* [gentoo-commits] gentoo-x86 commit in sci-biology/vienna-rna: ChangeLog vienna-rna-1.7.2.ebuild
@ 2008-10-06 22:34 Markus Dittrich (markusle)
0 siblings, 0 replies; 3+ messages in thread
From: Markus Dittrich (markusle) @ 2008-10-06 22:34 UTC (permalink / raw
To: gentoo-commits
markusle 08/10/06 22:34:27
Modified: ChangeLog vienna-rna-1.7.2.ebuild
Log:
Fixed ignored LDFLAGS issues and bogus detection of GD support. Also enabled the tests that come with the package.
(Portage version: 2.2_rc11/cvs/Linux 2.6.26-SENTINEL-2 i686)
Revision Changes Path
1.18 sci-biology/vienna-rna/ChangeLog
file : http://sources.gentoo.org/viewcvs.py/gentoo-x86/sci-biology/vienna-rna/ChangeLog?rev=1.18&view=markup
plain: http://sources.gentoo.org/viewcvs.py/gentoo-x86/sci-biology/vienna-rna/ChangeLog?rev=1.18&content-type=text/plain
diff : http://sources.gentoo.org/viewcvs.py/gentoo-x86/sci-biology/vienna-rna/ChangeLog?r1=1.17&r2=1.18
Index: ChangeLog
===================================================================
RCS file: /var/cvsroot/gentoo-x86/sci-biology/vienna-rna/ChangeLog,v
retrieving revision 1.17
retrieving revision 1.18
diff -u -r1.17 -r1.18
--- ChangeLog 29 Aug 2008 01:21:38 -0000 1.17
+++ ChangeLog 6 Oct 2008 22:34:27 -0000 1.18
@@ -1,6 +1,12 @@
# ChangeLog for sci-biology/vienna-rna
# Copyright 2000-2008 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/vienna-rna/ChangeLog,v 1.17 2008/08/29 01:21:38 markusle Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/vienna-rna/ChangeLog,v 1.18 2008/10/06 22:34:27 markusle Exp $
+
+ 06 Oct 2008; Markus Dittrich <markusle@gentoo.org>
+ +files/vienna-rna-1.7.2-LDFLAGS.patch,
+ +files/vienna-rna-1.7.2-disable-gd.patch, vienna-rna-1.7.2.ebuild:
+ Fixed ignored LDFLAGS issues and bogus detection of GD support. Also
+ enabled the tests that come with the package.
*vienna-rna-1.7.2 (28 Aug 2008)
1.2 sci-biology/vienna-rna/vienna-rna-1.7.2.ebuild
file : http://sources.gentoo.org/viewcvs.py/gentoo-x86/sci-biology/vienna-rna/vienna-rna-1.7.2.ebuild?rev=1.2&view=markup
plain: http://sources.gentoo.org/viewcvs.py/gentoo-x86/sci-biology/vienna-rna/vienna-rna-1.7.2.ebuild?rev=1.2&content-type=text/plain
diff : http://sources.gentoo.org/viewcvs.py/gentoo-x86/sci-biology/vienna-rna/vienna-rna-1.7.2.ebuild?r1=1.1&r2=1.2
Index: vienna-rna-1.7.2.ebuild
===================================================================
RCS file: /var/cvsroot/gentoo-x86/sci-biology/vienna-rna/vienna-rna-1.7.2.ebuild,v
retrieving revision 1.1
retrieving revision 1.2
diff -u -r1.1 -r1.2
--- vienna-rna-1.7.2.ebuild 29 Aug 2008 01:21:38 -0000 1.1
+++ vienna-rna-1.7.2.ebuild 6 Oct 2008 22:34:27 -0000 1.2
@@ -1,8 +1,8 @@
# Copyright 1999-2008 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/vienna-rna/vienna-rna-1.7.2.ebuild,v 1.1 2008/08/29 01:21:38 markusle Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/vienna-rna/vienna-rna-1.7.2.ebuild,v 1.2 2008/10/06 22:34:27 markusle Exp $
-inherit toolchain-funcs multilib eutils versionator
+inherit toolchain-funcs multilib eutils versionator autotools
DESCRIPTION="The Vienna RNA Package - RNA secondary structure prediction and comparison"
LICENSE="vienna-rna"
@@ -23,6 +23,13 @@
cd "${S}"
epatch "${FILESDIR}"/${PN}-1.6.5-c-fixes.patch
epatch "${FILESDIR}"/${P}-gcc4.3.patch
+ epatch "${FILESDIR}"/${P}-LDFLAGS.patch
+ epatch "${FILESDIR}"/${P}-disable-gd.patch
+ eautoreconf
+
+ # we need a separate eautoreconf in RNAforester
+ cd RNAforester
+ eautoreconf
}
src_compile() {
@@ -36,10 +43,15 @@
cd "${S}"/Readseq
sed -e "s:CC=cc:CC=$(tc-getCC):" -e "s:CFLAGS=:CFLAGS=${CFLAGS}:" \
-i Makefile || die "Failed patching readseq Makefile."
- make || die "Failed to compile readseq."
+ emake || die "Failed to compile readseq."
# TODO: Add (optional?) support for the NCBI toolkit.
}
+src_test() {
+ cd "${S}"/Perl && emake check || die "Perl tests failed"
+ cd "${S}"/Readseq && emake test || die "Readseq tests failed"
+}
+
src_install() {
make install DESTDIR="${D}" || die "Installation failed."
dodoc AUTHORS ChangeLog NEWS README THANKS \
^ permalink raw reply [flat|nested] 3+ messages in thread
* [gentoo-commits] gentoo-x86 commit in sci-biology/vienna-rna: ChangeLog vienna-rna-1.7.2.ebuild
@ 2008-10-09 13:03 Markus Dittrich (markusle)
0 siblings, 0 replies; 3+ messages in thread
From: Markus Dittrich (markusle) @ 2008-10-09 13:03 UTC (permalink / raw
To: gentoo-commits
markusle 08/10/09 13:03:30
Modified: ChangeLog vienna-rna-1.7.2.ebuild
Log:
Remove perlocal.pod file to avoid file collisions (see bug #240358).
(Portage version: 2.2_rc11/cvs/Linux 2.6.26-SENTINEL-2 i686)
Revision Changes Path
1.19 sci-biology/vienna-rna/ChangeLog
file : http://sources.gentoo.org/viewcvs.py/gentoo-x86/sci-biology/vienna-rna/ChangeLog?rev=1.19&view=markup
plain: http://sources.gentoo.org/viewcvs.py/gentoo-x86/sci-biology/vienna-rna/ChangeLog?rev=1.19&content-type=text/plain
diff : http://sources.gentoo.org/viewcvs.py/gentoo-x86/sci-biology/vienna-rna/ChangeLog?r1=1.18&r2=1.19
Index: ChangeLog
===================================================================
RCS file: /var/cvsroot/gentoo-x86/sci-biology/vienna-rna/ChangeLog,v
retrieving revision 1.18
retrieving revision 1.19
diff -u -r1.18 -r1.19
--- ChangeLog 6 Oct 2008 22:34:27 -0000 1.18
+++ ChangeLog 9 Oct 2008 13:03:30 -0000 1.19
@@ -1,6 +1,10 @@
# ChangeLog for sci-biology/vienna-rna
# Copyright 2000-2008 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/vienna-rna/ChangeLog,v 1.18 2008/10/06 22:34:27 markusle Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/vienna-rna/ChangeLog,v 1.19 2008/10/09 13:03:30 markusle Exp $
+
+ 09 Oct 2008; Markus Dittrich <markusle@gentoo.org>
+ vienna-rna-1.7.2.ebuild:
+ Remove perlocal.pod file to avoid file collisions (see bug #240358).
06 Oct 2008; Markus Dittrich <markusle@gentoo.org>
+files/vienna-rna-1.7.2-LDFLAGS.patch,
1.3 sci-biology/vienna-rna/vienna-rna-1.7.2.ebuild
file : http://sources.gentoo.org/viewcvs.py/gentoo-x86/sci-biology/vienna-rna/vienna-rna-1.7.2.ebuild?rev=1.3&view=markup
plain: http://sources.gentoo.org/viewcvs.py/gentoo-x86/sci-biology/vienna-rna/vienna-rna-1.7.2.ebuild?rev=1.3&content-type=text/plain
diff : http://sources.gentoo.org/viewcvs.py/gentoo-x86/sci-biology/vienna-rna/vienna-rna-1.7.2.ebuild?r1=1.2&r2=1.3
Index: vienna-rna-1.7.2.ebuild
===================================================================
RCS file: /var/cvsroot/gentoo-x86/sci-biology/vienna-rna/vienna-rna-1.7.2.ebuild,v
retrieving revision 1.2
retrieving revision 1.3
diff -u -r1.2 -r1.3
--- vienna-rna-1.7.2.ebuild 6 Oct 2008 22:34:27 -0000 1.2
+++ vienna-rna-1.7.2.ebuild 9 Oct 2008 13:03:30 -0000 1.3
@@ -1,8 +1,8 @@
# Copyright 1999-2008 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/vienna-rna/vienna-rna-1.7.2.ebuild,v 1.2 2008/10/06 22:34:27 markusle Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/vienna-rna/vienna-rna-1.7.2.ebuild,v 1.3 2008/10/09 13:03:30 markusle Exp $
-inherit toolchain-funcs multilib eutils versionator autotools
+inherit toolchain-funcs multilib eutils versionator autotools perl-module
DESCRIPTION="The Vienna RNA Package - RNA secondary structure prediction and comparison"
LICENSE="vienna-rna"
@@ -63,4 +63,7 @@
newdoc Readseq/Readme README.readseq && \
newdoc Readseq/Formats Formats.readseq \
|| die "Installing readseq Readme failed."
+
+ # remove perlocal.pod to avoid file collisions (see #240358)
+ fixlocalpod || die "Failed to remove perlocal.pod"
}
^ permalink raw reply [flat|nested] 3+ messages in thread
* [gentoo-commits] gentoo-x86 commit in sci-biology/vienna-rna: ChangeLog vienna-rna-1.7.2.ebuild
@ 2009-07-30 8:31 Samuli Suominen (ssuominen)
0 siblings, 0 replies; 3+ messages in thread
From: Samuli Suominen (ssuominen) @ 2009-07-30 8:31 UTC (permalink / raw
To: gentoo-commits
ssuominen 09/07/30 08:31:01
Modified: ChangeLog vienna-rna-1.7.2.ebuild
Log:
Fix building with GCC 4.4 and GLIBC 2.10+ wrt #274044. Rename getline to v_getline. Missing include.
(Portage version: 2.2_rc33/cvs/Linux x86_64)
Revision Changes Path
1.20 sci-biology/vienna-rna/ChangeLog
file : http://sources.gentoo.org/viewcvs.py/gentoo-x86/sci-biology/vienna-rna/ChangeLog?rev=1.20&view=markup
plain: http://sources.gentoo.org/viewcvs.py/gentoo-x86/sci-biology/vienna-rna/ChangeLog?rev=1.20&content-type=text/plain
diff : http://sources.gentoo.org/viewcvs.py/gentoo-x86/sci-biology/vienna-rna/ChangeLog?r1=1.19&r2=1.20
Index: ChangeLog
===================================================================
RCS file: /var/cvsroot/gentoo-x86/sci-biology/vienna-rna/ChangeLog,v
retrieving revision 1.19
retrieving revision 1.20
diff -u -r1.19 -r1.20
--- ChangeLog 9 Oct 2008 13:03:30 -0000 1.19
+++ ChangeLog 30 Jul 2009 08:31:01 -0000 1.20
@@ -1,6 +1,11 @@
# ChangeLog for sci-biology/vienna-rna
-# Copyright 2000-2008 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/vienna-rna/ChangeLog,v 1.19 2008/10/09 13:03:30 markusle Exp $
+# Copyright 1999-2009 Gentoo Foundation; Distributed under the GPL v2
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/vienna-rna/ChangeLog,v 1.20 2009/07/30 08:31:01 ssuominen Exp $
+
+ 30 Jul 2009; Samuli Suominen <ssuominen@gentoo.org>
+ vienna-rna-1.7.2.ebuild, +files/vienna-rna-1.7.2-gcc4.4.patch:
+ Fix building with GCC 4.4 and GLIBC 2.10+ wrt #274044. Rename getline to
+ v_getline. Missing include.
09 Oct 2008; Markus Dittrich <markusle@gentoo.org>
vienna-rna-1.7.2.ebuild:
1.4 sci-biology/vienna-rna/vienna-rna-1.7.2.ebuild
file : http://sources.gentoo.org/viewcvs.py/gentoo-x86/sci-biology/vienna-rna/vienna-rna-1.7.2.ebuild?rev=1.4&view=markup
plain: http://sources.gentoo.org/viewcvs.py/gentoo-x86/sci-biology/vienna-rna/vienna-rna-1.7.2.ebuild?rev=1.4&content-type=text/plain
diff : http://sources.gentoo.org/viewcvs.py/gentoo-x86/sci-biology/vienna-rna/vienna-rna-1.7.2.ebuild?r1=1.3&r2=1.4
Index: vienna-rna-1.7.2.ebuild
===================================================================
RCS file: /var/cvsroot/gentoo-x86/sci-biology/vienna-rna/vienna-rna-1.7.2.ebuild,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -r1.3 -r1.4
--- vienna-rna-1.7.2.ebuild 9 Oct 2008 13:03:30 -0000 1.3
+++ vienna-rna-1.7.2.ebuild 30 Jul 2009 08:31:01 -0000 1.4
@@ -1,6 +1,6 @@
-# Copyright 1999-2008 Gentoo Foundation
+# Copyright 1999-2009 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/vienna-rna/vienna-rna-1.7.2.ebuild,v 1.3 2008/10/09 13:03:30 markusle Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/vienna-rna/vienna-rna-1.7.2.ebuild,v 1.4 2009/07/30 08:31:01 ssuominen Exp $
inherit toolchain-funcs multilib eutils versionator autotools perl-module
@@ -16,7 +16,7 @@
DEPEND="dev-lang/perl
media-libs/gd"
-S="${WORKDIR}/ViennaRNA-${PV}"
+S=${WORKDIR}/ViennaRNA-${PV}
src_unpack() {
unpack ${A}
@@ -25,6 +25,7 @@
epatch "${FILESDIR}"/${P}-gcc4.3.patch
epatch "${FILESDIR}"/${P}-LDFLAGS.patch
epatch "${FILESDIR}"/${P}-disable-gd.patch
+ epatch "${FILESDIR}"/${P}-gcc4.4.patch
eautoreconf
# we need a separate eautoreconf in RNAforester
^ permalink raw reply [flat|nested] 3+ messages in thread
end of thread, other threads:[~2009-07-30 8:31 UTC | newest]
Thread overview: 3+ messages (download: mbox.gz follow: Atom feed
-- links below jump to the message on this page --
2008-10-09 13:03 [gentoo-commits] gentoo-x86 commit in sci-biology/vienna-rna: ChangeLog vienna-rna-1.7.2.ebuild Markus Dittrich (markusle)
-- strict thread matches above, loose matches on Subject: below --
2009-07-30 8:31 Samuli Suominen (ssuominen)
2008-10-06 22:34 Markus Dittrich (markusle)
This is a public inbox, see mirroring instructions
for how to clone and mirror all data and code used for this inbox