reinit the tree, so we can have metadata

8 files changed, 232 insertions, 0 deletions

diff --git a/sci-biology/eugene/Manifest b/sci-biology/eugene/Manifest
new file mode 100644
index 000000000000..86558b2b80a5
--- /dev/null
+++ b/sci-biology/eugene/Manifest
@@ -0,0 +1,10 @@
+AUX eugene-3.6-overflow.patch 252 SHA256 cc8795d5f4525a299bc3e17da1e26c1e5fe3ef0c2371c5bf9de36b5037972fc7 SHA512 ed39c8d4aa73ba9e378a025e740c50f1b431fbb4590e3e9204f789081c8b22aef05fb4ce9ac7a0f22015ee03f73392730894a8dea5f6f16cd4533172e46776ce WHIRLPOOL 775e4167b0efa7dfd1539b01c20f4ce268666840d5c2766222deadacfcc21cf6697c177efde0e777c398ad4c888ee3df1b57113b451b1700ca5965b718c8432f
+AUX eugene-3.6-plugins.patch 1784 SHA256 0ec9c0d2bf6009e89612c3d95711b211aefc267d3eb6b75bc6279318256bc46d SHA512 300601ee6abe469460ebbe29c45468d516e5e781ad4b0542e9590de38ba6e98e3697c5f6f92f83212a1aa6da5e0650636af279d82241277c0b43fb5472028fcc WHIRLPOOL 695b8efe382014c6e1c9c44bebab3ed417b7ad736fd7db5623911971926bab284e9bdfb2ee5061287c99a93433d060040285765f37e0b283ecd83717adca5359
+AUX eugene-4.1-format-security.patch 609 SHA256 391521469ce4c6df425084d9b2df611efe2721f563b15843f495064ed72d4553 SHA512 f4eedd5b70309d4b8eedce8f3a4f79b65e595d407e88fd79e7f4f2f8c98880432366124b7f0a34c9032c9a498a1db607b0cac20304e84ec01f736589924ff362 WHIRLPOOL 5b703b25d049f9f9fb78d543e72cde8130f9f1e116aac26e1c748897fe6558507d22f2ce08fc7c4e65568f5213fe4fc7de111a58043c88ee94586c4aca3f71e0
+AUX eugene-4.1d-Wformat.patch 2719 SHA256 14277b76320aed2551af0557c373431f556b4b39eac8b73365b373a253a6a543 SHA512 b235c11791caea63109009b858cde7ec179166640f009bf58caf33a8502345360efb71208a330572d7f870c468810bb9ab54db3e2af187a0d2baba7e12c6ff96 WHIRLPOOL be016418800bf8410bb637b2827ddec33366607dc4e0a0bdc014b1ab21599dbc0b26b5363c70d3c52d6da0b92d8119444addceeeac6466dbbdfe54137dec845b
+AUX eugene-4.1d-fix-c++14.patch 635 SHA256 80a443e3390ea4fcb13d74f7a3085d690d11409c4212ed35ab592116ff0760f4 SHA512 8ff6a8a2ee4b70b14d0fa9984c057307fe5b7d22e8a26969d82fb1ab7ee30a90cb3520ea8d3e16a59f09dfc46a3310cb43c621fabb31a39216209a4c3523e718 WHIRLPOOL b7c847f0bcf3386b585106345401f7742b0cf4de92556fc5ee98273c1f94ff619e2c640336c7d2d05205c797d6a17616e4775d06f7d1d49ef9cfcbc7015ad6a9
+DIST eugene-4.1d.tar.gz 7473965 SHA256 c160e6b4206e6700c866f38fee2c8fd0d69972d51ebc5b4cb7680774a419f4c0 SHA512 dab37930e211b3783954f6e4a762450760201b77e0b4214f16724516d9be583d0a7ec44a2f510e73f4370e9c2dc67a425456a057fdba8f51cb72386e16a26ef5 WHIRLPOOL 7ab116acd48648673d2cc633bae26908bf8250c5a17b9d5e8719dfd56edcdf716406b80af26a99700d9ec81e625737c57fe16493f670245f21999fef1c6911eb
+EBUILD eugene-4.1d.ebuild 893 SHA256 acf012e114990142a903232435a07e36368831cf4f05ff8746398380383ead3b SHA512 9db8db10b469392a9a124f02dcf1272307c6c44b9734d5f101dd13092701a16f64394408200731a63a14d5ff9e2f3ca83b2391b762b312f1a4d163dffa0b0822 WHIRLPOOL 28c67e6fe06406e0b6648ae6334d48c17f19b0a1959a02df38449553762f5543ef08f1a1cff64bd5f4668b5bc09ba4d9ec2f1b7d7d9ef24920d60a17dcfa9eae
+MISC ChangeLog 2831 SHA256 d9ac5006d8a7cd57a6b3a727b21556a20438a300f29b0cf10249ef8630cff0f3 SHA512 c7336aec414a57f81cd85c2b92556a0879bcbb9513b443439be282e02ae4073ce3b5dfad61d0265006a640586d8c0edc08ff6af081d2f794702e1d4b0191e177 WHIRLPOOL be4d86801ceb655f5017be4c527f2a992df7473b257b9febbec8809c1c918beef7844b70dca9c86e2cb0cfb8eb3c38d22b893989d2f4e55da570f0cbd3737e18
+MISC ChangeLog-2015 2009 SHA256 9cc7672d01f3ea069e1465072396b59e81cd8aff667ccf3e5c06776e0bbc571b SHA512 4c25d7d81ca0f63765b8635bff0043d9736e6cec7bc0ed5a4481309851e69bb7a059348e7d5b9a3b0073d68b5e04c3890349a9d0ba92d56f1c319500c58802c6 WHIRLPOOL 664c9da77c8e2bc49b29633d4f04cd9a2e1f1ed7e8f62c276cbe9865c7918ad6903e9cc78b87ac8788e56e331fc08eba18cbf864c0efcf8a72721460d1a82b32
+MISC metadata.xml 267 SHA256 b3535fccca0fc8511c1245214c1a7c105447b35f21093bda132991874ce82d48 SHA512 91ab266d9ab24401bc0fec759c5b6cfcf44a3c5669fc31c7301d79770839bb5dfa0e155d949392ef06176b4a0b2c32b91b1b54b0027f972db61f0a5e54644403 WHIRLPOOL d841a2f928c50434f2e8c65f583ea3aa2d04e5cebd664b1531ab5373260f735219131991000bbb2b21aa3add05dcdce29548b78eac8d8c0eced6dc5505b64e13
diff --git a/sci-biology/eugene/eugene-4.1d.ebuild b/sci-biology/eugene/eugene-4.1d.ebuild
new file mode 100644
index 000000000000..dbf8139e9e20
--- /dev/null
+++ b/sci-biology/eugene/eugene-4.1d.ebuild
@@ -0,0 +1,41 @@
+# Copyright 1999-2017 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+
+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-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/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>
diff --git a/sci-biology/eugene/metadata.xml b/sci-biology/eugene/metadata.xml
new file mode 100644
index 000000000000..959160fe46b1
--- /dev/null
+++ b/sci-biology/eugene/metadata.xml
@@ -0,0 +1,8 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+  <maintainer type="project">
+    <email>sci-biology@gentoo.org</email>
+    <name>Gentoo Biology Project</name>
+  </maintainer>
+</pkgmetadata>