diff options
author | V3n3RiX <venerix@koprulu.sector> | 2022-07-09 15:43:36 +0100 |
---|---|---|
committer | V3n3RiX <venerix@koprulu.sector> | 2022-07-09 15:43:36 +0100 |
commit | 2719f73b6813d11d13a9650cdd2ab8ec6e69385d (patch) | |
tree | 8c816148bcbd22757d892089c989ae614eae4f5a /sci-biology/eugene/files | |
parent | 0f558761aa2dee1017b4751e4017205e015a9560 (diff) |
gentoo resync : 09.07.2022
Diffstat (limited to 'sci-biology/eugene/files')
-rw-r--r-- | sci-biology/eugene/files/eugene-3.6-plugins.patch | 58 | ||||
-rw-r--r-- | sci-biology/eugene/files/eugene-4.1d-portable-getopt.patch | 74 |
2 files changed, 108 insertions, 24 deletions
diff --git a/sci-biology/eugene/files/eugene-3.6-plugins.patch b/sci-biology/eugene/files/eugene-3.6-plugins.patch index 1e910a13d5b1..e7424f73fc63 100644 --- a/sci-biology/eugene/files/eugene-3.6-plugins.patch +++ b/sci-biology/eugene/files/eugene-3.6-plugins.patch @@ -1,7 +1,36 @@ -http://bugs.gentoo.org/show_bug.cgi?id=297536 +https://bugs.gentoo.org/297536 ---- eugene-3.6/src/Makefile.am -+++ eugene-3.6/src/Makefile.am +--- a/configure.ac ++++ b/configure.ac +@@ -28,6 +28,7 @@ + AC_PROG_CC + AC_PROG_AWK + AC_PROG_LN_S ++AM_PROG_AR + AC_PROG_RANLIB + + +--- a/Makefile.am ++++ b/Makefile.am +@@ -137,7 +137,7 @@ + $(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 +@@ -160,6 +160,6 @@ + $(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 +--- a/src/Makefile.am ++++ b/src/Makefile.am @@ -20,7 +20,7 @@ SUBDIRS = Parametrization GDIF . SensorPlugins @@ -11,8 +40,8 @@ http://bugs.gentoo.org/show_bug.cgi?id=297536 AM_CFLAGS = bin_PROGRAMS = eugene ---- eugene-3.6/src/MSensor.cc -+++ eugene-3.6/src/MSensor.cc +--- a/src/MSensor.cc ++++ b/src/MSensor.cc @@ -97,7 +97,7 @@ std::string use_name; @@ -22,22 +51,3 @@ http://bugs.gentoo.org/show_bug.cgi?id=297536 // 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-4.1d-portable-getopt.patch b/sci-biology/eugene/files/eugene-4.1d-portable-getopt.patch new file mode 100644 index 000000000000..156cb4bbdfac --- /dev/null +++ b/sci-biology/eugene/files/eugene-4.1d-portable-getopt.patch @@ -0,0 +1,74 @@ +--- a/src/Param.h ++++ b/src/Param.h +@@ -28,26 +28,14 @@ + #include <vector> + #include <string> + #include <string.h> ++#include <unistd.h> + #ifdef HAVE_STRINGS_H + #include <strings.h> + #endif +-// MacOS-X has getopt() defined is stdlib and the library in the libSystem +-#ifndef __APPLE__ +-#ifdef HAVE_GETOPT_H +-#include <getopt.h> +-#else +-#ifndef HAVE_GETOPT +-#include "getopt.h" +-#endif +-#endif +-#endif + + #include "Const.h" + #include "System.h" + +-extern char *optarg; +-extern int optind; +- + + class ltstr + { +--- a/src/SensorPlugins/MarkovIMM/GetData/CEM.cc ++++ b/src/SensorPlugins/MarkovIMM/GetData/CEM.cc +@@ -22,18 +22,11 @@ + #include "../../../../config.h" + #endif + +-#ifdef HAVE_GETOPT_H +-#include <getopt.h> +-#else +-#ifndef HAVE_GETOPT +-#include "../../../getopt.h" +-#endif +-#endif +- + #include "../../../System.cc" + #include "../../../Const.h" + #include "../../0_SensorTk/EndianConv.h" + #include "strarray.h" ++#include "unistd.h" + #include <vector> + + // Constantes +--- a/src/SensorPlugins/MarkovIMM/GetData/TrainIMM.cc ++++ b/src/SensorPlugins/MarkovIMM/GetData/TrainIMM.cc +@@ -22,18 +22,11 @@ + #include "../../../../config.h" + #endif + +-#ifdef HAVE_GETOPT_H +-#include <getopt.h> +-#else +-#ifndef HAVE_GETOPT +-#include "../../../getopt.h" +-#endif +-#endif +- + #include "../../../System.cc" + #include "../../../Const.h" + #include "../../0_SensorTk/EndianConv.h" + #include "strarray.h" ++#include "unistd.h" + + + // Constantes |