
- 
--#include <core/system/FileMonitor.hpp>
--#include <core/StringUtils.hpp>
-+#include <core/BoostSignals.hpp>
- #include <core/Exec.hpp>
-+#include <core/StringUtils.hpp>
-+
-+#include <core/system/FileMonitor.hpp>
- 
- #include <session/SessionModuleContext.hpp>
- 
---- rstudio-1.1.463-orig/src/cpp/session/modules/rmarkdown/NotebookPlots.hpp	2018-10-25 09:42:55.000000000 +1100
-+++ rstudio-1.1.463/src/cpp/session/modules/rmarkdown/NotebookPlots.hpp	2018-11-17 21:24:35.296976391 +1100
-@@ -18,8 +18,10 @@
- #define SESSION_NOTEBOOK_PLOTS_HPP
- 
- #include <boost/function.hpp>
--#include <boost/signals/connection.hpp>
-+
-+#include <core/BoostSignals.hpp>
- #include <core/FilePath.hpp>
-+
- #include <r/RSexp.hpp>
- 
- #include "NotebookCapture.hpp"
-@@ -80,9 +82,9 @@
- 
-    unsigned lastOrdinal_;
- 
--   boost::signals::connection onBeforeNewPlot_;
--   boost::signals::connection onBeforeNewGridPage_;
--   boost::signals::connection onNewPlot_;
-+   RSTUDIO_BOOST_CONNECTION onBeforeNewPlot_;
-+   RSTUDIO_BOOST_CONNECTION onBeforeNewGridPage_;
-+   RSTUDIO_BOOST_CONNECTION onNewPlot_;
- 
-    double width_;
-    double height_;
---- rstudio-1.1.463-orig/src/cpp/session/modules/rmarkdown/NotebookQueue.cpp	2018-10-25 09:42:55.000000000 +1100
-+++ rstudio-1.1.463/src/cpp/session/modules/rmarkdown/NotebookQueue.cpp	2018-11-17 21:24:35.296976391 +1100
-@@ -87,7 +87,7 @@
-       pInput_->enque(kThreadQuitCommand);
- 
-       // unregister handlers
--      BOOST_FOREACH(boost::signals::connection connection, handlers_)
-+      BOOST_FOREACH(RSTUDIO_BOOST_CONNECTION connection, handlers_)
-       {
-          connection.disconnect();
-       }
-@@ -651,7 +651,7 @@
-    boost::shared_ptr<ChunkExecContext> execContext_;
- 
-    // registered signal handlers
--   std::vector<boost::signals::connection> handlers_;
-+   std::vector<RSTUDIO_BOOST_CONNECTION> handlers_;
- 
-    // the thread which submits console input, and the queue which feeds it
-    boost::thread console_;
---- rstudio-1.1.463-orig/src/cpp/session/modules/rmarkdown/SessionRmdNotebook.hpp	2018-10-25 09:42:55.000000000 +1100
-+++ rstudio-1.1.463/src/cpp/session/modules/rmarkdown/SessionRmdNotebook.hpp	2018-11-17 21:24:35.296976391 +1100
-@@ -18,7 +18,8 @@
- #define SESSION_RMARKDOWN_NOTEBOOK_HPP
- 
- #include <ctime>
--#include <boost/signals.hpp>
-+
-+#include <core/BoostSignals.hpp>
- #include <core/json/Json.hpp>
- 
- #define kChunkLibDir "lib"
-@@ -76,24 +77,24 @@
- struct Events : boost::noncopyable
- {
-    // Document {0}, chunk {1} from context id {3} execution completed
--   boost::signal<void(const std::string&, const std::string&,
-+   RSTUDIO_BOOST_SIGNAL<void(const std::string&, const std::string&,
-                       const std::string&)> 
-                 onChunkExecCompleted;
- 
-    // Document {0}, chunk {1} had console output of type {2} and text {3}
--   boost::signal<void(const std::string&, const std::string&, int, 
-+   RSTUDIO_BOOST_SIGNAL<void(const std::string&, const std::string&, int, 
-                 const std::string&)>
-                 onChunkConsoleOutput;
- 
--   boost::signal<void(const core::FilePath&, const core::FilePath&, 
-+   RSTUDIO_BOOST_SIGNAL<void(const core::FilePath&, const core::FilePath&, 
-                       const core::json::Value& metadata, unsigned ordinal)> 
-                          onPlotOutput;
--   boost::signal<void(const core::FilePath&, const core::FilePath&,
-+   RSTUDIO_BOOST_SIGNAL<void(const core::FilePath&, const core::FilePath&,
-                       const core::json::Value& metadata)> onHtmlOutput;
--   boost::signal<void(const core::json::Object&)> onErrorOutput;
--   boost::signal<void(const core::FilePath&, const core::FilePath&,
-+   RSTUDIO_BOOST_SIGNAL<void(const core::json::Object&)> onErrorOutput;
-+   RSTUDIO_BOOST_SIGNAL<void(const core::FilePath&, const core::FilePath&,
-                       const core::json::Value& metadata)> onDataOutput;
--   boost::signal<void(Condition condition, const std::string& message)> 
-+   RSTUDIO_BOOST_SIGNAL<void(Condition condition, const std::string& message)> 
-                          onCondition;
- };
- 

diff --git a/sci-mathematics/rstudio/files/rstudio-1.1.463-boost-1.69.0_p3.patch b/sci-mathematics/rstudio/files/rstudio-1.1.463-boost-1.69.0_p3.patch
deleted file mode 100644
index 961723fd224..00000000000
--- a/sci-mathematics/rstudio/files/rstudio-1.1.463-boost-1.69.0_p3.patch
+++ /dev/null
@@ -1,167 +0,0 @@
---- rstudio-1.1.463-orig/src/cpp/CMakeLists.txt	2018-11-17 21:24:35.285976284 +1100
-+++ rstudio-1.1.463/src/cpp/CMakeLists.txt	2018-11-17 21:41:02.712507842 +1100
-@@ -175,6 +175,9 @@
-       set(Boost_USE_STATIC_LIBS ON)
-       set(BOOST_INCLUDEDIR  ${RSTUDIO_TOOLS_BOOST}/include)
-       find_package(Boost ${BOOST_VERSION} REQUIRED)
-+      if(NOT Boost_VERSION VERSION_LESS 1.69.0)
-+         list(REMOVE_ITEM BOOST_LIBS signals)
-+      endif()
- 
-       # define library list manually (find_package doesn't always pick them up)
-       set(BOOST_LIB_DIR ${RSTUDIO_TOOLS_BOOST}/lib)
-@@ -184,11 +187,15 @@
-       message(STATUS "Using RStudio-provided Boost ${BOOST_VERSION}")
-    else()
-       add_definitions(-DRSTUDIO_BOOST_NAMESPACE=boost)
-+      find_package(Boost ${BOOST_VERSION} REQUIRED)
-+      if(NOT Boost_VERSION VERSION_LESS 1.69.0)
-+         list(REMOVE_ITEM BOOST_LIBS signals)
-+      endif()
-       find_package(Boost ${BOOST_VERSION} REQUIRED COMPONENTS ${BOOST_LIBS})
-       message(STATUS "Using system Boost ${BOOST_VERSION}")
-    endif()
- 
--   # WIN32 BOOST
-+# WIN32 BOOST
- else()
-    # hard-code to our own prebuilt boost libs
-    add_definitions(-DRSTUDIO_BOOST_NAMESPACE=rstudio_boost)
-@@ -211,14 +218,14 @@
- # allow opt-in to using Boost.Signals2
- # TODO: remove this in RStudio v1.3 and port to signals2
- if(NOT RSTUDIO_BOOST_SIGNALS_VERSION)
--   if (BOOST_VERSION VERSION_LESS 1.69.0)
-+   if (Boost_VERSION VERSION_LESS 1.69.0)
-       set(RSTUDIO_BOOST_SIGNALS_VERSION 1)
-    else()
-       set(RSTUDIO_BOOST_SIGNALS_VERSION 2)
-    endif()
- endif()
- 
--message(STATUS "Using Booost.Signals version ${RSTUDIO_BOOST_SIGNALS_VERSION}")
-+message(STATUS "Using Boost.Signals version ${RSTUDIO_BOOST_SIGNALS_VERSION}")
- add_definitions(-DRSTUDIO_BOOST_SIGNALS_VERSION=${RSTUDIO_BOOST_SIGNALS_VERSION})
- 
- # add boost as system include directory
---- rstudio-1.1.463-orig/src/cpp/core/include/core/r_util/RFunctionInformation.hpp	2018-10-25 09:42:55.000000000 +1100
-+++ rstudio-1.1.463/src/cpp/core/include/core/r_util/RFunctionInformation.hpp	2018-11-17 21:41:02.713507852 +1100
-@@ -75,9 +75,9 @@
-    const std::string& name() const { return name_; }
-    const boost::optional<std::string>& defaultValue() const { return defaultValue_; }
-    boost::tribool hasDefault() const { return hasDefault_; }
--   bool isUsed() const { return isUsed_; }
-+   bool isUsed() const { return bool(isUsed_); }
-    void setIsUsed(bool value) { isUsed_ = value; }
--   bool isMissingnessHandled() const { return isMissingnessHandled_; }
-+   bool isMissingnessHandled() const { return bool(isMissingnessHandled_); }
-    void setMissingnessHandled(bool value) { isMissingnessHandled_ = value; }
-    
- private:
-@@ -130,7 +130,7 @@
-    
-    bool isPrimitive()
-    {
--      return isPrimitive_ == true;
-+      return bool(isPrimitive_);
-    }
-    
-    void setIsPrimitive(bool isPrimitive)
---- rstudio-1.1.463-orig/src/cpp/session/modules/SessionRParser.cpp	2018-10-25 09:42:55.000000000 +1100
-+++ rstudio-1.1.463/src/cpp/session/modules/SessionRParser.cpp	2018-11-17 21:41:02.714507862 +1100
-@@ -390,7 +390,7 @@
-    if (!failed)
-    {
-       DEBUG("--- Found function in pkgInfo index: " << *fnInfo.binding());
--      return fnInfo.performsNse();
-+      return bool(fnInfo.performsNse());
-    }
-    
-    // Handle some special cases first.
---- rstudio-1.1.463-orig/src/tools/clang-ubsan-build	2018-10-25 09:42:55.000000000 +1100
-+++ rstudio-1.1.463/src/tools/clang-ubsan-build	2018-11-17 21:41:02.714507862 +1100
-@@ -10,19 +10,19 @@
- 
- : ${RSTUDIO_USE_LIBCXX="Yes"}
- : ${RSTUDIO_USE_SYSTEM_BOOST="Yes"}
--: ${RSTUDIO_BOOST_VERSION="1.56.0"}
-+: ${RSTUDIO_BOOST_REQUESTED_VERSION="1.56.0"}
- 
- mkdir -p "${BUILD_DIR}"
- cd "${BUILD_DIR}"
--cmake ../cpp                                                 \
--    -DLIBR_HOME="${R_HOME}"                                  \
--    -DCMAKE_C_COMPILER="${CC}"                               \
--    -DCMAKE_C_FLAGS="${ASANFLAGS} ${LDFLAGS}"                \
--    -DCMAKE_CXX_COMPILER="${CXX}"                            \
--    -DCMAKE_CXX_FLAGS="${ASANFLAGS} ${LDFLAGS}"              \
--    -DRSTUDIO_USE_LIBCXX="${RSTUDIO_USE_LIBCXX}"             \
--    -DRSTUDIO_USE_SYSTEM_BOOST="${RSTUDIO_USE_SYSTEM_BOOST}" \
--    -DRSTUDIO_BOOST_VERSION="${RSTUDIO_BOOST_VERSION}"       \
-+cmake ../cpp                                                               \
-+    -DLIBR_HOME="${R_HOME}"                                                \
-+    -DCMAKE_C_COMPILER="${CC}"                                             \
-+    -DCMAKE_C_FLAGS="${ASANFLAGS} ${LDFLAGS}"                              \
-+    -DCMAKE_CXX_COMPILER="${CXX}"                                          \
-+    -DCMAKE_CXX_FLAGS="${ASANFLAGS} ${LDFLAGS}"                            \
-+    -DRSTUDIO_USE_LIBCXX="${RSTUDIO_USE_LIBCXX}"                           \
-+    -DRSTUDIO_USE_SYSTEM_BOOST="${RSTUDIO_USE_SYSTEM_BOOST}"               \
-+    -DRSTUDIO_BOOST_REQUESTED_VERSION="${RSTUDIO_BOOST_REQUESTED_VERSION}" \
-     "$@"
- cd ..
- 
---- rstudio-1.1.463-orig/src/tools/gcc-ubsan-build	2018-10-25 09:42:55.000000000 +1100
-+++ rstudio-1.1.463/src/tools/gcc-ubsan-build	2018-11-17 21:41:02.715507871 +1100
-@@ -19,19 +19,19 @@
- # NOTE: Boost 1.50.0 not compatible with gcc-6
- : ${RSTUDIO_USE_LIBCXX="No"}
- : ${RSTUDIO_USE_SYSTEM_BOOST="Yes"}
--: ${RSTUDIO_BOOST_VERSION="1.54.0"}
-+: ${RSTUDIO_BOOST_REQUESTED_VERSION="1.54.0"}
- 
- mkdir -p "${BUILD_DIR}"
- cd "${BUILD_DIR}"
--cmake ../cpp                                                 \
--    -DLIBR_HOME="${R_HOME}"                                  \
--    -DCMAKE_C_COMPILER="${CC}"                               \
--    -DCMAKE_C_FLAGS="${ASANFLAGS} ${LDFLAGS}"                \
--    -DCMAKE_CXX_COMPILER="${CXX}"                            \
--    -DCMAKE_CXX_FLAGS="${ASANFLAGS} ${LDFLAGS}"              \
--    -DRSTUDIO_USE_LIBCXX="${RSTUDIO_USE_LIBCXX}"             \
--    -DRSTUDIO_USE_SYSTEM_BOOST="${RSTUDIO_USE_SYSTEM_BOOST}" \
--    -DRSTUDIO_BOOST_VERSION="${RSTUDIO_BOOST_VERSION}"       \
-+cmake ../cpp                                                               \
-+    -DLIBR_HOME="${R_HOME}"                                                \
-+    -DCMAKE_C_COMPILER="${CC}"                                             \
-+    -DCMAKE_C_FLAGS="${ASANFLAGS} ${LDFLAGS}"                              \
-+    -DCMAKE_CXX_COMPILER="${CXX}"                                          \
-+    -DCMAKE_CXX_FLAGS="${ASANFLAGS} ${LDFLAGS}"                            \
-+    -DRSTUDIO_USE_LIBCXX="${RSTUDIO_USE_LIBCXX}"                           \
-+    -DRSTUDIO_USE_SYSTEM_BOOST="${RSTUDIO_USE_SYSTEM_BOOST}"               \
-+    -DRSTUDIO_BOOST_REQUESTED_VERSION="${RSTUDIO_BOOST_REQUESTED_VERSION}" \
-     "$@"
- cd ..
- 
---- rstudio-1.1.463-orig/src/tools/xcode-ubsan-build	2018-10-25 09:42:55.000000000 +1100
-+++ rstudio-1.1.463/src/tools/xcode-ubsan-build	2018-11-17 21:41:02.715507871 +1100
-@@ -15,13 +15,13 @@
- # sanitizers released with newer versions of clang)
- mkdir -p "${BUILD_DIR}"
- cd "${BUILD_DIR}"
--cmake ../cpp -GXcode                 \
--    -DLIBR_HOME="${R_HOME}"          \
--    -DLIBR_INCLUDE_DIRS="${R_INCL}"  \
--    -DLIBR_DOC_DIR="${R_DOCS}"       \
--    -DRSTUDIO_USE_LIBCXX="Yes"       \
--    -DRSTUDIO_USE_SYSTEM_BOOST="Yes" \
--    -DRSTUDIO_BOOST_VERSION="1.56.0" \
-+cmake ../cpp -GXcode                           \
-+    -DLIBR_HOME="${R_HOME}"                    \
-+    -DLIBR_INCLUDE_DIRS="${R_INCL}"            \
-+    -DLIBR_DOC_DIR="${R_DOCS}"                 \
-+    -DRSTUDIO_USE_LIBCXX="Yes"                 \
-+    -DRSTUDIO_USE_SYSTEM_BOOST="Yes"           \
-+    -DRSTUDIO_BOOST_REQUESTED_VERSION="1.56.0" \
-     "$@"
- cmake ../cpp -DLIBR_LIBRARIES="${R_LIBS}/libR.dylib"
- cd ..

diff --git a/sci-mathematics/rstudio/files/rstudio-1.1.463-boost-1.70.0.patch b/sci-mathematics/rstudio/files/rstudio-1.1.463-boost-1.70.0.patch
deleted file mode 100644
index 320b823355a..00000000000
--- a/sci-mathematics/rstudio/files/rstudio-1.1.463-boost-1.70.0.patch
+++ /dev/null
@@ -1,46 +0,0 @@
---- rstudio-1.1.463-orig/src/cpp/ext/websocketpp/transport/asio/connection.hpp	2018-10-25 09:42:55.000000000 +1100
-+++ rstudio-1.1.463/src/cpp/ext/websocketpp/transport/asio/connection.hpp	2019-03-30 20:14:40.634057634 +1100
-@@ -296,7 +296,11 @@
-      */
-     timer_ptr set_timer(long duration, timer_handler callback) {
-         timer_ptr new_timer = lib::make_shared<boost::asio::deadline_timer>(
-+#if defined(BOOST_VERSION) && BOOST_VERSION >= 107000
-+            *m_io_service,
-+#else
-             lib::ref(*m_io_service),
-+#endif
-             boost::posix_time::milliseconds(duration)
-         );
- 
---- rstudio-1.1.463-orig/src/cpp/ext/websocketpp/transport/asio/endpoint.hpp	2018-10-25 09:42:55.000000000 +1100
-+++ rstudio-1.1.463/src/cpp/ext/websocketpp/transport/asio/endpoint.hpp	2019-03-30 20:14:36.319021594 +1100
-@@ -184,7 +184,12 @@
-         m_io_service = ptr;
-         m_external_io_service = true;
-         m_acceptor = lib::make_shared<boost::asio::ip::tcp::acceptor>(
--            lib::ref(*m_io_service));
-+#if defined(BOOST_VERSION) && BOOST_VERSION >= 107000
-+            *m_io_service
-+#else
-+            lib::ref(*m_io_service)
-+#endif
-+        );
- 
-         m_state = READY;
-         ec = lib::error_code();
---- rstudio-1.1.463-orig/src/cpp/ext/websocketpp/transport/asio/security/none.hpp	2018-10-25 09:42:55.000000000 +1100
-+++ rstudio-1.1.463/src/cpp/ext/websocketpp/transport/asio/security/none.hpp	2019-03-30 20:15:22.353406097 +1100
-@@ -167,7 +167,12 @@
-         }
- 
-         m_socket = lib::make_shared<boost::asio::ip::tcp::socket>(
--            lib::ref(*service));
-+#if defined(BOOST_VERSION) && BOOST_VERSION >= 107000
-+            *service
-+#else
-+            lib::ref(*service)
-+#endif
-+        );
- 
-         m_state = READY;
- 

diff --git a/sci-mathematics/rstudio/files/rstudio-1.1.463-fix-ptr-int-compare.patch b/sci-mathematics/rstudio/files/rstudio-1.1.463-fix-ptr-int-compare.patch
deleted file mode 100644
index 914cd942e8f..00000000000
--- a/sci-mathematics/rstudio/files/rstudio-1.1.463-fix-ptr-int-compare.patch
+++ /dev/null
@@ -1,13 +0,0 @@
---- rstudio-1.1.463-orig/src/cpp/server/ServerSecureKeyFile.cpp	2018-10-25 09:42:55.000000000 +1100
-+++ rstudio-1.1.463/src/cpp/server/ServerSecureKeyFile.cpp	2018-11-17 22:17:18.110012955 +1100
-@@ -79,8 +79,8 @@
-          return error;
- 
-       // change mode it so it is only readable and writeable by this user
--      if (changeFileMode(secureKeyPath,
--                         core::system::UserReadWriteMode) < 0)
-+      if (!!changeFileMode(secureKeyPath,
-+                           core::system::UserReadWriteMode))
-       {
-          return systemError(errno, ERROR_LOCATION);
-       }

diff --git a/sci-mathematics/rstudio/files/rstudio-1.2.1335-boost-1.72-filesystem.patch b/sci-mathematics/rstudio/files/rstudio-1.2.1335-boost-1.72-filesystem.patch
deleted file mode 100644
index b2c4d2392f6..00000000000
--- a/sci-mathematics/rstudio/files/rstudio-1.2.1335-boost-1.72-filesystem.patch
+++ /dev/null
@@ -1,31 +0,0 @@
-From a11d0454e5fe9c50005a03b9d9de84355df5c7fd Mon Sep 17 00:00:00 2001
-From: Kevin Ushey <kevinushey@gmail.com>
-Date: Fri, 15 Nov 2019 14:54:02 -0800
-Subject: [PATCH] avoid use of deprecated APIs
-
----
- src/cpp/core/FilePath.cpp | 4 +---
- 1 file changed, 1 insertion(+), 3 deletions(-)
-
-diff --git a/src/cpp/shared_core/FilePath.cpp b/src/cpp/shared_core/FilePath.cpp
-index 088366a9d6..495289e7fc 100644
---- a/src/cpp/core/FilePath.cpp
-+++ b/src/cpp/core/FilePath.cpp
-@@ -22,8 +22,6 @@
- #include <windows.h>
- #endif
- 
--#define BOOST_FILESYSTEM_NO_DEPRECATED
--
- #define BOOST_NO_CXX11_SCOPED_ENUMS
- #include <boost/filesystem.hpp>
- #undef BOOST_NO_CXX11_SCOPED_ENUMS
-@@ -1032,7 +1030,7 @@
-       {
-          // NOTE: The path gets round-tripped through toString/fromString, would
-          //   be nice to have a direct constructor
--         if (!iterationFunction(itr.level(),
-+         if (!iterationFunction(itr.depth(),
-                                 FilePath(BOOST_FS_PATH2STR(itr->path()))))
-          {
-             // end the iteration if requested

diff --git a/sci-mathematics/rstudio/files/rstudio-1.2.1335-fix-ptr-int-compare.patch b/sci-mathematics/rstudio/files/rstudio-1.2.1335-fix-ptr-int-compare.patch
deleted file mode 100644
index e38f5e0c444..00000000000
--- a/sci-mathematics/rstudio/files/rstudio-1.2.1335-fix-ptr-int-compare.patch
+++ /dev/null
@@ -1,13 +0,0 @@
---- rstudio-1.2.1335-orig/src/cpp/server_core/SecureKeyFile.cpp	2019-03-28 16:08:20.000000000 +1100
-+++ rstudio-1.2.1335/src/cpp/server_core/SecureKeyFile.cpp	2019-04-09 20:47:57.943317208 +1000
-@@ -68,8 +68,8 @@
-          return error;
- 
-       // change mode it so it is only readable and writeable by this user
--      if (changeFileMode(secureKeyPath,
--                         core::system::UserReadWriteMode) < 0)
-+      if (!!changeFileMode(secureKeyPath,
-+                           core::system::UserReadWriteMode))
-       {
-          return systemError(errno, ERROR_LOCATION);
-       }

diff --git a/sci-mathematics/rstudio/files/rstudio-1.2.1335-pandoc.patch b/sci-mathematics/rstudio/files/rstudio-1.2.1335-pandoc.patch
deleted file mode 100644
index e2fe83867bc..00000000000
--- a/sci-mathematics/rstudio/files/rstudio-1.2.1335-pandoc.patch
+++ /dev/null
@@ -1,32 +0,0 @@
---- rstudio-1.2.1335-orig/src/cpp/session/CMakeLists.txt	2019-03-28 16:08:20.000000000 +1100
-+++ rstudio-1.2.1335/src/cpp/session/CMakeLists.txt	2019-04-09 17:22:59.210201624 +1000
-@@ -25,9 +25,6 @@
- if(NOT EXISTS "${RSTUDIO_DEPENDENCIES_DIR}/common/mathjax-26")
-   message(FATAL_ERROR "Mathjax 2.6 not found (re-run install-dependencies script to install)")
- endif()
--if(NOT EXISTS "${RSTUDIO_DEPENDENCIES_DIR}/common/pandoc")
--  message(FATAL_ERROR "pandoc not found (re-run install-dependencies script to install)")
--endif()
- 
- # we often install embedded versions of these packages but don't do so currently
- 
-@@ -479,19 +476,6 @@
- install(DIRECTORY "resources/connections"
-         DESTINATION ${RSTUDIO_INSTALL_SUPPORTING}/resources)
- 
--# install pandoc
--if(WIN32)
--   set(PANDOC_VERSION "2.6" CACHE INTERNAL "Pandoc version")
--else()
--   set(PANDOC_VERSION "2.3.1" CACHE INTERNAL "Pandoc version")
--endif()
--
--set(PANDOC_BIN "${RSTUDIO_DEPENDENCIES_DIR}/common/pandoc/${PANDOC_VERSION}")
--file(GLOB PANDOC_FILES "${PANDOC_BIN}/pandoc*")
--install(FILES ${PANDOC_FILES}
--        PERMISSIONS OWNER_READ OWNER_WRITE OWNER_EXECUTE GROUP_READ GROUP_EXECUTE WORLD_READ WORLD_EXECUTE
--        DESTINATION  ${RSTUDIO_INSTALL_BIN}/pandoc)
--
- # install rmarkdown package
- # file(GLOB RMARKDOWN_PACKAGE "${RSTUDIO_DEPENDENCIES_DIR}/common/rmarkdown*.tar.gz")
- # install(FILES ${RMARKDOWN_PACKAGE}

diff --git a/sci-mathematics/rstudio/files/rstudio-1.2.1335-paths.patch b/sci-mathematics/rstudio/files/rstudio-1.2.1335-paths.patch
deleted file mode 100644
index ba66ef9f0ea..00000000000
--- a/sci-mathematics/rstudio/files/rstudio-1.2.1335-paths.patch
+++ /dev/null
@@ -1,118 +0,0 @@
---- rstudio-1.2.1335-orig/CMakeGlobals.txt	2019-03-28 16:08:20.000000000 +1100
-+++ rstudio-1.2.1335/CMakeGlobals.txt	2019-04-09 17:10:07.680657631 +1000
-@@ -161,7 +161,7 @@
-    set(RSTUDIO_INSTALL_SUPPORTING RStudio.app/Contents/Resources)
- else()
-    set(RSTUDIO_INSTALL_BIN bin)
--   set(RSTUDIO_INSTALL_SUPPORTING .)
-+   set(RSTUDIO_INSTALL_SUPPORTING ${DISTRO_SHARE})
- endif()
- 
- # if the install prefix is /usr/local then tweak as appropriate
---- rstudio-1.2.1335-orig/src/cpp/server/CMakeLists.txt	2019-03-28 16:08:20.000000000 +1100
-+++ rstudio-1.2.1335/src/cpp/server/CMakeLists.txt	2019-04-09 16:54:34.740739744 +1000
-@@ -194,7 +194,7 @@
-    configure_file(${CMAKE_CURRENT_SOURCE_DIR}/${RSERVER_INITD_DEBIAN_SCRIPT}.in
-                   ${CMAKE_CURRENT_BINARY_DIR}/${RSERVER_INITD_DEBIAN_SCRIPT})
-    install(PROGRAMS ${CMAKE_CURRENT_BINARY_DIR}/${RSERVER_INITD_DEBIAN_SCRIPT}
--           DESTINATION ${RSERVER_INITD_DEBIAN_DIR})
-+           DESTINATION ${DISTRO_SHARE}/${RSERVER_INITD_DEBIAN_DIR})
- 
-    # install configured redhat init.d script
-    set(RSERVER_INITD_REDHAT_DIR "extras/init.d/redhat")
-@@ -202,7 +202,7 @@
-    configure_file(${CMAKE_CURRENT_SOURCE_DIR}/${RSERVER_INITD_REDHAT_SCRIPT}.in
-                   ${CMAKE_CURRENT_BINARY_DIR}/${RSERVER_INITD_REDHAT_SCRIPT})
-    install(PROGRAMS ${CMAKE_CURRENT_BINARY_DIR}/${RSERVER_INITD_REDHAT_SCRIPT}
--           DESTINATION ${RSERVER_INITD_REDHAT_DIR})
-+           DESTINATION ${DISTRO_SHARE}/${RSERVER_INITD_REDHAT_DIR})
- 
-    # install configured suse init.d script
-    set(RSERVER_INITD_SUSE_DIR "extras/init.d/suse")
-@@ -210,13 +210,13 @@
-    configure_file(${CMAKE_CURRENT_SOURCE_DIR}/${RSERVER_INITD_SUSE_SCRIPT}.in
-                   ${CMAKE_CURRENT_BINARY_DIR}/${RSERVER_INITD_SUSE_SCRIPT})
-    install(PROGRAMS ${CMAKE_CURRENT_BINARY_DIR}/${RSERVER_INITD_SUSE_SCRIPT}
--           DESTINATION ${RSERVER_INITD_SUSE_DIR})
-+           DESTINATION ${DISTRO_SHARE}/${RSERVER_INITD_SUSE_DIR})
- 
-    # install pam profile
-    set(RSERVER_PAM_DIR "extras/pam")
-    set(RSERVER_PAM_PROFILE "${RSERVER_PAM_DIR}/rstudio")
-    install(FILES ${CMAKE_CURRENT_SOURCE_DIR}/${RSERVER_PAM_PROFILE}
--           DESTINATION ${RSERVER_PAM_DIR})
-+           DESTINATION ${DISTRO_SHARE}/${RSERVER_PAM_DIR})
- 
-    # install configured upstart profile
-    set(RSERVER_UPSTART_DIR "extras/upstart")
-@@ -224,12 +224,12 @@
-    configure_file(${CMAKE_CURRENT_SOURCE_DIR}/${RSERVER_UPSTART_PROFILE}.in
-                   ${CMAKE_CURRENT_BINARY_DIR}/${RSERVER_UPSTART_PROFILE})
-    install(FILES ${CMAKE_CURRENT_BINARY_DIR}/${RSERVER_UPSTART_PROFILE}
--           DESTINATION ${RSERVER_UPSTART_DIR})
-+           DESTINATION ${DISTRO_SHARE}/${RSERVER_UPSTART_DIR})
-    set(RSERVER_UPSTART_PROFILE_REDHAT "${RSERVER_UPSTART_DIR}/rstudio-server.redhat.conf")
-    configure_file(${CMAKE_CURRENT_SOURCE_DIR}/${RSERVER_UPSTART_PROFILE_REDHAT}.in
-                   ${CMAKE_CURRENT_BINARY_DIR}/${RSERVER_UPSTART_PROFILE_REDHAT})
-    install(FILES ${CMAKE_CURRENT_BINARY_DIR}/${RSERVER_UPSTART_PROFILE_REDHAT}
--           DESTINATION ${RSERVER_UPSTART_DIR})
-+           DESTINATION ${DISTRO_SHARE}/${RSERVER_UPSTART_DIR})
- 
-     # install configured systemd profile
-    set(RSERVER_SYSTEMD_DIR "extras/systemd")
---- rstudio-1.2.1335-orig/src/cpp/server/ServerOptions.cpp	2019-03-28 16:08:20.000000000 +1100
-+++ rstudio-1.2.1335/src/cpp/server/ServerOptions.cpp	2019-04-09 16:54:34.740739744 +1000
-@@ -389,8 +389,8 @@
- 
-    // convert relative paths by completing from the system installation
-    // path (this allows us to be relocatable)
--   resolvePath(resourcePath, &wwwLocalPath_);
--   resolvePath(resourcePath, &wwwSymbolMapsPath_);
-+   resolvePath(resourcePath.childPath(DISTRO_SHARE), &wwwLocalPath_);
-+   resolvePath(resourcePath.childPath(DISTRO_SHARE), &wwwSymbolMapsPath_);
-    resolvePath(binaryPath, &authPamHelperPath_);
-    resolvePath(binaryPath, &rsessionPath_);
-    resolvePath(binaryPath, &rldpathPath_);
---- rstudio-1.2.1335-orig/src/cpp/session/SessionOptions.cpp	2019-03-28 16:08:20.000000000 +1100
-+++ rstudio-1.2.1335/src/cpp/session/SessionOptions.cpp	2019-04-09 17:17:06.035206050 +1000
-@@ -53,7 +53,7 @@
- namespace session {  
- 
- namespace {
--const char* const kDefaultPandocPath = "bin/pandoc";
-+const char* const kDefaultPandocPath = "bin";
- const char* const kDefaultPostbackPath = "bin/postback/rpostback";
- const char* const kDefaultRsclangPath = "bin/rsclang";
- 
-@@ -569,14 +569,14 @@
-    }
-    
-    // convert relative paths by completing from the app resource path
--   resolvePath(resourcePath_, &rResourcesPath_);
--   resolvePath(resourcePath_, &agreementFilePath_);
--   resolvePath(resourcePath_, &wwwLocalPath_);
--   resolvePath(resourcePath_, &wwwSymbolMapsPath_);
--   resolvePath(resourcePath_, &coreRSourcePath_);
--   resolvePath(resourcePath_, &modulesRSourcePath_);
--   resolvePath(resourcePath_, &sessionLibraryPath_);
--   resolvePath(resourcePath_, &sessionPackageArchivesPath_);
-+   resolvePath(resourcePath_.childPath(DISTRO_SHARE), &rResourcesPath_);
-+   resolvePath(resourcePath_.childPath(DISTRO_SHARE), &agreementFilePath_);
-+   resolvePath(resourcePath_.childPath(DISTRO_SHARE), &wwwLocalPath_);
-+   resolvePath(resourcePath_.childPath(DISTRO_SHARE), &wwwSymbolMapsPath_);
-+   resolvePath(resourcePath_.childPath(DISTRO_SHARE), &coreRSourcePath_);
-+   resolvePath(resourcePath_.childPath(DISTRO_SHARE), &modulesRSourcePath_);
-+   resolvePath(resourcePath_.childPath(DISTRO_SHARE), &sessionLibraryPath_);
-+   resolvePath(resourcePath_.childPath(DISTRO_SHARE), &sessionPackageArchivesPath_);
-    resolvePostbackPath(resourcePath_, &rpostbackPath_);
- #ifdef _WIN32
-    resolvePath(resourcePath_, &consoleIoPath_);
-@@ -601,7 +601,7 @@
-    }
-    winptyPath_ = pty.complete(completion).absolutePath();
- #endif // _WIN32
--   resolvePath(resourcePath_, &hunspellDictionariesPath_);
-+   resolvePath(resourcePath_.childPath(DISTRO_SHARE), &hunspellDictionariesPath_);
-    resolvePath(resourcePath_, &mathjaxPath_);
-    resolvePath(resourcePath_, &libclangHeadersPath_);
-    resolvePandocPath(resourcePath_, &pandocPath_);

diff --git a/sci-mathematics/rstudio/files/rstudio-1.2.1335-prefs.patch b/sci-mathematics/rstudio/files/rstudio-1.2.1335-prefs.patch
deleted file mode 100644
index e72df553eeb..00000000000
--- a/sci-mathematics/rstudio/files/rstudio-1.2.1335-prefs.patch
+++ /dev/null
@@ -1,53 +0,0 @@
---- rstudio-1.2.1335-orig/src/gwt/build.xml	2019-03-28 16:08:20.000000000 +1100
-+++ rstudio-1.2.1335/src/gwt/build.xml	2019-04-09 16:44:15.089471934 +1000
-@@ -34,6 +34,7 @@
-    <property name="gwt.extra.args" value=""/>
-    <property name="gwt.main.module" value="org.rstudio.studio.RStudio"/>
-    <property name="ace.bin" value="${src.dir}/org/rstudio/studio/client/workbench/views/source/editors/text/ace"/>
-+   <property environment="env"/>
- 
-    <path id="project.class.path">
-      <pathelement location="${build.dir}"/>
-@@ -112,8 +113,10 @@
-             <pathelement location="${src.dir}"/>
-             <path refid="project.class.path"/>
-          </classpath>
-+         <jvmarg value="-Duser.home=${env.T}"/>
-          <!-- add jvmarg -Xss16M or similar if you see a StackOverflowError -->
-          <jvmarg value="-Xmx1536M"/>
-+         <jvmarg value="-Djava.util.prefs.userRoot=${env.T}"/>
-          <arg value="-war"/>
-          <arg value="${www.dir}"/>
-          <arg value="-localWorkers"/>
-@@ -154,6 +157,7 @@
-             <pathelement location="${src.dir}"/>
-             <path refid="project.class.path"/>
-          </classpath>
-+         <jvmarg value="-Duser.home=${env.T}"/>
-          <jvmarg value="-Xmx2048M"/>
-          <arg value="-style"/>
-          <arg value="PRETTY"/>
-@@ -176,6 +180,7 @@
-             <pathelement location="src"/>
-             <path refid="project.class.path"/>
-          </classpath>
-+         <jvmarg value="-Duser.home=${env.T}"/>
-          <jvmarg value="-Xmx2048M"/>
-          <arg value="-style"/>
-          <arg value="PRETTY"/>
-@@ -202,6 +207,7 @@
-             <pathelement location="src"/>
-             <path refid="project.class.path"/>
-          </classpath>
-+         <jvmarg value="-Duser.home=${env.T}"/>
-          <jvmarg value="-Xmx2048M"/>
-       	<arg value="-src"/>
-       	<arg value = "src"/>
-@@ -237,6 +243,7 @@
-             <pathelement location="${test.dir}"/>
-             <pathelement location="${src.dir}"/>
-         </classpath>
-+        <jvmarg value="-Duser.home=${env.T}"/>
-         <classpath refid="project.class.path"/>
-         <classpath refid="unittest.class.path"/>
-         <arg value="org.rstudio.studio.client.RStudioUnitTestSuite"/>

diff --git a/sci-mathematics/rstudio/rstudio-1.1.463-r1.ebuild b/sci-mathematics/rstudio/rstudio-1.1.463-r1.ebuild
deleted file mode 100644
index 8b60b2efe5b..00000000000
--- a/sci-mathematics/rstudio/rstudio-1.1.463-r1.ebuild
+++ /dev/null
@@ -1,255 +0,0 @@
-# Copyright 1999-2020 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-inherit eutils user cmake-utils gnome2-utils pam xdg-utils java-pkg-2 pax-utils qmake-utils vcs-clean
-
-# TODO
-# * package gin and gwt
-# * use dict from tree, linguas
-# * do src_test (use junit from tree?)
-
-# update from scripts in dependencies/common
-# egrep '(GWT_SDK_VER=|GIN_VER=|SELENIUM_VER=|CHROMEDRIVER_VER=)' dependencies/common/install-gwt
-GWT_VER=2.7.0
-GIN_VER=1.5
-SELENIUM_VER=2.37.0
-CHROMEDRIVER_VER=2.7
-# grep 'PANDOC_VERSION=' dependencies/common/install-pandoc
-PANDOC_VER=1.19.2.1
-# ls dependencies/common/*.tar.gz
-PACKRAT_VER=0.98.1000
-RMARKDOWN_VER=0.98.1000
-SHINYAPPS_VER=0.98.1000
-RSCONNECT_VER=0.4.1.4_fcac892a69817febd7b655b189bf57193260cda0
-
-DESCRIPTION="IDE for the R language"
-HOMEPAGE="
-	http://www.rstudio.org
-	https://github.com/rstudio/rstudio/"
-SRC_URI="
-	https://github.com/rstudio/rstudio/archive/v${PV}.tar.gz -> ${P}.tar.gz
-	https://s3.amazonaws.com/rstudio-buildtools/gin-${GIN_VER}.zip
-	https://s3.amazonaws.com/rstudio-buildtools/gwt-${GWT_VER}.zip
-	https://s3.amazonaws.com/rstudio-buildtools/selenium-java-${SELENIUM_VER}.zip
-	https://s3.amazonaws.com/rstudio-buildtools/selenium-server-standalone-${SELENIUM_VER}.jar
-	https://s3.amazonaws.com/rstudio-buildtools/chromedriver-linux
-	https://s3.amazonaws.com/rstudio-dictionaries/core-dictionaries.zip
-	https://dev.gentoo.org/~gienah/distfiles/packrat-${PACKRAT_VER}.tar.gz
-	https://dev.gentoo.org/~gienah/distfiles/rmarkdown-${RMARKDOWN_VER}.tar.gz
-	https://dev.gentoo.org/~gienah/distfiles/shinyapps-${SHINYAPPS_VER}.tar.gz
-	https://dev.gentoo.org/~gienah/distfiles/rsconnect_${RSCONNECT_VER}.tar.gz
-"
-
-LICENSE="AGPL-3"
-SLOT="0"
-KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
-IUSE="dedicated libressl server"
-
-QT_VER=5.4
-QT_SLOT=5
-RDEPEND="
-	>=app-text/pandoc-${PANDOC_VER}
-	dev-haskell/pandoc-citeproc
-	>=dev-lang/R-2.11.1
-	>=dev-libs/boost-1.63:=
-	>=dev-libs/mathjax-2.7.4
-	sys-apps/util-linux
-	>=sys-devel/clang-3.5.0:*
-	sys-libs/zlib
-	>=virtual/jre-1.8:=
-	x11-libs/pango
-	!dedicated? (
-		>=dev-qt/qtcore-${QT_VER}:${QT_SLOT}
-		>=dev-qt/qtdeclarative-${QT_VER}:${QT_SLOT}
-		>=dev-qt/qtdbus-${QT_VER}:${QT_SLOT}
-		>=dev-qt/qtgui-${QT_VER}:${QT_SLOT}
-		>=dev-qt/qtnetwork-${QT_VER}:${QT_SLOT}
-		>=dev-qt/qtopengl-${QT_VER}:${QT_SLOT}
-		>=dev-qt/qtpositioning-${QT_VER}:${QT_SLOT}
-		>=dev-qt/qtprintsupport-${QT_VER}:${QT_SLOT}
-		>=dev-qt/qtsingleapplication-2.6.1_p20150629[X,qt5(+)]
-		>=dev-qt/qtsensors-${QT_VER}:${QT_SLOT}
-		>=dev-qt/qtsql-${QT_VER}:${QT_SLOT}
-		>=dev-qt/qtsvg-${QT_VER}:${QT_SLOT}
-		>=dev-qt/qtwebchannel-${QT_VER}:${QT_SLOT}
-		>=dev-qt/qtwebkit-${QT_VER}:${QT_SLOT}
-		>=dev-qt/qtwidgets-${QT_VER}:${QT_SLOT}
-		>=dev-qt/qtxml-${QT_VER}:${QT_SLOT}
-		>=dev-qt/qtxmlpatterns-${QT_VER}:${QT_SLOT}
-		server? ( sys-libs/pam )
-	)
-	dedicated? ( sys-libs/pam )
-	!libressl? ( dev-libs/openssl:0= )
-	libressl? ( dev-libs/libressl:0= )"
-DEPEND="${RDEPEND}
-	app-arch/unzip
-	dev-java/ant-core
-	>=virtual/jdk-1.8:=
-	virtual/pkgconfig"
-#	test? ( dev-java/junit:4 )
-
-PATCHES=(
-		"${FILESDIR}/${PN}-0.99.879-prefs.patch"
-		"${FILESDIR}/${PN}-1.0.44-paths.patch"
-		"${FILESDIR}/${PN}-1.1.357-clang-pandoc.patch"
-		"${FILESDIR}/${PN}-0.98.490-linker_flags.patch"
-		"${FILESDIR}/${PN}-0.99.473-qtsingleapplication.patch"
-		"${FILESDIR}/${PN}-1.0.44-systemd.patch"
-		"${FILESDIR}/${PN}-1.1.453-boost-1.67.0.patch"
-		"${FILESDIR}/${PN}-1.1.453-core.patch"
-		"${FILESDIR}/${PN}-1.1.463-boost-1.69.0_p1.patch"
-		"${FILESDIR}/${PN}-1.1.463-boost-1.69.0_p2.patch"
-		"${FILESDIR}/${PN}-1.1.463-boost-1.69.0_p3.patch"
-		"${FILESDIR}/${PN}-1.1.463-fix-ptr-int-compare.patch"
-		"${FILESDIR}/${PN}-1.1.463-boost-1.70.0.patch"
-)
-
-src_unpack() {
-	unpack ${P}.tar.gz gwt-${GWT_VER}.zip
-	cd "${S}" || die
-	mkdir -p src/gwt/lib/{gin,gwt} \
-		dependencies/common/dictionaries \
-		src/gwt/lib/selenium/${SELENIUM_VER} \
-		src/gwt/lib/selenium/chromedriver/${CHROMEDRIVER_VER} || die
-	mv ../gwt-${GWT_VER} src/gwt/lib/gwt/${GWT_VER} || die
-	unzip -qd src/gwt/lib/gin/${GIN_VER} \
-		"${DISTDIR}"/gin-${GIN_VER}.zip || die
-	unzip -qd dependencies/common/dictionaries \
-		"${DISTDIR}"/core-dictionaries.zip || die
-	unzip -qd src/gwt/lib/selenium/${SELENIUM_VER} \
-		"${DISTDIR}"/selenium-java-${SELENIUM_VER}.zip || die
-	cp "${DISTDIR}"/selenium-server-standalone-${SELENIUM_VER}.jar \
-		src/gwt/lib/selenium/${SELENIUM_VER}/ || die
-	cp "${DISTDIR}"/chromedriver-linux \
-		src/gwt/lib/selenium/chromedriver/${CHROMEDRIVER_VER}/ || die
-	cd dependencies/common || die
-	unpack packrat-${PACKRAT_VER}.tar.gz
-	unpack rmarkdown-${RMARKDOWN_VER}.tar.gz
-	unpack shinyapps-${SHINYAPPS_VER}.tar.gz
-	unpack rsconnect_${RSCONNECT_VER}.tar.gz
-	cp "${DISTDIR}"/rmarkdown-${RMARKDOWN_VER}.tar.gz \
-		. || die
-	cp "${DISTDIR}"/packrat-${PACKRAT_VER}.tar.gz \
-		. || die
-	cp "${DISTDIR}"/shinyapps-${SHINYAPPS_VER}.tar.gz \
-		. || die
-	cp "${DISTDIR}"/rsconnect_${RSCONNECT_VER}.tar.gz \
-		. || die
-}
-
-src_prepare() {
-	cmake-utils_src_prepare
-	java-pkg-2_src_prepare
-	egit_clean
-
-	# Enable CMake to install our .service file for systemd usage
-	mkdir -vp "${S}/src/cpp/server/lib/systemd/system" || die
-	cp -v "${FILESDIR}/rstudio-server.service.in" "${S}/src/cpp/server/lib/systemd/system/" || die
-
-	# Adding -DDISTRO_SHARE=... to append-flags breaks cmake so using
-	# this sed hack for now. ~RMH
-	sed -i \
-		-e "s|DISTRO_SHARE|\"share/${PN}\"|g" \
-		src/cpp/server/ServerOptions.cpp \
-		src/cpp/session/SessionOptions.cpp || die
-
-	# use mathjax from system
-	ln -sf "${EPREFIX}"/usr/share/mathjax dependencies/common/mathjax-26 || die
-
-	# make sure icons and mime stuff are with prefix
-	sed -i \
-		-e "s:/usr:${EPREFIX}/usr:g" \
-		CMakeGlobals.txt src/cpp/desktop/CMakeLists.txt || die
-
-	# On Gentoo the rstudio-server configuration file is /etc/conf.d/rstudio-server.conf
-	sed -e "s@/etc/rstudio/rserver.conf@${EROOT}/etc/conf.d/rstudio-server.conf@" \
-		-i src/cpp/server/ServerOptions.cpp \
-		|| die
-
-	# Set the rsession.conf file location for Gentoo prefix
-	sed -e "s@/etc/rstudio/rsession.conf@${EROOT}/etc/rstudio/rsession.conf@" \
-		-i src/cpp/session/SessionOptions.cpp \
-		|| die
-
-	# dev-qt/qtsingleapplication-2.6.1_p20150629 does not provide a cmake module.
-	# It provides a library that has its version number appended to the end,
-	# which is difficult to handle in cmake, as find_library does not support
-	# searching for wildcard library names. So I find the library name from the
-	# qmake spec, and then sed this into the patched src/cpp/desktop/CMakeLists.txt.
-	rm -rf "${S}"/src/cpp/desktop/3rdparty || die
-	local s=$(grep '\-lQt$${QT_MAJOR_VERSION}Solutions_SingleApplication' \
-				   $(qt5_get_mkspecsdir)/features/qtsingleapplication.prf \
-					 | sed -e 's@\$\${QT_MAJOR_VERSION}@5@' \
-						   -e 's@LIBS \*= -l@@')
-	sed -e "s@Qt5Solutions_SingleApplication-2.6@${s}@g" \
-		-i "${S}"/src/cpp/desktop/CMakeLists.txt \
-		|| die
-
-	# The git commit for tag: git rev-list -n 1 v${PV}
-	sed -e 's@git ARGS rev-parse HEAD@echo ARGS 6871a99b32add885fe6fa3d50fe15f62346142e7@'\
-		-i "${S}"/CMakeLists.txt \
-		"${S}"/CMakeGlobals.txt \
-		|| die
-}
-
-src_configure() {
-	export RSTUDIO_VERSION_MAJOR=$(ver_cut 1)
-	export RSTUDIO_VERSION_MINOR=$(ver_cut 2)
-	export RSTUDIO_VERSION_PATCH=$(ver_cut 3)
-
-	local mycmakeargs=(
-		-DDISTRO_SHARE=share/${PN}
-		-DRSTUDIO_INSTALL_FREEDESKTOP="$(usex !dedicated "ON" "OFF")"
-		-DRSTUDIO_TARGET=$(usex dedicated "Server" "$(usex server "Development" "Desktop")")
-		-DQT_QMAKE_EXECUTABLE=$(qt5_get_bindir)/qmake
-		-DRSTUDIO_VERIFY_R_VERSION=FALSE
-		)
-
-	cmake-utils_src_configure
-}
-
-src_compile() {
-	# Avoid the rest of the oracle-jdk-bin-1.8.0.60 sandbox violations F: mkdir S: deny
-	# P: /root/.oracle_jre_usage.
-	export ANT_OPTS="-Duser.home=${T}"
-	cmake-utils_src_compile
-}
-
-src_install() {
-	export ANT_OPTS="-Duser.home=${T}"
-	cmake-utils_src_install
-	pax-mark m "${ED}/usr/bin/rstudio"
-	doconfd "${FILESDIR}"/rstudio-server.conf
-	dodir /etc/rstudio
-	insinto /etc/rstudio
-	doins "${FILESDIR}"/rsession.conf
-	dosym ../conf.d/rstudio-server.conf /etc/rstudio/rserver.conf
-	if use dedicated || use server; then
-		dopamd src/cpp/server/extras/pam/rstudio
-		newinitd "${FILESDIR}"/rstudio-server.initd rstudio-server
-	fi
-}
-
-pkg_preinst() {
-	use dedicated || gnome2_icon_savelist
-	java-pkg-2_pkg_preinst
-}
-
-pkg_postinst() {
-	use dedicated || { xdg_desktop_database_update
-		xdg_mimeinfo_database_update
-		gnome2_icon_cache_update ;}
-
-	if use dedicated || use server; then
-		enewgroup rstudio-server
-		enewuser rstudio-server -1 -1 -1 rstudio-server
-	fi
-}
-
-pkg_postrm() {
-	use dedicated || { xdg_desktop_database_update
-		xdg_mimeinfo_database_update
-		gnome2_icon_cache_update ;}
-}

diff --git a/sci-mathematics/rstudio/rstudio-1.2.1335.ebuild b/sci-mathematics/rstudio/rstudio-1.2.1335.ebuild
deleted file mode 100644
index 2ba27bd5148..00000000000
--- a/sci-mathematics/rstudio/rstudio-1.2.1335.ebuild
+++ /dev/null
@@ -1,254 +0,0 @@
-# Copyright 1999-2019 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-inherit eutils user cmake-utils gnome2-utils pam xdg-utils java-pkg-2 pax-utils qmake-utils vcs-clean
-
-# TODO
-# * package gin and gwt
-# * use dict from tree, linguas
-# * do src_test (use junit from tree?)
-
-# update from scripts in dependencies/common
-# egrep '(GWT_SDK_VER=|GIN_VER=|SELENIUM_VER=|CHROMEDRIVER_VER=)' dependencies/common/install-gwt
-GWT_VER=2.8.1
-GIN_VER=2.1.2
-SELENIUM_VER=2.37.0
-CHROMEDRIVER_VER=2.7
-# grep 'PANDOC_VERSION=' dependencies/common/install-pandoc
-# It should be PANDOC_VER=2.3.1 however >=app-text/pandoc-2.3.1 is not yet in portage
-PANDOC_VER=1.19.2.1
-# ls dependencies/common/*.tar.gz
-PACKRAT_VER=0.98.1000
-RMARKDOWN_VER=0.98.1000
-SHINYAPPS_VER=0.98.1000
-RSCONNECT_VER=0.4.1.4_fcac892a69817febd7b655b189bf57193260cda0
-
-DESCRIPTION="IDE for the R language"
-HOMEPAGE="
-	http://www.rstudio.org
-	https://github.com/rstudio/rstudio/"
-SRC_URI="
-	https://github.com/rstudio/rstudio/archive/v${PV}.tar.gz -> ${P}.tar.gz
-	https://s3.amazonaws.com/rstudio-buildtools/gin-${GIN_VER}.zip
-	https://s3.amazonaws.com/rstudio-buildtools/gwt-${GWT_VER}.zip
-	https://s3.amazonaws.com/rstudio-buildtools/selenium-java-${SELENIUM_VER}.zip
-	https://s3.amazonaws.com/rstudio-buildtools/selenium-server-standalone-${SELENIUM_VER}.jar
-	https://s3.amazonaws.com/rstudio-buildtools/chromedriver-linux
-	https://s3.amazonaws.com/rstudio-dictionaries/core-dictionaries.zip
-	https://dev.gentoo.org/~gienah/distfiles/packrat-${PACKRAT_VER}.tar.gz
-	https://dev.gentoo.org/~gienah/distfiles/rmarkdown-${RMARKDOWN_VER}.tar.gz
-	https://dev.gentoo.org/~gienah/distfiles/shinyapps-${SHINYAPPS_VER}.tar.gz
-	https://dev.gentoo.org/~gienah/distfiles/rsconnect_${RSCONNECT_VER}.tar.gz
-"
-
-LICENSE="AGPL-3"
-SLOT="0"
-KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
-IUSE="dedicated libressl server"
-
-QT_VER=5.4
-QT_SLOT=5
-RDEPEND="
-	>=app-text/pandoc-${PANDOC_VER}
-	dev-haskell/pandoc-citeproc
-	>=dev-lang/R-2.11.1
-	>=dev-libs/boost-1.63:=
-	>=dev-libs/mathjax-2.7.4
-	sys-apps/util-linux
-	>=sys-devel/clang-3.5.0:*
-	sys-libs/zlib
-	>=virtual/jre-1.8:=
-	x11-libs/pango
-	!dedicated? (
-		>=dev-qt/qtcore-${QT_VER}:${QT_SLOT}
-		>=dev-qt/qtdeclarative-${QT_VER}:${QT_SLOT}
-		>=dev-qt/qtdbus-${QT_VER}:${QT_SLOT}
-		>=dev-qt/qtgui-${QT_VER}:${QT_SLOT}
-		>=dev-qt/qtnetwork-${QT_VER}:${QT_SLOT}
-		>=dev-qt/qtopengl-${QT_VER}:${QT_SLOT}
-		>=dev-qt/qtpositioning-${QT_VER}:${QT_SLOT}
-		>=dev-qt/qtprintsupport-${QT_VER}:${QT_SLOT}
-		>=dev-qt/qtsingleapplication-2.6.1_p20150629[X,qt5(+)]
-		>=dev-qt/qtsensors-${QT_VER}:${QT_SLOT}
-		>=dev-qt/qtsql-${QT_VER}:${QT_SLOT}
-		>=dev-qt/qtsvg-${QT_VER}:${QT_SLOT}
-		>=dev-qt/qtwebchannel-${QT_VER}:${QT_SLOT}
-		>=dev-qt/qtwebengine-${QT_VER}:${QT_SLOT}[widgets]
-		>=dev-qt/qtwidgets-${QT_VER}:${QT_SLOT}
-		>=dev-qt/qtxml-${QT_VER}:${QT_SLOT}
-		>=dev-qt/qtxmlpatterns-${QT_VER}:${QT_SLOT}
-		server? ( sys-libs/pam )
-	)
-	dedicated? ( sys-libs/pam )
-	!libressl? ( dev-libs/openssl:0= )
-	libressl? ( dev-libs/libressl:0= )"
-DEPEND="${RDEPEND}
-	app-arch/unzip
-	dev-java/ant-core
-	>=virtual/jdk-1.8:=
-	virtual/pkgconfig"
-#	test? ( dev-java/junit:4 )
-
-PATCHES=(
-	"${FILESDIR}"/${PN}-1.2.1335-prefs.patch
-	"${FILESDIR}"/${PN}-1.2.1335-paths.patch
-	"${FILESDIR}"/${PN}-1.2.1335-pandoc.patch
-	"${FILESDIR}"/${PN}-1.2.1335-linker_flags.patch
-	"${FILESDIR}"/${PN}-1.2.1335-qtsingleapplication.patch
-	"${FILESDIR}"/${PN}-1.0.44-systemd.patch
-	"${FILESDIR}"/${PN}-1.2.1335-core.patch
-	"${FILESDIR}"/${PN}-1.2.1335-fix-ptr-int-compare.patch
-	"${FILESDIR}"/${PN}-1.2.1335-boost-1.70.0_p1.patch
-	"${FILESDIR}"/${PN}-1.2.1335-boost-1.70.0_p2.patch
-	"${FILESDIR}"/${PN}-1.2.1335-boost-1.72-filesystem.patch
-)
-
-src_unpack() {
-	unpack ${P}.tar.gz gwt-${GWT_VER}.zip
-	cd "${S}" || die
-	mkdir -p src/gwt/lib/{gin,gwt} \
-		dependencies/common/dictionaries \
-		src/gwt/lib/selenium/${SELENIUM_VER} \
-		src/gwt/lib/selenium/chromedriver/${CHROMEDRIVER_VER} || die
-	mv ../gwt-${GWT_VER} src/gwt/lib/gwt/${GWT_VER} || die
-	unzip -qd src/gwt/lib/gin/${GIN_VER} \
-		"${DISTDIR}"/gin-${GIN_VER}.zip || die
-	unzip -qd dependencies/common/dictionaries \
-		"${DISTDIR}"/core-dictionaries.zip || die
-	unzip -qd src/gwt/lib/selenium/${SELENIUM_VER} \
-		"${DISTDIR}"/selenium-java-${SELENIUM_VER}.zip || die
-	cp "${DISTDIR}"/selenium-server-standalone-${SELENIUM_VER}.jar \
-		src/gwt/lib/selenium/${SELENIUM_VER}/ || die
-	cp "${DISTDIR}"/chromedriver-linux \
-		src/gwt/lib/selenium/chromedriver/${CHROMEDRIVER_VER}/ || die
-	cd dependencies/common || die
-	unpack packrat-${PACKRAT_VER}.tar.gz
-	unpack rmarkdown-${RMARKDOWN_VER}.tar.gz
-	unpack shinyapps-${SHINYAPPS_VER}.tar.gz
-	unpack rsconnect_${RSCONNECT_VER}.tar.gz
-	cp "${DISTDIR}"/rmarkdown-${RMARKDOWN_VER}.tar.gz \
-		. || die
-	cp "${DISTDIR}"/packrat-${PACKRAT_VER}.tar.gz \
-		. || die
-	cp "${DISTDIR}"/shinyapps-${SHINYAPPS_VER}.tar.gz \
-		. || die
-	cp "${DISTDIR}"/rsconnect_${RSCONNECT_VER}.tar.gz \
-		. || die
-}
-
-src_prepare() {
-	cmake-utils_src_prepare
-	java-pkg-2_src_prepare
-	egit_clean
-
-	# Enable CMake to install our .service file for systemd usage
-	mkdir -vp "${S}/src/cpp/server/lib/systemd/system" || die
-	cp -v "${FILESDIR}/rstudio-server.service.in" "${S}/src/cpp/server/lib/systemd/system/" || die
-
-	# Adding -DDISTRO_SHARE=... to append-flags breaks cmake so using
-	# this sed hack for now. ~RMH
-	sed -i \
-		-e "s|DISTRO_SHARE|\"share/${PN}\"|g" \
-		src/cpp/server/ServerOptions.cpp \
-		src/cpp/session/SessionOptions.cpp || die
-
-	# use mathjax from system
-	ln -sf "${EPREFIX}"/usr/share/mathjax dependencies/common/mathjax-26 || die
-
-	# make sure icons and mime stuff are with prefix
-	sed -i \
-		-e "s:/usr:${EPREFIX}/usr:g" \
-		CMakeGlobals.txt src/cpp/desktop/CMakeLists.txt || die
-
-	# On Gentoo the rstudio-server configuration file is /etc/conf.d/rstudio-server.conf
-	sed -e "s@/etc/rstudio/rserver.conf@${EROOT}/etc/conf.d/rstudio-server.conf@" \
-		-i src/cpp/server/ServerOptions.cpp \
-		|| die
-
-	# Set the rsession.conf file location for Gentoo prefix
-	sed -e "s@/etc/rstudio/rsession.conf@${EROOT}/etc/rstudio/rsession.conf@" \
-		-i src/cpp/session/SessionOptions.cpp \
-		|| die
-
-	# dev-qt/qtsingleapplication-2.6.1_p20150629 does not provide a cmake module.
-	# It provides a library that has its version number appended to the end,
-	# which is difficult to handle in cmake, as find_library does not support
-	# searching for wildcard library names. So I find the library name from the
-	# qmake spec, and then sed this into the patched src/cpp/desktop/CMakeLists.txt.
-	rm -rf "${S}"/src/cpp/desktop/3rdparty || die
-	local s=$(grep '\-lQt$${QT_MAJOR_VERSION}Solutions_SingleApplication' \
-				   $(qt5_get_mkspecsdir)/features/qtsingleapplication.prf \
-					 | sed -e 's@\$\${QT_MAJOR_VERSION}@5@' \
-						   -e 's@LIBS \*= -l@@')
-	sed -e "s@Qt5Solutions_SingleApplication-2.6@${s}@g" \
-		-i "${S}"/src/cpp/desktop/CMakeLists.txt \
-		|| die
-
-	# The git commit for tag: git rev-list -n 1 v${PV}
-	sed -e 's@git ARGS rev-parse HEAD@echo ARGS 6871a99b32add885fe6fa3d50fe15f62346142e7@'\
-		-i "${S}"/CMakeLists.txt \
-		"${S}"/CMakeGlobals.txt \
-		|| die
-}
-
-src_configure() {
-	export RSTUDIO_VERSION_MAJOR=$(ver_cut 1)
-	export RSTUDIO_VERSION_MINOR=$(ver_cut 2)
-	export RSTUDIO_VERSION_PATCH=$(ver_cut 3)
-
-	local mycmakeargs=(
-		-DDISTRO_SHARE=share/${PN}
-		-DRSTUDIO_INSTALL_FREEDESKTOP="$(usex !dedicated "ON" "OFF")"
-		-DRSTUDIO_TARGET=$(usex dedicated "Server" "$(usex server "Development" "Desktop")")
-		-DQT_QMAKE_EXECUTABLE=$(qt5_get_bindir)/qmake
-		-DRSTUDIO_VERIFY_R_VERSION=FALSE
-		)
-
-	cmake-utils_src_configure
-}
-
-src_compile() {
-	# Avoid the rest of the oracle-jdk-bin-1.8.0.60 sandbox violations F: mkdir S: deny
-	# P: /root/.oracle_jre_usage.
-	export ANT_OPTS="-Duser.home=${T}"
-	cmake-utils_src_compile
-}
-
-src_install() {
-	export ANT_OPTS="-Duser.home=${T}"
-	cmake-utils_src_install
-	pax-mark m "${ED}/usr/bin/rstudio"
-	doconfd "${FILESDIR}"/rstudio-server.conf
-	dodir /etc/rstudio
-	insinto /etc/rstudio
-	doins "${FILESDIR}"/rsession.conf
-	dosym ../conf.d/rstudio-server.conf /etc/rstudio/rserver.conf
-	if use dedicated || use server; then
-		dopamd src/cpp/server/extras/pam/rstudio
-		newinitd "${FILESDIR}"/rstudio-server.initd rstudio-server
-	fi
-}
-
-pkg_preinst() {
-	use dedicated || gnome2_icon_savelist
-	java-pkg-2_pkg_preinst
-}
-
-pkg_postinst() {
-	use dedicated || { xdg_desktop_database_update
-		xdg_mimeinfo_database_update
-		gnome2_icon_cache_update ;}
-
-	if use dedicated || use server; then
-		enewgroup rstudio-server
-		enewuser rstudio-server -1 -1 -1 rstudio-server
-	fi
-}
-
-pkg_postrm() {
-	use dedicated || { xdg_desktop_database_update
-		xdg_mimeinfo_database_update
-		gnome2_icon_cache_update ;}
-}


^ permalink raw reply related	[flat|nested] 12+ messages in thread

* [gentoo-commits] repo/gentoo:master commit in: sci-mathematics/rstudio/, sci-mathematics/rstudio/files/
@ 2020-05-25 12:00 Mark Wright
  0 siblings, 0 replies; 12+ messages in thread
From: Mark Wright @ 2020-05-25 12:00 UTC (permalink / raw
  To: gentoo-commits

commit:     3baafff326dfe64a021b28d36a48751e81e95c32
Author:     Mark Wright <gienah <AT> gentoo <DOT> org>
AuthorDate: Mon May 25 11:58:49 2020 +0000
Commit:     Mark Wright <gienah <AT> gentoo <DOT> org>
CommitDate: Mon May 25 11:59:45 2020 +0000
URL:        https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=3baafff3

sci-mathematics/rstudio: Bump to 1.3.959

Package-Manager: Portage-2.3.100, Repoman-2.3.22
Signed-off-by: Mark Wright <gienah <AT> gentoo.org>

 sci-mathematics/rstudio/Manifest                   |   1 +
 .../rstudio/files/rstudio-1.3.959-R-4.0.0.patch    | 106 ++++++++++
 .../rstudio/files/rstudio-1.3.959-core.patch       | 184 ++++++++++++++++
 .../files/rstudio-1.3.959-pandoc-mathjax.patch     |  42 ++++
 .../rstudio/files/rstudio-1.3.959-paths.patch      | 118 +++++++++++
 .../rstudio/files/rstudio-1.3.959-prefs.patch      |  68 ++++++
 .../rstudio-1.3.959-qtsingleapplication.patch      |  60 ++++++
 sci-mathematics/rstudio/rstudio-1.3.959.ebuild     | 231 +++++++++++++++++++++
 8 files changed, 810 insertions(+)

diff --git a/sci-mathematics/rstudio/Manifest b/sci-mathematics/rstudio/Manifest
index 6821cacc59b..063f6280255 100644
--- a/sci-mathematics/rstudio/Manifest
+++ b/sci-mathematics/rstudio/Manifest
@@ -1,3 +1,4 @@
 DIST core-dictionaries.zip 876339 BLAKE2B f29afcbf5a7f8ec635e5a5b248d978af286d18488f54c9a09a2b95fde19b796e4473e5846402a46dd24b71c6e4167512539aaa32ab6d99713d500a80aaf46796 SHA512 9c5830cc9fed575e223f1c61f02e48c5aea6801bb0cd2586f02437c17fdffdb1d36c396d5a8ecbe02ba01196e73458304345b1f6b92c052bc7a7d05961fac2c9
 DIST rstudio-1.2.5033.tar.gz 20456976 BLAKE2B 3cbca6a5180690104dddf1456168bd38708d4152ed9b7a167035dd66e270aeb6405169d34461cbd899738be1872607e3f3b6f81ff0b3c9e6a9ed965a889b1393 SHA512 3569d4fed342275a9905c87e4f97be63b6391d2c37f75397e06201a7c31f80d94799214f51ff8e57d458ef18d5e54afe1ec8a7c56ac05ed8b8225ecca72d1daf
 DIST rstudio-1.2.5042.tar.gz 20456999 BLAKE2B 3251ab2511daefefa395256fedb273ecc36dbc8118457474e3647f7616baea91301e597896582ad4b191195fc7baf17645c4c25b9a957a0c17a6251151b1dd87 SHA512 e09f2360abecde0c16e240e6838efb270a355bec3d3982ffde2b01b32b21e9281fef465734edbfeb5e05375529cc7f06d5b5d41304f367982f53ae7ad98e20f9
+DIST rstudio-1.3.959.tar.gz 89639419 BLAKE2B d45b2c1b0e426ddb5a945e59a8127ddfd47f6230ef0929639c4b525382ae57437a273df6ade85cfbf3a29911cf0158ee2e0808bfa94e783d70d4615f6c228f31 SHA512 e5d8bfe16011790ff4723c731043f44070d8fe48f85c5a9ab8389c9a2b7a1d3813e9362063ec4c6a6ca3b0a0857e2190481cbb74191650a129c0d2e10b342fac

diff --git a/sci-mathematics/rstudio/files/rstudio-1.3.959-R-4.0.0.patch b/sci-mathematics/rstudio/files/rstudio-1.3.959-R-4.0.0.patch
new file mode 100644
index 00000000000..dc35d0ce008
--- /dev/null
+++ b/sci-mathematics/rstudio/files/rstudio-1.3.959-R-4.0.0.patch
@@ -0,0 +1,106 @@
+From 71b1a935762efd24a79de193662450de5a89f67e Mon Sep 17 00:00:00 2001
+From: Jonathan McPherson <jonathan@rstudio.com>
+Date: Tue, 14 Jan 2020 12:53:20 -0800
+Subject: [PATCH] use R_NoSave over R_Slave for R 4.0+
+
+---
+ src/cpp/r/CMakeLists.txt             | 12 ++++++++++++
+ src/cpp/r/config.h.in                |  8 +++++++-
+ src/cpp/r/session/REmbeddedPosix.cpp | 20 ++++++++++++++------
+ 3 files changed, 33 insertions(+), 7 deletions(-)
+
+diff --git a/src/cpp/r/CMakeLists.txt b/src/cpp/r/CMakeLists.txt
+index 6984ae309c..29784b8b67 100644
+--- a/src/cpp/r/CMakeLists.txt
++++ b/src/cpp/r/CMakeLists.txt
+@@ -15,6 +15,18 @@
+ 
+ project (R)
+ 
++# find the version of R in play
++find_package(LibR REQUIRED)
++execute_process(
++    COMMAND "${LIBR_EXECUTABLE}" "--vanilla" "--slave" "-e" "cat(as.character(getRversion()))"
++    OUTPUT_VARIABLE LIBR_VERSION)
++
++# parse and save the R version to a variable
++string(REPLACE "." ";" R_VERSION_LIST "${LIBR_VERSION}")
++list(GET R_VERSION_LIST 0 R_VERSION_MAJOR)
++list(GET R_VERSION_LIST 1 R_VERSION_MINOR)
++list(GET R_VERSION_LIST 2 R_VERSION_PATCH)
++
+ # include files
+ file(GLOB_RECURSE R_HEADER_FILES "*.h*")
+ 
+diff --git a/src/cpp/r/config.h.in b/src/cpp/r/config.h.in
+index 6ba67c8e09..00bc8b6191 100644
+--- a/src/cpp/r/config.h.in
++++ b/src/cpp/r/config.h.in
+@@ -1,7 +1,7 @@
+ /*
+  * config.h.in
+  *
+- * Copyright (C) 2009-12 by RStudio, PBC
++ * Copyright (C) 2009-20 by RStudio, Inc.
+  *
+  * Unless you have received this program directly from RStudio pursuant
+  * to the terms of a commercial license agreement with RStudio, then
+@@ -16,4 +16,10 @@
+ 
+ #cmakedefine PANGO_CAIRO_FOUND
+ 
++// Important: These variables represent the version of R found during
++// compile/link time, NOT the version of R present at runtime.
++#define R_VERSION_MAJOR ${R_VERSION_MAJOR}
++#define R_VERSION_MINOR ${R_VERSION_MINOR}
++#define R_VERSION_PATCH ${R_VERSION_PATCH}
++
+ 
+diff --git a/src/cpp/r/session/REmbeddedPosix.cpp b/src/cpp/r/session/REmbeddedPosix.cpp
+index ac71b94522..73e2e2ce7f 100644
+--- a/src/cpp/r/session/REmbeddedPosix.cpp
++++ b/src/cpp/r/session/REmbeddedPosix.cpp
+@@ -1,7 +1,7 @@
+ /*
+  * REmbeddedPosix.cpp
+  *
+- * Copyright (C) 2009-19 by RStudio, PBC
++ * Copyright (C) 2009-20 by RStudio, Inc.
+  *
+  * Unless you have received this program directly from RStudio pursuant
+  * to the terms of a commercial license agreement with RStudio, then
+@@ -38,6 +38,8 @@ extern "C" void (*ptr_R_ProcessEvents)(void);
+ extern "C"  typedef void (*ptr_QuartzCocoa_SetupEventLoop)(int, unsigned long);
+ #endif
+ 
++#include "config.h"
++
+ extern int R_running_as_main_program;  // from unix/system.c
+ 
+ using namespace rstudio::core;
+@@ -103,14 +105,20 @@ void runEmbeddedR(const core::FilePath& /*rHome*/,    // ignored on posix
+    //
+    structRstart rp;
+    Rstart Rp = &rp;
+-   R_DefParams(Rp) ;
+-   Rp->R_Slave = FALSE ;
++   R_DefParams(Rp);
++#if R_VERSION_MAJOR > 3
++   // R 4.0 and above use --no-echo to suppress output
++   Rp->R_NoEcho = FALSE;
++#else
++   // R 3.x and below use --slave
++   Rp->R_Slave = FALSE;
++#endif
+    Rp->R_Quiet = quiet ? TRUE : FALSE;
+-   Rp->R_Interactive = TRUE ;
+-   Rp->SaveAction = defaultSaveAction ;
++   Rp->R_Interactive = TRUE;
++   Rp->SaveAction = defaultSaveAction;
+    Rp->RestoreAction = SA_NORESTORE; // handled within initialize()
+    Rp->LoadInitFile = loadInitFile ? TRUE : FALSE;
+-   R_SetParams(Rp) ;
++   R_SetParams(Rp);
+ 
+    // redirect console
+    R_Interactive = TRUE; // should have also been set by call to Rf_initialize_R

diff --git a/sci-mathematics/rstudio/files/rstudio-1.3.959-core.patch b/sci-mathematics/rstudio/files/rstudio-1.3.959-core.patch
new file mode 100644
index 00000000000..0f6af4ef7f1
--- /dev/null
+++ b/sci-mathematics/rstudio/files/rstudio-1.3.959-core.patch
@@ -0,0 +1,184 @@
+--- rstudio-1.3.959-orig/src/cpp/session/SessionClientInit.cpp	2020-05-19 04:11:10.000000000 +1000
++++ rstudio-1.3.959/src/cpp/session/SessionClientInit.cpp	2020-05-24 17:21:56.960469575 +1000
+@@ -91,13 +91,13 @@
+       boost::shared_ptr<http::Cookie>* pCookie)
+ {
+    // extract the base URL
+-   json::JsonRpcRequest request;
++   core::json::JsonRpcRequest request;
+    Error error = parseJsonRpcRequest(ptrConnection->request().body(), &request);
+    if (error)
+       return error;
+    std::string baseURL;
+ 
+-   error = json::readParams(request.params, &baseURL);
++   error = core::json::readParams(request.params, &baseURL);
+    if (error)
+       return error;
+ 
+@@ -143,7 +143,7 @@
+    if (options.programMode() == kSessionProgramModeServer && 
+        !core::http::validateCSRFHeaders(ptrConnection->request()))
+    {
+-      ptrConnection->sendJsonRpcError(Error(json::errc::Unauthorized, ERROR_LOCATION));
++      ptrConnection->sendJsonRpcError(Error(core::json::errc::Unauthorized, ERROR_LOCATION));
+       return;
+    }
+ 
+@@ -173,12 +173,12 @@
+    }
+ 
+    // prepare session info 
+-   json::Object sessionInfo ;
++   core::json::Object sessionInfo ;
+    sessionInfo["clientId"] = clientId;
+    sessionInfo["mode"] = options.programMode();
+ 
+    // build initialization options for client
+-   json::Object initOptions;
++   core::json::Object initOptions;
+    initOptions["restore_workspace"] = options.rRestoreWorkspace();
+    initOptions["run_rprofile"] = options.rRunRprofile();
+    sessionInfo["init_options"] = initOptions;
+@@ -194,8 +194,8 @@
+    }
+ 
+    // temp dir
+-   FilePath tempDir = rstudio::r::session::utils::tempDir();
+-   Error error = tempDir.ensureDirectory();
++   core::FilePath tempDir = rstudio::r::session::utils::tempDir();
++   core::Error error = tempDir.ensureDirectory();
+    if (error)
+       LOG_ERROR(error);
+    sessionInfo["temp_dir"] = tempDir.getAbsolutePath();
+@@ -213,12 +213,12 @@
+    sessionInfo["prompt"] = rstudio::r::options::getOption<std::string>("prompt");
+ 
+    // client state
+-   json::Object clientStateObject;
++   core::json::Object clientStateObject;
+    rstudio::r::session::clientState().currentState(&clientStateObject);
+    sessionInfo["client_state"] = clientStateObject;
+    
+    // source documents
+-   json::Array jsonDocs;
++   core::json::Array jsonDocs;
+    error = modules::source::clientInitDocuments(&jsonDocs);
+    if (error)
+       LOG_ERROR(error);
+@@ -243,7 +243,7 @@
+    if (resumed)
+    {
+       // console actions
+-      json::Object actionsObject;
++     core::json::Object actionsObject;
+       consoleActions.asJson(&actionsObject);
+       sessionInfo["console_actions"] = actionsObject;
+    }
+@@ -310,12 +310,12 @@
+    }
+    else
+    {
+-      sessionInfo["active_project_file"] = json::Value();
+-      sessionInfo["project_ui_prefs"] = json::Value();
+-      sessionInfo["project_open_docs"] = json::Value();
++      sessionInfo["active_project_file"] = core::json::Value();
++      sessionInfo["project_ui_prefs"] = core::json::Value();
++      sessionInfo["project_open_docs"] = core::json::Value();
+       sessionInfo["project_supports_sharing"] = false;
+       sessionInfo["project_owned_by_user"] = false;
+-      sessionInfo["project_user_data_directory"] = json::Value();
++      sessionInfo["project_user_data_directory"] = core::json::Value();
+    }
+ 
+    sessionInfo["system_encoding"] = std::string(::locale2charset(nullptr));
+@@ -352,20 +352,20 @@
+       sessionInfo["build_tools_bookdown_website"] =
+                               module_context::isBookdownWebsite();
+ 
+-      FilePath buildTargetDir = projects::projectContext().buildTargetPath();
++      core::FilePath buildTargetDir = projects::projectContext().buildTargetPath();
+       if (!buildTargetDir.isEmpty())
+       {
+          sessionInfo["build_target_dir"] = module_context::createAliasedPath(
+                                                                 buildTargetDir);
+-         sessionInfo["has_pkg_src"] = (type == r_util::kBuildTypePackage) &&
++         sessionInfo["has_pkg_src"] = (type == core::r_util::kBuildTypePackage) &&
+             buildTargetDir.completeChildPath("src").exists();
+          sessionInfo["has_pkg_vig"] =
+-               (type == r_util::kBuildTypePackage) &&
++               (type == core::r_util::kBuildTypePackage) &&
+                   buildTargetDir.completeChildPath("vignettes").exists();
+       }
+       else
+       {
+-         sessionInfo["build_target_dir"] = json::Value();
++         sessionInfo["build_target_dir"] = core::json::Value();
+          sessionInfo["has_pkg_src"] = false;
+          sessionInfo["has_pkg_vig"] = false;
+       }
+@@ -373,9 +373,9 @@
+    }
+    else
+    {
+-      sessionInfo["build_tools_type"] = r_util::kBuildTypeNone;
++      sessionInfo["build_tools_type"] = core::r_util::kBuildTypeNone;
+       sessionInfo["build_tools_bookdown_website"] = false;
+-      sessionInfo["build_target_dir"] = json::Value();
++      sessionInfo["build_target_dir"] = core::json::Value();
+       sessionInfo["has_pkg_src"] = false;
+       sessionInfo["has_pkg_vig"] = false;
+    }
+@@ -384,7 +384,7 @@
+    sessionInfo["presentation_commands"] = options.allowPresentationCommands();
+ 
+    sessionInfo["tutorial_api_available"] = false;
+-   sessionInfo["tutorial_api_client_origin"] = json::Value();
++   sessionInfo["tutorial_api_client_origin"] = core::json::Value();
+ 
+    sessionInfo["build_state"] = modules::build::buildStateAsJson();
+    sessionInfo["devtools_installed"] = module_context::isMinimumDevtoolsInstalled();
+@@ -395,7 +395,7 @@
+ 
+    // console history -- we do this at the end because
+    // restoreBuildRestartContext may have reset it
+-   json::Array historyArray;
++   core::json::Array historyArray;
+    rstudio::r::session::consoleHistory().asJson(&historyArray);
+    sessionInfo["console_history"] = historyArray;
+    sessionInfo["console_history_capacity"] =
+@@ -470,14 +470,14 @@
+ 
+    sessionInfo["multi_session"] = options.multiSession();
+ 
+-   json::Object rVersionsJson;
++   core::json::Object rVersionsJson;
+    rVersionsJson["r_version"] = module_context::rVersion();
+    rVersionsJson["r_version_label"] = module_context::rVersionLabel();
+    rVersionsJson["r_home_dir"] = module_context::rHomeDir();
+    sessionInfo["r_versions_info"] = rVersionsJson;
+ 
+    sessionInfo["show_user_home_page"] = options.showUserHomePage();
+-   sessionInfo["user_home_page_url"] = json::Value();
++   sessionInfo["user_home_page_url"] = core::json::Value();
+    
+    sessionInfo["r_addins"] = modules::r_addins::addinRegistryAsJson();
+    sessionInfo["package_provided_extensions"] = modules::ppe::indexer().getPayload();
+@@ -501,7 +501,7 @@
+ 
+    sessionInfo["launcher_jobs_enabled"] = modules::overlay::launcherJobsFeatureDisplayed();
+ 
+-   json::Object packageDependencies;
++   core::json::Object packageDependencies;
+    error = modules::dependency_list::getDependencyList(&packageDependencies);
+    if (error)
+       LOG_ERROR(error);
+@@ -529,7 +529,7 @@
+ 
+    // create response  (we always set kEventsPending to false so that the client
+    // won't poll for events until it is ready)
+-   json::JsonRpcResponse jsonRpcResponse;
++   core::json::JsonRpcResponse jsonRpcResponse;
+    jsonRpcResponse.setField(kEventsPending, "false");
+    jsonRpcResponse.setResult(sessionInfo);
+ 

diff --git a/sci-mathematics/rstudio/files/rstudio-1.3.959-pandoc-mathjax.patch b/sci-mathematics/rstudio/files/rstudio-1.3.959-pandoc-mathjax.patch
new file mode 100644
index 00000000000..d8718dda9b1
--- /dev/null
+++ b/sci-mathematics/rstudio/files/rstudio-1.3.959-pandoc-mathjax.patch
@@ -0,0 +1,42 @@
+--- rstudio-1.3.959-orig/src/cpp/session/CMakeLists.txt	2020-05-19 04:11:10.000000000 +1000
++++ rstudio-1.3.959/src/cpp/session/CMakeLists.txt	2020-05-24 18:54:40.444955162 +1000
+@@ -22,12 +22,6 @@
+ if(NOT EXISTS "${RSTUDIO_DEPENDENCIES_DIR}/common/dictionaries")
+   message(FATAL_ERROR "Dictionaries not found (re-run install-dependencies script to install)")
+ endif()
+-if(NOT EXISTS "${RSTUDIO_DEPENDENCIES_DIR}/common/mathjax-27")
+-  message(FATAL_ERROR "Mathjax 2.7 not found (re-run install-dependencies script to install)")
+-endif()
+-if(NOT EXISTS "${RSTUDIO_DEPENDENCIES_DIR}/common/pandoc")
+-  message(FATAL_ERROR "pandoc not found (re-run install-dependencies script to install)")
+-endif()
+ 
+ # verify embedded packages are available
+ foreach(PKG ${RSTUDIO_EMBEDDED_PACKAGES})
+@@ -500,10 +494,6 @@
+    install(DIRECTORY "${RSTUDIO_DEPENDENCIES_DIR}/common/dictionaries"
+            DESTINATION "${RSTUDIO_INSTALL_SUPPORTING}/resources")
+ 
+-   # install mathjax for local html preview
+-   install(DIRECTORY "${RSTUDIO_DEPENDENCIES_DIR}/common/mathjax-27"
+-           DESTINATION "${RSTUDIO_INSTALL_SUPPORTING}/resources")
+-
+    # icons for database connections
+    install(DIRECTORY "resources/connections"
+            DESTINATION ${RSTUDIO_INSTALL_SUPPORTING}/resources)
+@@ -516,15 +506,6 @@
+    install(DIRECTORY "resources/dependencies"
+            DESTINATION ${RSTUDIO_INSTALL_SUPPORTING}/resources)
+ 
+-   # install pandoc
+-   set(PANDOC_VERSION "2.7.3" CACHE INTERNAL "Pandoc version")
+-
+-   set(PANDOC_BIN "${RSTUDIO_DEPENDENCIES_DIR}/common/pandoc/${PANDOC_VERSION}")
+-   file(GLOB PANDOC_FILES "${PANDOC_BIN}/pandoc*")
+-   install(FILES ${PANDOC_FILES}
+-           PERMISSIONS OWNER_READ OWNER_WRITE OWNER_EXECUTE GROUP_READ GROUP_EXECUTE WORLD_READ WORLD_EXECUTE
+-           DESTINATION  ${RSTUDIO_INSTALL_BIN}/pandoc)
+-
+    # install embedded packages
+    foreach(PKG ${RSTUDIO_EMBEDDED_PACKAGES})
+       file(GLOB PKG_FILES "${RSTUDIO_DEPENDENCIES_DIR}/common/${PKG}*.tar.gz")

diff --git a/sci-mathematics/rstudio/files/rstudio-1.3.959-paths.patch b/sci-mathematics/rstudio/files/rstudio-1.3.959-paths.patch
new file mode 100644
index 00000000000..175d52f7149
--- /dev/null
+++ b/sci-mathematics/rstudio/files/rstudio-1.3.959-paths.patch
@@ -0,0 +1,118 @@
+--- rstudio-1.3.959-orig/CMakeGlobals.txt	2020-05-19 04:11:10.000000000 +1000
++++ rstudio-1.3.959/CMakeGlobals.txt	2020-05-25 19:30:10.711859714 +1000
+@@ -181,7 +181,7 @@
+    else()
+      set(RSTUDIO_INSTALL_BIN bin)
+    endif()
+-   set(RSTUDIO_INSTALL_SUPPORTING .)
++   set(RSTUDIO_INSTALL_SUPPORTING ${DISTRO_SHARE})
+ endif()
+ 
+ # if the install prefix is /usr/local then tweak as appropriate
+--- rstudio-1.3.959-orig/src/cpp/server/CMakeLists.txt	2020-05-19 04:11:10.000000000 +1000
++++ rstudio-1.3.959/src/cpp/server/CMakeLists.txt	2020-05-25 19:30:10.711859714 +1000
+@@ -190,7 +190,7 @@
+    configure_file(${CMAKE_CURRENT_SOURCE_DIR}/${RSERVER_INITD_DEBIAN_SCRIPT}.in
+                   ${CMAKE_CURRENT_BINARY_DIR}/${RSERVER_INITD_DEBIAN_SCRIPT})
+    install(PROGRAMS ${CMAKE_CURRENT_BINARY_DIR}/${RSERVER_INITD_DEBIAN_SCRIPT}
+-           DESTINATION ${RSERVER_INITD_DEBIAN_DIR})
++           DESTINATION ${DISTRO_SHARE}/${RSERVER_INITD_DEBIAN_DIR})
+ 
+    # install configured redhat init.d script
+    set(RSERVER_INITD_REDHAT_DIR "extras/init.d/redhat")
+@@ -198,7 +198,7 @@
+    configure_file(${CMAKE_CURRENT_SOURCE_DIR}/${RSERVER_INITD_REDHAT_SCRIPT}.in
+                   ${CMAKE_CURRENT_BINARY_DIR}/${RSERVER_INITD_REDHAT_SCRIPT})
+    install(PROGRAMS ${CMAKE_CURRENT_BINARY_DIR}/${RSERVER_INITD_REDHAT_SCRIPT}
+-           DESTINATION ${RSERVER_INITD_REDHAT_DIR})
++           DESTINATION ${DISTRO_SHARE}/${RSERVER_INITD_REDHAT_DIR})
+ 
+    # install configured suse init.d script
+    set(RSERVER_INITD_SUSE_DIR "extras/init.d/suse")
+@@ -206,13 +206,13 @@
+    configure_file(${CMAKE_CURRENT_SOURCE_DIR}/${RSERVER_INITD_SUSE_SCRIPT}.in
+                   ${CMAKE_CURRENT_BINARY_DIR}/${RSERVER_INITD_SUSE_SCRIPT})
+    install(PROGRAMS ${CMAKE_CURRENT_BINARY_DIR}/${RSERVER_INITD_SUSE_SCRIPT}
+-           DESTINATION ${RSERVER_INITD_SUSE_DIR})
++           DESTINATION ${DISTRO_SHARE}/${RSERVER_INITD_SUSE_DIR})
+ 
+    # install pam profile
+    set(RSERVER_PAM_DIR "extras/pam")
+    set(RSERVER_PAM_PROFILE "${RSERVER_PAM_DIR}/rstudio")
+    install(FILES ${CMAKE_CURRENT_SOURCE_DIR}/${RSERVER_PAM_PROFILE}
+-           DESTINATION ${RSERVER_PAM_DIR})
++           DESTINATION ${DISTRO_SHARE}/${RSERVER_PAM_DIR})
+ 
+    # install configured upstart profile
+    set(RSERVER_UPSTART_DIR "extras/upstart")
+@@ -220,12 +220,12 @@
+    configure_file(${CMAKE_CURRENT_SOURCE_DIR}/${RSERVER_UPSTART_PROFILE}.in
+                   ${CMAKE_CURRENT_BINARY_DIR}/${RSERVER_UPSTART_PROFILE})
+    install(FILES ${CMAKE_CURRENT_BINARY_DIR}/${RSERVER_UPSTART_PROFILE}
+-           DESTINATION ${RSERVER_UPSTART_DIR})
++           DESTINATION ${DISTRO_SHARE}/${RSERVER_UPSTART_DIR})
+    set(RSERVER_UPSTART_PROFILE_REDHAT "${RSERVER_UPSTART_DIR}/rstudio-server.redhat.conf")
+    configure_file(${CMAKE_CURRENT_SOURCE_DIR}/${RSERVER_UPSTART_PROFILE_REDHAT}.in
+                   ${CMAKE_CURRENT_BINARY_DIR}/${RSERVER_UPSTART_PROFILE_REDHAT})
+    install(FILES ${CMAKE_CURRENT_BINARY_DIR}/${RSERVER_UPSTART_PROFILE_REDHAT}
+-           DESTINATION ${RSERVER_UPSTART_DIR})
++           DESTINATION ${DISTRO_SHARE}/${RSERVER_UPSTART_DIR})
+ 
+     # install configured systemd profile
+    set(RSERVER_SYSTEMD_DIR "extras/systemd")
+--- rstudio-1.3.959-orig/src/cpp/server/ServerOptions.cpp	2020-05-19 04:11:10.000000000 +1000
++++ rstudio-1.3.959/src/cpp/server/ServerOptions.cpp	2020-05-25 19:34:19.377675880 +1000
+@@ -442,8 +442,8 @@
+ 
+    // convert relative paths by completing from the system installation
+    // path (this allows us to be relocatable)
+-   resolvePath(resourcePath, &wwwLocalPath_);
+-   resolvePath(resourcePath, &wwwSymbolMapsPath_);
++   resolvePath(resourcePath.completeChildPath(DISTRO_SHARE), &wwwLocalPath_);
++   resolvePath(resourcePath.completeChildPath(DISTRO_SHARE), &wwwSymbolMapsPath_);
+    resolvePath(binaryPath, &authPamHelperPath_);
+    resolvePath(binaryPath, &rsessionPath_);
+    resolvePath(binaryPath, &rldpathPath_);
+--- rstudio-1.3.959-orig/src/cpp/session/SessionOptions.cpp	2020-05-19 04:11:10.000000000 +1000
++++ rstudio-1.3.959/src/cpp/session/SessionOptions.cpp	2020-05-25 19:33:58.318606745 +1000
+@@ -52,7 +52,7 @@
+ namespace session {  
+ 
+ namespace {
+-const char* const kDefaultPandocPath = "bin/pandoc";
++const char* const kDefaultPandocPath = "bin";
+ const char* const kDefaultPostbackPath = "bin/postback/rpostback";
+ const char* const kDefaultRsclangPath = "bin/rsclang";
+ 
+@@ -586,14 +586,14 @@
+    }
+    
+    // convert relative paths by completing from the app resource path
+-   resolvePath(resourcePath_, &rResourcesPath_);
+-   resolvePath(resourcePath_, &agreementFilePath_);
+-   resolvePath(resourcePath_, &wwwLocalPath_);
+-   resolvePath(resourcePath_, &wwwSymbolMapsPath_);
+-   resolvePath(resourcePath_, &coreRSourcePath_);
+-   resolvePath(resourcePath_, &modulesRSourcePath_);
+-   resolvePath(resourcePath_, &sessionLibraryPath_);
+-   resolvePath(resourcePath_, &sessionPackageArchivesPath_);
++   resolvePath(resourcePath_.completeChildPath(DISTRO_SHARE), &rResourcesPath_);
++   resolvePath(resourcePath_.completeChildPath(DISTRO_SHARE), &agreementFilePath_);
++   resolvePath(resourcePath_.completeChildPath(DISTRO_SHARE), &wwwLocalPath_);
++   resolvePath(resourcePath_.completeChildPath(DISTRO_SHARE), &wwwSymbolMapsPath_);
++   resolvePath(resourcePath_.completeChildPath(DISTRO_SHARE), &coreRSourcePath_);
++   resolvePath(resourcePath_.completeChildPath(DISTRO_SHARE), &modulesRSourcePath_);
++   resolvePath(resourcePath_.completeChildPath(DISTRO_SHARE), &sessionLibraryPath_);
++   resolvePath(resourcePath_.completeChildPath(DISTRO_SHARE), &sessionPackageArchivesPath_);
+    resolvePostbackPath(resourcePath_, &rpostbackPath_);
+ #ifdef _WIN32
+    resolvePath(resourcePath_, &consoleIoPath_);
+@@ -626,7 +626,7 @@
+    }
+    winptyPath_ = pty.completePath(completion).getAbsolutePath();
+ #endif // _WIN32
+-   resolvePath(resourcePath_, &hunspellDictionariesPath_);
++   resolvePath(resourcePath_.completeChildPath(DISTRO_SHARE), &hunspellDictionariesPath_);
+    resolvePath(resourcePath_, &mathjaxPath_);
+    resolvePath(resourcePath_, &libclangHeadersPath_);
+    resolvePandocPath(resourcePath_, &pandocPath_);

diff --git a/sci-mathematics/rstudio/files/rstudio-1.3.959-prefs.patch b/sci-mathematics/rstudio/files/rstudio-1.3.959-prefs.patch
new file mode 100644
index 00000000000..4f961394769
--- /dev/null
+++ b/sci-mathematics/rstudio/files/rstudio-1.3.959-prefs.patch
@@ -0,0 +1,68 @@
+--- rstudio-1.3.959-orig/src/gwt/build.xml	2020-05-19 04:11:10.000000000 +1000
++++ rstudio-1.3.959/src/gwt/build.xml	2020-05-25 17:38:28.911881424 +1000
+@@ -28,19 +28,37 @@
+             classname="com.google.javascript.jscomp.ant.CompileTask"
+             classpath="${tools.dir}/compiler/compiler.jar"/>
+ 
++   <!-- Configure path to aopalliance -->
++   <property name="aopalliance.sdk" value="@GENTOO_PORTAGE_EPREFIX@/usr/share/aopalliance-1/lib"/>
++
++   <!-- Configure path to javax-inject -->
++   <property name="javax.inject" value="@GENTOO_PORTAGE_EPREFIX@/usr/share/javax-inject/lib"/>
++
++   <!-- Configure path to validation-api -->
++   <property name="validation.api" value="@GENTOO_PORTAGE_EPREFIX@/usr/share/validation-api-1.0/lib"/>
++   <property name="validation.api.sources" value="@GENTOO_PORTAGE_EPREFIX@/usr/share/validation-api-1.0/sources"/>
++
+    <!-- Configure path to GWT SDK -->
+    <property name="gwt.sdk" value="${lib.dir}/gwt/gwt-rstudio-1.3"/>
++   <!-- Configure path to Google Gin -->
++   <property name="gin.sdk" value="@GENTOO_PORTAGE_EPREFIX@/usr/share/gin-2.1/lib"/>
++
+    <property name="gwt.extra.args" value=""/>
+    <property name="gwt.main.module" value="org.rstudio.studio.RStudio"/>
+    <property name="ace.bin" value="${src.dir}/org/rstudio/studio/client/workbench/views/source/editors/text/ace"/>
++   <property environment="env"/>
+ 
+    <!-- configure code server -->
+    <property name="bind.address" value="127.0.0.1"/>
+ 
+    <path id="project.class.path">
+      <pathelement location="${build.dir}"/>
++      <fileset dir="${aopalliance.sdk}" includes="*.jar"/>
++      <fileset dir="${javax.inject}" includes="*.jar"/>
++      <fileset dir="${validation.api}" includes="*.jar"/>
++      <fileset dir="${validation.api.sources}" includes="*.zip"/>
+       <fileset dir="${gwt.sdk}" includes="*.jar"/>
+-      <fileset dir="${lib.dir}/gin/2.1.2" includes="*.jar"/>
++      <fileset dir="${gin.sdk}" includes="*.jar"/>
+    </path>
+ 
+    <path id="test.class.path">
+@@ -114,8 +132,10 @@
+             <pathelement location="${src.dir}"/>
+             <path refid="project.class.path"/>
+          </classpath>
++         <jvmarg value="-Duser.home=${env.T}"/>
+          <!-- add jvmarg -Xss16M or similar if you see a StackOverflowError -->
+          <jvmarg value="-Xmx1536M"/>
++         <jvmarg value="-Djava.util.prefs.userRoot=${env.T}"/>
+          <arg value="-war"/>
+          <arg value="${www.dir}"/>
+          <arg value="-localWorkers"/>
+@@ -168,6 +188,7 @@
+             <pathelement location="${src.dir}"/>
+             <path refid="project.class.path"/>
+          </classpath>
++         <jvmarg value="-Duser.home=${env.T}"/>
+          <jvmarg value="-Xmx2048M"/>
+          <arg value="-style"/>
+          <arg value="PRETTY"/>
+@@ -212,6 +233,7 @@
+             <pathelement location="${test.dir}"/>
+             <pathelement location="${src.dir}"/>
+         </classpath>
++        <jvmarg value="-Duser.home=${env.T}"/>
+         <classpath refid="project.class.path"/>
+         <classpath refid="unittest.class.path"/>
+         <arg value="org.rstudio.studio.client.RStudioUnitTestSuite"/>

diff --git a/sci-mathematics/rstudio/files/rstudio-1.3.959-qtsingleapplication.patch b/sci-mathematics/rstudio/files/rstudio-1.3.959-qtsingleapplication.patch
new file mode 100644
index 00000000000..3ced4f9afa1
--- /dev/null
+++ b/sci-mathematics/rstudio/files/rstudio-1.3.959-qtsingleapplication.patch
@@ -0,0 +1,60 @@
+--- rstudio-1.3.959-orig/src/cpp/desktop/CMakeLists.txt	2020-05-19 04:11:10.000000000 +1000
++++ rstudio-1.3.959/src/cpp/desktop/CMakeLists.txt	2020-05-24 17:15:47.039422975 +1000
+@@ -138,6 +138,13 @@
+ get_filename_component(QT_LIBRARY_PATH "${QT_BIN_DIR}/../lib"     ABSOLUTE CACHE)
+ get_filename_component(QT_INSTALL_PATH "${QT_BIN_DIR}/.."         ABSOLUTE CACHE)
+ 
++find_path(QTSINGLEAPPLIB_INCLUDE_DIR NAMES QtSingleApplication
++  PATH_SUFFIXES QtSolutions
++  PATHS
++  /usr/include/qt5)
++find_library(QTSINGLEAPPLIB Qt5Solutions_SingleApplication-2.6
++  libQt5Solutions_SingleApplication-2.6)
++
+ # disable clang warnings for qt sources
+ if(APPLE)
+    add_definitions(-Wno-unused-private-field
+@@ -156,7 +163,6 @@
+ 
+ set(MOC_DESKTOP_HEADER_FILES ${DESKTOP_HEADER_FILES})
+ list(REMOVE_ITEM MOC_DESKTOP_HEADER_FILES
+-  ${CMAKE_CURRENT_SOURCE_DIR}/3rdparty/qtsingleapplication/qtlockedfile.h
+   ${CMAKE_CURRENT_SOURCE_DIR}/DesktopDetectRHome.hpp
+   ${CMAKE_CURRENT_SOURCE_DIR}/DesktopOptions.hpp
+   ${CMAKE_CURRENT_SOURCE_DIR}/DesktopRVersion.hpp
+@@ -225,8 +231,6 @@
+   DesktopSynctex.cpp
+   DesktopJobLauncherOverlay.cpp
+   RemoteDesktopSessionLauncherOverlay.cpp
+-  3rdparty/qtsingleapplication/qtsingleapplication.cpp
+-  3rdparty/qtsingleapplication/qtlocalpeer.cpp
+ )
+ 
+ if(WIN32)
+@@ -283,6 +287,7 @@
+   ${OPENSSL_INCLUDE_DIR}
+   ${CMAKE_CURRENT_SOURCE_DIR}
+   ${CMAKE_CURRENT_BINARY_DIR}
++  ${QTSINGLEAPPLIB_INCLUDE_DIR}
+   ${EXT_SOURCE_DIR}
+   ${SESSION_SOURCE_DIR}/include
+   ${TESTS_INCLUDE_DIR}
+@@ -386,6 +391,7 @@
+    # set link dependencies
+    target_link_libraries(rstudio
+       ${RSTUDIO_QTMODULES}
++      ${QTSINGLEAPPLIB}
+       ${QT_LIBRARIES}
+       ${Boost_LIBRARIES}
+       rstudio-core
+--- rstudio-1.3.959-orig/src/cpp/desktop/DesktopPosixApplication.hpp	2020-05-19 04:11:10.000000000 +1000
++++ rstudio-1.3.959/src/cpp/desktop/DesktopPosixApplication.hpp	2020-05-24 17:13:22.050016953 +1000
+@@ -16,7 +16,7 @@
+ #ifndef DESKTOP_POSIX_APPLICATION_HPP
+ #define DESKTOP_POSIX_APPLICATION_HPP
+ 
+-#include "3rdparty/qtsingleapplication/QtSingleApplication"
++#include <QtSingleApplication>
+ 
+ #include "DesktopApplicationLaunch.hpp"
+ 

diff --git a/sci-mathematics/rstudio/rstudio-1.3.959.ebuild b/sci-mathematics/rstudio/rstudio-1.3.959.ebuild
new file mode 100644
index 00000000000..d708ec5bd51
--- /dev/null
+++ b/sci-mathematics/rstudio/rstudio-1.3.959.ebuild
@@ -0,0 +1,231 @@
+# Copyright 1999-2020 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=7
+
+inherit eutils cmake-utils pam xdg-utils java-pkg-2 java-ant-2 pax-utils prefix qmake-utils vcs-clean
+
+# TODO
+# * use dict from tree, linguas
+# * do src_test (use junit from tree?)
+
+GIN_VER=2.1.2
+# grep 'PANDOC_VERSION=' dependencies/common/install-pandoc
+# It should be PANDOC_VER=2.7.3 however >=app-text/pandoc-2.7.3 is not yet in portage
+PANDOC_VER=1.19.2.1
+# grep -5 QT_CANDIDATES src/cpp/desktop/CMakeLists.txt
+QT_VER=5.12.6
+QT_SLOT=5
+
+DESCRIPTION="IDE for the R language"
+HOMEPAGE="
+	http://www.rstudio.org
+	https://github.com/rstudio/rstudio/"
+SRC_URI="
+	https://github.com/rstudio/rstudio/archive/v${PV}.tar.gz -> ${P}.tar.gz
+	https://s3.amazonaws.com/rstudio-dictionaries/core-dictionaries.zip
+"
+
+LICENSE="AGPL-3"
+SLOT="0"
+KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
+IUSE="dedicated libressl server"
+
+RDEPEND="
+	>=app-text/pandoc-${PANDOC_VER}
+	dev-java/aopalliance:1
+	dev-java/gin:2.1
+	dev-java/javax-inject
+	=dev-java/validation-api-1.0*:1.0[source]
+	dev-haskell/pandoc-citeproc
+	dev-lang/R
+	dev-libs/boost:=
+	>=dev-libs/mathjax-2.7.4
+	sys-apps/util-linux
+	sys-devel/clang:*
+	sys-libs/zlib
+	>=virtual/jre-1.8:=
+	x11-libs/pango
+	!dedicated? (
+		>=dev-qt/qtcore-${QT_VER}:${QT_SLOT}
+		>=dev-qt/qtdeclarative-${QT_VER}:${QT_SLOT}
+		>=dev-qt/qtdbus-${QT_VER}:${QT_SLOT}
+		>=dev-qt/qtgui-${QT_VER}:${QT_SLOT}
+		>=dev-qt/qtnetwork-${QT_VER}:${QT_SLOT}
+		>=dev-qt/qtopengl-${QT_VER}:${QT_SLOT}
+		>=dev-qt/qtpositioning-${QT_VER}:${QT_SLOT}
+		>=dev-qt/qtprintsupport-${QT_VER}:${QT_SLOT}
+		>=dev-qt/qtsingleapplication-2.6.1_p20150629[X,qt5(+)]
+		>=dev-qt/qtsensors-${QT_VER}:${QT_SLOT}
+		>=dev-qt/qtsql-${QT_VER}:${QT_SLOT}
+		>=dev-qt/qtsvg-${QT_VER}:${QT_SLOT}
+		>=dev-qt/qtwebchannel-${QT_VER}:${QT_SLOT}
+		>=dev-qt/qtwebengine-${QT_VER}:${QT_SLOT}[widgets]
+		>=dev-qt/qtwidgets-${QT_VER}:${QT_SLOT}
+		>=dev-qt/qtxml-${QT_VER}:${QT_SLOT}
+		>=dev-qt/qtxmlpatterns-${QT_VER}:${QT_SLOT}
+		server? ( sys-libs/pam )
+	)
+	dedicated? ( sys-libs/pam )
+	dedicated? (
+		sys-libs/pam
+		acct-user/rstudio-server
+		acct-group/rstudio-server
+	)
+	server? (
+		acct-user/rstudio-server
+		acct-group/rstudio-server
+	)
+	!libressl? ( dev-libs/openssl:0= )
+	libressl? ( dev-libs/libressl:0= )"
+DEPEND="${RDEPEND}
+	app-arch/unzip
+	dev-java/ant-core
+	>=virtual/jdk-1.8:=
+	virtual/pkgconfig"
+#	test? ( dev-java/junit:4 )
+
+PATCHES=(
+	"${FILESDIR}"/${PN}-1.3.959-prefs.patch
+	"${FILESDIR}"/${PN}-1.3.959-paths.patch
+	"${FILESDIR}"/${PN}-1.3.959-pandoc-mathjax.patch
+	"${FILESDIR}"/${PN}-1.2.1335-linker_flags.patch
+	"${FILESDIR}"/${PN}-1.3.959-qtsingleapplication.patch
+	"${FILESDIR}"/${PN}-1.0.44-systemd.patch
+	"${FILESDIR}"/${PN}-1.3.959-core.patch
+	"${FILESDIR}"/${PN}-1.2.5042-boost-1.73.0.patch
+	"${FILESDIR}"/${PN}-1.3.959-R-4.0.0.patch
+)
+
+src_unpack() {
+	unpack ${P}.tar.gz
+	cd "${S}" || die
+	mkdir -p dependencies/common/dictionaries
+	unzip -qd dependencies/common/dictionaries \
+		"${DISTDIR}"/core-dictionaries.zip || die
+}
+
+src_prepare() {
+	cmake-utils_src_prepare
+	java-pkg-2_src_prepare
+	egit_clean
+
+	# Enable CMake to install our .service file for systemd usage
+	mkdir -vp "${S}/src/cpp/server/lib/systemd/system" || die
+	cp -v "${FILESDIR}/rstudio-server.service.in" "${S}/src/cpp/server/lib/systemd/system/" || die
+
+	# Adding -DDISTRO_SHARE=... to append-flags breaks cmake so using
+	# this sed hack for now. ~RMH
+	sed -i \
+		-e "s|DISTRO_SHARE|\"share/${PN}\"|g" \
+		src/cpp/server/ServerOptions.cpp \
+		src/cpp/session/SessionOptions.cpp || die
+
+	# use mathjax from system
+	ln -sf "${EPREFIX}"/usr/share/mathjax dependencies/common/mathjax-26 || die
+
+	# make sure icons and mime stuff are with prefix
+	sed -i \
+		-e "s:/usr:${EPREFIX}/usr:g" \
+		CMakeGlobals.txt src/cpp/desktop/CMakeLists.txt || die
+
+	# install themes in /etc/rstudio/extra/sthemes instead of /usr/extra/themes
+	sed -i \
+		-e "s@\(DESTINATION \"\)\(extras/themes\"\)@\1${EROOT}/etc/rstudio/\2@" \
+		src/cpp/server/CMakeLists.txt || die
+
+	# On Gentoo the rstudio-server configuration file is /etc/conf.d/rstudio-server.conf
+	sed -e "s@/etc/rstudio/rserver.conf@${EROOT}/etc/conf.d/rstudio-server.conf@" \
+		-i src/cpp/server/ServerOptions.cpp \
+		|| die
+
+	# Set the rsession.conf file location for Gentoo prefix
+	sed -e "s@/etc/rstudio/rsession.conf@${EROOT}/etc/rstudio/rsession.conf@" \
+		-i src/cpp/session/SessionOptions.cpp \
+		|| die
+
+	# dev-qt/qtsingleapplication-2.6.1_p20150629 does not provide a cmake module.
+	# It provides a library that has its version number appended to the end,
+	# which is difficult to handle in cmake, as find_library does not support
+	# searching for wildcard library names. So I find the library name from the
+	# qmake spec, and then sed this into the patched src/cpp/desktop/CMakeLists.txt.
+	rm -rf "${S}"/src/cpp/desktop/3rdparty || die
+	local s=$(grep '\-lQt$${QT_MAJOR_VERSION}Solutions_SingleApplication' \
+				   $(qt5_get_mkspecsdir)/features/qtsingleapplication.prf \
+					 | sed -e 's@\$\${QT_MAJOR_VERSION}@5@' \
+						   -e 's@LIBS \*= -l@@')
+	sed -e "s@Qt5Solutions_SingleApplication-2.6@${s}@g" \
+		-i "${S}"/src/cpp/desktop/CMakeLists.txt \
+		|| die
+
+	# The git commit for tag: git rev-list -n 1 v${PV}
+	sed -e 's@git ARGS rev-parse HEAD@echo ARGS 3a09be39fd51a8fafa8ae330007937d31924b395@'\
+		-i "${S}"/CMakeLists.txt \
+		"${S}"/CMakeGlobals.txt \
+		|| die
+
+	eprefixify src/gwt/build.xml
+}
+
+src_configure() {
+	export RSTUDIO_VERSION_MAJOR=$(ver_cut 1)
+	export RSTUDIO_VERSION_MINOR=$(ver_cut 2)
+	export RSTUDIO_VERSION_PATCH=$(ver_cut 3)
+
+	local mycmakeargs=(
+		-DDISTRO_SHARE=share/${PN}
+		-DRSTUDIO_TARGET=$(usex dedicated "Server" "$(usex server "Development" "Desktop")")
+		-DRSTUDIO_VERIFY_R_VERSION=FALSE
+		-DRSTUDIO_USE_SYSTEM_BOOST=TRUE
+		)
+
+	if use !dedicated; then
+		mycmakeargs+=(
+			-DRSTUDIO_INSTALL_FREEDESKTOP="$(usex !dedicated "ON" "OFF")"
+			-DQT_QMAKE_EXECUTABLE=$(qt5_get_bindir)/qmake
+		)
+	fi
+	cmake-utils_src_configure
+}
+
+src_compile() {
+	local JAVA_ANT_REWRITE_CLASSPATH="yes"
+	local EANT_BUILD_XML="src/gwt/build.xml"
+	local EANT_BUILD_TARGET="clean"
+	java-pkg-2_src_compile
+
+	# Avoid the rest of the oracle-jdk-bin-1.8.0.60 sandbox violations F: mkdir S: deny
+	# P: /root/.oracle_jre_usage.
+	export ANT_OPTS="-Duser.home=${T}"
+	cmake-utils_src_compile
+}
+
+src_install() {
+	export ANT_OPTS="-Duser.home=${T}"
+	cmake-utils_src_install
+	use dedicated || pax-mark m "${ED}/usr/bin/rstudio"
+	doconfd "${FILESDIR}"/rstudio-server.conf
+	insinto /etc/rstudio
+	doins "${FILESDIR}"/rsession.conf
+	dosym ../conf.d/rstudio-server.conf /etc/rstudio/rserver.conf
+	if use dedicated || use server; then
+		dopamd src/cpp/server/extras/pam/rstudio
+		newinitd "${FILESDIR}"/rstudio-server.initd rstudio-server
+	fi
+}
+
+pkg_preinst() {
+	java-pkg-2_pkg_preinst
+}
+
+pkg_postinst() {
+	use dedicated || { xdg_desktop_database_update
+		xdg_mimeinfo_database_update
+		xdg_icon_cache_update ;}
+}
+
+pkg_postrm() {
+	use dedicated || { xdg_desktop_database_update
+		xdg_mimeinfo_database_update
+		xdg_icon_cache_update ;}
+}


^ permalink raw reply related	[flat|nested] 12+ messages in thread

* [gentoo-commits] repo/gentoo:master commit in: sci-mathematics/rstudio/, sci-mathematics/rstudio/files/
@ 2020-07-17 10:50 Mark Wright
  0 siblings, 0 replies; 12+ messages in thread
From: Mark Wright @ 2020-07-17 10:50 UTC (permalink / raw
  To: gentoo-commits

commit:     9a942b9f13c331d304201d35fe1a0f78491291b3
Author:     Mark Wright <gienah <AT> gentoo <DOT> org>
AuthorDate: Fri Jul 17 10:46:53 2020 +0000
Commit:     Mark Wright <gienah <AT> gentoo <DOT> org>
CommitDate: Fri Jul 17 10:48:00 2020 +0000
URL:        https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=9a942b9f

sci-mathematics/rstudio: Bump to rstudio-1.3.1056

Package-Manager: Portage-2.3.103, Repoman-2.3.23
Signed-off-by: Mark Wright <gienah <AT> gentoo.org>

 sci-mathematics/rstudio/Manifest                   |   1 +
 .../rstudio/files/rstudio-1.3.1056-R-4.0.0.patch   |  58 ++++++
 .../files/rstudio-1.3.1056-boost-1.74.0.patch      |  30 +++
 sci-mathematics/rstudio/rstudio-1.3.1056.ebuild    | 232 +++++++++++++++++++++
 4 files changed, 321 insertions(+)

diff --git a/sci-mathematics/rstudio/Manifest b/sci-mathematics/rstudio/Manifest
index 063f6280255..686f27d6dda 100644
--- a/sci-mathematics/rstudio/Manifest
+++ b/sci-mathematics/rstudio/Manifest
@@ -1,4 +1,5 @@
 DIST core-dictionaries.zip 876339 BLAKE2B f29afcbf5a7f8ec635e5a5b248d978af286d18488f54c9a09a2b95fde19b796e4473e5846402a46dd24b71c6e4167512539aaa32ab6d99713d500a80aaf46796 SHA512 9c5830cc9fed575e223f1c61f02e48c5aea6801bb0cd2586f02437c17fdffdb1d36c396d5a8ecbe02ba01196e73458304345b1f6b92c052bc7a7d05961fac2c9
 DIST rstudio-1.2.5033.tar.gz 20456976 BLAKE2B 3cbca6a5180690104dddf1456168bd38708d4152ed9b7a167035dd66e270aeb6405169d34461cbd899738be1872607e3f3b6f81ff0b3c9e6a9ed965a889b1393 SHA512 3569d4fed342275a9905c87e4f97be63b6391d2c37f75397e06201a7c31f80d94799214f51ff8e57d458ef18d5e54afe1ec8a7c56ac05ed8b8225ecca72d1daf
 DIST rstudio-1.2.5042.tar.gz 20456999 BLAKE2B 3251ab2511daefefa395256fedb273ecc36dbc8118457474e3647f7616baea91301e597896582ad4b191195fc7baf17645c4c25b9a957a0c17a6251151b1dd87 SHA512 e09f2360abecde0c16e240e6838efb270a355bec3d3982ffde2b01b32b21e9281fef465734edbfeb5e05375529cc7f06d5b5d41304f367982f53ae7ad98e20f9
+DIST rstudio-1.3.1056.tar.gz 89584544 BLAKE2B 0e758ad97f9faa2d3932a49dafd92bc21199a5c0a20e2d8480267ebbb7cd11dc38596b4bb697e04add7bfe6b126f7b2ae6675040a0ac8caca5a5cf737f5ad6eb SHA512 8a9077c2ae021e0cf4cca41b374a50534087b35fd2c1e4b18bdd5ba3672e1ab275046e483ec8a3aba729a8e39f961149fb03a053ea005d8a32873b51201baca2
 DIST rstudio-1.3.959.tar.gz 89639419 BLAKE2B d45b2c1b0e426ddb5a945e59a8127ddfd47f6230ef0929639c4b525382ae57437a273df6ade85cfbf3a29911cf0158ee2e0808bfa94e783d70d4615f6c228f31 SHA512 e5d8bfe16011790ff4723c731043f44070d8fe48f85c5a9ab8389c9a2b7a1d3813e9362063ec4c6a6ca3b0a0857e2190481cbb74191650a129c0d2e10b342fac

diff --git a/sci-mathematics/rstudio/files/rstudio-1.3.1056-R-4.0.0.patch b/sci-mathematics/rstudio/files/rstudio-1.3.1056-R-4.0.0.patch
new file mode 100644
index 00000000000..662089e93a0
--- /dev/null
+++ b/sci-mathematics/rstudio/files/rstudio-1.3.1056-R-4.0.0.patch
@@ -0,0 +1,58 @@
+From 71b1a935762efd24a79de193662450de5a89f67e Mon Sep 17 00:00:00 2001
+From: Jonathan McPherson <jonathan@rstudio.com>
+Date: Tue, 14 Jan 2020 12:53:20 -0800
+Subject: [PATCH] use R_NoSave over R_Slave for R 4.0+
+
+---
+ src/cpp/r/CMakeLists.txt             | 12 ++++++++++++
+ src/cpp/r/config.h.in                |  8 +++++++-
+ src/cpp/r/session/REmbeddedPosix.cpp | 20 ++++++++++++++------
+ 3 files changed, 33 insertions(+), 7 deletions(-)
+
+diff --git a/src/cpp/r/CMakeLists.txt b/src/cpp/r/CMakeLists.txt
+index 6984ae309c..29784b8b67 100644
+--- a/src/cpp/r/CMakeLists.txt
++++ b/src/cpp/r/CMakeLists.txt
+@@ -15,6 +15,18 @@
+ 
+ project (R)
+ 
++# find the version of R in play
++find_package(LibR REQUIRED)
++execute_process(
++    COMMAND "${LIBR_EXECUTABLE}" "--vanilla" "--slave" "-e" "cat(as.character(getRversion()))"
++    OUTPUT_VARIABLE LIBR_VERSION)
++
++# parse and save the R version to a variable
++string(REPLACE "." ";" R_VERSION_LIST "${LIBR_VERSION}")
++list(GET R_VERSION_LIST 0 R_VERSION_MAJOR)
++list(GET R_VERSION_LIST 1 R_VERSION_MINOR)
++list(GET R_VERSION_LIST 2 R_VERSION_PATCH)
++
+ # include files
+ file(GLOB_RECURSE R_HEADER_FILES "*.h*")
+ 
+diff --git a/src/cpp/r/config.h.in b/src/cpp/r/config.h.in
+index 6ba67c8e09..00bc8b6191 100644
+--- a/src/cpp/r/config.h.in
++++ b/src/cpp/r/config.h.in
+@@ -1,7 +1,7 @@
+ /*
+  * config.h.in
+  *
+- * Copyright (C) 2009-12 by RStudio, PBC
++ * Copyright (C) 2009-20 by RStudio, Inc.
+  *
+  * Unless you have received this program directly from RStudio pursuant
+  * to the terms of a commercial license agreement with RStudio, then
+@@ -16,4 +16,10 @@
+ 
+ #cmakedefine PANGO_CAIRO_FOUND
+ 
++// Important: These variables represent the version of R found during
++// compile/link time, NOT the version of R present at runtime.
++#define R_VERSION_MAJOR ${R_VERSION_MAJOR}
++#define R_VERSION_MINOR ${R_VERSION_MINOR}
++#define R_VERSION_PATCH ${R_VERSION_PATCH}
++
+ 

diff --git a/sci-mathematics/rstudio/files/rstudio-1.3.1056-boost-1.74.0.patch b/sci-mathematics/rstudio/files/rstudio-1.3.1056-boost-1.74.0.patch
new file mode 100644
index 00000000000..2fde3119e2a
--- /dev/null
+++ b/sci-mathematics/rstudio/files/rstudio-1.3.1056-boost-1.74.0.patch
@@ -0,0 +1,30 @@
+--- rstudio-1.3.1056-orig/src/cpp/core/file_lock/FileLock.cpp	2020-07-08 08:25:03.000000000 +1000
++++ rstudio-1.3.1056/src/cpp/core/file_lock/FileLock.cpp	2020-07-17 18:01:57.016882590 +1000
+@@ -26,6 +26,7 @@
+ #include <core/system/Environment.hpp>
+ 
+ #include <boost/algorithm/string.hpp>
++#include <boost/bind.hpp>
+ 
+ // borrowed from SessionConstants.hpp
+ #define kRStudioSessionRoute "RSTUDIO_SESSION_ROUTE"
+--- rstudio-1.3.1056-orig/src/cpp/core/HtmlUtils.cpp	2020-07-08 08:25:03.000000000 +1000
++++ rstudio-1.3.1056/src/cpp/core/HtmlUtils.cpp	2020-07-17 18:01:58.129886387 +1000
+@@ -19,6 +19,7 @@
+ 
+ #include <boost/format.hpp>
+ #include <boost/algorithm/string/predicate.hpp>
++#include <boost/bind.hpp>
+ 
+ #include <core/Base64.hpp>
+ #include <core/FileSerializer.hpp>
+--- rstudio-1.3.1056-orig/src/cpp/r/session/RStdCallbacks.cpp	2020-07-08 08:25:03.000000000 +1000
++++ rstudio-1.3.1056/src/cpp/r/session/RStdCallbacks.cpp	2020-07-17 18:32:09.044071640 +1000
+@@ -19,6 +19,7 @@
+ 
+ #include <boost/function.hpp>
+ #include <boost/regex.hpp>
++#include <boost/bind.hpp>
+ 
+ #include <r/RExec.hpp>
+ #include <r/ROptions.hpp>

diff --git a/sci-mathematics/rstudio/rstudio-1.3.1056.ebuild b/sci-mathematics/rstudio/rstudio-1.3.1056.ebuild
new file mode 100644
index 00000000000..49d75885be5
--- /dev/null
+++ b/sci-mathematics/rstudio/rstudio-1.3.1056.ebuild
@@ -0,0 +1,232 @@
+# Copyright 1999-2020 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=7
+
+inherit eutils cmake pam xdg-utils java-pkg-2 java-ant-2 pax-utils prefix qmake-utils vcs-clean
+
+# TODO
+# * use dict from tree, linguas
+# * do src_test (use junit from tree?)
+
+GIN_VER=2.1.2
+# grep 'PANDOC_VERSION=' dependencies/common/install-pandoc
+# It should be PANDOC_VER=2.7.3 however >=app-text/pandoc-2.7.3 is not yet in portage
+PANDOC_VER=1.19.2.1
+# grep -5 QT_CANDIDATES src/cpp/desktop/CMakeLists.txt
+QT_VER=5.12.6
+QT_SLOT=5
+
+DESCRIPTION="IDE for the R language"
+HOMEPAGE="
+	http://www.rstudio.org
+	https://github.com/rstudio/rstudio/"
+SRC_URI="
+	https://github.com/rstudio/rstudio/archive/v${PV}.tar.gz -> ${P}.tar.gz
+	https://s3.amazonaws.com/rstudio-dictionaries/core-dictionaries.zip
+"
+
+LICENSE="AGPL-3"
+SLOT="0"
+KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
+IUSE="dedicated libressl server"
+
+RDEPEND="
+	>=app-text/pandoc-${PANDOC_VER}
+	dev-java/aopalliance:1
+	dev-java/gin:2.1
+	dev-java/javax-inject
+	=dev-java/validation-api-1.0*:1.0[source]
+	dev-haskell/pandoc-citeproc
+	dev-lang/R
+	dev-libs/boost:=
+	>=dev-libs/mathjax-2.7.4
+	sys-apps/util-linux
+	sys-devel/clang:*
+	sys-libs/zlib
+	>=virtual/jre-1.8:=
+	x11-libs/pango
+	!dedicated? (
+		>=dev-qt/qtcore-${QT_VER}:${QT_SLOT}
+		>=dev-qt/qtdeclarative-${QT_VER}:${QT_SLOT}
+		>=dev-qt/qtdbus-${QT_VER}:${QT_SLOT}
+		>=dev-qt/qtgui-${QT_VER}:${QT_SLOT}
+		>=dev-qt/qtnetwork-${QT_VER}:${QT_SLOT}
+		>=dev-qt/qtopengl-${QT_VER}:${QT_SLOT}
+		>=dev-qt/qtpositioning-${QT_VER}:${QT_SLOT}
+		>=dev-qt/qtprintsupport-${QT_VER}:${QT_SLOT}
+		>=dev-qt/qtsingleapplication-2.6.1_p20150629[X,qt5(+)]
+		>=dev-qt/qtsensors-${QT_VER}:${QT_SLOT}
+		>=dev-qt/qtsql-${QT_VER}:${QT_SLOT}
+		>=dev-qt/qtsvg-${QT_VER}:${QT_SLOT}
+		>=dev-qt/qtwebchannel-${QT_VER}:${QT_SLOT}
+		>=dev-qt/qtwebengine-${QT_VER}:${QT_SLOT}[widgets]
+		>=dev-qt/qtwidgets-${QT_VER}:${QT_SLOT}
+		>=dev-qt/qtxml-${QT_VER}:${QT_SLOT}
+		>=dev-qt/qtxmlpatterns-${QT_VER}:${QT_SLOT}
+		server? ( sys-libs/pam )
+	)
+	dedicated? ( sys-libs/pam )
+	dedicated? (
+		sys-libs/pam
+		acct-user/rstudio-server
+		acct-group/rstudio-server
+	)
+	server? (
+		acct-user/rstudio-server
+		acct-group/rstudio-server
+	)
+	!libressl? ( dev-libs/openssl:0= )
+	libressl? ( dev-libs/libressl:0= )"
+DEPEND="${RDEPEND}
+	app-arch/unzip
+	dev-java/ant-core
+	>=virtual/jdk-1.8:=
+	virtual/pkgconfig"
+#	test? ( dev-java/junit:4 )
+
+PATCHES=(
+	"${FILESDIR}"/${PN}-1.3.959-prefs.patch
+	"${FILESDIR}"/${PN}-1.3.959-paths.patch
+	"${FILESDIR}"/${PN}-1.3.959-pandoc-mathjax.patch
+	"${FILESDIR}"/${PN}-1.2.1335-linker_flags.patch
+	"${FILESDIR}"/${PN}-1.3.959-qtsingleapplication.patch
+	"${FILESDIR}"/${PN}-1.0.44-systemd.patch
+	"${FILESDIR}"/${PN}-1.3.959-core.patch
+	"${FILESDIR}"/${PN}-1.2.5042-boost-1.73.0.patch
+	"${FILESDIR}"/${PN}-1.3.1056-R-4.0.0.patch
+	"${FILESDIR}"/${PN}-1.3.1056-boost-1.74.0.patch
+)
+
+src_unpack() {
+	unpack ${P}.tar.gz
+	cd "${S}" || die
+	mkdir -p dependencies/common/dictionaries
+	unzip -qd dependencies/common/dictionaries \
+		"${DISTDIR}"/core-dictionaries.zip || die
+}
+
+src_prepare() {
+	cmake_src_prepare
+	java-pkg-2_src_prepare
+	egit_clean
+
+	# Enable CMake to install our .service file for systemd usage
+	mkdir -vp "${S}/src/cpp/server/lib/systemd/system" || die
+	cp -v "${FILESDIR}/rstudio-server.service.in" "${S}/src/cpp/server/lib/systemd/system/" || die
+
+	# Adding -DDISTRO_SHARE=... to append-flags breaks cmake so using
+	# this sed hack for now. ~RMH
+	sed -i \
+		-e "s|DISTRO_SHARE|\"share/${PN}\"|g" \
+		src/cpp/server/ServerOptions.cpp \
+		src/cpp/session/SessionOptions.cpp || die
+
+	# use mathjax from system
+	ln -sf "${EPREFIX}"/usr/share/mathjax dependencies/common/mathjax-26 || die
+
+	# make sure icons and mime stuff are with prefix
+	sed -i \
+		-e "s:/usr:${EPREFIX}/usr:g" \
+		CMakeGlobals.txt src/cpp/desktop/CMakeLists.txt || die
+
+	# install themes in /etc/rstudio/extra/sthemes instead of /usr/extra/themes
+	sed -i \
+		-e "s@\(DESTINATION \"\)\(extras/themes\"\)@\1${EROOT}/etc/rstudio/\2@" \
+		src/cpp/server/CMakeLists.txt || die
+
+	# On Gentoo the rstudio-server configuration file is /etc/conf.d/rstudio-server.conf
+	sed -e "s@/etc/rstudio/rserver.conf@${EROOT}/etc/conf.d/rstudio-server.conf@" \
+		-i src/cpp/server/ServerOptions.cpp \
+		|| die
+
+	# Set the rsession.conf file location for Gentoo prefix
+	sed -e "s@/etc/rstudio/rsession.conf@${EROOT}/etc/rstudio/rsession.conf@" \
+		-i src/cpp/session/SessionOptions.cpp \
+		|| die
+
+	# dev-qt/qtsingleapplication-2.6.1_p20150629 does not provide a cmake module.
+	# It provides a library that has its version number appended to the end,
+	# which is difficult to handle in cmake, as find_library does not support
+	# searching for wildcard library names. So I find the library name from the
+	# qmake spec, and then sed this into the patched src/cpp/desktop/CMakeLists.txt.
+	rm -rf "${S}"/src/cpp/desktop/3rdparty || die
+	local s=$(grep '\-lQt$${QT_MAJOR_VERSION}Solutions_SingleApplication' \
+				   $(qt5_get_mkspecsdir)/features/qtsingleapplication.prf \
+					 | sed -e 's@\$\${QT_MAJOR_VERSION}@5@' \
+						   -e 's@LIBS \*= -l@@')
+	sed -e "s@Qt5Solutions_SingleApplication-2.6@${s}@g" \
+		-i "${S}"/src/cpp/desktop/CMakeLists.txt \
+		|| die
+
+	# The git commit for tag: git rev-list -n 1 v${PV}
+	sed -e 's@git ARGS rev-parse HEAD@echo ARGS 5a4dee980c998d9a270a83b582b367126f3914cf@'\
+		-i "${S}"/CMakeLists.txt \
+		"${S}"/CMakeGlobals.txt \
+		|| die
+
+	eprefixify src/gwt/build.xml
+}
+
+src_configure() {
+	export RSTUDIO_VERSION_MAJOR=$(ver_cut 1)
+	export RSTUDIO_VERSION_MINOR=$(ver_cut 2)
+	export RSTUDIO_VERSION_PATCH=$(ver_cut 3)
+
+	local mycmakeargs=(
+		-DDISTRO_SHARE=share/${PN}
+		-DRSTUDIO_TARGET=$(usex dedicated "Server" "$(usex server "Development" "Desktop")")
+		-DRSTUDIO_VERIFY_R_VERSION=FALSE
+		-DRSTUDIO_USE_SYSTEM_BOOST=TRUE
+		)
+
+	if use !dedicated; then
+		mycmakeargs+=(
+			-DRSTUDIO_INSTALL_FREEDESKTOP="$(usex !dedicated "ON" "OFF")"
+			-DQT_QMAKE_EXECUTABLE=$(qt5_get_bindir)/qmake
+		)
+	fi
+	cmake_src_configure
+}
+
+src_compile() {
+	local JAVA_ANT_REWRITE_CLASSPATH="yes"
+	local EANT_BUILD_XML="src/gwt/build.xml"
+	local EANT_BUILD_TARGET="clean"
+	java-pkg-2_src_compile
+
+	# Avoid the rest of the oracle-jdk-bin-1.8.0.60 sandbox violations F: mkdir S: deny
+	# P: /root/.oracle_jre_usage.
+	export ANT_OPTS="-Duser.home=${T}"
+	cmake_src_compile
+}
+
+src_install() {
+	export ANT_OPTS="-Duser.home=${T}"
+	cmake_src_install
+	use dedicated || pax-mark m "${ED}/usr/bin/rstudio"
+	doconfd "${FILESDIR}"/rstudio-server.conf
+	insinto /etc/rstudio
+	doins "${FILESDIR}"/rsession.conf
+	dosym ../conf.d/rstudio-server.conf /etc/rstudio/rserver.conf
+	if use dedicated || use server; then
+		dopamd src/cpp/server/extras/pam/rstudio
+		newinitd "${FILESDIR}"/rstudio-server.initd rstudio-server
+	fi
+}
+
+pkg_preinst() {
+	java-pkg-2_pkg_preinst
+}
+
+pkg_postinst() {
+	use dedicated || { xdg_desktop_database_update
+		xdg_mimeinfo_database_update
+		xdg_icon_cache_update ;}
+}
+
+pkg_postrm() {
+	use dedicated || { xdg_desktop_database_update
+		xdg_mimeinfo_database_update
+		xdg_icon_cache_update ;}
+}


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