diff options
Diffstat (limited to 'sci-biology')
5 files changed, 142 insertions, 68 deletions
diff --git a/sci-biology/infernal/files/infernal-1.0.2-fix-build-system.patch b/sci-biology/infernal/files/infernal-1.0.2-fix-build-system.patch new file mode 100644 index 000000000000..41ab3103594b --- /dev/null +++ b/sci-biology/infernal/files/infernal-1.0.2-fix-build-system.patch @@ -0,0 +1,135 @@ +* Fix parallel build +* Respect AR +* Respect DESTDIR +* Respect LDFLAGS + +--- a/easel/Makefile.in ++++ b/easel/Makefile.in +@@ -17,7 +17,6 @@ + # + CC = @CC@ + CFLAGS = @CFLAGS@ +-AR = @AR@ rcv + LN = ln + RANLIB = @RANLIB@ + LDFLAGS = -static @LDFLAGS@ +@@ -132,13 +131,13 @@ + esl_wuss.o + + all: libeasel.a +- (cd miniapps; make) ++ $(MAKE) -C miniapps + + .c.o: + ${CC} -I. ${CFLAGS} ${SIMDFLAGS} ${DEFS} -c $< + + libeasel.a: $(OBJS) +- $(AR) libeasel.a $(OBJS) ++ $(AR) rcv libeasel.a $(OBJS) + $(RANLIB) libeasel.a + chmod 644 libeasel.a + +--- a/easel/testsuite/Makefile.in ++++ b/easel/testsuite/Makefile.in +@@ -15,7 +15,6 @@ + LIBS = @LIBGSL@ @LIBS@ -lm + MPILIBS = @MPILIBS@ + +-AR = @AR@ rcv + RANLIB = @RANLIB@ + + ESLDIR = .. +--- a/iinfernal-1/Makefile.in ++++ b/iinfernal-1/Makefile.in +@@ -20,7 +20,6 @@ + # only used for building the testsuite anyway... e.g. we + # make a "libhmmer.a" library for building the testsuite. + # +-AR = @AR@ rcv + RANLIB = @RANLIB@ + + MPILIBS = @MPILIBS@ +@@ -63,7 +62,7 @@ + module: libinfernal.a + + libinfernal.a: $(OBJS) +- $(AR) libinfernal.a $(OBJS) ++ $(AR) rcv libinfernal.a $(OBJS) + $(RANLIB) libinfernal.a + chmod 644 libinfernal.a + +--- a/Makefile.in ++++ b/Makefile.in +@@ -82,9 +82,10 @@ + all: core + + core: +- (cd easel; make CC="$(CC)" CFLAGS="$(CFLAGS)"; make) +- (cd src; make CC="$(CC)" CFLAGS="$(CFLAGS)"; make module) +- (cd testsuite; make CC="$(CC)" CFLAGS="$(CFLAGS)") ++ $(MAKE) -C easel ++ $(MAKE) -C src ++ $(MAKE) -C src module ++ $(MAKE) -C testsuite + + #.PHONY: $(RIGFILTERS) + #$(RIGFILTERS): core +@@ -202,9 +203,9 @@ + # "make install" installs the programs in BINDIR + # + install: +- mkdir -p ${BINDIR} ++ mkdir -p $(DESTDIR)${BINDIR} + for file in $(PROGS); do\ +- cp src/$$file $(BINDIR)/;\ ++ cp src/$$file $(DESTDIR)$(BINDIR)/;\ + done + # if test -d $(RIGFILTERS); then\ + # for file in $(RFPROGS); do\ +--- a/rigfilters/cfsqp/Makefile.in ++++ b/rigfilters/cfsqp/Makefile.in +@@ -24,7 +24,6 @@ + ## archiving command, and ranlib command. + # these are used to create the libcfsqp.a library, necessary for cm2hmm + # +-AR = @AR@ rcv + RANLIB = @RANLIB@ + + OBJS = cfsqp.o\ +@@ -41,7 +40,7 @@ + all: libcfsqp.a + + libcfsqp.a: $(OBJS) ${HDRS} +- $(AR) libcfsqp.a $(OBJS) ++ $(AR) rcv libcfsqp.a $(OBJS) + $(RANLIB) libcfsqp.a + chmod 644 libcfsqp.a + +--- a/src/Makefile.in ++++ b/src/Makefile.in +@@ -27,7 +27,6 @@ + # only used for building the testsuite anyway... e.g. we + # make a "libinfernal.a" library for building the testsuite. + # +-AR = @AR@ rcv + RANLIB = @RANLIB@ + + # configuration for optional MPI functionality +@@ -86,7 +85,7 @@ + all: $(PROGS) + + $(PROGS): @EXEC_DEPENDENCY@ $(OBJS) ${HDRS} +- $(CC) $(CFLAGS) $(DEFS) $(MYLIBDIR) -o $@ $@.o $(OBJS) $(MYLIBS) $(LIBS) $(MPILIBS) ++ $(CC) $(LDFLAGS) $(CFLAGS) $(DEFS) $(MYLIBDIR) -o $@ $@.o $(OBJS) $(MYLIBS) $(LIBS) $(MPILIBS) + + + ################################################################# +@@ -95,7 +94,7 @@ + module: libinfernal.a + + libinfernal.a: $(OBJS) ${HDRS} +- $(AR) libinfernal.a $(OBJS) ++ $(AR) rcv libinfernal.a $(OBJS) + $(RANLIB) libinfernal.a + chmod 644 libinfernal.a + diff --git a/sci-biology/infernal/files/infernal-1.0.2-ldflags.patch b/sci-biology/infernal/files/infernal-1.0.2-ldflags.patch deleted file mode 100644 index f688dce152ed..000000000000 --- a/sci-biology/infernal/files/infernal-1.0.2-ldflags.patch +++ /dev/null @@ -1,15 +0,0 @@ -Respect LDFLAGS - -http://bugs.gentoo.org/show_bug.cgi?id=338177 - ---- a/src/Makefile.in -+++ b/src/Makefile.in -@@ -86,7 +86,7 @@ - all: $(PROGS) - - $(PROGS): @EXEC_DEPENDENCY@ $(OBJS) ${HDRS} -- $(CC) $(CFLAGS) $(DEFS) $(MYLIBDIR) -o $@ $@.o $(OBJS) $(MYLIBS) $(LIBS) $(MPILIBS) -+ $(CC) $(LDFLAGS) $(CFLAGS) $(DEFS) $(MYLIBDIR) -o $@ $@.o $(OBJS) $(MYLIBS) $(LIBS) $(MPILIBS) - - - ################################################################# diff --git a/sci-biology/infernal/files/infernal-1.0.2-parallel-build.patch b/sci-biology/infernal/files/infernal-1.0.2-parallel-build.patch deleted file mode 100644 index 67ffa6fda7f6..000000000000 --- a/sci-biology/infernal/files/infernal-1.0.2-parallel-build.patch +++ /dev/null @@ -1,31 +0,0 @@ -Fix parallel build - -http://bugs.gentoo.org/show_bug.cgi?id=311919 - ---- a/Makefile.in -+++ b/Makefile.in -@@ -82,9 +82,10 @@ - all: core - - core: -- (cd easel; make CC="$(CC)" CFLAGS="$(CFLAGS)"; make) -- (cd src; make CC="$(CC)" CFLAGS="$(CFLAGS)"; make module) -- (cd testsuite; make CC="$(CC)" CFLAGS="$(CFLAGS)") -+ $(MAKE) -C easel -+ $(MAKE) -C src -+ $(MAKE) -C src module -+ $(MAKE) -C testsuite - - #.PHONY: $(RIGFILTERS) - #$(RIGFILTERS): core ---- a/easel/Makefile.in -+++ b/easel/Makefile.in -@@ -132,7 +132,7 @@ - esl_wuss.o - - all: libeasel.a -- (cd miniapps; make) -+ $(MAKE) -C miniapps - - .c.o: - ${CC} -I. ${CFLAGS} ${SIMDFLAGS} ${DEFS} -c $< diff --git a/sci-biology/infernal/files/infernal-1.0.2-respect-DESTDIR.patch b/sci-biology/infernal/files/infernal-1.0.2-respect-DESTDIR.patch deleted file mode 100644 index ea465e592ffa..000000000000 --- a/sci-biology/infernal/files/infernal-1.0.2-respect-DESTDIR.patch +++ /dev/null @@ -1,16 +0,0 @@ -Build system does not respect DESTDIR by default. - ---- a/Makefile.in -+++ b/Makefile.in -@@ -203,9 +203,9 @@ - # "make install" installs the programs in BINDIR - # - install: -- mkdir -p ${BINDIR} -+ mkdir -p $(DESTDIR)${BINDIR} - for file in $(PROGS); do\ -- cp src/$$file $(BINDIR)/;\ -+ cp src/$$file $(DESTDIR)$(BINDIR)/;\ - done - # if test -d $(RIGFILTERS); then\ - # for file in $(RFPROGS); do\ diff --git a/sci-biology/infernal/infernal-1.0.2-r1.ebuild b/sci-biology/infernal/infernal-1.0.2-r1.ebuild index e906c23024ff..2e96418b6bb9 100644 --- a/sci-biology/infernal/infernal-1.0.2-r1.ebuild +++ b/sci-biology/infernal/infernal-1.0.2-r1.ebuild @@ -1,7 +1,9 @@ -# Copyright 1999-2017 Gentoo Foundation +# Copyright 1999-2020 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 -EAPI=6 +EAPI=7 + +inherit toolchain-funcs DESCRIPTION="Inference of RNA alignments" HOMEPAGE="http://infernal.janelia.org/" @@ -9,21 +11,20 @@ SRC_URI="ftp://selab.janelia.org/pub/software/${PN}/${P}.tar.gz" LICENSE="GPL-3" SLOT="0" -IUSE="mpi" KEYWORDS="amd64 x86" +IUSE="mpi" RDEPEND="mpi? ( virtual/mpi )" DEPEND="${RDEPEND}" PATCHES=( - "${FILESDIR}"/${P}-parallel-build.patch + "${FILESDIR}"/${P}-fix-build-system.patch "${FILESDIR}"/${P}-overflows.patch "${FILESDIR}"/${P}-perl-5.16-2.patch - "${FILESDIR}"/${P}-ldflags.patch - "${FILESDIR}"/${P}-respect-DESTDIR.patch ) src_configure() { + tc-export AR econf $(use_enable mpi) } |