proj/gentoo: Initial commit

This commit represents a new era for Gentoo:
Storing the gentoo-x86 tree in Git, as converted from CVS.

This commit is the start of the NEW history.
Any historical data is intended to be grafted onto this point.

Creation process:
1. Take final CVS checkout snapshot
2. Remove ALL ChangeLog* files
3. Transform all Manifests to thin
4. Remove empty Manifests
5. Convert all stale $Header$/$Id$ CVS keywords to non-expanded Git $Id$
5.1. Do not touch files with -kb/-ko keyword flags.

Signed-off-by: Robin H. Johnson <robbat2@gentoo.org>
X-Thanks: Alec Warner <antarus@gentoo.org> - did the GSoC 2006 migration tests
X-Thanks: Robin H. Johnson <robbat2@gentoo.org> - infra guy, herding this project
X-Thanks: Nguyen Thai Ngoc Duy <pclouds@gentoo.org> - Former Gentoo developer, wrote Git features for the migration
X-Thanks: Brian Harring <ferringb@gentoo.org> - wrote much python to improve cvs2svn
X-Thanks: Rich Freeman <rich0@gentoo.org> - validation scripts
X-Thanks: Patrick Lauer <patrick@gentoo.org> - Gentoo dev, running new 2014 work in migration
X-Thanks: Michał Górny <mgorny@gentoo.org> - scripts, QA, nagging
X-Thanks: All of other Gentoo developers - many ideas and lots of paint on the bikeshed

9 files changed, 340 insertions, 0 deletions

diff --git a/sci-biology/arb/Manifest b/sci-biology/arb/Manifest
new file mode 100644
index 000000000000..7ec0fa4e73a4
--- /dev/null
+++ b/sci-biology/arb/Manifest
@@ -0,0 +1,7 @@
+DIST arb-5.1-glibc2.10.patch.bz2 24659 SHA256 1153e3efe73c1027972ee1b2789ee9841749c0bd2cbb2cc3ad8cd53586ff6f2f
+DIST arb-5.1-linker.patch.bz2 4406 SHA256 62080367ebd11ed3c9991bfb872e083e2d747264a400178ab0ec11a3502f3d43
+DIST arb-5.1.tgz 9727285 SHA256 7f0a2411e7b95b94f23c51211461047eb74ffd3dd632552a82425cf903f89dbf
+DIST arb-5.2-linker.patch.bz2 4441 SHA256 3b804fca56e920f83b79f7cdfb124769bfa677a3f2216021eed04ba76ac886c6 SHA512 6afae76a4b403ad3139abd4535b5da8bbf2d16aa5f49e30c86c8f186ac585de6c789e8fa4e402576a67ce8c58468e626a46bde5cfae5869ea2c046a1492fa903 WHIRLPOOL 95435cfc7f5a530442ad294cb8cd79a666f54cc3c99195e9c05a923e41b0211e5bad7b67cd4d8c5ee37ef30de22fba4472dc8990d95aaf3c8d3edb2d3d26c984
+DIST arb-5.2.tgz 9729004 SHA256 cd68cfae317aae378da69c4c4ec8036a2babec064896d0b9d845fac2133f6edd SHA512 d1f9f7273645af7da0e949971b705303f0715ac98869acc0f75d62bfe88751709f5d5dbbc3079b0abe461ddce8262b165426e347ad28bc28a55cdf6c29b5ff56 WHIRLPOOL ec5422b4b689a77b479231c04d7b5a2f4f0ef23cd06b024920432134132d7c2c5b24c407b2561074a41606e7945ce88970789f5db82e43cc9ef9313ea48c0583
+DIST arb-5.3-linker.patch.xz 3604 SHA256 09580d0c1ff54c4956382cef850aecb9008e62e083f3246604cac72f06d05e95 SHA512 8eb072cd5a3c13b2a6ad0e40f3b155096168dbd70a6e13878d4a62e563903742442373a5e3032d6f78beefe774943fef86f6060e89acd0d18b95a7c0d4a8dec7 WHIRLPOOL f77d767c5b5c911ba3ddc9ef5b3e482cb1975b5d56f50b76166bd4a0b55e251e73eeee46709147207b2f3553d482bab99398d8bd03aef8f0b79928a8a66d0bfe
+DIST arb-5.3.tgz 9543106 SHA256 c40a3f33f39996e3e331fb41acd452e5a20b7e638b856b0b66ea8e07c977abf8 SHA512 faa924b9c6f437f77ed637798c6fe5fe5c2e6a0f2efc9c1f735133fab9c037c7039fc4ef6f6e5b0408fc39ea5c69c747b1887689f4621b608add593d77930282 WHIRLPOOL 9b4723043b4f8b9a68973f49cb7dc8c3cf3558ff646d20f7d4f20f6e4797b6c9a986fdb1dc47178f2c80251db59f61dffd1b01bbdd880f864fc749ef59e62958
diff --git a/sci-biology/arb/arb-5.1-r1.ebuild b/sci-biology/arb/arb-5.1-r1.ebuild
new file mode 100644
index 000000000000..7db2d798ec55
--- /dev/null
+++ b/sci-biology/arb/arb-5.1-r1.ebuild
@@ -0,0 +1,78 @@
+# Copyright 1999-2012 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=2
+
+inherit eutils toolchain-funcs
+
+DESCRIPTION="Tools for DNA/RNA sequence database handling and data analysis, phylogenetic analysis"
+HOMEPAGE="http://www.arb-home.de/"
+SRC_URI="
+	http://download.arb-home.de/release/arb_${PV}/arbsrc.tgz -> ${P}.tgz
+	mirror://gentoo/${P}-glibc2.10.patch.bz2
+	http://dev.gentoo.org/~jlec/${P}-linker.patch.bz2"
+
+LICENSE="arb"
+SLOT="0"
+IUSE="+opengl"
+KEYWORDS="~amd64 ~x86"
+
+DEPEND="
+	app-text/sablotron
+	media-libs/libpng
+	media-libs/tiff
+	www-client/lynx
+	x11-libs/libXaw
+	x11-libs/libXpm
+	x11-libs/motif:0
+	opengl? (
+		media-libs/glew
+		media-libs/freeglut
+		|| (
+			media-libs/mesa[motif]
+			( media-libs/mesa x11-libs/libGLw ) ) )"
+RDEPEND="${DEPEND}
+	sci-visualization/gnuplot"
+# Recommended: libmotif3 gv xfig xterm treetool java
+
+src_unpack() {
+	unpack ${A}
+	mv arbsrc* ${P}
+}
+
+src_prepare() {
+	epatch \
+		"${WORKDIR}"/${P}-glibc2.10.patch\
+		"${WORKDIR}"/${P}-linker.patch \
+		"${FILESDIR}"/${PV}-libs.patch \
+		"${FILESDIR}"/${PV}-bfr-overflow.patch
+	sed -i \
+		-e 's/all: checks/all:/' \
+		-e "s/GCC:=.*/GCC=$(tc-getCC) ${CFLAGS}/" \
+		-e "s/GPP:=.*/GPP=$(tc-getCXX) ${CXXFLAGS}/" \
+		-e 's/--export-dynamic/-Wl,--export-dynamic/g' \
+		"${S}/Makefile" || die
+	cp config.makefile.template config.makefile
+	sed -i -e '/^[ \t]*read/ d' -e 's/SHELL_ANS=0/SHELL_ANS=1/' "${S}/arb_install.sh" || die
+	use amd64 && sed -i -e 's/ARB_64 := 0/ARB_64 := 1/' config.makefile
+	use opengl || sed -i -e 's/OPENGL := 1/OPENGL := 0/' config.makefile
+	emake ARBHOME="${S}" links || die
+}
+
+src_compile() {
+	emake ARBHOME="${S}" PATH="${PATH}:${S}/bin" LD_LIBRARY_PATH="${LD_LIBRARY_PATH}:${S}/lib" tarfile || die
+	use amd64 && mv arb.tgz arb.64.gentoo.tgz
+	use x86 && mv arb.tgz arb.32.gentoo.tgz
+	ln -s arb.*.tgz arb.tgz || die
+}
+
+src_install() {
+	ARBHOME="${D}/opt/arb" "${S}/arb_install.sh" || die
+	cat <<- EOF > "${S}/99${PN}"
+	ARBHOME=/opt/arb
+	PATH=/opt/arb/bin
+	LD_LIBRARY_PATH=/opt/arb/lib
+	EOF
+	doenvd "${S}/99${PN}" || die
+}
diff --git a/sci-biology/arb/arb-5.2.ebuild b/sci-biology/arb/arb-5.2.ebuild
new file mode 100644
index 000000000000..97f7dc5dfbdd
--- /dev/null
+++ b/sci-biology/arb/arb-5.2.ebuild
@@ -0,0 +1,80 @@
+# Copyright 1999-2012 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=4
+
+inherit eutils toolchain-funcs
+
+DESCRIPTION="Tools for DNA/RNA sequence database handling and data analysis, phylogenetic analysis"
+HOMEPAGE="http://www.arb-home.de/"
+SRC_URI="
+	http://download.arb-home.de/release/arb_${PV}/arbsrc.tgz -> ${P}.tgz
+	http://dev.gentoo.org/~jlec/distfiles/${P}-linker.patch.bz2"
+
+SLOT="0"
+LICENSE="arb"
+IUSE="+opengl"
+KEYWORDS="~amd64 ~x86"
+
+CDEPEND="app-text/sablotron
+	media-libs/libpng
+	media-libs/tiff
+	www-client/lynx
+	x11-libs/libXaw
+	x11-libs/libXpm
+	x11-libs/motif:0
+	opengl? (
+		media-libs/glew
+		media-libs/freeglut
+		|| (
+			media-libs/mesa[motif]
+			( media-libs/mesa x11-libs/libGLw ) ) )"
+DEPEND="${CDEPEND}
+	sys-process/time"
+RDEPEND="${CDEPEND}
+	sci-visualization/gnuplot"
+# Recommended: libmotif3 gv xfig xterm treetool java
+
+src_unpack() {
+	unpack ${A}
+	mv arbsrc* ${P}
+}
+
+src_prepare() {
+	epatch \
+		"${WORKDIR}"/${P}-linker.patch \
+		"${FILESDIR}"/5.1-libs.patch \
+		"${FILESDIR}"/5.1-bfr-overflow.patch \
+		"${FILESDIR}"/${PV}-libpng15.patch \
+		"${FILESDIR}"/${P}-gcc-47.patch
+	sed \
+		-e 's/all: checks/all:/' \
+		-e "s/GCC:=.*/GCC=$(tc-getCC) ${CFLAGS}/" \
+		-e "s/GPP:=.*/GPP=$(tc-getCXX) ${CXXFLAGS}/" \
+		-e 's:-O4::g' \
+		-e 's:-pipe::g' \
+		-i "${S}/Makefile" || die
+	cp config.makefile.template config.makefile
+	sed -i -e '/^[ \t]*read/ d' -e 's/SHELL_ANS=0/SHELL_ANS=1/' "${S}/arb_install.sh" || die
+	use amd64 && sed -i -e 's/ARB_64 := 0/ARB_64 := 1/' config.makefile
+	use opengl || sed -i -e 's/OPENGL := 1/OPENGL := 0/' config.makefile
+	emake ARBHOME="${S}" links
+}
+
+src_compile() {
+	emake ARBHOME="${S}" PATH="${PATH}:${S}/bin" LD_LIBRARY_PATH="${LD_LIBRARY_PATH}:${S}/lib" tarfile
+	use amd64 && mv arb.tgz arb.64.gentoo.tgz
+	use x86 && mv arb.tgz arb.32.gentoo.tgz
+	ln -s arb.*.tgz arb.tgz || die
+}
+
+src_install() {
+	ARBHOME="${D}/opt/arb" "${S}/arb_install.sh" || die
+	cat <<- EOF > "${S}/99${PN}"
+	ARBHOME=/opt/arb
+	PATH=/opt/arb/bin
+	LD_LIBRARY_PATH=/opt/arb/lib
+	EOF
+	doenvd "${S}/99${PN}"
+}
diff --git a/sci-biology/arb/arb-5.3.ebuild b/sci-biology/arb/arb-5.3.ebuild
new file mode 100644
index 000000000000..97f8b78ddca2
--- /dev/null
+++ b/sci-biology/arb/arb-5.3.ebuild
@@ -0,0 +1,78 @@
+# Copyright 1999-2012 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=4
+
+inherit eutils toolchain-funcs
+
+DESCRIPTION="Tools for DNA/RNA sequence database handling and data analysis, phylogenetic analysis"
+HOMEPAGE="http://www.arb-home.de/"
+SRC_URI="
+	http://download.arb-home.de/release/arb_${PV}/arbsrc.tgz -> ${P}.tgz
+	http://dev.gentoo.org/~jlec/distfiles/${P}-linker.patch.xz"
+
+SLOT="0"
+LICENSE="arb"
+IUSE="+opengl"
+KEYWORDS="~amd64 ~x86"
+
+CDEPEND="app-text/sablotron
+	media-libs/libpng
+	media-libs/tiff
+	www-client/lynx
+	x11-libs/libXaw
+	x11-libs/libXpm
+	x11-libs/motif:0
+	opengl? (
+		media-libs/glew
+		media-libs/freeglut
+		|| (
+			media-libs/mesa[motif]
+			( media-libs/mesa x11-libs/libGLw ) ) )"
+DEPEND="${CDEPEND}
+	sys-process/time"
+RDEPEND="${CDEPEND}
+	sci-visualization/gnuplot"
+# Recommended: libmotif3 gv xfig xterm treetool java
+
+src_unpack() {
+	unpack ${A}
+	mv arbsrc* ${P}
+}
+
+src_prepare() {
+	epatch \
+		"${WORKDIR}"/${P}-linker.patch \
+		"${FILESDIR}"/5.1-libs.patch \
+		"${FILESDIR}"/5.1-bfr-overflow.patch \
+		"${FILESDIR}"/5.2-libpng15.patch \
+		"${FILESDIR}"/${PN}-5.2-gcc-47.patch
+	sed \
+		-e 's/all: checks/all:/' \
+		-e "s/GCC:=.*/GCC=$(tc-getCC) ${CFLAGS}/" \
+		-e "s/GPP:=.*/GPP=$(tc-getCXX) ${CXXFLAGS}/" \
+		-i "${S}/Makefile" || die
+	cp config.makefile.template config.makefile
+	sed -i -e '/^[ \t]*read/ d' -e 's/SHELL_ANS=0/SHELL_ANS=1/' "${S}/arb_install.sh" || die
+	use amd64 && sed -i -e 's/ARB_64 := 0/ARB_64 := 1/' config.makefile
+	use opengl || sed -i -e 's/OPENGL := 1/OPENGL := 0/' config.makefile
+	emake ARBHOME="${S}" links
+}
+
+src_compile() {
+	emake ARBHOME="${S}" PATH="${PATH}:${S}/bin" LD_LIBRARY_PATH="${LD_LIBRARY_PATH}:${S}/lib" tarfile
+	use amd64 && mv arb.tgz arb.64.gentoo.tgz
+	use x86 && mv arb.tgz arb.32.gentoo.tgz
+	ln -s arb.*.tgz arb.tgz || die
+}
+
+src_install() {
+	ARBHOME="${D}/opt/arb" "${S}/arb_install.sh" || die
+	cat <<- EOF > "${S}/99${PN}"
+	ARBHOME=/opt/arb
+	PATH=/opt/arb/bin
+	LD_LIBRARY_PATH=/opt/arb/lib
+	EOF
+	doenvd "${S}/99${PN}"
+}
diff --git a/sci-biology/arb/files/5.1-bfr-overflow.patch b/sci-biology/arb/files/5.1-bfr-overflow.patch
new file mode 100644
index 000000000000..21d21f5ac17f
--- /dev/null
+++ b/sci-biology/arb/files/5.1-bfr-overflow.patch
@@ -0,0 +1,16 @@
+ ARB_GDE/GDE_HGLfile.cxx |    2 +-
+ 1 files changed, 1 insertions(+), 1 deletions(-)
+
+diff --git a/ARB_GDE/GDE_HGLfile.cxx b/ARB_GDE/GDE_HGLfile.cxx
+index e353a89..f69635a 100644
+--- a/ARB_GDE/GDE_HGLfile.cxx
++++ b/ARB_GDE/GDE_HGLfile.cxx
+@@ -494,7 +494,7 @@ void ReadGDE(char *filename,NA_Alignment *dataset,int type)
+             if(this_elem->id[0] == '\0')
+                 strncpy(this_elem->id,uniqueID(),79);
+             if(this_elem->short_name[0] == '\0')
+-                strncpy(this_elem->short_name,this_elem->id,79);
++                strncpy(this_elem->short_name,this_elem->id,31);
+             if(this_elem->seqlen == 0)
+                 this_elem->protect=
+                     PROT_BASE_CHANGES+
diff --git a/sci-biology/arb/files/5.1-libs.patch b/sci-biology/arb/files/5.1-libs.patch
new file mode 100644
index 000000000000..bf0bacad3286
--- /dev/null
+++ b/sci-biology/arb/files/5.1-libs.patch
@@ -0,0 +1,16 @@
+diff --git a/SOURCE_TOOLS/provide_libs.pl b/SOURCE_TOOLS/provide_libs.pl
+index b653a66..b346c96 100644
+--- a/SOURCE_TOOLS/provide_libs.pl
++++ b/SOURCE_TOOLS/provide_libs.pl
+@@ -118,11 +118,6 @@ sub provide_libs($$$) {
+   foreach my $lib (keys %needed_by) {
+     update_lib($lib, $bindir.'/'.$needed_by{$lib}, $addlibsdir);
+   }
+-  if ($opengl==1) {
+-    foreach my $lib (keys %needed_by_opengl) {
+-      update_lib($lib, $bindir.'/'.$needed_by_opengl{$lib}, $addlibsdir);
+-    }
+-  }
+ }
+ 
+ sub main() {
diff --git a/sci-biology/arb/files/5.2-libpng15.patch b/sci-biology/arb/files/5.2-libpng15.patch
new file mode 100644
index 000000000000..3d750e76efe3
--- /dev/null
+++ b/sci-biology/arb/files/5.2-libpng15.patch
@@ -0,0 +1,45 @@
+Fix building with libpng-1.5
+
+https://bugs.gentoo.org/show_bug.cgi?id=378353
+
+Patch written by Samuli Suominen <ssuominen@gentoo.org>
+--- a/GL/glpng/glpng.c
++++ b/GL/glpng/glpng.c
+@@ -285,7 +285,7 @@
+     endinfo = png_create_info_struct(png);
+ 
+     // DH: added following lines
+-    if (setjmp(png->jmpbuf))
++    if (setjmp(png_jmpbuf(png)))
+     {
+         png_destroy_read_struct(&png, &info, &endinfo);
+         return 0;
+@@ -390,7 +390,7 @@
+     endinfo = png_create_info_struct(png);
+ 
+     // DH: added following lines
+-    if (setjmp(png->jmpbuf))
++    if (setjmp(png_jmpbuf(png)))
+     {
+         png_destroy_read_struct(&png, &info, &endinfo);
+         return 0;
+@@ -569,7 +569,7 @@
+ #define ALPHA *q
+ 
+                 switch (trans) {
+-                    case PNG_CALLBACK:
++                    case PNG_CALLBACKT:
+                         FORSTART
+                             ALPHA = AlphaCallback((unsigned char) r, (unsigned char) g, (unsigned char) b);
+                         FOREND
+--- a/GL/glpng/glpng.h
++++ b/GL/glpng/glpng.h
+@@ -57,7 +57,7 @@
+ #define PNG_SIMPLEMIPMAP PNG_SIMPLEMIPMAPS
+ 
+     /* Transparency parameters */
+-#define PNG_CALLBACK  -3 /* Call the callback function to generate alpha   */
++#define PNG_CALLBACKT  -3 /* Call the callback function to generate alpha   */
+ #define PNG_ALPHA     -2 /* Use alpha channel in PNG file, if there is one */
+ #define PNG_SOLID     -1 /* No transparency                                */
+ #define PNG_STENCIL    0 /* Sets alpha to 0 for r=g=b=0, 1 otherwise       */
diff --git a/sci-biology/arb/files/arb-5.2-gcc-47.patch b/sci-biology/arb/files/arb-5.2-gcc-47.patch
new file mode 100644
index 000000000000..186e78e450b3
--- /dev/null
+++ b/sci-biology/arb/files/arb-5.2-gcc-47.patch
@@ -0,0 +1,15 @@
+ AWTI/AWTI_import.cxx |    1 +
+ 1 files changed, 1 insertions(+), 0 deletions(-)
+
+diff --git a/AWTI/AWTI_import.cxx b/AWTI/AWTI_import.cxx
+index 8e730ac..e3f9ff4 100644
+--- a/AWTI/AWTI_import.cxx
++++ b/AWTI/AWTI_import.cxx
+@@ -12,6 +12,7 @@
+ #include <GEN.hxx>
+ 
+ #include <climits>
++#include <unistd.h>
+ 
+ using namespace std;
+ 
diff --git a/sci-biology/arb/metadata.xml b/sci-biology/arb/metadata.xml
new file mode 100644
index 000000000000..f17a827e3101
--- /dev/null
+++ b/sci-biology/arb/metadata.xml
@@ -0,0 +1,5 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+  <herd>sci-biology</herd>
+</pkgmetadata>