commit: 5bd35d2287f51fa70024ffc977d34d8e15d8a168
Author: David Seifert gentoo org>
AuthorDate: Sat Sep 24 14:20:44 2016 +
Commit: David Seifert gentoo org>
CommitDate: Sat Sep 24 19:02:03 2016 +
URL:https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=5bd35d22
sci-biology/eugene: Bump to 4.1d from science-overlay
Gentoo-bug: 594700
* EAPI=6
* Fix -Wformat warnings
Package-Manager: portage-2.3.1
sci-biology/eugene/Manifest| 1 +
sci-biology/eugene/eugene-4.1d.ebuild | 42 +++
sci-biology/eugene/files/eugene-4.1d-Wformat.patch | 84 ++
.../eugene/files/eugene-4.1d-fix-c++14.patch | 17 +
4 files changed, 144 insertions(+)
diff --git a/sci-biology/eugene/Manifest b/sci-biology/eugene/Manifest
index 015da1f..d017c65 100644
--- a/sci-biology/eugene/Manifest
+++ b/sci-biology/eugene/Manifest
@@ -1 +1,2 @@
DIST eugene-4.1.tar.gz 7393361 SHA256
faff769f68e1ab1fdec61be34ec7fef3c73805734199765ba11cf1ea9c02f800 SHA512
f4bcf63103754f8fb577d311d181375732411fa926fb0cef86fcd00c373ed5cc5637f1b55fa375a4bb14c5181f7de1dc244570f74cdd1887b6107d5c6cea37b3
WHIRLPOOL
32f4539456c243dd3c6a9d5a986fea210e53e5566aaa0849a26f34832957100623570a0814193059420d53e553247584360635706844ed0ec55c4cc65e235ad4
+DIST eugene-4.1d.tar.gz 7473965 SHA256
c160e6b4206e6700c866f38fee2c8fd0d69972d51ebc5b4cb7680774a419f4c0 SHA512
dab37930e211b3783954f6e4a762450760201b77e0b4214f16724516d9be583d0a7ec44a2f510e73f4370e9c2dc67a425456a057fdba8f51cb72386e16a26ef5
WHIRLPOOL
7ab116acd48648673d2cc633bae26908bf8250c5a17b9d5e8719dfd56edcdf716406b80af26a99700d9ec81e625737c57fe16493f670245f21999fef1c6911eb
diff --git a/sci-biology/eugene/eugene-4.1d.ebuild
b/sci-biology/eugene/eugene-4.1d.ebuild
new file mode 100644
index ..55a73bc
--- /dev/null
+++ b/sci-biology/eugene/eugene-4.1d.ebuild
@@ -0,0 +1,42 @@
+# Copyright 1999-2016 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=6
+
+inherit autotools
+
+DESCRIPTION="Prokaryotic and Eukaryotic gene predictor"
+HOMEPAGE="http://eugene.toulouse.inra.fr/;
+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"
+
+PATCHES=(
+ #
https://mulcyber.toulouse.inra.fr/tracker/index.php?func=detail=1170
+ "${FILESDIR}"/${PN}-3.6-overflow.patch
+ "${FILESDIR}"/${PN}-3.6-plugins.patch
+ "${FILESDIR}"/${PN}-4.1-format-security.patch
+ "${FILESDIR}"/${PN}-4.1d-fix-c++14.patch
+ "${FILESDIR}"/${PN}-4.1d-Wformat.patch
+)
+
+src_prepare() {
+ default
+ sed \
+ -e '/SUBDIRS/ s/doc//' \
+ -e '/INSTALL.*doc/ s/\(.*\)//' \
+ -i Makefile.am || die
+ eautoreconf
+}
diff --git a/sci-biology/eugene/files/eugene-4.1d-Wformat.patch
b/sci-biology/eugene/files/eugene-4.1d-Wformat.patch
new file mode 100644
index ..ab6d2bd
--- /dev/null
+++ b/sci-biology/eugene/files/eugene-4.1d-Wformat.patch
@@ -0,0 +1,84 @@
+Fix -Wformat warnings caused by wrong printf specifiers:
+* Sensor.Riken.cc:95:61: warning: format ‘%d’ expects argument of type ‘int’,
but
+* argument 3 has type ‘std::vector::size_type {aka long unsigned
int}’ [-Wformat=]
+*fprintf(stderr, "%d RAFL EST pairs read, ", RAFLtmp.size());
+
+--- a/src/Hits.cc
b/src/Hits.cc
+@@ -163,7 +163,7 @@
+ if (ThisHit != NULL)
+ for (int i=0; i<*NumHits-1; i++) ThisHit = ThisHit->Next;
+
+-while ((read=fscanf(HitFile,"%d %d %d %lf %d %s %d %d %as\n", , ,
++while ((read=fscanf(HitFile,"%d %d %d %lf %d %s %d %d %ss\n", , ,
+ , , , HitId, ,
,HSP)) >= 8)
+ {
+ if (HSP) fprintf(stderr, "%s", HSP);
+--- a/src/SensorPlugins/Est/Sensor.Est.cc
b/src/SensorPlugins/Est/Sensor.Est.cc
+@@ -1353,13 +1353,13 @@
+ exit(2);
+ }
+
+- fprintf(fp, "vPos %d\n", vPos.size());
++ fprintf(fp, "vPos %zu\n", vPos.size());
+ for (int i=0; i< vPos.size();i++ )
+ {
+ fprintf(fp, "vPos %d\t%d\n",i, vPos[i]);
+ }
+
+- fprintf(fp, "vESTMatch %d\n", vESTMatch.size());
++ fprintf(fp, "vESTMatch %zu\n", vESTMatch.size());
+ for (int i=0; i< vESTMatch.size();i++ )
+ {
+ fprintf(fp, "vESTMatch %d\t\n", vESTMatch[i]);
+--- a/src/SensorPlugins/Riken/Sensor.Riken.cc
b/src/SensorPlugins/Riken/Sensor.Riken.cc
+@@ -92,7 +92,7 @@
+
+
+
+- fprintf(stderr, "%d RAFL EST pairs read, ", RAFLtmp.size());
++ fprintf(stderr, "%zu RAFL EST pairs read, ", RAFLtmp.size());
+
+ sort(RAFLtmp.begin(), RAFLtmp.end(), Before);
+
+@@ -148,7 +148,7 @@
+ }
+ }
+
+- fprintf(stderr,"resulting %d\n",RAFL.size());
++ fprintf(stderr,"resulting %zu\n",RAFL.size());
+ fflush(stderr);
+
+ //for (RAFLtmpindice=0; RAFLtmpindice<
