diff options
Diffstat (limited to 'sci-biology')
| -rw-r--r-- | sci-biology/primer3/ChangeLog | 6 | ||||
| -rw-r--r-- | sci-biology/primer3/Manifest | 14 | ||||
| -rw-r--r-- | sci-biology/primer3/metadata.xml | 4 | ||||
| -rw-r--r-- | sci-biology/primer3/primer3-2.3.1.ebuild | 19 | ||||
| -rw-r--r-- | sci-biology/primer3/primer3-2.3.4.ebuild | 5 |
5 files changed, 26 insertions, 22 deletions
diff --git a/sci-biology/primer3/ChangeLog b/sci-biology/primer3/ChangeLog index ecdf98c67cab..8448af12eed4 100644 --- a/sci-biology/primer3/ChangeLog +++ b/sci-biology/primer3/ChangeLog @@ -1,6 +1,10 @@ # 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 1.33 2012/12/12 12:27:49 jlec Exp $ +# $Header: /var/cvsroot/gentoo-x86/sci-biology/primer3/ChangeLog,v 1.34 2012/12/12 13:10:00 jlec Exp $ + + 12 Dec 2012; Justin Lecher <jlec@gentoo.org> primer3-2.3.1.ebuild, + primer3-2.3.4.ebuild, metadata.xml: + Fix test *primer3-2.3.4 (12 Dec 2012) diff --git a/sci-biology/primer3/Manifest b/sci-biology/primer3/Manifest index 274825699645..172fbc308462 100644 --- a/sci-biology/primer3/Manifest +++ b/sci-biology/primer3/Manifest @@ -9,14 +9,14 @@ DIST primer3-2.3.1.tar.gz 2539917 SHA256 34a27e5c442e41fca1202be4fbe90f97c791fa9 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 -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 +EBUILD primer3-2.3.1.ebuild 1145 SHA256 2ad27b842299f1bc97ca8a0a09ad72f336403ca70c28e0115d3d186d5961c786 SHA512 1f398bcedf28494b85b829b24c6c6960634bc112d19bdea88125a91aa9ea3fe8ae0f4fda331901d7da112792077690f9d5d9eca85917b500bded1c7eb3a0cb77 WHIRLPOOL fb027bd48ce3d688329c4da2d9a8b749944f7981d87422c163e92f74650a98e3ff8aff4b85c021f13655028759bf761bd54cfa6b636d5f27d589fa4a92fbaa03 +EBUILD primer3-2.3.4.ebuild 1138 SHA256 7b6ce1f2801634df77987ed5ebbb7b5f4e8dc5d32dca1adb81fbb9ebe5ee6fd2 SHA512 7ca9fd25169c521229fb41f422e367ac66ccaa6bc383fb21ac2dd3569607a45cb262f52d8024a2563d72f5994d37f542ce2d0ebc1772c3d1c1294f4ee3278c34 WHIRLPOOL d53d8073181fd3b9f6e88f0df6de5fbd3fc98688165300fb833dc2e6712035e80d539318ba52e77a7abd1e9beeedd73b3fb36d9181336ab1d89ba9d21b285991 +MISC ChangeLog 5329 SHA256 b4934f9dde4752095efb2fec065792b6c1b6218cf5b2faf04b08eb187cf2dfee SHA512 45dcfb2a07236643bf5de9f7909a52be622f30a34e058810a61424c10aff930fd57e0026c9aff73c5500736ae64aa84a93c5232db8d914498ab42597cf759450 WHIRLPOOL b213ba9095f5a18a20b06e2983bbbdf3c165860541ebd0b0ea8370292938203d01f2a7a20411ee6aaeea4c638e660d3476cf61351a7fd21afaeb22323f176497 +MISC metadata.xml 626 SHA256 7f92fdb9d901cce63f02bce075366ea0fcd34c54809c6cff6a5074671e528c97 SHA512 cd1df947da6ce9bfc424658af5149a431f9f049938d74b0ff83e5fe585829006dc4c4707833e7b4308242fed6e92b3c83263754aadadb2e22c76cf964c32fc25 WHIRLPOOL 5a8f088e9fb2a29b73cc6ad8da1808314f38f04e611b96a76de1054c290fbb662177b757c8a198885fa03c0f881376cebe95906606279193d2852f443176ef04 -----BEGIN PGP SIGNATURE----- Version: GnuPG v2.0.19 (GNU/Linux) -iEYEAREIAAYFAlDIeEYACgkQgAnW8HDreRZjrwCgx4sJHPLMT0hmo70fCjVfieZV -JmsAoMgwBpVcfNtWaEElyAPTFxd8zVVC -=IODu +iEYEAREIAAYFAlDIgikACgkQgAnW8HDreRZJcgCaAt1S4KR00skQ/rF53yULytHu +Rf8AoLbI5XpaYhwxHjS8aTjLzE7i8nAh +=IMmA -----END PGP SIGNATURE----- diff --git a/sci-biology/primer3/metadata.xml b/sci-biology/primer3/metadata.xml index ab4edb62b7b6..a72b3a5d05f6 100644 --- a/sci-biology/primer3/metadata.xml +++ b/sci-biology/primer3/metadata.xml @@ -1,8 +1,8 @@ <?xml version="1.0" encoding="UTF-8"?> <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> - <herd>sci-biology</herd> - <longdescription> + <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; diff --git a/sci-biology/primer3/primer3-2.3.1.ebuild b/sci-biology/primer3/primer3-2.3.1.ebuild index c42182fb1bbe..590d4105ac07 100644 --- a/sci-biology/primer3/primer3-2.3.1.ebuild +++ b/sci-biology/primer3/primer3-2.3.1.ebuild @@ -1,14 +1,14 @@ # Copyright 1999-2012 Gentoo Foundation # Distributed under the terms of the GNU General Public License v2 -# $Header: /var/cvsroot/gentoo-x86/sci-biology/primer3/primer3-2.3.1.ebuild,v 1.1 2012/07/19 12:21:52 jlec Exp $ +# $Header: /var/cvsroot/gentoo-x86/sci-biology/primer3/primer3-2.3.1.ebuild,v 1.2 2012/12/12 13:10:00 jlec Exp $ EAPI=4 -inherit toolchain-funcs +inherit eutils toolchain-funcs DESCRIPTION="Primer Design for PCR reactions" HOMEPAGE="http://primer3.sourceforge.net/" -SRC_URI="mirror://sourceforge/${PN}/${P}.tar.gz" +SRC_URI="mirror://sourceforge/${PN}/${PV}/${P}.tar.gz" SLOT="0" LICENSE="GPL-2" @@ -19,15 +19,13 @@ DEPEND="dev-lang/perl" RDEPEND="" src_prepare() { + epatch "${FILESDIR}"/${PN}-2.3.4-buildsystem.patch + if [[ ${CHOST} == *-darwin* ]]; then sed -e "s:LIBOPTS ='-static':LIBOPTS =:" -i Makefile || die fi - perl -i -ne 's/\$\(CPP\)/'$(tc-getCXX)'/; print unless /^(CC|CPP|CFLAGS|LDFLAGS)\s*=/' src/Makefile || die - sed \ - -e '/oligotm/s:-o $@:$(LDFLAGS) -o $@:g' \ - -e '/long_seq_tm_test/s:-o $@:$(LDFLAGS) -o $@:g' \ - -e 's:CFLAGS:CXXFLAGS:g' \ - -i src/Makefile || die + + tc-export CC CXX AR RANLIB } src_compile() { @@ -35,7 +33,8 @@ src_compile() { } src_test () { - emake -C test + emake -C test | tee "${T}"/test.log + grep -q "\[FAILED\]" && die "test failed. See "${T}"/test.log" } src_install () { diff --git a/sci-biology/primer3/primer3-2.3.4.ebuild b/sci-biology/primer3/primer3-2.3.4.ebuild index 86815c57eaee..628c567c378d 100644 --- a/sci-biology/primer3/primer3-2.3.4.ebuild +++ b/sci-biology/primer3/primer3-2.3.4.ebuild @@ -1,6 +1,6 @@ # 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 $ +# $Header: /var/cvsroot/gentoo-x86/sci-biology/primer3/primer3-2.3.4.ebuild,v 1.2 2012/12/12 13:10:00 jlec Exp $ EAPI=4 @@ -33,7 +33,8 @@ src_compile() { } src_test () { - emake -C test + emake -C test | tee "${T}"/test.log + grep -q "\[FAILED\]" && die "test failed. See "${T}"/test.log" } src_install () { |