gentoo resync : 09.07.2022

4 files changed, 117 insertions, 33 deletions

diff --git a/sci-biology/eugene/Manifest b/sci-biology/eugene/Manifest
index ad0cf62db829..78dd82270c34 100644
--- a/sci-biology/eugene/Manifest
+++ b/sci-biology/eugene/Manifest
@@ -1,8 +1,9 @@
 AUX eugene-3.6-overflow.patch 252 BLAKE2B 83b82992d734996b2878028329642ec015a53f6b281255637e5b99eb1d69eea0a6d44b03a2f24959eebc426553835142b479636a629023731d5a2d05ad2b5064 SHA512 ed39c8d4aa73ba9e378a025e740c50f1b431fbb4590e3e9204f789081c8b22aef05fb4ce9ac7a0f22015ee03f73392730894a8dea5f6f16cd4533172e46776ce
-AUX eugene-3.6-plugins.patch 1784 BLAKE2B 88ab82e4a1f351587108371ef545ae630277ddb1d4d5bdd31dfa58bc705ec2f06b92723622c37b7f2ac917bc18f089060d2a4c0f2ea3a6e3aa4af288429e13f9 SHA512 300601ee6abe469460ebbe29c45468d516e5e781ad4b0542e9590de38ba6e98e3697c5f6f92f83212a1aa6da5e0650636af279d82241277c0b43fb5472028fcc
+AUX eugene-3.6-plugins.patch 1843 BLAKE2B 8bf8f09a43ec35838058094188973f985f69992e7f273b5c40f71abf39b498ec9bad1f8c8db9f0b1f5ec77796abefbf150afa9dc3a6764d33d16c3bdc175f87d SHA512 66d9191656821ec958804462aec83885560dfa35f075e1b012401d9ee4b86368b83005353d0093af0b95dc313b1fee6995f981504737242820125c5ead20ae9c
 AUX eugene-4.1-format-security.patch 609 BLAKE2B 1571c5c3af87e5ea49fa1f5b5ce19487c1493aa85e8f7782645874abf62c9e5d09e2e8c4c6aa2c5f44aedba257859d0245fcbbd28ae57d24dae118c562561a3a SHA512 f4eedd5b70309d4b8eedce8f3a4f79b65e595d407e88fd79e7f4f2f8c98880432366124b7f0a34c9032c9a498a1db607b0cac20304e84ec01f736589924ff362
 AUX eugene-4.1d-Wformat.patch 2719 BLAKE2B 6dbdcb4e9946d0245eeeca1ff23b5d52ff3b37a64cbd88838229836323959325c7f54c9b00dec0abc02c218c4761ddef00def7f111c41df628af6d06f2147a6e SHA512 b235c11791caea63109009b858cde7ec179166640f009bf58caf33a8502345360efb71208a330572d7f870c468810bb9ab54db3e2af187a0d2baba7e12c6ff96
 AUX eugene-4.1d-fix-c++14.patch 635 BLAKE2B d6e72bd7e4b80f21ebbc78cfc5f791fa23b0c22cd3414a5ecaaf50c54e1789625901bd0f9a5357f523de5dbca02d75229557d8a032f2e7cdd345e7dae3dbe19d SHA512 8ff6a8a2ee4b70b14d0fa9984c057307fe5b7d22e8a26969d82fb1ab7ee30a90cb3520ea8d3e16a59f09dfc46a3310cb43c621fabb31a39216209a4c3523e718
+AUX eugene-4.1d-portable-getopt.patch 1433 BLAKE2B 8de256a490936a6c893c055917919a7cfc6a510675b4c12021d7cedb8a6cdf4aa73fb60d6ae4186b1df7abb784da09a9dc440464d8cbd90ac5d9ea758262391e SHA512 6a365eed393a27c080ec6f0eaa288a88e7909daa657637cb819aeb3e908934f8f228bd1026205402bc180e54c4ffe56be5ff5eedc95d3817b65da08774c9496c
 DIST eugene-4.1d.tar.gz 7473965 BLAKE2B 537ba871b701a5c199791809f76ea883ff77fe768e27a69b95186ef82ab32cab9b5761405a9fadfeea9f58fe88cadce83bba4b1fa6cba5f4ede2347a516d1df0 SHA512 dab37930e211b3783954f6e4a762450760201b77e0b4214f16724516d9be583d0a7ec44a2f510e73f4370e9c2dc67a425456a057fdba8f51cb72386e16a26ef5
-EBUILD eugene-4.1d.ebuild 893 BLAKE2B 5aec582935c0e5e2c6ea9a14ed06a14d65c2759a3bfa1fda5fa940f1f700fc0bcf198bb65d47996afa4adc719bf9d40613bb635089e59cddea566518702d4f77 SHA512 9db8db10b469392a9a124f02dcf1272307c6c44b9734d5f101dd13092701a16f64394408200731a63a14d5ff9e2f3ca83b2391b762b312f1a4d163dffa0b0822
+EBUILD eugene-4.1d-r1.ebuild 950 BLAKE2B 33eeae7972f006763a905f06542482714564d8b46d05485886f9441520a3ec9e39620a583ec66d097bc2a26b62ccf953fcc2699075426b8b855541c0af26fd48 SHA512 95ef458f3af2b1ab478d239ebb83cf64105c3b9128e06e72642d0e559ef405beb7e6b2b494320a7a866a108498715408ee693111a0b3ebd5e02297c156811cd0
 MISC metadata.xml 268 BLAKE2B a4d67334cdad8626d60e46b677ee1c83f569e5e20b3739a7664bb33be1829f8478af35e135bf734a6ff151b8543ea6c4ecafbf822cee8189f7e7096bd9698711 SHA512 59d3d8213b1a219396b74b6f4188c01e1cb4eb1c63e6792ce1e7fdb8000d1a4625919337ff77288ca7f7e07d9753f481d2381a06f554012633cd678194c980de
diff --git a/sci-biology/eugene/eugene-4.1d.ebuild b/sci-biology/eugene/eugene-4.1d-r1.ebuild
index dbf8139e9e20..b1d9f409c096 100644
--- a/sci-biology/eugene/eugene-4.1d.ebuild
+++ b/sci-biology/eugene/eugene-4.1d-r1.ebuild
@@ -1,7 +1,7 @@
-# Copyright 1999-2017 Gentoo Foundation
+# Copyright 1999-2022 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
-EAPI=6
+EAPI=8
 
 inherit autotools
 
@@ -12,16 +12,13 @@ SRC_URI="https://mulcyber.toulouse.inra.fr/frs/download.php/1359/${P}.tar.gz"
 LICENSE="Artistic"
 SLOT="0"
 KEYWORDS="amd64 x86"
-IUSE=""
+RESTRICT="test"
 
 DEPEND="
 	media-libs/gd[png]
-	media-libs/libpng:0=
-	"
+	media-libs/libpng:="
 RDEPEND="${DEPEND}"
 
-RESTRICT="test"
-
 PATCHES=(
 	# https://mulcyber.toulouse.inra.fr/tracker/index.php?func=detail&aid=1170
 	"${FILESDIR}"/${PN}-3.6-overflow.patch
@@ -29,6 +26,7 @@ PATCHES=(
 	"${FILESDIR}"/${PN}-4.1-format-security.patch
 	"${FILESDIR}"/${PN}-4.1d-fix-c++14.patch
 	"${FILESDIR}"/${PN}-4.1d-Wformat.patch
+	"${FILESDIR}"/${PN}-4.1d-portable-getopt.patch
 )
 
 src_prepare() {
@@ -37,5 +35,6 @@ src_prepare() {
 		-e '/SUBDIRS/ s/doc//' \
 		-e '/INSTALL.*doc/ s/\(.*\)//' \
 		-i Makefile.am || die
+	rm src/getopt.h || die
 	eautoreconf
 }
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