diff options
author | Olivier Fisette <ribosome@gentoo.org> | 2006-01-21 18:05:18 +0000 |
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committer | Olivier Fisette <ribosome@gentoo.org> | 2006-01-21 18:05:18 +0000 |
commit | 33452c6605bc5e419a26b0bf6eb1df07434f90a8 (patch) | |
tree | c4b87821c25c8e8e10c0ccb3735af98cb30c14cc /sci-biology | |
parent | Added modular X dependencies and cleaned up older versions. Closing bug #119... (diff) | |
download | gentoo-2-33452c6605bc5e419a26b0bf6eb1df07434f90a8.tar.gz gentoo-2-33452c6605bc5e419a26b0bf6eb1df07434f90a8.tar.bz2 gentoo-2-33452c6605bc5e419a26b0bf6eb1df07434f90a8.zip |
Removed obsolete version
(Portage version: 2.0.53)
Diffstat (limited to 'sci-biology')
-rw-r--r-- | sci-biology/hmmer/ChangeLog | 6 | ||||
-rw-r--r-- | sci-biology/hmmer/files/Makefile-hmmer-2.2g.patch | 33 | ||||
-rw-r--r-- | sci-biology/hmmer/files/digest-hmmer-2.3.2 | 1 | ||||
-rw-r--r-- | sci-biology/hmmer/hmmer-2.3.2.ebuild | 41 | ||||
-rw-r--r-- | sci-biology/phylip/ChangeLog | 5 | ||||
-rw-r--r-- | sci-biology/phylip/files/digest-phylip-3.64 | 1 | ||||
-rw-r--r-- | sci-biology/phylip/phylip-3.64.ebuild | 43 | ||||
-rw-r--r-- | sci-biology/prints/ChangeLog | 5 | ||||
-rw-r--r-- | sci-biology/prints/files/digest-prints-37.0 | 6 | ||||
-rw-r--r-- | sci-biology/prints/prints-37.0.ebuild | 44 |
10 files changed, 13 insertions, 172 deletions
diff --git a/sci-biology/hmmer/ChangeLog b/sci-biology/hmmer/ChangeLog index 9c6b451e2327..23e3fd2a5d4c 100644 --- a/sci-biology/hmmer/ChangeLog +++ b/sci-biology/hmmer/ChangeLog @@ -1,6 +1,10 @@ # ChangeLog for sci-biology/hmmer # Copyright 2000-2006 Gentoo Foundation; Distributed under the GPL v2 -# $Header: /var/cvsroot/gentoo-x86/sci-biology/hmmer/ChangeLog,v 1.10 2006/01/21 16:48:49 ribosome Exp $ +# $Header: /var/cvsroot/gentoo-x86/sci-biology/hmmer/ChangeLog,v 1.11 2006/01/21 18:01:18 ribosome Exp $ + + 21 Jan 2006; Olivier Fisette <ribosome@gentoo.org> + -files/Makefile-hmmer-2.2g.patch, -hmmer-2.3.2.ebuild: + Removed obsolete version. *hmmer-2.3.2-r2 (21 Jan 2006) diff --git a/sci-biology/hmmer/files/Makefile-hmmer-2.2g.patch b/sci-biology/hmmer/files/Makefile-hmmer-2.2g.patch deleted file mode 100644 index fe9c8fdbcbfa..000000000000 --- a/sci-biology/hmmer/files/Makefile-hmmer-2.2g.patch +++ /dev/null @@ -1,33 +0,0 @@ ---- Makefile.in.orig 2003-05-05 15:21:41.000000000 +0100 -+++ Makefile.in 2003-05-05 15:22:11.000000000 +0100 -@@ -84,6 +84,12 @@ - sindex\ - shuffle\ - sreformat -+SQUIDMANS = afetch\ -+ alistat\ -+ seqstat\ -+ sfetch\ -+ shuffle\ -+ sreformat - - # all: Compile everything (except the testsuite), - # and stick the supported programs in binaries/ -@@ -146,13 +152,14 @@ - for file in $(PROGS) $(SQUIDPROGS) $(PVMPROGS); do\ - cp binaries/$$file $(BINDIR)/;\ - done -- for file in hmmer $(PROGS) $(SQUIDPROGS); do\ -+ for file in hmmer $(PROGS); do\ - $(INSTMAN) documentation/man/$$file.man $(MANDIR)/man$(MANSUFFIX)/$$file.$(MANSUFFIX);\ -+ chmod 0644 $(MANDIR)/man$(MANSUFFIX)/$$file.$(MANSUFFIX);\ - done -- for file in $(SQUIDPROGS); do\ -+ for file in $(SQUIDMANS); do\ - $(INSTMAN) squid/Man/$$file.man $(MANDIR)/man$(MANSUFFIX)/$$file.$(MANSUFFIX);\ -+ chmod 0644 $(MANDIR)/man$(MANSUFFIX)/$$file.$(MANSUFFIX);\ - done -- - # "make clean" removes almost everything except configuration files - # and binaries. - clean: diff --git a/sci-biology/hmmer/files/digest-hmmer-2.3.2 b/sci-biology/hmmer/files/digest-hmmer-2.3.2 deleted file mode 100644 index a923f14534a4..000000000000 --- a/sci-biology/hmmer/files/digest-hmmer-2.3.2 +++ /dev/null @@ -1 +0,0 @@ -MD5 5f073340c0cf761288f961a73821228a hmmer-2.3.2.tar.gz 1024933 diff --git a/sci-biology/hmmer/hmmer-2.3.2.ebuild b/sci-biology/hmmer/hmmer-2.3.2.ebuild deleted file mode 100644 index 2720112a39cb..000000000000 --- a/sci-biology/hmmer/hmmer-2.3.2.ebuild +++ /dev/null @@ -1,41 +0,0 @@ -# Copyright 1999-2005 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.ebuild,v 1.2 2005/02/08 00:15:30 augustus Exp $ - -DESCRIPTION="HMMER - Biological sequence analysis with profile HMMs" -HOMEPAGE="http://hmmer.wustl.edu/" -SRC_URI="ftp://ftp.genetics.wustl.edu/pub/eddy/${PN}/${PV}/${P}.tar.gz" -LICENSE="GPL-2" - -SLOT="0" -KEYWORDS="x86 amd64 ~ppc-macos ~ppc" -IUSE="" - -src_compile() { - ./configure \ - --host=${CHOST} \ - --prefix=${D}/usr \ - --exec_prefix=${D}/usr \ - --mandir=${D}/usr/share/man || die - -# econf || die - emake || die -} - -src_install() { - einstall || die - - dodoc 00README NOTES - - insinto /usr/share/doc/${PF} - doins Userguide.pdf - - cd squid - - dobin afetch alistat compalign compstruct revcomp seqstat seqsplit sfetch shuffle sreformat sindex weight translate - dolib libsquid.a -} - -src_test() { - make check -} diff --git a/sci-biology/phylip/ChangeLog b/sci-biology/phylip/ChangeLog index 064eb6f8a7e9..401599638066 100644 --- a/sci-biology/phylip/ChangeLog +++ b/sci-biology/phylip/ChangeLog @@ -1,6 +1,9 @@ # ChangeLog for sci-biology/phylip # Copyright 2000-2006 Gentoo Foundation; Distributed under the GPL v2 -# $Header: /var/cvsroot/gentoo-x86/sci-biology/phylip/ChangeLog,v 1.20 2006/01/21 16:19:44 grobian Exp $ +# $Header: /var/cvsroot/gentoo-x86/sci-biology/phylip/ChangeLog,v 1.21 2006/01/21 18:04:13 ribosome Exp $ + + 21 Jan 2006; Olivier Fisette <ribosome@gentoo.org> -phylip-3.64.ebuild: + Removed obsolete version. 21 Jan 2006; Hasan Khalil <gongloo@gentoo.org> phylip-3.64.ebuild: Dropping ppc-macos stable keyword as a result of X11 bug(s). #115468 diff --git a/sci-biology/phylip/files/digest-phylip-3.64 b/sci-biology/phylip/files/digest-phylip-3.64 deleted file mode 100644 index c15a42204d75..000000000000 --- a/sci-biology/phylip/files/digest-phylip-3.64 +++ /dev/null @@ -1 +0,0 @@ -MD5 57337d9e4a0a4a0ae60a75e8f1ad9413 phylip-3.64.tar.gz 1054390 diff --git a/sci-biology/phylip/phylip-3.64.ebuild b/sci-biology/phylip/phylip-3.64.ebuild deleted file mode 100644 index 4d2fadfeb373..000000000000 --- a/sci-biology/phylip/phylip-3.64.ebuild +++ /dev/null @@ -1,43 +0,0 @@ -# Copyright 1999-2006 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 -# $Header: /var/cvsroot/gentoo-x86/sci-biology/phylip/phylip-3.64.ebuild,v 1.5 2006/01/21 15:59:51 gongloo Exp $ - -inherit toolchain-funcs - -DESCRIPTION="PHYLIP - The PHYLogeny Inference Package" -HOMEPAGE="http://evolution.genetics.washington.edu/phylip.html" -SRC_URI="ftp://evolution.genetics.washington.edu/pub/${PN}/${P}.tar.gz" -LICENSE="freedist" - -SLOT="0" -KEYWORDS="ppc ~ppc-macos x86" -IUSE="" - -DEPEND="virtual/libc - virtual/x11" - -S=${WORKDIR}/${P}/src - -src_compile() { - sed -e "s/CFLAGS =/CFLAGS = ${CFLAGS}/" \ - -e "s/CC = cc/CC = $(tc-getCC)/" \ - -e "s/DC = cc/DC = $(tc-getCC)/" \ - -i Makefile || die - mkdir ../fonts - emake -j1 all put || die - mv ../exe/font* ../fonts -} - -src_install() -{ - cd ${WORKDIR}/${P} - - dobin exe/* - - dohtml phylip.html - insinto /usr/share/doc/${PF}/html/doc - doins doc/* - - insinto /usr/share/${PN}/fonts - doins fonts/* -} diff --git a/sci-biology/prints/ChangeLog b/sci-biology/prints/ChangeLog index b1bc27eff880..bdb48a45bd51 100644 --- a/sci-biology/prints/ChangeLog +++ b/sci-biology/prints/ChangeLog @@ -1,6 +1,9 @@ # ChangeLog for sci-biology/prints # Copyright 2000-2006 Gentoo Foundation; Distributed under the GPL v2 -# $Header: /var/cvsroot/gentoo-x86/sci-biology/prints/ChangeLog,v 1.16 2006/01/14 09:42:48 grobian Exp $ +# $Header: /var/cvsroot/gentoo-x86/sci-biology/prints/ChangeLog,v 1.17 2006/01/21 18:05:18 ribosome Exp $ + + 21 Jan 2006; Olivier Fisette <ribosome@gentoo.org> -prints-37.0.ebuild: + Removed obsolete version. 14 Jan 2006; Fabian Groffen <grobian@gentoo.org> prints-38.0.ebuild: Marked ppc-macos stable for bug #115453 diff --git a/sci-biology/prints/files/digest-prints-37.0 b/sci-biology/prints/files/digest-prints-37.0 deleted file mode 100644 index 660c4ee3c1ef..000000000000 --- a/sci-biology/prints/files/digest-prints-37.0 +++ /dev/null @@ -1,6 +0,0 @@ -MD5 8d15b420f8fb946085364b95550557c9 newpr.lis.gz 1446 -MD5 0b250e6966d83573609d6afe3f6442ce prints37_0.all.fasta.Z 19434403 -MD5 750992359d84739bf9d08894271c34ad prints37_0.dat.gz 7145345 -MD5 4b25791302554f8ea87358156b2b6b89 prints37_0.lis.gz 30354 -MD5 72215bb4d79ba0e2503ecb6614f74834 prints37_0.nam.gz 584 -MD5 2472d9ba65b3bfc4cd054f18d5b26a67 prints37_0.vsn.gz 73 diff --git a/sci-biology/prints/prints-37.0.ebuild b/sci-biology/prints/prints-37.0.ebuild deleted file mode 100644 index 02ff6f3a5fbc..000000000000 --- a/sci-biology/prints/prints-37.0.ebuild +++ /dev/null @@ -1,44 +0,0 @@ -# Copyright 1999-2005 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 -# $Header: /var/cvsroot/gentoo-x86/sci-biology/prints/prints-37.0.ebuild,v 1.10 2005/11/19 18:22:33 blubb Exp $ - -DESCRIPTION="A protein motif fingerprint database" -HOMEPAGE="http://www.bioinf.man.ac.uk/dbbrowser/PRINTS/" -SRC_URI="ftp://ftp.ebi.ac.uk/pub/databases/${PN}/newpr.lis.gz - ftp://ftp.ebi.ac.uk/pub/databases/${PN}/${PN}37_0.all.fasta.Z - ftp://ftp.ebi.ac.uk/pub/databases/${PN}/${PN}37_0.dat.gz - ftp://ftp.ebi.ac.uk/pub/databases/${PN}/${PN}37_0.lis.gz - ftp://ftp.ebi.ac.uk/pub/databases/${PN}/${PN}37_0.nam.gz - ftp://ftp.ebi.ac.uk/pub/databases/${PN}/${PN}37_0.vsn.gz" -LICENSE="public-domain" -SLOT="0" -KEYWORDS="amd64 ppc ppc-macos ppc64 x86" -IUSE="emboss minimal" -# Minimal build keeps only the indexed files (if applicable) and the documentation. -# The non-indexed database is not installed. - -DEPEND="emboss? ( sci-biology/emboss )" - -S=${WORKDIR} - -src_compile() { - if use emboss; then - mkdir PRINTS - echo - einfo "Indexing PRINTS for usage with EMBOSS." - EMBOSS_DATA=. printsextract -auto -infile prints37_0.dat || die \ - "Indexing PRINTS failed." - echo - fi -} - -src_install() { - if ! use minimal; then - insinto /usr/share/${PN} - doins ${PN}37_0.{all.fasta,dat,lis,nam,vsn} newpr.lis - fi - if use emboss; then - insinto /usr/share/EMBOSS/data/PRINTS - doins PRINTS/* - fi -} |