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author | Robin H. Johnson <robbat2@gentoo.org> | 2015-08-08 13:49:04 -0700 |
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committer | Robin H. Johnson <robbat2@gentoo.org> | 2015-08-08 17:38:18 -0700 |
commit | 56bd759df1d0c750a065b8c845e93d5dfa6b549d (patch) | |
tree | 3f91093cdb475e565ae857f1c5a7fd339e2d781e /sci-biology/eugene | |
download | gentoo-56bd759df1d0c750a065b8c845e93d5dfa6b549d.tar.gz gentoo-56bd759df1d0c750a065b8c845e93d5dfa6b549d.tar.bz2 gentoo-56bd759df1d0c750a065b8c845e93d5dfa6b549d.zip |
proj/gentoo: Initial commit
This commit represents a new era for Gentoo:
Storing the gentoo-x86 tree in Git, as converted from CVS.
This commit is the start of the NEW history.
Any historical data is intended to be grafted onto this point.
Creation process:
1. Take final CVS checkout snapshot
2. Remove ALL ChangeLog* files
3. Transform all Manifests to thin
4. Remove empty Manifests
5. Convert all stale $Header$/$Id$ CVS keywords to non-expanded Git $Id$
5.1. Do not touch files with -kb/-ko keyword flags.
Signed-off-by: Robin H. Johnson <robbat2@gentoo.org>
X-Thanks: Alec Warner <antarus@gentoo.org> - did the GSoC 2006 migration tests
X-Thanks: Robin H. Johnson <robbat2@gentoo.org> - infra guy, herding this project
X-Thanks: Nguyen Thai Ngoc Duy <pclouds@gentoo.org> - Former Gentoo developer, wrote Git features for the migration
X-Thanks: Brian Harring <ferringb@gentoo.org> - wrote much python to improve cvs2svn
X-Thanks: Rich Freeman <rich0@gentoo.org> - validation scripts
X-Thanks: Patrick Lauer <patrick@gentoo.org> - Gentoo dev, running new 2014 work in migration
X-Thanks: Michał Górny <mgorny@gentoo.org> - scripts, QA, nagging
X-Thanks: All of other Gentoo developers - many ideas and lots of paint on the bikeshed
Diffstat (limited to 'sci-biology/eugene')
-rw-r--r-- | sci-biology/eugene/Manifest | 1 | ||||
-rw-r--r-- | sci-biology/eugene/eugene-4.1.ebuild | 37 | ||||
-rw-r--r-- | sci-biology/eugene/files/eugene-3.6-overflow.patch | 13 | ||||
-rw-r--r-- | sci-biology/eugene/files/eugene-3.6-plugins.patch | 43 | ||||
-rw-r--r-- | sci-biology/eugene/files/eugene-4.1-format-security.patch | 16 | ||||
-rw-r--r-- | sci-biology/eugene/metadata.xml | 5 |
6 files changed, 115 insertions, 0 deletions
diff --git a/sci-biology/eugene/Manifest b/sci-biology/eugene/Manifest new file mode 100644 index 000000000000..015da1fb031b --- /dev/null +++ b/sci-biology/eugene/Manifest @@ -0,0 +1 @@ +DIST eugene-4.1.tar.gz 7393361 SHA256 faff769f68e1ab1fdec61be34ec7fef3c73805734199765ba11cf1ea9c02f800 SHA512 f4bcf63103754f8fb577d311d181375732411fa926fb0cef86fcd00c373ed5cc5637f1b55fa375a4bb14c5181f7de1dc244570f74cdd1887b6107d5c6cea37b3 WHIRLPOOL 32f4539456c243dd3c6a9d5a986fea210e53e5566aaa0849a26f34832957100623570a0814193059420d53e553247584360635706844ed0ec55c4cc65e235ad4 diff --git a/sci-biology/eugene/eugene-4.1.ebuild b/sci-biology/eugene/eugene-4.1.ebuild new file mode 100644 index 000000000000..088ecc7a1a8b --- /dev/null +++ b/sci-biology/eugene/eugene-4.1.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="Eukaryotic gene predictor" +HOMEPAGE="http://www.inra.fr/mia/T/EuGene/" +SRC_URI="https://mulcyber.toulouse.inra.fr/frs/download.php/1157/${P}.tar.gz" + +LICENSE="Artistic" +SLOT="0" +KEYWORDS="amd64 x86" +IUSE="" + +DEPEND=" + media-libs/gd[png] + media-libs/libpng:0= + " +RDEPEND="${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 \ + "${FILESDIR}"/${P}-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 000000000000..7222530ad771 --- /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 000000000000..1e910a13d5b1 --- /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 000000000000..e6e4a6cc8bd7 --- /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 000000000000..f17a827e3101 --- /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> |