commit: 5bd35d2287f51fa70024ffc977d34d8e15d8a168 Author: David Seifert <soap <AT> gentoo <DOT> org> AuthorDate: Sat Sep 24 14:20:44 2016 +0000 Commit: David Seifert <soap <AT> gentoo <DOT> org> CommitDate: Sat Sep 24 19:02:03 2016 +0000 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 00000000..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&aid=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 00000000..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<RAFLgene>::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", &deb, &fin, ++ while ((read=fscanf(HitFile,"%d %d %d %lf %d %s %d %d %ss\n", &deb, &fin, + &poids, &evalue, &phase, HitId, &HSPDeb, &HSPFin,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< (int)RAFL.size(); RAFLtmpindice++) { +--- a/src/SensorPlugins/SMachine/Sensor.SMachine.cc ++++ b/src/SensorPlugins/SMachine/Sensor.SMachine.cc +@@ -197,7 +197,7 @@ + fclose(fp); + + if (end ==2) { +- fprintf(stderr, "Error in SpliceMachine splice site file %s, line %d\n", name, len); ++ fprintf(stderr, "Error in SpliceMachine splice site file %s, line %zu\n", name, len); + exit(2); + } + } +--- a/src/SoTerms.cc ++++ b/src/SoTerms.cc +@@ -67,14 +67,14 @@ + j++; + if (line[0] == 'i' && line[1] == 'd') + { +- i = sscanf(line, "id: %s", &value); ++ i = sscanf(line, "id: %s", value); + if (i > 0) + { + char soId[60]; + char soName[60]; + strcpy (soId, value ); + fgets (line, MAX_LINE, fp); +- i = sscanf(line, "name: %s", &value); ++ i = sscanf(line, "name: %s", value); + strcpy (soName, value ); + idToName_[to_string(soId)]=to_string(soName); + nameToId_[to_string(soName)]=to_string(soId); diff --git a/sci-biology/eugene/files/eugene-4.1d-fix-c++14.patch b/sci-biology/eugene/files/eugene-4.1d-fix-c++14.patch new file mode 100644 index 00000000..a27261c --- /dev/null +++ b/sci-biology/eugene/files/eugene-4.1d-fix-c++14.patch @@ -0,0 +1,17 @@ +Fix building with C++14, which errors out due to collisions with isinf +from cmath. We don't need to fix ancient broken OSX toolchains. +See also: https://bugs.gentoo.org/show_bug.cgi?id=594700 + +--- a/src/SensorPlugins/Tester/Sensor.Tester.cc ++++ b/src/SensorPlugins/Tester/Sensor.Tester.cc +@@ -18,9 +18,7 @@ + // ------------------------------------------------------------------ + + // MacOS-X kludge. cmath undefines these macros. Turn them into inlines +-#include <math.h> +-inline int (isinf)(double r) { return isinf(r); } +-inline int (isnan)(double r) { return isnan(r); } ++#include <cmath> + + #include <iomanip> + #include <fstream>
