* [gentoo-commits] proj/sci:master commit in: sci-biology/codonw/
@ 2015-06-05 6:21 Justin Lecher
0 siblings, 0 replies; 8+ messages in thread
From: Justin Lecher @ 2015-06-05 6:21 UTC (permalink / raw
To: gentoo-commits
commit: b227f985711f1cfb5fac1f68edcb816b5ae150d6
Author: Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Sat May 30 05:52:06 2015 +0000
Commit: Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Fri Jun 5 06:21:03 2015 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=b227f985
sci-biology/codonw: Workaround file collision by appending PN to every command, bug #344713, bug #550388
Package-Manager: portage-2.2.20
sci-biology/codonw/ChangeLog | 8 +++++++-
.../codonw/{codonw-1.4.4-r1.ebuild => codonw-1.4.4-r2.ebuild} | 8 +++++---
sci-biology/codonw/metadata.xml | 10 +++++-----
3 files changed, 17 insertions(+), 9 deletions(-)
diff --git a/sci-biology/codonw/ChangeLog b/sci-biology/codonw/ChangeLog
index 00b6629..ee52e96 100644
--- a/sci-biology/codonw/ChangeLog
+++ b/sci-biology/codonw/ChangeLog
@@ -2,6 +2,13 @@
# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2
# $Header: $
+*codonw-1.4.4-r2 (30 May 2015)
+
+ 30 May 2015; Justin Lecher <jlec@gentoo.org> +codonw-1.4.4-r2.ebuild,
+ -codonw-1.4.4-r1.ebuild, metadata.xml:
+ sci-biology/codonw: Workaround file collision by appending PN to every
+ command, bug #344713, bug #550388
+
10 Jan 2015; Marius Brehler <marbre@linux.sungazer.de>
condow-1.4.4-r1.ebuild:
Move to EAPI=5.
@@ -14,4 +21,3 @@
28 Feb 2009; Andrey Kislyuk <weaver@gentoo.org> ChangeLog:
New package sci-biology/codonw, ebuild written by me
-
diff --git a/sci-biology/codonw/codonw-1.4.4-r1.ebuild b/sci-biology/codonw/codonw-1.4.4-r2.ebuild
similarity index 89%
rename from sci-biology/codonw/codonw-1.4.4-r1.ebuild
rename to sci-biology/codonw/codonw-1.4.4-r2.ebuild
index 85c0c5e..99c6994 100644
--- a/sci-biology/codonw/codonw-1.4.4-r1.ebuild
+++ b/sci-biology/codonw/codonw-1.4.4-r2.ebuild
@@ -20,7 +20,8 @@ KEYWORDS="~amd64 ~x86"
S=${WORKDIR}/codonW
src_prepare() {
- sed -e 's/$(CC) -c/& -DBSD/' \
+ sed \
+ -e 's/$(CC) -c/& -DBSD/' \
-e 's/$(CFLAGS) $(objects)/$(CFLAGS) $(LDFLAGS) $(objects)/' \
-i Makefile || die
}
@@ -30,10 +31,11 @@ src_compile() {
}
src_install() {
- dobin codonw
+ local i
+ dobin ${PN}
# woohoo watch out for collisions
for i in rscu cu aau raau tidy reader cutab cutot transl bases base3s dinuc cai fop gc3s gc cbi enc; do
- dosym codonw /usr/bin/${i}
+ dosym codonw /usr/bin/${i}-${PN}
done
dodoc *.txt
}
diff --git a/sci-biology/codonw/metadata.xml b/sci-biology/codonw/metadata.xml
index 3302123..fc7c769 100644
--- a/sci-biology/codonw/metadata.xml
+++ b/sci-biology/codonw/metadata.xml
@@ -1,9 +1,9 @@
<?xml version="1.0" encoding="UTF-8"?>
<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
<pkgmetadata>
- <maintainer>
- <email>weaver@gentoo.org</email>
- <name>Andrey Kislyuk</name>
- </maintainer>
- <herd>sci-biology</herd>
+ <maintainer>
+ <email>weaver@gentoo.org</email>
+ <name>Andrey Kislyuk</name>
+ </maintainer>
+ <herd>sci-biology</herd>
</pkgmetadata>
^ permalink raw reply related [flat|nested] 8+ messages in thread* [gentoo-commits] proj/sci:master commit in: sci-biology/codonw/
@ 2023-02-19 4:45 Horea Christian
0 siblings, 0 replies; 8+ messages in thread
From: Horea Christian @ 2023-02-19 4:45 UTC (permalink / raw
To: gentoo-commits
commit: 307e9fc6df28cae1f1bb5e53219ae537256c16a9
Author: Horea Christian <chr <AT> chymera <DOT> eu>
AuthorDate: Sun Feb 19 04:44:56 2023 +0000
Commit: Horea Christian <horea.christ <AT> gmail <DOT> com>
CommitDate: Sun Feb 19 04:44:56 2023 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=307e9fc6
sci-biology/codonw: update SRC_URI
Signed-off-by: Horea Christian <chr <AT> chymera.eu>
sci-biology/codonw/codonw-1.4.4-r2.ebuild | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/sci-biology/codonw/codonw-1.4.4-r2.ebuild b/sci-biology/codonw/codonw-1.4.4-r2.ebuild
index b3b761a6b..49bf65452 100644
--- a/sci-biology/codonw/codonw-1.4.4-r2.ebuild
+++ b/sci-biology/codonw/codonw-1.4.4-r2.ebuild
@@ -8,7 +8,7 @@ inherit toolchain-funcs
DESCRIPTION="Multivariate statistical analysis of codon and amino acid usage"
HOMEPAGE="https://codonw.sourceforge.net/"
SRC_URI="mirror://sourceforge/${PN}/CodonWSourceCode_${PV//./_}.tar.gz
- http://codonw.sourceforge.net/JohnPedenThesisPressOpt_water.pdf"
+ https://codonw.sourceforge.net/JohnPedenThesisPressOpt_water.pdf"
LICENSE="GPL-2"
SLOT="0"
^ permalink raw reply related [flat|nested] 8+ messages in thread* [gentoo-commits] proj/sci:master commit in: sci-biology/codonw/
@ 2023-02-19 4:44 Horea Christian
0 siblings, 0 replies; 8+ messages in thread
From: Horea Christian @ 2023-02-19 4:44 UTC (permalink / raw
To: gentoo-commits
commit: 31dcd0c56eccb45cd15109287b93a00eb24368ec
Author: Horea Christian <chr <AT> chymera <DOT> eu>
AuthorDate: Sun Feb 19 04:44:04 2023 +0000
Commit: Horea Christian <horea.christ <AT> gmail <DOT> com>
CommitDate: Sun Feb 19 04:44:09 2023 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=31dcd0c5
sci-biology/codonw: fixed HOMEPAGE HTTPS redirect
Signed-off-by: Horea Christian <chr <AT> chymera.eu>
sci-biology/codonw/codonw-1.4.4-r2.ebuild | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/sci-biology/codonw/codonw-1.4.4-r2.ebuild b/sci-biology/codonw/codonw-1.4.4-r2.ebuild
index 6478e9169..b3b761a6b 100644
--- a/sci-biology/codonw/codonw-1.4.4-r2.ebuild
+++ b/sci-biology/codonw/codonw-1.4.4-r2.ebuild
@@ -6,7 +6,7 @@ EAPI=7
inherit toolchain-funcs
DESCRIPTION="Multivariate statistical analysis of codon and amino acid usage"
-HOMEPAGE="http://codonw.sourceforge.net/"
+HOMEPAGE="https://codonw.sourceforge.net/"
SRC_URI="mirror://sourceforge/${PN}/CodonWSourceCode_${PV//./_}.tar.gz
http://codonw.sourceforge.net/JohnPedenThesisPressOpt_water.pdf"
^ permalink raw reply related [flat|nested] 8+ messages in thread* [gentoo-commits] proj/sci:master commit in: sci-biology/codonw/
@ 2021-01-24 14:08 Andrew Ammerlaan
0 siblings, 0 replies; 8+ messages in thread
From: Andrew Ammerlaan @ 2021-01-24 14:08 UTC (permalink / raw
To: gentoo-commits
commit: a445fcecd4358c0cee3f88fd59aca14f0af0b68a
Author: Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net>
AuthorDate: Sun Jan 24 14:08:50 2021 +0000
Commit: Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net>
CommitDate: Sun Jan 24 14:08:50 2021 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=a445fcec
sci-biology/codonw: EAPI bump
Package-Manager: Portage-3.0.14, Repoman-3.0.2
Signed-off-by: Andrew Ammerlaan <andrewammerlaan <AT> riseup.net>
sci-biology/codonw/codonw-1.4.4-r2.ebuild | 13 ++++++-------
1 file changed, 6 insertions(+), 7 deletions(-)
diff --git a/sci-biology/codonw/codonw-1.4.4-r2.ebuild b/sci-biology/codonw/codonw-1.4.4-r2.ebuild
index a6c680eb5..6478e9169 100644
--- a/sci-biology/codonw/codonw-1.4.4-r2.ebuild
+++ b/sci-biology/codonw/codonw-1.4.4-r2.ebuild
@@ -1,15 +1,13 @@
-# Copyright 1999-2015 Gentoo Foundation
+# Copyright 1999-2021 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
-EAPI=5
+EAPI=7
-inherit toolchain-funcs versionator
-
-MY_PV=$(replace_all_version_separators '_')
+inherit toolchain-funcs
DESCRIPTION="Multivariate statistical analysis of codon and amino acid usage"
HOMEPAGE="http://codonw.sourceforge.net/"
-SRC_URI="mirror://sourceforge/${PN}/CodonWSourceCode_${MY_PV}.tar.gz
+SRC_URI="mirror://sourceforge/${PN}/CodonWSourceCode_${PV//./_}.tar.gz
http://codonw.sourceforge.net/JohnPedenThesisPressOpt_water.pdf"
LICENSE="GPL-2"
@@ -17,13 +15,14 @@ SLOT="0"
IUSE=""
KEYWORDS="~amd64 ~x86"
-S=${WORKDIR}/codonW
+S="${WORKDIR}/codonW"
src_prepare() {
sed \
-e 's/$(CC) -c/& -DBSD/' \
-e 's/$(CFLAGS) $(objects)/$(CFLAGS) $(LDFLAGS) $(objects)/' \
-i Makefile || die
+ default
}
src_compile() {
^ permalink raw reply related [flat|nested] 8+ messages in thread* [gentoo-commits] proj/sci:master commit in: sci-biology/codonw/
@ 2015-11-15 18:53 Martin Mokrejs
0 siblings, 0 replies; 8+ messages in thread
From: Martin Mokrejs @ 2015-11-15 18:53 UTC (permalink / raw
To: gentoo-commits
commit: a08742af9a713a34c87c6e97a33d129036099a8a
Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Sun Nov 15 18:52:39 2015 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Sun Nov 15 18:52:39 2015 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=a08742af
sci-biology/codonw: add original Thesis of John Peden describing codonw package in more detail
Package-Manager: portage-2.2.18
sci-biology/codonw/ChangeLog | 5 +++++
sci-biology/codonw/codonw-1.4.4-r2.ebuild | 5 +++--
2 files changed, 8 insertions(+), 2 deletions(-)
diff --git a/sci-biology/codonw/ChangeLog b/sci-biology/codonw/ChangeLog
index ab9070f..4bcea2c 100644
--- a/sci-biology/codonw/ChangeLog
+++ b/sci-biology/codonw/ChangeLog
@@ -2,6 +2,11 @@
# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2
# $Id$
+ 15 Nov 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
+ codonw-1.4.4-r2.ebuild:
+ sci-biology/codonw: add original Thesis of John Peden describing codonw
+ package in more detail
+
08 Jun 2015; Justin Lecher <jlec@gentoo.org> metadata.xml:
sci-biology/codonw: Updating remote-id in metadata.xml
diff --git a/sci-biology/codonw/codonw-1.4.4-r2.ebuild b/sci-biology/codonw/codonw-1.4.4-r2.ebuild
index 3c228bd..152d75e 100644
--- a/sci-biology/codonw/codonw-1.4.4-r2.ebuild
+++ b/sci-biology/codonw/codonw-1.4.4-r2.ebuild
@@ -10,7 +10,8 @@ MY_PV=$(replace_all_version_separators '_')
DESCRIPTION="Multivariate statistical analysis of codon and amino acid usage"
HOMEPAGE="http://codonw.sourceforge.net/"
-SRC_URI="mirror://sourceforge/${PN}/CodonWSourceCode_${MY_PV}.tar.gz"
+SRC_URI="mirror://sourceforge/${PN}/CodonWSourceCode_${MY_PV}.tar.gz
+ http://codonw.sourceforge.net/JohnPedenThesisPressOpt_water.pdf"
LICENSE="GPL-2"
SLOT="0"
@@ -37,5 +38,5 @@ src_install() {
for i in rscu cu aau raau tidy reader cutab cutot transl bases base3s dinuc cai fop gc3s gc cbi enc; do
dosym codonw /usr/bin/${i}-${PN}
done
- dodoc *.txt
+ dodoc *.txt "${DISTDIR}"/JohnPedenThesisPressOpt_water.pdf
}
^ permalink raw reply related [flat|nested] 8+ messages in thread* [gentoo-commits] proj/sci:master commit in: sci-biology/codonw/
@ 2015-01-11 9:09 Justin Lecher
0 siblings, 0 replies; 8+ messages in thread
From: Justin Lecher @ 2015-01-11 9:09 UTC (permalink / raw
To: gentoo-commits
commit: e95477b2468656bfdb318892b538e7e29e733d4a
Author: Marius Brehler <marbre <AT> linux <DOT> sungazer <DOT> de>
AuthorDate: Sat Jan 10 16:00:59 2015 +0000
Commit: Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Sat Jan 10 16:00:59 2015 +0000
URL: http://sources.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=e95477b2
sci-biology/codonw: Drop unnecessary dies
---
sci-biology/codonw/codonw-1.4.4-r1.ebuild | 8 ++++----
1 file changed, 4 insertions(+), 4 deletions(-)
diff --git a/sci-biology/codonw/codonw-1.4.4-r1.ebuild b/sci-biology/codonw/codonw-1.4.4-r1.ebuild
index 50e2f9c..85c0c5e 100644
--- a/sci-biology/codonw/codonw-1.4.4-r1.ebuild
+++ b/sci-biology/codonw/codonw-1.4.4-r1.ebuild
@@ -26,14 +26,14 @@ src_prepare() {
}
src_compile() {
- emake CC="$(tc-getCC)" CFLAGS="${CFLAGS}" || die
+ emake CC="$(tc-getCC)" CFLAGS="${CFLAGS}"
}
src_install() {
- dobin codonw || die
+ dobin codonw
# woohoo watch out for collisions
for i in rscu cu aau raau tidy reader cutab cutot transl bases base3s dinuc cai fop gc3s gc cbi enc; do
- dosym codonw /usr/bin/${i} || die
+ dosym codonw /usr/bin/${i}
done
- dodoc *.txt || die
+ dodoc *.txt
}
^ permalink raw reply related [flat|nested] 8+ messages in thread* [gentoo-commits] proj/sci:master commit in: sci-biology/codonw/
@ 2015-01-11 9:09 Justin Lecher
0 siblings, 0 replies; 8+ messages in thread
From: Justin Lecher @ 2015-01-11 9:09 UTC (permalink / raw
To: gentoo-commits
commit: 2b3e8f43608da0a1585a5bf5a37cb21a09b9e1e8
Author: Marius Brehler <marbre <AT> linux <DOT> sungazer <DOT> de>
AuthorDate: Sat Jan 10 15:40:35 2015 +0000
Commit: Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Sat Jan 10 15:40:35 2015 +0000
URL: http://sources.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=2b3e8f43
sci-biology/codonw: Move to EAPI=5
---
sci-biology/codonw/ChangeLog | 6 +++++-
sci-biology/codonw/codonw-1.4.4-r1.ebuild | 4 ++--
2 files changed, 7 insertions(+), 3 deletions(-)
diff --git a/sci-biology/codonw/ChangeLog b/sci-biology/codonw/ChangeLog
index d2f9cc3..00b6629 100644
--- a/sci-biology/codonw/ChangeLog
+++ b/sci-biology/codonw/ChangeLog
@@ -1,7 +1,11 @@
# ChangeLog for sci-biology/codonw
-# Copyright 1999-2010 Gentoo Foundation; Distributed under the GPL v2
+# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2
# $Header: $
+ 10 Jan 2015; Marius Brehler <marbre@linux.sungazer.de>
+ condow-1.4.4-r1.ebuild:
+ Move to EAPI=5.
+
*codonw-1.4.4-r1 (08 Nov 2010)
08 Nov 2010; Kacper Kowalik <xarthisius@gentoo.org> -codonw-1.4.4.ebuild,
diff --git a/sci-biology/codonw/codonw-1.4.4-r1.ebuild b/sci-biology/codonw/codonw-1.4.4-r1.ebuild
index f7f48e1..50e2f9c 100644
--- a/sci-biology/codonw/codonw-1.4.4-r1.ebuild
+++ b/sci-biology/codonw/codonw-1.4.4-r1.ebuild
@@ -1,8 +1,8 @@
-# Copyright 1999-2014 Gentoo Foundation
+# Copyright 1999-2015 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
# $Header: $
-EAPI=2
+EAPI=5
inherit toolchain-funcs versionator
^ permalink raw reply related [flat|nested] 8+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/codonw/
@ 2011-06-24 17:09 Justin Lecher
0 siblings, 0 replies; 8+ messages in thread
From: Justin Lecher @ 2011-06-24 17:09 UTC (permalink / raw
To: gentoo-commits
commit: e7c0c8fb5f351bcd20bc06f0c193dbda04f7115b
Author: Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Fri Jun 24 12:50:05 2011 +0000
Commit: Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Fri Jun 24 12:50:05 2011 +0000
URL: http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=e7c0c8fb
Sort inherit and/or USE
(Portage version: 2.2.0_alpha41/git/Linux x86_64, signed Manifest commit with key 70EB7916)
---
sci-biology/codonw/codonw-1.4.4-r1.ebuild | 2 +-
1 files changed, 1 insertions(+), 1 deletions(-)
diff --git a/sci-biology/codonw/codonw-1.4.4-r1.ebuild b/sci-biology/codonw/codonw-1.4.4-r1.ebuild
index 3563ddf..05ed6ea 100644
--- a/sci-biology/codonw/codonw-1.4.4-r1.ebuild
+++ b/sci-biology/codonw/codonw-1.4.4-r1.ebuild
@@ -4,7 +4,7 @@
EAPI=2
-inherit versionator toolchain-funcs
+inherit toolchain-funcs versionator
MY_PV=$(replace_all_version_separators '_')
^ permalink raw reply related [flat|nested] 8+ messages in thread
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