[gentoo-commits] repo/gentoo:master commit in: sci-biology/transfac/, profiles/
commit: 0c9a8d595bc0e9f73ec77071ff9f5a798e8443b4
Author: Jakov Smolić gentoo org>
AuthorDate: Tue Aug 9 07:11:00 2022 +
Commit: Jakov Smolić gentoo org>
CommitDate: Tue Aug 9 07:11:00 2022 +
URL:https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=0c9a8d59
sci-biology/transfac: treeclean
Closes: https://bugs.gentoo.org/361411
Signed-off-by: Jakov Smolić gentoo.org>
profiles/package.mask | 5
sci-biology/transfac/Manifest | 1 -
sci-biology/transfac/metadata.xml | 16 ---
sci-biology/transfac/transfac-3.2-r2.ebuild | 42 -
4 files changed, 64 deletions(-)
diff --git a/profiles/package.mask b/profiles/package.mask
index 1345f899a433..15577ff6c56f 100644
--- a/profiles/package.mask
+++ b/profiles/package.mask
@@ -498,11 +498,6 @@ dev-libs/ucommon
# Removal on 2022-08-10.
dev-php/pecl-geoip
-# David Seifert (2022-07-11)
-# Crashes with latest emboss, no other distro packages this,
-# ancient release, bug #361411, removal on 2022-08-10.
-sci-biology/transfac
-
# Fabian Groffen (2022-07-02)
# Segfaults handling SPF validations (warn on permerror), like the
# previous release, better not to trust your important mail to
diff --git a/sci-biology/transfac/Manifest b/sci-biology/transfac/Manifest
deleted file mode 100644
index 78b209e166c0..
--- a/sci-biology/transfac/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST transfac32.tar.Z 3346266 BLAKE2B
3bd6cfacd7e4ea75946dce5e77bae84a7d199daa84750fe21cd3c393fa66cdf09518a4043ac15f2fbe7bc19f001482e14b65743f1a89aec34bcb28409277370e
SHA512
d7004f90e57fa2b8839714e50b9ce1f67357db404adc1a5caddd1e9b86c8e3e9f4e85bbda15c4d6afed85da82ae8615f63260f9a3df9cfd79897d38896893b9f
diff --git a/sci-biology/transfac/metadata.xml
b/sci-biology/transfac/metadata.xml
deleted file mode 100644
index daa74b549bb1..
--- a/sci-biology/transfac/metadata.xml
+++ /dev/null
@@ -1,16 +0,0 @@
-
-https://www.gentoo.org/dtd/metadata.dtd;>
-
-
- sci-biol...@gentoo.org
- Gentoo Biology Project
-
-
- TRANSFAC® is a database of eukaryotic transcription factors, of
their
- genomic binding sites and DNA-binding profiles. TRANSFAC 3.2 is
an old
- public version available at the European Bioinformatics
Institute.
- TRANSFAC® is currently maintained by the BIOBASE company.
Altough they
- offer public access to a more recent version of the database,
they
- offer no free downloadable version.
-
-
diff --git a/sci-biology/transfac/transfac-3.2-r2.ebuild
b/sci-biology/transfac/transfac-3.2-r2.ebuild
deleted file mode 100644
index 2fce474da2ad..
--- a/sci-biology/transfac/transfac-3.2-r2.ebuild
+++ /dev/null
@@ -1,42 +0,0 @@
-# Copyright 1999-2022 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=8
-
-DESCRIPTION="A database of eucaryotic transcription factors"
-HOMEPAGE="http://www.gene-regulation.com/pub/databases.html;
-SRC_URI="ftp://ftp.ebi.ac.uk/pub/databases/${PN}/${PN}32.tar.Z;
-S="${WORKDIR}"
-
-LICENSE="public-domain"
-SLOT="3"
-# Minimal build keeps only the indexed files (if applicable) and the
documentation.
-# The non-indexed database is not installed.
-KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
-IUSE="emboss minimal"
-
-BDEPEND="emboss? ( sci-biology/emboss )"
-RDEPEND="${BDEPEND}"
-
-src_compile() {
- if use emboss; then
- einfo
- einfo "Indexing TRANSFAC for usage with EMBOSS"
- EMBOSS_DATA="." tfextract -auto -infile class.dat || die
"Indexing TRANSFAC failed"
- einfo
- fi
-}
-
-src_install() {
- newdoc readme.txt README
-
- if ! use minimal; then
- insinto /usr/share/transfac-${SLOT}
- doins *.dat
- fi
-
- if use emboss; then
- insinto /usr/share/EMBOSS/data
- doins tf*
- fi
-}
[gentoo-commits] repo/gentoo:master commit in: sci-biology/transfac/
commit: 4345375f01e657175dc4e9199884ffbea67d68e5
Author: David Seifert gentoo org>
AuthorDate: Thu Jul 7 19:57:13 2022 +
Commit: David Seifert gentoo org>
CommitDate: Thu Jul 7 19:57:13 2022 +
URL:https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=4345375f
sci-biology/transfac: update EAPI 6 -> 8
Signed-off-by: David Seifert gentoo.org>
.../{transfac-3.2-r1.ebuild => transfac-3.2-r2.ebuild} | 13 ++---
1 file changed, 6 insertions(+), 7 deletions(-)
diff --git a/sci-biology/transfac/transfac-3.2-r1.ebuild
b/sci-biology/transfac/transfac-3.2-r2.ebuild
similarity index 84%
rename from sci-biology/transfac/transfac-3.2-r1.ebuild
rename to sci-biology/transfac/transfac-3.2-r2.ebuild
index 91b16f4b4fe4..2fce474da2ad 100644
--- a/sci-biology/transfac/transfac-3.2-r1.ebuild
+++ b/sci-biology/transfac/transfac-3.2-r2.ebuild
@@ -1,11 +1,12 @@
-# Copyright 1999-2017 Gentoo Foundation
+# Copyright 1999-2022 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
-EAPI=6
+EAPI=8
DESCRIPTION="A database of eucaryotic transcription factors"
HOMEPAGE="http://www.gene-regulation.com/pub/databases.html;
SRC_URI="ftp://ftp.ebi.ac.uk/pub/databases/${PN}/${PN}32.tar.Z;
+S="${WORKDIR}"
LICENSE="public-domain"
SLOT="3"
@@ -14,10 +15,8 @@ SLOT="3"
KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
IUSE="emboss minimal"
-DEPEND="emboss? ( sci-biology/emboss )"
-RDEPEND="${DEPEND}"
-
-S=${WORKDIR}
+BDEPEND="emboss? ( sci-biology/emboss )"
+RDEPEND="${BDEPEND}"
src_compile() {
if use emboss; then
@@ -32,7 +31,7 @@ src_install() {
newdoc readme.txt README
if ! use minimal; then
- insinto /usr/share/${PN}-${SLOT}
+ insinto /usr/share/transfac-${SLOT}
doins *.dat
fi
[gentoo-commits] repo/gentoo:master commit in: sci-biology/transfac/
commit: 5baee74fbdce4cfcfc16da6700c613ddaa770cbb
Author: David Seifert gentoo org>
AuthorDate: Sat Feb 25 20:09:17 2017 +
Commit: David Seifert gentoo org>
CommitDate: Sat Feb 25 20:10:20 2017 +
URL:https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=5baee74f
sci-biology/transfac: Modernise to EAPI 6
Package-Manager: Portage-2.3.3, Repoman-2.3.1
...{transfac-3.2.ebuild => transfac-3.2-r1.ebuild} | 27 --
1 file changed, 15 insertions(+), 12 deletions(-)
diff --git a/sci-biology/transfac/transfac-3.2.ebuild
b/sci-biology/transfac/transfac-3.2-r1.ebuild
similarity index 77%
rename from sci-biology/transfac/transfac-3.2.ebuild
rename to sci-biology/transfac/transfac-3.2-r1.ebuild
index 9b6e76ce87..7c98be79ed 100644
--- a/sci-biology/transfac/transfac-3.2.ebuild
+++ b/sci-biology/transfac/transfac-3.2-r1.ebuild
@@ -2,40 +2,43 @@
# Distributed under the terms of the GNU General Public License v2
# $Id$
+EAPI=6
+
DESCRIPTION="A database of eucaryotic transcription factors"
HOMEPAGE="http://www.gene-regulation.com/pub/databases.html;
SRC_URI="ftp://ftp.ebi.ac.uk/pub/databases/${PN}/${PN}32.tar.Z;
-LICENSE="public-domain"
+LICENSE="public-domain"
SLOT="3"
-KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
-IUSE="emboss minimal"
# Minimal build keeps only the indexed files (if applicable) and the
documentation.
# The non-indexed database is not installed.
+KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
+IUSE="emboss minimal"
DEPEND="emboss? ( sci-biology/emboss )"
-
RDEPEND="${DEPEND}"
-S="${WORKDIR}"
+S=${WORKDIR}
src_compile() {
if use emboss; then
- echo
- einfo "Indexing TRANSFAC for usage with EMBOSS."
- EMBOSS_DATA=. tfextract -auto -infile class.dat || die \
- "Indexing TRANSFAC failed."
- echo
+ einfo
+ einfo "Indexing TRANSFAC for usage with EMBOSS"
+ EMBOSS_DATA="." tfextract -auto -infile class.dat || die
"Indexing TRANSFAC failed"
+ einfo
fi
}
src_install() {
+ newdoc readme.txt README
+
if ! use minimal; then
insinto /usr/share/${PN}-${SLOT}
- doins *.dat || die
+ doins *.dat
fi
+
if use emboss; then
insinto /usr/share/EMBOSS/data
- doins tf* || die
+ doins tf*
fi
}
[gentoo-commits] repo/gentoo:master commit in: sci-biology/transfac/
commit: 5d9128bb235538e20ab004fae572007f8084562d
Author: David Seifert gentoo org>
AuthorDate: Sun Feb 19 18:41:36 2017 +
Commit: David Seifert gentoo org>
CommitDate: Sun Feb 19 18:43:39 2017 +
URL:https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=5d9128bb
sci-biology/transfac: Drop to unstable
Package-Manager: Portage-2.3.3, Repoman-2.3.1
Closes: https://github.com/gentoo/gentoo/pull/3937
sci-biology/transfac/transfac-3.2.ebuild | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/sci-biology/transfac/transfac-3.2.ebuild
b/sci-biology/transfac/transfac-3.2.ebuild
index f35476ca5a..9b6e76ce87 100644
--- a/sci-biology/transfac/transfac-3.2.ebuild
+++ b/sci-biology/transfac/transfac-3.2.ebuild
@@ -8,7 +8,7 @@ SRC_URI="ftp://ftp.ebi.ac.uk/pub/databases/${PN}/${PN}32.tar.Z;
LICENSE="public-domain"
SLOT="3"
-KEYWORDS="amd64 x86 ~amd64-linux ~x86-linux ~ppc-macos ~sparc-solaris"
+KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
IUSE="emboss minimal"
# Minimal build keeps only the indexed files (if applicable) and the
documentation.
# The non-indexed database is not installed.
