diff options
| -rw-r--r-- | sci-biology/hmmer/ChangeLog | 6 | ||||
| -rw-r--r-- | sci-biology/hmmer/Manifest | 21 | ||||
| -rw-r--r-- | sci-biology/hmmer/files/hmmer-3.0-fix_tests.patch | 23 | ||||
| -rw-r--r-- | sci-biology/hmmer/hmmer-2.3.2-r1.ebuild | 10 | ||||
| -rw-r--r-- | sci-biology/hmmer/hmmer-2.3.2-r2.ebuild | 10 | ||||
| -rw-r--r-- | sci-biology/hmmer/hmmer-3.0.ebuild | 16 |
6 files changed, 64 insertions, 22 deletions
diff --git a/sci-biology/hmmer/ChangeLog b/sci-biology/hmmer/ChangeLog index ffdbdb428829..42334f40b8ec 100644 --- a/sci-biology/hmmer/ChangeLog +++ b/sci-biology/hmmer/ChangeLog @@ -1,6 +1,10 @@ # ChangeLog for sci-biology/hmmer # Copyright 1999-2010 Gentoo Foundation; Distributed under the GPL v2 -# $Header: /var/cvsroot/gentoo-x86/sci-biology/hmmer/ChangeLog,v 1.29 2010/07/16 21:56:53 hwoarang Exp $ +# $Header: /var/cvsroot/gentoo-x86/sci-biology/hmmer/ChangeLog,v 1.30 2010/07/18 10:20:59 xarthisius Exp $ + + 18 Jul 2010; Kacper Kowalik <xarthisius@gentoo.org> hmmer-2.3.2-r1.ebuild, + hmmer-2.3.2-r2.ebuild, hmmer-3.0.ebuild, +files/hmmer-3.0-fix_tests.patch: + Fix tests that use gsl. Make repoman happy. 16 Jul 2010; Markos Chandras <hwoarang@gentoo.org> hmmer-3.0.ebuild: Stable on amd64 wrt bug #328419 diff --git a/sci-biology/hmmer/Manifest b/sci-biology/hmmer/Manifest index 657a407c9d0c..77569a6d979b 100644 --- a/sci-biology/hmmer/Manifest +++ b/sci-biology/hmmer/Manifest @@ -1,7 +1,20 @@ +-----BEGIN PGP SIGNED MESSAGE----- +Hash: SHA1 + +AUX hmmer-3.0-fix_tests.patch 873 RMD160 a41d05e24c4b7a971be14cc9bc25b6f5d9659022 SHA1 e399425bb460c0e94ff1cabf16d0d94d3018edff SHA256 bcf31054c0b646973faa97c27c03dc80c335c43e5e07816a10a65bd596e65d44 DIST hmmer-2.3.2.tar.gz 1024933 RMD160 4bf25fc71f332849c76b0a05bca24e88241cee67 SHA1 aa34cb97cbc43ff3bd92dd111ba5677298fe2d40 SHA256 d20e1779fcdff34ab4e986ea74a6c4ac5c5f01da2993b14e92c94d2f076828b4 DIST hmmer-3.0.tar.gz 3952015 RMD160 681967fd0d2c0104ca9e080688d9652a187a8b45 SHA1 77803c0bdb3ab07b7051a4c68c0564de31940c6d SHA256 6977e6473fcb554b1d5a86dc9edffffa53918c1bd88d7fd20d7499f1ba719e83 -EBUILD hmmer-2.3.2-r1.ebuild 1158 RMD160 b7e130b6b8ea46f1c2b8ecc4073820ef5ee429e9 SHA1 9da503dfe5df93dabe896d4911e0a180c824dba9 SHA256 7b1c363372b53e63da3ee7edb04bec7b8dee6606bf936205b32aaca780215bac -EBUILD hmmer-2.3.2-r2.ebuild 1158 RMD160 12e1bc9bbef0d97b86bf4cabf40803ca28add539 SHA1 fdb710ae9b4f534342bc9798ba6334434e29bb7f SHA256 e637aada0386e9de663ae00dbe0af1a60c68d197c096d2f8a8b9991556e548da -EBUILD hmmer-3.0.ebuild 938 RMD160 dd9db5ebff0ac577463780eb984e1723e795cedb SHA1 e7206a516b5ff4d90727d208ff1c4a59927e608c SHA256 dd66a072fad45480c6cf2d32d655d215754f155916896f9aedf21d10f861fc35 -MISC ChangeLog 4476 RMD160 8d4441d101156954de13dc994839e92549876b66 SHA1 f64a43cce014985eb17cfc7381908e176f4c3f48 SHA256 b80f7dbd7a1f3df804e2beba0597be681856c193e0b12ccfa2e01e880bfd9985 +EBUILD hmmer-2.3.2-r1.ebuild 1167 RMD160 d886db50357d8b0dbb7f8e29bb1712d238ce96d7 SHA1 d8097ea91f630ec34745e65457441f21eea39eac SHA256 1271485785e17ec569eb0d365fba45c69b139b07cb10895915e9a5310d2ef670 +EBUILD hmmer-2.3.2-r2.ebuild 1167 RMD160 e848760e79a34acd82231ce5a53de3c6dec454dc SHA1 9f931c5ccf043dab0b0c061401cf569537094da6 SHA256 c20259de9eaf43c769a1a6b84f10da749018e10e32ae2e04e51995f0b4fd00d9 +EBUILD hmmer-3.0.ebuild 995 RMD160 9415f5f53db707ab7a623d3756e3fc417a783429 SHA1 dc77bfe2ac53ce3f27724682fe1aa606b12d0b57 SHA256 5a4a08636830af2fdc5760d6b6141e2e1e9fd446caa1f72b1f547e9a9ee7daaf +MISC ChangeLog 4679 RMD160 a3773ca9554db15061ce945b6d059a91ebe5f4c6 SHA1 79765217c42ea7cbf76bfc03060e77670d031abc SHA256 ee0663b108356638f64745780d3d6f9f56f8cb892251f53bae1c4bae1f7b22c5 MISC metadata.xml 277 RMD160 a018c1e9848781266ea1b6f0f6637de4f4883ca4 SHA1 62f5832f9fbeed814bae04f46e6a4815ce8e27fa SHA256 1faaa440fc96892d78af96f5450e6931f482410380abcbb5d608138c29799eb4 +-----BEGIN PGP SIGNATURE----- +Version: GnuPG v2.0.15 (GNU/Linux) + +iJwEAQECAAYFAkxC1ZUACgkQIiMqcbOVdxTdmQP8DFHNNCDdSfK9v6N11cEQ2nWC +3qDy0quUqbNfxuM1eqrYKAfSkJ0YL62OzRfgII2J/sNpxwtLuN4JspfKPNGMNZwC +bKJaTm0V/ERFoD1ZSNydzptFkoBvCnR7LRMobg7owh3d3MkWFa0Ij4TtWtWTIN77 +AQ/lw2MGof6JWOlAc+k= +=T0KT +-----END PGP SIGNATURE----- diff --git a/sci-biology/hmmer/files/hmmer-3.0-fix_tests.patch b/sci-biology/hmmer/files/hmmer-3.0-fix_tests.patch new file mode 100644 index 000000000000..983827b0bd46 --- /dev/null +++ b/sci-biology/hmmer/files/hmmer-3.0-fix_tests.patch @@ -0,0 +1,23 @@ +--- easel/Makefile.in ++++ easel/Makefile.in +@@ -26,8 +26,7 @@ + LDFLAGS = @LDFLAGS@ + SIMDFLAGS= @SIMD_CFLAGS@ + CPPFLAGS = @CPPFLAGS@ +-LIBGSL = @LIBGSL@ +-LIBS = @LIBS@ @PTHREAD_LIBS@ ++LIBS = @LIBS@ @LIBGSL@ @PTHREAD_LIBS@ + + # Other tools + # +@@ -252,8 +251,8 @@ + else \ + DFILE=${srcdir}/esl_$${BASENAME}.c ;\ + fi;\ +- echo ${CC} ${CFLAGS} ${SIMDFLAGS} ${DEFS} ${LDFLAGS} -o $@ -I. -I${srcdir} -L. -D$${DFLAG} $${DFILE} -leasel -lm;\ +- ${CC} ${CFLAGS} ${SIMDFLAGS} ${DEFS} ${LDFLAGS} -o $@ -I. -I${srcdir} -L. -D$${DFLAG} $${DFILE} -leasel -lm ++ echo ${CC} ${CFLAGS} ${SIMDFLAGS} ${DEFS} ${LDFLAGS} -o $@ -I. -I${srcdir} -L. -D$${DFLAG} $${DFILE} -leasel -lm ${LIBS};\ ++ ${CC} ${CFLAGS} ${SIMDFLAGS} ${DEFS} ${LDFLAGS} -o $@ -I. -I${srcdir} -L. -D$${DFLAG} $${DFILE} -leasel -lm ${LIBS} + + + # install: installs libeasel.a in ${libdir}/ diff --git a/sci-biology/hmmer/hmmer-2.3.2-r1.ebuild b/sci-biology/hmmer/hmmer-2.3.2-r1.ebuild index 41c59662726c..b186e1e6a093 100644 --- a/sci-biology/hmmer/hmmer-2.3.2-r1.ebuild +++ b/sci-biology/hmmer/hmmer-2.3.2-r1.ebuild @@ -1,6 +1,6 @@ -# Copyright 1999-2008 Gentoo Foundation +# Copyright 1999-2010 Gentoo Foundation # Distributed under the terms of the GNU General Public License v2 -# $Header: /var/cvsroot/gentoo-x86/sci-biology/hmmer/hmmer-2.3.2-r1.ebuild,v 1.11 2008/02/07 14:39:22 grobian Exp $ +# $Header: /var/cvsroot/gentoo-x86/sci-biology/hmmer/hmmer-2.3.2-r1.ebuild,v 1.12 2010/07/18 10:20:59 xarthisius Exp $ DESCRIPTION="Sequence analysis using profile hidden Markov models" LICENSE="GPL-2" @@ -16,9 +16,9 @@ DEPEND="pvm? ( sys-cluster/pvm )" src_compile() { ./configure \ --host=${CHOST} \ - --prefix=${D}/usr \ - --exec_prefix=${D}/usr \ - --mandir=${D}/usr/share/man \ + --prefix="${D}"/usr \ + --exec_prefix="${D}"/usr \ + --mandir="${D}"/usr/share/man \ --enable-lfs \ $(use_enable pvm) \ $(use_enable threads) || die diff --git a/sci-biology/hmmer/hmmer-2.3.2-r2.ebuild b/sci-biology/hmmer/hmmer-2.3.2-r2.ebuild index ec8cd3e0ded0..64ece5e99184 100644 --- a/sci-biology/hmmer/hmmer-2.3.2-r2.ebuild +++ b/sci-biology/hmmer/hmmer-2.3.2-r2.ebuild @@ -1,6 +1,6 @@ -# Copyright 1999-2008 Gentoo Foundation +# Copyright 1999-2010 Gentoo Foundation # Distributed under the terms of the GNU General Public License v2 -# $Header: /var/cvsroot/gentoo-x86/sci-biology/hmmer/hmmer-2.3.2-r2.ebuild,v 1.7 2008/02/07 14:39:22 grobian Exp $ +# $Header: /var/cvsroot/gentoo-x86/sci-biology/hmmer/hmmer-2.3.2-r2.ebuild,v 1.8 2010/07/18 10:20:59 xarthisius Exp $ DESCRIPTION="Sequence analysis using profile hidden Markov models" LICENSE="GPL-2" @@ -16,9 +16,9 @@ DEPEND="pvm? ( sys-cluster/pvm )" src_compile() { econf \ --host=${CHOST} \ - --prefix=${D}/usr \ - --exec_prefix=${D}/usr \ - --mandir=${D}/usr/share/man \ + --prefix="${D}"/usr \ + --exec_prefix="${D}"/usr \ + --mandir="${D}"/usr/share/man \ --enable-lfs \ $(use_enable pvm) \ $(use_enable threads) || die diff --git a/sci-biology/hmmer/hmmer-3.0.ebuild b/sci-biology/hmmer/hmmer-3.0.ebuild index f8e3c212be6e..8611cccff9fc 100644 --- a/sci-biology/hmmer/hmmer-3.0.ebuild +++ b/sci-biology/hmmer/hmmer-3.0.ebuild @@ -1,9 +1,11 @@ # Copyright 1999-2010 Gentoo Foundation # Distributed under the terms of the GNU General Public License v2 -# $Header: /var/cvsroot/gentoo-x86/sci-biology/hmmer/hmmer-3.0.ebuild,v 1.2 2010/07/16 21:56:53 hwoarang Exp $ +# $Header: /var/cvsroot/gentoo-x86/sci-biology/hmmer/hmmer-3.0.ebuild,v 1.3 2010/07/18 10:20:59 xarthisius Exp $ EAPI="2" +inherit eutils + DESCRIPTION="Sequence analysis using profile hidden Markov models" HOMEPAGE="http://hmmer.janelia.org/" SRC_URI="ftp://selab.janelia.org/pub/software/hmmer3/${PV}/${P}.tar.gz" @@ -17,22 +19,22 @@ DEPEND="mpi? ( virtual/mpi ) gsl? ( >=sci-libs/gsl-1.12 )" RDEPEND="${DEPEND}" +src_prepare() { + epatch "${FILESDIR}"/${P}-fix_tests.patch +} + src_configure() { econf $(use_enable sse) \ $(use_enable mpi) \ $(use_enable threads) \ - $(use_with gsl) || die + $(use_with gsl) } src_install() { - einstall || die + emake DESTDIR="${D}" install || die dolib src/libhmmer.a || die dolib easel/libeasel.a || die insinto /usr/share/${PN} doins -r tutorial || die dodoc RELEASE-NOTES Userguide.pdf } - -src_test() { - emake check || die -} |