From 73c1e487f0d8fc8c14f39c83e729c95acaf6be0d Mon Sep 17 00:00:00 2001 From: Martin Mokrejs Date: Mon, 6 Feb 2012 19:21:43 +0100 Subject: two more Makefiles needed a DESTDIR patch, in conjunction with an ugly symlink hack in one can build the stuff; dobin does not transfer symliks so every binary appears installed 3 times; upstream bug http://jira.be-md.ncbi.nlm.nih.gov/browse/TR-10207 (Portage version: 2.1.10.45/git/Linux x86_64, unsigned Manifest commit) --- sci-biology/sra_sdk/ChangeLog | 8 +++ sci-biology/sra_sdk/files/libs_sra_Makefile.patch | 77 ++++++++++++++++++++++ .../sra_sdk/files/tools_vdb-vcopy_Makefile.patch | 12 ++++ sci-biology/sra_sdk/sra_sdk-2.1.9.ebuild | 44 +++++-------- 4 files changed, 112 insertions(+), 29 deletions(-) create mode 100644 sci-biology/sra_sdk/files/libs_sra_Makefile.patch create mode 100644 sci-biology/sra_sdk/files/tools_vdb-vcopy_Makefile.patch (limited to 'sci-biology') diff --git a/sci-biology/sra_sdk/ChangeLog b/sci-biology/sra_sdk/ChangeLog index 0b2163fbf..9ac722a7b 100644 --- a/sci-biology/sra_sdk/ChangeLog +++ b/sci-biology/sra_sdk/ChangeLog @@ -2,6 +2,14 @@ # Copyright 1999-2012 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 06 Feb 2012; Martin Mokrejs + sra_sdk-2.1.9.ebuild, +files/libs_sra_Makefile.patch, + +files/tools_vdb-vcopy_Makefile.patch: + two more Makefiles needed a DESTDIR patch, in conjunction with an ugly + symlink hack in one can build the stuff; dobin does not transfer symliks so + every binary appears installed 3 times; upstream bug + http://jira.be-md.ncbi.nlm.nih.gov/browse/TR-10207 + *sra_sdk-2.1.9 (06 Feb 2012) 06 Feb 2012; Martin Mokrejs diff --git a/sci-biology/sra_sdk/files/libs_sra_Makefile.patch b/sci-biology/sra_sdk/files/libs_sra_Makefile.patch new file mode 100644 index 000000000..44acc42b0 --- /dev/null +++ b/sci-biology/sra_sdk/files/libs_sra_Makefile.patch @@ -0,0 +1,77 @@ +diff -u -w sra_sdk-2.1.9/work/sra_sdk-2.1.9/libs/sra/Makefile sra_sdk-2.1.9/work/sra_sdk-2.1.9/libs/sra/Makefile +--- sra_sdk-2.1.9/work/sra_sdk-2.1.9/libs/sra/Makefile 2011-12-02 21:30:12.000000000 +0100 ++++ sra_sdk-2.1.9/work/sra_sdk-2.1.9/libs/sra/Makefile 2012-02-06 18:38:45.000000000 +0100 +@@ -100,7 +100,7 @@ + $(addsuffix .$(LOBX),$(SRAPATH_SRC)) + + $(LIBDIR)/libsrapath.$(LIBX): $(SRAPATH_OBJ) +- $(LD) --slib -o $@ $^ ++ $(LD) --slib -o $(DESTDIR)$@ $^ + + libsrapath.vers.h: + @ true +@@ -138,10 +138,10 @@ + -dklib + + $(LIBDIR)/libsra-schema.$(SHLX): $(SRA_SCHEMA_OBJ) +- $(LD) --dlib --vers $(SRCDIR) -o $@ $^ $(SRA_SCHEMA_LIB) ++ $(LD) --dlib --vers $(SRCDIR) -o $(DESTDIR)$@ $^ $(SRA_SCHEMA_LIB) + + $(LIBDIR)/libwsra-schema.$(SHLX): $(WSRA_SCHEMA_OBJ) +- $(LD) --dlib --vers $(SRCDIR) -o $@ $^ $(WSRA_SCHEMA_LIB) ++ $(LD) --dlib --vers $(SRCDIR) -o $(DESTDIR)$@ $^ $(WSRA_SCHEMA_LIB) + + SRASCHEMA_SRC = \ + sraschema-stub +@@ -168,10 +168,10 @@ + $(addsuffix .$(LOBX),$(WSRASCHEMA_SRC)) + + $(LIBDIR)/libsraschema.$(LIBX): $(SRASCHEMA_OBJ) $(SRASCHEMA_DEPS) +- $(LD) --slib -o $@ $(SRASCHEMA_OBJ) $(SRA_SCHEMA_LIB) ++ $(LD) --slib -o $(DESTDIR)$@ $(SRASCHEMA_OBJ) $(SRA_SCHEMA_LIB) + + $(LIBDIR)/libwsraschema.$(LIBX): $(WSRASCHEMA_OBJ) $(WSRASCHEMA_DEPS) +- $(LD) --slib -o $@ $(WSRASCHEMA_OBJ) $(WSRA_SCHEMA_LIB) ++ $(LD) --slib -o $(DESTDIR)$@ $(WSRASCHEMA_OBJ) $(WSRA_SCHEMA_LIB) + + libsraschema_tag: + @ $(TOP)/build/tag-module.sh $(MODULE) libsraschema $(SRASCHEMA_OBJ) +@@ -205,10 +205,10 @@ + -dklib + + $(LIBDIR)/libsradb.$(SHLX): $(SRADB_OBJ) +- $(LD) --dlib --vers $(SRCDIR) -o $@ $^ $(SRADB_LIB) ++ $(LD) --dlib --vers $(SRCDIR) -o $(DESTDIR)$@ $^ $(SRADB_LIB) + + $(LIBDIR)/libsradb.$(LIBX): $(SRADB_OBJ) +- $(LD) --slib --vers $(SRCDIR) -o $@ $^ $(SRADB_LIB) ++ $(LD) --slib --vers $(SRCDIR) -o $(DESTDIR)$@ $^ $(SRADB_LIB) + + libsradb_tag: $(SRADB_TAGS) + @ $(TOP)/build/tag-module.sh $(MODULE) libsradb $(SRADB_OBJ) +@@ -236,10 +236,10 @@ + -dklib + + $(LIBDIR)/libwsradb.$(SHLX): $(WSRADB_OBJ) +- $(LD) --dlib --vers $(SRCDIR) -o $@ $^ $(WSRADB_LIB) ++ $(LD) --dlib --vers $(SRCDIR) -o $(DESTDIR)$@ $^ $(WSRADB_LIB) + + $(LIBDIR)/libwsradb.$(LIBX): $(WSRADB_OBJ) +- $(LD) --slib --vers $(SRCDIR) -o $@ $^ $(WSRADB_LIB) ++ $(LD) --slib --vers $(SRCDIR) -o $(DESTDIR)$@ $^ $(WSRADB_LIB) + + libwsradb_tag: $(WSRADB_TAGS) + @ $(TOP)/build/tag-module.sh $(MODULE) libwsradb $(WSRADB_OBJ) +@@ -266,10 +266,10 @@ + -dklib + + $(LIBDIR)/libsrareader.$(SHLX): $(SRAREADER_OBJ) +- $(LD) --dlib --vers $(SRCDIR) -o $@ $^ $(SRAREADER_LIB) ++ $(LD) --dlib --vers $(SRCDIR) -o $(DESTDIR)$@ $^ $(SRAREADER_LIB) + + $(LIBDIR)/libsrareader.$(LIBX): $(SRAREADER_OBJ) +- $(LD) --slib --vers $(SRCDIR) -o $@ $^ $(SRAREADER_LIB) ++ $(LD) --slib --vers $(SRCDIR) -o $(DESTDIR)$@ $^ $(SRAREADER_LIB) + + libsrareader_tag: + @ $(TOP)/build/tag-module.sh $(MODULE) libsrareader $(SRAREADER_OBJ) diff --git a/sci-biology/sra_sdk/files/tools_vdb-vcopy_Makefile.patch b/sci-biology/sra_sdk/files/tools_vdb-vcopy_Makefile.patch new file mode 100644 index 000000000..738d67cbd --- /dev/null +++ b/sci-biology/sra_sdk/files/tools_vdb-vcopy_Makefile.patch @@ -0,0 +1,12 @@ +diff -u -w sra_sdk-2.1.9/work/sra_sdk-2.1.9/tools/vdb-copy/Makefile sra_sdk-2.1.9/work/sra_sdk-2.1.9/tools/vdb-copy/Makefile +--- sra_sdk-2.1.9/work/sra_sdk-2.1.9/tools/vdb-copy/Makefile 2011-12-02 22:00:36.000000000 +0100 ++++ sra_sdk-2.1.9/work/sra_sdk-2.1.9/tools/vdb-copy/Makefile 2012-02-06 18:39:05.000000000 +0100 +@@ -89,7 +89,7 @@ + $(BINDIR)/vdb-copy: $(NCBIDIR)/vdb-copy.kfg + + $(NCBIDIR)/vdb-copy.kfg: $(SRCDIR)/vdb-copy.kfg +- cp $^ $@ ++ cp $^ $(DESTDIR)$@ + + VDB_COPY_SRC = \ + num-gen \ diff --git a/sci-biology/sra_sdk/sra_sdk-2.1.9.ebuild b/sci-biology/sra_sdk/sra_sdk-2.1.9.ebuild index 92d51bf2c..fcc74cbdc 100644 --- a/sci-biology/sra_sdk/sra_sdk-2.1.9.ebuild +++ b/sci-biology/sra_sdk/sra_sdk-2.1.9.ebuild @@ -14,7 +14,7 @@ SRC_URI="http://trace.ncbi.nlm.nih.gov/Traces/sra/static/sra_sdk-"${PV}".tar.gz" LICENSE="public-domain" SLOT="0" #KEYWORDS="" -KEYWORDS="~amd64 ~x86" +KEYWORDS="~amd64" IUSE="static" DEPEND="app-shells/bash @@ -28,12 +28,14 @@ RDEPEND="${DEPEND}" src_prepare(){ epatch "${FILESDIR}"/sra_sdk-destdir.patch || die + epatch "${FILESDIR}"/tools_vdb-vcopy_Makefile.patch || die + epatch "${FILESDIR}"/libs_sra_Makefile.patch || die + mkdir -p /var/tmp/portage/sci-biology/"${P}"/image//var/tmp/portage/sci-biology/ + ln -s /var/tmp/portage/sci-biology/"${P}" /var/tmp/portage/sci-biology/"${P}"/image//var/tmp/portage/sci-biology/"${P}" + } src_compile(){ - # -I/usr/include/libxml2 - # -I/var/tmp/portage/sci-biology/sra_sdk-2.0.1/work/sra_sdk-2.0.1/interfaces/os/unix - # COMP env variable may have 'GCC' or 'ICC' values if use static; then emake static LIBDIR=/lib64 DESTDIR="${D}" @@ -46,35 +48,19 @@ src_compile(){ } src_install(){ - # for details see "${WORKDIR}"/sra_sdk-2.1.6/README-build - + rm -rf /var/tmp/portage/sci-biology/"${P}"/image//var # BUG: at the moment every binary is installed three times, e.g.: # -rwxr-xr-x 1 root root 1797720 Sep 23 01:31 abi-dump # -rwxr-xr-x 1 root root 1797720 Sep 23 01:31 abi-dump.2 # -rwxr-xr-x 1 root root 1797720 Sep 23 01:31 abi-dump.2.1.6 if use amd64; then - dobin "${WORKDIR}"/objdir/linux/pub/gcc/x86_64/bin/* - insinto /usr/bin/ncbi - dobin "${WORKDIR}"/objdir/linux/pub/gcc/x86_64/bin/ncbi/* - elif use x86; then - dobin "${WORKDIR}"/objdir/linux/pub/gcc/i386/bin/* - insinto /usr/bin/ncbi - dobin "${WORKDIR}"/objdir/linux/pub/gcc/i386/bin/ncbi/* + mkdir "${D}"/usr + mkdir "${D}"/usr/bin + dobin "${WORKDIR}"/objdir/linux/rel/gcc/x86_64/bin/* + # for f in ${W}/objdir/linux/rel/gcc/i386/bin/*; do if [ ! -l "$f" ]; then cp "$f" ${D}/usr/bin || die "copy failed" ; fi; done + + dolib "${WORKDIR}"/objdir/linux/rel/gcc/x86_64/ilib/* + dolib "${WORKDIR}"/objdir/linux/rel/gcc/x86_64/mod/* + dolib "${WORKDIR}"/objdir/linux/rel/gcc/x86_64/wmod/* fi - - # mkdir -p ${D}/usr/bin || die - # for f in ${W}/objdir/linux/rel/gcc/i386/bin/*; do if [ ! -l "$f" ]; then cp "$f" ${D}/usr/bin || die "copy failed" ; fi; done - - # looks the binaries have the folllowing libs statically linked in so we do NOT need these files - # mkdir -p ${D}/usr/ilib || die - # dolib ${W}/objdir/linux/rel/gcc/i386/ilib/* - # insinto "${D}"/usr/lib/ncbi - # doins ${W}/objdir/linux/rel/gcc/i386/ilib/ncbi/* - - # mkdir -p ${D}/usr/lib || die - # dolib ${W}/objdir/linux/rel/gcc/i386/lib/* - # insinto "${D}"/usr/lib/ncbi - # doins ${W}/objdir/linux/rel/gcc/i386/lib/ncbi/* - - # same for mod/ and wmod/ subdirs } -- cgit v1.2.3-65-gdbad