commit: 2c862807546f666b21c5ab2c01ba3a1402f5c38a Author: Andreas Sturmlechner <asturm <AT> gentoo <DOT> org> AuthorDate: Mon May 19 20:38:27 2025 +0000 Commit: Andreas Sturmlechner <asturm <AT> gentoo <DOT> org> CommitDate: Tue May 20 19:12:22 2025 +0000 URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=2c862807
sci-biology/augustus: drop 2.5.5 Signed-off-by: Andreas Sturmlechner <asturm <AT> gentoo.org> sci-biology/augustus/Manifest | 1 - sci-biology/augustus/augustus-2.5.5.ebuild | 50 ------- .../augustus/files/augustus-2.5.5-sane-build.patch | 156 --------------------- 3 files changed, 207 deletions(-) diff --git a/sci-biology/augustus/Manifest b/sci-biology/augustus/Manifest index 7bba72327fb5..178d054cf6f7 100644 --- a/sci-biology/augustus/Manifest +++ b/sci-biology/augustus/Manifest @@ -1,3 +1,2 @@ DIST augustus-3.4.0.tar.gz 221652100 BLAKE2B dfc8c98107f5a955f688f3d2976ca936faf2ef7004095f6b9d7c1902a36ca5d3c9aef59cab1b82b56cd5c2abc7b67195c5030111ed68557d53128814b1bf6bab SHA512 ca1df1016589f55527a883429edd5024cbc32c1b32036c81f9df5e0967a7d194f5b7a82109e924f380627427d9731caa478e63cad8cd804c01521aed76d8c4a6 DIST augustus-3.5.0.tar.gz 225918930 BLAKE2B 26e934f3d3f50d183fb0ee7874352c5ac9af9877eaa40a9a6195ae79cfd9a78a321bd9261e8bd3435b1d4984589d0bdd4e0821ba6600c717d6afd95f511702de SHA512 0869e54b3126b3ab2f6fb2c28ff07b779265a139968e5277352f5230d3c317415324ca61dce4a0cd6c3f1fb5399447ae815bec7732a285ce652cf44e6cd23e5d -DIST augustus.2.5.5.tar.gz 70826249 BLAKE2B 3f3f1537c5c614f00298e1835eeb7bbe968987c3e0dee13299e1e26b4abf198d8635a93121b11722d2c90b63ff54cf153c72716d01c3ca033481bb54357b7bcf SHA512 33eb05d5c90200d2fc17026743d3a25e73aa3e217b8546f0bed4c94bcb460597d853377a67896e52e45ead5d736d13ed3b2c91b31fed8216da2920c825e8c20f diff --git a/sci-biology/augustus/augustus-2.5.5.ebuild b/sci-biology/augustus/augustus-2.5.5.ebuild deleted file mode 100644 index ed345330c4a7..000000000000 --- a/sci-biology/augustus/augustus-2.5.5.ebuild +++ /dev/null @@ -1,50 +0,0 @@ -# Copyright 1999-2023 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=7 - -inherit toolchain-funcs - -DESCRIPTION="Eukaryotic gene predictor" -HOMEPAGE="http://augustus.gobics.de/"; -SRC_URI="http://augustus.gobics.de/binaries/${PN}.${PV}.tar.gz"; - -LICENSE="Artistic" -SLOT="0" -KEYWORDS="amd64 ~x86" -IUSE="examples" - -S="${WORKDIR}/${PN}.${PV}" -PATCHES=( "${FILESDIR}"/${P}-sane-build.patch ) - -src_configure() { - tc-export CC CXX -} - -src_compile() { - emake clean - default -} - -src_install() { - dobin bin/* - - exeinto /usr/libexec/${PN} - doexe scripts/*.p* - - insinto /usr/libexec/${PN} - doins scripts/*.conf - - insinto /usr/share/${PN} - doins -r config - - echo "AUGUSTUS_CONFIG_PATH=\"/usr/share/${PN}/config\"" > 99${PN} || die - doenvd 99${PN} - - dodoc -r README.TXT HISTORY.TXT docs/*.{pdf,txt} - - if use examples; then - insinto /usr/share/${PN}/ - doins -r docs/tutorial examples - fi -} diff --git a/sci-biology/augustus/files/augustus-2.5.5-sane-build.patch b/sci-biology/augustus/files/augustus-2.5.5-sane-build.patch deleted file mode 100644 index 39cd0762b1c1..000000000000 --- a/sci-biology/augustus/files/augustus-2.5.5-sane-build.patch +++ /dev/null @@ -1,156 +0,0 @@ - Makefile | 8 +++--- - scripts/Makefile | 6 +++- - scripts/aln2wig/Makefile | 8 +++--- - scripts/compileSpliceCands/Makefile | 6 ++-- - src/Makefile | 43 ++++++++++++++++++---------------- - 5 files changed, 38 insertions(+), 33 deletions(-) - -diff --git a/Makefile b/Makefile -index e23a667..64610c8 100644 ---- a/Makefile -+++ b/Makefile -@@ -3,9 +3,9 @@ - # - - all: -- cd src && ${MAKE} -- cd scripts && ${MAKE} -+ $(MAKE) -C src -+ $(MAKE) -C scripts - - clean: -- cd src && ${MAKE} clean -- cd scripts && ${MAKE} clean -+ $(MAKE) -C src clean -+ $(MAKE) -C scripts clean -diff --git a/scripts/Makefile b/scripts/Makefile -index 6d4dd67..ab6a885 100644 ---- a/scripts/Makefile -+++ b/scripts/Makefile -@@ -1,5 +1,7 @@ - all : -- cd aln2wig && ${MAKE} -+ $(MAKE) -C aln2wig -+ $(MAKE) -C compileSpliceCands - - clean : -- cd aln2wig && ${MAKE} clean -+ $(MAKE) -C aln2wig clean -+ $(MAKE) -C compileSpliceCands -diff --git a/scripts/aln2wig/Makefile b/scripts/aln2wig/Makefile -index 64d09f5..9752980 100644 ---- a/scripts/aln2wig/Makefile -+++ b/scripts/aln2wig/Makefile -@@ -1,10 +1,10 @@ --CFLAGS := -Wall -Wno-unused-result -Wno-sign-compare -ansi -pedantic -O2 -ggdb -+CFLAGS += -Wall -Wno-unused-result -Wno-sign-compare -ansi -pedantic - - psl2wig : aln2wig.o -- gcc $(CFLAGS) -o aln2wig aln2wig.o; -- cp aln2wig ../../bin -+ $(CC) $(CFLAGS) $(LDFLAGS) -o aln2wig aln2wig.o; -+ cp aln2wig ../../bin/ - psl2wig.o : aln2wig.c -- gcc $(CFLAGS) -c aln2wig.c -+ $(CC) $(CFLAGS) -c aln2wig.c - - all : psl2wig - -diff --git a/scripts/compileSpliceCands/Makefile b/scripts/compileSpliceCands/Makefile -index cddada5..8079791 100644 ---- a/scripts/compileSpliceCands/Makefile -+++ b/scripts/compileSpliceCands/Makefile -@@ -1,8 +1,8 @@ - compileSpliceCands : compileSpliceCands.o list.h list.o -- gcc -o compileSpliceCands compileSpliceCands.o list.o; --# cp compileSpliceCands ../../bin -+ $(CC) $(CFLAGS) $(LDFLAGS) -o compileSpliceCands compileSpliceCands.o list.o; -+ cp compileSpliceCands ../../bin/ - compileSpliceCands.o : compileSpliceCands.c -- gcc -Wall -pedantic -ansi -c compileSpliceCands.c -+ $(CC) $(CFLAGS) -Wall -pedantic -ansi -c compileSpliceCands.c - - all : compileSpliceCands - -diff --git a/src/Makefile b/src/Makefile -index 71795b6..732b953 100644 ---- a/src/Makefile -+++ b/src/Makefile -@@ -6,8 +6,8 @@ - # a strict signed-only usage strategy to avoid mistakes since we are not warned about this. - # - In the current version, the order of object files in $(OBJS) IS IMPORTANT (see lldouble.hh) - # --CC = g++ --CFLAGS := -Wall -Wno-sign-compare -ansi -pedantic -O2 ${CFLAGS} -static # -pg -DDEBUG -g -ggdb -static -+CXX ?= g++ -+CXXFLAGS += -Wall -Wno-sign-compare -ansi -pedantic # -pg -DDEBUG -g -ggdb -static - INCLS = -I../include -I. - LIBS = # -lcwd - OBJS = genbank.o properties.o pp_profile.o pp_hitseq.o pp_scoring.o statemodel.o namgene.o \ -@@ -18,45 +18,48 @@ TOBJS = commontrain.o igenictrain.o introntrain.o exontrain.o utrtrain.o # conte - PROGR = augustus etraining consensusFinder curve2hints fastBlockSearch prepareAlign - INFO = cflags - --all: $(OBJS) $(TOBJS) $(DUMOBJS) $(PROGR) info -+all: $(OBJS) $(TOBJS) $(DUMOBJS) $(PROGR) info bin - - .SUFFIXES: - .SUFFIXES: .cc .o .so - - .cc.o: -- $(CC) -c $(CFLAGS) -o $@ $< $(INCLS) -+ $(CXX) -c $(CXXFLAGS) -o $@ $< $(INCLS) - --augustus: augustus.cc $(OBJS) $(DUMOBJS) -- $(CC) $(CFLAGS) -o $@ $^ $(INCLS) $(LIBS) -+bin: $(PROGR) -+ cp $(PROGR) ../bin/ -+ -+augustus: augustus.o $(OBJS) $(DUMOBJS) -+ $(CXX) $(CXXFLAGS) $(LDFLAGS) -o $@ $^ $(INCLS) $(LIBS) - cp augustus ../bin/ - --etraining: etraining.cc $(TOBJS) $(OBJS) -- $(CC) $(CFLAGS) -o $@ $^ $(INCLS) $(LIBS) -+etraining: etraining.o $(TOBJS) $(OBJS) -+ $(CXX) $(CXXFLAGS) $(LDFLAGS) -o $@ $^ $(INCLS) $(LIBS) - cp etraining ../bin/ - --evaluate: evaluate.cc $(OBJS) $(DUMOBJS) -- $(CC) $(CFLAGS) -o $@ $^ $(INCLS) $(LIBS) -+evaluate: evaluate.o $(OBJS) $(DUMOBJS) -+ $(CXX) $(CXXFLAGS) $(LDFLAGS) -o $@ $^ $(INCLS) $(LIBS) - --consensusFinder: consensusFinder.cc consensus.o -- $(CC) $(CFLAGS) -o $@ $^ $(INCLS) $(LIBS) -+consensusFinder: consensusFinder.o consensus.o -+ $(CXX) $(CXXFLAGS) $(LDFLAGS) -o $@ $^ $(INCLS) $(LIBS) - --curve2hints: curve2hints.cc exon_seg.o -- $(CC) $(CFLAGS) -o $@ $^ $(INCLS) $(LIBS) -+curve2hints: curve2hints.o exon_seg.o -+ $(CXX) $(CXXFLAGS) $(LDFLAGS) -o $@ $^ $(INCLS) $(LIBS) - --fastBlockSearch: fastBlockSearch.cc pp_fastBlockSearcher.o \ -+fastBlockSearch: fastBlockSearch.o pp_fastBlockSearcher.o \ - types.o properties.o geneticcode.o pp_profile.o lldouble.o -- $(CC) $(CFLAGS) -o $@ $^ $(INCLS) $(LIBS) -+ $(CXX) $(CXXFLAGS) $(LDFLAGS) -o $@ $^ $(INCLS) $(LIBS) - cp fastBlockSearch ../bin/ - --prepareAlign: pp_prepare_align.cc -- $(CC) $(CFLAGS) -o $@ $^ -+prepareAlign: pp_prepare_align.o -+ $(CXX) $(CXXFLAGS) $(LDFLAGS) -o $@ $^ - cp prepareAlign ../bin/ - - info: -- echo "$(CFLAGS)" > $(INFO) -+ echo "$(CXXFLAGS)" > $(INFO) - - clean: -- rm -f $(PROGR) $(OBJS) $(DUMOBJS) $(TOBJS) consensus.o exon_seg.o pp_fastBlockSearcher.o $(INFO) -+ rm -f $(PROGR) $(OBJS) $(DUMOBJS) $(TOBJS) consensus.o exon_seg.o pp_fastBlockSearcher.o $(INFO) ../bin/* - - tidy: clean - rm -f *~ *.o *.rej *.orig ../include/*~ ../include/*.orig ../include/*.rej $(INFO)
