sci-biology/eugene: Bump to 4.1d from science-overlay

Gentoo-bug: 594700
* EAPI=6
* Fix -Wformat warnings

Package-Manager: portage-2.3.1

4 files changed, 144 insertions, 0 deletions

diff --git a/sci-biology/eugene/Manifest b/sci-biology/eugene/Manifest
index 015da1fb031b..d017c6516a49 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 000000000000..55a73bc3c4cd
--- /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 000000000000..ab6d2bd1d2ee
--- /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 000000000000..a27261c68c06
--- /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>