[gentoo-commits] proj/sci:master commit in: sci-biology/ncbi-tools++/

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* [gentoo-commits] proj/sci:master commit in: sci-biology/ncbi-tools++/
@ 2013-01-07 23:00 Martin Mokrejs
  0 siblings, 0 replies; 49+ messages in thread
From: Martin Mokrejs @ 2013-01-07 23:00 UTC (permalink / raw
  To: gentoo-commits

commit:     4ef26689d731fc16766d88682ec2fc8903fcfcde
Author:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Mon Jan  7 22:59:45 2013 +0000
Commit:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Mon Jan  7 22:59:45 2013 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=4ef26689

reverting to --no-as-needed LDFLAG

---
 sci-biology/ncbi-tools++/ncbi-tools++-9.0.0.ebuild |    6 ++----
 1 files changed, 2 insertions(+), 4 deletions(-)

diff --git a/sci-biology/ncbi-tools++/ncbi-tools++-9.0.0.ebuild b/sci-biology/ncbi-tools++/ncbi-tools++-9.0.0.ebuild
index fa05240..f93b1aa 100644
--- a/sci-biology/ncbi-tools++/ncbi-tools++-9.0.0.ebuild
+++ b/sci-biology/ncbi-tools++/ncbi-tools++-9.0.0.ebuild
@@ -131,7 +131,7 @@ RDEPEND="${DEPEND}"
 S="${WORKDIR}/${MY_P}"
 
 src_prepare() {
-#	filter-ldflags -Wl,--as-needed
+	filter-ldflags -Wl,--as-needed
 #	append-ldflags -Wl,--no-undefined
 	sed -i -e 's/-print-file-name=libstdc++.a//' \
 		-e '/sed/ s/\([gO]\[0-9\]\)\*/\1\\+/' \
@@ -283,10 +283,8 @@ src_configure() {
 		--with-lfs \
 		--prefix="${ED}"/usr \
 		--libdir="${ED}"/usr/$(get_libdir)/"${PN}" \
-		${myconf} LDFLAGS="-Wl,--as-needed" \
+		${myconf} LDFLAGS="-Wl,--no-as-needed" \
 		|| die
-
-		# ${myconf} LDFLAGS="-Wl,--no-as-needed"
 }
 
 src_compile() {


^ permalink raw reply related	[flat|nested] 49+ messages in thread

* [gentoo-commits] proj/sci:master commit in: sci-biology/ncbi-tools++/
@ 2013-01-29 21:23 Justin Lecher
  0 siblings, 0 replies; 49+ messages in thread
From: Justin Lecher @ 2013-01-29 21:23 UTC (permalink / raw
  To: gentoo-commits

commit:     22fd8327e252d7cf356f2337cafed02bef31a42d
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Tue Jan 29 21:23:35 2013 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Tue Jan 29 21:23:35 2013 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=22fd8327

my version

Signed-off-by: Justin Lecher <jlec <AT> gentoo.org>

---
 .../ncbi-tools++/ncbi-tools++-9.0.0-r1.ebuild      |  345 ++++++++++++++++++++
 1 files changed, 345 insertions(+), 0 deletions(-)

diff --git a/sci-biology/ncbi-tools++/ncbi-tools++-9.0.0-r1.ebuild b/sci-biology/ncbi-tools++/ncbi-tools++-9.0.0-r1.ebuild
new file mode 100644
index 0000000..9806b41
--- /dev/null
+++ b/sci-biology/ncbi-tools++/ncbi-tools++-9.0.0-r1.ebuild
@@ -0,0 +1,345 @@
+# Copyright 1999-2012 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/ncbi-tools++/ncbi-tools++-0.2010.06.15-r1.ebuild,v 1.3 2012/11/05 11:22:49 jlec Exp $
+
+EAPI=5
+
+inherit eutils flag-o-matic multilib toolchain-funcs
+
+MY_TAG="Jun_15_2010"
+MY_Y="${MY_TAG/*_/}"
+MY_PV="9_0_0"
+MY_P="ncbi_cxx--${MY_PV}"
+#ftp://ftp.ncbi.nlm.nih.gov/toolbox/ncbi_tools++/ARCHIVE/9_0_0/ncbi_cxx--9_0_0.tar.gz
+
+
+DESCRIPTION="NCBI C++ Toolkit, including NCBI BLAST+"
+HOMEPAGE="http://www.ncbi.nlm.nih.gov/books/bv.fcgi?rid=toolkit"
+SRC_URI="
+	ftp://ftp.ncbi.nih.gov/toolbox/ncbi_tools++/ARCHIVE/${MY_PV}/ncbi_cxx--${MY_PV}.tar.gz"
+#	http://dev.gentoo.org/~jlec/distfiles/${PN}-${PV#0.}-asneeded.patch.xz"
+
+LICENSE="public-domain"
+SLOT="0"
+IUSE="
+	debug static-libs static threads pch
+	test wxwidgets odbc
+	berkdb boost bzip2 cppunit curl expat fastcgi fltk freetype ftds gif 
+	glut gnutls hdf5 icu jpeg lzo mesa mysql muparser opengl pcre png python
+	sablotron sqlite sqlite3 ssl tiff xerces xalan xml xpm xslt X"
+#KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
+KEYWORDS=""
+
+# sys-libs/db should be compiled with USE=cxx
+DEPEND="
+	berkdb? ( sys-libs/db:4.3[cxx] )
+	ftds? ( dev-db/freetds )
+	boost? ( dev-libs/boost )
+	curl? ( net-misc/curl )
+	sqlite? ( dev-db/sqlite )
+	sqlite3? ( dev-db/sqlite:3 )
+	mysql? ( virtual/mysql )
+	gnutls? ( net-libs/gnutls )
+	ssl? ( dev-libs/openssl )
+	fltk? ( x11-libs/fltk )
+	opengl? ( virtual/opengl )
+	mesa? ( media-libs/mesa )
+	glut? ( media-libs/freeglut )
+	freetype? ( media-libs/freetype )
+	fastcgi? ( www-apache/mod_fastcgi )
+	python? ( dev-lang/python )
+	cppunit? ( dev-util/cppunit )
+	icu? ( dev-libs/icu )
+	expat? ( dev-libs/expat )
+	sablotron? ( app-text/sablotron )
+	xml? ( dev-libs/libxml2 )
+	xslt? ( dev-libs/libxslt )
+	xerces? ( dev-libs/xerces-c )
+	xalan? ( dev-libs/xalan-c )
+	muparser? ( dev-cpp/muParser )
+	hdf5? ( sci-libs/hdf5 )
+	gif? ( media-libs/giflib )
+	jpeg? ( virtual/jpeg )
+	png? ( media-libs/libpng )
+	tiff? ( media-libs/tiff )
+	xpm? ( x11-libs/libXpm )
+	dev-libs/lzo
+	app-arch/bzip2
+	dev-libs/libpcre"
+# USE flags which should be added somehow: wxWindows wxWidgets SP ORBacus ODBC OEChem sge
+
+# configure options, may want to expose some
+#  --without-debug         build non-debug versions of libs and apps
+#  --without-optimization  turn off optimization flags in non-debug mode
+#  --with-profiling        build profiled versions of libs and apps
+#  --with-tcheck(=DIR)     build for Intel Thread Checker (in DIR)
+#  --with-dll              build all libraries as DLLs
+#  --with-static           build all libraries statically even if --with-dll
+#  --with-static-exe       build all executables as statically as possible
+#  --with-plugin-auto-load always enable the plugin manager by default
+#  --with-bin-release      build executables suitable for public release
+#  --with-mt               compile in a MultiThread-safe manner
+#  --with-64               compile to 64-bit code
+#  --with-universal        build universal binaries on Mac OS X
+#  --with-universal=CPUs   build universal binaries targeting the given CPUs
+#  --without-exe           do not build executables
+#  --with-runpath=         hard-code the runtime path to DLLs
+#  --with-lfs              enable large file support to the extent possible
+#  --with-extra-action=    script to call after the configuration is complete
+#  --with-autodep          automatic generation of dependencies (GNU make)
+#  --with-build-root=DIR   specify a non-default build directory name
+#  --with-fake-root=DIR    appear to have been built under DIR
+#  --without-suffix        no Release/Debug, MT or DLL sfx in the build dir name
+#  --with-hostspec         add full host specs to the build dir name
+#  --without-version       don't always include the cplr ver in the bd name
+#  --with-build-root-sfx=X add a user-specified suffix to the build dir name
+#  --without-execopy       do not copy built executables to the BIN area
+#  --with-bincopy          populate lib and bin with copies, not hard links
+#  --with-lib-rebuilds     ensure that apps use up-to-date libraries
+#  --with-lib-rebuilds=ask ask whether to update each app's libraries
+#  --without-deactivation  keep old copies of libraries that no longer build
+#  --without-makefile-auto-update  do not auto-update generated makefiles
+#  --with-projects=FILE    build projects listed in FILE by default
+#  --without-flat-makefile do not generate an all-encompassing flat makefile
+#  --with-configure-dialog allow interactive flat makefile project selection
+#  --with-saved-settings=F load configuration settings from the file F
+#  --with-check            run test suite after the build
+#  --with-check-tools=...  use the specified tools for testing
+#  --with-ncbi-public      ensure compatibility for all in-house platforms
+#  --with-strip            strip binaries at build time
+#  --with-pch              use precompiled headers if possible
+#  --with-caution          cancel configuration unconditionally when in doubt
+#  --without-caution       proceed without asking when in doubt
+#  --without-ccache        do not automatically use ccache if available
+#  --without-distcc        do not automatically use distcc if available
+#  --without-ncbi-c        do not use NCBI C Toolkit
+#  --without-sss           do not use NCBI SSS libraries
+#  --without-utils         do not use NCBI SSS UTIL library
+#  --without-sssdb         do not use NCBI SSS DB library
+#  --with-included-sss     use the in-tree copy of SSS
+
+#  --without-local-lbsm    turn off support for IPC with locally running LBSMD
+#  --without-ncbi-crypt    use a dummy stubbed-out version of ncbi_crypt
+#  --without-connext       do not build non-public CONNECT library extensions
+#  --without-serial        do not build the serialization library and tools
+#  --without-objects       do not generate/build serializeable objects from ASNs
+#  --without-dbapi         do not build database connectivity libraries
+#  --without-app           do not build standalone applications like ID1_FETCH
+#  --without-ctools        do not build NCBI C Toolkit based projects
+#  --without-gui           do not build most graphical projects
+#  --without-algo          do not build CPU-intensive algorithms
+#  --without-internal      do not build internal projects
+#  --with-gbench           ensure that Genome Workbench can be built
+#  --without-gbench        do not build Genome Workbench
+
+RDEPEND="${DEPEND}"
+
+S="${WORKDIR}/${MY_P}"
+
+src_prepare() {
+#	filter-ldflags -Wl,--as-needed
+#	append-ldflags -Wl,--no-undefined
+#	sed -i -e 's/-print-file-name=libstdc++.a//' \
+#		-e '/sed/ s/\([gO]\[0-9\]\)\*/\1\\+/' \
+#		src/build-system/configure || die
+#	epatch \
+#		"${FILESDIR}"/${PN}-${PV#0.}-fix-order-of-libs.patch \
+#		"${FILESDIR}"/curl-types.patch \
+#		"${FILESDIR}"/malloc_initialize_upstream_fix.patch \
+#		"${FILESDIR}"/respect_CXXFLAGS_configure.ac.patch \
+#		"${FILESDIR}"/respect_CXXFLAGS_configure.patch \
+#		"${FILESDIR}"/report_project_settings_configure.ac.patch \
+#		"${FILESDIR}"/report_project_settings_configure.patch \
+#		"${FILESDIR}"/make_install.patch
+
+#		"${FILESDIR}"/${PN}-${PV#0.}-disable_test_compress.patch
+
+
+#		"${FILESDIR}"/${PN}-${PV#0.}-gcc46.patch \
+#		"${FILESDIR}"/${PN}-${PV#0.}-gcc47.patch \
+#		"${WORKDIR}"/${PN}-${PV#0.}-asneeded.patch \
+#		"${FILESDIR}"/${PN}-${PV#0.}-libpng15.patch \
+#		"${FILESDIR}"/${PN}-${PV#0.}-glibc-214.patch
+
+#	use prefix && append-ldflags -Wl,-rpath,"${EPREFIX}/usr/$(get_libdir)/${PN}"
+	tc-export CXX CC
+}
+
+src_configure() {
+	local myconf=()
+	#--without-optimization  turn off optimization flags in non-debug mode
+	#--with-profiling        build profiled versions of libs and apps
+	#--with-tcheck(=DIR)     build for Intel Thread Checker (in DIR)
+	#--with-plugin-auto-load always enable the plugin manager by default
+	#--with-bundles          build bundles in addition to dylibs on Mac OS X
+	#--with-bin-release      build executables suitable for public release
+	#	no dll and such
+	#--with-64               compile to 64-bit code
+	# --with-universal        build universal binaries on Mac OS X
+	# --with-universal=CPUs   build universal binaries targeting the given CPUs
+	# --without-exe           do not build executables
+	#--with-relative-runpath=P specify an executable-relative DLL search path
+	# --with-hard-runpath     hard-code runtime path, ignoring LD_LIBRARY_PATH
+	# --with-limited-linker   don't attempt to build especially large projects
+	#--with-extra-action=    script to call after the configuration is complete
+	#--with-autodep          automatic generation of dependencies (GNU make)
+	# --with-fake-root=DIR    appear to have been built under DIR
+	#--with-build-root-sfx=X add a user-specified suffix to the build dir name
+	# --without-execopy       do not copy built executables to the BIN area
+	#--with-lib-rebuilds     ensure that apps use up-to-date libraries
+	# --with-lib-rebuilds=ask ask whether to update each app's libraries
+	# --without-deactivation  keep old copies of libraries that no longer build
+	# --without-makefile-auto-update  do not auto-update generated makefiles
+	# --with-projects=FILE    build projects listed in FILE by default
+	# --without-flat-makefile do not generate an all-encompassing flat makefile
+	# --with-configure-dialog allow interactive flat makefile project selection
+	# --with-saved-settings=F load configuration settings from the file F
+	#-with-check-tools=...  use the specified tools for testing
+	# --with-ncbi-public      ensure compatibility for all in-house platforms
+	#--with-sybase-local=DIR use local SYBASE install (DIR is optional)
+	# --with-sybase-new       use newer SYBASE install (12.5 rather than 12.0)
+	#--without-ftds-renamed  do not rename Sybase DBLIB symbols in built-in FTDS
+	#--without-sp            do not use SP libraries
+	#--without-orbacus       do not use ORBacus CORBA libraries
+	# --with-orbacus=DIR      use ORBacus installation in DIR
+	#--with-jni(=JDK-DIR)    build Java bindings (against the JDK in JDK-DIR)
+	#--with-sablot=DIR       use Sablotron installation in DIR
+	# --without-sablot,       do not use Sablotron
+	#--with-oechem=DIR       use OpenEye OEChem installation in DIR
+	# --without-oechem        do not use OEChem
+	# --with-sge=DIR          use Sun Grid Engine installation in DIR
+	# --without-sge           do not use Sun Grid Engine
+	#--with-magic=DIR        use libmagic installation in DIR
+	# --without-magic         do not use libmagic
+	#--without-local-lbsm    turn off support for IPC with locally running LBSMD
+	# --without-ncbi-crypt    use a dummy stubbed-out version of ncbi_crypt
+	# --without-connext       do not build non-public CONNECT library extensions
+	# --without-serial        do not build the serialization library and tools
+	# --without-objects       do not generate/build serializeable objects from ASNs
+	# --without-dbapi         do not build database connectivity libraries
+	# --without-app           do not build standalone applications like ID1_FETCH
+	# --without-gui           do not build most graphical projects
+	# --without-algo          do not build CPU-intensive algorithms
+	#--without-internal      do not build internal projects
+	# --with-gbench           ensure that Genome Workbench can be built
+	# --without-gbench        do not build Genome Workbench
+	myconf+=(
+	--with-dll
+	--with-lfs
+	--with-build-root="${S}"_build
+	--without-suffix
+	--without-hostspec
+	--without-version
+	--with-bincopy
+	--without-strip
+	--without-ccache
+	--without-distcc
+	--with-ncbi-c
+	--without-ctools
+	--with-sss
+	--with-utils
+	--with-sssdb
+	--with-included-sss
+	--with-z="${EPREFIX}"/usr
+	--with-bz2="${EPREFIX}"/usr
+	--with-muparser="${EPREFIX}"/usr
+	--without-sybase
+#	--with-3psw=std:netopt
+	$(use_with debug)
+	$(use_with debug max-debug)
+	$(use_with debug symbols)
+	$(use_with static-libs static)
+	$(use_with static static-exe)
+	$(use_with threads mt)
+	$(use_with prefix runpath "${EPREFIX}/usr/$(get_libdir)/ncbi_cxx")
+	$(use_with test check)
+	$(use_with pch)
+	$(use_with lzo lzo "${EPREFIX}"/usr)
+	$(use_with pcre pcre "${EPREFIX}"/usr)
+	$(use_with gnutls gnutls "${EPREFIX}"/usr)
+	$(use_with ssl openssl "${EPREFIX}"/usr)
+	$(use_with ftds ftds "${EPREFIX}"/usr)
+	$(use_with mysql mysql "${EPREFIX}"/usr)
+	$(use_with fltk fltk "${EPREFIX}"/usr)
+	$(use_with opengl opengl "${EPREFIX}"/usr)
+	$(use_with mesa mesa "${EPREFIX}"/usr)
+	$(use_with opengl glut "${EPREFIX}"/usr)
+	$(use_with opengl glew "${EPREFIX}"/usr)
+	$(use_with opengl glew-m)
+	$(use_with wxwidgets wxwidgets "${EPREFIX}"/usr)
+	$(use_with wxwidgets wxwidgets-ucs)
+	$(use_with freetype freetype "${EPREFIX}"/usr)
+	$(use_with fastcgi fastcgi "${EPREFIX}"/usr)
+	$(use_with berkdb bdb "${EPREFIX}"/usr)
+	$(use_with odbc odbc "${EPREFIX}"/usr)
+	$(use_with python python "${EPREFIX}"/usr)
+	$(use_with boost boost "${EPREFIX}"/usr)
+	$(use_with sqlite sqlite3 "${EPREFIX}"/usr)
+	$(use_with icu icu "${EPREFIX}"/usr)
+	$(use_with expat expat "${EPREFIX}"/usr)
+	$(use_with xml libxml2 "${EPREFIX}"/usr)
+	$(use_with xml libxslt "${EPREFIX}"/usr)
+	$(use_with xerces xerces "${EPREFIX}"/usr)
+	$(use_with hdf5 hdf5 "${EPREFIX}"/usr)
+	$(use_with xalan xalan "${EPREFIX}"/usr)
+	$(use_with gif gif "${EPREFIX}"/usr)
+	$(use_with jpeg jpeg "${EPREFIX}"/usr)
+	$(use_with tiff tiff "${EPREFIX}"/usr)
+	$(use_with png png "${EPREFIX}"/usr)
+	$(use_with xpm xpm "${EPREFIX}"/usr)
+	$(use_with curl curl "${EPREFIX}"/usr)
+	$(use_with X x "${EPREFIX}"/usr)
+	)
+
+	# http://www.ncbi.nlm.nih.gov/books/NBK7167/
+	use test ||	myconf+=( --with-projects="${FILESDIR}"/disable-testsuite-compilation.txt )
+
+	# TODO
+    # copy optimization -O options from CXXFLAGS to DEF_FAST_FLAGS and pass that also to configure
+	# otherwise your -O2 will be dropped in some subdirectories and repalced by e.g. -O9
+
+	"${S}"/configure \
+	--prefix="${EPREFIX}"/usr \
+	--build=x86_64-pc-linux-gnu \
+	--host=x86_64-pc-linux-gnu \
+	--infodir=/usr/share/info \
+	--datadir=/usr/share \
+	--sysconfdir=/etc \
+	--localstatedir=/var/lib \
+	--libdir=/usr/lib64 \
+	${myconf[@]} || die
+#--without-debug \
+#		--with-bin-release \
+#		--with-bincopy \
+#		--without-static \
+#		--with-dll \
+#		--with-mt \
+#		--with-lfs \
+#		--prefix="${ED}"/usr \
+#		--libdir="${ED}"/usr/$(get_libdir)/"${PN}" \
+#		${myconf} LDFLAGS="-Wl,--no-as-needed" \
+#		|| die
+#	econf ${myconf[@]}
+}
+
+src_compile() {
+	# all_r would ignore the --with-projects contents and build more
+	# emake all_r -C GCC*-Release*/build || die
+	# all_p with compile only selected/required components
+	emake all_p -C GCC*-Release*/build || die "gcc-4.5.3 crashes at src/objects/valerr/ValidError.cpp:226:1: internal compiler error: Segmentation fault, right?"
+}
+
+src_install() {
+	emake install || die
+	# File collisions with sci-biology/ncbi-tools
+	rm -f "${ED}"/usr/bin/{asn2asn,rpsblast,test_regexp}
+	mv "${ED}"/usr/bin/seedtop "${ED}"/usr/bin/seedtop2
+
+	echo "LDPATH=${EPREFIX}/usr/$(get_libdir)/${PN}" > ${S}/99${PN}
+	doenvd "${S}/99${PN}"
+}
+
+pkg_postinst() {
+	einfo 'Please run "source /etc/profile" before using this package in the current shell.'
+	einfo 'Documentation is at http://www.ncbi.nlm.nih.gov/books/NBK7167/'
+}


^ permalink raw reply related	[flat|nested] 49+ messages in thread

* [gentoo-commits] proj/sci:master commit in: sci-biology/ncbi-tools++/
@ 2013-03-03 17:52 Justin Lecher
  0 siblings, 0 replies; 49+ messages in thread
From: Justin Lecher @ 2013-03-03 17:52 UTC (permalink / raw
  To: gentoo-commits

commit:     49b25fad765eaac9aed591426a7554281ca070db
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Sun Mar  3 16:32:10 2013 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Sun Mar  3 16:32:10 2013 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=49b25fad

sci-biology/ncbi-tools++: Clean whitespace errors

Package-Manager: portage-2.2.0_alpha164
RepoMan-Options: --force

---
 sci-biology/ncbi-tools++/ChangeLog                 |    4 ++++
 .../ncbi-tools++/ncbi-tools++-9.0.0-r1.ebuild      |    8 +++-----
 sci-biology/ncbi-tools++/ncbi-tools++-9.0.0.ebuild |    6 ++----
 3 files changed, 9 insertions(+), 9 deletions(-)

diff --git a/sci-biology/ncbi-tools++/ChangeLog b/sci-biology/ncbi-tools++/ChangeLog
index 2a2744a..99af26d 100644
--- a/sci-biology/ncbi-tools++/ChangeLog
+++ b/sci-biology/ncbi-tools++/ChangeLog
@@ -2,6 +2,10 @@
 # Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2
 # $Header: $
 
+  03 Mar 2013; Justin Lecher <jlec@gentoo.org> ncbi-tools++-9.0.0.ebuild,
+  ncbi-tools++-9.0.0-r1.ebuild:
+  Clean whitespace errors
+
   03 Mar 2013; Justin Lecher <jlec@gentoo.org> +metadata.xml:
   Add metadata.xml
 

diff --git a/sci-biology/ncbi-tools++/ncbi-tools++-9.0.0-r1.ebuild b/sci-biology/ncbi-tools++/ncbi-tools++-9.0.0-r1.ebuild
index 439e917..eada94b 100644
--- a/sci-biology/ncbi-tools++/ncbi-tools++-9.0.0-r1.ebuild
+++ b/sci-biology/ncbi-tools++/ncbi-tools++-9.0.0-r1.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2012 Gentoo Foundation
+# Copyright 1999-2013 Gentoo Foundation
 # Distributed under the terms of the GNU General Public License v2
 # $Header: /var/cvsroot/gentoo-x86/sci-biology/ncbi-tools++/ncbi-tools++-0.2010.06.15-r1.ebuild,v 1.3 2012/11/05 11:22:49 jlec Exp $
 
@@ -12,7 +12,6 @@ MY_PV="9_0_0"
 MY_P="ncbi_cxx--${MY_PV}"
 #ftp://ftp.ncbi.nlm.nih.gov/toolbox/ncbi_tools++/ARCHIVE/9_0_0/ncbi_cxx--9_0_0.tar.gz
 
-
 DESCRIPTION="NCBI C++ Toolkit, including NCBI BLAST+"
 HOMEPAGE="http://www.ncbi.nlm.nih.gov/books/bv.fcgi?rid=toolkit"
 SRC_URI="
@@ -24,7 +23,7 @@ SLOT="0"
 IUSE="
 	debug static-libs static threads pch
 	test wxwidgets odbc
-	berkdb boost bzip2 cppunit curl expat fastcgi fltk freetype ftds gif 
+	berkdb boost bzip2 cppunit curl expat fastcgi fltk freetype ftds gif
 	glut gnutls hdf5 icu jpeg lzo mesa mysql muparser opengl pcre png python
 	sablotron sqlite sqlite3 ssl tiff xerces xalan xml xpm xslt X"
 #KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
@@ -90,7 +89,6 @@ src_prepare() {
 
 #		"${FILESDIR}"/${PN}-${PV#0.}-disable_test_compress.patch
 
-
 #		"${FILESDIR}"/${PN}-${PV#0.}-gcc46.patch \
 #		"${FILESDIR}"/${PN}-${PV#0.}-gcc47.patch \
 #		"${WORKDIR}"/${PN}-${PV#0.}-asneeded.patch \
@@ -243,7 +241,7 @@ src_configure() {
 	use test ||	myconf+=( --with-projects="${FILESDIR}"/disable-testsuite-compilation.txt )
 
 	# TODO
-    # copy optimization -O options from CXXFLAGS to DEF_FAST_FLAGS and pass that also to configure
+	# copy optimization -O options from CXXFLAGS to DEF_FAST_FLAGS and pass that also to configure
 	# otherwise your -O2 will be dropped in some subdirectories and repalced by e.g. -O9
 
 	einfo "bash ./src/build-system/configure --srcdir="${S}" --prefix="${EPREFIX}"/usr --libdir=/usr/lib64 ${myconf[@]}"

diff --git a/sci-biology/ncbi-tools++/ncbi-tools++-9.0.0.ebuild b/sci-biology/ncbi-tools++/ncbi-tools++-9.0.0.ebuild
index f93b1aa..09f183a 100644
--- a/sci-biology/ncbi-tools++/ncbi-tools++-9.0.0.ebuild
+++ b/sci-biology/ncbi-tools++/ncbi-tools++-9.0.0.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2012 Gentoo Foundation
+# Copyright 1999-2013 Gentoo Foundation
 # Distributed under the terms of the GNU General Public License v2
 # $Header: /var/cvsroot/gentoo-x86/sci-biology/ncbi-tools++/ncbi-tools++-0.2010.06.15-r1.ebuild,v 1.3 2012/11/05 11:22:49 jlec Exp $
 
@@ -12,7 +12,6 @@ MY_PV="9_0_0"
 MY_P="ncbi_cxx--${MY_PV}"
 #ftp://ftp.ncbi.nlm.nih.gov/toolbox/ncbi_tools++/ARCHIVE/9_0_0/ncbi_cxx--9_0_0.tar.gz
 
-
 DESCRIPTION="NCBI C++ Toolkit, including NCBI BLAST+"
 HOMEPAGE="http://www.ncbi.nlm.nih.gov/books/bv.fcgi?rid=toolkit"
 SRC_URI="
@@ -148,7 +147,6 @@ src_prepare() {
 
 #		"${FILESDIR}"/${PN}-${PV#0.}-disable_test_compress.patch
 
-
 #		"${FILESDIR}"/${PN}-${PV#0.}-gcc46.patch \
 #		"${FILESDIR}"/${PN}-${PV#0.}-gcc47.patch \
 #		"${WORKDIR}"/${PN}-${PV#0.}-asneeded.patch \
@@ -271,7 +269,7 @@ src_configure() {
 	fi
 
 	# TODO
-    # copy optimization -O options from CXXFLAGS to DEF_FAST_FLAGS and pass that also to configure
+	# copy optimization -O options from CXXFLAGS to DEF_FAST_FLAGS and pass that also to configure
 	# otherwise your -O2 will be dropped in some subdirectories and repalced by e.g. -O9
 
 	"${S}"/configure --without-debug \


^ permalink raw reply related	[flat|nested] 49+ messages in thread

* [gentoo-commits] proj/sci:master commit in: sci-biology/ncbi-tools++/
@ 2013-03-03 17:52 Justin Lecher
  0 siblings, 0 replies; 49+ messages in thread
From: Justin Lecher @ 2013-03-03 17:52 UTC (permalink / raw
  To: gentoo-commits

commit:     6814d886acb1a78640b5e8f85926c9b62a0b432e
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Sun Mar  3 17:37:26 2013 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Sun Mar  3 17:37:26 2013 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=6814d886

sci-biology/ncbi-tools++: Document USE

Package-Manager: portage-2.2.0_alpha164
RepoMan-Options: --force

---
 sci-biology/ncbi-tools++/ChangeLog    |    3 +++
 sci-biology/ncbi-tools++/metadata.xml |   30 ++++++++++++++++++++++++++++++
 2 files changed, 33 insertions(+), 0 deletions(-)

diff --git a/sci-biology/ncbi-tools++/ChangeLog b/sci-biology/ncbi-tools++/ChangeLog
index 99af26d..ab4e4ea 100644
--- a/sci-biology/ncbi-tools++/ChangeLog
+++ b/sci-biology/ncbi-tools++/ChangeLog
@@ -2,6 +2,9 @@
 # Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2
 # $Header: $
 
+  03 Mar 2013; Justin Lecher <jlec@gentoo.org> metadata.xml:
+  Document USE
+
   03 Mar 2013; Justin Lecher <jlec@gentoo.org> ncbi-tools++-9.0.0.ebuild,
   ncbi-tools++-9.0.0-r1.ebuild:
   Clean whitespace errors

diff --git a/sci-biology/ncbi-tools++/metadata.xml b/sci-biology/ncbi-tools++/metadata.xml
index fc7c769..250e068 100644
--- a/sci-biology/ncbi-tools++/metadata.xml
+++ b/sci-biology/ncbi-tools++/metadata.xml
@@ -6,4 +6,34 @@
     <name>Andrey Kislyuk</name>
   </maintainer>
   <herd>sci-biology</herd>
+  <use>
+    <flag name="boost">Undocumented USE</flag>
+  </use>
+  <use>
+    <flag name="cppunit">Undocumented USE</flag>
+  </use>
+  <use>
+    <flag name="freetype">Undocumented USE</flag>
+  </use>
+  <use>
+    <flag name="ftds">Undocumented USE</flag>
+  </use>
+  <use>
+    <flag name="mesa">Undocumented USE</flag>
+  </use>
+  <use>
+    <flag name="muparser">Undocumented USE</flag>
+  </use>
+  <use>
+    <flag name="sablotron">Undocumented USE</flag>
+  </use>
+  <use>
+    <flag name="xerces">Undocumented USE</flag>
+  </use>
+  <use>
+    <flag name="xalan">Undocumented USE</flag>
+  </use>
+  <use>
+    <flag name="xslt">Undocumented USE</flag>
+  </use>
 </pkgmetadata>


^ permalink raw reply related	[flat|nested] 49+ messages in thread

* [gentoo-commits] proj/sci:master commit in: sci-biology/ncbi-tools++/
@ 2013-04-01 13:26 Justin Lecher
  0 siblings, 0 replies; 49+ messages in thread
From: Justin Lecher @ 2013-04-01 13:26 UTC (permalink / raw
  To: gentoo-commits

commit:     2b64eb561a6fb14fd4af81a272d17ac9590f0a23
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Mon Apr  1 13:26:22 2013 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Mon Apr  1 13:26:22 2013 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=2b64eb56

sci-biology/ncbi-tools++: Some Prefix love

Package-Manager: portage-2.2.0_alpha170
RepoMan-Options: --force

---
 sci-biology/ncbi-tools++/ChangeLog                 |    7 ++
 .../ncbi-tools++/ncbi-tools++-9.0.0-r1.ebuild      |   87 +++++++++++---------
 2 files changed, 55 insertions(+), 39 deletions(-)

diff --git a/sci-biology/ncbi-tools++/ChangeLog b/sci-biology/ncbi-tools++/ChangeLog
index ab4e4ea..234411a 100644
--- a/sci-biology/ncbi-tools++/ChangeLog
+++ b/sci-biology/ncbi-tools++/ChangeLog
@@ -2,6 +2,13 @@
 # Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2
 # $Header: $
 
+  01 Apr 2013; Justin Lecher <jlec@gentoo.org> ncbi-tools++-9.0.0-r1.ebuild:
+  Some Prefix love
+
+  01 Apr 2013; Justin Lecher <jlec@gentoo.org> ncbi-tools++-9.0.0-r1.ebuild:
+  Some Prefix love
+
+
   03 Mar 2013; Justin Lecher <jlec@gentoo.org> metadata.xml:
   Document USE
 

diff --git a/sci-biology/ncbi-tools++/ncbi-tools++-9.0.0-r1.ebuild b/sci-biology/ncbi-tools++/ncbi-tools++-9.0.0-r1.ebuild
index eada94b..9a2f8da 100644
--- a/sci-biology/ncbi-tools++/ncbi-tools++-9.0.0-r1.ebuild
+++ b/sci-biology/ncbi-tools++/ncbi-tools++-9.0.0-r1.ebuild
@@ -104,6 +104,8 @@ src_prepare() {
 	epatch ${PATCHES[@]}
 
 	tc-export CXX CC
+
+
 #	cd src/build-system || die
 #	eaclocal -I.
 #	eautoconf
@@ -184,9 +186,9 @@ src_configure() {
 #	--with-sssutils
 #	--with-sssdb
 #	--with-included-sss
-	--with-z="${EPREFIX}"/usr
-	--with-bz2="${EPREFIX}"/usr
-	--with-muparser="${EPREFIX}"/usr
+	--with-z="${EPREFIX}/usr"
+	--with-bz2="${EPREFIX}/usr"
+	--with-muparser="${EPREFIX}/usr"
 	--without-sybase
 	--with-autodep
 #	--with-3psw=std:netopt favor standard (system) builds of the above pkgs
@@ -199,41 +201,41 @@ src_configure() {
 	$(use_with prefix runpath "${EPREFIX}/usr/$(get_libdir)/ncbi_cxx")
 	$(use_with test check)
 	$(use_with pch)
-	$(use_with lzo lzo "${EPREFIX}"/usr)
-	$(use_with pcre pcre "${EPREFIX}"/usr)
-	$(use_with gnutls gnutls "${EPREFIX}"/usr)
-	$(use_with ssl openssl "${EPREFIX}"/usr)
-	$(use_with ftds ftds "${EPREFIX}"/usr)
-	$(use_with mysql mysql "${EPREFIX}"/usr)
-	$(use_with fltk fltk "${EPREFIX}"/usr)
-	$(use_with opengl opengl "${EPREFIX}"/usr)
-	$(use_with mesa mesa "${EPREFIX}"/usr)
-	$(use_with opengl glut "${EPREFIX}"/usr)
-	$(use_with opengl glew "${EPREFIX}"/usr)
+	$(use_with lzo lzo "${EPREFIX}/usr")
+	$(use_with pcre pcre "${EPREFIX}/usr")
+	$(use_with gnutls gnutls "${EPREFIX}/usr")
+	$(use_with ssl openssl "${EPREFIX}/usr")
+	$(use_with ftds ftds "${EPREFIX}/usr")
+	$(use_with mysql mysql "${EPREFIX}/usr")
+	$(use_with fltk fltk "${EPREFIX}/usr")
+	$(use_with opengl opengl "${EPREFIX}/usr")
+	$(use_with mesa mesa "${EPREFIX}/usr")
+	$(use_with opengl glut "${EPREFIX}/usr")
+	$(use_with opengl glew "${EPREFIX}/usr")
 	$(use_with opengl glew-mx)
-	$(use_with wxwidgets wxwidgets "${EPREFIX}"/usr)
+	$(use_with wxwidgets wxwidgets "${EPREFIX}/usr")
 	$(use_with wxwidgets wxwidgets-ucs)
-	$(use_with freetype freetype "${EPREFIX}"/usr)
-	$(use_with fastcgi fastcgi "${EPREFIX}"/usr)
-	$(use_with berkdb bdb "${EPREFIX}"/usr)
-	$(use_with odbc odbc "${EPREFIX}"/usr)
-	$(use_with python python "${EPREFIX}"/usr)
-	$(use_with boost boost "${EPREFIX}"/usr)
-	$(use_with sqlite sqlite3 "${EPREFIX}"/usr)
-	$(use_with icu icu "${EPREFIX}"/usr)
-	$(use_with expat expat "${EPREFIX}"/usr)
-	$(use_with xml libxml "${EPREFIX}"/usr)
-	$(use_with xml libxslt "${EPREFIX}"/usr)
-	$(use_with xerces xerces "${EPREFIX}"/usr)
-	$(use_with hdf5 hdf5 "${EPREFIX}"/usr)
-	$(use_with xalan xalan "${EPREFIX}"/usr)
-#	$(use_with gif gif "${EPREFIX}"/usr)
-	$(use_with jpeg jpeg "${EPREFIX}"/usr)
-	$(use_with tiff tiff "${EPREFIX}"/usr)
-	$(use_with png png "${EPREFIX}"/usr)
-	$(use_with xpm xpm "${EPREFIX}"/usr)
-	$(use_with curl curl "${EPREFIX}"/usr)
-#	$(use_with X x "${EPREFIX}"/usr)
+	$(use_with freetype freetype "${EPREFIX}/usr")
+	$(use_with fastcgi fastcgi "${EPREFIX}/usr")
+	$(use_with berkdb bdb "${EPREFIX}/usr")
+	$(use_with odbc odbc "${EPREFIX}/usr")
+	$(use_with python python "${EPREFIX}/usr")
+	$(use_with boost boost "${EPREFIX}/usr")
+	$(use_with sqlite sqlite3 "${EPREFIX}/usr")
+	$(use_with icu icu "${EPREFIX}/usr")
+	$(use_with expat expat "${EPREFIX}/usr")
+	$(use_with xml libxml "${EPREFIX}/usr")
+	$(use_with xml libxslt "${EPREFIX}/usr")
+	$(use_with xerces xerces "${EPREFIX}/usr")
+	$(use_with hdf5 hdf5 "${EPREFIX}/usr")
+	$(use_with xalan xalan "${EPREFIX}/usr")
+#	$(use_with gif gif "${EPREFIX}/usr")
+	$(use_with jpeg jpeg "${EPREFIX}/usr")
+	$(use_with tiff tiff "${EPREFIX}/usr")
+	$(use_with png png "${EPREFIX}/usr")
+	$(use_with xpm xpm "${EPREFIX}/usr")
+	$(use_with curl curl "${EPREFIX}/usr")
+#	$(use_with X x "${EPREFIX}/usr")
 	$(use_with X x)
 	)
 
@@ -244,14 +246,14 @@ src_configure() {
 	# copy optimization -O options from CXXFLAGS to DEF_FAST_FLAGS and pass that also to configure
 	# otherwise your -O2 will be dropped in some subdirectories and repalced by e.g. -O9
 
-	einfo "bash ./src/build-system/configure --srcdir="${S}" --prefix="${EPREFIX}"/usr --libdir=/usr/lib64 ${myconf[@]}"
+	einfo "bash ./src/build-system/configure --srcdir="${S}" --prefix="${EPREFIX}/usr" --libdir=/usr/lib64 ${myconf[@]}"
 
 #	bash \
 #		./src/build-system/configure \
 #	cd src/build-system || die
 	econf \
 		--srcdir="${S}" \
-		--prefix="${EPREFIX}"/usr \
+		--prefix="${EPREFIX}/usr" \
 		--libdir=/usr/lib64 \
 		${myconf[@]} || die
 #--without-debug \
@@ -278,7 +280,14 @@ src_compile() {
 }
 
 src_install() {
-	emake install || die
+	rm -rvf "${S}"_build/lib/ncbi || die
+	emake install prefix="${ED}/usr" libdir="${ED}/usr/$(get_libdir)/${PN}"
+
+#	dobin "${S}"_build/bin/*
+#	dolib.so "${S}"_build/lib/*so*
+#	dolib.a "${S}"_build/lib/*.a
+#	doheader "${S}"_build/inc/*
+
 	# File collisions with sci-biology/ncbi-tools
 	rm -f "${ED}"/usr/bin/{asn2asn,rpsblast,test_regexp}
 	mv "${ED}"/usr/bin/seedtop "${ED}"/usr/bin/seedtop2


^ permalink raw reply related	[flat|nested] 49+ messages in thread

* [gentoo-commits] proj/sci:master commit in: sci-biology/ncbi-tools++/
@ 2013-06-12 20:04 Justin Lecher
  0 siblings, 0 replies; 49+ messages in thread
From: Justin Lecher @ 2013-06-12 20:04 UTC (permalink / raw
  To: gentoo-commits

commit:     5b52557e87bd23e7b860e6c8bfc195c653d4536d
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Wed Jun 12 18:57:31 2013 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Wed Jun 12 18:57:31 2013 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=5b52557e

sci-biology/ncbi-tools++: Drop autotools.eclass

Package-Manager: portage-2.2.0_alpha179
RepoMan-Options: --force

---
 sci-biology/ncbi-tools++/ChangeLog                    | 3 +++
 sci-biology/ncbi-tools++/ncbi-tools++-9.0.0-r1.ebuild | 2 +-
 2 files changed, 4 insertions(+), 1 deletion(-)

diff --git a/sci-biology/ncbi-tools++/ChangeLog b/sci-biology/ncbi-tools++/ChangeLog
index 234411a..83c7679 100644
--- a/sci-biology/ncbi-tools++/ChangeLog
+++ b/sci-biology/ncbi-tools++/ChangeLog
@@ -2,6 +2,9 @@
 # Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2
 # $Header: $
 
+  12 Jun 2013; Justin Lecher <jlec@gentoo.org> ncbi-tools++-9.0.0-r1.ebuild:
+  Drop autotools.eclass
+
   01 Apr 2013; Justin Lecher <jlec@gentoo.org> ncbi-tools++-9.0.0-r1.ebuild:
   Some Prefix love
 

diff --git a/sci-biology/ncbi-tools++/ncbi-tools++-9.0.0-r1.ebuild b/sci-biology/ncbi-tools++/ncbi-tools++-9.0.0-r1.ebuild
index 9a2f8da..11d6fd0 100644
--- a/sci-biology/ncbi-tools++/ncbi-tools++-9.0.0-r1.ebuild
+++ b/sci-biology/ncbi-tools++/ncbi-tools++-9.0.0-r1.ebuild
@@ -4,7 +4,7 @@
 
 EAPI=5
 
-inherit autotools eutils flag-o-matic multilib toolchain-funcs
+inherit eutils flag-o-matic multilib toolchain-funcs
 
 MY_TAG="Jun_15_2010"
 MY_Y="${MY_TAG/*_/}"


^ permalink raw reply related	[flat|nested] 49+ messages in thread

* [gentoo-commits] proj/sci:master commit in: sci-biology/ncbi-tools++/
@ 2013-06-12 20:07 Justin Lecher
  0 siblings, 0 replies; 49+ messages in thread
From: Justin Lecher @ 2013-06-12 20:07 UTC (permalink / raw
  To: gentoo-commits

commit:     bc92c82534cb0dae36a4001b184e11fd719e8d86
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Wed Jun 12 20:06:37 2013 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Wed Jun 12 20:06:37 2013 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=bc92c825

sci-biology/ncbi-tools++: Drop empty line

Package-Manager: portage-2.2.0_alpha179
RepoMan-Options: --force

---
 sci-biology/ncbi-tools++/ChangeLog                    | 3 +++
 sci-biology/ncbi-tools++/ncbi-tools++-9.0.0-r1.ebuild | 1 -
 2 files changed, 3 insertions(+), 1 deletion(-)

diff --git a/sci-biology/ncbi-tools++/ChangeLog b/sci-biology/ncbi-tools++/ChangeLog
index 83c7679..270521c 100644
--- a/sci-biology/ncbi-tools++/ChangeLog
+++ b/sci-biology/ncbi-tools++/ChangeLog
@@ -3,6 +3,9 @@
 # $Header: $
 
   12 Jun 2013; Justin Lecher <jlec@gentoo.org> ncbi-tools++-9.0.0-r1.ebuild:
+  Drop empty line
+
+  12 Jun 2013; Justin Lecher <jlec@gentoo.org> ncbi-tools++-9.0.0-r1.ebuild:
   Drop autotools.eclass
 
   01 Apr 2013; Justin Lecher <jlec@gentoo.org> ncbi-tools++-9.0.0-r1.ebuild:

diff --git a/sci-biology/ncbi-tools++/ncbi-tools++-9.0.0-r1.ebuild b/sci-biology/ncbi-tools++/ncbi-tools++-9.0.0-r1.ebuild
index 11d6fd0..8c190e4 100644
--- a/sci-biology/ncbi-tools++/ncbi-tools++-9.0.0-r1.ebuild
+++ b/sci-biology/ncbi-tools++/ncbi-tools++-9.0.0-r1.ebuild
@@ -105,7 +105,6 @@ src_prepare() {
 
 	tc-export CXX CC
 
-
 #	cd src/build-system || die
 #	eaclocal -I.
 #	eautoconf


^ permalink raw reply related	[flat|nested] 49+ messages in thread

* [gentoo-commits] proj/sci:master commit in: sci-biology/ncbi-tools++/
@ 2013-09-13 20:21 Martin Mokrejs
  0 siblings, 0 replies; 49+ messages in thread
From: Martin Mokrejs @ 2013-09-13 20:21 UTC (permalink / raw
  To: gentoo-commits

commit:     16bbfdefcf0e1b35ba1502f6c8948d6d60c9e5ed
Author:     Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Fri Sep 13 20:23:24 2013 +0000
Commit:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Fri Sep 13 20:23:24 2013 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=16bbfdef

Remove redundant connect from DLL_LIB lines.

---
 sci-biology/ncbi-tools++/ChangeLog | 16 ++++++++++++++++
 1 file changed, 16 insertions(+)

diff --git a/sci-biology/ncbi-tools++/ChangeLog b/sci-biology/ncbi-tools++/ChangeLog
index 2e245b3..b737081 100644
--- a/sci-biology/ncbi-tools++/ChangeLog
+++ b/sci-biology/ncbi-tools++/ChangeLog
@@ -3,6 +3,22 @@
 # $Header: $
 
   13 Sep 2013; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
+  ncbi-tools++-9.0.0-r1.ebuild, ncbi-tools++-12.0.0.ebuild,
+  files/ncbi-tools++-9.0.0-as-needed.patch,
+  +files/ncbi-tools++-9.0.0-fix-undef-reference-to-GenBankReaders_Register_Id1.
+  patch, files/ncbi-tools++-12.0.0-as-needed.patch:
+  files/ncbi-tools++-12.0.0-as-needed.patch
+  files/ncbi-tools++-9.0.0-as-needed.patch
+  
+  Remove redundant connect per message from Aaron Ucko <ucko@ncbi.nlm.nih.gov>:
+  
+  > +DLL_LIB  = xncbi xutil seqset connect xconnect xnetblast
+  Then simply remove connect, which is redundant with xconnect.  (connect
+  consists of code shared with NCBI's C Toolkit; xconnect adds a C++
+  layer.)
+
+
+  13 Sep 2013; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
   ncbi-tools++-12.0.0.ebuild,
   +files/ncbi-tools++-12.0.0-fix-creaders-linking.patch:
   No, the fix-creaders-linking is needed for 12.0.0 as well.


^ permalink raw reply related	[flat|nested] 49+ messages in thread

* [gentoo-commits] proj/sci:master commit in: sci-biology/ncbi-tools++/
@ 2013-09-13 20:23 Martin Mokrejs
  0 siblings, 0 replies; 49+ messages in thread
From: Martin Mokrejs @ 2013-09-13 20:23 UTC (permalink / raw
  To: gentoo-commits

commit:     cbacda12d70dc97ab35fe390abf09d44502b1c3d
Author:     Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Fri Sep 13 20:24:36 2013 +0000
Commit:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Fri Sep 13 20:24:36 2013 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=cbacda12

fix version number in the ebuild

---
 sci-biology/ncbi-tools++/ncbi-tools++-12.0.0.ebuild | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/sci-biology/ncbi-tools++/ncbi-tools++-12.0.0.ebuild b/sci-biology/ncbi-tools++/ncbi-tools++-12.0.0.ebuild
index 33ee6fb..0549445 100644
--- a/sci-biology/ncbi-tools++/ncbi-tools++-12.0.0.ebuild
+++ b/sci-biology/ncbi-tools++/ncbi-tools++-12.0.0.ebuild
@@ -8,7 +8,7 @@ inherit eutils flag-o-matic multilib toolchain-funcs
 
 MY_TAG="Jun_15_2010"
 MY_Y="${MY_TAG/*_/}"
-MY_PV="9_0_0"
+MY_PV="12_0_0"
 MY_P="ncbi_cxx--${MY_PV}"
 #ftp://ftp.ncbi.nlm.nih.gov/toolbox/ncbi_tools++/ARCHIVE/9_0_0/ncbi_cxx--9_0_0.tar.gz
 


^ permalink raw reply related	[flat|nested] 49+ messages in thread

* [gentoo-commits] proj/sci:master commit in: sci-biology/ncbi-tools++/
@ 2013-09-14  8:44 Martin Mokrejs
  0 siblings, 0 replies; 49+ messages in thread
From: Martin Mokrejs @ 2013-09-14  8:44 UTC (permalink / raw
  To: gentoo-commits

commit:     5c30b638891d5120f4a6757229945f6103dffa43
Author:     Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Sat Sep 14 08:46:29 2013 +0000
Commit:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Sat Sep 14 08:46:29 2013 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=5c30b638

Support at least when user passes USE='gnutls -ssl -openssl' but what we really want is to prefer gnutls over openssl if both are available on the system.

---
 sci-biology/ncbi-tools++/ChangeLog                    | 6 ++++++
 sci-biology/ncbi-tools++/ncbi-tools++-9.0.0-r1.ebuild | 7 ++++++-
 2 files changed, 12 insertions(+), 1 deletion(-)

diff --git a/sci-biology/ncbi-tools++/ChangeLog b/sci-biology/ncbi-tools++/ChangeLog
index 7f94502..3da37d9 100644
--- a/sci-biology/ncbi-tools++/ChangeLog
+++ b/sci-biology/ncbi-tools++/ChangeLog
@@ -3,6 +3,12 @@
 # $Header: $
 
   14 Sep 2013; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
+  ncbi-tools++-9.0.0-r1.ebuild:
+  Support at least when user passes USE="gnutls -ssl -openssl" but what we
+  really want is to prefer gnutls over openssl if both are available on the
+  system.
+
+  14 Sep 2013; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
   ncbi-tools++-9.0.0-r1.ebuild,
   +files/ncbi-tools++-9.0.0-remove-LZO-definition-upstream.patch:
   Add upstream ncbi-tools++-9.0.0-remove-LZO-definition-upstream.patch with

diff --git a/sci-biology/ncbi-tools++/ncbi-tools++-9.0.0-r1.ebuild b/sci-biology/ncbi-tools++/ncbi-tools++-9.0.0-r1.ebuild
index 1a34f35..4e1ee2e 100644
--- a/sci-biology/ncbi-tools++/ncbi-tools++-9.0.0-r1.ebuild
+++ b/sci-biology/ncbi-tools++/ncbi-tools++-9.0.0-r1.ebuild
@@ -24,7 +24,7 @@ IUSE="
 	debug static-libs static threads pch
 	test wxwidgets odbc
 	berkdb boost bzip2 cppunit curl expat fastcgi fltk freetype ftds gif
-	glut gnutls hdf5 icu jpeg mesa mysql muparser opengl pcre png python
+	glut gnutls hdf5 icu lzo jpeg mesa mysql muparser opengl pcre png python
 	sablotron sqlite sqlite3 ssl tiff xerces xalan xml xpm xslt X"
 #KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
 KEYWORDS=""
@@ -64,6 +64,7 @@ DEPEND="
 	png? ( media-libs/libpng )
 	tiff? ( media-libs/tiff )
 	xpm? ( x11-libs/libXpm )
+	dev-libs/lzo
 	app-arch/bzip2
 	dev-libs/libpcre"
 # USE flags which should be added somehow: wxWindows wxWidgets SP ORBacus ODBC OEChem sge
@@ -206,6 +207,9 @@ src_configure() {
 #
 	--with-flat-makefile
 #	--with-3psw=std:netopt favor standard (system) builds of the above pkgs
+
+
+# TODO: should improve the ssl/openssl/gmutls logic like is in net-misc/vpnc
 	$(use_with debug)
 	$(use_with debug max-debug)
 	$(use_with debug symbols)
@@ -215,6 +219,7 @@ src_configure() {
 	$(use_with prefix runpath "${EPREFIX}/usr/$(get_libdir)/ncbi_cxx")
 	$(use_with test check)
 	$(use_with pch)
+	$(use_with lzo lzo "${EPREFIX}/usr")
 	$(use_with pcre pcre "${EPREFIX}/usr")
 	$(use_with gnutls gnutls "${EPREFIX}/usr")
 	$(use_with ssl openssl "${EPREFIX}/usr")


^ permalink raw reply related	[flat|nested] 49+ messages in thread

* [gentoo-commits] proj/sci:master commit in: sci-biology/ncbi-tools++/
@ 2014-03-25 10:49 Martin Mokrejs
  0 siblings, 0 replies; 49+ messages in thread
From: Martin Mokrejs @ 2014-03-25 10:49 UTC (permalink / raw
  To: gentoo-commits

commit:     44ffc4b87ef68b5dc623060f5335ba44339abb19
Author:     Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Tue Mar 25 10:48:44 2014 +0000
Commit:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Tue Mar 25 10:48:44 2014 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=44ffc4b8

sci-biology/ncbi-tools++: add deps on jpeg-turbo

---
 sci-biology/ncbi-tools++/ncbi-tools++-12.0.0.ebuild | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/sci-biology/ncbi-tools++/ncbi-tools++-12.0.0.ebuild b/sci-biology/ncbi-tools++/ncbi-tools++-12.0.0.ebuild
index bde00f8..69aea50 100644
--- a/sci-biology/ncbi-tools++/ncbi-tools++-12.0.0.ebuild
+++ b/sci-biology/ncbi-tools++/ncbi-tools++-12.0.0.ebuild
@@ -60,7 +60,7 @@ DEPEND="
 	muparser? ( dev-cpp/muParser )
 	hdf5? ( sci-libs/hdf5 )
 	gif? ( media-libs/giflib )
-	jpeg? ( virtual/jpeg )
+	jpeg? ( media-libs/jpeg || ( media-libs/libjpeg-turbo ) )
 	png? ( media-libs/libpng )
 	tiff? ( media-libs/tiff )
 	xpm? ( x11-libs/libXpm )


^ permalink raw reply related	[flat|nested] 49+ messages in thread

* [gentoo-commits] proj/sci:master commit in: sci-biology/ncbi-tools++/
@ 2014-05-06 16:44 Justin Lecher
  0 siblings, 0 replies; 49+ messages in thread
From: Justin Lecher @ 2014-05-06 16:44 UTC (permalink / raw
  To: gentoo-commits

commit:     3a46fa5d7e08ae791daad0e9455c739a03e6ff97
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Tue May  6 07:10:48 2014 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Tue May  6 07:11:00 2014 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=3a46fa5d

Configure works

Signed-off-by: Justin Lecher <jlec <AT> gentoo.org>

---
 sci-biology/ncbi-tools++/ncbi-tools++-12.0.0.ebuild | 16 ++++++++--------
 1 file changed, 8 insertions(+), 8 deletions(-)

diff --git a/sci-biology/ncbi-tools++/ncbi-tools++-12.0.0.ebuild b/sci-biology/ncbi-tools++/ncbi-tools++-12.0.0.ebuild
index 69aea50..d4a5085 100644
--- a/sci-biology/ncbi-tools++/ncbi-tools++-12.0.0.ebuild
+++ b/sci-biology/ncbi-tools++/ncbi-tools++-12.0.0.ebuild
@@ -60,7 +60,7 @@ DEPEND="
 	muparser? ( dev-cpp/muParser )
 	hdf5? ( sci-libs/hdf5 )
 	gif? ( media-libs/giflib )
-	jpeg? ( media-libs/jpeg || ( media-libs/libjpeg-turbo ) )
+	jpeg? ( virtual/jpeg )
 	png? ( media-libs/libpng )
 	tiff? ( media-libs/tiff )
 	xpm? ( x11-libs/libXpm )
@@ -70,7 +70,7 @@ DEPEND="
 # USE flags which should be added somehow: wxWindows wxWidgets SP ORBacus ODBC OEChem sge
 
 
-# seems muParser is required, also glew is required. configure exitss otherwise
+# seems muParser is required, also glew is required. configure exits otherwise
 
 RDEPEND="${DEPEND}"
 
@@ -116,9 +116,8 @@ src_prepare() {
 	tc-export CXX CC
 
 	cd src/build-system || die
-	eautoreconf
-#	eaclocal -I.
-#	eautoconf
+#	eautoreconf
+	eautoconf
 }
 
 src_configure() {
@@ -258,9 +257,10 @@ src_configure() {
 
 	einfo "bash ./src/build-system/configure --srcdir="${S}" --prefix="${EPREFIX}/usr" --libdir=/usr/lib64 ${myconf[@]}"
 
-#	bash \
-#		./src/build-system/configure \
-	econf \
+#	ECONF_SOURCE="src/build-system" \
+#		econf \
+	bash \
+		./src/build-system/configure \
 		--srcdir="${S}" \
 		--prefix="${EPREFIX}/usr" \
 		--libdir=/usr/lib64 \


^ permalink raw reply related	[flat|nested] 49+ messages in thread

* [gentoo-commits] proj/sci:master commit in: sci-biology/ncbi-tools++/
@ 2014-06-02 12:08 Martin Mokrejs
  0 siblings, 0 replies; 49+ messages in thread
From: Martin Mokrejs @ 2014-06-02 12:08 UTC (permalink / raw
  To: gentoo-commits

commit:     cb2f6200cc1de77fcdb6b3ac1b5b1d835ab4225f
Author:     Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Mon Jun  2 12:06:58 2014 +0000
Commit:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Mon Jun  2 12:06:58 2014 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=cb2f6200

sci-biology/ncbi-tools++: added a note about a taxonomy database add-on not yet installed by Gentoo

---
 sci-biology/ncbi-tools++/ncbi-tools++-12.0.0.ebuild   | 3 +++
 sci-biology/ncbi-tools++/ncbi-tools++-9.0.0-r1.ebuild | 4 ++++
 sci-biology/ncbi-tools++/ncbi-tools++-9.0.0.ebuild    | 5 +++++
 3 files changed, 12 insertions(+)

diff --git a/sci-biology/ncbi-tools++/ncbi-tools++-12.0.0.ebuild b/sci-biology/ncbi-tools++/ncbi-tools++-12.0.0.ebuild
index d4a5085..3b19a93 100644
--- a/sci-biology/ncbi-tools++/ncbi-tools++-12.0.0.ebuild
+++ b/sci-biology/ncbi-tools++/ncbi-tools++-12.0.0.ebuild
@@ -18,6 +18,8 @@ SRC_URI="
 	ftp://ftp.ncbi.nih.gov/toolbox/ncbi_tools++/ARCHIVE/${MY_PV}/ncbi_cxx--${MY_PV}.tar.gz"
 #	http://dev.gentoo.org/~jlec/distfiles/${PN}-${PV#0.}-asneeded.patch.xz"
 
+# should also install ftp://ftp.ncbi.nlm.nih.gov/blast/db/taxdb.tar.gz
+# see http://www.biostars.org/p/76551/ and http://blastedbio.blogspot.cz/2012/05/blast-tabular-missing-descriptions.html
 LICENSE="public-domain"
 SLOT="0"
 IUSE="
@@ -271,6 +273,7 @@ src_configure() {
 #		--without-static \
 #		--with-dll \
 #		--with-mt \
+#		--with-openmp \
 #		--with-lfs \
 #		--prefix="${ED}"/usr \
 #		--libdir="${ED}"/usr/$(get_libdir)/"${PN}" \

diff --git a/sci-biology/ncbi-tools++/ncbi-tools++-9.0.0-r1.ebuild b/sci-biology/ncbi-tools++/ncbi-tools++-9.0.0-r1.ebuild
index 7b3ba9e..89ae176 100644
--- a/sci-biology/ncbi-tools++/ncbi-tools++-9.0.0-r1.ebuild
+++ b/sci-biology/ncbi-tools++/ncbi-tools++-9.0.0-r1.ebuild
@@ -18,6 +18,9 @@ SRC_URI="
 	ftp://ftp.ncbi.nih.gov/toolbox/ncbi_tools++/ARCHIVE/${MY_PV}/ncbi_cxx--${MY_PV}.tar.gz"
 #	http://dev.gentoo.org/~jlec/distfiles/${PN}-${PV#0.}-asneeded.patch.xz"
 
+# should also install ftp://ftp.ncbi.nlm.nih.gov/blast/db/taxdb.tar.gz
+# see http://www.biostars.org/p/76551/ and http://blastedbio.blogspot.cz/2012/05/blast-tabular-missing-descriptions.html
+
 LICENSE="public-domain"
 SLOT="0"
 IUSE="
@@ -281,6 +284,7 @@ src_configure() {
 #		--without-static \
 #		--with-dll \
 #		--with-mt \
+#		--with-openmp \
 #		--with-lfs \
 #		--prefix="${ED}"/usr \
 #		--libdir="${ED}"/usr/$(get_libdir)/"${PN}" \

diff --git a/sci-biology/ncbi-tools++/ncbi-tools++-9.0.0.ebuild b/sci-biology/ncbi-tools++/ncbi-tools++-9.0.0.ebuild
index 2824e09..8020276 100644
--- a/sci-biology/ncbi-tools++/ncbi-tools++-9.0.0.ebuild
+++ b/sci-biology/ncbi-tools++/ncbi-tools++-9.0.0.ebuild
@@ -18,6 +18,9 @@ SRC_URI="
 	ftp://ftp.ncbi.nih.gov/toolbox/ncbi_tools++/ARCHIVE/${MY_PV}/ncbi_cxx--${MY_PV}.tar.gz"
 #	http://dev.gentoo.org/~jlec/distfiles/${PN}-${PV#0.}-asneeded.patch.xz"
 
+# should also install ftp://ftp.ncbi.nlm.nih.gov/blast/db/taxdb.tar.gz
+# see http://www.biostars.org/p/76551/ and http://blastedbio.blogspot.cz/2012/05/blast-tabular-missing-descriptions.html
+
 LICENSE="public-domain"
 SLOT="0"
 IUSE="berkdb boost bzip2 cppunit curl expat fastcgi fltk freetype ftds gif glut gnutls hdf5 icu jpeg lzo mesa mysql muparser opengl pcre png python sablotron sqlite sqlite3 ssl tiff xerces xalan xml xpm xslt X"
@@ -283,6 +286,8 @@ src_configure() {
 		--libdir="${ED}"/usr/$(get_libdir)/"${PN}" \
 		${myconf} LDFLAGS="-Wl,--no-as-needed" \
 		|| die
+
+	# --with-openmp
 }
 
 src_compile() {


^ permalink raw reply related	[flat|nested] 49+ messages in thread

* [gentoo-commits] proj/sci:master commit in: sci-biology/ncbi-tools++/
@ 2014-06-23 16:18 Martin Mokrejs
  0 siblings, 0 replies; 49+ messages in thread
From: Martin Mokrejs @ 2014-06-23 16:18 UTC (permalink / raw
  To: gentoo-commits

commit:     41e720e3552ebd75742dba2126eeffed95ce6769
Author:     Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Mon Jun 23 16:17:38 2014 +0000
Commit:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Mon Jun 23 16:17:38 2014 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=41e720e3

updating the ChangeLog to note where the ncbi-tools++-12.0.0-support-autoconf-2.60.patch comes from

---
 sci-biology/ncbi-tools++/ChangeLog | 9 ++++++++-
 1 file changed, 8 insertions(+), 1 deletion(-)

diff --git a/sci-biology/ncbi-tools++/ChangeLog b/sci-biology/ncbi-tools++/ChangeLog
index 3da37d9..5abfefa 100644
--- a/sci-biology/ncbi-tools++/ChangeLog
+++ b/sci-biology/ncbi-tools++/ChangeLog
@@ -1,7 +1,14 @@
 # ChangeLog for sci-biology/ncbi-tools++
-# Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2
+# Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2
 # $Header: $
 
+  23 Jun 2014; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> ChangeLog:
+  add patches for 12.0.0 to support autoconf-2.60 (so far 2.59 was needed),
+  patches from upstream:
+  http://www.ncbi.nlm.nih.gov/viewvc/v1?view=revision&revision=62745
+  http://www.ncbi.nlm.nih.gov/viewvc/v1?view=revision&revision=62750
+  http://www.ncbi.nlm.nih.gov/viewvc/v1?view=revision&revision=62760
+
   14 Sep 2013; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
   ncbi-tools++-9.0.0-r1.ebuild:
   Support at least when user passes USE="gnutls -ssl -openssl" but what we


^ permalink raw reply related	[flat|nested] 49+ messages in thread

* [gentoo-commits] proj/sci:master commit in: sci-biology/ncbi-tools++/
@ 2014-06-25 21:02 Martin Mokrejs
  0 siblings, 0 replies; 49+ messages in thread
From: Martin Mokrejs @ 2014-06-25 21:02 UTC (permalink / raw
  To: gentoo-commits

commit:     3f54d211a74334d29b3c624edc1c96743aa8785b
Author:     Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Wed Jun 25 21:02:00 2014 +0000
Commit:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Wed Jun 25 21:02:00 2014 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=3f54d211

sci-biology/ncbi-tools++-12.0.0: install colliding files under a name suffixed by a plus sign

---
 sci-biology/ncbi-tools++/ncbi-tools++-12.0.0.ebuild | 8 ++++++--
 1 file changed, 6 insertions(+), 2 deletions(-)

diff --git a/sci-biology/ncbi-tools++/ncbi-tools++-12.0.0.ebuild b/sci-biology/ncbi-tools++/ncbi-tools++-12.0.0.ebuild
index 8ee3f16..6de9b4f 100644
--- a/sci-biology/ncbi-tools++/ncbi-tools++-12.0.0.ebuild
+++ b/sci-biology/ncbi-tools++/ncbi-tools++-12.0.0.ebuild
@@ -339,8 +339,12 @@ src_install() {
 #	doheader "${S}"_build/inc/*
 
 	# File collisions with sci-biology/ncbi-tools
-	rm -f "${ED}"/usr/bin/{asn2asn,rpsblast,test_regexp}
-	mv "${ED}"/usr/bin/seedtop "${ED}"/usr/bin/seedtop2
+	#rm -f "${ED}"/usr/bin/{asn2asn,rpsblast,test_regexp,vecscreen}
+	mv "${ED}"/usr/bin/asn2asn "${ED}"/usr/bin/asn2asn+
+	mv "${ED}"/usr/bin/rpsblast "${ED}"/usr/bin/rpsblast+
+	mv "${ED}"/usr/bin/test_regexp "${ED}"/usr/bin/test_regexp+
+	mv "${ED}"/usr/bin/vecscreen "${ED}"/usr/bin/vecscreen+
+	mv "${ED}"/usr/bin/seedtop "${ED}"/usr/bin/seedtop+
 
 	echo "LDPATH=${EPREFIX}/usr/$(get_libdir)/${PN}" > ${S}/99${PN}
 	doenvd "${S}/99${PN}"


^ permalink raw reply related	[flat|nested] 49+ messages in thread

* [gentoo-commits] proj/sci:master commit in: sci-biology/ncbi-tools++/
@ 2014-06-26 13:30 Martin Mokrejs
  0 siblings, 0 replies; 49+ messages in thread
From: Martin Mokrejs @ 2014-06-26 13:30 UTC (permalink / raw
  To: gentoo-commits

commit:     29634acbbe011256ad517af5f0d946c876e7ba12
Author:     Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Thu Jun 26 13:29:31 2014 +0000
Commit:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Thu Jun 26 13:29:31 2014 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=29634acb

sci-biology/ncbi-tools++-12.0.0: cleanup comments and shutdown a false alarm message from mv

---
 sci-biology/ncbi-tools++/ncbi-tools++-12.0.0.ebuild | 3 +--
 1 file changed, 1 insertion(+), 2 deletions(-)

diff --git a/sci-biology/ncbi-tools++/ncbi-tools++-12.0.0.ebuild b/sci-biology/ncbi-tools++/ncbi-tools++-12.0.0.ebuild
index d8b7d97..535b992 100644
--- a/sci-biology/ncbi-tools++/ncbi-tools++-12.0.0.ebuild
+++ b/sci-biology/ncbi-tools++/ncbi-tools++-12.0.0.ebuild
@@ -336,10 +336,9 @@ src_install() {
 #	doheader "${S}"_build/inc/*
 
 	# File collisions with sci-biology/ncbi-tools
-	#rm -f "${ED}"/usr/bin/{asn2asn,rpsblast,test_regexp,vecscreen}
 	mv "${ED}"/usr/bin/asn2asn "${ED}"/usr/bin/asn2asn+
 	mv "${ED}"/usr/bin/rpsblast "${ED}"/usr/bin/rpsblast+
-	mv "${ED}"/usr/bin/test_regexp "${ED}"/usr/bin/test_regexp+
+	mv -f "${ED}"/usr/bin/test_regexp "${ED}"/usr/bin/test_regexp+ # drop the eventually mistakenly compiled binaries
 	mv "${ED}"/usr/bin/vecscreen "${ED}"/usr/bin/vecscreen+
 	mv "${ED}"/usr/bin/seedtop "${ED}"/usr/bin/seedtop+
 


^ permalink raw reply related	[flat|nested] 49+ messages in thread

* [gentoo-commits] proj/sci:master commit in: sci-biology/ncbi-tools++/
@ 2014-06-26 14:32 Martin Mokrejs
  0 siblings, 0 replies; 49+ messages in thread
From: Martin Mokrejs @ 2014-06-26 14:32 UTC (permalink / raw
  To: gentoo-commits

commit:     a2f461519e3a62831c5d05b9ef0016e9eaf61adc
Author:     Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Thu Jun 26 14:31:53 2014 +0000
Commit:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Thu Jun 26 14:31:53 2014 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=a2f46151

sci-biology/ncbi-tools++-12.0.0: dropped altogether openssl-related USE flags and configure arguments (per upstream info nothing in the public code uses openssl and the configure test is there for their internal reasonings); dropped gnutls[lzo] requirement which was only need for unpatched 9.0.0 version; however, --with-lzo is still advantageous for http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/doxyhtml/group__Compression.htmlhttp://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/doxyhtml/group__CompressionStreams.html

---
 sci-biology/ncbi-tools++/ncbi-tools++-12.0.0.ebuild | 4 +---
 1 file changed, 1 insertion(+), 3 deletions(-)

diff --git a/sci-biology/ncbi-tools++/ncbi-tools++-12.0.0.ebuild b/sci-biology/ncbi-tools++/ncbi-tools++-12.0.0.ebuild
index 535b992..f8a3956 100644
--- a/sci-biology/ncbi-tools++/ncbi-tools++-12.0.0.ebuild
+++ b/sci-biology/ncbi-tools++/ncbi-tools++-12.0.0.ebuild
@@ -40,7 +40,6 @@ DEPEND="
 	sqlite? ( dev-db/sqlite )
 	sqlite3? ( dev-db/sqlite:3 )
 	mysql? ( virtual/mysql )
-	ssl? ( dev-libs/openssl )
 	fltk? ( x11-libs/fltk )
 	opengl? ( virtual/opengl media-libs/glew )
 	mesa? ( media-libs/mesa
@@ -49,7 +48,7 @@ DEPEND="
 	glut? ( media-libs/freeglut )
 	freetype? ( media-libs/freetype )
 	fastcgi? ( www-apache/mod_fastcgi )
-	gnutls? ( net-libs/gnutls[lzo] )
+	gnutls? ( net-libs/gnutls )
 	python? ( dev-lang/python )
 	cppunit? ( dev-util/cppunit )
 	icu? ( dev-libs/icu )
@@ -227,7 +226,6 @@ src_configure() {
 	$(use_with lzo lzo "${EPREFIX}/usr")
 	$(use_with pcre pcre "${EPREFIX}/usr")
 	$(use_with gnutls gnutls "${EPREFIX}/usr")
-	$(use_with ssl openssl "${EPREFIX}/usr")
 	$(use_with ftds ftds "${EPREFIX}/usr")
 	$(use_with mysql mysql "${EPREFIX}/usr")
 	$(usex fltk --with-fltk="${EPREFIX}/usr" "")


^ permalink raw reply related	[flat|nested] 49+ messages in thread

* [gentoo-commits] proj/sci:master commit in: sci-biology/ncbi-tools++/
@ 2014-06-26 14:38 Martin Mokrejs
  0 siblings, 0 replies; 49+ messages in thread
From: Martin Mokrejs @ 2014-06-26 14:38 UTC (permalink / raw
  To: gentoo-commits

commit:     4093a5178b56aba0459005460bf7dd5f3d2beba0
Author:     Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Thu Jun 26 14:38:00 2014 +0000
Commit:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Thu Jun 26 14:38:00 2014 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=4093a517

sci-biology/ncbi-tools++-9.0.0*: dropped altogether openssl-related USE flags and configure arguments (per upstream info nothing in the public code uses openssl and the configure test is there for their internal reasonings); dropped gnutls[lzo] requirement which was only need for unpatched 9.0.0 version; however, --with-lzo is still advantageous for http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/doxyhtml/group__Compression.htmlhttp://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/doxyhtml/group__CompressionStreams.html

---
 sci-biology/ncbi-tools++/ncbi-tools++-9.0.0-r1.ebuild |  8 +++-----
 sci-biology/ncbi-tools++/ncbi-tools++-9.0.0.ebuild    | 10 ++--------
 2 files changed, 5 insertions(+), 13 deletions(-)

diff --git a/sci-biology/ncbi-tools++/ncbi-tools++-9.0.0-r1.ebuild b/sci-biology/ncbi-tools++/ncbi-tools++-9.0.0-r1.ebuild
index 89ae176..953b011 100644
--- a/sci-biology/ncbi-tools++/ncbi-tools++-9.0.0-r1.ebuild
+++ b/sci-biology/ncbi-tools++/ncbi-tools++-9.0.0-r1.ebuild
@@ -28,7 +28,7 @@ IUSE="
 	test wxwidgets odbc
 	berkdb boost bzip2 cppunit curl expat fastcgi fltk freetype ftds gif
 	glut gnutls hdf5 icu lzo jpeg mesa mysql muparser opengl pcre png python
-	sablotron sqlite sqlite3 ssl tiff xerces xalan xml xpm xslt X"
+	sablotron sqlite sqlite3 tiff xerces xalan xml xpm xslt X"
 #KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
 KEYWORDS=""
 
@@ -42,7 +42,6 @@ DEPEND="
 	sqlite3? ( dev-db/sqlite:3 )
 	mysql? ( virtual/mysql )
 	gnutls? ( net-libs/gnutls )
-	ssl? ( dev-libs/openssl )
 	fltk? ( x11-libs/fltk )
 	opengl? ( virtual/opengl )
 	mesa? ( media-libs/mesa
@@ -67,7 +66,7 @@ DEPEND="
 	png? ( media-libs/libpng )
 	tiff? ( media-libs/tiff )
 	xpm? ( x11-libs/libXpm )
-	dev-libs/lzo
+	lzo? ( dev-libs/lzo )
 	app-arch/bzip2
 	dev-libs/libpcre"
 # USE flags which should be added somehow: wxWindows wxWidgets SP ORBacus ODBC OEChem sge
@@ -212,7 +211,7 @@ src_configure() {
 #	--with-3psw=std:netopt favor standard (system) builds of the above pkgs
 
 
-# TODO: should improve the ssl/openssl/gmutls logic like is in net-misc/vpnc
+# Note: only care about gnutls, nothing actually uses openssl except a forgotten configure test
 	$(use_with debug)
 	$(use_with debug max-debug)
 	$(use_with debug symbols)
@@ -225,7 +224,6 @@ src_configure() {
 	$(use_with lzo lzo "${EPREFIX}/usr")
 	$(use_with pcre pcre "${EPREFIX}/usr")
 	$(use_with gnutls gnutls "${EPREFIX}/usr")
-	$(use_with ssl openssl "${EPREFIX}/usr")
 	$(use_with ftds ftds "${EPREFIX}/usr")
 	$(use_with mysql mysql "${EPREFIX}/usr")
 	$(use_with fltk fltk "${EPREFIX}/usr")

diff --git a/sci-biology/ncbi-tools++/ncbi-tools++-9.0.0.ebuild b/sci-biology/ncbi-tools++/ncbi-tools++-9.0.0.ebuild
index 8020276..b9f8047 100644
--- a/sci-biology/ncbi-tools++/ncbi-tools++-9.0.0.ebuild
+++ b/sci-biology/ncbi-tools++/ncbi-tools++-9.0.0.ebuild
@@ -23,7 +23,7 @@ SRC_URI="
 
 LICENSE="public-domain"
 SLOT="0"
-IUSE="berkdb boost bzip2 cppunit curl expat fastcgi fltk freetype ftds gif glut gnutls hdf5 icu jpeg lzo mesa mysql muparser opengl pcre png python sablotron sqlite sqlite3 ssl tiff xerces xalan xml xpm xslt X"
+IUSE="berkdb boost bzip2 cppunit curl expat fastcgi fltk freetype ftds gif glut gnutls hdf5 icu jpeg lzo mesa mysql muparser opengl pcre png python sablotron sqlite sqlite3 tiff xerces xalan xml xpm xslt X"
 #KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
 KEYWORDS=""
 
@@ -36,7 +36,6 @@ DEPEND="berkdb? ( sys-libs/db:4.3 )
 	sqlite3? ( dev-db/sqlite:3 )
 	mysql? ( virtual/mysql )
 	gnutls? ( net-libs/gnutls )
-	ssl? ( dev-libs/openssl )
 	fltk? ( x11-libs/fltk )
 	opengl? ( virtual/opengl )
 	mesa? ( media-libs/mesa )
@@ -59,7 +58,7 @@ DEPEND="berkdb? ( sys-libs/db:4.3 )
 	png? ( media-libs/libpng )
 	tiff? ( media-libs/tiff )
 	xpm? ( x11-libs/libXpm )
-	dev-libs/lzo
+	lzo? ( dev-libs/lzo )
 	app-arch/bzip2
 	dev-libs/libpcre"
 # USE flags which should be added somehow: wxWindows wxWidgets SP ORBacus ODBC OEChem sge
@@ -182,11 +181,6 @@ src_configure() {
 	else
 		myconf="--without-gnutls"
 	fi
-	if use ssl; then
-		myconf="--with-openssl"
-	else
-		myconf="--without-openssl"
-	fi
 	if ! use sqlite; then
 		myconf="--without-sqlite"
 	fi


^ permalink raw reply related	[flat|nested] 49+ messages in thread

* [gentoo-commits] proj/sci:master commit in: sci-biology/ncbi-tools++/
@ 2014-06-26 15:09 Martin Mokrejs
  0 siblings, 0 replies; 49+ messages in thread
From: Martin Mokrejs @ 2014-06-26 15:09 UTC (permalink / raw
  To: gentoo-commits

commit:     47da4cc7e724f425a41f532ce56155fff072657b
Author:     Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Thu Jun 26 15:09:03 2014 +0000
Commit:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Thu Jun 26 15:09:03 2014 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=47da4cc7

sci-biology/ncbi-tools++-12.0.0: dropping :%=% from LIB settings

---
 sci-biology/ncbi-tools++/ncbi-tools++-12.0.0.ebuild | 1 +
 1 file changed, 1 insertion(+)

diff --git a/sci-biology/ncbi-tools++/ncbi-tools++-12.0.0.ebuild b/sci-biology/ncbi-tools++/ncbi-tools++-12.0.0.ebuild
index f8a3956..218278d 100644
--- a/sci-biology/ncbi-tools++/ncbi-tools++-12.0.0.ebuild
+++ b/sci-biology/ncbi-tools++/ncbi-tools++-12.0.0.ebuild
@@ -112,6 +112,7 @@ src_prepare() {
 		"${FILESDIR}"/${P}-more-patches.patch
 		"${FILESDIR}"/${P}-linkage-tuneups-addons.patch
 		"${FILESDIR}"/${P}-configure.patch
+		"${FILESDIR}"/${P}-drop-STATIC-from-LIB.patch
 		)
 #       "${FILESDIR}"/${P}-as-needed.patch
 #       "${FILESDIR}"/${P}-fix-creaders-linking.patch


^ permalink raw reply related	[flat|nested] 49+ messages in thread

* [gentoo-commits] proj/sci:master commit in: sci-biology/ncbi-tools++/
@ 2014-06-26 17:31 Martin Mokrejs
  0 siblings, 0 replies; 49+ messages in thread
From: Martin Mokrejs @ 2014-06-26 17:31 UTC (permalink / raw
  To: gentoo-commits

commit:     f18aa6a66c0e20b32d49289548aff679a8092be9
Author:     Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Thu Jun 26 17:31:01 2014 +0000
Commit:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Thu Jun 26 17:31:01 2014 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=f18aa6a6

sci-biology/ncbi-tools++-12.0.0: added a blocker with sci-biology/sra_sdk

---
 sci-biology/ncbi-tools++/ncbi-tools++-12.0.0.ebuild | 1 +
 1 file changed, 1 insertion(+)

diff --git a/sci-biology/ncbi-tools++/ncbi-tools++-12.0.0.ebuild b/sci-biology/ncbi-tools++/ncbi-tools++-12.0.0.ebuild
index 218278d..cce77ab 100644
--- a/sci-biology/ncbi-tools++/ncbi-tools++-12.0.0.ebuild
+++ b/sci-biology/ncbi-tools++/ncbi-tools++-12.0.0.ebuild
@@ -33,6 +33,7 @@ KEYWORDS=""
 
 # sys-libs/db should be compiled with USE=cxx
 DEPEND="
+	!sci-biology/sra_sdk
 	berkdb? ( sys-libs/db:4.3[cxx] )
 	ftds? ( dev-db/freetds )
 	boost? ( dev-libs/boost )


^ permalink raw reply related	[flat|nested] 49+ messages in thread

* [gentoo-commits] proj/sci:master commit in: sci-biology/ncbi-tools++/
@ 2014-06-26 19:04 Martin Mokrejs
  0 siblings, 0 replies; 49+ messages in thread
From: Martin Mokrejs @ 2014-06-26 19:04 UTC (permalink / raw
  To: gentoo-commits

commit:     19b0ba203ab340ea1b4f4ea9f950b3024905127f
Author:     Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Thu Jun 26 19:04:06 2014 +0000
Commit:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Thu Jun 26 19:04:06 2014 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=19b0ba20

sci-biology/ncbi-tools++-12.0.0: drop forgotten IUSE=ssl

---
 sci-biology/ncbi-tools++/ncbi-tools++-12.0.0.ebuild | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/sci-biology/ncbi-tools++/ncbi-tools++-12.0.0.ebuild b/sci-biology/ncbi-tools++/ncbi-tools++-12.0.0.ebuild
index cce77ab..ebc9c33 100644
--- a/sci-biology/ncbi-tools++/ncbi-tools++-12.0.0.ebuild
+++ b/sci-biology/ncbi-tools++/ncbi-tools++-12.0.0.ebuild
@@ -27,7 +27,7 @@ IUSE="
 	test wxwidgets odbc
 	berkdb boost bzip2 cppunit curl expat fastcgi fltk freetype ftds gif
 	glut gnutls hdf5 icu jpeg lzo mesa mysql muparser opengl pcre png python
-	sablotron sqlite sqlite3 ssl tiff xerces xalan xml xpm xslt X"
+	sablotron sqlite sqlite3 tiff xerces xalan xml xpm xslt X"
 #KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
 KEYWORDS=""
 


^ permalink raw reply related	[flat|nested] 49+ messages in thread

* [gentoo-commits] proj/sci:master commit in: sci-biology/ncbi-tools++/
@ 2014-06-26 19:49 Martin Mokrejs
  0 siblings, 0 replies; 49+ messages in thread
From: Martin Mokrejs @ 2014-06-26 19:49 UTC (permalink / raw
  To: gentoo-commits

commit:     2513d463dc99aaf7b5f70f2689f97af7de3c4483
Author:     Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Thu Jun 26 19:48:49 2014 +0000
Commit:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Thu Jun 26 19:48:49 2014 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=2513d463

sci-biology/ncbi-tools++: dropped USE=ftds as it is useless and recommended by upstream to be disabled altogether

---
 sci-biology/ncbi-tools++/ncbi-tools++-12.0.0.ebuild   | 14 ++++++--------
 sci-biology/ncbi-tools++/ncbi-tools++-9.0.0-r1.ebuild | 13 ++++++-------
 sci-biology/ncbi-tools++/ncbi-tools++-9.0.0.ebuild    | 14 +++++---------
 3 files changed, 17 insertions(+), 24 deletions(-)

diff --git a/sci-biology/ncbi-tools++/ncbi-tools++-12.0.0.ebuild b/sci-biology/ncbi-tools++/ncbi-tools++-12.0.0.ebuild
index ebc9c33..23ff5d8 100644
--- a/sci-biology/ncbi-tools++/ncbi-tools++-12.0.0.ebuild
+++ b/sci-biology/ncbi-tools++/ncbi-tools++-12.0.0.ebuild
@@ -25,8 +25,8 @@ SLOT="0"
 IUSE="
 	debug static-libs static threads pch
 	test wxwidgets odbc
-	berkdb boost bzip2 cppunit curl expat fastcgi fltk freetype ftds gif
-	glut gnutls hdf5 icu jpeg lzo mesa mysql muparser opengl pcre png python
+	berkdb boost bzip2 cppunit curl expat fastcgi fltk freetype gif
+	glut gnutls hdf5 icu jpeg lzo osmesa mysql muparser opengl pcre png python
 	sablotron sqlite sqlite3 tiff xerces xalan xml xpm xslt X"
 #KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
 KEYWORDS=""
@@ -35,7 +35,6 @@ KEYWORDS=""
 DEPEND="
 	!sci-biology/sra_sdk
 	berkdb? ( sys-libs/db:4.3[cxx] )
-	ftds? ( dev-db/freetds )
 	boost? ( dev-libs/boost )
 	curl? ( net-misc/curl )
 	sqlite? ( dev-db/sqlite )
@@ -43,7 +42,7 @@ DEPEND="
 	mysql? ( virtual/mysql )
 	fltk? ( x11-libs/fltk )
 	opengl? ( virtual/opengl media-libs/glew )
-	mesa? ( media-libs/mesa
+	osmesa? ( media-libs/mesa
 		media-libs/glew
 	)
 	glut? ( media-libs/freeglut )
@@ -70,7 +69,8 @@ DEPEND="
 	app-arch/bzip2
 	dev-libs/libpcre"
 # USE flags which should be added somehow: wxWindows wxWidgets SP ORBacus ODBC OEChem sge
-
+# Intentionally omitted USE flags:
+#   ftds? ( dev-db/freetds ) # useless, no real apps use it outside NCBI
 
 # seems muParser is required, also glew is required. configure exits otherwise if these are explicitly passed to it (due to USE flag enabled)
 
@@ -168,7 +168,6 @@ src_configure() {
 	#--with-ncbi-public      ensure compatibility for all in-house platforms
 	#--with-sybase-local=DIR use local SYBASE install (DIR is optional)
 	#--with-sybase-new       use newer SYBASE install (12.5 rather than 12.0)
-	#--without-ftds-renamed  do not rename Sybase DBLIB symbols in built-in FTDS
 	#--without-sp            do not use SP libraries
 	#--without-orbacus       do not use ORBacus CORBA libraries
 	#--with-orbacus=DIR      use ORBacus installation in DIR
@@ -228,11 +227,10 @@ src_configure() {
 	$(use_with lzo lzo "${EPREFIX}/usr")
 	$(use_with pcre pcre "${EPREFIX}/usr")
 	$(use_with gnutls gnutls "${EPREFIX}/usr")
-	$(use_with ftds ftds "${EPREFIX}/usr")
 	$(use_with mysql mysql "${EPREFIX}/usr")
 	$(usex fltk --with-fltk="${EPREFIX}/usr" "")
 	$(use_with opengl opengl "${EPREFIX}/usr")
-	$(use_with mesa mesa "${EPREFIX}/usr")
+	$(use_with osmesa mesa "${EPREFIX}/usr")
 	$(use_with opengl glut "${EPREFIX}/usr")
 	$(use_with opengl glew "${EPREFIX}/usr")
 	$(use_with opengl glew-mx)

diff --git a/sci-biology/ncbi-tools++/ncbi-tools++-9.0.0-r1.ebuild b/sci-biology/ncbi-tools++/ncbi-tools++-9.0.0-r1.ebuild
index 953b011..44c444e 100644
--- a/sci-biology/ncbi-tools++/ncbi-tools++-9.0.0-r1.ebuild
+++ b/sci-biology/ncbi-tools++/ncbi-tools++-9.0.0-r1.ebuild
@@ -26,8 +26,8 @@ SLOT="0"
 IUSE="
 	debug static-libs static threads pch
 	test wxwidgets odbc
-	berkdb boost bzip2 cppunit curl expat fastcgi fltk freetype ftds gif
-	glut gnutls hdf5 icu lzo jpeg mesa mysql muparser opengl pcre png python
+	berkdb boost bzip2 cppunit curl expat fastcgi fltk freetype gif
+	glut gnutls hdf5 icu lzo jpeg osmesa mysql muparser opengl pcre png python
 	sablotron sqlite sqlite3 tiff xerces xalan xml xpm xslt X"
 #KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
 KEYWORDS=""
@@ -35,7 +35,6 @@ KEYWORDS=""
 # sys-libs/db should be compiled with USE=cxx
 DEPEND="
 	berkdb? ( sys-libs/db:4.3[cxx] )
-	ftds? ( dev-db/freetds )
 	boost? ( dev-libs/boost )
 	curl? ( net-misc/curl )
 	sqlite? ( dev-db/sqlite )
@@ -44,7 +43,7 @@ DEPEND="
 	gnutls? ( net-libs/gnutls )
 	fltk? ( x11-libs/fltk )
 	opengl? ( virtual/opengl )
-	mesa? ( media-libs/mesa
+	osmesa? ( media-libs/osmesa
 		media-libs/glew
 	)
 	glut? ( media-libs/freeglut )
@@ -70,6 +69,8 @@ DEPEND="
 	app-arch/bzip2
 	dev-libs/libpcre"
 # USE flags which should be added somehow: wxWindows wxWidgets SP ORBacus ODBC OEChem sge
+# Intentionally omitted USE flags:
+#	ftds? ( dev-db/freetds ) # useless, no real apps use it outside NCBI
 
 
 # seems muParser is required, also glew is required. configure exitss otherwise
@@ -154,7 +155,6 @@ src_configure() {
 	#--with-ncbi-public      ensure compatibility for all in-house platforms
 	#--with-sybase-local=DIR use local SYBASE install (DIR is optional)
 	#--with-sybase-new       use newer SYBASE install (12.5 rather than 12.0)
-	#--without-ftds-renamed  do not rename Sybase DBLIB symbols in built-in FTDS
 	#--without-sp            do not use SP libraries
 	#--without-orbacus       do not use ORBacus CORBA libraries
 	#--with-orbacus=DIR      use ORBacus installation in DIR
@@ -224,11 +224,10 @@ src_configure() {
 	$(use_with lzo lzo "${EPREFIX}/usr")
 	$(use_with pcre pcre "${EPREFIX}/usr")
 	$(use_with gnutls gnutls "${EPREFIX}/usr")
-	$(use_with ftds ftds "${EPREFIX}/usr")
 	$(use_with mysql mysql "${EPREFIX}/usr")
 	$(use_with fltk fltk "${EPREFIX}/usr")
 	$(use_with opengl opengl "${EPREFIX}/usr")
-	$(use_with mesa mesa "${EPREFIX}/usr")
+	$(use_with osmesa mesa "${EPREFIX}/usr")
 	$(use_with opengl glut "${EPREFIX}/usr")
 	$(use_with opengl glew "${EPREFIX}/usr")
 	$(use_with opengl glew-mx)

diff --git a/sci-biology/ncbi-tools++/ncbi-tools++-9.0.0.ebuild b/sci-biology/ncbi-tools++/ncbi-tools++-9.0.0.ebuild
index b9f8047..89b6a96 100644
--- a/sci-biology/ncbi-tools++/ncbi-tools++-9.0.0.ebuild
+++ b/sci-biology/ncbi-tools++/ncbi-tools++-9.0.0.ebuild
@@ -23,13 +23,12 @@ SRC_URI="
 
 LICENSE="public-domain"
 SLOT="0"
-IUSE="berkdb boost bzip2 cppunit curl expat fastcgi fltk freetype ftds gif glut gnutls hdf5 icu jpeg lzo mesa mysql muparser opengl pcre png python sablotron sqlite sqlite3 tiff xerces xalan xml xpm xslt X"
+IUSE="berkdb boost bzip2 cppunit curl expat fastcgi fltk freetype gif glut gnutls hdf5 icu jpeg lzo osmesa mysql muparser opengl pcre png python sablotron sqlite sqlite3 tiff xerces xalan xml xpm xslt X"
 #KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
 KEYWORDS=""
 
 # sys-libs/db should be compiled with USE=cxx
 DEPEND="berkdb? ( sys-libs/db:4.3 )
-	ftds? ( dev-db/freetds )
 	boost? ( dev-libs/boost )
 	curl? ( net-misc/curl )
 	sqlite? ( dev-db/sqlite )
@@ -38,7 +37,7 @@ DEPEND="berkdb? ( sys-libs/db:4.3 )
 	gnutls? ( net-libs/gnutls )
 	fltk? ( x11-libs/fltk )
 	opengl? ( virtual/opengl )
-	mesa? ( media-libs/mesa )
+	osmesa? ( media-libs/mesa )
 	glut? ( media-libs/freeglut )
 	freetype? ( media-libs/freetype )
 	fastcgi? ( www-apache/mod_fastcgi )
@@ -62,6 +61,8 @@ DEPEND="berkdb? ( sys-libs/db:4.3 )
 	app-arch/bzip2
 	dev-libs/libpcre"
 # USE flags which should be added somehow: wxWindows wxWidgets SP ORBacus ODBC OEChem sge
+# Intentionally omitted USE flags:
+#   ftds? ( dev-db/freetds ) # useless, no real apps use it outside NCBI
 
 # configure options, may want to expose some
 #  --without-debug         build non-debug versions of libs and apps
@@ -171,11 +172,6 @@ src_configure() {
 	if ! use curl; then
 		myconf="--without-curl"
 	fi
-	if use ftds; then
-		myconf="--with-ftds"
-	else
-		myconf="--without-ftds"
-	fi
 	if use gnutls; then
 		myconf="--with-gnutls"
 	else
@@ -196,7 +192,7 @@ src_configure() {
 	if ! use opengl; then
 		myconf="--without-opengl"
 	fi
-	if ! use mesa; then
+	if ! use osmesa; then
 		myconf="--without-mesa"
 	fi
 	if ! use glut; then


^ permalink raw reply related	[flat|nested] 49+ messages in thread

* [gentoo-commits] proj/sci:master commit in: sci-biology/ncbi-tools++/
@ 2014-06-26 20:45 Martin Mokrejs
  0 siblings, 0 replies; 49+ messages in thread
From: Martin Mokrejs @ 2014-06-26 20:45 UTC (permalink / raw
  To: gentoo-commits

commit:     0fc3dc7cd2dabc62b52e5fdba7acc838263e07f4
Author:     Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Thu Jun 26 20:44:53 2014 +0000
Commit:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Thu Jun 26 20:44:53 2014 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=0fc3dc7c

sci-biology/ncbi-tools++: bring back USE=mesa although it is about OSMesa

---
 sci-biology/ncbi-tools++/ncbi-tools++-12.0.0.ebuild   | 8 +++-----
 sci-biology/ncbi-tools++/ncbi-tools++-9.0.0-r1.ebuild | 6 +++---
 sci-biology/ncbi-tools++/ncbi-tools++-9.0.0.ebuild    | 6 +++---
 3 files changed, 9 insertions(+), 11 deletions(-)

diff --git a/sci-biology/ncbi-tools++/ncbi-tools++-12.0.0.ebuild b/sci-biology/ncbi-tools++/ncbi-tools++-12.0.0.ebuild
index 3429e05..8280670 100644
--- a/sci-biology/ncbi-tools++/ncbi-tools++-12.0.0.ebuild
+++ b/sci-biology/ncbi-tools++/ncbi-tools++-12.0.0.ebuild
@@ -26,7 +26,7 @@ IUSE="
 	debug static-libs static threads pch
 	test wxwidgets odbc
 	berkdb boost bzip2 cppunit curl expat fastcgi fltk freetype gif
-	glut gnutls hdf5 icu jpeg lzo osmesa mysql muparser opengl pcre png python
+	glut gnutls hdf5 icu jpeg lzo mesa mysql muparser opengl pcre png python
 	sablotron sqlite sqlite3 tiff xerces xalan xml xpm xslt X"
 #KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
 KEYWORDS=""
@@ -42,9 +42,7 @@ DEPEND="
 	mysql? ( virtual/mysql )
 	fltk? ( x11-libs/fltk )
 	opengl? ( virtual/opengl media-libs/glew )
-	osmesa? ( media-libs/mesa
-		media-libs/glew
-	)
+	mesa? ( media-libs/mesa )
 	glut? ( media-libs/freeglut )
 	freetype? ( media-libs/freetype )
 	fastcgi? ( www-apache/mod_fastcgi )
@@ -231,7 +229,7 @@ src_configure() {
 	$(use_with mysql mysql "${EPREFIX}/usr")
 	$(usex fltk --with-fltk="${EPREFIX}/usr" "")
 	$(use_with opengl opengl "${EPREFIX}/usr")
-	$(use_with osmesa mesa "${EPREFIX}/usr")
+	$(use_with mesa mesa "${EPREFIX}/usr")
 	$(use_with opengl glut "${EPREFIX}/usr")
 	$(use_with opengl glew "${EPREFIX}/usr")
 	$(use_with opengl glew-mx)

diff --git a/sci-biology/ncbi-tools++/ncbi-tools++-9.0.0-r1.ebuild b/sci-biology/ncbi-tools++/ncbi-tools++-9.0.0-r1.ebuild
index 44c444e..e0ca14c 100644
--- a/sci-biology/ncbi-tools++/ncbi-tools++-9.0.0-r1.ebuild
+++ b/sci-biology/ncbi-tools++/ncbi-tools++-9.0.0-r1.ebuild
@@ -27,7 +27,7 @@ IUSE="
 	debug static-libs static threads pch
 	test wxwidgets odbc
 	berkdb boost bzip2 cppunit curl expat fastcgi fltk freetype gif
-	glut gnutls hdf5 icu lzo jpeg osmesa mysql muparser opengl pcre png python
+	glut gnutls hdf5 icu lzo jpeg mesa mysql muparser opengl pcre png python
 	sablotron sqlite sqlite3 tiff xerces xalan xml xpm xslt X"
 #KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
 KEYWORDS=""
@@ -43,7 +43,7 @@ DEPEND="
 	gnutls? ( net-libs/gnutls )
 	fltk? ( x11-libs/fltk )
 	opengl? ( virtual/opengl )
-	osmesa? ( media-libs/osmesa
+	mesa? ( media-libs/mesa
 		media-libs/glew
 	)
 	glut? ( media-libs/freeglut )
@@ -227,7 +227,7 @@ src_configure() {
 	$(use_with mysql mysql "${EPREFIX}/usr")
 	$(use_with fltk fltk "${EPREFIX}/usr")
 	$(use_with opengl opengl "${EPREFIX}/usr")
-	$(use_with osmesa mesa "${EPREFIX}/usr")
+	$(use_with mesa mesa "${EPREFIX}/usr")
 	$(use_with opengl glut "${EPREFIX}/usr")
 	$(use_with opengl glew "${EPREFIX}/usr")
 	$(use_with opengl glew-mx)

diff --git a/sci-biology/ncbi-tools++/ncbi-tools++-9.0.0.ebuild b/sci-biology/ncbi-tools++/ncbi-tools++-9.0.0.ebuild
index 89b6a96..ab553c5 100644
--- a/sci-biology/ncbi-tools++/ncbi-tools++-9.0.0.ebuild
+++ b/sci-biology/ncbi-tools++/ncbi-tools++-9.0.0.ebuild
@@ -23,7 +23,7 @@ SRC_URI="
 
 LICENSE="public-domain"
 SLOT="0"
-IUSE="berkdb boost bzip2 cppunit curl expat fastcgi fltk freetype gif glut gnutls hdf5 icu jpeg lzo osmesa mysql muparser opengl pcre png python sablotron sqlite sqlite3 tiff xerces xalan xml xpm xslt X"
+IUSE="berkdb boost bzip2 cppunit curl expat fastcgi fltk freetype gif glut gnutls hdf5 icu jpeg lzo mesa mysql muparser opengl pcre png python sablotron sqlite sqlite3 tiff xerces xalan xml xpm xslt X"
 #KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
 KEYWORDS=""
 
@@ -37,7 +37,7 @@ DEPEND="berkdb? ( sys-libs/db:4.3 )
 	gnutls? ( net-libs/gnutls )
 	fltk? ( x11-libs/fltk )
 	opengl? ( virtual/opengl )
-	osmesa? ( media-libs/mesa )
+	mesa? ( media-libs/mesa )
 	glut? ( media-libs/freeglut )
 	freetype? ( media-libs/freetype )
 	fastcgi? ( www-apache/mod_fastcgi )
@@ -192,7 +192,7 @@ src_configure() {
 	if ! use opengl; then
 		myconf="--without-opengl"
 	fi
-	if ! use osmesa; then
+	if ! use mesa; then
 		myconf="--without-mesa"
 	fi
 	if ! use glut; then


^ permalink raw reply related	[flat|nested] 49+ messages in thread

* [gentoo-commits] proj/sci:master commit in: sci-biology/ncbi-tools++/
@ 2014-06-26 21:06 Martin Mokrejs
  0 siblings, 0 replies; 49+ messages in thread
From: Martin Mokrejs @ 2014-06-26 21:06 UTC (permalink / raw
  To: gentoo-commits

commit:     7d0dda709757bcc413823ffd963152c024551303
Author:     Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Thu Jun 26 21:05:51 2014 +0000
Commit:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Thu Jun 26 21:05:51 2014 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=7d0dda70

sci-biology/ncbi-tools++: so require media-libs/mesa[osmesa] for USE=mesa

---
 sci-biology/ncbi-tools++/ncbi-tools++-12.0.0.ebuild   | 2 +-
 sci-biology/ncbi-tools++/ncbi-tools++-9.0.0-r1.ebuild | 2 +-
 sci-biology/ncbi-tools++/ncbi-tools++-9.0.0.ebuild    | 2 +-
 3 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/sci-biology/ncbi-tools++/ncbi-tools++-12.0.0.ebuild b/sci-biology/ncbi-tools++/ncbi-tools++-12.0.0.ebuild
index 8280670..d304579 100644
--- a/sci-biology/ncbi-tools++/ncbi-tools++-12.0.0.ebuild
+++ b/sci-biology/ncbi-tools++/ncbi-tools++-12.0.0.ebuild
@@ -42,7 +42,7 @@ DEPEND="
 	mysql? ( virtual/mysql )
 	fltk? ( x11-libs/fltk )
 	opengl? ( virtual/opengl media-libs/glew )
-	mesa? ( media-libs/mesa )
+	mesa? ( media-libs/mesa[osmesa] )
 	glut? ( media-libs/freeglut )
 	freetype? ( media-libs/freetype )
 	fastcgi? ( www-apache/mod_fastcgi )

diff --git a/sci-biology/ncbi-tools++/ncbi-tools++-9.0.0-r1.ebuild b/sci-biology/ncbi-tools++/ncbi-tools++-9.0.0-r1.ebuild
index e0ca14c..a618abb 100644
--- a/sci-biology/ncbi-tools++/ncbi-tools++-9.0.0-r1.ebuild
+++ b/sci-biology/ncbi-tools++/ncbi-tools++-9.0.0-r1.ebuild
@@ -43,7 +43,7 @@ DEPEND="
 	gnutls? ( net-libs/gnutls )
 	fltk? ( x11-libs/fltk )
 	opengl? ( virtual/opengl )
-	mesa? ( media-libs/mesa
+	mesa? ( media-libs/mesa[osmesa]
 		media-libs/glew
 	)
 	glut? ( media-libs/freeglut )

diff --git a/sci-biology/ncbi-tools++/ncbi-tools++-9.0.0.ebuild b/sci-biology/ncbi-tools++/ncbi-tools++-9.0.0.ebuild
index ab553c5..db91131 100644
--- a/sci-biology/ncbi-tools++/ncbi-tools++-9.0.0.ebuild
+++ b/sci-biology/ncbi-tools++/ncbi-tools++-9.0.0.ebuild
@@ -37,7 +37,7 @@ DEPEND="berkdb? ( sys-libs/db:4.3 )
 	gnutls? ( net-libs/gnutls )
 	fltk? ( x11-libs/fltk )
 	opengl? ( virtual/opengl )
-	mesa? ( media-libs/mesa )
+	mesa? ( media-libs/mesa[osmesa] )
 	glut? ( media-libs/freeglut )
 	freetype? ( media-libs/freetype )
 	fastcgi? ( www-apache/mod_fastcgi )


^ permalink raw reply related	[flat|nested] 49+ messages in thread

* [gentoo-commits] proj/sci:master commit in: sci-biology/ncbi-tools++/
@ 2014-06-26 21:26 Martin Mokrejs
  0 siblings, 0 replies; 49+ messages in thread
From: Martin Mokrejs @ 2014-06-26 21:26 UTC (permalink / raw
  To: gentoo-commits

commit:     e5e343c4a4dd2e5df08f92798c800e2ecaf5f4f7
Author:     Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Thu Jun 26 21:25:35 2014 +0000
Commit:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Thu Jun 26 21:25:35 2014 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=e5e343c4

sci-biology/ncbi-tools++-12.0.0: improved comment text

---
 sci-biology/ncbi-tools++/ncbi-tools++-12.0.0.ebuild | 5 ++++-
 1 file changed, 4 insertions(+), 1 deletion(-)

diff --git a/sci-biology/ncbi-tools++/ncbi-tools++-12.0.0.ebuild b/sci-biology/ncbi-tools++/ncbi-tools++-12.0.0.ebuild
index d304579..3c28096 100644
--- a/sci-biology/ncbi-tools++/ncbi-tools++-12.0.0.ebuild
+++ b/sci-biology/ncbi-tools++/ncbi-tools++-12.0.0.ebuild
@@ -68,7 +68,10 @@ DEPEND="
 	dev-libs/libpcre"
 # USE flags which should be added somehow: wxWindows wxWidgets SP ORBacus ODBC OEChem sge
 # Intentionally omitted USE flags:
-#   ftds? ( dev-db/freetds ) # useless, no real apps use it outside NCBI
+#   ftds? ( dev-db/freetds ) # support for outside FreeTDS installations is currently broken.
+#                              The default (heavily patched) embedded copy should work, or you can
+#                              leave it off altogether -- the only public apps that make use of it are
+#                              samples and tests, since NCBI's database servers are of course firewalled.
 
 # seems muParser is required, also glew is required. configure exits otherwise if these are explicitly passed to it (due to USE flag enabled)
 


^ permalink raw reply related	[flat|nested] 49+ messages in thread

* [gentoo-commits] proj/sci:master commit in: sci-biology/ncbi-tools++/
@ 2014-10-10  6:27 Justin Lecher
  0 siblings, 0 replies; 49+ messages in thread
From: Justin Lecher @ 2014-10-10  6:27 UTC (permalink / raw
  To: gentoo-commits

commit:     5b06e2557cb96c8fb6f7aae9cc43662175579b17
Author:     mschubert <mschu.dev <AT> gmail <DOT> com>
AuthorDate: Thu Oct  9 21:32:01 2014 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Thu Oct  9 21:32:01 2014 +0000
URL:        http://sources.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=5b06e255

ncbi-tools++: fix prefix libdir, muparser/hdf5 use flags

---
 sci-biology/ncbi-tools++/ncbi-tools++-12.0.0.ebuild | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/sci-biology/ncbi-tools++/ncbi-tools++-12.0.0.ebuild b/sci-biology/ncbi-tools++/ncbi-tools++-12.0.0.ebuild
index 450ec1f..b019bc6 100644
--- a/sci-biology/ncbi-tools++/ncbi-tools++-12.0.0.ebuild
+++ b/sci-biology/ncbi-tools++/ncbi-tools++-12.0.0.ebuild
@@ -57,7 +57,7 @@ DEPEND="
 	xerces? ( dev-libs/xerces-c )
 	xalan? ( dev-libs/xalan-c )
 	muparser? ( dev-cpp/muParser )
-	hdf5? ( sci-libs/hdf5 )
+	hdf5? ( sci-libs/hdf5[cxx] )
 	gif? ( media-libs/giflib )
 	jpeg? ( virtual/jpeg )
 	png? ( media-libs/libpng )
@@ -212,7 +212,6 @@ src_configure() {
 #	--with-included-sss
 	--with-z="${EPREFIX}/usr"
 	--with-bz2="${EPREFIX}/usr"
-	--with-muparser="${EPREFIX}/usr"
 	--without-sybase
 	--with-autodep
 #	--with-3psw=std:netopt favor standard (system) builds of the above pkgs
@@ -222,13 +221,14 @@ src_configure() {
 	$(use_with static-libs static)
 	$(use_with static static-exe)
 	$(use_with threads mt)
-	$(use_with prefix runpath "${EPREFIX}/usr/$(get_libdir)/ncbi_cxx")
+	$(use_with prefix runpath "${EPREFIX}/usr/$(get_libdir)/${PN}")
 	$(use_with test check)
 	$(use_with pch)
 	$(use_with lzo lzo "${EPREFIX}/usr")
 	$(use_with pcre pcre "${EPREFIX}/usr")
 	$(use_with gnutls gnutls "${EPREFIX}/usr")
 	$(use_with mysql mysql "${EPREFIX}/usr")
+	$(use_with muparser muparser "${EPREFIX}/usr")
 	$(usex fltk --with-fltk="${EPREFIX}/usr" "")
 	$(use_with opengl opengl "${EPREFIX}/usr")
 	$(use_with mesa mesa "${EPREFIX}/usr")


^ permalink raw reply related	[flat|nested] 49+ messages in thread

* [gentoo-commits] proj/sci:master commit in: sci-biology/ncbi-tools++/
@ 2015-02-18 16:41 Justin Lecher
  0 siblings, 0 replies; 49+ messages in thread
From: Justin Lecher @ 2015-02-18 16:41 UTC (permalink / raw
  To: gentoo-commits

commit:     abea2757044d9b4ee86ceea1a0f6afe974c03f62
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Wed Feb 18 13:29:11 2015 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Wed Feb 18 13:29:11 2015 +0000
URL:        http://sources.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=abea2757

sci-biology/ncbi-tools++: fix SLOT operators; correct python deps

Package-Manager: portage-2.2.17

---
 sci-biology/ncbi-tools++/ChangeLog                  |  5 ++++-
 sci-biology/ncbi-tools++/ncbi-tools++-12.0.0.ebuild | 18 +++++++++++-------
 2 files changed, 15 insertions(+), 8 deletions(-)

diff --git a/sci-biology/ncbi-tools++/ChangeLog b/sci-biology/ncbi-tools++/ChangeLog
index 65f0990..44abaa2 100644
--- a/sci-biology/ncbi-tools++/ChangeLog
+++ b/sci-biology/ncbi-tools++/ChangeLog
@@ -1,7 +1,10 @@
 # ChangeLog for sci-biology/ncbi-tools++
-# Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2
+# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2
 # $Header: $
 
+  18 Feb 2015; Justin Lecher <jlec@gentoo.org> ncbi-tools++-12.0.0.ebuild:
+  sci-biology/ncbi-tools++: fix SLOT operators; correct python deps
+
   16 Sep 2014; Christoph Junghans <ottxor@gentoo.org>
   -files/ncbi-tools++-12.0.0-as-needed.patch,
   -files/ncbi-tools++-9.0.0-as-needed.patch,

diff --git a/sci-biology/ncbi-tools++/ncbi-tools++-12.0.0.ebuild b/sci-biology/ncbi-tools++/ncbi-tools++-12.0.0.ebuild
index b019bc6..b2933a4 100644
--- a/sci-biology/ncbi-tools++/ncbi-tools++-12.0.0.ebuild
+++ b/sci-biology/ncbi-tools++/ncbi-tools++-12.0.0.ebuild
@@ -1,10 +1,12 @@
-# Copyright 1999-2014 Gentoo Foundation
+# Copyright 1999-2015 Gentoo Foundation
 # Distributed under the terms of the GNU General Public License v2
 # $Header: $
 
 EAPI=5
 
-inherit eutils flag-o-matic multilib toolchain-funcs
+PYTHON_COMPAT=( python2_7 )
+
+inherit eutils flag-o-matic multilib python-single-r1 toolchain-funcs
 
 MY_TAG="Jun_15_2010"
 MY_Y="${MY_TAG/*_/}"
@@ -31,13 +33,15 @@ IUSE="
 #KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
 KEYWORDS=""
 
+REQUIRED_USE="${PYTHON_REQUIRED_USE}"
+
 # sys-libs/db should be compiled with USE=cxx
 DEPEND="
 	!sci-biology/sra_sdk
 	berkdb? ( sys-libs/db:4.3[cxx] )
 	boost? ( dev-libs/boost )
 	curl? ( net-misc/curl )
-	sqlite? ( dev-db/sqlite )
+	sqlite? ( dev-db/sqlite:0 )
 	sqlite3? ( dev-db/sqlite:3 )
 	mysql? ( virtual/mysql )
 	fltk? ( x11-libs/fltk )
@@ -47,7 +51,7 @@ DEPEND="
 	freetype? ( media-libs/freetype )
 	fastcgi? ( www-apache/mod_fastcgi )
 	gnutls? ( net-libs/gnutls )
-	python? ( dev-lang/python )
+	python? ( ${PYTHON_DEPS} )
 	cppunit? ( dev-util/cppunit )
 	icu? ( dev-libs/icu )
 	expat? ( dev-libs/expat )
@@ -59,9 +63,9 @@ DEPEND="
 	muparser? ( dev-cpp/muParser )
 	hdf5? ( sci-libs/hdf5[cxx] )
 	gif? ( media-libs/giflib )
-	jpeg? ( virtual/jpeg )
-	png? ( media-libs/libpng )
-	tiff? ( media-libs/tiff )
+	jpeg? ( virtual/jpeg:0= )
+	png? ( media-libs/libpng:0= )
+	tiff? ( media-libs/tiff:0= )
 	xpm? ( x11-libs/libXpm )
 	dev-libs/lzo
 	app-arch/bzip2


^ permalink raw reply related	[flat|nested] 49+ messages in thread

* [gentoo-commits] proj/sci:master commit in: sci-biology/ncbi-tools++/
@ 2015-04-17 21:59 Martin Mokrejs
  0 siblings, 0 replies; 49+ messages in thread
From: Martin Mokrejs @ 2015-04-17 21:59 UTC (permalink / raw
  To: gentoo-commits

commit:     3b861411b3276f99250fa28b5615513590a38270
Author:     Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Fri Apr 17 21:34:52 2015 +0000
Commit:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Fri Apr 17 21:34:52 2015 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=3b861411

sci-biology/ncbi-tools++: re-added KEYWORDS

Package-Manager: portage-2.2.18

 sci-biology/ncbi-tools++/ChangeLog                  | 4 ++++
 sci-biology/ncbi-tools++/ncbi-tools++-12.0.0.ebuild | 3 ++-
 2 files changed, 6 insertions(+), 1 deletion(-)

diff --git a/sci-biology/ncbi-tools++/ChangeLog b/sci-biology/ncbi-tools++/ChangeLog
index 44abaa2..ccef946 100644
--- a/sci-biology/ncbi-tools++/ChangeLog
+++ b/sci-biology/ncbi-tools++/ChangeLog
@@ -2,6 +2,10 @@
 # Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2
 # $Header: $
 
+  17 Apr 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
+  ncbi-tools++-12.0.0.ebuild:
+  sci-biology/ncbi-tools++: re-added KEYWORDS
+
   18 Feb 2015; Justin Lecher <jlec@gentoo.org> ncbi-tools++-12.0.0.ebuild:
   sci-biology/ncbi-tools++: fix SLOT operators; correct python deps
 

diff --git a/sci-biology/ncbi-tools++/ncbi-tools++-12.0.0.ebuild b/sci-biology/ncbi-tools++/ncbi-tools++-12.0.0.ebuild
index b2933a4..efe49f7 100644
--- a/sci-biology/ncbi-tools++/ncbi-tools++-12.0.0.ebuild
+++ b/sci-biology/ncbi-tools++/ncbi-tools++-12.0.0.ebuild
@@ -14,6 +14,7 @@ MY_PV="12_0_0"
 MY_P="ncbi_cxx--${MY_PV}"
 #ftp://ftp.ncbi.nlm.nih.gov/toolbox/ncbi_tools++/ARCHIVE/9_0_0/ncbi_cxx--9_0_0.tar.gz
 
+# for example sci-biology/ncbi-tools++-12.0.0 contains blastn-2.2.28+
 DESCRIPTION="NCBI C++ Toolkit, including NCBI BLAST+"
 HOMEPAGE="http://www.ncbi.nlm.nih.gov/books/bv.fcgi?rid=toolkit"
 SRC_URI="
@@ -31,7 +32,7 @@ IUSE="
 	glut gnutls hdf5 icu jpeg lzo mesa mysql muparser opengl pcre png python
 	sablotron sqlite sqlite3 tiff xerces xalan xml xpm xslt X"
 #KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
-KEYWORDS=""
+KEYWORDS="~amd64"
 
 REQUIRED_USE="${PYTHON_REQUIRED_USE}"
 


^ permalink raw reply related	[flat|nested] 49+ messages in thread

* [gentoo-commits] proj/sci:master commit in: sci-biology/ncbi-tools++/
@ 2015-06-24  9:51 Justin Lecher
  0 siblings, 0 replies; 49+ messages in thread
From: Justin Lecher @ 2015-06-24  9:51 UTC (permalink / raw
  To: gentoo-commits

commit:     879ae552d91f82bacace60a97757f862a461ee83
Author:     Horea Christian <h.chr <AT> mail <DOT> ru>
AuthorDate: Tue Jun 23 15:20:25 2015 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Tue Jun 23 15:20:25 2015 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=879ae552

added dep needed at build-time

Package-Manager: portage-2.2.20

 sci-biology/ncbi-tools++/ChangeLog                  | 3 +++
 sci-biology/ncbi-tools++/ncbi-tools++-12.0.0.ebuild | 1 +
 2 files changed, 4 insertions(+)

diff --git a/sci-biology/ncbi-tools++/ChangeLog b/sci-biology/ncbi-tools++/ChangeLog
index 0267684..b59d8f9 100644
--- a/sci-biology/ncbi-tools++/ChangeLog
+++ b/sci-biology/ncbi-tools++/ChangeLog
@@ -2,6 +2,9 @@
 # Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2
 # $Header: $
 
+  23 Jun 2015; Horea Christian <h.chr@mail.ru> ncbi-tools++-12.0.0.ebuild:
+  added dep needed at build-time
+
   11 Jun 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
   +files/ncbi-tools++-12.0.0-bdb6.patch, ncbi-tools++-12.0.0.ebuild:
   sci-biology/ncbi-tools++: added upstream patch to compile against sys-

diff --git a/sci-biology/ncbi-tools++/ncbi-tools++-12.0.0.ebuild b/sci-biology/ncbi-tools++/ncbi-tools++-12.0.0.ebuild
index 2948c74..f65f979 100644
--- a/sci-biology/ncbi-tools++/ncbi-tools++-12.0.0.ebuild
+++ b/sci-biology/ncbi-tools++/ncbi-tools++-12.0.0.ebuild
@@ -39,6 +39,7 @@ REQUIRED_USE="${PYTHON_REQUIRED_USE}"
 # sys-libs/db should be compiled with USE=cxx
 DEPEND="
 	!sci-biology/sra_sdk
+	app-arch/cpio
 	berkdb? ( sys-libs/db:4.3[cxx] )
 	boost? ( dev-libs/boost )
 	curl? ( net-misc/curl )


^ permalink raw reply related	[flat|nested] 49+ messages in thread

* [gentoo-commits] proj/sci:master commit in: sci-biology/ncbi-tools++/
@ 2015-07-17  0:40 Andrew Savchenko
  0 siblings, 0 replies; 49+ messages in thread
From: Andrew Savchenko @ 2015-07-17  0:40 UTC (permalink / raw
  To: gentoo-commits

commit:     635c7ada0349d113b3e112a4cd0d41a27c7c51e6
Author:     Andrew Savchenko <bircoph <AT> gmail <DOT> com>
AuthorDate: Fri Jul 17 00:39:45 2015 +0000
Commit:     Andrew Savchenko <bircoph <AT> gentoo <DOT> org>
CommitDate: Fri Jul 17 00:39:45 2015 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=635c7ada

Fix repoman fatal error (invalid USE description)

 sci-biology/ncbi-tools++/ChangeLog    | 3 +++
 sci-biology/ncbi-tools++/metadata.xml | 3 +++
 2 files changed, 6 insertions(+)

diff --git a/sci-biology/ncbi-tools++/ChangeLog b/sci-biology/ncbi-tools++/ChangeLog
index b59d8f9..ca8db9d 100644
--- a/sci-biology/ncbi-tools++/ChangeLog
+++ b/sci-biology/ncbi-tools++/ChangeLog
@@ -2,6 +2,9 @@
 # Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2
 # $Header: $
 
+  17 Jul 2015; Andrew Savchenko <bircoph@gentoo.org> metadata.xml:
+  Add sqlite3 flag description.
+
   23 Jun 2015; Horea Christian <h.chr@mail.ru> ncbi-tools++-12.0.0.ebuild:
   added dep needed at build-time
 

diff --git a/sci-biology/ncbi-tools++/metadata.xml b/sci-biology/ncbi-tools++/metadata.xml
index 30500b6..4d49b51 100644
--- a/sci-biology/ncbi-tools++/metadata.xml
+++ b/sci-biology/ncbi-tools++/metadata.xml
@@ -25,6 +25,9 @@
     <flag name="sablotron">Undocumented USE</flag>
   </use>
   <use>
+    <flag name="sqlite3">Add support for <pkg>dev-db/sqlite:3</pkg></flag>
+  </use>
+  <use>
     <flag name="xerces">Undocumented USE</flag>
   </use>
   <use>


^ permalink raw reply related	[flat|nested] 49+ messages in thread

* [gentoo-commits] proj/sci:master commit in: sci-biology/ncbi-tools++/
@ 2016-01-06  8:49 Justin Lecher
  0 siblings, 0 replies; 49+ messages in thread
From: Justin Lecher @ 2016-01-06  8:49 UTC (permalink / raw
  To: gentoo-commits

commit:     b9a147bbcb472ff957ec8552b6893351e062cba2
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Wed Jan  6 08:48:53 2016 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Wed Jan  6 08:49:05 2016 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=b9a147bb

sci-biology/ncbi-tools++: Drop sqlite-2 support

Package-Manager: portage-2.2.26
Signed-off-by: Justin Lecher <jlec <AT> gentoo.org>

 sci-biology/ncbi-tools++/metadata.xml               | 3 ---
 sci-biology/ncbi-tools++/ncbi-tools++-12.0.0.ebuild | 7 +++----
 2 files changed, 3 insertions(+), 7 deletions(-)

diff --git a/sci-biology/ncbi-tools++/metadata.xml b/sci-biology/ncbi-tools++/metadata.xml
index 4d49b51..30500b6 100644
--- a/sci-biology/ncbi-tools++/metadata.xml
+++ b/sci-biology/ncbi-tools++/metadata.xml
@@ -25,9 +25,6 @@
     <flag name="sablotron">Undocumented USE</flag>
   </use>
   <use>
-    <flag name="sqlite3">Add support for <pkg>dev-db/sqlite:3</pkg></flag>
-  </use>
-  <use>
     <flag name="xerces">Undocumented USE</flag>
   </use>
   <use>

diff --git a/sci-biology/ncbi-tools++/ncbi-tools++-12.0.0.ebuild b/sci-biology/ncbi-tools++/ncbi-tools++-12.0.0.ebuild
index 1b0c24e..7159951 100644
--- a/sci-biology/ncbi-tools++/ncbi-tools++-12.0.0.ebuild
+++ b/sci-biology/ncbi-tools++/ncbi-tools++-12.0.0.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2015 Gentoo Foundation
+# Copyright 1999-2016 Gentoo Foundation
 # Distributed under the terms of the GNU General Public License v2
 # $Id$
 
@@ -30,7 +30,7 @@ IUSE="
 	test wxwidgets odbc
 	berkdb boost bzip2 cppunit curl expat fastcgi fltk freetype gif
 	glut gnutls hdf5 icu jpeg lzo mesa mysql muparser opengl pcre png python
-	sablotron sqlite sqlite3 tiff xerces xalan xml xpm xslt X"
+	sablotron sqlite tiff xerces xalan xml xpm xslt X"
 #KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
 KEYWORDS="~amd64"
 
@@ -43,8 +43,7 @@ DEPEND="
 	berkdb? ( sys-libs/db:4.3[cxx] )
 	boost? ( dev-libs/boost )
 	curl? ( net-misc/curl )
-	sqlite? ( dev-db/sqlite:0 )
-	sqlite3? ( dev-db/sqlite:3 )
+	sqlite? ( dev-db/sqlite:3 )
 	mysql? ( virtual/mysql )
 	fltk? ( x11-libs/fltk )
 	opengl? ( virtual/opengl media-libs/glew )


^ permalink raw reply related	[flat|nested] 49+ messages in thread

* [gentoo-commits] proj/sci:master commit in: sci-biology/ncbi-tools++/
@ 2016-08-23 20:17 Justin Lecher
  0 siblings, 0 replies; 49+ messages in thread
From: Justin Lecher @ 2016-08-23 20:17 UTC (permalink / raw
  To: gentoo-commits

commit:     d54c7320a32ad973252bc1cbcb8cb3d7a32aed62
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Tue Aug 23 20:15:13 2016 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Tue Aug 23 20:17:16 2016 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=d54c7320

sci-biology/ncbi-tools++: Drop obsolete dep

Package-Manager: portage-2.3.0
Signed-off-by: Justin Lecher <jlec <AT> gentoo.org>

 sci-biology/ncbi-tools++/ncbi-tools++-12.0.0.ebuild | 1 -
 1 file changed, 1 deletion(-)

diff --git a/sci-biology/ncbi-tools++/ncbi-tools++-12.0.0.ebuild b/sci-biology/ncbi-tools++/ncbi-tools++-12.0.0.ebuild
index 7159951..5e5684b 100644
--- a/sci-biology/ncbi-tools++/ncbi-tools++-12.0.0.ebuild
+++ b/sci-biology/ncbi-tools++/ncbi-tools++-12.0.0.ebuild
@@ -50,7 +50,6 @@ DEPEND="
 	mesa? ( media-libs/mesa[osmesa] )
 	glut? ( media-libs/freeglut )
 	freetype? ( media-libs/freetype )
-	fastcgi? ( www-apache/mod_fastcgi )
 	gnutls? ( net-libs/gnutls )
 	python? ( ${PYTHON_DEPS} )
 	cppunit? ( dev-util/cppunit )


^ permalink raw reply related	[flat|nested] 49+ messages in thread

* [gentoo-commits] proj/sci:master commit in: sci-biology/ncbi-tools++/
@ 2016-08-23 20:17 Justin Lecher
  0 siblings, 0 replies; 49+ messages in thread
From: Justin Lecher @ 2016-08-23 20:17 UTC (permalink / raw
  To: gentoo-commits

commit:     9d6cc9b456888a65bad46444f380e7e0cc59dae3
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Tue Aug 23 20:16:51 2016 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Tue Aug 23 20:17:16 2016 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=9d6cc9b4

sci-biology/ncbi-tools++: Fix SLOT operators

Package-Manager: portage-2.3.0
Signed-off-by: Justin Lecher <jlec <AT> gentoo.org>

 sci-biology/ncbi-tools++/ncbi-tools++-12.0.0.ebuild | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/sci-biology/ncbi-tools++/ncbi-tools++-12.0.0.ebuild b/sci-biology/ncbi-tools++/ncbi-tools++-12.0.0.ebuild
index 5e5684b..c9f6911 100644
--- a/sci-biology/ncbi-tools++/ncbi-tools++-12.0.0.ebuild
+++ b/sci-biology/ncbi-tools++/ncbi-tools++-12.0.0.ebuild
@@ -46,7 +46,7 @@ DEPEND="
 	sqlite? ( dev-db/sqlite:3 )
 	mysql? ( virtual/mysql )
 	fltk? ( x11-libs/fltk )
-	opengl? ( virtual/opengl media-libs/glew )
+	opengl? ( virtual/opengl media-libs/glew:0= )
 	mesa? ( media-libs/mesa[osmesa] )
 	glut? ( media-libs/freeglut )
 	freetype? ( media-libs/freetype )


^ permalink raw reply related	[flat|nested] 49+ messages in thread

* [gentoo-commits] proj/sci:master commit in: sci-biology/ncbi-tools++/
@ 2016-12-03 11:34 Martin Mokrejs
  0 siblings, 0 replies; 49+ messages in thread
From: Martin Mokrejs @ 2016-12-03 11:34 UTC (permalink / raw
  To: gentoo-commits

commit:     0d1b801349367e3210c3feb0247936d51efdcdc5
Author:     Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Sat Dec  3 11:33:53 2016 +0000
Commit:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Sat Dec  3 11:33:53 2016 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=0d1b8013

sci-biology/ncbi-tools++: add a comment about >=gcc-5.3.0 incompatibility

Package-Manager: portage-2.3.2

 sci-biology/ncbi-tools++/ncbi-tools++-12.0.0.ebuild | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/sci-biology/ncbi-tools++/ncbi-tools++-12.0.0.ebuild b/sci-biology/ncbi-tools++/ncbi-tools++-12.0.0.ebuild
index 1236c13..8902d3e 100644
--- a/sci-biology/ncbi-tools++/ncbi-tools++-12.0.0.ebuild
+++ b/sci-biology/ncbi-tools++/ncbi-tools++-12.0.0.ebuild
@@ -329,6 +329,9 @@ src_compile() {
 	# 
 	# To take full advantage of --with-flat-makefile, you'll need the following (instead of 'emake all_p -C "${S}"_build/build') and call configure --with-flat-makefile:
 	emake -C "${S}"_build/build -f Makefile.flat
+	#
+	# >=gcc-5.3.0 is not supported, see also bug #579248#c8
+	# configure: error: Do not know how to build MT-safe with compiler /usr/bin/x86_64-pc-linux-gnu-g++  5.3.0
 }
 
 src_install() {


^ permalink raw reply related	[flat|nested] 49+ messages in thread

* [gentoo-commits] proj/sci:master commit in: sci-biology/ncbi-tools++/
@ 2017-03-14 23:08 Martin Mokrejs
  0 siblings, 0 replies; 49+ messages in thread
From: Martin Mokrejs @ 2017-03-14 23:08 UTC (permalink / raw
  To: gentoo-commits

commit:     a83e16235eb2a5fcadacac3570df72f70e0d21fd
Author:     Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Tue Mar 14 23:07:53 2017 +0000
Commit:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Tue Mar 14 23:07:53 2017 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=a83e1623

sci-biology/ncbi-tools++-12.0.0: do not force --without-downloaded-vdb

This configure flag appeared only in more recent versions.

Package-Manager: Portage-2.3.3, Repoman-2.3.1

 sci-biology/ncbi-tools++/ncbi-tools++-12.0.0.ebuild | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/sci-biology/ncbi-tools++/ncbi-tools++-12.0.0.ebuild b/sci-biology/ncbi-tools++/ncbi-tools++-12.0.0.ebuild
index 5c91c1b0c..14e1fabda 100644
--- a/sci-biology/ncbi-tools++/ncbi-tools++-12.0.0.ebuild
+++ b/sci-biology/ncbi-tools++/ncbi-tools++-12.0.0.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2016 Gentoo Foundation
+# Copyright 1999-2017 Gentoo Foundation
 # Distributed under the terms of the GNU General Public License v2
 
 EAPI=5
@@ -220,11 +220,12 @@ src_configure() {
 	--without-sybase
 	--with-autodep
 #	--with-3psw=std:netopt favor standard (system) builds of the above pkgs
+	# --without-downloaded-vdb is not available in 12.0.0 release yet
 	# preventing executing git to checkout during configure phase ncbi-vdb sources
 	# resulting in 'checking for ncbi-vdb... no' and
 	# '^PACKAGES:'
 	# '^  disabled: ... VDB'
-	--without-downloaded-vdb
+	# --without-downloaded-vdb
 	$(use_with debug)
 	$(use_with debug max-debug)
 	$(use_with debug symbols)


^ permalink raw reply related	[flat|nested] 49+ messages in thread

* [gentoo-commits] proj/sci:master commit in: sci-biology/ncbi-tools++/
@ 2017-03-27  5:35 Martin Mokrejs
  0 siblings, 0 replies; 49+ messages in thread
From: Martin Mokrejs @ 2017-03-27  5:35 UTC (permalink / raw
  To: gentoo-commits

commit:     eb01dd274c938f4b647546b9ec2924d2ee3f5876
Author:     Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Mon Mar 27 05:35:10 2017 +0000
Commit:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Mon Mar 27 05:35:10 2017 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=eb01dd27

sci-biology/ncbi-tools++: avoid file collision, KEYWORDS added back

Package-Manager: Portage-2.3.5, Repoman-2.3.1

 sci-biology/ncbi-tools++/ncbi-tools++-18.0.0.ebuild | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/sci-biology/ncbi-tools++/ncbi-tools++-18.0.0.ebuild b/sci-biology/ncbi-tools++/ncbi-tools++-18.0.0.ebuild
index 10e1b7228..ec3852d76 100644
--- a/sci-biology/ncbi-tools++/ncbi-tools++-18.0.0.ebuild
+++ b/sci-biology/ncbi-tools++/ncbi-tools++-18.0.0.ebuild
@@ -30,8 +30,7 @@ IUSE="
 	berkdb boost bzip2 cppunit curl expat fastcgi fltk freetype gif
 	glut gnutls hdf5 icu jpeg lzo mesa mysql muparser opengl pcre png python
 	sablotron sqlite tiff xerces xalan xml xpm xslt X"
-#KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
-KEYWORDS=""
+KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
 
 REQUIRED_USE="${PYTHON_REQUIRED_USE}"
 
@@ -363,6 +362,7 @@ src_install() {
 	mv -f "${ED}"/usr/bin/test_regexp "${ED}"/usr/bin/test_regexp+ # drop the eventually mistakenly compiled binaries
 	mv "${ED}"/usr/bin/vecscreen "${ED}"/usr/bin/vecscreen+
 	mv "${ED}"/usr/bin/seedtop "${ED}"/usr/bin/seedtop+
+	mv "${ED}"/usr/bin/idfetch "${ED}"/usr/bin/idfetch+ # new in ncbi-tools++-18.0.0
 
 	echo "LDPATH=${EPREFIX}/usr/$(get_libdir)/${PN}" > ${S}/99${PN}
 	doenvd "${S}/99${PN}"


^ permalink raw reply related	[flat|nested] 49+ messages in thread

* [gentoo-commits] proj/sci:master commit in: sci-biology/ncbi-tools++/
@ 2017-04-11  8:41 Martin Mokrejs
  0 siblings, 0 replies; 49+ messages in thread
From: Martin Mokrejs @ 2017-04-11  8:41 UTC (permalink / raw
  To: gentoo-commits

commit:     ad511c8fb80754d29a9fa8e2b10e87be87d073ad
Author:     Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Tue Apr 11 08:41:28 2017 +0000
Commit:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Tue Apr 11 08:41:28 2017 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=ad511c8f

sci-biology/ncbi-tools++: add note on idfetch collision by upstream

Package-Manager: Portage-2.3.5, Repoman-2.3.2

 sci-biology/ncbi-tools++/ncbi-tools++-18.0.0.ebuild | 6 ++++++
 1 file changed, 6 insertions(+)

diff --git a/sci-biology/ncbi-tools++/ncbi-tools++-18.0.0.ebuild b/sci-biology/ncbi-tools++/ncbi-tools++-18.0.0.ebuild
index ec3852d76..3f1fc7bd1 100644
--- a/sci-biology/ncbi-tools++/ncbi-tools++-18.0.0.ebuild
+++ b/sci-biology/ncbi-tools++/ncbi-tools++-18.0.0.ebuild
@@ -362,6 +362,12 @@ src_install() {
 	mv -f "${ED}"/usr/bin/test_regexp "${ED}"/usr/bin/test_regexp+ # drop the eventually mistakenly compiled binaries
 	mv "${ED}"/usr/bin/vecscreen "${ED}"/usr/bin/vecscreen+
 	mv "${ED}"/usr/bin/seedtop "${ED}"/usr/bin/seedtop+
+	#
+	# idfetch collides with idfetch from ncbi-tools-2.2.26
+	# Although the two idfetch implementations do deliberately have several
+	# options in common, the C++ version is not yet a full drop-in replacement
+	# for the C version (and will never entirely be, due to fundamental
+	# differences between the two toolkits' argument-parsing conventions).
 	mv "${ED}"/usr/bin/idfetch "${ED}"/usr/bin/idfetch+ # new in ncbi-tools++-18.0.0
 
 	echo "LDPATH=${EPREFIX}/usr/$(get_libdir)/${PN}" > ${S}/99${PN}


^ permalink raw reply related	[flat|nested] 49+ messages in thread

* [gentoo-commits] proj/sci:master commit in: sci-biology/ncbi-tools++/
@ 2019-03-30  0:13 Martin Mokrejs
  0 siblings, 0 replies; 49+ messages in thread
From: Martin Mokrejs @ 2019-03-30  0:13 UTC (permalink / raw
  To: gentoo-commits

commit:     220946d413cfcfa399e3609f2b215eabdc8df3a8
Author:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Sat Mar 30 00:13:51 2019 +0000
Commit:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Sat Mar 30 00:13:51 2019 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=220946d4

sci-biology/ncbi-tools++: version bump

It does not link if older version is installed because linker
picks up older version of libraries and obviously does not find
newly added functions.

Upstream says:
Please try either supplying an LD_RUN_PATH environment setting
or a -Wl,-rpath-link,... flag pointing at your build tree's lib
directory.  Also, please bear in mind that adding the old
installation's library directory to the central search path largely
defeats the purpose of making it a separate directory.

Package-Manager: Portage-2.3.62, Repoman-2.3.12
Signed-off-by: Martin Mokrejs <mmokrejs <AT> fold.natur.cuni.cz>

 .../ncbi-tools++/ncbi-tools++-22.0.0.ebuild        | 380 +++++++++++++++++++++
 1 file changed, 380 insertions(+)

diff --git a/sci-biology/ncbi-tools++/ncbi-tools++-22.0.0.ebuild b/sci-biology/ncbi-tools++/ncbi-tools++-22.0.0.ebuild
new file mode 100644
index 000000000..585042f9f
--- /dev/null
+++ b/sci-biology/ncbi-tools++/ncbi-tools++-22.0.0.ebuild
@@ -0,0 +1,380 @@
+# Copyright 1999-2019 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=5
+
+PYTHON_COMPAT=( python2_7 )
+
+inherit eutils flag-o-matic multilib python-single-r1 toolchain-funcs
+
+MY_TAG="Mar_28_2019"
+MY_Y="${MY_TAG/*_/}"
+MY_PV="22_0_0"
+MY_P="ncbi_cxx--${MY_PV}"
+
+# for example sci-biology/ncbi-tools++-12.0.0 contains blastn-2.2.28+
+DESCRIPTION="NCBI C++ Toolkit, including NCBI BLAST+"
+HOMEPAGE="http://www.ncbi.nlm.nih.gov/books/bv.fcgi?rid=toolkit"
+# https://ncbi.github.io/cxx-toolkit/pages/release_notes
+SRC_URI="
+	ftp://ftp.ncbi.nih.gov/toolbox/ncbi_tools++/ARCHIVE/2019/${MY_TAG}/ncbi_cxx--${MY_PV}.tar.gz"
+#	http://dev.gentoo.org/~jlec/distfiles/${PN}-${PV#0.}-asneeded.patch.xz"
+
+# should also install ftp://ftp.ncbi.nlm.nih.gov/blast/db/taxdb.tar.gz
+# see http://www.biostars.org/p/76551/ and http://blastedbio.blogspot.cz/2012/05/blast-tabular-missing-descriptions.html
+LICENSE="public-domain"
+SLOT="0"
+IUSE="
+	debug static-libs static threads pch
+	test wxwidgets odbc
+	berkdb boost bzip2 cppunit curl expat fastcgi fltk freetype gif
+	glut gnutls hdf5 icu jpeg lzo mesa mysql muparser opengl pcre png python
+	sablotron sqlite tiff xerces xalan xml xpm xslt X"
+KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
+
+REQUIRED_USE="${PYTHON_REQUIRED_USE}"
+
+# sys-libs/db should be compiled with USE=cxx
+DEPEND="
+	!sci-biology/sra_sdk
+	app-arch/cpio
+	berkdb? ( sys-libs/db:4.3[cxx] )
+	boost? ( dev-libs/boost )
+	curl? ( net-misc/curl )
+	sqlite? ( >=dev-db/sqlite-3.6.6:3 )
+	mysql? ( virtual/mysql )
+	fltk? ( x11-libs/fltk )
+	opengl? ( virtual/opengl media-libs/glew:0= )
+	mesa? ( media-libs/mesa[osmesa] )
+	glut? ( media-libs/freeglut )
+	freetype? ( media-libs/freetype )
+	gnutls? ( net-libs/gnutls )
+	python? ( ${PYTHON_DEPS} )
+	cppunit? ( dev-util/cppunit )
+	icu? ( dev-libs/icu )
+	expat? ( dev-libs/expat )
+	sablotron? ( app-text/sablotron )
+	xml? ( dev-libs/libxml2 )
+	xslt? ( >=dev-libs/libxslt-1.1.14 )
+	xerces? ( dev-libs/xerces-c )
+	xalan? ( dev-libs/xalan-c )
+	muparser? ( dev-cpp/muParser )
+	hdf5? ( sci-libs/hdf5[cxx] )
+	gif? ( media-libs/giflib )
+	jpeg? ( virtual/jpeg:0= )
+	png? ( media-libs/libpng:0= )
+	tiff? ( media-libs/tiff:0= )
+	xpm? ( x11-libs/libXpm )
+	>=dev-libs/lzo-2.0
+	app-arch/bzip2
+	dev-libs/libpcre"
+# USE flags which should be added somehow: wxWindows wxWidgets SP ORBacus ODBC OEChem sge
+# Intentionally omitted USE flags:
+#   ftds? ( dev-db/freetds ) # support for outside FreeTDS installations is currently broken.
+#                              The default (heavily patched) embedded copy should work, or you can
+#                              leave it off altogether -- the only public apps that make use of it are
+#                              samples and tests, since NCBI's database servers are of course firewalled.
+
+# seems muParser is required, also glew is required. configure exits otherwise if these are explicitly passed to it (due to USE flag enabled)
+
+RDEPEND="${DEPEND}"
+
+S="${WORKDIR}/${MY_P}"
+
+src_prepare() {
+#	filter-ldflags -Wl,--as-needed
+#	append-ldflags -Wl,--no-undefined
+#	sed -i -e 's/-print-file-name=libstdc++.a//' \
+#		-e '/sed/ s/\([gO]\[0-9\]\)\*/\1\\+/' \
+#		src/build-system/configure || die
+#	epatch \
+#		"${FILESDIR}"/${PN}-${PV#0.}-fix-order-of-libs.patch \
+#		"${FILESDIR}"/curl-types.patch \
+#		"${FILESDIR}"/malloc_initialize_upstream_fix.patch \
+#		"${FILESDIR}"/respect_CXXFLAGS_configure.ac.patch \
+#		"${FILESDIR}"/respect_CXXFLAGS_configure.patch \
+#		"${FILESDIR}"/report_project_settings_configure.ac.patch \
+#		"${FILESDIR}"/report_project_settings_configure.patch \
+#		"${FILESDIR}"/make_install.patch
+
+#		"${FILESDIR}"/${PN}-${PV#0.}-disable_test_compress.patch
+
+#		"${FILESDIR}"/${PN}-${PV#0.}-gcc46.patch \
+#		"${FILESDIR}"/${PN}-${PV#0.}-gcc47.patch \
+#		"${WORKDIR}"/${PN}-${PV#0.}-asneeded.patch \
+#		"${FILESDIR}"/${PN}-${PV#0.}-libpng15.patch \
+#		"${FILESDIR}"/${PN}-${PV#0.}-glibc-214.patch
+
+#	use prefix && append-ldflags -Wl,-rpath,"${EPREFIX}/usr/$(get_libdir)/${PN}"
+
+# The conf-opts.patch and as-needed.patch need to be adjusted for 12.0.0 line numbers
+#	local PATCHES=(
+#		"${FILESDIR}"/${P}-configure.patch
+#		"${FILESDIR}"/${P}-fix-install.patch
+#		"${FILESDIR}"/${P}-never_build_test_boost.patch # bug #579248
+#		"${FILESDIR}"/${P}-fix-annotwriter-linking.patch
+#		"${FILESDIR}"/${P}-fix-undefined-xobjread.patch
+#		"${FILESDIR}"/${P}-fix-apps-blast-linking.patch
+#		"${FILESDIR}"/${P}-fix-sample-app-cgi-linking.patch
+#		"${FILESDIR}"/${P}-fix-app-compartp-linking.patch
+#		"${FILESDIR}"/${P}-fix-app-convert_seq-linking.patch
+#		"${FILESDIR}"/${P}-fix-app-hfilter-linking.patch
+#		"${FILESDIR}"/${P}-fix-app-igblast-linking.patch
+#		"${FILESDIR}"/${P}-fix-ncfetch-linking.patch
+#		"${FILESDIR}"/${P}-fix-netcache_cgi_sample-linking.patch
+#		"${FILESDIR}"/${P}-fix-netstorage_gc-linking.patch
+#		"${FILESDIR}"/${P}-fix-speedtest-linking.patch
+#		"${FILESDIR}"/${P}-fix-splign-linking.patch
+#		"${FILESDIR}"/${P}-fix-srcchk-linking.patch
+#		"${FILESDIR}"/${P}-fix-app-rmblastn-linking.patch
+#		"${FILESDIR}"/${P}-remove-old-symlinks.patch
+#		"${FILESDIR}"/${P}-fix-app-table2asn-linking.patch
+#		"${FILESDIR}"/${P}-fix-app-tls-linking.patch
+#		"${FILESDIR}"/${P}-fix-app-vecscreen-linking.patch
+#		"${FILESDIR}"/${P}-fix-app-blast_sample-linking.patch
+#		)
+	#ncbi-tools++-18.0.0-fix-undefined-lxncbi.patch
+#	epatch ${PATCHES[@]}
+	# make sure this one is the last one and contains the actual patches applied unless we can have autoconf-2.59 or 2.60
+	# https://bugs.gentoo.org/show_bug.cgi?id=514706
+
+	tc-export CXX CC
+
+	cd src/build-system || die
+#	eautoreconf
+
+	# Temporarily disabling eautoconf because we patch configure via ${P}-support-autoconf-2.60.patch
+	# eautoconf # keep it disabled until we can ensure 2.59 is installed
+	# beware 12.0.0. and previous required autoconf-2.59, a patch for 12.0.0 brings autoconf-2.60 support
+}
+
+# possibly place modified contents of ${W}/src/build-system/config.site.ncbi and {W}/src/build-system/config.site.ex into ${W}/src/build-system/config.site
+src_configure() {
+	local myconf=()
+	#--without-optimization  turn off optimization flags in non-debug mode
+	#--with-profiling        build profiled versions of libs and apps
+	#--with-tcheck(=DIR)     build for Intel Thread Checker (in DIR)
+	#--with-plugin-auto-load always enable the plugin manager by default
+	#--with-bundles          build bundles in addition to dylibs on Mac OS X
+	#--with-bin-release      build executables suitable for public release
+	#	no dll and such
+	#--with-64               compile to 64-bit code
+	#--with-universal        build universal binaries on Mac OS X
+	#--with-universal=CPUs   build universal binaries targeting the given CPUs
+	#--without-exe           do not build executables
+	#--with-relative-runpath=P specify an executable-relative DLL search path
+	#--with-hard-runpath     hard-code runtime path, ignoring LD_LIBRARY_PATH
+	#--with-limited-linker   don't attempt to build especially large projects
+	#--with-extra-action=    script to call after the configuration is complete
+	#--with-autodep          automatic generation of dependencies (GNU make)
+	#--with-fake-root=DIR    appear to have been built under DIR
+	#--with-build-root-sfx=X add a user-specified suffix to the build dir name
+	#--without-execopy       do not copy built executables to the BIN area
+	#--with-lib-rebuilds     ensure that apps use up-to-date libraries
+	#--with-lib-rebuilds=ask ask whether to update each app's libraries
+	#--without-deactivation  keep old copies of libraries that no longer build
+	#--without-makefile-auto-update  do not auto-update generated makefiles
+	#--with-projects=FILE    build projects listed in FILE by default
+	#--without-flat-makefile do not generate an all-encompassing flat makefile
+	#--with-configure-dialog allow interactive flat makefile project selection
+	#--with-saved-settings=F load configuration settings from the file F
+	#--with-check-tools=...  use the specified tools for testing
+	#--with-ncbi-public      ensure compatibility for all in-house platforms
+	#--with-sybase-local=DIR use local SYBASE install (DIR is optional)
+	#--with-sybase-new       use newer SYBASE install (12.5 rather than 12.0)
+	#--without-sp            do not use SP libraries
+	#--without-orbacus       do not use ORBacus CORBA libraries
+	#--with-orbacus=DIR      use ORBacus installation in DIR
+	#--with-jni(=JDK-DIR)    build Java bindings (against the JDK in JDK-DIR)
+	#--with-sablot=DIR       use Sablotron installation in DIR
+	#--without-sablot,       do not use Sablotron
+	#--with-oechem=DIR       use OpenEye OEChem installation in DIR
+	#--without-oechem        do not use OEChem
+	#--with-sge=DIR          use Sun Grid Engine installation in DIR
+	#--without-sge           do not use Sun Grid Engine
+	#--with-magic=DIR        use libmagic installation in DIR
+	#--without-magic         do not use libmagic
+	#--without-local-lbsm    turn off support for IPC with locally running LBSMD
+	#--without-ncbi-crypt    use a dummy stubbed-out version of ncbi_crypt
+	#--without-connext       do not build non-public CONNECT library extensions
+	#--without-serial        do not build the serialization library and tools
+	#--without-objects       do not generate/build serializeable objects from ASNs
+	#--without-dbapi         do not build database connectivity libraries
+	#--without-app           do not build standalone applications like ID1_FETCH
+	#--without-gui           do not build most graphical projects
+	#--without-algo          do not build CPU-intensive algorithms
+	#--without-internal      do not build internal projects
+	#--with-gbench           ensure that Genome Workbench can be built
+	#--without-gbench        do not build Genome Workbench
+	myconf+=(
+	--with-dll
+	--with-lfs
+	--with-build-root="${S}"_build
+	--without-suffix
+	--without-hostspec
+	--without-version
+	--with-bincopy
+	--without-strip
+	--without-ccache
+	--without-distcc
+#	--with-ncbi-c
+	--without-ctools
+#	--with-sss
+#	--with-sssutils
+#	--with-sssdb
+#	--with-included-sss
+	--with-z="${EPREFIX}/usr"
+	--with-bz2="${EPREFIX}/usr"
+	--without-sybase
+	--with-autodep
+#	--with-3psw=std:netopt favor standard (system) builds of the above pkgs
+	# --without-downloaded-vdb is not available in 12.0.0 release yet
+	# preventing executing git to checkout during configure phase ncbi-vdb sources
+	# resulting in 'checking for ncbi-vdb... no' and
+	# '^PACKAGES:'
+	# '^  disabled: ... VDB'
+	--without-downloaded-vdb
+	$(use_with debug)
+#	$(use_with debug max-debug) # broken in 22.0.0 as it triggers need for https://github.com/google/sanitizers/wiki/AddressSanitizer
+	$(use_with debug symbols)
+	$(use_with static-libs static)
+	$(use_with static static-exe)
+	$(use_with threads mt)
+	$(use_with prefix runpath "${EPREFIX}/usr/$(get_libdir)/${PN}")
+	$(use_with test check)
+	$(use_with pch)
+	$(use_with lzo lzo "${EPREFIX}/usr")
+	$(use_with pcre pcre "${EPREFIX}/usr")
+	$(use_with gnutls gnutls "${EPREFIX}/usr")
+	$(use_with mysql mysql "${EPREFIX}/usr")
+	$(use_with muparser muparser "${EPREFIX}/usr")
+	$(usex fltk --with-fltk="${EPREFIX}/usr" "")
+	$(use_with opengl opengl "${EPREFIX}/usr")
+	$(use_with mesa mesa "${EPREFIX}/usr")
+	$(use_with opengl glut "${EPREFIX}/usr")
+	$(use_with opengl glew "${EPREFIX}/usr")
+	$(use_with opengl glew-mx)
+	$(use_with wxwidgets wxwidgets "${EPREFIX}/usr")
+	$(use_with wxwidgets wxwidgets-ucs)
+	$(use_with freetype freetype "${EPREFIX}/usr")
+	$(use_with fastcgi fastcgi "${EPREFIX}/usr")
+	$(use_with berkdb bdb "${EPREFIX}/usr")
+	$(usex odbc --with-odbc="${EPREFIX}/usr" "")
+	$(use_with python python "${EPREFIX}/usr")
+	$(use_with boost boost "${EPREFIX}/usr")
+	$(use_with sqlite sqlite3 "${EPREFIX}/usr")
+	$(use_with icu icu "${EPREFIX}/usr")
+	$(use_with expat expat "${EPREFIX}/usr")
+	$(use_with xml libxml "${EPREFIX}/usr")
+	$(use_with xml libxslt "${EPREFIX}/usr")
+	$(use_with xerces xerces "${EPREFIX}/usr")
+	$(use_with hdf5 hdf5 "${EPREFIX}/usr")
+	$(use_with xalan xalan "${EPREFIX}/usr")
+#	$(use_with gif gif "${EPREFIX}/usr") # prevent compilation failure in "ncbi-tools++-12.0.0/src/util/image/image_io_gif.cpp:351: error: 'QuantizeBuffer' was not declared in this scope"
+	--without-gif
+	$(use_with jpeg jpeg "${EPREFIX}/usr")
+	$(use_with tiff tiff "${EPREFIX}/usr")
+	$(use_with png png "${EPREFIX}/usr")
+	$(use_with xpm xpm "${EPREFIX}/usr")
+	$(use_with curl curl "${EPREFIX}/usr")
+#	$(use_with X x "${EPREFIX}/usr")
+#	$(use_with X x) # there is no --with-x option
+	)
+
+	# http://www.ncbi.nlm.nih.gov/books/NBK7167/
+	use test ||	myconf+=( --with-projects="${FILESDIR}"/disable-testsuite-compilation.txt )
+
+	# TODO
+	# copy optimization -O options from CXXFLAGS to DEF_FAST_FLAGS and pass that also to configure
+	# otherwise your -O2 will be dropped in some subdirectories and replaced by e.g. -O9
+
+	einfo "bash ./src/build-system/configure --srcdir="${S}" --prefix="${EPREFIX}/usr" --libdir=/usr/lib64 ${myconf[@]}"
+
+#	ECONF_SOURCE="src/build-system" \
+#		econf \
+	bash \
+		./src/build-system/configure \
+		--srcdir="${S}" \
+		--prefix="${EPREFIX}/usr" \
+		--libdir=/usr/lib64 \
+		--with-flat-makefile \
+		${myconf[@]} || die
+#--without-debug \
+#		--with-bin-release \
+#		--with-bincopy \
+#		--without-static \
+#		--with-dll \
+#		--with-mt \
+#		--with-openmp \
+#		--with-lfs \
+#		--prefix="${ED}"/usr \
+#		--libdir="${ED}"/usr/$(get_libdir)/"${PN}" \
+#		${myconf} LDFLAGS="-Wl,--no-as-needed" \
+#		|| die
+#	econf ${myconf[@]}
+}
+
+src_compile() {
+	## all_r would ignore the --with-projects contents and build more
+	## emake all_r -C GCC*-Release*/build || die
+	## all_p with compile only selected/required components
+	##cd "${S}"_build &&\
+	##emake all_p -C GCC*-Release*/build || die "gcc-4.5.3 crashes at src/objects/valerr/ValidError.cpp:226:1: internal compiler error: Segmentation fault, right?"
+	#emake all_p -C "${S}"_build/build
+
+	#
+	# Re: /usr/lib64/ncbi-tools++/libdbapi_driver.so: undefined reference to `ncbi::NcbiGetlineEOL(std::istream&, std::string&)'
+	#
+	# The next release should automatically address such underlinking, albeit
+	# only in --with-flat-makefile configurations.  For now (12.0.0), you'll need to
+	# add or extend more DLL_LIB settings, to which end you may find the
+	# resources at http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/depgraphs/
+	# helpful.  For instance,
+	#
+	# http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/depgraphs/dbapi_driver.html
+	#
+	# indicates that src/dbapi/driver/Makefile.dbapi_driver.lib should set
+	#
+	# DLL_LIB = xncbi
+	#
+	# (You can find the path to that makefile by examining
+	# .../status/.dbapi_driver.dep or .../build/Makefile.flat.)
+	#
+	# To take full advantage of --with-flat-makefile, you'll need the following (instead of 'emake all_p -C "${S}"_build/build') and call configure --with-flat-makefile:
+	emake -C "${S}"_build/build -f Makefile.flat
+	#
+	# >=gcc-5.3.0 is not supported, see also bug #579248#c8
+	# configure: error: Do not know how to build MT-safe with compiler /usr/bin/x86_64-pc-linux-gnu-g++  5.3.0
+}
+
+src_install() {
+	rm -rvf "${S}"_build/lib/ncbi || die
+	emake install prefix="${ED}/usr" libdir="${ED}/usr/$(get_libdir)/${PN}"
+
+#	dobin "${S}"_build/bin/*
+#	dolib.so "${S}"_build/lib/*so*
+#	dolib.a "${S}"_build/lib/*.a
+#	doheader "${S}"_build/inc/*
+
+	# File collisions with sci-biology/ncbi-tools
+	mv "${ED}"/usr/bin/asn2asn "${ED}"/usr/bin/asn2asn+
+	mv "${ED}"/usr/bin/rpsblast "${ED}"/usr/bin/rpsblast+
+	mv -f "${ED}"/usr/bin/test_regexp "${ED}"/usr/bin/test_regexp+ # drop the eventually mistakenly compiled binaries
+	mv "${ED}"/usr/bin/vecscreen "${ED}"/usr/bin/vecscreen+
+	mv "${ED}"/usr/bin/seedtop "${ED}"/usr/bin/seedtop+
+	#
+	# idfetch collides with idfetch from ncbi-tools-2.2.26
+	# Although the two idfetch implementations do deliberately have several
+	# options in common, the C++ version is not yet a full drop-in replacement
+	# for the C version (and will never entirely be, due to fundamental
+	# differences between the two toolkits' argument-parsing conventions).
+	mv "${ED}"/usr/bin/idfetch "${ED}"/usr/bin/idfetch+ # new in ncbi-tools++-18.0.0
+
+	echo "LDPATH=${EPREFIX}/usr/$(get_libdir)/${PN}" > ${S}/99${PN}
+	doenvd "${S}/99${PN}"
+}
+
+pkg_postinst() {
+	einfo 'Please run "source /etc/profile" before using this package in the current shell.'
+	einfo 'Documentation is at http://www.ncbi.nlm.nih.gov/books/NBK7167/'
+}


^ permalink raw reply related	[flat|nested] 49+ messages in thread

* [gentoo-commits] proj/sci:master commit in: sci-biology/ncbi-tools++/
@ 2019-03-30  6:42 Martin Mokrejs
  0 siblings, 0 replies; 49+ messages in thread
From: Martin Mokrejs @ 2019-03-30  6:42 UTC (permalink / raw
  To: gentoo-commits

commit:     a6b601e64f7b9313fc7d7c2fec43d0f4d4d7ec1f
Author:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Sat Mar 30 06:42:42 2019 +0000
Commit:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Sat Mar 30 06:42:42 2019 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=a6b601e6

sci-biology/ncbi-tools++: document possible issue with builds

I have the following defined due to ncbi-tools++-18.0.0 installed
on my system:

/usr/lib/gcc/x86_64-pc-linux-gnu/8.3.0/32:
/usr/lib/gcc/x86_64-pc-linux-gnu/8.3.0:
/usr/lib/gcc/x86_64-pc-linux-gnu/7.3.0/32:
/usr/lib/gcc/x86_64-pc-linux-gnu/7.3.0:
/usr/lib/llvm/7/lib32:
/usr/lib/llvm/7/lib64:
/usr/lib64/itcl4.1.1:
/usr/lib64/itk4.1.0:
/lib64:
/usr/lib64:
/usr/local/lib64:
/lib32:
/usr/lib32:
/usr/lib64/rust-1.29.2:
/usr/lib64/R/lib:
/usr/lib64/fltk:
/usr/lib64/ncbi-tools++:
/usr/lib64/staden:

grep: /etc: No such file or directory
grep: /etc/env.d: No such file or directory
/etc/env.d/99ncbi-tools++:LDPATH=/usr/lib64/ncbi-tools++
...

That in turn makes linker pick "${WORKDIR}"/ncbi_cxx--22_0_0_build/lib/*
files but later overrides some of them with /usr/lib64/ncbi-tools++/*,
depending on the ordering of -lXXXXXX arguments.

Package-Manager: Portage-2.3.62, Repoman-2.3.12
Signed-off-by: Martin Mokrejs <mmokrejs <AT> fold.natur.cuni.cz>

 sci-biology/ncbi-tools++/ncbi-tools++-12.0.0.ebuild | 5 +++--
 sci-biology/ncbi-tools++/ncbi-tools++-18.0.0.ebuild | 5 +++--
 sci-biology/ncbi-tools++/ncbi-tools++-22.0.0.ebuild | 3 ++-
 3 files changed, 8 insertions(+), 5 deletions(-)

diff --git a/sci-biology/ncbi-tools++/ncbi-tools++-12.0.0.ebuild b/sci-biology/ncbi-tools++/ncbi-tools++-12.0.0.ebuild
index 14e1fabda..68341a338 100644
--- a/sci-biology/ncbi-tools++/ncbi-tools++-12.0.0.ebuild
+++ b/sci-biology/ncbi-tools++/ncbi-tools++-12.0.0.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2017 Gentoo Foundation
+# Copyright 1999-2019 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
 EAPI=5
@@ -36,11 +36,12 @@ KEYWORDS="~amd64"
 REQUIRED_USE="${PYTHON_REQUIRED_USE}"
 
 # sys-libs/db should be compiled with USE=cxx
+# dev-libs/boost must have Boost.Test suite, probably dev-libs/boost[test] then?
 DEPEND="
 	!sci-biology/sra_sdk
 	app-arch/cpio
 	berkdb? ( sys-libs/db:4.3[cxx] )
-	boost? ( dev-libs/boost )
+	boost? ( dev-libs/boost[tools] )
 	curl? ( net-misc/curl )
 	sqlite? ( dev-db/sqlite:3 )
 	mysql? ( virtual/mysql )

diff --git a/sci-biology/ncbi-tools++/ncbi-tools++-18.0.0.ebuild b/sci-biology/ncbi-tools++/ncbi-tools++-18.0.0.ebuild
index 3f1fc7bd1..c737392fd 100644
--- a/sci-biology/ncbi-tools++/ncbi-tools++-18.0.0.ebuild
+++ b/sci-biology/ncbi-tools++/ncbi-tools++-18.0.0.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2017 Gentoo Foundation
+# Copyright 1999-2019 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
 EAPI=5
@@ -35,11 +35,12 @@ KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
 REQUIRED_USE="${PYTHON_REQUIRED_USE}"
 
 # sys-libs/db should be compiled with USE=cxx
+# dev-libs/boost must have Boost.Test suite, probably dev-libs/boost[test] then?
 DEPEND="
 	!sci-biology/sra_sdk
 	app-arch/cpio
 	berkdb? ( sys-libs/db:4.3[cxx] )
-	boost? ( dev-libs/boost )
+	boost? ( dev-libs/boost[tools] )
 	curl? ( net-misc/curl )
 	sqlite? ( dev-db/sqlite:3 )
 	mysql? ( virtual/mysql )

diff --git a/sci-biology/ncbi-tools++/ncbi-tools++-22.0.0.ebuild b/sci-biology/ncbi-tools++/ncbi-tools++-22.0.0.ebuild
index 585042f9f..971789fb4 100644
--- a/sci-biology/ncbi-tools++/ncbi-tools++-22.0.0.ebuild
+++ b/sci-biology/ncbi-tools++/ncbi-tools++-22.0.0.ebuild
@@ -35,11 +35,12 @@ KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
 REQUIRED_USE="${PYTHON_REQUIRED_USE}"
 
 # sys-libs/db should be compiled with USE=cxx
+# dev-libs/boost must have Boost.Test suite, probably dev-libs/boost[test] then?
 DEPEND="
 	!sci-biology/sra_sdk
 	app-arch/cpio
 	berkdb? ( sys-libs/db:4.3[cxx] )
-	boost? ( dev-libs/boost )
+	boost? ( dev-libs/boost[tools] )
 	curl? ( net-misc/curl )
 	sqlite? ( >=dev-db/sqlite-3.6.6:3 )
 	mysql? ( virtual/mysql )


^ permalink raw reply related	[flat|nested] 49+ messages in thread

* [gentoo-commits] proj/sci:master commit in: sci-biology/ncbi-tools++/
@ 2021-01-05 18:22 Andrew Ammerlaan
  0 siblings, 0 replies; 49+ messages in thread
From: Andrew Ammerlaan @ 2021-01-05 18:22 UTC (permalink / raw
  To: gentoo-commits

commit:     704db64ed869a89a3b0df65fb1e183816604b075
Author:     Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net>
AuthorDate: Tue Jan  5 10:05:05 2021 +0000
Commit:     Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net>
CommitDate: Tue Jan  5 18:21:54 2021 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=704db64e

sci-biology/ncbi-tools++: depend on gcc<10, bump py targets

Closes: https://github.com/gentoo/sci/pull/1014
Package-Manager: Portage-3.0.12, Repoman-3.0.2
Signed-off-by: Andrew Ammerlaan <andrewammerlaan <AT> riseup.net>

 .../ncbi-tools++/ncbi-tools++-12.0.0.ebuild        | 32 ++++++------
 .../ncbi-tools++/ncbi-tools++-18.0.0.ebuild        | 60 +++++++++++-----------
 .../ncbi-tools++/ncbi-tools++-22.0.0.ebuild        | 12 +++--
 3 files changed, 55 insertions(+), 49 deletions(-)

diff --git a/sci-biology/ncbi-tools++/ncbi-tools++-12.0.0.ebuild b/sci-biology/ncbi-tools++/ncbi-tools++-12.0.0.ebuild
index 68341a338..0aa05e878 100644
--- a/sci-biology/ncbi-tools++/ncbi-tools++-12.0.0.ebuild
+++ b/sci-biology/ncbi-tools++/ncbi-tools++-12.0.0.ebuild
@@ -1,7 +1,7 @@
-# Copyright 1999-2019 Gentoo Authors
+# Copyright 1999-2021 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
-EAPI=5
+EAPI=7
 
 PYTHON_COMPAT=( python2_7 )
 
@@ -38,6 +38,7 @@ REQUIRED_USE="${PYTHON_REQUIRED_USE}"
 # sys-libs/db should be compiled with USE=cxx
 # dev-libs/boost must have Boost.Test suite, probably dev-libs/boost[test] then?
 DEPEND="
+	<sys-devel/gcc-10:=
 	!sci-biology/sra_sdk
 	app-arch/cpio
 	berkdb? ( sys-libs/db:4.3[cxx] )
@@ -83,7 +84,21 @@ RDEPEND="${DEPEND}"
 
 S="${WORKDIR}/${MY_P}"
 
+PATCHES=(
+		"${FILESDIR}"/${P}-conf-opts.patch
+		"${FILESDIR}"/${P}-fix-svn-URL-upstream.patch
+		"${FILESDIR}"/${P}-linkage-tuneups.patch
+		"${FILESDIR}"/${P}-more-patches.patch
+		"${FILESDIR}"/${P}-linkage-tuneups-addons.patch
+		"${FILESDIR}"/${P}-configure.patch
+		"${FILESDIR}"/${P}-drop-STATIC-from-LIB.patch
+		"${FILESDIR}"/${P}-fix-install.patch
+		"${FILESDIR}"/${P}-bdb6.patch
+		"${FILESDIR}"/${P}-never_build_test_boost.patch # bug #579248
+		)
+
 src_prepare() {
+	default
 #	filter-ldflags -Wl,--as-needed
 #	append-ldflags -Wl,--no-undefined
 #	sed -i -e 's/-print-file-name=libstdc++.a//' \
@@ -110,24 +125,11 @@ src_prepare() {
 #	use prefix && append-ldflags -Wl,-rpath,"${EPREFIX}/usr/$(get_libdir)/${PN}"
 
 # The conf-opts.patch and as-needed.patch need to be adjusted for 12.0.0 line numbers
-	local PATCHES=(
-		"${FILESDIR}"/${P}-conf-opts.patch
-		"${FILESDIR}"/${P}-fix-svn-URL-upstream.patch
-		"${FILESDIR}"/${P}-linkage-tuneups.patch
-		"${FILESDIR}"/${P}-more-patches.patch
-		"${FILESDIR}"/${P}-linkage-tuneups-addons.patch
-		"${FILESDIR}"/${P}-configure.patch
-		"${FILESDIR}"/${P}-drop-STATIC-from-LIB.patch
-		"${FILESDIR}"/${P}-fix-install.patch
-		"${FILESDIR}"/${P}-bdb6.patch
-		"${FILESDIR}"/${P}-never_build_test_boost.patch # bug #579248
-		)
 #       "${FILESDIR}"/${P}-as-needed.patch
 #       "${FILESDIR}"/${P}-fix-creaders-linking.patch
 #       "${FILESDIR}"/${P}-fix-FreeTDS-upstream.patch
 #		)
 		# "${FILESDIR}"/${P}-support-autoconf-2.60.patch
-	epatch ${PATCHES[@]}
 	# make sure this one is the last one and contains the actual patches applied unless we can have autoconf-2.59 or 2.60
 	# https://bugs.gentoo.org/show_bug.cgi?id=514706
 

diff --git a/sci-biology/ncbi-tools++/ncbi-tools++-18.0.0.ebuild b/sci-biology/ncbi-tools++/ncbi-tools++-18.0.0.ebuild
index c737392fd..c3014adca 100644
--- a/sci-biology/ncbi-tools++/ncbi-tools++-18.0.0.ebuild
+++ b/sci-biology/ncbi-tools++/ncbi-tools++-18.0.0.ebuild
@@ -1,7 +1,7 @@
-# Copyright 1999-2019 Gentoo Authors
+# Copyright 1999-2021 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
-EAPI=5
+EAPI=7
 
 PYTHON_COMPAT=( python2_7 )
 
@@ -30,13 +30,14 @@ IUSE="
 	berkdb boost bzip2 cppunit curl expat fastcgi fltk freetype gif
 	glut gnutls hdf5 icu jpeg lzo mesa mysql muparser opengl pcre png python
 	sablotron sqlite tiff xerces xalan xml xpm xslt X"
-KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
+KEYWORDS="~amd64 ~x86"
 
 REQUIRED_USE="${PYTHON_REQUIRED_USE}"
 
 # sys-libs/db should be compiled with USE=cxx
 # dev-libs/boost must have Boost.Test suite, probably dev-libs/boost[test] then?
 DEPEND="
+	<sys-devel/gcc-10:=
 	!sci-biology/sra_sdk
 	app-arch/cpio
 	berkdb? ( sys-libs/db:4.3[cxx] )
@@ -82,7 +83,34 @@ RDEPEND="${DEPEND}"
 
 S="${WORKDIR}/${MY_P}"
 
+PATCHES=(
+		"${FILESDIR}"/${P}-configure.patch
+		"${FILESDIR}"/${P}-fix-install.patch
+		"${FILESDIR}"/${P}-never_build_test_boost.patch # bug #579248
+		"${FILESDIR}"/${P}-fix-annotwriter-linking.patch
+		"${FILESDIR}"/${P}-fix-undefined-xobjread.patch
+		"${FILESDIR}"/${P}-fix-apps-blast-linking.patch
+		"${FILESDIR}"/${P}-fix-sample-app-cgi-linking.patch
+		"${FILESDIR}"/${P}-fix-app-compartp-linking.patch
+		"${FILESDIR}"/${P}-fix-app-convert_seq-linking.patch
+		"${FILESDIR}"/${P}-fix-app-hfilter-linking.patch
+		"${FILESDIR}"/${P}-fix-app-igblast-linking.patch
+		"${FILESDIR}"/${P}-fix-ncfetch-linking.patch
+		"${FILESDIR}"/${P}-fix-netcache_cgi_sample-linking.patch
+		"${FILESDIR}"/${P}-fix-netstorage_gc-linking.patch
+		"${FILESDIR}"/${P}-fix-speedtest-linking.patch
+		"${FILESDIR}"/${P}-fix-splign-linking.patch
+		"${FILESDIR}"/${P}-fix-srcchk-linking.patch
+		"${FILESDIR}"/${P}-fix-app-rmblastn-linking.patch
+		"${FILESDIR}"/${P}-remove-old-symlinks.patch
+		"${FILESDIR}"/${P}-fix-app-table2asn-linking.patch
+		"${FILESDIR}"/${P}-fix-app-tls-linking.patch
+		"${FILESDIR}"/${P}-fix-app-vecscreen-linking.patch
+		"${FILESDIR}"/${P}-fix-app-blast_sample-linking.patch
+		)
+
 src_prepare() {
+	default
 #	filter-ldflags -Wl,--as-needed
 #	append-ldflags -Wl,--no-undefined
 #	sed -i -e 's/-print-file-name=libstdc++.a//' \
@@ -109,33 +137,7 @@ src_prepare() {
 #	use prefix && append-ldflags -Wl,-rpath,"${EPREFIX}/usr/$(get_libdir)/${PN}"
 
 # The conf-opts.patch and as-needed.patch need to be adjusted for 12.0.0 line numbers
-	local PATCHES=(
-		"${FILESDIR}"/${P}-configure.patch
-		"${FILESDIR}"/${P}-fix-install.patch
-		"${FILESDIR}"/${P}-never_build_test_boost.patch # bug #579248
-		"${FILESDIR}"/${P}-fix-annotwriter-linking.patch
-		"${FILESDIR}"/${P}-fix-undefined-xobjread.patch
-		"${FILESDIR}"/${P}-fix-apps-blast-linking.patch
-		"${FILESDIR}"/${P}-fix-sample-app-cgi-linking.patch
-		"${FILESDIR}"/${P}-fix-app-compartp-linking.patch
-		"${FILESDIR}"/${P}-fix-app-convert_seq-linking.patch
-		"${FILESDIR}"/${P}-fix-app-hfilter-linking.patch
-		"${FILESDIR}"/${P}-fix-app-igblast-linking.patch
-		"${FILESDIR}"/${P}-fix-ncfetch-linking.patch
-		"${FILESDIR}"/${P}-fix-netcache_cgi_sample-linking.patch
-		"${FILESDIR}"/${P}-fix-netstorage_gc-linking.patch
-		"${FILESDIR}"/${P}-fix-speedtest-linking.patch
-		"${FILESDIR}"/${P}-fix-splign-linking.patch
-		"${FILESDIR}"/${P}-fix-srcchk-linking.patch
-		"${FILESDIR}"/${P}-fix-app-rmblastn-linking.patch
-		"${FILESDIR}"/${P}-remove-old-symlinks.patch
-		"${FILESDIR}"/${P}-fix-app-table2asn-linking.patch
-		"${FILESDIR}"/${P}-fix-app-tls-linking.patch
-		"${FILESDIR}"/${P}-fix-app-vecscreen-linking.patch
-		"${FILESDIR}"/${P}-fix-app-blast_sample-linking.patch
-		)
 	#ncbi-tools++-18.0.0-fix-undefined-lxncbi.patch
-	epatch ${PATCHES[@]}
 	# make sure this one is the last one and contains the actual patches applied unless we can have autoconf-2.59 or 2.60
 	# https://bugs.gentoo.org/show_bug.cgi?id=514706
 

diff --git a/sci-biology/ncbi-tools++/ncbi-tools++-22.0.0.ebuild b/sci-biology/ncbi-tools++/ncbi-tools++-22.0.0.ebuild
index 0c0e1b24c..ffa36ad4d 100644
--- a/sci-biology/ncbi-tools++/ncbi-tools++-22.0.0.ebuild
+++ b/sci-biology/ncbi-tools++/ncbi-tools++-22.0.0.ebuild
@@ -1,9 +1,9 @@
-# Copyright 1999-2019 Gentoo Authors
+# Copyright 1999-2021 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
-EAPI=5
+EAPI=7
 
-PYTHON_COMPAT=( python2_7 )
+PYTHON_COMPAT=( python3_{7,8,9} )
 
 inherit eutils flag-o-matic multilib python-single-r1 toolchain-funcs
 
@@ -30,13 +30,14 @@ IUSE="
 	berkdb boost bzip2 cppunit curl expat fastcgi fltk freetype gif
 	glut gnutls hdf5 icu jpeg lzo mesa mysql muparser opengl pcre png python
 	sablotron sqlite tiff xerces xalan xml xpm xslt X"
-KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
+KEYWORDS="~amd64 ~x86"
 
 REQUIRED_USE="${PYTHON_REQUIRED_USE}"
 
 # sys-libs/db should be compiled with USE=cxx
 # dev-libs/boost must have Boost.Test suite, probably dev-libs/boost[test] then?
 DEPEND="
+	<sys-devel/gcc-10:=
 	!sci-biology/sra_sdk
 	app-arch/cpio
 	berkdb? ( sys-libs/db:4.3[cxx] )
@@ -83,6 +84,7 @@ RDEPEND="${DEPEND}"
 S="${WORKDIR}/${MY_P}"
 
 src_prepare() {
+	default
 #	filter-ldflags -Wl,--as-needed
 #	append-ldflags -Wl,--no-undefined
 #	sed -i -e 's/-print-file-name=libstdc++.a//' \
@@ -254,7 +256,7 @@ src_configure() {
 	$(use_with mesa mesa "${EPREFIX}/usr")
 	$(use_with opengl glut "${EPREFIX}/usr")
 	$(use_with opengl glew "${EPREFIX}/usr")
-	$(use_with opengl glew-mx)
+#	$(use_with opengl glew-mx) can't find this with any version of media-libs/glew installed: explicitly specified, but no usable version found.
 	$(use_with wxwidgets wxwidgets "${EPREFIX}/usr")
 	$(use_with wxwidgets wxwidgets-ucs)
 	$(use_with freetype freetype "${EPREFIX}/usr")


^ permalink raw reply related	[flat|nested] 49+ messages in thread

* [gentoo-commits] proj/sci:master commit in: sci-biology/ncbi-tools++/
@ 2021-01-10 19:09 Andrew Ammerlaan
  0 siblings, 0 replies; 49+ messages in thread
From: Andrew Ammerlaan @ 2021-01-10 19:09 UTC (permalink / raw
  To: gentoo-commits

commit:     e92721e59c64fec4feb78285e58ef0956f8e03fd
Author:     Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net>
AuthorDate: Sun Jan 10 19:08:32 2021 +0000
Commit:     Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net>
CommitDate: Sun Jan 10 19:08:32 2021 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=e92721e5

sci-biology/ncbi-tools++: add RESTRICT="!test? ( test )"

Package-Manager: Portage-3.0.12, Repoman-3.0.2
Signed-off-by: Andrew Ammerlaan <andrewammerlaan <AT> riseup.net>

 sci-biology/ncbi-tools++/ncbi-tools++-12.0.0.ebuild | 1 +
 sci-biology/ncbi-tools++/ncbi-tools++-18.0.0.ebuild | 1 +
 sci-biology/ncbi-tools++/ncbi-tools++-22.0.0.ebuild | 1 +
 3 files changed, 3 insertions(+)

diff --git a/sci-biology/ncbi-tools++/ncbi-tools++-12.0.0.ebuild b/sci-biology/ncbi-tools++/ncbi-tools++-12.0.0.ebuild
index 0aa05e878..b5986637b 100644
--- a/sci-biology/ncbi-tools++/ncbi-tools++-12.0.0.ebuild
+++ b/sci-biology/ncbi-tools++/ncbi-tools++-12.0.0.ebuild
@@ -32,6 +32,7 @@ IUSE="
 	sablotron sqlite tiff xerces xalan xml xpm xslt X"
 #KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
 KEYWORDS="~amd64"
+RESTRICT="!test? ( test )"
 
 REQUIRED_USE="${PYTHON_REQUIRED_USE}"
 

diff --git a/sci-biology/ncbi-tools++/ncbi-tools++-18.0.0.ebuild b/sci-biology/ncbi-tools++/ncbi-tools++-18.0.0.ebuild
index c3014adca..6285e3cc9 100644
--- a/sci-biology/ncbi-tools++/ncbi-tools++-18.0.0.ebuild
+++ b/sci-biology/ncbi-tools++/ncbi-tools++-18.0.0.ebuild
@@ -31,6 +31,7 @@ IUSE="
 	glut gnutls hdf5 icu jpeg lzo mesa mysql muparser opengl pcre png python
 	sablotron sqlite tiff xerces xalan xml xpm xslt X"
 KEYWORDS="~amd64 ~x86"
+RESTRICT="!test? ( test )"
 
 REQUIRED_USE="${PYTHON_REQUIRED_USE}"
 

diff --git a/sci-biology/ncbi-tools++/ncbi-tools++-22.0.0.ebuild b/sci-biology/ncbi-tools++/ncbi-tools++-22.0.0.ebuild
index ffa36ad4d..9e9a5935f 100644
--- a/sci-biology/ncbi-tools++/ncbi-tools++-22.0.0.ebuild
+++ b/sci-biology/ncbi-tools++/ncbi-tools++-22.0.0.ebuild
@@ -31,6 +31,7 @@ IUSE="
 	glut gnutls hdf5 icu jpeg lzo mesa mysql muparser opengl pcre png python
 	sablotron sqlite tiff xerces xalan xml xpm xslt X"
 KEYWORDS="~amd64 ~x86"
+RESTRICT="!test? ( test )"
 
 REQUIRED_USE="${PYTHON_REQUIRED_USE}"
 


^ permalink raw reply related	[flat|nested] 49+ messages in thread

* [gentoo-commits] proj/sci:master commit in: sci-biology/ncbi-tools++/
@ 2021-01-13 21:06 Andrew Ammerlaan
  0 siblings, 0 replies; 49+ messages in thread
From: Andrew Ammerlaan @ 2021-01-13 21:06 UTC (permalink / raw
  To: gentoo-commits

commit:     06a5e1e5fb052973398a5eb69620ebd425e78a11
Author:     Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net>
AuthorDate: Wed Jan 13 21:01:10 2021 +0000
Commit:     Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net>
CommitDate: Wed Jan 13 21:01:10 2021 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=06a5e1e5

sci-biology/ncbi-tools++: use https for homepage

Package-Manager: Portage-3.0.13, Repoman-3.0.2
Signed-off-by: Andrew Ammerlaan <andrewammerlaan <AT> riseup.net>

 sci-biology/ncbi-tools++/ncbi-tools++-12.0.0.ebuild | 2 +-
 sci-biology/ncbi-tools++/ncbi-tools++-18.0.0.ebuild | 2 +-
 sci-biology/ncbi-tools++/ncbi-tools++-22.0.0.ebuild | 2 +-
 3 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/sci-biology/ncbi-tools++/ncbi-tools++-12.0.0.ebuild b/sci-biology/ncbi-tools++/ncbi-tools++-12.0.0.ebuild
index b5986637b..0946bcbc8 100644
--- a/sci-biology/ncbi-tools++/ncbi-tools++-12.0.0.ebuild
+++ b/sci-biology/ncbi-tools++/ncbi-tools++-12.0.0.ebuild
@@ -15,7 +15,7 @@ MY_P="ncbi_cxx--${MY_PV}"
 
 # for example sci-biology/ncbi-tools++-12.0.0 contains blastn-2.2.28+
 DESCRIPTION="NCBI C++ Toolkit, including NCBI BLAST+"
-HOMEPAGE="http://www.ncbi.nlm.nih.gov/books/bv.fcgi?rid=toolkit"
+HOMEPAGE="https://www.ncbi.nlm.nih.gov/books/bv.fcgi?rid=toolkit"
 SRC_URI="
 	ftp://ftp.ncbi.nih.gov/toolbox/ncbi_tools++/ARCHIVE/${MY_PV}/ncbi_cxx--${MY_PV}.tar.gz"
 #	http://dev.gentoo.org/~jlec/distfiles/${PN}-${PV#0.}-asneeded.patch.xz"

diff --git a/sci-biology/ncbi-tools++/ncbi-tools++-18.0.0.ebuild b/sci-biology/ncbi-tools++/ncbi-tools++-18.0.0.ebuild
index 6285e3cc9..def493d90 100644
--- a/sci-biology/ncbi-tools++/ncbi-tools++-18.0.0.ebuild
+++ b/sci-biology/ncbi-tools++/ncbi-tools++-18.0.0.ebuild
@@ -15,7 +15,7 @@ MY_P="ncbi_cxx--${MY_PV}"
 
 # for example sci-biology/ncbi-tools++-12.0.0 contains blastn-2.2.28+
 DESCRIPTION="NCBI C++ Toolkit, including NCBI BLAST+"
-HOMEPAGE="http://www.ncbi.nlm.nih.gov/books/bv.fcgi?rid=toolkit"
+HOMEPAGE="https://www.ncbi.nlm.nih.gov/books/bv.fcgi?rid=toolkit"
 SRC_URI="
 	ftp://ftp.ncbi.nih.gov/toolbox/ncbi_tools++/ARCHIVE/2017/Jan_10_2017/ncbi_cxx--${MY_PV}.tar.gz"
 #	http://dev.gentoo.org/~jlec/distfiles/${PN}-${PV#0.}-asneeded.patch.xz"

diff --git a/sci-biology/ncbi-tools++/ncbi-tools++-22.0.0.ebuild b/sci-biology/ncbi-tools++/ncbi-tools++-22.0.0.ebuild
index 9e9a5935f..7d64f01a0 100644
--- a/sci-biology/ncbi-tools++/ncbi-tools++-22.0.0.ebuild
+++ b/sci-biology/ncbi-tools++/ncbi-tools++-22.0.0.ebuild
@@ -14,7 +14,7 @@ MY_P="ncbi_cxx--${MY_PV}"
 
 # for example sci-biology/ncbi-tools++-12.0.0 contains blastn-2.2.28+
 DESCRIPTION="NCBI C++ Toolkit, including NCBI BLAST+"
-HOMEPAGE="http://www.ncbi.nlm.nih.gov/books/bv.fcgi?rid=toolkit"
+HOMEPAGE="https://www.ncbi.nlm.nih.gov/books/bv.fcgi?rid=toolkit"
 # https://ncbi.github.io/cxx-toolkit/pages/release_notes
 SRC_URI="
 	ftp://ftp.ncbi.nih.gov/toolbox/ncbi_tools++/ARCHIVE/2019/${MY_TAG}/ncbi_cxx--${MY_PV}.tar.gz"


^ permalink raw reply related	[flat|nested] 49+ messages in thread

* [gentoo-commits] proj/sci:master commit in: sci-biology/ncbi-tools++/
@ 2021-01-19 17:16 Andrew Ammerlaan
  0 siblings, 0 replies; 49+ messages in thread
From: Andrew Ammerlaan @ 2021-01-19 17:16 UTC (permalink / raw
  To: gentoo-commits

commit:     3c9aa1b79108b8d09e8857231b9ea17433da8b85
Author:     Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net>
AuthorDate: Tue Jan 19 17:14:56 2021 +0000
Commit:     Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net>
CommitDate: Tue Jan 19 17:14:56 2021 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=3c9aa1b7

sci-biology/ncbi-tools++: update HOMEPAGE

Package-Manager: Portage-3.0.13, Repoman-3.0.2
Signed-off-by: Andrew Ammerlaan <andrewammerlaan <AT> riseup.net>

 sci-biology/ncbi-tools++/ncbi-tools++-12.0.0.ebuild | 2 +-
 sci-biology/ncbi-tools++/ncbi-tools++-18.0.0.ebuild | 2 +-
 sci-biology/ncbi-tools++/ncbi-tools++-22.0.0.ebuild | 2 +-
 3 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/sci-biology/ncbi-tools++/ncbi-tools++-12.0.0.ebuild b/sci-biology/ncbi-tools++/ncbi-tools++-12.0.0.ebuild
index 0946bcbc8..ed50801fc 100644
--- a/sci-biology/ncbi-tools++/ncbi-tools++-12.0.0.ebuild
+++ b/sci-biology/ncbi-tools++/ncbi-tools++-12.0.0.ebuild
@@ -15,7 +15,7 @@ MY_P="ncbi_cxx--${MY_PV}"
 
 # for example sci-biology/ncbi-tools++-12.0.0 contains blastn-2.2.28+
 DESCRIPTION="NCBI C++ Toolkit, including NCBI BLAST+"
-HOMEPAGE="https://www.ncbi.nlm.nih.gov/books/bv.fcgi?rid=toolkit"
+HOMEPAGE="https://ncbi.github.io/cxx-toolkit/"
 SRC_URI="
 	ftp://ftp.ncbi.nih.gov/toolbox/ncbi_tools++/ARCHIVE/${MY_PV}/ncbi_cxx--${MY_PV}.tar.gz"
 #	http://dev.gentoo.org/~jlec/distfiles/${PN}-${PV#0.}-asneeded.patch.xz"

diff --git a/sci-biology/ncbi-tools++/ncbi-tools++-18.0.0.ebuild b/sci-biology/ncbi-tools++/ncbi-tools++-18.0.0.ebuild
index def493d90..0aacd0511 100644
--- a/sci-biology/ncbi-tools++/ncbi-tools++-18.0.0.ebuild
+++ b/sci-biology/ncbi-tools++/ncbi-tools++-18.0.0.ebuild
@@ -15,7 +15,7 @@ MY_P="ncbi_cxx--${MY_PV}"
 
 # for example sci-biology/ncbi-tools++-12.0.0 contains blastn-2.2.28+
 DESCRIPTION="NCBI C++ Toolkit, including NCBI BLAST+"
-HOMEPAGE="https://www.ncbi.nlm.nih.gov/books/bv.fcgi?rid=toolkit"
+HOMEPAGE="https://ncbi.github.io/cxx-toolkit/"
 SRC_URI="
 	ftp://ftp.ncbi.nih.gov/toolbox/ncbi_tools++/ARCHIVE/2017/Jan_10_2017/ncbi_cxx--${MY_PV}.tar.gz"
 #	http://dev.gentoo.org/~jlec/distfiles/${PN}-${PV#0.}-asneeded.patch.xz"

diff --git a/sci-biology/ncbi-tools++/ncbi-tools++-22.0.0.ebuild b/sci-biology/ncbi-tools++/ncbi-tools++-22.0.0.ebuild
index 7d64f01a0..004cc7086 100644
--- a/sci-biology/ncbi-tools++/ncbi-tools++-22.0.0.ebuild
+++ b/sci-biology/ncbi-tools++/ncbi-tools++-22.0.0.ebuild
@@ -14,7 +14,7 @@ MY_P="ncbi_cxx--${MY_PV}"
 
 # for example sci-biology/ncbi-tools++-12.0.0 contains blastn-2.2.28+
 DESCRIPTION="NCBI C++ Toolkit, including NCBI BLAST+"
-HOMEPAGE="https://www.ncbi.nlm.nih.gov/books/bv.fcgi?rid=toolkit"
+HOMEPAGE="https://ncbi.github.io/cxx-toolkit/"
 # https://ncbi.github.io/cxx-toolkit/pages/release_notes
 SRC_URI="
 	ftp://ftp.ncbi.nih.gov/toolbox/ncbi_tools++/ARCHIVE/2019/${MY_TAG}/ncbi_cxx--${MY_PV}.tar.gz"


^ permalink raw reply related	[flat|nested] 49+ messages in thread

* [gentoo-commits] proj/sci:master commit in: sci-biology/ncbi-tools++/
@ 2021-02-01  4:33 Andrew Ammerlaan
  0 siblings, 0 replies; 49+ messages in thread
From: Andrew Ammerlaan @ 2021-02-01  4:33 UTC (permalink / raw
  To: gentoo-commits

commit:     e8d4a8bc048182c0db34a3b995ac6a5c24fcdbb8
Author:     Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net>
AuthorDate: Mon Feb  1 04:32:58 2021 +0000
Commit:     Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net>
CommitDate: Mon Feb  1 04:32:58 2021 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=e8d4a8bc

sci-biology/ncbi-tools++: drop py2 only version

Package-Manager: Portage-3.0.14, Repoman-3.0.2
Signed-off-by: Andrew Ammerlaan <andrewammerlaan <AT> riseup.net>

 .../ncbi-tools++/ncbi-tools++-12.0.0.ebuild        | 369 ---------------------
 .../ncbi-tools++/ncbi-tools++-18.0.0.ebuild        |   2 +-
 2 files changed, 1 insertion(+), 370 deletions(-)

diff --git a/sci-biology/ncbi-tools++/ncbi-tools++-12.0.0.ebuild b/sci-biology/ncbi-tools++/ncbi-tools++-12.0.0.ebuild
deleted file mode 100644
index ed50801fc..000000000
--- a/sci-biology/ncbi-tools++/ncbi-tools++-12.0.0.ebuild
+++ /dev/null
@@ -1,369 +0,0 @@
-# Copyright 1999-2021 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-PYTHON_COMPAT=( python2_7 )
-
-inherit eutils flag-o-matic multilib python-single-r1 toolchain-funcs
-
-MY_TAG="Jun_15_2010"
-MY_Y="${MY_TAG/*_/}"
-MY_PV="12_0_0"
-MY_P="ncbi_cxx--${MY_PV}"
-#ftp://ftp.ncbi.nlm.nih.gov/toolbox/ncbi_tools++/ARCHIVE/9_0_0/ncbi_cxx--9_0_0.tar.gz
-
-# for example sci-biology/ncbi-tools++-12.0.0 contains blastn-2.2.28+
-DESCRIPTION="NCBI C++ Toolkit, including NCBI BLAST+"
-HOMEPAGE="https://ncbi.github.io/cxx-toolkit/"
-SRC_URI="
-	ftp://ftp.ncbi.nih.gov/toolbox/ncbi_tools++/ARCHIVE/${MY_PV}/ncbi_cxx--${MY_PV}.tar.gz"
-#	http://dev.gentoo.org/~jlec/distfiles/${PN}-${PV#0.}-asneeded.patch.xz"
-
-# should also install ftp://ftp.ncbi.nlm.nih.gov/blast/db/taxdb.tar.gz
-# see http://www.biostars.org/p/76551/ and http://blastedbio.blogspot.cz/2012/05/blast-tabular-missing-descriptions.html
-LICENSE="public-domain"
-SLOT="0"
-IUSE="
-	debug static-libs static threads pch
-	test wxwidgets odbc
-	berkdb boost bzip2 cppunit curl expat fastcgi fltk freetype gif
-	glut gnutls hdf5 icu jpeg lzo mesa mysql muparser opengl pcre png python
-	sablotron sqlite tiff xerces xalan xml xpm xslt X"
-#KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
-KEYWORDS="~amd64"
-RESTRICT="!test? ( test )"
-
-REQUIRED_USE="${PYTHON_REQUIRED_USE}"
-
-# sys-libs/db should be compiled with USE=cxx
-# dev-libs/boost must have Boost.Test suite, probably dev-libs/boost[test] then?
-DEPEND="
-	<sys-devel/gcc-10:=
-	!sci-biology/sra_sdk
-	app-arch/cpio
-	berkdb? ( sys-libs/db:4.3[cxx] )
-	boost? ( dev-libs/boost[tools] )
-	curl? ( net-misc/curl )
-	sqlite? ( dev-db/sqlite:3 )
-	mysql? ( virtual/mysql )
-	fltk? ( x11-libs/fltk )
-	opengl? ( virtual/opengl media-libs/glew:0= )
-	mesa? ( media-libs/mesa[osmesa] )
-	glut? ( media-libs/freeglut )
-	freetype? ( media-libs/freetype )
-	gnutls? ( net-libs/gnutls )
-	python? ( ${PYTHON_DEPS} )
-	cppunit? ( dev-util/cppunit )
-	icu? ( dev-libs/icu )
-	expat? ( dev-libs/expat )
-	sablotron? ( app-text/sablotron )
-	xml? ( dev-libs/libxml2 )
-	xslt? ( dev-libs/libxslt )
-	xerces? ( dev-libs/xerces-c )
-	xalan? ( dev-libs/xalan-c )
-	muparser? ( dev-cpp/muParser )
-	hdf5? ( sci-libs/hdf5[cxx] )
-	gif? ( media-libs/giflib )
-	jpeg? ( virtual/jpeg:0= )
-	png? ( media-libs/libpng:0= )
-	tiff? ( media-libs/tiff:0= )
-	xpm? ( x11-libs/libXpm )
-	dev-libs/lzo
-	app-arch/bzip2
-	dev-libs/libpcre"
-# USE flags which should be added somehow: wxWindows wxWidgets SP ORBacus ODBC OEChem sge
-# Intentionally omitted USE flags:
-#   ftds? ( dev-db/freetds ) # support for outside FreeTDS installations is currently broken.
-#                              The default (heavily patched) embedded copy should work, or you can
-#                              leave it off altogether -- the only public apps that make use of it are
-#                              samples and tests, since NCBI's database servers are of course firewalled.
-
-# seems muParser is required, also glew is required. configure exits otherwise if these are explicitly passed to it (due to USE flag enabled)
-
-RDEPEND="${DEPEND}"
-
-S="${WORKDIR}/${MY_P}"
-
-PATCHES=(
-		"${FILESDIR}"/${P}-conf-opts.patch
-		"${FILESDIR}"/${P}-fix-svn-URL-upstream.patch
-		"${FILESDIR}"/${P}-linkage-tuneups.patch
-		"${FILESDIR}"/${P}-more-patches.patch
-		"${FILESDIR}"/${P}-linkage-tuneups-addons.patch
-		"${FILESDIR}"/${P}-configure.patch
-		"${FILESDIR}"/${P}-drop-STATIC-from-LIB.patch
-		"${FILESDIR}"/${P}-fix-install.patch
-		"${FILESDIR}"/${P}-bdb6.patch
-		"${FILESDIR}"/${P}-never_build_test_boost.patch # bug #579248
-		)
-
-src_prepare() {
-	default
-#	filter-ldflags -Wl,--as-needed
-#	append-ldflags -Wl,--no-undefined
-#	sed -i -e 's/-print-file-name=libstdc++.a//' \
-#		-e '/sed/ s/\([gO]\[0-9\]\)\*/\1\\+/' \
-#		src/build-system/configure || die
-#	epatch \
-#		"${FILESDIR}"/${PN}-${PV#0.}-fix-order-of-libs.patch \
-#		"${FILESDIR}"/curl-types.patch \
-#		"${FILESDIR}"/malloc_initialize_upstream_fix.patch \
-#		"${FILESDIR}"/respect_CXXFLAGS_configure.ac.patch \
-#		"${FILESDIR}"/respect_CXXFLAGS_configure.patch \
-#		"${FILESDIR}"/report_project_settings_configure.ac.patch \
-#		"${FILESDIR}"/report_project_settings_configure.patch \
-#		"${FILESDIR}"/make_install.patch
-
-#		"${FILESDIR}"/${PN}-${PV#0.}-disable_test_compress.patch
-
-#		"${FILESDIR}"/${PN}-${PV#0.}-gcc46.patch \
-#		"${FILESDIR}"/${PN}-${PV#0.}-gcc47.patch \
-#		"${WORKDIR}"/${PN}-${PV#0.}-asneeded.patch \
-#		"${FILESDIR}"/${PN}-${PV#0.}-libpng15.patch \
-#		"${FILESDIR}"/${PN}-${PV#0.}-glibc-214.patch
-
-#	use prefix && append-ldflags -Wl,-rpath,"${EPREFIX}/usr/$(get_libdir)/${PN}"
-
-# The conf-opts.patch and as-needed.patch need to be adjusted for 12.0.0 line numbers
-#       "${FILESDIR}"/${P}-as-needed.patch
-#       "${FILESDIR}"/${P}-fix-creaders-linking.patch
-#       "${FILESDIR}"/${P}-fix-FreeTDS-upstream.patch
-#		)
-		# "${FILESDIR}"/${P}-support-autoconf-2.60.patch
-	# make sure this one is the last one and contains the actual patches applied unless we can have autoconf-2.59 or 2.60
-	# https://bugs.gentoo.org/show_bug.cgi?id=514706
-
-	tc-export CXX CC
-
-	cd src/build-system || die
-#	eautoreconf
-
-	# Temporarily disabling eautoconf because we patch configure via ${P}-support-autoconf-2.60.patch
-	# eautoconf # keep it disabled until we can ensure 2.59 is installed
-	# beware 12.0.0. and previous required autoconf-2.59, a patch for 12.0.0 brings autoconf-2.60 support
-}
-
-# possibly place modified contents of ${W}/src/build-system/config.site.ncbi and {W}/src/build-system/config.site.ex into ${W}/src/build-system/config.site
-src_configure() {
-	local myconf=()
-	#--without-optimization  turn off optimization flags in non-debug mode
-	#--with-profiling        build profiled versions of libs and apps
-	#--with-tcheck(=DIR)     build for Intel Thread Checker (in DIR)
-	#--with-plugin-auto-load always enable the plugin manager by default
-	#--with-bundles          build bundles in addition to dylibs on Mac OS X
-	#--with-bin-release      build executables suitable for public release
-	#	no dll and such
-	#--with-64               compile to 64-bit code
-	#--with-universal        build universal binaries on Mac OS X
-	#--with-universal=CPUs   build universal binaries targeting the given CPUs
-	#--without-exe           do not build executables
-	#--with-relative-runpath=P specify an executable-relative DLL search path
-	#--with-hard-runpath     hard-code runtime path, ignoring LD_LIBRARY_PATH
-	#--with-limited-linker   don't attempt to build especially large projects
-	#--with-extra-action=    script to call after the configuration is complete
-	#--with-autodep          automatic generation of dependencies (GNU make)
-	#--with-fake-root=DIR    appear to have been built under DIR
-	#--with-build-root-sfx=X add a user-specified suffix to the build dir name
-	#--without-execopy       do not copy built executables to the BIN area
-	#--with-lib-rebuilds     ensure that apps use up-to-date libraries
-	#--with-lib-rebuilds=ask ask whether to update each app's libraries
-	#--without-deactivation  keep old copies of libraries that no longer build
-	#--without-makefile-auto-update  do not auto-update generated makefiles
-	#--with-projects=FILE    build projects listed in FILE by default
-	#--without-flat-makefile do not generate an all-encompassing flat makefile
-	#--with-configure-dialog allow interactive flat makefile project selection
-	#--with-saved-settings=F load configuration settings from the file F
-	#--with-check-tools=...  use the specified tools for testing
-	#--with-ncbi-public      ensure compatibility for all in-house platforms
-	#--with-sybase-local=DIR use local SYBASE install (DIR is optional)
-	#--with-sybase-new       use newer SYBASE install (12.5 rather than 12.0)
-	#--without-sp            do not use SP libraries
-	#--without-orbacus       do not use ORBacus CORBA libraries
-	#--with-orbacus=DIR      use ORBacus installation in DIR
-	#--with-jni(=JDK-DIR)    build Java bindings (against the JDK in JDK-DIR)
-	#--with-sablot=DIR       use Sablotron installation in DIR
-	#--without-sablot,       do not use Sablotron
-	#--with-oechem=DIR       use OpenEye OEChem installation in DIR
-	#--without-oechem        do not use OEChem
-	#--with-sge=DIR          use Sun Grid Engine installation in DIR
-	#--without-sge           do not use Sun Grid Engine
-	#--with-magic=DIR        use libmagic installation in DIR
-	#--without-magic         do not use libmagic
-	#--without-local-lbsm    turn off support for IPC with locally running LBSMD
-	#--without-ncbi-crypt    use a dummy stubbed-out version of ncbi_crypt
-	#--without-connext       do not build non-public CONNECT library extensions
-	#--without-serial        do not build the serialization library and tools
-	#--without-objects       do not generate/build serializeable objects from ASNs
-	#--without-dbapi         do not build database connectivity libraries
-	#--without-app           do not build standalone applications like ID1_FETCH
-	#--without-gui           do not build most graphical projects
-	#--without-algo          do not build CPU-intensive algorithms
-	#--without-internal      do not build internal projects
-	#--with-gbench           ensure that Genome Workbench can be built
-	#--without-gbench        do not build Genome Workbench
-	myconf+=(
-	--with-dll
-	--with-lfs
-	--with-build-root="${S}"_build
-	--without-suffix
-	--without-hostspec
-	--without-version
-	--with-bincopy
-	--without-strip
-	--without-ccache
-	--without-distcc
-#	--with-ncbi-c
-	--without-ctools
-#	--with-sss
-#	--with-sssutils
-#	--with-sssdb
-#	--with-included-sss
-	--with-z="${EPREFIX}/usr"
-	--with-bz2="${EPREFIX}/usr"
-	--without-sybase
-	--with-autodep
-#	--with-3psw=std:netopt favor standard (system) builds of the above pkgs
-	# --without-downloaded-vdb is not available in 12.0.0 release yet
-	# preventing executing git to checkout during configure phase ncbi-vdb sources
-	# resulting in 'checking for ncbi-vdb... no' and
-	# '^PACKAGES:'
-	# '^  disabled: ... VDB'
-	# --without-downloaded-vdb
-	$(use_with debug)
-	$(use_with debug max-debug)
-	$(use_with debug symbols)
-	$(use_with static-libs static)
-	$(use_with static static-exe)
-	$(use_with threads mt)
-	$(use_with prefix runpath "${EPREFIX}/usr/$(get_libdir)/${PN}")
-	$(use_with test check)
-	$(use_with pch)
-	$(use_with lzo lzo "${EPREFIX}/usr")
-	$(use_with pcre pcre "${EPREFIX}/usr")
-	$(use_with gnutls gnutls "${EPREFIX}/usr")
-	$(use_with mysql mysql "${EPREFIX}/usr")
-	$(use_with muparser muparser "${EPREFIX}/usr")
-	$(usex fltk --with-fltk="${EPREFIX}/usr" "")
-	$(use_with opengl opengl "${EPREFIX}/usr")
-	$(use_with mesa mesa "${EPREFIX}/usr")
-	$(use_with opengl glut "${EPREFIX}/usr")
-	$(use_with opengl glew "${EPREFIX}/usr")
-	$(use_with opengl glew-mx)
-	$(use_with wxwidgets wxwidgets "${EPREFIX}/usr")
-	$(use_with wxwidgets wxwidgets-ucs)
-	$(use_with freetype freetype "${EPREFIX}/usr")
-	$(use_with fastcgi fastcgi "${EPREFIX}/usr")
-	$(use_with berkdb bdb "${EPREFIX}/usr")
-	$(usex odbc --with-odbc="${EPREFIX}/usr" "")
-	$(use_with python python "${EPREFIX}/usr")
-	$(use_with boost boost "${EPREFIX}/usr")
-	$(use_with sqlite sqlite3 "${EPREFIX}/usr")
-	$(use_with icu icu "${EPREFIX}/usr")
-	$(use_with expat expat "${EPREFIX}/usr")
-	$(use_with xml libxml "${EPREFIX}/usr")
-	$(use_with xml libxslt "${EPREFIX}/usr")
-	$(use_with xerces xerces "${EPREFIX}/usr")
-	$(use_with hdf5 hdf5 "${EPREFIX}/usr")
-	$(use_with xalan xalan "${EPREFIX}/usr")
-#	$(use_with gif gif "${EPREFIX}/usr") # prevent compilation failure in "ncbi-tools++-12.0.0/src/util/image/image_io_gif.cpp:351: error: 'QuantizeBuffer' was not declared in this scope"
-	--without-gif
-	$(use_with jpeg jpeg "${EPREFIX}/usr")
-	$(use_with tiff tiff "${EPREFIX}/usr")
-	$(use_with png png "${EPREFIX}/usr")
-	$(use_with xpm xpm "${EPREFIX}/usr")
-	$(use_with curl curl "${EPREFIX}/usr")
-#	$(use_with X x "${EPREFIX}/usr")
-#	$(use_with X x) # there is no --with-x option
-	)
-
-	# http://www.ncbi.nlm.nih.gov/books/NBK7167/
-	use test ||	myconf+=( --with-projects="${FILESDIR}"/disable-testsuite-compilation.txt )
-
-	# TODO
-	# copy optimization -O options from CXXFLAGS to DEF_FAST_FLAGS and pass that also to configure
-	# otherwise your -O2 will be dropped in some subdirectories and replaced by e.g. -O9
-
-	einfo "bash ./src/build-system/configure --srcdir="${S}" --prefix="${EPREFIX}/usr" --libdir=/usr/lib64 ${myconf[@]}"
-
-#	ECONF_SOURCE="src/build-system" \
-#		econf \
-	bash \
-		./src/build-system/configure \
-		--srcdir="${S}" \
-		--prefix="${EPREFIX}/usr" \
-		--libdir=/usr/lib64 \
-		--with-flat-makefile \
-		${myconf[@]} || die
-#--without-debug \
-#		--with-bin-release \
-#		--with-bincopy \
-#		--without-static \
-#		--with-dll \
-#		--with-mt \
-#		--with-openmp \
-#		--with-lfs \
-#		--prefix="${ED}"/usr \
-#		--libdir="${ED}"/usr/$(get_libdir)/"${PN}" \
-#		${myconf} LDFLAGS="-Wl,--no-as-needed" \
-#		|| die
-#	econf ${myconf[@]}
-}
-
-src_compile() {
-	## all_r would ignore the --with-projects contents and build more
-	## emake all_r -C GCC*-Release*/build || die
-	## all_p with compile only selected/required components
-	##cd "${S}"_build &&\
-	##emake all_p -C GCC*-Release*/build || die "gcc-4.5.3 crashes at src/objects/valerr/ValidError.cpp:226:1: internal compiler error: Segmentation fault, right?"
-	#emake all_p -C "${S}"_build/build
-
-	#
-	# Re: /usr/lib64/ncbi-tools++/libdbapi_driver.so: undefined reference to `ncbi::NcbiGetlineEOL(std::istream&, std::string&)'
-	#
-	# The next release should automatically address such underlinking, albeit
-	# only in --with-flat-makefile configurations.  For now (12.0.0), you'll need to
-	# add or extend more DLL_LIB settings, to which end you may find the
-	# resources at http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/depgraphs/
-	# helpful.  For instance,
-	#
-	# http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/depgraphs/dbapi_driver.html
-	#
-	# indicates that src/dbapi/driver/Makefile.dbapi_driver.lib should set
-	#
-	# DLL_LIB = xncbi
-	#
-	# (You can find the path to that makefile by examining
-	# .../status/.dbapi_driver.dep or .../build/Makefile.flat.)
-	#
-	# To take full advantage of --with-flat-makefile, you'll need the following (instead of 'emake all_p -C "${S}"_build/build') and call configure --with-flat-makefile:
-	emake -C "${S}"_build/build -f Makefile.flat
-	#
-	# >=gcc-5.3.0 is not supported, see also bug #579248#c8
-	# configure: error: Do not know how to build MT-safe with compiler /usr/bin/x86_64-pc-linux-gnu-g++  5.3.0
-}
-
-src_install() {
-	rm -rvf "${S}"_build/lib/ncbi || die
-	emake install prefix="${ED}/usr" libdir="${ED}/usr/$(get_libdir)/${PN}"
-
-#	dobin "${S}"_build/bin/*
-#	dolib.so "${S}"_build/lib/*so*
-#	dolib.a "${S}"_build/lib/*.a
-#	doheader "${S}"_build/inc/*
-
-	# File collisions with sci-biology/ncbi-tools
-	mv "${ED}"/usr/bin/asn2asn "${ED}"/usr/bin/asn2asn+
-	mv "${ED}"/usr/bin/rpsblast "${ED}"/usr/bin/rpsblast+
-	mv -f "${ED}"/usr/bin/test_regexp "${ED}"/usr/bin/test_regexp+ # drop the eventually mistakenly compiled binaries
-	mv "${ED}"/usr/bin/vecscreen "${ED}"/usr/bin/vecscreen+
-	mv "${ED}"/usr/bin/seedtop "${ED}"/usr/bin/seedtop+
-
-	echo "LDPATH=${EPREFIX}/usr/$(get_libdir)/${PN}" > ${S}/99${PN}
-	doenvd "${S}/99${PN}"
-}
-
-pkg_postinst() {
-	einfo 'Please run "source /etc/profile" before using this package in the current shell.'
-	einfo 'Documentation is at http://www.ncbi.nlm.nih.gov/books/NBK7167/'
-}

diff --git a/sci-biology/ncbi-tools++/ncbi-tools++-18.0.0.ebuild b/sci-biology/ncbi-tools++/ncbi-tools++-18.0.0.ebuild
index 0aacd0511..5c0b619df 100644
--- a/sci-biology/ncbi-tools++/ncbi-tools++-18.0.0.ebuild
+++ b/sci-biology/ncbi-tools++/ncbi-tools++-18.0.0.ebuild
@@ -3,7 +3,7 @@
 
 EAPI=7
 
-PYTHON_COMPAT=( python2_7 )
+PYTHON_COMPAT=( python3_{7,8,9} )
 
 inherit eutils flag-o-matic multilib python-single-r1 toolchain-funcs
 


^ permalink raw reply related	[flat|nested] 49+ messages in thread

* [gentoo-commits] proj/sci:master commit in: sci-biology/ncbi-tools++/
@ 2021-03-16 18:49 Andrew Ammerlaan
  0 siblings, 0 replies; 49+ messages in thread
From: Andrew Ammerlaan @ 2021-03-16 18:49 UTC (permalink / raw
  To: gentoo-commits

commit:     2705ca6b2ce3442eea8d893134c41fa7b68d2ada
Author:     Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net>
AuthorDate: Tue Mar 16 18:49:40 2021 +0000
Commit:     Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net>
CommitDate: Tue Mar 16 18:49:40 2021 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=2705ca6b

sci-biology/ncbi-tools++: drop python support on 12.0.0

is python2

Package-Manager: Portage-3.0.17, Repoman-3.0.2
Signed-off-by: Andrew Ammerlaan <andrewammerlaan <AT> riseup.net>

 sci-biology/ncbi-tools++/ncbi-tools++-12.0.0.ebuild | 12 ++++--------
 sci-biology/ncbi-tools++/ncbi-tools++-18.0.0.ebuild |  2 +-
 2 files changed, 5 insertions(+), 9 deletions(-)

diff --git a/sci-biology/ncbi-tools++/ncbi-tools++-12.0.0.ebuild b/sci-biology/ncbi-tools++/ncbi-tools++-12.0.0.ebuild
index ed50801fc..fa1caf715 100644
--- a/sci-biology/ncbi-tools++/ncbi-tools++-12.0.0.ebuild
+++ b/sci-biology/ncbi-tools++/ncbi-tools++-12.0.0.ebuild
@@ -3,9 +3,7 @@
 
 EAPI=7
 
-PYTHON_COMPAT=( python2_7 )
-
-inherit eutils flag-o-matic multilib python-single-r1 toolchain-funcs
+inherit flag-o-matic multilib toolchain-funcs
 
 MY_TAG="Jun_15_2010"
 MY_Y="${MY_TAG/*_/}"
@@ -28,14 +26,12 @@ IUSE="
 	debug static-libs static threads pch
 	test wxwidgets odbc
 	berkdb boost bzip2 cppunit curl expat fastcgi fltk freetype gif
-	glut gnutls hdf5 icu jpeg lzo mesa mysql muparser opengl pcre png python
+	glut gnutls hdf5 icu jpeg lzo mesa mysql muparser opengl pcre png
 	sablotron sqlite tiff xerces xalan xml xpm xslt X"
 #KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
 KEYWORDS="~amd64"
 RESTRICT="!test? ( test )"
 
-REQUIRED_USE="${PYTHON_REQUIRED_USE}"
-
 # sys-libs/db should be compiled with USE=cxx
 # dev-libs/boost must have Boost.Test suite, probably dev-libs/boost[test] then?
 DEPEND="
@@ -53,7 +49,6 @@ DEPEND="
 	glut? ( media-libs/freeglut )
 	freetype? ( media-libs/freetype )
 	gnutls? ( net-libs/gnutls )
-	python? ( ${PYTHON_DEPS} )
 	cppunit? ( dev-util/cppunit )
 	icu? ( dev-libs/icu )
 	expat? ( dev-libs/expat )
@@ -256,7 +251,8 @@ src_configure() {
 	$(use_with fastcgi fastcgi "${EPREFIX}/usr")
 	$(use_with berkdb bdb "${EPREFIX}/usr")
 	$(usex odbc --with-odbc="${EPREFIX}/usr" "")
-	$(use_with python python "${EPREFIX}/usr")
+	# is python2
+	--without-python
 	$(use_with boost boost "${EPREFIX}/usr")
 	$(use_with sqlite sqlite3 "${EPREFIX}/usr")
 	$(use_with icu icu "${EPREFIX}/usr")

diff --git a/sci-biology/ncbi-tools++/ncbi-tools++-18.0.0.ebuild b/sci-biology/ncbi-tools++/ncbi-tools++-18.0.0.ebuild
index 0aacd0511..5c0b619df 100644
--- a/sci-biology/ncbi-tools++/ncbi-tools++-18.0.0.ebuild
+++ b/sci-biology/ncbi-tools++/ncbi-tools++-18.0.0.ebuild
@@ -3,7 +3,7 @@
 
 EAPI=7
 
-PYTHON_COMPAT=( python2_7 )
+PYTHON_COMPAT=( python3_{7,8,9} )
 
 inherit eutils flag-o-matic multilib python-single-r1 toolchain-funcs
 


^ permalink raw reply related	[flat|nested] 49+ messages in thread

* [gentoo-commits] proj/sci:master commit in: sci-biology/ncbi-tools++/
@ 2021-03-16 18:49 Andrew Ammerlaan
  0 siblings, 0 replies; 49+ messages in thread
From: Andrew Ammerlaan @ 2021-03-16 18:49 UTC (permalink / raw
  To: gentoo-commits

commit:     6ae264536af8017178293a0f35242f4dfcd9e453
Author:     Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net>
AuthorDate: Tue Mar 16 18:46:32 2021 +0000
Commit:     Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net>
CommitDate: Tue Mar 16 18:46:32 2021 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=6ae26453

Revert "sci-biology/ncbi-tools++: drop py2 only version"

This reverts commit e8d4a8bc048182c0db34a3b995ac6a5c24fcdbb8.

Signed-off-by: Andrew Ammerlaan <andrewammerlaan <AT> riseup.net>

 ...++-18.0.0.ebuild => ncbi-tools++-12.0.0.ebuild} | 51 ++++++++--------------
 .../ncbi-tools++/ncbi-tools++-18.0.0.ebuild        |  2 +-
 2 files changed, 19 insertions(+), 34 deletions(-)

diff --git a/sci-biology/ncbi-tools++/ncbi-tools++-18.0.0.ebuild b/sci-biology/ncbi-tools++/ncbi-tools++-12.0.0.ebuild
similarity index 89%
copy from sci-biology/ncbi-tools++/ncbi-tools++-18.0.0.ebuild
copy to sci-biology/ncbi-tools++/ncbi-tools++-12.0.0.ebuild
index 5c0b619df..ed50801fc 100644
--- a/sci-biology/ncbi-tools++/ncbi-tools++-18.0.0.ebuild
+++ b/sci-biology/ncbi-tools++/ncbi-tools++-12.0.0.ebuild
@@ -3,13 +3,13 @@
 
 EAPI=7
 
-PYTHON_COMPAT=( python3_{7,8,9} )
+PYTHON_COMPAT=( python2_7 )
 
 inherit eutils flag-o-matic multilib python-single-r1 toolchain-funcs
 
 MY_TAG="Jun_15_2010"
 MY_Y="${MY_TAG/*_/}"
-MY_PV="18_0_0"
+MY_PV="12_0_0"
 MY_P="ncbi_cxx--${MY_PV}"
 #ftp://ftp.ncbi.nlm.nih.gov/toolbox/ncbi_tools++/ARCHIVE/9_0_0/ncbi_cxx--9_0_0.tar.gz
 
@@ -17,7 +17,7 @@ MY_P="ncbi_cxx--${MY_PV}"
 DESCRIPTION="NCBI C++ Toolkit, including NCBI BLAST+"
 HOMEPAGE="https://ncbi.github.io/cxx-toolkit/"
 SRC_URI="
-	ftp://ftp.ncbi.nih.gov/toolbox/ncbi_tools++/ARCHIVE/2017/Jan_10_2017/ncbi_cxx--${MY_PV}.tar.gz"
+	ftp://ftp.ncbi.nih.gov/toolbox/ncbi_tools++/ARCHIVE/${MY_PV}/ncbi_cxx--${MY_PV}.tar.gz"
 #	http://dev.gentoo.org/~jlec/distfiles/${PN}-${PV#0.}-asneeded.patch.xz"
 
 # should also install ftp://ftp.ncbi.nlm.nih.gov/blast/db/taxdb.tar.gz
@@ -30,7 +30,8 @@ IUSE="
 	berkdb boost bzip2 cppunit curl expat fastcgi fltk freetype gif
 	glut gnutls hdf5 icu jpeg lzo mesa mysql muparser opengl pcre png python
 	sablotron sqlite tiff xerces xalan xml xpm xslt X"
-KEYWORDS="~amd64 ~x86"
+#KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
+KEYWORDS="~amd64"
 RESTRICT="!test? ( test )"
 
 REQUIRED_USE="${PYTHON_REQUIRED_USE}"
@@ -85,29 +86,16 @@ RDEPEND="${DEPEND}"
 S="${WORKDIR}/${MY_P}"
 
 PATCHES=(
+		"${FILESDIR}"/${P}-conf-opts.patch
+		"${FILESDIR}"/${P}-fix-svn-URL-upstream.patch
+		"${FILESDIR}"/${P}-linkage-tuneups.patch
+		"${FILESDIR}"/${P}-more-patches.patch
+		"${FILESDIR}"/${P}-linkage-tuneups-addons.patch
 		"${FILESDIR}"/${P}-configure.patch
+		"${FILESDIR}"/${P}-drop-STATIC-from-LIB.patch
 		"${FILESDIR}"/${P}-fix-install.patch
+		"${FILESDIR}"/${P}-bdb6.patch
 		"${FILESDIR}"/${P}-never_build_test_boost.patch # bug #579248
-		"${FILESDIR}"/${P}-fix-annotwriter-linking.patch
-		"${FILESDIR}"/${P}-fix-undefined-xobjread.patch
-		"${FILESDIR}"/${P}-fix-apps-blast-linking.patch
-		"${FILESDIR}"/${P}-fix-sample-app-cgi-linking.patch
-		"${FILESDIR}"/${P}-fix-app-compartp-linking.patch
-		"${FILESDIR}"/${P}-fix-app-convert_seq-linking.patch
-		"${FILESDIR}"/${P}-fix-app-hfilter-linking.patch
-		"${FILESDIR}"/${P}-fix-app-igblast-linking.patch
-		"${FILESDIR}"/${P}-fix-ncfetch-linking.patch
-		"${FILESDIR}"/${P}-fix-netcache_cgi_sample-linking.patch
-		"${FILESDIR}"/${P}-fix-netstorage_gc-linking.patch
-		"${FILESDIR}"/${P}-fix-speedtest-linking.patch
-		"${FILESDIR}"/${P}-fix-splign-linking.patch
-		"${FILESDIR}"/${P}-fix-srcchk-linking.patch
-		"${FILESDIR}"/${P}-fix-app-rmblastn-linking.patch
-		"${FILESDIR}"/${P}-remove-old-symlinks.patch
-		"${FILESDIR}"/${P}-fix-app-table2asn-linking.patch
-		"${FILESDIR}"/${P}-fix-app-tls-linking.patch
-		"${FILESDIR}"/${P}-fix-app-vecscreen-linking.patch
-		"${FILESDIR}"/${P}-fix-app-blast_sample-linking.patch
 		)
 
 src_prepare() {
@@ -138,7 +126,11 @@ src_prepare() {
 #	use prefix && append-ldflags -Wl,-rpath,"${EPREFIX}/usr/$(get_libdir)/${PN}"
 
 # The conf-opts.patch and as-needed.patch need to be adjusted for 12.0.0 line numbers
-	#ncbi-tools++-18.0.0-fix-undefined-lxncbi.patch
+#       "${FILESDIR}"/${P}-as-needed.patch
+#       "${FILESDIR}"/${P}-fix-creaders-linking.patch
+#       "${FILESDIR}"/${P}-fix-FreeTDS-upstream.patch
+#		)
+		# "${FILESDIR}"/${P}-support-autoconf-2.60.patch
 	# make sure this one is the last one and contains the actual patches applied unless we can have autoconf-2.59 or 2.60
 	# https://bugs.gentoo.org/show_bug.cgi?id=514706
 
@@ -237,7 +229,7 @@ src_configure() {
 	# resulting in 'checking for ncbi-vdb... no' and
 	# '^PACKAGES:'
 	# '^  disabled: ... VDB'
-	--without-downloaded-vdb
+	# --without-downloaded-vdb
 	$(use_with debug)
 	$(use_with debug max-debug)
 	$(use_with debug symbols)
@@ -366,13 +358,6 @@ src_install() {
 	mv -f "${ED}"/usr/bin/test_regexp "${ED}"/usr/bin/test_regexp+ # drop the eventually mistakenly compiled binaries
 	mv "${ED}"/usr/bin/vecscreen "${ED}"/usr/bin/vecscreen+
 	mv "${ED}"/usr/bin/seedtop "${ED}"/usr/bin/seedtop+
-	#
-	# idfetch collides with idfetch from ncbi-tools-2.2.26
-	# Although the two idfetch implementations do deliberately have several
-	# options in common, the C++ version is not yet a full drop-in replacement
-	# for the C version (and will never entirely be, due to fundamental
-	# differences between the two toolkits' argument-parsing conventions).
-	mv "${ED}"/usr/bin/idfetch "${ED}"/usr/bin/idfetch+ # new in ncbi-tools++-18.0.0
 
 	echo "LDPATH=${EPREFIX}/usr/$(get_libdir)/${PN}" > ${S}/99${PN}
 	doenvd "${S}/99${PN}"

diff --git a/sci-biology/ncbi-tools++/ncbi-tools++-18.0.0.ebuild b/sci-biology/ncbi-tools++/ncbi-tools++-18.0.0.ebuild
index 5c0b619df..0aacd0511 100644
--- a/sci-biology/ncbi-tools++/ncbi-tools++-18.0.0.ebuild
+++ b/sci-biology/ncbi-tools++/ncbi-tools++-18.0.0.ebuild
@@ -3,7 +3,7 @@
 
 EAPI=7
 
-PYTHON_COMPAT=( python3_{7,8,9} )
+PYTHON_COMPAT=( python2_7 )
 
 inherit eutils flag-o-matic multilib python-single-r1 toolchain-funcs
 


^ permalink raw reply related	[flat|nested] 49+ messages in thread

* [gentoo-commits] proj/sci:master commit in: sci-biology/ncbi-tools++/
@ 2021-07-03 10:44 Andrew Ammerlaan
  0 siblings, 0 replies; 49+ messages in thread
From: Andrew Ammerlaan @ 2021-07-03 10:44 UTC (permalink / raw
  To: gentoo-commits

commit:     a973f78a36d58a3bc23bb99eb241b819a6b8bfcb
Author:     Andrew Ammerlaan <andrewammerlaan <AT> gentoo <DOT> org>
AuthorDate: Sat Jul  3 10:43:23 2021 +0000
Commit:     Andrew Ammerlaan <andrewammerlaan <AT> gentoo <DOT> org>
CommitDate: Sat Jul  3 10:43:23 2021 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=a973f78a

sci-biology/ncbi-tools++: allow newer versions of sys-libs/db

Package-Manager: Portage-3.0.20, Repoman-3.0.3
Signed-off-by: Andrew Ammerlaan <andrewammerlaan <AT> gentoo.org>

 sci-biology/ncbi-tools++/ncbi-tools++-12.0.0.ebuild | 2 +-
 sci-biology/ncbi-tools++/ncbi-tools++-18.0.0.ebuild | 2 +-
 sci-biology/ncbi-tools++/ncbi-tools++-22.0.0.ebuild | 2 +-
 3 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/sci-biology/ncbi-tools++/ncbi-tools++-12.0.0.ebuild b/sci-biology/ncbi-tools++/ncbi-tools++-12.0.0.ebuild
index fa1caf715..41e8bdd05 100644
--- a/sci-biology/ncbi-tools++/ncbi-tools++-12.0.0.ebuild
+++ b/sci-biology/ncbi-tools++/ncbi-tools++-12.0.0.ebuild
@@ -38,7 +38,7 @@ DEPEND="
 	<sys-devel/gcc-10:=
 	!sci-biology/sra_sdk
 	app-arch/cpio
-	berkdb? ( sys-libs/db:4.3[cxx] )
+	berkdb? ( sys-libs/db:=[cxx] )
 	boost? ( dev-libs/boost[tools] )
 	curl? ( net-misc/curl )
 	sqlite? ( dev-db/sqlite:3 )

diff --git a/sci-biology/ncbi-tools++/ncbi-tools++-18.0.0.ebuild b/sci-biology/ncbi-tools++/ncbi-tools++-18.0.0.ebuild
index 5c0b619df..55d0aa6ba 100644
--- a/sci-biology/ncbi-tools++/ncbi-tools++-18.0.0.ebuild
+++ b/sci-biology/ncbi-tools++/ncbi-tools++-18.0.0.ebuild
@@ -41,7 +41,7 @@ DEPEND="
 	<sys-devel/gcc-10:=
 	!sci-biology/sra_sdk
 	app-arch/cpio
-	berkdb? ( sys-libs/db:4.3[cxx] )
+	berkdb? ( sys-libs/db:=[cxx] )
 	boost? ( dev-libs/boost[tools] )
 	curl? ( net-misc/curl )
 	sqlite? ( dev-db/sqlite:3 )

diff --git a/sci-biology/ncbi-tools++/ncbi-tools++-22.0.0.ebuild b/sci-biology/ncbi-tools++/ncbi-tools++-22.0.0.ebuild
index 004cc7086..1f34de56e 100644
--- a/sci-biology/ncbi-tools++/ncbi-tools++-22.0.0.ebuild
+++ b/sci-biology/ncbi-tools++/ncbi-tools++-22.0.0.ebuild
@@ -41,7 +41,7 @@ DEPEND="
 	<sys-devel/gcc-10:=
 	!sci-biology/sra_sdk
 	app-arch/cpio
-	berkdb? ( sys-libs/db:4.3[cxx] )
+	berkdb? ( sys-libs/db:=[cxx] )
 	boost? ( dev-libs/boost[tools] )
 	curl? ( net-misc/curl )
 	sqlite? ( >=dev-db/sqlite-3.6.6:3 )


^ permalink raw reply related	[flat|nested] 49+ messages in thread

* [gentoo-commits] proj/sci:master commit in: sci-biology/ncbi-tools++/
@ 2021-08-31  9:45 Andrew Ammerlaan
  0 siblings, 0 replies; 49+ messages in thread
From: Andrew Ammerlaan @ 2021-08-31  9:45 UTC (permalink / raw
  To: gentoo-commits

commit:     248040a4f0ee09c35dcb76de2e385f3e685b9363
Author:     Andrew Ammerlaan <andrewammerlaan <AT> gentoo <DOT> org>
AuthorDate: Tue Aug 31 09:37:09 2021 +0000
Commit:     Andrew Ammerlaan <andrewammerlaan <AT> gentoo <DOT> org>
CommitDate: Tue Aug 31 09:37:09 2021 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=248040a4

sci-biology/ncbi-tools++: add MissingUseDepDefault

Package-Manager: Portage-3.0.22, Repoman-3.0.3
Signed-off-by: Andrew Ammerlaan <andrewammerlaan <AT> gentoo.org>

 sci-biology/ncbi-tools++/ncbi-tools++-12.0.0.ebuild | 2 +-
 sci-biology/ncbi-tools++/ncbi-tools++-18.0.0.ebuild | 2 +-
 sci-biology/ncbi-tools++/ncbi-tools++-22.0.0.ebuild | 2 +-
 3 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/sci-biology/ncbi-tools++/ncbi-tools++-12.0.0.ebuild b/sci-biology/ncbi-tools++/ncbi-tools++-12.0.0.ebuild
index 41e8bdd05..e646cd099 100644
--- a/sci-biology/ncbi-tools++/ncbi-tools++-12.0.0.ebuild
+++ b/sci-biology/ncbi-tools++/ncbi-tools++-12.0.0.ebuild
@@ -38,7 +38,7 @@ DEPEND="
 	<sys-devel/gcc-10:=
 	!sci-biology/sra_sdk
 	app-arch/cpio
-	berkdb? ( sys-libs/db:=[cxx] )
+	berkdb? ( sys-libs/db:=[cxx(-)] )
 	boost? ( dev-libs/boost[tools] )
 	curl? ( net-misc/curl )
 	sqlite? ( dev-db/sqlite:3 )

diff --git a/sci-biology/ncbi-tools++/ncbi-tools++-18.0.0.ebuild b/sci-biology/ncbi-tools++/ncbi-tools++-18.0.0.ebuild
index 55d0aa6ba..e6f233bc7 100644
--- a/sci-biology/ncbi-tools++/ncbi-tools++-18.0.0.ebuild
+++ b/sci-biology/ncbi-tools++/ncbi-tools++-18.0.0.ebuild
@@ -41,7 +41,7 @@ DEPEND="
 	<sys-devel/gcc-10:=
 	!sci-biology/sra_sdk
 	app-arch/cpio
-	berkdb? ( sys-libs/db:=[cxx] )
+	berkdb? ( sys-libs/db:=[cxx(-)] )
 	boost? ( dev-libs/boost[tools] )
 	curl? ( net-misc/curl )
 	sqlite? ( dev-db/sqlite:3 )

diff --git a/sci-biology/ncbi-tools++/ncbi-tools++-22.0.0.ebuild b/sci-biology/ncbi-tools++/ncbi-tools++-22.0.0.ebuild
index 1f34de56e..f98fd4282 100644
--- a/sci-biology/ncbi-tools++/ncbi-tools++-22.0.0.ebuild
+++ b/sci-biology/ncbi-tools++/ncbi-tools++-22.0.0.ebuild
@@ -41,7 +41,7 @@ DEPEND="
 	<sys-devel/gcc-10:=
 	!sci-biology/sra_sdk
 	app-arch/cpio
-	berkdb? ( sys-libs/db:=[cxx] )
+	berkdb? ( sys-libs/db:=[cxx(-)] )
 	boost? ( dev-libs/boost[tools] )
 	curl? ( net-misc/curl )
 	sqlite? ( >=dev-db/sqlite-3.6.6:3 )


^ permalink raw reply related	[flat|nested] 49+ messages in thread

* [gentoo-commits] proj/sci:master commit in: sci-biology/ncbi-tools++/
@ 2022-01-25 19:15 Andrew Ammerlaan
  0 siblings, 0 replies; 49+ messages in thread
From: Andrew Ammerlaan @ 2022-01-25 19:15 UTC (permalink / raw
  To: gentoo-commits

commit:     f958fa4fa89d4d466be60d52c7d51ce5c71ae816
Author:     Andrew Ammerlaan <andrewammerlaan <AT> gentoo <DOT> org>
AuthorDate: Tue Jan 25 16:21:44 2022 +0000
Commit:     Andrew Ammerlaan <andrewammerlaan <AT> gentoo <DOT> org>
CommitDate: Tue Jan 25 16:21:44 2022 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=f958fa4f

sci-biology/ncbi-tools++: drop non-existing blocker

Package-Manager: Portage-3.0.30, Repoman-3.0.3
Signed-off-by: Andrew Ammerlaan <andrewammerlaan <AT> gentoo.org>

 sci-biology/ncbi-tools++/ncbi-tools++-12.0.0.ebuild | 3 +--
 sci-biology/ncbi-tools++/ncbi-tools++-18.0.0.ebuild | 3 +--
 sci-biology/ncbi-tools++/ncbi-tools++-22.0.0.ebuild | 3 +--
 3 files changed, 3 insertions(+), 6 deletions(-)

diff --git a/sci-biology/ncbi-tools++/ncbi-tools++-12.0.0.ebuild b/sci-biology/ncbi-tools++/ncbi-tools++-12.0.0.ebuild
index 6daf7b3f0..272177f97 100644
--- a/sci-biology/ncbi-tools++/ncbi-tools++-12.0.0.ebuild
+++ b/sci-biology/ncbi-tools++/ncbi-tools++-12.0.0.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2021 Gentoo Authors
+# Copyright 1999-2022 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
 EAPI=7
@@ -36,7 +36,6 @@ RESTRICT="!test? ( test )"
 # dev-libs/boost must have Boost.Test suite, probably dev-libs/boost[test] then?
 DEPEND="
 	<sys-devel/gcc-10:=
-	!sci-biology/sra_sdk
 	app-arch/cpio
 	berkdb? ( sys-libs/db:=[cxx(-)] )
 	boost? ( dev-libs/boost[tools] )

diff --git a/sci-biology/ncbi-tools++/ncbi-tools++-18.0.0.ebuild b/sci-biology/ncbi-tools++/ncbi-tools++-18.0.0.ebuild
index e2db30639..052d8d429 100644
--- a/sci-biology/ncbi-tools++/ncbi-tools++-18.0.0.ebuild
+++ b/sci-biology/ncbi-tools++/ncbi-tools++-18.0.0.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2021 Gentoo Authors
+# Copyright 1999-2022 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
 EAPI=7
@@ -39,7 +39,6 @@ REQUIRED_USE="${PYTHON_REQUIRED_USE}"
 # dev-libs/boost must have Boost.Test suite, probably dev-libs/boost[test] then?
 DEPEND="
 	<sys-devel/gcc-10:=
-	!sci-biology/sra_sdk
 	app-arch/cpio
 	berkdb? ( sys-libs/db:=[cxx(-)] )
 	boost? ( dev-libs/boost[tools] )

diff --git a/sci-biology/ncbi-tools++/ncbi-tools++-22.0.0.ebuild b/sci-biology/ncbi-tools++/ncbi-tools++-22.0.0.ebuild
index 7df161c99..9acd9924c 100644
--- a/sci-biology/ncbi-tools++/ncbi-tools++-22.0.0.ebuild
+++ b/sci-biology/ncbi-tools++/ncbi-tools++-22.0.0.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2021 Gentoo Authors
+# Copyright 1999-2022 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
 EAPI=7
@@ -39,7 +39,6 @@ REQUIRED_USE="${PYTHON_REQUIRED_USE}"
 # dev-libs/boost must have Boost.Test suite, probably dev-libs/boost[test] then?
 DEPEND="
 	<sys-devel/gcc-10:=
-	!sci-biology/sra_sdk
 	app-arch/cpio
 	berkdb? ( sys-libs/db:=[cxx(-)] )
 	boost? ( dev-libs/boost[tools] )


^ permalink raw reply related	[flat|nested] 49+ messages in thread

end of thread, other threads:[~2022-01-25 19:15 UTC | newest]

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