gentoo auto-resync : 12:03:2024 - 12:46:41

6 files changed, 234 insertions, 2 deletions

diff --git a/sci-biology/Manifest.gz b/sci-biology/Manifest.gz
index e479838ad584..895adecb6204 100644
--- a/sci-biology/Manifest.gz
+++ b/sci-biology/Manifest.gz
diff --git a/sci-biology/glimmerhmm/Manifest b/sci-biology/glimmerhmm/Manifest
index f0f760cdd059..8c778076076c 100644
--- a/sci-biology/glimmerhmm/Manifest
+++ b/sci-biology/glimmerhmm/Manifest
@@ -1,5 +1,9 @@
+AUX 0001-fix-ridiculous-ODR-violation.patch 782 BLAKE2B 0a52cfe41e595c0717fe977d74c50c46cb74ffb0da182a987c3e57b69e048468e12b2e506953a562fc7159253ca7d38849c262ca68fb988ddd68e2f1404ac35b SHA512 b65d906b290a2e008711bead679d9f7f85bf1289fdf729d9242c36aaa0f332b0ebef021b5c4d43c3e2ba1d892becd2e652bc0db752213bef39ca5973192dbde1
 AUX 3.0.1-gentoo.patch 4235 BLAKE2B 8263516018df83c39da08e906bcdbfb8445ef26c064a82d8edf547fba5b569921905dd32476a99726f1864cc24ec5464fbc48db55e08cca0b9555647dddae120 SHA512 e0350a4b604fe76462bbb7139264a9b2916c050c335589031bdca0cf0c6a653bbf84d9827f5c2096ff13f1007d4ef2e93698814758f787a98e4dd818be44bc3d
+AUX 3.0.4-gentoo.patch 4318 BLAKE2B 6389fddbca39f6acdabf066b0de488423b0e10068e038fc25520a2ee3a1ab592f008b699d48c235de5deff31ca8569a0a2cec24e558c3684420eaddc82f649b4 SHA512 ed08d5ccd3a756e013b6883297436348e5d296f5d8f7647c17552db00ccf553d149d5bae2ca598b1546e016e79002ad5cd35c95fa7175b530673531c084426aa
 AUX glimmerhmm-3.0.1-fix-data-path.patch 512 BLAKE2B fc37954be58eaaec074fbb3ff9a8109907fc71be39365aa07e62c884a78c910d0ffcceaee907736107b56d97f0e7c9baf30f9fd71f239ede6cebe4bc9bcfb59e SHA512 0e1b65887a7a27c8d9adbf88a904ddbb4afc56e5052a6693ca57ae160bc9c6dab8589b633d364aead873fc1aaa671580bfc0deed9bde153f5069a0351244ef51
 DIST GlimmerHMM-3.0.1.tar.gz 45475952 BLAKE2B 355f4e9f26c31167e0935de8012fa99a243838d0dd47e0e46ae4cb1df4eaf188a13fb365025bc4be82805c89f36f534a9907030515f96b9422340e9e966f4ea6 SHA512 15307d1982527bd83433882552cd3e12c76a65a2a119b6911a748dc801f80b1fc5732cb769a52e5c6281bdd48cf619a02edbd1b96ee40319fc620a3a7cdd82b7
-EBUILD glimmerhmm-3.0.1-r1.ebuild 990 BLAKE2B af2935449242c6324045c64c9a91a6d6f887891dcfbee89817c067c0c7a65792614f8244af428608f8d2b0fe5e4cc0939f56ef99b567ebfee678a2948f93bc5c SHA512 a17e8d42120751084bb2330ceb57d87b48dcb3e3e2222577f350a69a37777a38a3b9dd323bd055f7e8248b3c286021249577f43f895d0dd49fd4aa77dc624037
+DIST GlimmerHMM-3.0.4.tar.gz 45692137 BLAKE2B e271ea506e77d0038e343030be1875de0c92265ac2808cf35b7ba872a2d2f9416d645cd373f2ba6816f8352b4367a3a7c878c4dea772fcadf8954aabd91fca64 SHA512 e10d89550c938faf4b1e2a259213ad88a7443b7597cf753c7041698ac78d468f4ed93e0f7736640cd2fe97abe227d54eb7feca1fe7450d72f83896a94ef7a70b
+EBUILD glimmerhmm-3.0.1-r1.ebuild 1045 BLAKE2B 75db2c6d64bea85d6b81c945187b9bf873ca6449a508725b5e2d1a795db2d173b7fe429d4fb95ce73fdc0b21ebfb7fd49aed65abe3a819ba1fceacc59a823651 SHA512 064be899038c26379614d1ff8a4362a985470095dc13d117ea7c5d6d6e77e7bf647fae0c55139b1b673426d7fbbc0e170ee96c5f1a8eb7e85619a3a94cb1096f
+EBUILD glimmerhmm-3.0.4.ebuild 1041 BLAKE2B e85b71d13b684d0e54ec617745eb46be858ccc4e7b000138942ceb987bd434563860f4abe4bfafa2aafa128294b9103a728334cdab4881d2d281af0cfaf603fa SHA512 ae38017c8cbed502ee1d5c8775d3641c778b486373db9cc609bcb965463fdd88579cfe42114a78a6b538aeb62dc365f263bd9a0872d359d55ed6e49b0ca9a986
 MISC metadata.xml 268 BLAKE2B a4d67334cdad8626d60e46b677ee1c83f569e5e20b3739a7664bb33be1829f8478af35e135bf734a6ff151b8543ea6c4ecafbf822cee8189f7e7096bd9698711 SHA512 59d3d8213b1a219396b74b6f4188c01e1cb4eb1c63e6792ce1e7fdb8000d1a4625919337ff77288ca7f7e07d9753f481d2381a06f554012633cd678194c980de
diff --git a/sci-biology/glimmerhmm/files/0001-fix-ridiculous-ODR-violation.patch b/sci-biology/glimmerhmm/files/0001-fix-ridiculous-ODR-violation.patch
new file mode 100644
index 000000000000..58fa92819b59
--- /dev/null
+++ b/sci-biology/glimmerhmm/files/0001-fix-ridiculous-ODR-violation.patch
@@ -0,0 +1,27 @@
+From 282b1a113e002d8b90dedb6a5b6a6dc35e7310d1 Mon Sep 17 00:00:00 2001
+From: Eli Schwartz <eschwartz93@gmail.com>
+Date: Tue, 12 Mar 2024 01:45:16 -0400
+Subject: [PATCH] fix ridiculous ODR violation
+
+The return value of a function defined in another file is whatever that
+file defines, not "void because we didn't assign it to anything".
+---
+ sources/oc1.h | 2 +-
+ 1 file changed, 1 insertion(+), 1 deletion(-)
+
+diff --git a/sources/oc1.h b/sources/oc1.h
+index 7b068c8..e28017d 100644
+--- a/sources/oc1.h
++++ b/sources/oc1.h
+@@ -49,7 +49,7 @@ struct tree_node
+   EDGE edge; /* used only in the display module. */
+  };
+ 
+-void error(char *);
++int error(char *);
+ void free_ivector(int *,int,int);
+ void free_vector(float *,int,int);
+ void free_dvector(double*,int,float);
+-- 
+2.43.2
+
diff --git a/sci-biology/glimmerhmm/files/3.0.4-gentoo.patch b/sci-biology/glimmerhmm/files/3.0.4-gentoo.patch
new file mode 100644
index 000000000000..d3838b1dc9bc
--- /dev/null
+++ b/sci-biology/glimmerhmm/files/3.0.4-gentoo.patch
@@ -0,0 +1,153 @@
+diff --git a/sources/makefile b/sources/makefile
+index f287d71..c560f48 100644
+--- a/sources/makefile
++++ b/sources/makefile
+@@ -2,25 +2,22 @@
+ 
+ 
+ 
+-CC=g++
+-CFLAGS=-g
+-
+ all: glimmerhmm
+ 
+ glimmerhmm: glimmerhmm.o graph.o sites.o tree_util_prob.o util.o
+-	$(CC) $(CFLAGS) -o glimmerhmm glimmerhmm.o graph.o sites.o tree_util_prob.o util.o  -lm 
++	$(CXX) $(CXXFLAGS) $(LDFLAGS) -o glimmerhmm glimmerhmm.o graph.o sites.o tree_util_prob.o util.o  -lm 
+ 
+ glimmerhmm.o: glimmerhmm.c
+-	$(CC) $(CFLAGS) -c glimmerhmm.c
++	$(CXX) $(CXXFLAGS) -c glimmerhmm.c
+ 
+ graph.o: graph.c 
+-	$(CC) $(CFLAGS) -c graph.c
++	$(CXX) $(CXXFLAGS) -c graph.c
+ 
+ sites.o: sites.c
+-	$(CC) $(CFLAGS) -c sites.c
++	$(CXX) $(CXXFLAGS) -c sites.c
+ 
+ tree_util_prob.o: tree_util_prob.c
+-	$(CC) $(CFLAGS) -c tree_util_prob.c
++	$(CXX) $(CXXFLAGS) -c tree_util_prob.c
+ 
+ util.o: util.c
+-	$(CC) $(CFLAGS) -c util.c
++	$(CXX) $(CXXFLAGS) -c util.c
+diff --git a/train/makefile b/train/makefile
+index 56eaa13..d660cf1 100644
+--- a/train/makefile
++++ b/train/makefile
+@@ -2,11 +2,8 @@
+ 
+ # C compiler
+ 
+-C       = gcc 
+-CC      = g++ 
+ #CFLAGS  = -O1 ${SEARCHDIRS}
+ #CFLAGS  = -O3 -g -Wall
+-CFLAGS = -Wall -g
+ LIBS    = -lm
+ 
+ MAKEFILE= makefile
+@@ -16,67 +13,79 @@ all:    build-icm build-icm-noframe build1 build2 falsecomp findsites karlin sco
+ 
+ 
+ misc.o: misc.c
+-	${C} ${CFLAGS} -c misc.c
++	$(CC) $(CFLAGS) -c misc.c
+ 
+ build-icm.o: build-icm.c
+-	${C} ${CFLAGS} -c build-icm.c
++	$(CC) $(CFLAGS) -c build-icm.c
+ 
+ build-icm: build-icm.o misc.o
+-	$(C) ${CFLAGS} -o $@ build-icm.o misc.o $(LIBS)
++	$(CC) $(CFLAGS) $(LDFLAGS) -o $@ build-icm.o misc.o $(LIBS)
+ 
+ build-icm-noframe.o: build-icm-noframe.c
+-	${C} ${CFLAGS} -c build-icm-noframe.c
++	$(CC) $(CFLAGS) -c build-icm-noframe.c
+ 
+ build-icm-noframe: build-icm-noframe.o misc.o
+-	$(C) ${CFLAGS} -o $@ build-icm-noframe.o misc.o $(LIBS)
++	$(CC) $(CFLAGS) $(LDFLAGS) -o $@ build-icm-noframe.o misc.o $(LIBS)
+ 
+ build1: build1.o
+-	${CC} ${CFLAGS} build1.c -o build1 $(LIBS)
++	$(CXX) $(CXXFLAGS) $(LDFLAGS) build1.o -o build1 $(LIBS)
+ 
+ build2: build2.o
+-	${CC} ${CFLAGS} build2.c -o build2 $(LIBS)
++	$(CXX) $(CXXFLAGS) $(LDFLAGS) build2.o -o build2 $(LIBS)
+ 
+ falsecomp: falsecomp.o
+-	${CC} ${CFLAGS} falsecomp.c -o falsecomp $(LIBS)
++	$(CXX) $(CXXFLAGS) $(LDFLAGS) falsecomp.o -o falsecomp $(LIBS)
+ 
+ findsites: findsites.o
+-	${CC} ${CFLAGS} findsites.c -o findsites $(LIBS)
++	$(CXX) $(CXXFLAGS) $(LDFLAGS) findsites.o -o findsites $(LIBS)
+ 
+ karlin: karlin.o
+-	${CC} ${CFLAGS} karlin.c -o karlin $(LIBS)
++	$(CXX) $(CXXFLAGS) $(LDFLAGS) karlin.o -o karlin $(LIBS)
+ 
+ score: score.o
+-	${CC} ${CFLAGS} score.c -o score $(LIBS)
++	$(CXX) $(CXXFLAGS) $(LDFLAGS) score.o -o score $(LIBS)
+ 
+ score2: score2.o
+-	${CC} ${CFLAGS} score2.c -o score2 $(LIBS)
++	$(CXX) $(CXXFLAGS) $(LDFLAGS) score2.o -o score2 $(LIBS)
+ 
+ scoreATG: scoreATG.o
+-	${CC} ${CFLAGS} scoreATG.c -o scoreATG $(LIBS)
++	$(CXX) $(CXXFLAGS) $(LDFLAGS) scoreATG.o -o scoreATG $(LIBS)
+ 
+ scoreATG2: scoreATG2.o
+-	${CC} ${CFLAGS} scoreATG2.c -o scoreATG2 $(LIBS)
++	$(CXX) $(CXXFLAGS) $(LDFLAGS) scoreATG2.o -o scoreATG2 $(LIBS)
+ 
+ scoreSTOP: scoreSTOP.o
+-	${CC} ${CFLAGS} scoreSTOP.c -o scoreSTOP $(LIBS)
++	$(CXX) $(CXXFLAGS) $(LDFLAGS) scoreSTOP.o -o scoreSTOP $(LIBS)
+ 
+ escoreSTOP2: scoreSTOP2.o
+-	${CC} ${CFLAGS} scoreSTOP2.c -o scoreSTOP2 $(LIBS)
++	$(CXX) $(CXXFLAGS) $(LDFLAGS) scoreSTOP2.o -o scoreSTOP2 $(LIBS)
+ 
+ rfapp: erfapp.o
+-	${CC} ${CFLAGS} erfapp.c -o erfapp $(LIBS)
++	$(CXX) $(CXXFLAGS) $(LDFLAGS) erfapp.c -o erfapp $(LIBS)
+ 
+ sites.o: sites.c
+-	${CC} ${CFLAGS} -c sites.c
++	$(CXX) $(CXXFLAGS) -c sites.c
++
++scoreATG.o: scoreATG.c
++	$(CXX) $(CXXFLAGS) -c scoreATG.c
++       
++scoreSTOP.o: scoreSTOP.c
++	$(CXX) $(CXXFLAGS) -c scoreSTOP.c
++
++scoreSTOP2.o: scoreSTOP2.c
++	$(CXX) $(CXXFLAGS) -c scoreSTOP2.c
++
++scoreATG2.o: scoreATG2.c
++	$(CXX) $(CXXFLAGS) -c scoreATG2.c
+ 
+ utils.o: utils.c 
+-	${CC} ${CFLAGS} -c utils.c
++	$(CXX) $(CXXFLAGS) -c utils.c
+ 
+ splicescore.o: splicescore.c
+-	${CC} ${CFLAGS} -c splicescore.c
++	$(CXX) $(CXXFLAGS) -c splicescore.c
+ 
+ splicescore: splicescore.o sites.o utils.o
+-	${CC} splicescore.o sites.o utils.o -o splicescore $(LIBS)
++	$(CXX) $(CXXFLAGS) $(LDFLAGS) splicescore.o sites.o utils.o -o splicescore $(LIBS)
+ .PHONY : clean
+ clean::
+ 	/bin/rm -f core* splicescore *.o score build? build-icm \
diff --git a/sci-biology/glimmerhmm/glimmerhmm-3.0.1-r1.ebuild b/sci-biology/glimmerhmm/glimmerhmm-3.0.1-r1.ebuild
index b6fc54eb65b1..d118ce0996da 100644
--- a/sci-biology/glimmerhmm/glimmerhmm-3.0.1-r1.ebuild
+++ b/sci-biology/glimmerhmm/glimmerhmm-3.0.1-r1.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2023 Gentoo Authors
+# Copyright 1999-2024 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
 EAPI=7
@@ -20,6 +20,7 @@ S="${WORKDIR}/${MY_P}"
 PATCHES=(
 	"${FILESDIR}"/${PV}-gentoo.patch
 	"${FILESDIR}"/${PN}-3.0.1-fix-data-path.patch
+	"${FILESDIR}"/0001-fix-ridiculous-ODR-violation.patch
 )
 
 src_configure() {
diff --git a/sci-biology/glimmerhmm/glimmerhmm-3.0.4.ebuild b/sci-biology/glimmerhmm/glimmerhmm-3.0.4.ebuild
new file mode 100644
index 000000000000..829e79d4db85
--- /dev/null
+++ b/sci-biology/glimmerhmm/glimmerhmm-3.0.4.ebuild
@@ -0,0 +1,47 @@
+# Copyright 1999-2024 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+inherit toolchain-funcs
+
+MY_P=GlimmerHMM
+
+DESCRIPTION="A eukaryotic gene finding system from TIGR"
+HOMEPAGE="http://www.cbcb.umd.edu/software/GlimmerHMM/"
+SRC_URI="https://ccb.jhu.edu/software/glimmerhmm/dl/${MY_P}-${PV}.tar.gz"
+S="${WORKDIR}/${MY_P}"
+
+LICENSE="Artistic"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+
+PATCHES=(
+	"${FILESDIR}"/${PV}-gentoo.patch
+	"${FILESDIR}"/${PN}-3.0.1-fix-data-path.patch
+	"${FILESDIR}"/0001-fix-ridiculous-ODR-violation.patch
+)
+
+src_configure() {
+	tc-export CC CXX
+}
+
+src_compile() {
+	emake -C sources
+	emake -C train
+}
+
+src_install() {
+	dobin sources/glimmerhmm train/trainGlimmerHMM
+
+	insinto /usr/share/${PN}/lib
+	doins train/*.pm
+
+	insinto /usr/share/${PN}/models
+	doins -r trained_dir/.
+
+	exeinto /usr/libexec/${PN}/training_utils
+	doexe train/{build{1,2,-icm,-icm-noframe},erfapp,falsecomp,findsites,karlin,score,score{2,ATG,ATG2,STOP,STOP2},splicescore}
+
+	dodoc README.first train/readme.train
+}