sci-biology/primer3: Version Bump, #446982; cleaned old

(Portage version: 2.2.0_alpha148/cvs/Linux x86_64, signed Manifest commit with key 70EB7916)

4 files changed, 191 insertions, 42 deletions

diff --git a/sci-biology/primer3/ChangeLog b/sci-biology/primer3/ChangeLog
index c8a7df6ca87e..ecdf98c67cab 100644
--- a/sci-biology/primer3/ChangeLog
+++ b/sci-biology/primer3/ChangeLog
@@ -1,6 +1,12 @@
 # ChangeLog for sci-biology/primer3
 # Copyright 1999-2012 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/primer3/ChangeLog,v 1.32 2012/07/19 12:21:52 jlec Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/primer3/ChangeLog,v 1.33 2012/12/12 12:27:49 jlec Exp $
+
+*primer3-2.3.4 (12 Dec 2012)
+
+  12 Dec 2012; Justin Lecher <jlec@gentoo.org> -primer3-1.1.4-r2.ebuild,
+  +primer3-2.3.4.ebuild, +files/primer3-2.3.4-buildsystem.patch:
+  Version Bump, #446982; cleaned old
 
 *primer3-2.3.1 (19 Jul 2012)
 
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..51ab913b48cf
--- /dev/null
+++ b/sci-biology/primer3/files/primer3-2.3.4-buildsystem.patch
@@ -0,0 +1,139 @@
+ src/Makefile | 59 ++++++++++++++++++++++++++++++-----------------------------
+ 1 file changed, 30 insertions(+), 29 deletions(-)
+
+diff --git a/src/Makefile b/src/Makefile
+index 607ab45..b23ec23 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'
+ 
+@@ -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/primer3-1.1.4-r2.ebuild b/sci-biology/primer3/primer3-1.1.4-r2.ebuild
deleted file mode 100644
index 0076c5ed19fb..000000000000
--- a/sci-biology/primer3/primer3-1.1.4-r2.ebuild
+++ /dev/null
@@ -1,41 +0,0 @@
-# Copyright 1999-2011 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/primer3/primer3-1.1.4-r2.ebuild,v 1.2 2011/11/23 08:10:50 jlec Exp $
-
-EAPI="3"
-
-inherit eutils toolchain-funcs
-
-DESCRIPTION="Primer Design for PCR reactions"
-HOMEPAGE="http://primer3.sourceforge.net/"
-SRC_URI="mirror://sourceforge/${PN}/${P}.tar.gz"
-
-SLOT="0"
-LICENSE="whitehead"
-IUSE=""
-KEYWORDS="~amd64 ~ppc ~ppc64 ~sparc ~x86 ~amd64-linux ~x86-linux ~ppc-macos ~sparc-solaris"
-
-DEPEND="dev-lang/perl"
-RDEPEND=""
-
-S=${WORKDIR}/src
-
-src_prepare() {
-
-	[[ ${CHOST} == *-darwin* ]] && \
-		sed -e "s:LIBOPTS ='-static':LIBOPTS =:" -i Makefile
-	epatch "${FILESDIR}"/${P}-ldflags.patch
-}
-
-src_compile() {
-	emake -e CC="$(tc-getCC)" || die
-}
-
-src_test () {
-	emake primer_test || die
-}
-
-src_install () {
-	dobin long_seq_tm_test ntdpal oligotm primer3_core || die
-	dodoc ../{how-to-cite.txt,README.txt,example} || die
-}
diff --git a/sci-biology/primer3/primer3-2.3.4.ebuild b/sci-biology/primer3/primer3-2.3.4.ebuild
new file mode 100644
index 000000000000..86815c57eaee
--- /dev/null
+++ b/sci-biology/primer3/primer3-2.3.4.ebuild
@@ -0,0 +1,45 @@
+# Copyright 1999-2012 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/primer3/primer3-2.3.4.ebuild,v 1.1 2012/12/12 12:27:49 jlec Exp $
+
+EAPI=4
+
+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}"/${P}-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
+}
+
+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
+}