From 0c97119fc8982c1a6f367de25542834e4dd6cda4 Mon Sep 17 00:00:00 2001 From: V3n3RiX Date: Tue, 12 Mar 2024 12:46:41 +0000 Subject: gentoo auto-resync : 12:03:2024 - 12:46:41 --- sci-biology/Manifest.gz | Bin 19323 -> 19325 bytes sci-biology/glimmerhmm/Manifest | 6 +- .../files/0001-fix-ridiculous-ODR-violation.patch | 27 ++++ sci-biology/glimmerhmm/files/3.0.4-gentoo.patch | 153 +++++++++++++++++++++ sci-biology/glimmerhmm/glimmerhmm-3.0.1-r1.ebuild | 3 +- sci-biology/glimmerhmm/glimmerhmm-3.0.4.ebuild | 47 +++++++ 6 files changed, 234 insertions(+), 2 deletions(-) create mode 100644 sci-biology/glimmerhmm/files/0001-fix-ridiculous-ODR-violation.patch create mode 100644 sci-biology/glimmerhmm/files/3.0.4-gentoo.patch create mode 100644 sci-biology/glimmerhmm/glimmerhmm-3.0.4.ebuild (limited to 'sci-biology') diff --git a/sci-biology/Manifest.gz b/sci-biology/Manifest.gz index e479838ad584..895adecb6204 100644 Binary files a/sci-biology/Manifest.gz and b/sci-biology/Manifest.gz differ 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 +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 +} -- cgit v1.2.3