diff options
author | V3n3RiX <venerix@redcorelinux.org> | 2017-10-09 18:53:29 +0100 |
---|---|---|
committer | V3n3RiX <venerix@redcorelinux.org> | 2017-10-09 18:53:29 +0100 |
commit | 4f2d7949f03e1c198bc888f2d05f421d35c57e21 (patch) | |
tree | ba5f07bf3f9d22d82e54a462313f5d244036c768 /sci-biology/eugene/files |
reinit the tree, so we can have metadata
Diffstat (limited to 'sci-biology/eugene/files')
5 files changed, 173 insertions, 0 deletions
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> |