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| author |   David Seifert <soap@gentoo.org> | 2022-07-07 21:56:48 +0200 |
|---|---|---|
| committer | David Seifert <soap@gentoo.org> | 2022-07-07 21:56:48 +0200 |
| commit | 823eb4522246d520868149c751ee325c7b75b742 (patch) | |
| tree | bed9a3505eec69b6dbd14858c5a85fd15f5d060c /sci-biology | |
| parent | sci-biology/clustal-omega: update EAPI 6 -> 8 (diff) | |
| download | gentoo-823eb4522246d520868149c751ee325c7b75b742.tar.gz gentoo-823eb4522246d520868149c751ee325c7b75b742.tar.bz2 gentoo-823eb4522246d520868149c751ee325c7b75b742.zip | |
sci-biology/clustalw: update EAPI 6 -> 8 (1.83)
Closes: https://bugs.gentoo.org/741180
Signed-off-by: David Seifert <soap@gentoo.org>
Diffstat (limited to 'sci-biology')
| -rw-r--r-- | sci-biology/clustalw/clustalw-1.83-r4.ebuild | 23 | ||||
| -rw-r--r-- | sci-biology/clustalw/files/1.83-as-needed.patch | 31 | ||||
| -rw-r--r-- | sci-biology/clustalw/files/1.83-clang.patch | 11 |
3 files changed, 48 insertions, 17 deletions
diff --git a/sci-biology/clustalw/clustalw-1.83-r4.ebuild b/sci-biology/clustalw/clustalw-1.83-r4.ebuild index 076f16300b3a..62c59747adf3 100644 --- a/sci-biology/clustalw/clustalw-1.83-r4.ebuild +++ b/sci-biology/clustalw/clustalw-1.83-r4.ebuild @@ -1,34 +1,35 @@ -# Copyright 1999-2021 Gentoo Authors +# Copyright 1999-2022 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 -EAPI=6 +EAPI=8 inherit toolchain-funcs DESCRIPTION="General purpose multiple alignment program for DNA and proteins" HOMEPAGE="http://www.embl-heidelberg.de/~seqanal/" SRC_URI="ftp://ftp.ebi.ac.uk/pub/software/unix/clustalw/${PN}${PV}.UNIX.tar.gz" +S="${WORKDIR}/${PN}${PV}" LICENSE="clustalw" SLOT="1" KEYWORDS="amd64 ~ppc ppc64 sparc x86 ~amd64-linux ~x86-linux ~ppc-macos ~sparc-solaris" -IUSE="" -S="${WORKDIR}"/${PN}${PV} - -PATCHES=( "${FILESDIR}"/${PV}-as-needed.patch ) +PATCHES=( + "${FILESDIR}"/${PV}-as-needed.patch + "${FILESDIR}"/${PV}-clang.patch +) src_prepare() { default - - sed \ - -e "/^CC/s:cc:$(tc-getCC):g" \ - -i makefile || die sed \ - -e "s%clustalw_help%/usr/share/doc/${PF}/clustalw_help%" \ + -e "s|clustalw_help|${EPREFIX}/usr/share/doc/${PF}/clustalw_help|" \ -i clustalw.c || die } +src_configure() { + tc-export CC +} + src_install() { dobin clustalw dodoc README clustalv.doc clustalw{.doc,.ms,_help} diff --git a/sci-biology/clustalw/files/1.83-as-needed.patch b/sci-biology/clustalw/files/1.83-as-needed.patch index 9bb35b43f24a..54b78b0811e0 100644 --- a/sci-biology/clustalw/files/1.83-as-needed.patch +++ b/sci-biology/clustalw/files/1.83-as-needed.patch @@ -1,17 +1,36 @@ --- a/makefile +++ b/makefile -@@ -11,11 +11,11 @@ +@@ -10,25 +10,22 @@ + HEADERS = general.h clustalw.h - CC = cc +-CC = cc -CFLAGS = -c -O -LFLAGS = -O -lm -+CFLAGS += -c -+LIBS = -lm ++# C99 for gets() ++CFLAGS += -std=gnu99 ++LIBS += -lm clustalw : $(OBJECTS) amenu.o clustalw.o - $(CC) -o $@ $(OBJECTS) amenu.o clustalw.o $(LFLAGS) -+ $(CC) $(LDFLAGS) -o $@ $(OBJECTS) amenu.o clustalw.o $(LIBS) ++ $(CC) $(LDFLAGS) $(CFLAGS) -o $@ $(OBJECTS) amenu.o clustalw.o $(LIBS) interface.o : interface.c $(HEADERS) param.h - $(CC) $(CFLAGS) $*.c +- $(CC) $(CFLAGS) $*.c ++ $(CC) $(CFLAGS) $(CPPFLAGS) -c $< + + amenu.o : amenu.c $(HEADERS) param.h +- $(CC) $(CFLAGS) $*.c ++ $(CC) $(CFLAGS) $(CPPFLAGS) -c $< + + readmat.o : readmat.c $(HEADERS) matrices.h +- $(CC) $(CFLAGS) $*.c ++ $(CC) $(CFLAGS) $(CPPFLAGS) -c $< + + trees.o : trees.c $(HEADERS) dayhoff.h +- $(CC) $(CFLAGS) $*.c +- +-.c.o : +- $(CC) $(CFLAGS) $? ++ $(CC) $(CFLAGS) $(CPPFLAGS) -c $< + diff --git a/sci-biology/clustalw/files/1.83-clang.patch b/sci-biology/clustalw/files/1.83-clang.patch new file mode 100644 index 000000000000..ea1202079d9e --- /dev/null +++ b/sci-biology/clustalw/files/1.83-clang.patch @@ -0,0 +1,11 @@ +--- a/interface.c ++++ b/interface.c +@@ -210,7 +210,7 @@ + Boolean name1 = FALSE; + sint ajb; + +- if(args[0]==NULL) return; ++ if(args[0]==NULL) return 0; + + + |