* [gentoo-commits] proj/sci:master commit in: sci-biology/eugene/files/, sci-biology/eugene/
@ 2016-02-10 13:12 Martin Mokrejs
0 siblings, 0 replies; 2+ messages in thread
From: Martin Mokrejs @ 2016-02-10 13:12 UTC (permalink / raw
To: gentoo-commits
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commit: 197707f97ff7246be0dd4dbc187c0682b2d7a639
Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Wed Feb 10 13:09:45 2016 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Wed Feb 10 13:09:45 2016 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=197707f9
sci-biology/eugene: version bump
Package-Manager: portage-2.2.26
sci-biology/eugene/eugene-4.1d.ebuild | 37 +++++++++++++++++++
sci-biology/eugene/files/eugene-3.6-overflow.patch | 13 +++++++
sci-biology/eugene/files/eugene-3.6-plugins.patch | 43 ++++++++++++++++++++++
.../eugene/files/eugene-4.1-format-security.patch | 16 ++++++++
sci-biology/eugene/metadata.xml | 5 +++
5 files changed, 114 insertions(+)
diff --git a/sci-biology/eugene/eugene-4.1d.ebuild b/sci-biology/eugene/eugene-4.1d.ebuild
new file mode 100644
index 0000000..a2fb281
--- /dev/null
+++ b/sci-biology/eugene/eugene-4.1d.ebuild
@@ -0,0 +1,37 @@
+# Copyright 1999-2015 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=5
+
+inherit autotools eutils
+
+DESCRIPTION="Prokaryotic and Eukaryotic gene predictor"
+HOMEPAGE="http://www.inra.fr/mia/T/EuGene/"
+SRC_URI="https://mulcyber.toulouse.inra.fr/frs/download.php/1359/${P}.tar.gz"
+
+LICENSE="Artistic"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+IUSE=""
+
+DEPEND="
+ media-libs/gd[png]
+ media-libs/libpng:0=
+ "
+RDEPEND="${DEPEND}"
+
+RESTRICT="test"
+
+src_prepare() {
+ # https://mulcyber.toulouse.inra.fr/tracker/index.php?func=detail&aid=1170
+ epatch \
+ "${FILESDIR}"/${PN}-3.6-overflow.patch \
+ "${FILESDIR}"/${PN}-3.6-plugins.patch \
+ "${FILESDIR}"/${PN}-4.1-format-security.patch
+ sed \
+ -e '/SUBDIRS/ s/doc//' \
+ -e '/INSTALL.*doc/ s/\(.*\)//' \
+ -i Makefile.am || die
+ eautoreconf
+}
diff --git a/sci-biology/eugene/files/eugene-3.6-overflow.patch b/sci-biology/eugene/files/eugene-3.6-overflow.patch
new file mode 100644
index 0000000..7222530
--- /dev/null
+++ b/sci-biology/eugene/files/eugene-3.6-overflow.patch
@@ -0,0 +1,13 @@
+http://bugs.gentoo.org/show_bug.cgi?id=336607
+
+--- eugene-3.6/src/Sensor.cc
++++ eugene-3.6/src/Sensor.cc
+@@ -224,7 +224,7 @@
+ //--------------------------
+ void Signals :: PrintS ()
+ {
+- char t[7];
++ char t[10];
+ char s = '+';
+
+ switch (type) {
diff --git a/sci-biology/eugene/files/eugene-3.6-plugins.patch b/sci-biology/eugene/files/eugene-3.6-plugins.patch
new file mode 100644
index 0000000..1e910a1
--- /dev/null
+++ b/sci-biology/eugene/files/eugene-3.6-plugins.patch
@@ -0,0 +1,43 @@
+http://bugs.gentoo.org/show_bug.cgi?id=297536
+
+--- eugene-3.6/src/Makefile.am
++++ eugene-3.6/src/Makefile.am
+@@ -20,7 +20,7 @@
+
+ SUBDIRS = Parametrization GDIF . SensorPlugins
+
+-AM_CXXFLAGS = $(eugene_cxxflags) -DDEFAULT_EUGENE_DIR=\"${pkgdatadir}\"
++AM_CXXFLAGS = $(eugene_cxxflags) -DDEFAULT_EUGENE_DIR=\"${pkgdatadir}\" -DLIB_DIR=\"${libdir}\"
+ AM_CFLAGS =
+
+ bin_PROGRAMS = eugene
+--- eugene-3.6/src/MSensor.cc
++++ eugene-3.6/src/MSensor.cc
+@@ -97,7 +97,7 @@
+ std::string use_name;
+
+ if (!IsInitialized) {
+- PluginsDir = (std::string)PAR.getC("eugene_dir")+"/"+PLUGINS_DIR+"/";
++ PluginsDir = (std::string)LIB_DIR+"/eugene/"+PLUGINS_DIR+"/";
+
+ // On récupère les couples nom de sensor/priorité du .par
+ PAR.ResetIter();
+--- eugene-3.6/Makefile.am
++++ eugene-3.6/Makefile.am
+@@ -125,7 +125,7 @@
+ $(INSTALL) -d $(DESTDIR)/$(pkgdatadir)/web/Style
+ $(INSTALL) -d $(DESTDIR)/$(pkgdatadir)/web/Javascripts
+ $(INSTALL) -d $(DESTDIR)/$(pkgdatadir)/web/Images
+- $(INSTALL) -d $(DESTDIR)/$(pkgdatadir)/plugins
++ $(INSTALL) -d $(DESTDIR)/$(libdir)/eugene/plugins
+ $(INSTALL) -d $(DESTDIR)/$(pkgdatadir)/cfg
+ $(INSTALL) -d $(DESTDIR)/$(pkgdatadir)/models
+ $(INSTALL) -d $(DESTDIR)/$(pkgdatadir)/models/WAM
+@@ -144,6 +144,6 @@
+ $(INSTALL) -m 644 $(srcdir)/web/Images/*jpg $(DESTDIR)/$(pkgdatadir)/web/Images
+ $(INSTALL) -m 644 $(srcdir)/cfg/*.obo $(DESTDIR)/$(pkgdatadir)/cfg
+ $(INSTALL) -m 644 $(srcdir)/cfg/*.par $(DESTDIR)/$(pkgdatadir)/cfg
+- $(INSTALL) src/SensorPlugins/*/*.so $(DESTDIR)/$(pkgdatadir)/plugins
++ $(INSTALL) src/SensorPlugins/*/*.so $(DESTDIR)/$(libdir)/eugene/plugins
+ $(INSTALL) $(srcdir)/Procedures/Eval/egn_* $(DESTDIR)/$(pkgdatadir)/Procedures/Eval
+ $(INSTALL) $(srcdir)/Procedures/Get/egn_* $(DESTDIR)/$(pkgdatadir)/Procedures/Get
diff --git a/sci-biology/eugene/files/eugene-4.1-format-security.patch b/sci-biology/eugene/files/eugene-4.1-format-security.patch
new file mode 100644
index 0000000..e6e4a6c
--- /dev/null
+++ b/sci-biology/eugene/files/eugene-4.1-format-security.patch
@@ -0,0 +1,16 @@
+ src/Hits.cc | 2 +-
+ 1 file changed, 1 insertion(+), 1 deletion(-)
+
+diff --git a/src/Hits.cc b/src/Hits.cc
+index edfe178..b228be6 100755
+--- a/src/Hits.cc
++++ b/src/Hits.cc
+@@ -166,7 +166,7 @@ Hits* Hits::ReadFromFile(FILE* HitFile, int *NumHits, int level, int margin, int
+ while ((read=fscanf(HitFile,"%d %d %d %lf %d %s %d %d %as\n", &deb, &fin,
+ &poids, &evalue, &phase, HitId, &HSPDeb, &HSPFin,HSP)) >= 8)
+ {
+- if (HSP) fprintf(stderr,HSP);
++ if (HSP) fprintf(stderr, "%s", HSP);
+ if (phase < 0 && deb > fin)
+ {
+ int tmp = deb;
diff --git a/sci-biology/eugene/metadata.xml b/sci-biology/eugene/metadata.xml
new file mode 100644
index 0000000..f17a827
--- /dev/null
+++ b/sci-biology/eugene/metadata.xml
@@ -0,0 +1,5 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+ <herd>sci-biology</herd>
+</pkgmetadata>
^ permalink raw reply related [flat|nested] 2+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/eugene/files/, sci-biology/eugene/
@ 2020-09-22 11:12 Aisha Tammy
0 siblings, 0 replies; 2+ messages in thread
From: Aisha Tammy @ 2020-09-22 11:12 UTC (permalink / raw
To: gentoo-commits
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commit: b85d0f1063db0059bd57d983bd5b9f899b4941b8
Author: Aisha Tammy <gentoo <AT> aisha <DOT> cc>
AuthorDate: Tue Sep 22 11:06:46 2020 +0000
Commit: Aisha Tammy <gentoo <AT> aisha <DOT> cc>
CommitDate: Tue Sep 22 11:06:46 2020 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=b85d0f10
sci-biology/eugene: drop package
present in ::gentoo
Package-Manager: Portage-3.0.7, Repoman-3.0.1
Signed-off-by: Aisha Tammy <gentoo <AT> aisha.cc>
sci-biology/eugene/eugene-4.1d.ebuild | 36 ------------------
sci-biology/eugene/files/eugene-3.6-overflow.patch | 13 -------
sci-biology/eugene/files/eugene-3.6-plugins.patch | 43 ----------------------
.../eugene/files/eugene-4.1-format-security.patch | 16 --------
sci-biology/eugene/metadata.xml | 12 ------
5 files changed, 120 deletions(-)
diff --git a/sci-biology/eugene/eugene-4.1d.ebuild b/sci-biology/eugene/eugene-4.1d.ebuild
deleted file mode 100644
index e90ec89b4..000000000
--- a/sci-biology/eugene/eugene-4.1d.ebuild
+++ /dev/null
@@ -1,36 +0,0 @@
-# Copyright 1999-2015 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-inherit autotools eutils
-
-DESCRIPTION="Prokaryotic and Eukaryotic gene predictor"
-HOMEPAGE="http://www.inra.fr/mia/T/EuGene/"
-SRC_URI="https://mulcyber.toulouse.inra.fr/frs/download.php/1359/${P}.tar.gz"
-
-LICENSE="Artistic"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE=""
-
-DEPEND="
- media-libs/gd[png]
- media-libs/libpng:0=
- "
-RDEPEND="${DEPEND}"
-
-RESTRICT="test"
-
-src_prepare() {
- # https://mulcyber.toulouse.inra.fr/tracker/index.php?func=detail&aid=1170
- epatch \
- "${FILESDIR}"/${PN}-3.6-overflow.patch \
- "${FILESDIR}"/${PN}-3.6-plugins.patch \
- "${FILESDIR}"/${PN}-4.1-format-security.patch
- sed \
- -e '/SUBDIRS/ s/doc//' \
- -e '/INSTALL.*doc/ s/\(.*\)//' \
- -i Makefile.am || die
- eautoreconf
-}
diff --git a/sci-biology/eugene/files/eugene-3.6-overflow.patch b/sci-biology/eugene/files/eugene-3.6-overflow.patch
deleted file mode 100644
index 7222530ad..000000000
--- a/sci-biology/eugene/files/eugene-3.6-overflow.patch
+++ /dev/null
@@ -1,13 +0,0 @@
-http://bugs.gentoo.org/show_bug.cgi?id=336607
-
---- eugene-3.6/src/Sensor.cc
-+++ eugene-3.6/src/Sensor.cc
-@@ -224,7 +224,7 @@
- //--------------------------
- void Signals :: PrintS ()
- {
-- char t[7];
-+ char t[10];
- char s = '+';
-
- switch (type) {
diff --git a/sci-biology/eugene/files/eugene-3.6-plugins.patch b/sci-biology/eugene/files/eugene-3.6-plugins.patch
deleted file mode 100644
index 1e910a13d..000000000
--- a/sci-biology/eugene/files/eugene-3.6-plugins.patch
+++ /dev/null
@@ -1,43 +0,0 @@
-http://bugs.gentoo.org/show_bug.cgi?id=297536
-
---- eugene-3.6/src/Makefile.am
-+++ eugene-3.6/src/Makefile.am
-@@ -20,7 +20,7 @@
-
- SUBDIRS = Parametrization GDIF . SensorPlugins
-
--AM_CXXFLAGS = $(eugene_cxxflags) -DDEFAULT_EUGENE_DIR=\"${pkgdatadir}\"
-+AM_CXXFLAGS = $(eugene_cxxflags) -DDEFAULT_EUGENE_DIR=\"${pkgdatadir}\" -DLIB_DIR=\"${libdir}\"
- AM_CFLAGS =
-
- bin_PROGRAMS = eugene
---- eugene-3.6/src/MSensor.cc
-+++ eugene-3.6/src/MSensor.cc
-@@ -97,7 +97,7 @@
- std::string use_name;
-
- if (!IsInitialized) {
-- PluginsDir = (std::string)PAR.getC("eugene_dir")+"/"+PLUGINS_DIR+"/";
-+ PluginsDir = (std::string)LIB_DIR+"/eugene/"+PLUGINS_DIR+"/";
-
- // On récupère les couples nom de sensor/priorité du .par
- PAR.ResetIter();
---- eugene-3.6/Makefile.am
-+++ eugene-3.6/Makefile.am
-@@ -125,7 +125,7 @@
- $(INSTALL) -d $(DESTDIR)/$(pkgdatadir)/web/Style
- $(INSTALL) -d $(DESTDIR)/$(pkgdatadir)/web/Javascripts
- $(INSTALL) -d $(DESTDIR)/$(pkgdatadir)/web/Images
-- $(INSTALL) -d $(DESTDIR)/$(pkgdatadir)/plugins
-+ $(INSTALL) -d $(DESTDIR)/$(libdir)/eugene/plugins
- $(INSTALL) -d $(DESTDIR)/$(pkgdatadir)/cfg
- $(INSTALL) -d $(DESTDIR)/$(pkgdatadir)/models
- $(INSTALL) -d $(DESTDIR)/$(pkgdatadir)/models/WAM
-@@ -144,6 +144,6 @@
- $(INSTALL) -m 644 $(srcdir)/web/Images/*jpg $(DESTDIR)/$(pkgdatadir)/web/Images
- $(INSTALL) -m 644 $(srcdir)/cfg/*.obo $(DESTDIR)/$(pkgdatadir)/cfg
- $(INSTALL) -m 644 $(srcdir)/cfg/*.par $(DESTDIR)/$(pkgdatadir)/cfg
-- $(INSTALL) src/SensorPlugins/*/*.so $(DESTDIR)/$(pkgdatadir)/plugins
-+ $(INSTALL) src/SensorPlugins/*/*.so $(DESTDIR)/$(libdir)/eugene/plugins
- $(INSTALL) $(srcdir)/Procedures/Eval/egn_* $(DESTDIR)/$(pkgdatadir)/Procedures/Eval
- $(INSTALL) $(srcdir)/Procedures/Get/egn_* $(DESTDIR)/$(pkgdatadir)/Procedures/Get
diff --git a/sci-biology/eugene/files/eugene-4.1-format-security.patch b/sci-biology/eugene/files/eugene-4.1-format-security.patch
deleted file mode 100644
index e6e4a6cc8..000000000
--- a/sci-biology/eugene/files/eugene-4.1-format-security.patch
+++ /dev/null
@@ -1,16 +0,0 @@
- src/Hits.cc | 2 +-
- 1 file changed, 1 insertion(+), 1 deletion(-)
-
-diff --git a/src/Hits.cc b/src/Hits.cc
-index edfe178..b228be6 100755
---- a/src/Hits.cc
-+++ b/src/Hits.cc
-@@ -166,7 +166,7 @@ Hits* Hits::ReadFromFile(FILE* HitFile, int *NumHits, int level, int margin, int
- while ((read=fscanf(HitFile,"%d %d %d %lf %d %s %d %d %as\n", &deb, &fin,
- &poids, &evalue, &phase, HitId, &HSPDeb, &HSPFin,HSP)) >= 8)
- {
-- if (HSP) fprintf(stderr,HSP);
-+ if (HSP) fprintf(stderr, "%s", HSP);
- if (phase < 0 && deb > fin)
- {
- int tmp = deb;
diff --git a/sci-biology/eugene/metadata.xml b/sci-biology/eugene/metadata.xml
deleted file mode 100644
index 138cb7705..000000000
--- a/sci-biology/eugene/metadata.xml
+++ /dev/null
@@ -1,12 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
- <maintainer type="person">
- <email>mmokrejs@fold.natur.cuni.cz</email>
- <name>Martin Mokrejs</name>
- </maintainer>
- <maintainer type="project">
- <email>sci-biology@gentoo.org</email>
- <name>Gentoo Biology Project</name>
- </maintainer>
-</pkgmetadata>
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