Removed obsolete version

(Portage version: 2.0.53)

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
-}