diff options
| -rw-r--r-- | sci-biology/primer3/ChangeLog | 8 | ||||
| -rw-r--r-- | sci-biology/primer3/Manifest | 14 | ||||
| -rw-r--r-- | sci-biology/primer3/files/primer3-2.3.4-buildsystem.patch | 139 | ||||
| -rw-r--r-- | sci-biology/primer3/primer3-1.1.4-r2.ebuild | 41 | ||||
| -rw-r--r-- | sci-biology/primer3/primer3-2.3.4.ebuild | 45 |
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 +JmsAoMgwBpVcfNtWaEElyAPTFxd8zVVC +=IODu -----END PGP SIGNATURE----- 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 +} |