From 431536b65f189da968a7891f6b379fe64285f05b Mon Sep 17 00:00:00 2001 From: "Justin Lecher (jlec)" Date: Wed, 11 Nov 2009 23:18:56 +0100 Subject: fasta version bump and fix of chatastrophic ebuild, src_test is still broken (Portage version: 2.2_rc49/git/Linux x86_64) (Signed Manifest commit) --- sci-biology/fasta/ChangeLog | 11 +++- sci-biology/fasta/Manifest | 21 +++++--- sci-biology/fasta/fasta-35.3.6.ebuild | 51 ------------------ sci-biology/fasta/fasta-35.4.8.ebuild | 52 ------------------ sci-biology/fasta/fasta-35.4.9.ebuild | 79 ++++++++++++++++++++++++++++ sci-biology/fasta/files/35.4.9-ldflags.patch | 26 +++++++++ 6 files changed, 130 insertions(+), 110 deletions(-) delete mode 100644 sci-biology/fasta/fasta-35.3.6.ebuild delete mode 100644 sci-biology/fasta/fasta-35.4.8.ebuild create mode 100644 sci-biology/fasta/fasta-35.4.9.ebuild create mode 100644 sci-biology/fasta/files/35.4.9-ldflags.patch diff --git a/sci-biology/fasta/ChangeLog b/sci-biology/fasta/ChangeLog index e1143c67b..4fb40ad41 100644 --- a/sci-biology/fasta/ChangeLog +++ b/sci-biology/fasta/ChangeLog @@ -1,7 +1,16 @@ # ChangeLog for sci-biology/fasta -# Copyright 1999-2008 Gentoo Foundation; Distributed under the GPL v2 +# Copyright 1999-2009 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ +*fasta-35.4.9 (11 Nov 2009) + + 11 Nov 2009; Justin Lecher (jlec) + +files/35.4.9-ldflags.patch, -fasta-35.3.6.ebuild, -fasta-35.4.8.ebuild, + +fasta-35.4.9.ebuild: + Version bump + Fix of the ebuild + src_test is broken + 06 Jul 2008; Jeff Gardner ChangeLog: Initial import, thanks to Jose Maria Fernandez Gonzalez. diff --git a/sci-biology/fasta/Manifest b/sci-biology/fasta/Manifest index 261337882..006c5c2a1 100644 --- a/sci-biology/fasta/Manifest +++ b/sci-biology/fasta/Manifest @@ -1,6 +1,15 @@ -DIST fasta-35.3.6.tar.gz 614606 RMD160 f0d8a5514a430d592a030afd69348413d1ac8c63 SHA1 335f2f3732f9b03ba0d6102fd94674f5ac616297 SHA256 4525232e2a1a42388921760d75c5ece6e058d9ce2c35cba074ce544d6e56df15 -DIST fasta-35.4.8.tar.gz 630387 RMD160 9504f8924594cfa2fc8c7d21dd7da2e80ff678f4 SHA1 f076dde53c4f59887828bf919e3060831912aea9 SHA256 2347ca3af2c9f3ee43148852cd31dc7a89a2cb5d130280d0ec0d3287cb833d33 -EBUILD fasta-35.3.6.ebuild 1171 RMD160 058a268f6e8f9d2dcf4f4479303d6b328d5f1a05 SHA1 446781c0ce28898309b77c1311f83580f16a5537 SHA256 2456a736004083126ac3041773810bc612b66e3af0f77fd3bed85467000fcc3c -EBUILD fasta-35.4.8.ebuild 1185 RMD160 1beb885b72ccf998bce824ade6e6677f7730369e SHA1 9b194bcac3617962802a0f412d7f6ddf11403dc8 SHA256 e030d3e8c7b2d4b686cfda5896a71f899c3c9ab1599d343444f3092ac219f4cb -MISC ChangeLog 237 RMD160 a2ce23a123f5d353398a267d84bc81663f034abc SHA1 103e50d0f241a7e4d467f627cf98983056e640b8 SHA256 002d044f54613ed80b5b8e261d91f0d56f90cb42745a044560090dc1d3749b80 -MISC metadata.xml 307 RMD160 0993f9568f191dc314f2f742417cca45456af8ff SHA1 94fe99112096a2e23c199fbf22aa8ad8be475b7e SHA256 e998d3ee356e25351b86abf709647bde3856ccceafce876ff17dbd8ea0a8d41b +-----BEGIN PGP SIGNED MESSAGE----- +Hash: SHA1 + +AUX 35.4.9-ldflags.patch 1036 RMD160 49cfa8e067824012b46086e6878699dcadf2938e SHA1 1013030756dfadf0ef9d04305e4500701c9a3561 SHA256 21b6c290ca565c50376da61cd980f21f7a96598ea5da046294321d8d6be5d5fe +DIST fasta-35.4.9.tar.gz 631440 RMD160 753d18142932e88b0f2e3d82e460063331be7fce SHA1 bd3d0c5c8419159f4fd80ea1a4557e4a36cd49d1 SHA256 49d18880e20c6ee717844884746415916ca4c29b368c1e7458f6782795543966 +EBUILD fasta-35.4.9.ebuild 1486 RMD160 180a8defedde7717d5eb50235c33c040b406e5ce SHA1 31a0286083c507b09b75baefbd444b76d6586a4f SHA256 c41c71ca8a230a4a7ce97db15aa260b77556e350226aa5030e5d729cbaf09be6 +MISC ChangeLog 479 RMD160 5b17cd6f9bd7672043bd273a7ecc0ef8b88beaaf SHA1 02c07c282c0a6765c92936b262deab5d67c57472 SHA256 4e97be28c22a28f0b9a18236e14b124399f9106ffdf09a10fd2baf521577faf5 +MISC metadata.xml 382 RMD160 75d40acc3b5a8fb8ea656817aa204cc524ef7059 SHA1 7c7a5b42930a24b3fb2609716b7238ba3193e18d SHA256 2d9cc9ccec1bcd41294ff75ff29b4b449868a1dc2cd763ac28ee946a90611185 +-----BEGIN PGP SIGNATURE----- +Version: GnuPG v2.0.11 (GNU/Linux) + +iEYEARECAAYFAkr7OFAACgkQgAnW8HDreRbVBwCfe5Y3N++g1NsYPolLntfFIJ+/ +uwAAn3WjHRZTa1D+NvAhT1R749Vcuk30 +=KYb6 +-----END PGP SIGNATURE----- diff --git a/sci-biology/fasta/fasta-35.3.6.ebuild b/sci-biology/fasta/fasta-35.3.6.ebuild deleted file mode 100644 index 39c6c5247..000000000 --- a/sci-biology/fasta/fasta-35.3.6.ebuild +++ /dev/null @@ -1,51 +0,0 @@ -# Copyright 1999-2008 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 -# $Header: $ - -DESCRIPTION="FASTA is a DNA and Protein sequence alignment software package" -HOMEPAGE="http://fasta.bioch.virginia.edu/fasta_www2/fasta_down.shtml" -SRC_URI="http://faculty.virginia.edu/wrpearson/${PN}/${PN}3/${P}.tar.gz" - -LICENSE="fasta" -SLOT="0" -KEYWORDS="~x86 ~amd64" -IUSE="debug icc sse2" - -DEPEND="icc? ( dev-lang/icc )" -RDEPEND="" - -CC_ALT= -CFLAGS_ALT= -ALT= - -if use debug ; then - CFLAGS_ALT=-g -DDEBUG -fi - -if use icc ; then - CC_ALT=icc - ALT="${ALT}_icc" -else - CC_ALT=gcc -fi - -if use sse2 ; then - ALT="${ALT}_sse2" - CFLAGS_ALT="${CFLAGS_ALT} -msse2" - if ! use icc ; then - CFLAGS_ALT="${CFLAGS_ALT} -ffast-math" - fi -fi - -src_compile() { - einfo "Using $CC_ALT compiler" - make -f Makefile.linux${ALT} CC="${CC_ALT} ${CFLAGS}" all -} - -src_install() { - dodir /usr/bin - make -f Makefile.linux${ALT} CC="${CC_ALT} ${CFLAGS}" XDIR="${D}/usr/bin" install - doman fasta3.1 fasta35.1 fastf3.1 fasts3.1 map_db.1 prss3.1 ps_lav.1 pvcomp.1 - dodoc COPYRIGHT FASTA_LIST README README.versions fasta20.doc - dohtml changes_v34.html changes_v35.html search.html -} diff --git a/sci-biology/fasta/fasta-35.4.8.ebuild b/sci-biology/fasta/fasta-35.4.8.ebuild deleted file mode 100644 index 403d84073..000000000 --- a/sci-biology/fasta/fasta-35.4.8.ebuild +++ /dev/null @@ -1,52 +0,0 @@ -# Copyright 1999-2008 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 -# $Header: $ - -DESCRIPTION="FASTA is a DNA and Protein sequence alignment software package" -HOMEPAGE="http://fasta.bioch.virginia.edu/fasta_www2/fasta_down.shtml" -SRC_URI="http://faculty.virginia.edu/wrpearson/${PN}/${PN}3/${P}.tar.gz" - -LICENSE="fasta" -SLOT="0" -KEYWORDS="~x86 ~amd64" -IUSE="debug icc sse2" - -DEPEND="icc? ( dev-lang/icc )" -RDEPEND="" - -CC_ALT= -CFLAGS_ALT= -ALT= - -if use debug ; then - CFLAGS_ALT=-g -DDEBUG -fi - -if use icc ; then - CC_ALT=icc - ALT="${ALT}_icc" -else - CC_ALT=gcc -fi - -if use sse2 ; then - ALT="${ALT}_sse2" - CFLAGS_ALT="${CFLAGS_ALT} -msse2" - if ! use icc ; then - CFLAGS_ALT="${CFLAGS_ALT} -ffast-math" - fi -fi - -src_compile() { - einfo "Using $CC_ALT compiler" -# cd src - make -f make/Makefile.linux${ALT} CC="${CC_ALT} ${CFLAGS}" all -} - -src_install() { - dodir /usr/bin - make -f Makefile.linux${ALT} CC="${CC_ALT} ${CFLAGS}" XDIR="${D}/usr/bin" install - doman fasta3.1 fasta35.1 fastf3.1 fasts3.1 map_db.1 prss3.1 ps_lav.1 pvcomp.1 - dodoc COPYRIGHT FASTA_LIST README README.versions fasta20.doc - dohtml changes_v34.html changes_v35.html search.html -} diff --git a/sci-biology/fasta/fasta-35.4.9.ebuild b/sci-biology/fasta/fasta-35.4.9.ebuild new file mode 100644 index 000000000..c57529f9c --- /dev/null +++ b/sci-biology/fasta/fasta-35.4.9.ebuild @@ -0,0 +1,79 @@ +# Copyright 1999-2009 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Header: $ + +EAPI="2" + +inherit eutils + +DESCRIPTION="FASTA is a DNA and Protein sequence alignment software package" +HOMEPAGE="http://fasta.bioch.virginia.edu/fasta_www2/fasta_down.shtml" +SRC_URI="http://faculty.virginia.edu/wrpearson/${PN}/${PN}3/${P}.tar.gz" + +LICENSE="fasta" +SLOT="0" +KEYWORDS="~x86 ~amd64" +IUSE="debug icc sse2 test" + +DEPEND=" + icc? ( dev-lang/icc ) + test? ( app-shells/tcsh )" +RDEPEND="" + +src_prepare() { + CC_ALT= + CFLAGS_ALT= + ALT= + + if use debug ; then + CFLAGS_ALT="-g -DDEBUG" + fi + + if use icc ; then + CC_ALT=icc + ALT="${ALT}_icc" + else + CC_ALT=gcc + + case $(uname -m) in + + i*86 ) + ALT="32";; + + x86_64 ) + ALT="64";; + + esac + fi + + if use sse2 ; then + ALT="${ALT}_sse2" + CFLAGS_ALT="${CFLAGS_ALT} -msse2" + if ! use icc ; then + CFLAGS_ALT="${CFLAGS_ALT} -ffast-math" + fi + fi + + export CC_ALT="${CC_ALT}" + export CFLAGS_ALT="${CFLAGS_ALT}" + export ALT="${ALT}" + + epatch "${FILESDIR}"/${PV}-ldflags.patch +} + +src_compile() { + einfo "Using $CC_ALT compiler" + cd src + make -f ../make/Makefile.linux${ALT} CC="${CC_ALT} ${CFLAGS} ${CFLAGS_ALT}" HFLAGS="${LDFLAGS} -o" all || die +} + +src_test() { + cd test + PATH="${S}/bin:${PATH}" csh test.sh +} + +src_install() { + dobin bin/* || die + doman doc/{prss3.1,fasta35.1,pvcomp.1,fasts3.1,fastf3.1,ps_lav.1,map_db.1} || die + dodoc FASTA_LIST README doc/{README.versions,readme*,fasta*,changes*} || die +} diff --git a/sci-biology/fasta/files/35.4.9-ldflags.patch b/sci-biology/fasta/files/35.4.9-ldflags.patch new file mode 100644 index 000000000..c3b7a9b56 --- /dev/null +++ b/sci-biology/fasta/files/35.4.9-ldflags.patch @@ -0,0 +1,26 @@ +diff --git a/make/Makefile.pcom b/make/Makefile.pcom +index a808667..405be95 100644 +--- a/make/Makefile.pcom ++++ b/make/Makefile.pcom +@@ -274,16 +274,16 @@ print_pssm : print_pssm.c getseq.c karlin.c apam.c + $(CC) -o print_pssm $(CFLAGS) print_pssm.c getseq.c karlin.c apam.c $(LIB_M) + + map_db : map_db.c uascii.h ncbl2_head.h +- $(CC) $(CFLAGS) -o $(BIN)/map_db map_db.c ++ $(CC) $(CFLAGS) $(HFLAGS) $(BIN)/map_db map_db.c + + list_db : list_db.c +- $(CC) $(CFLAGS) -o $(BIN)/list_db list_db.c ++ $(CC) $(CFLAGS) $(HFLAGS) $(BIN)/list_db list_db.c + + lav2ps : lav2plt.o lavplt_ps.o +- $(CC) -DUNIX -o $(BIN)/lav2ps lav2plt.o lavplt_ps.o -lm ++ $(CC) -DUNIX $(HFLAGS) $(BIN)/lav2ps lav2plt.o lavplt_ps.o -lm + + lav2svg : lav2plt.o lavplt_svg.o +- $(CC) -DUNIX -o $(BIN)/lav2svg lav2plt.o lavplt_svg.o -lm ++ $(CC) -DUNIX $(HFLAGS) $(BIN)/lav2svg lav2plt.o lavplt_svg.o -lm + + res_stats : res_stats.o scale_se.o +- $(CC) -DUNIX -o $(BIN)/res_stats res_stats.o scale_se.o -lm ++ $(CC) -DUNIX $(HFLAGS) $(BIN)/res_stats res_stats.o scale_se.o -lm -- cgit v1.2.3-65-gdbad