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

Package-Manager: portage-2.2.0_alpha148/cvs/Linux x86_64
Manifest-Sign-Key: 0x70EB7916

5 files changed, 198 insertions, 49 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/Manifest b/sci-biology/primer3/Manifest
index 5fba31cd1566..274825699645 100644
--- a/sci-biology/primer3/Manifest
+++ b/sci-biology/primer3/Manifest
@@ -2,21 +2,21 @@
 Hash: SHA256
 
 AUX primer3-1.1.4-ldflags.patch 882 SHA256 10ef0f1491df83c60f5919fcc461a0864e12a0303d8242f4e3ea1c2f8963c436 SHA512 8e9d48b8c504db96a3e632189527e4bab54765686d153560d415c2ef0d7bc5f8d0e6ba350fd571b6d1c3386ef745be108f866b52ceebab0f0412155bf079a306 WHIRLPOOL b6fb36622c44d078052e9a09f4389d6e6cdb63d1a7bd45dc6b016767b369954a8040c6ac01bb8131520034863edc9ac246b94fd64265118890224e7dc73227f6
-DIST primer3-1.1.4.tar.gz 974628 SHA256 1cb045791afd3c4033956a65687ca0c1b1a6607ac84705bf4ed7d7151691980b
+AUX primer3-2.3.4-buildsystem.patch 5086 SHA256 69753406bccdbc27723ae2e579dd0e301334cfa1fa9a755c6688afd13a20121d SHA512 02dbd00d51626c2dd826dd42fad138da58b2b3d0bfd06c31dafa1b64697c86999a4165d1a866c15f84699fa13296102e21cce39ea3d00e28a7007d69ba40f96f WHIRLPOOL 7d1038388398dff811ff14094b952610e01c27816fa012d1d561ee43c2e63632582348c7d190c9dfc986f7092f3dc7f17747b1036233e07783b43ba5f9f92daa
 DIST primer3-2.2.3.tar.gz 2284282 SHA256 2e68d638119bfcac12571da351cf261e28a3dd4b32c89074ce17065931a98774
 DIST primer3-2.3.0.tar.gz 2596929 SHA256 6b6721f8ae3b45dc8ac81d6a230012f79d56f840274e88dc5001ec718625e834 SHA512 56c67e19749d55e10bf2eb5728de0a8d72d4b016b477928e737b3485e583e3060faca2a13f0ad46f75e60d591e72dd0970dfef9acd65151463270a731a4e53f8 WHIRLPOOL b455046c268cba17b7d79730d39e350a6e85ce0caa649e2d585cac3905c9d47480cf3d9c6158bc7556c2a8cad2feaed767d03f6b099baa07f7069c105c06546f
 DIST primer3-2.3.1.tar.gz 2539917 SHA256 34a27e5c442e41fca1202be4fbe90f97c791fa93e2235e28b625574ccf90c137 SHA512 ff035fc1bc96ff4ce1fa29d867f01fc2df62e3bcff23de62c753cef3a92a7209ef8fda27dc19cdf0173aa98c5b2fa36ad0b58cca9a7d225be26f3ebc970b08f8 WHIRLPOOL c2801ea96733729121a70ef77a710d1e0668ecdc5243ef70b4073930b421b708bf771805eec8d26d39af12f1d5b57dbbaf0384d565e887d26b916149dd5e23d2
-EBUILD primer3-1.1.4-r2.ebuild 966 SHA256 fb2ea764406931476ae46e9878aa3591b8a23f972be52b57a76ae4fa2085347a SHA512 a28dd5694d5ba255775929c2b8c99980d8b150da6c930f9bc57d522d7371c992157e5dc4e4397b70799c1f86165ce449e17fe37ee48fd0180e9000f9d5c9fe7e WHIRLPOOL 317a0a0d6f5a1999ea7521156ae52c07671030623e263d791304a9e4f659a2dc1ee206a3d1a5b1040a4fb8d2d2617192228422ed2dafc077101eb8bef9049e6c
+DIST primer3-2.3.4.tar.gz 2525173 SHA256 0f03dab554acb4073c1f59df280df7151cb96925c5218d56cdae6b051feb3d38 SHA512 ebf5cbfb3d0cafcb57131b377f57ca7972e61bbfdadf94511d60247c8011adcb1f3f88ffe1a41eb59e24ff1a5c00c9f088a57e1a9d1fc69b923e4cd157663d79 WHIRLPOOL 2a1f22f6d79e84c8920509e000f4653bd5a4b8e4fb6056811d95071fa6a86a347581b4868d5ed515343911c3a328b4ab425503253bfd717816962b6374d13a4c
 EBUILD primer3-2.2.3.ebuild 1335 SHA256 ed8de7c2dc7e7250de0e73f8af2298e6d8b385155c6a3605f1a539c20ec7dedd SHA512 de7d2f048a5750852798ec417d34cdacf46199609f21cb594c991ff0b87253779b9931c42bc2d3b867eb1a74011977aa5106fbf00866adbd76ca1c1d249cfa93 WHIRLPOOL f3a165d8e9454769fe3b088cba39006c0e74456d2cc645006c450e94aaf026fab7b1ade349548673d22137c2be9be3f50c0ad64558bd61b76f71dd9d025a7d3c
 EBUILD primer3-2.3.0.ebuild 1231 SHA256 dec94ce5572c2292dff38d7977c960553c381572d77cbd0fe6967e837f0eaab5 SHA512 01115f231f73058fa22b00e994736ca67b84fd992f7a4a876401bcf2d3b01b5cd844e67cf2082dfba4d1241dce76328ee767b6152b862241ce0e954cfc607846 WHIRLPOOL ccaec6f4314601d21a4fda99349bb0f3e088cac77a7b9ad0d9a63a3c6b0c6c7c60200630b4682df2b66b9983569aaa5d0846282dbfcfe8f2eab5c86e1e5c3efb
 EBUILD primer3-2.3.1.ebuild 1232 SHA256 1467ebb2358bfedb25614ececcbce97db77ab9c60f37cb191f8fc27f70c62334 SHA512 21851efb4eff25de612a45b234b54fd00b2f3698736febc930b4c03b39908868c9346f8fb8c8f37db2712d42ef4e699651b5e8267f174545b9f469e1283a6952 WHIRLPOOL ef533f563f9e4c21bcd558cb9dc9984e771d9357619c9ff157c18fec067beed87b49a05db778fdec04d51507e7582100d1bf1d9c8cc4ef789df786c624dd840d
-MISC ChangeLog 5004 SHA256 59990c21ec8aeec1d3c635c79af54ddf9ccc4919975df197138e112928494c55 SHA512 64774ebe370bbecc470ed05014b74d65ff73fa7b07f81f98dcd3a50abf8cfbc254c7af6a1ac1e04d9755db1d5dffe785b8d6969e5bed934f17f40e678d02c587 WHIRLPOOL d6d59690f5e4b290e3c488de1c58cad59ff34a3c33b54bece525e5f067924f5ec4424994d6db10c863592b73799bab83ad68f61fadd17e2bb41a8a70cdc8fa78
+EBUILD primer3-2.3.4.ebuild 1052 SHA256 6a7f0a427d89f8dafe17581720585b0da681c208019cbdf24b733900f0eb85a2 SHA512 bf5ca3eb8a9329f101cf62fc1dde92c3971a9a29339ef164a747b7de32640e54f1145ec29deaf3d18f86e52d3a48635fa39a41d8b57a3f653168821355425928 WHIRLPOOL c64ae784d8d2f2b803020dfe88667d0332617d92747d593d27d8bd830ed2143a1ad142c608731ce8894560a84ef124d05d839b7bf92e104e5845b2cb364084ba
+MISC ChangeLog 5210 SHA256 ae7bb616067bc922bebca320ad278bdda7d4aa3216d206dadd2de3dbc6214e32 SHA512 715a4dd5509362a7efbce170935502e8a3a92afd0915c8f01e4522f989a0a2afd929d69a855b3fa84154c4ced3389ddc12ba37476d430d09d243c3c7edce87bb WHIRLPOOL e5c0b24d127f7553f5de39996c734659a0ec48db105e6f9ba769302483d280036028d6bb73932bd2b35ebc594d211a8d6b91b36130ee15190cd347c6cb4022f2
 MISC metadata.xml 624 SHA256 f612edc94f6538c9acf99caadc2a7d6e33cac6f933db9deafae777c7a45505bb SHA512 91b936b1814b144e4f0655ec1d45ef2221ea3e1346027c8ee6e5f4938c0fe8479131aa1abf7b45e7814ab85224cb4a63b64437c2958befb91d2963b2853d1a92 WHIRLPOOL 7e23f7b6826e38e21310c9be5db74b6fa7b0de7027ea1280e223df867f6287a2fa9c0afb62bdb8a4dc85dae93afe1502cc5280b3106ed15378a86516312b47b9
 -----BEGIN PGP SIGNATURE-----
 Version: GnuPG v2.0.19 (GNU/Linux)
-Comment: GPGTools - http://gpgtools.org
 
-iEYEAREIAAYFAlAH++YACgkQgAnW8HDreRYagACfeBe04cCFwZKxmdk7fr8qQC9M
-GjQAnjo07cx1LoBrg8qshkTShJ8V3ssh
-=yatg
+iEYEAREIAAYFAlDIeEYACgkQgAnW8HDreRZjrwCgx4sJHPLMT0hmo70fCjVfieZV
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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
+}