[gentoo-commits] proj/sci:fixing commit in: sci-biology/tablet-bin/

[gentoo-commits] proj/sci:fixing commit in: sci-biology/tablet-bin/

[Justin Lecher]

commit:     934f6a25f442f4d0310e33e512ecabfa65f9cb4b
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Sun Jun 16 09:19:16 2013 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Sun Jun 16 09:19:16 2013 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=934f6a25

sci-biology/tablet-bin: Version BUmp; BUmp to EAPI5 and python-r1.eclass

Package-Manager: portage-2.2.0_alpha179

---
 sci-biology/tablet-bin/ChangeLog                   |  6 ++-
 sci-biology/tablet-bin/metadata.xml                | 10 ++--
 .../tablet-bin/tablet-bin-1.11.05.03.ebuild        | 62 ----------------------
 ...1.11.01.ebuild => tablet-bin-1.13.05.17.ebuild} | 57 ++++++++++++++------
 4 files changed, 50 insertions(+), 85 deletions(-)

diff --git a/sci-biology/tablet-bin/ChangeLog b/sci-biology/tablet-bin/ChangeLog
index 3205cfc..52a442d 100644
--- a/sci-biology/tablet-bin/ChangeLog
+++ b/sci-biology/tablet-bin/ChangeLog
@@ -1,7 +1,11 @@
 # ChangeLog for sci-biology/tablet-bin
-# Copyright 1999-2012 Gentoo Foundation; Distributed under the GPL v2
+# Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2
 # $Header: $
 
+  16 Jun 2013; Justin Lecher <jlec@gentoo.org> -tablet-bin-1.11.05.03.ebuild,
+  -tablet-bin-1.11.11.01.ebuild, +tablet-bin-1.13.05.17.ebuild, metadata.xml:
+  Version BUmp; BUmp to EAPI5 and python-r1.eclass
+
   07 Feb 2012; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
   tablet-bin-1.11.11.01.ebuild:
   adjust PATH to point to the installation place

diff --git a/sci-biology/tablet-bin/metadata.xml b/sci-biology/tablet-bin/metadata.xml
index 07b5255..2bc8930 100644
--- a/sci-biology/tablet-bin/metadata.xml
+++ b/sci-biology/tablet-bin/metadata.xml
@@ -1,9 +1,9 @@
 <?xml version="1.0" encoding="UTF-8"?>
 <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
 <pkgmetadata>
-	<herd>sci-biology</herd>
-	<maintainer>
-		<email>mmokrejs@fold.natur.cuni.cz</email>
-		<name>Martin Mokrejs</name>
-	</maintainer>
+  <herd>sci-biology</herd>
+  <maintainer>
+    <email>mmokrejs@fold.natur.cuni.cz</email>
+    <name>Martin Mokrejs</name>
+  </maintainer>
 </pkgmetadata>

diff --git a/sci-biology/tablet-bin/tablet-bin-1.11.05.03.ebuild b/sci-biology/tablet-bin/tablet-bin-1.11.05.03.ebuild
deleted file mode 100644
index 32cc463e..0000000
--- a/sci-biology/tablet-bin/tablet-bin-1.11.05.03.ebuild
+++ /dev/null
@@ -1,62 +0,0 @@
-# Copyright 1999-2011 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Header: $
-
-EAPI=3
-
-inherit java-pkg-2 python
-
-DESCRIPTION="Viewer of next generation sequence assemblies and alignments."
-HOMEPAGE="http://bioinf.scri.ac.uk/tablet/"
-SRC_URI="http://bioinf.scri.ac.uk/tablet/installers/tablet_linux_x86_1_11_05_03.sh
-		http://bioinf.scri.ac.uk/tablet/additional/coveragestats.py"
-
-# Upstream says regarding source code unavailability:
-# Tablet uses a modified version of the BSD License which has been edited to
-# remove references to distribution and use in source forms. This means that
-# we are happy for you to distribute and use Tablet however you please, but we
-# do not (yet) want to make the source code publicly available.
-
-# The licence file itself is in the installer, and ends up on disk after
-# installation at /opt/Tablet/docs/tablet.html
-# The original BSD licence was modified to remove references to distribution
-# and use in source forms, because we cannot make the source code available
-# for Tablet.
-
-LICENSE="Tablet"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE=""
-
-DEPEND=""
-RDEPEND="${DEPEND}
-		virtual/jre
-		dev-lang/python"
-
-src_install() {
-	# In theory it seems this binary package could be installed through ant
-	# instead of the install4j package which is not easy to be forced
-	# non-interactive. The below approach via install4j is not ideal but works.
-	sed "s#\"\${D}\"#"${D}"#g" "${FILESDIR}"/response.varfile > "${DISTDIR}"/response.varfile || die "sed failed"
-
-	# the intallation script somehow does not pickup
-	# -varfile="${DISTDIR}"/response.varfile from the commandline and therefore
-	# we place the file rather directly into the place where it should reside.
-	# In the file you can read details how the variables were mangled. For
-	# example, the trick with sys.symlinkDir in the response.varfile is to
-	# disable the installation process to symlink from /usr/local/bin/table to
-	# /opt/Tablet/tablet. That was logged in that file with the following line:
-	#
-	# /var/tmp/portage/sci-biology/tablet-bin-1.11.02.18/image/opt/Tablet/.install4j/installation.log: Variable changed: sys.symlinkDir=/usr/local/bin[class java.lang.String]
-	#
-	# The file is then left on the installed system in "${D}"/opt/Tablet/.install4j/response.varfile
-	mkdir -p "${D}"/opt/Tablet/.install4j || die "Cannot pre-create	"${D}"/opt/Tablet/.install4j/"
-	cat "${DISTDIR}"/response.varfile >	"${D}"/opt/Tablet/.install4j/response.varfile || die "Cannot write	"${D}"/opt/Tablet/.install4j/response.varfile"
-
-	# make sure we force java to point a to $HOME which is inside our sanbox
-	# directory area. We force -Duser.home . It seems also -Dinstall4j.userHome
-	# could be done based on the figure shown at http://resources.ej-technologies.com/install4j/help/doc/
-	sed "s#/bin/java\" -Dinstall4j.jvmDir#/bin/java\" -Duser.home="${D}"/../temp -Dinstall4j.jvmDir#" -i "${DISTDIR}"/tablet_linux_x86_1_11_05_03.sh || die "failed to set userHome value"
-	sh "${DISTDIR}"/tablet_linux_x86_1_11_05_03.sh -q -overwrite -varfile="${DISTDIR}"/response.varfile --destination="${D}"/opt/Tablet -dir "${D}"/opt/Tablet || die "Failed to run the self-extracting exe file"
-	dobin "${DISTDIR}"/coveragestats.py
-}

diff --git a/sci-biology/tablet-bin/tablet-bin-1.11.11.01.ebuild b/sci-biology/tablet-bin/tablet-bin-1.13.05.17.ebuild
similarity index 65%
rename from sci-biology/tablet-bin/tablet-bin-1.11.11.01.ebuild
rename to sci-biology/tablet-bin/tablet-bin-1.13.05.17.ebuild
index 3e6d6e6..e3be7e5 100644
--- a/sci-biology/tablet-bin/tablet-bin-1.11.11.01.ebuild
+++ b/sci-biology/tablet-bin/tablet-bin-1.13.05.17.ebuild
@@ -1,15 +1,18 @@
-# Copyright 1999-2012 Gentoo Foundation
+# Copyright 1999-2013 Gentoo Foundation
 # Distributed under the terms of the GNU General Public License v2
 # $Header: $
 
-EAPI=3
+EAPI=5
 
-inherit java-pkg-2 python
+PYTHON_COMPAT=( python{2_6,2_7} )
+
+inherit java-pkg-2 python-r1
 
 DESCRIPTION="Viewer of next generation sequence assemblies and alignments."
 HOMEPAGE="http://bioinf.scri.ac.uk/tablet/"
-SRC_URI="http://bioinf.scri.ac.uk/tablet/installers/tablet_linux_x86_1_11_11_01.sh
-		http://bioinf.scri.ac.uk/tablet/additional/coveragestats.py"
+SRC_URI="
+	http://bioinf.scri.ac.uk/tablet/installers/tablet_linux_x86_$(replace_all_version_separators _).sh -> ${P}.sh
+	http://bioinf.scri.ac.uk/tablet/additional/coveragestats.py"
 
 # Upstream says regarding source code unavailability:
 # Tablet uses a modified version of the BSD License which has been edited to
@@ -28,12 +31,20 @@ SLOT="0"
 KEYWORDS="~amd64 ~x86"
 IUSE=""
 
-DEPEND=""
+REQUIRED_USE="${PYTHON_REQUIRED_USE}"
+
+DEPEND="${PYTHON_DEPS}"
 RDEPEND="${DEPEND}
-		virtual/jre
-		dev-lang/python"
+		virtual/jre"
 
-MYPV="$(replace_all_version_separators '_')"
+S="${WORKDIR}"
+
+src_unpack() {
+	local file
+	for file in ${A}; do
+		cp "${DISTDIR}"/${file} ${WORKDIR} || die
+	done
+}
 
 pkg_setup() {
 	einfo "Fixing java access violations ..."
@@ -45,7 +56,7 @@ src_install() {
 	# In theory it seems this binary package could be installed through ant
 	# instead of the install4j package which is not easy to be forced
 	# non-interactive. The below approach via install4j is not ideal but works.
-	sed "s#\"\${D}\"#"${D}"#g" "${FILESDIR}"/response.varfile > "${DISTDIR}"/response.varfile || die "sed failed"
+	sed "s#\"\${D}\"#"${D}"#g" "${FILESDIR}"/response.varfile > "${WORKDIR}"/response.varfile || die "sed failed"
 
 	# the intallation script somehow does not pickup
 	# -varfile="${DISTDIR}"/response.varfile from the commandline and therefore
@@ -55,19 +66,31 @@ src_install() {
 	# disable the installation process to symlink from /usr/local/bin/table to
 	# /opt/Tablet/tablet. That was logged in that file with the following line:
 	#
-	# /var/tmp/portage/sci-biology/tablet-bin-1.11.02.18/image/opt/Tablet/.install4j/installation.log: Variable changed: sys.symlinkDir=/usr/local/bin[class java.lang.String]
+	# /var/tmp/portage/sci-biology/tablet-bin-1.11.02.18/image/opt/Tablet/.install4j/installation.log:
+	#	Variable changed: sys.symlinkDir=/usr/local/bin[class java.lang.String]
 	#
 	# The file is then left on the installed system in "${D}"/opt/Tablet/.install4j/response.varfile
-	mkdir -p "${D}"/opt/Tablet/.install4j || die "Cannot pre-create	"${D}"/opt/Tablet/.install4j/"
-	cat "${DISTDIR}"/response.varfile >	"${D}"/opt/Tablet/.install4j/response.varfile || die "Cannot write	"${D}"/opt/Tablet/.install4j/response.varfile"
+	dodir /opt/Tablet/.install4j
+	cat "${WORKDIR}"/response.varfile > "${ED}"/opt/Tablet/.install4j/response.varfile || die
 
 	# make sure we force java to point a to $HOME which is inside our sanbox
 	# directory area. We force -Duser.home . It seems also -Dinstall4j.userHome
 	# could be done based on the figure shown at http://resources.ej-technologies.com/install4j/help/doc/
-	sed "s#/bin/java\" -Dinstall4j.jvmDir#/bin/java\" -Duser.home="${TMPDIR}" -Dinstall4j.jvmDir#" -i "${DISTDIR}"/tablet_linux_x86_"${MYPV}".sh || die "failed to set userHome value"
-	sh "${DISTDIR}"/tablet_linux_x86_"${MYPV}".sh -q -overwrite -varfile="${DISTDIR}"/response.varfile --destination="${D}"/opt/Tablet -dir "${D}"/opt/Tablet || die "Failed to run the self-extracting exe file"
-	dobin "${DISTDIR}"/coveragestats.py
+	sed \
+		-e "s#/bin/java\" -Dinstall4j.jvmDir#/bin/java\" -Duser.home="${TMPDIR}" -Dinstall4j.jvmDir#" \
+		-i "${WORKDIR}"/${P}.sh || die
+	sh \
+		"${WORKDIR}"/${P}.sh \
+		-q -overwrite \
+		-varfile="${DISTDIR}"/response.varfile \
+		--destination="${ED}"/opt/Tablet \
+		-dir "${ED}"/opt/Tablet || die
+
+	rm -rvf "${ED}"/opt/Tablet/jre || die
+
+
+	python_foreach_impl python_doscript "${WORKDIR}"/coveragestats.py
 
-	echo "PATH=/opt/Tablet" > 99Tablet
+	echo "PATH=${EPREFIX}/opt/Tablet" > 99Tablet
 	doenvd 99Tablet || die
 }

[gentoo-commits] proj/sci:fixing commit in: sci-biology/tablet-bin/

[Justin Lecher]

commit:     4f67d2aba3097729635a0367b94287ad10bfd373
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Sun Jun 16 11:15:49 2013 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Sun Jun 16 11:15:49 2013 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=4f67d2ab

sci-biology/tablet-bin: Version BUmp; BUmp to EAPI5 and python-r1.eclass; drop addpredict

Package-Manager: portage-2.2.0_alpha180

---
 sci-biology/tablet-bin/ChangeLog                    |  3 +++
 sci-biology/tablet-bin/tablet-bin-1.13.05.17.ebuild | 13 +++----------
 2 files changed, 6 insertions(+), 10 deletions(-)

diff --git a/sci-biology/tablet-bin/ChangeLog b/sci-biology/tablet-bin/ChangeLog
index 52a442d..87308e6 100644
--- a/sci-biology/tablet-bin/ChangeLog
+++ b/sci-biology/tablet-bin/ChangeLog
@@ -2,6 +2,9 @@
 # Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2
 # $Header: $
 
+  16 Jun 2013; Justin Lecher <jlec@gentoo.org> tablet-bin-1.13.05.17.ebuild:
+  Version BUmp; BUmp to EAPI5 and python-r1.eclass; drop addpredict
+
   16 Jun 2013; Justin Lecher <jlec@gentoo.org> -tablet-bin-1.11.05.03.ebuild,
   -tablet-bin-1.11.11.01.ebuild, +tablet-bin-1.13.05.17.ebuild, metadata.xml:
   Version BUmp; BUmp to EAPI5 and python-r1.eclass

diff --git a/sci-biology/tablet-bin/tablet-bin-1.13.05.17.ebuild b/sci-biology/tablet-bin/tablet-bin-1.13.05.17.ebuild
index e3be7e5..762e888 100644
--- a/sci-biology/tablet-bin/tablet-bin-1.13.05.17.ebuild
+++ b/sci-biology/tablet-bin/tablet-bin-1.13.05.17.ebuild
@@ -42,21 +42,15 @@ S="${WORKDIR}"
 src_unpack() {
 	local file
 	for file in ${A}; do
-		cp "${DISTDIR}"/${file} ${WORKDIR} || die
+		cp "${DISTDIR}"/${file} "${WORKDIR}" || die
 	done
 }
 
-pkg_setup() {
-	einfo "Fixing java access violations ..."
-	# bug 387227
-	addpredict /proc/self/coredump_filter
-}
-
 src_install() {
 	# In theory it seems this binary package could be installed through ant
 	# instead of the install4j package which is not easy to be forced
 	# non-interactive. The below approach via install4j is not ideal but works.
-	sed "s#\"\${D}\"#"${D}"#g" "${FILESDIR}"/response.varfile > "${WORKDIR}"/response.varfile || die "sed failed"
+	sed "s#\"\${D}\"#\"${D}\"#g" "${FILESDIR}"/response.varfile > "${WORKDIR}"/response.varfile || die "sed failed"
 
 	# the intallation script somehow does not pickup
 	# -varfile="${DISTDIR}"/response.varfile from the commandline and therefore
@@ -86,8 +80,7 @@ src_install() {
 		--destination="${ED}"/opt/Tablet \
 		-dir "${ED}"/opt/Tablet || die
 
-	rm -rvf "${ED}"/opt/Tablet/jre || die
-
+	rm -rf "${ED}"/opt/Tablet/jre || die
 
 	python_foreach_impl python_doscript "${WORKDIR}"/coveragestats.py