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

6 files changed, 283 insertions, 0 deletions

diff --git a/sci-biology/primer3/Manifest b/sci-biology/primer3/Manifest
new file mode 100644
index 000000000000..19da14fe3f93
--- /dev/null
+++ b/sci-biology/primer3/Manifest
@@ -0,0 +1,2 @@
+DIST primer3-2.3.5.tar.gz 1655871 SHA256 e0c06a36dc384f656835a8d5ecb4b5069493b7dd98775b38a233863ab591c54b SHA512 e64c27eea0258af913304963254494d6c874e7776b09a14ee9a273f1a3cdfa908acf92b78affc0102f06df17effbf011181c60d97ebd0a645044df7a28b41fec WHIRLPOOL 321069f568fad409b31f2fd4caa36f1128523383f5b294dffc68d57a67489ee2ac17d53bedd8e36df9b688c43c06c91f47bdaf81b4fda6597d916ea06643e666
+DIST primer3-src-2.3.6.tar.gz 1667573 SHA256 2ff54faf957f0d7e4c79d9536fa1027b028bc5e4c6005f142df42ef85562ecd4 SHA512 671b420f3bc9b6b9972e19a757925ada170e5f8c0e3e8a90630a48e6cde44abc0e1e09b9ea90129f94b58f835e30440f3d91c14fb4b796fd94eb478b2ca28ead WHIRLPOOL 61bbc676c38b1b96806c9ac54d130aae936a5406213759613a3be76016cdd4ebf76c5a54d1ceffc7bd2634829d9aef9d64f87cc85289793b40ab031e01a5917f
diff --git a/sci-biology/primer3/files/primer3-1.1.4-ldflags.patch b/sci-biology/primer3/files/primer3-1.1.4-ldflags.patch
new file mode 100644
index 000000000000..66a5a52d4e8e
--- /dev/null
+++ b/sci-biology/primer3/files/primer3-1.1.4-ldflags.patch
@@ -0,0 +1,25 @@
+Respect LDFLAGS
+
+http://bugs.gentoo.org/show_bug.cgi?id=335225
+
+--- src/Makefile
++++ src/Makefile
+@@ -103,10 +103,10 @@
+ 	$(CC) $(LDFLAGS) -o $@ ntdpal_main.o dpal.o

+ 

+ oligotm: oligotm_main.c oligotm.h $(OLIGOTM_LIB)

+-	$(CC) $(CFLAGS) -o $@ oligotm_main.c $(OLIGOTM_LIB) $(LIBOPTS) $(LDLIBS)

++	$(CC) $(LDFLAGS) $(CFLAGS) -o $@ oligotm_main.c $(OLIGOTM_LIB) $(LIBOPTS) $(LDLIBS)

+ 

+ long_seq_tm_test: long_seq_tm_test_main.c oligotm.o

+-	$(CC) $(CFLAGS) -o $@ long_seq_tm_test_main.c oligotm.o $(LIBOPTS) $(LDLIBS)

++	$(CC) $(LDFLAGS) $(CFLAGS) -o $@ long_seq_tm_test_main.c oligotm.o $(LIBOPTS) $(LDLIBS)

+ 

+ boulder_input.o: boulder_input.c boulder_input.h primer3.h primer3_release.h dpal.h

+ 	$(CC) -c $(CFLAGS) $(P_DEFINES) -o $@ boulder_input.c

+@@ -136,4 +136,4 @@
+ primer_test: test

+ 

+ test: $(PRIMER_EXE) ntdpal

+-	cd ../test; make test

++	$(MAKE) -C ../test test

diff --git a/sci-biology/primer3/files/primer3-2.3.4-buildsystem.patch b/sci-biology/primer3/files/primer3-2.3.4-buildsystem.patch
new file mode 100644
index 000000000000..cf47b35af502
--- /dev/null
+++ b/sci-biology/primer3/files/primer3-2.3.4-buildsystem.patch
@@ -0,0 +1,148 @@
+ src/Makefile | 61 ++++++++++++++++++++++++++++++------------------------------
+ 1 file changed, 31 insertions(+), 30 deletions(-)
+
+diff --git a/src/Makefile b/src/Makefile
+index 607ab45..a88adf4 100644
+--- a/src/Makefile
++++ b/src/Makefile
+@@ -52,15 +52,16 @@ TESTOPTS=
+ WINMAKE=mingw32-make
+ 
+ LDLIBS     = -lm
+-AR         = ar
+-CC         = gcc
+-CPP        = g++
+-O_OPTS     = -O2
+-CC_OPTS    = -g -Wall -D__USE_FIXED_PROTOTYPES__
+-P_DEFINES  =
++AR         ?= ar
++CC         ?= gcc
++CXX        ?= g++
++O_OPTS     ?= 
++CC_OPTS    ?= -Wall -D__USE_FIXED_PROTOTYPES__
++P_DEFINES  ?=
+ 
+-CFLAGS  = $(CC_OPTS) $(O_OPTS)
+-LDFLAGS = -g
++CFLAGS    += $(CC_OPTS) $(O_OPTS)
++CXXFLAGS  += $(CC_OPTS) $(O_OPTS)
++LDFLAGS   +=
+ # Note, for profiling, use
+ # make O_OPTS='-pg -O0' LDFLAGS='-g -pg'
+ 
+@@ -92,7 +93,7 @@ LIBPRIMER3      = libprimer3.a
+ LIBPRIMER3_DYN  = libprimer3.so.1.0.0
+ LIBRARIES       = $(LIBPRIMER3) $(LIBDPAL) $(LIBTHAL) $(LIBOLIGOTM) 
+ DYNLIBS         = $(LIBPRIMER3_DYN) $(LIBDPAL_DYN) $(LIBTHAL_DYN) $(LIBOLIGOTM_DYN)
+-RANLIB          = ranlib
++RANLIB          ?= ranlib
+ 
+ PRIMER_OBJECTS1=primer3_boulder_main.o\
+                 format_output.o\
+@@ -127,85 +128,85 @@ $(LIBOLIGOTM): oligotm.o
+ 	$(RANLIB) $@
+ 
+ $(LIBOLIGOTM_LIB): oligotm.o
+-	$(CC) -shared -W1,-soname,liboligotm.so.1 -o $(LIBOLIGOTM_DYN) oligotm.o
++	$(CC) $(LDFLAGS) -shared -W1,-soname,liboligotm.so.1 -o $(LIBOLIGOTM_DYN) oligotm.o
+ 
+ $(LIBDPAL): dpal_primer.o
+ 	$(AR) rv $@ dpal_primer.o
+ 	$(RANLIB) $@
+ 
+ $(LIBDPAL_DYN): dpal_primer.o
+-	$(CC) -shared -W1,-soname,libdpal.so.1 -o $(LIBDPAL_DYN_LIB) dpal_primer.o
++	$(CC) $(LDFLAGS) -shared -W1,-soname,libdpal.so.1 -o $(LIBDPAL_DYN_LIB) dpal_primer.o
+ 
+ $(LIBTHAL): thal_primer.o
+ 	$(AR) rv $@ thal_primer.o
+ 	$(RANLIB) $@
+ 
+ $(LIBTHAL_DYN): thal_primer.o
+-	$(CC) -shared -W1,-soname,libthal.so.1 -o $(LIBTHAL_DYN_LIB) thal_primer.o
++	$(CC) $(LDFLAGS) -shared -W1,-soname,libthal.so.1 -o $(LIBTHAL_DYN_LIB) thal_primer.o
+ 
+ $(LIBPRIMER3): libprimer3.o p3_seq_lib.o
+ 	$(AR) rv $@ libprimer3.o p3_seq_lib.o
+ 	$(RANLIB) $@
+ 
+ $(LIBPRIMER3_DYN): libprimer3.o p3_seq_lib.o
+-	$(CC) -shared -W1,-soname,liprimer3.so.1 -o $(LIBPRIMER3_DYN) libprimer3.o p3_seq_lib.o
++	$(CC) $(LDFLAGS) -shared -W1,-soname,liprimer3.so.1 -o $(LIBPRIMER3_DYN) libprimer3.o p3_seq_lib.o
+ 
+ $(PRIMER_EXE): $(PRIMER_OBJECTS)
+-	$(CPP) $(LDFLAGS) -o $@ $(PRIMER_OBJECTS) $(LIBOPTS) $(LDLIBS)
++	$(CXX) $(LDFLAGS) -o $@ $(PRIMER_OBJECTS) $(LIBOPTS) $(LDLIBS)
+ 
+ libprimer3.o: libprimer3.c libprimer3.h p3_seq_lib.h dpal.h thal.h oligotm.h
+-	$(CPP) -c $(CFLAGS) -Wno-deprecated $(P_DEFINES) -o $@ libprimer3.c
++	$(CXX) -c $(CXXFLAGS) -Wno-deprecated $(P_DEFINES) -o $@ libprimer3.c
+ 
+ $(NTDPAL_EXE): ntdpal_main.o dpal.o
+-	$(CPP) $(LDFLAGS) -o $@ ntdpal_main.o dpal.o
++	$(CXX) $(LDFLAGS) -o $@ ntdpal_main.o dpal.o
+ 
+ $(NTTHAL_EXE): thal_main.o thal.o
+-	$(CPP) $(LDFLAGS) -o $@ thal_main.o thal.o $(LDLIBS)
++	$(CXX) $(LDFLAGS) -o $@ thal_main.o thal.o $(LDLIBS)
+ 
+ $(OLIGOTM_EXE): oligotm_main.c oligotm.h $(LIBOLIGOTM)
+-	$(CPP) $(CFLAGS) -o $@ oligotm_main.c $(LIBOLIGOTM) $(LIBOPTS) $(LDLIBS)
++	$(CXX) $(CXXFLAGS) $(LDFLAGS) -o $@ oligotm_main.c $(LIBOLIGOTM) $(LIBOPTS) $(LDLIBS)
+ 
+ $(LONG_SEQ_EXE): long_seq_tm_test_main.c oligotm.o
+-	$(CPP) $(CFLAGS) -o $@ long_seq_tm_test_main.c oligotm.o $(LIBOPTS) $(LDLIBS)
++	$(CXX) $(CXXFLAGS) $(LDFLAGS) -o $@ long_seq_tm_test_main.c oligotm.o $(LIBOPTS) $(LDLIBS)
+ 
+ read_boulder.o: read_boulder.c read_boulder.h libprimer3.h dpal.h thal.h p3_seq_lib.h 
+-	$(CPP) -c $(CFLAGS) $(P_DEFINES) -o $@ read_boulder.c
++	$(CXX) -c $(CXXFLAGS) $(P_DEFINES) -o $@ read_boulder.c
+ 
+ print_boulder.o: print_boulder.c print_boulder.h libprimer3.h p3_seq_lib.h 
+-	$(CPP) -c $(CFLAGS) $(P_DEFINES) -o $@ print_boulder.c
++	$(CXX) -c $(CXXFLAGS) $(P_DEFINES) -o $@ print_boulder.c
+ 
+ dpal.o: dpal.c dpal.h
+-	$(CPP) -c $(CFLAGS) -o $@ dpal.c
++	$(CXX) -c $(CXXFLAGS) -o $@ dpal.c
+ 
+ # We use '-ffloat-store' on windows to prevent undesirable
+ # precision which may lead to differences in floating point results.
+ thal.o: thal.c thal.h
+-	$(CPP) -c $(CFLAGS) -ffloat-store -o $@ thal.c
++	$(CXX) -c $(CXXFLAGS) -ffloat-store -o $@ thal.c
+ 
+ p3_seq_lib.o: p3_seq_lib.c p3_seq_lib.h libprimer3.h
+-	$(CPP) -c $(CFLAGS) -o $@ p3_seq_lib.c
++	$(CXX) -c $(CXXFLAGS) -o $@ p3_seq_lib.c
+ 
+ dpal_primer.o: dpal.c dpal.h
+-	$(CPP) -c $(CFLAGS) $(P_DEFINES) -o $@ dpal.c
++	$(CXX) -c $(CXXFLAGS) $(P_DEFINES) -o $@ dpal.c
+ 
+ thal_primer.o: thal.c thal.h
+-	$(CPP) -c $(CFLAGS) -ffloat-store $(P_DEFINES) -o $@ thal.c
++	$(CXX) -c $(CXXFLAGS) -ffloat-store $(P_DEFINES) -o $@ thal.c
+ 
+ format_output.o: format_output.c format_output.h libprimer3.h dpal.h thal.h p3_seq_lib.h 
+-	$(CPP) -c $(CFLAGS) $(P_DEFINES) -o $@ format_output.c
++	$(CXX) -c $(CXXFLAGS) $(P_DEFINES) -o $@ format_output.c
+ 
+ ntdpal_main.o: ntdpal_main.c dpal.h
+-	$(CPP) -c $(CC_OPTS) -o $@ ntdpal_main.c
++	$(CXX) -c $(CXXFLAGS) -o $@ ntdpal_main.c
+ 
+ thal_main.o: thal_main.c thal.h
+-	$(CPP) -c $(CFLAGS) -o $@ thal_main.c
++	$(CXX) -c $(CXXFLAGS) -o $@ thal_main.c
+ # We use CC_OPTS above rather than CFLAGS because
+ # gcc 2.7.2 crashes while compiling ntdpal_main.c with -O2
+ 
+ oligotm.o: oligotm.c oligotm.h
+ 
+ primer3_boulder_main.o: primer3_boulder_main.c libprimer3.h dpal.h thal.h oligotm.h format_output.h print_boulder.h read_boulder.h
+-	$(CPP) -c $(CFLAGS) $(P_DEFINES) primer3_boulder_main.c
++	$(CXX) -c $(CXXFLAGS) $(P_DEFINES) primer3_boulder_main.c
+ 
+ primer_test: test
+ 
diff --git a/sci-biology/primer3/metadata.xml b/sci-biology/primer3/metadata.xml
new file mode 100644
index 000000000000..1fbadfaf3b77
--- /dev/null
+++ b/sci-biology/primer3/metadata.xml
@@ -0,0 +1,16 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+  <herd>sci-biology</herd>
+  <longdescription>
+		Primer3 picks primers for PCR reactions, considering: oligonucleotide
+		melting temperature, size, GC content, and primer-dimer possibilities;
+		PCR product size; positional constraints within the source sequence;
+		and miscellaneous other constraints. All of these criteria are
+		user-specifiable as constraints, and some are specifiable as terms in
+		an objective function that characterizes an optimal primer pair.
+	</longdescription>
+  <upstream>
+    <remote-id type="sourceforge">primer3</remote-id>
+  </upstream>
+</pkgmetadata>
diff --git a/sci-biology/primer3/primer3-2.3.5.ebuild b/sci-biology/primer3/primer3-2.3.5.ebuild
new file mode 100644
index 000000000000..4135610c2524
--- /dev/null
+++ b/sci-biology/primer3/primer3-2.3.5.ebuild
@@ -0,0 +1,46 @@
+# Copyright 1999-2015 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=5
+
+inherit eutils toolchain-funcs
+
+DESCRIPTION="Primer Design for PCR reactions"
+HOMEPAGE="http://primer3.sourceforge.net/"
+SRC_URI="mirror://sourceforge/${PN}/${PV}/${P}.tar.gz"
+
+SLOT="0"
+LICENSE="GPL-2"
+IUSE=""
+KEYWORDS="amd64 ppc ~ppc64 ~sparc x86 ~amd64-linux ~x86-linux ~ppc-macos ~sparc-solaris"
+
+DEPEND="dev-lang/perl"
+RDEPEND=""
+
+src_prepare() {
+	epatch "${FILESDIR}"/${PN}-2.3.4-buildsystem.patch
+
+	if [[ ${CHOST} == *-darwin* ]]; then
+		sed -e "s:LIBOPTS ='-static':LIBOPTS =:" -i Makefile || die
+	fi
+
+	tc-export CC CXX AR RANLIB
+}
+
+src_compile() {
+	emake -C src
+}
+
+src_test () {
+	emake -C test | tee "${T}"/test.log
+	grep -q "\[FAILED\]" && die "test failed. See "${T}"/test.log"
+}
+
+src_install () {
+	dobin src/{long_seq_tm_test,ntdpal,oligotm,primer3_core}
+	dodoc src/release_notes.txt example
+	insinto /opt/primer3_config
+	doins -r src/primer3_config/* primer3*settings.txt
+	dohtml primer3_manual.htm
+}
diff --git a/sci-biology/primer3/primer3-2.3.6.ebuild b/sci-biology/primer3/primer3-2.3.6.ebuild
new file mode 100644
index 000000000000..9ba9ff0796c3
--- /dev/null
+++ b/sci-biology/primer3/primer3-2.3.6.ebuild
@@ -0,0 +1,46 @@
+# Copyright 1999-2015 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=5
+
+inherit eutils toolchain-funcs
+
+DESCRIPTION="Primer Design for PCR reactions"
+HOMEPAGE="http://primer3.sourceforge.net/"
+SRC_URI="mirror://sourceforge/${PN}/${PV}/${PN}-src-${PV}.tar.gz"
+
+SLOT="0"
+LICENSE="GPL-2"
+IUSE=""
+KEYWORDS="~amd64 ~ppc ~ppc64 ~sparc ~x86 ~amd64-linux ~x86-linux ~ppc-macos ~sparc-solaris"
+
+DEPEND="dev-lang/perl"
+RDEPEND=""
+
+src_prepare() {
+	epatch "${FILESDIR}"/${PN}-2.3.4-buildsystem.patch
+
+	if [[ ${CHOST} == *-darwin* ]]; then
+		sed -e "s:LIBOPTS ='-static':LIBOPTS =:" -i Makefile || die
+	fi
+
+	tc-export CC CXX AR RANLIB
+}
+
+src_compile() {
+	emake -C src
+}
+
+src_test () {
+	emake -C test | tee "${T}"/test.log
+	grep -q "\[FAILED\]" && die "test failed. See "${T}"/test.log"
+}
+
+src_install () {
+	dobin src/{long_seq_tm_test,ntdpal,oligotm,primer3_core}
+	dodoc src/release_notes.txt example
+	insinto /opt/primer3_config
+	doins -r src/primer3_config/* primer3*settings.txt
+	dohtml primer3_manual.htm
+}