From mboxrd@z Thu Jan 1 00:00:00 1970 Received: from pigeon.gentoo.org ([208.92.234.80] helo=lists.gentoo.org) by finch.gentoo.org with esmtp (Exim 4.60) (envelope-from ) id 1RuTCT-0001rI-32 for garchives@archives.gentoo.org; Mon, 06 Feb 2012 18:22:01 +0000 Received: from pigeon.gentoo.org (localhost [127.0.0.1]) by pigeon.gentoo.org (Postfix) with SMTP id 7094BE0773; Mon, 6 Feb 2012 18:21:53 +0000 (UTC) Received: from smtp.gentoo.org (smtp.gentoo.org [140.211.166.183]) by pigeon.gentoo.org (Postfix) with ESMTP id 310ABE0773 for ; Mon, 6 Feb 2012 18:21:52 +0000 (UTC) Received: from pelican.gentoo.org (unknown [66.219.59.40]) (using TLSv1 with cipher AECDH-AES256-SHA (256/256 bits)) (No client certificate requested) by smtp.gentoo.org (Postfix) with ESMTPS id 3DF421B4066 for ; Mon, 6 Feb 2012 18:21:52 +0000 (UTC) Received: from localhost.localdomain (localhost [127.0.0.1]) by pelican.gentoo.org (Postfix) with ESMTP id AFB2880043 for ; Mon, 6 Feb 2012 18:21:51 +0000 (UTC) From: "Martin Mokrejs" To: gentoo-commits@lists.gentoo.org Content-type: text/plain; charset=UTF-8 Reply-To: gentoo-dev@lists.gentoo.org, "Martin Mokrejs" Message-ID: <73c1e487f0d8fc8c14f39c83e729c95acaf6be0d.mmokrejs@gentoo> Subject: [gentoo-commits] proj/sci:master commit in: sci-biology/sra_sdk/files/, sci-biology/sra_sdk/ X-VCS-Repository: proj/sci X-VCS-Files: sci-biology/sra_sdk/ChangeLog sci-biology/sra_sdk/files/libs_sra_Makefile.patch sci-biology/sra_sdk/files/tools_vdb-vcopy_Makefile.patch sci-biology/sra_sdk/sra_sdk-2.1.9.ebuild X-VCS-Directories: sci-biology/sra_sdk/files/ sci-biology/sra_sdk/ X-VCS-Committer: mmokrejs X-VCS-Committer-Name: Martin Mokrejs X-VCS-Revision: 73c1e487f0d8fc8c14f39c83e729c95acaf6be0d Date: Mon, 6 Feb 2012 18:21:51 +0000 (UTC) Precedence: bulk List-Post: List-Help: List-Unsubscribe: List-Subscribe: List-Id: Gentoo Linux mail X-BeenThere: gentoo-commits@lists.gentoo.org Content-Transfer-Encoding: quoted-printable X-Archives-Salt: 57a010e5-59c7-43f9-8ecb-e6299ba0a9c8 X-Archives-Hash: af52ba5b38fcd37fb49c06940b103c47 commit: 73c1e487f0d8fc8c14f39c83e729c95acaf6be0d Author: Martin Mokrejs fold natur cuni cz> AuthorDate: Mon Feb 6 18:21:43 2012 +0000 Commit: Martin Mokrejs fold natur cuni cz> CommitDate: Mon Feb 6 18:21:43 2012 +0000 URL: http://git.overlays.gentoo.org/gitweb/?p=3Dproj/sci.git;a=3Dc= ommit;h=3D73c1e487 two more Makefiles needed a DESTDIR patch, in conjunction with an ugly sy= mlink hack in one can build the stuff; dobin does not transfer symliks s= o 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(-) diff --git a/sci-biology/sra_sdk/ChangeLog b/sci-biology/sra_sdk/ChangeLo= g index 0b2163f..9ac722a 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: $ =20 + 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 symli= ks 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) =20 06 Feb 2012; Martin Mokrejs diff --git a/sci-biology/sra_sdk/files/libs_sra_Makefile.patch b/sci-biol= ogy/sra_sdk/files/libs_sra_Makefile.patch new file mode 100644 index 0000000..44acc42 --- /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)) +=20 + $(LIBDIR)/libsrapath.$(LIBX): $(SRAPATH_OBJ) +- $(LD) --slib -o $@ $^ ++ $(LD) --slib -o $(DESTDIR)$@ $^ +=20 + libsrapath.vers.h: + @ true +@@ -138,10 +138,10 @@ + -dklib +=20 + $(LIBDIR)/libsra-schema.$(SHLX): $(SRA_SCHEMA_OBJ) +- $(LD) --dlib --vers $(SRCDIR) -o $@ $^ $(SRA_SCHEMA_LIB) ++ $(LD) --dlib --vers $(SRCDIR) -o $(DESTDIR)$@ $^ $(SRA_SCHEMA_LIB) +=20 + $(LIBDIR)/libwsra-schema.$(SHLX): $(WSRA_SCHEMA_OBJ) +- $(LD) --dlib --vers $(SRCDIR) -o $@ $^ $(WSRA_SCHEMA_LIB) ++ $(LD) --dlib --vers $(SRCDIR) -o $(DESTDIR)$@ $^ $(WSRA_SCHEMA_LIB) +=20 + SRASCHEMA_SRC =3D \ + sraschema-stub +@@ -168,10 +168,10 @@ + $(addsuffix .$(LOBX),$(WSRASCHEMA_SRC)) +=20 + $(LIBDIR)/libsraschema.$(LIBX): $(SRASCHEMA_OBJ) $(SRASCHEMA_DEPS) +- $(LD) --slib -o $@ $(SRASCHEMA_OBJ) $(SRA_SCHEMA_LIB) ++ $(LD) --slib -o $(DESTDIR)$@ $(SRASCHEMA_OBJ) $(SRA_SCHEMA_LIB) +=20 + $(LIBDIR)/libwsraschema.$(LIBX): $(WSRASCHEMA_OBJ) $(WSRASCHEMA_DEPS) +- $(LD) --slib -o $@ $(WSRASCHEMA_OBJ) $(WSRA_SCHEMA_LIB) ++ $(LD) --slib -o $(DESTDIR)$@ $(WSRASCHEMA_OBJ) $(WSRA_SCHEMA_LIB) +=20 + libsraschema_tag: + @ $(TOP)/build/tag-module.sh $(MODULE) libsraschema $(SRASCHEMA_OBJ) +@@ -205,10 +205,10 @@ + -dklib +=20 + $(LIBDIR)/libsradb.$(SHLX): $(SRADB_OBJ) +- $(LD) --dlib --vers $(SRCDIR) -o $@ $^ $(SRADB_LIB) ++ $(LD) --dlib --vers $(SRCDIR) -o $(DESTDIR)$@ $^ $(SRADB_LIB) +=20 + $(LIBDIR)/libsradb.$(LIBX): $(SRADB_OBJ) +- $(LD) --slib --vers $(SRCDIR) -o $@ $^ $(SRADB_LIB) ++ $(LD) --slib --vers $(SRCDIR) -o $(DESTDIR)$@ $^ $(SRADB_LIB) +=20 + libsradb_tag: $(SRADB_TAGS) + @ $(TOP)/build/tag-module.sh $(MODULE) libsradb $(SRADB_OBJ) +@@ -236,10 +236,10 @@ + -dklib +=20 + $(LIBDIR)/libwsradb.$(SHLX): $(WSRADB_OBJ) +- $(LD) --dlib --vers $(SRCDIR) -o $@ $^ $(WSRADB_LIB) ++ $(LD) --dlib --vers $(SRCDIR) -o $(DESTDIR)$@ $^ $(WSRADB_LIB) +=20 + $(LIBDIR)/libwsradb.$(LIBX): $(WSRADB_OBJ) +- $(LD) --slib --vers $(SRCDIR) -o $@ $^ $(WSRADB_LIB) ++ $(LD) --slib --vers $(SRCDIR) -o $(DESTDIR)$@ $^ $(WSRADB_LIB) +=20 + libwsradb_tag: $(WSRADB_TAGS) + @ $(TOP)/build/tag-module.sh $(MODULE) libwsradb $(WSRADB_OBJ) +@@ -266,10 +266,10 @@ + -dklib +=20 + $(LIBDIR)/libsrareader.$(SHLX): $(SRAREADER_OBJ) +- $(LD) --dlib --vers $(SRCDIR) -o $@ $^ $(SRAREADER_LIB) ++ $(LD) --dlib --vers $(SRCDIR) -o $(DESTDIR)$@ $^ $(SRAREADER_LIB) +=20 + $(LIBDIR)/libsrareader.$(LIBX): $(SRAREADER_OBJ) +- $(LD) --slib --vers $(SRCDIR) -o $@ $^ $(SRAREADER_LIB) ++ $(LD) --slib --vers $(SRCDIR) -o $(DESTDIR)$@ $^ $(SRAREADER_LIB) +=20 + 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/s= ci-biology/sra_sdk/files/tools_vdb-vcopy_Makefile.patch new file mode 100644 index 0000000..738d67c --- /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=20 +=20 + $(NCBIDIR)/vdb-copy.kfg: $(SRCDIR)/vdb-copy.kfg +- cp $^ $@ ++ cp $^ $(DESTDIR)$@ +=20 + VDB_COPY_SRC =3D \ + num-gen \ diff --git a/sci-biology/sra_sdk/sra_sdk-2.1.9.ebuild b/sci-biology/sra_s= dk/sra_sdk-2.1.9.ebuild index 92d51bf..fcc74cb 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=3D"http://trace.ncbi.nlm.nih.gov/Traces/sra/sta= tic/sra_sdk-"${PV}".tar.gz" LICENSE=3D"public-domain" SLOT=3D"0" #KEYWORDS=3D"" -KEYWORDS=3D"~amd64 ~x86" +KEYWORDS=3D"~amd64" IUSE=3D"static" =20 DEPEND=3D"app-shells/bash @@ -28,12 +28,14 @@ RDEPEND=3D"${DEPEND}" =20 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/"${P}" + } =20 src_compile(){ - # -I/usr/include/libxml2 - # -I/var/tmp/portage/sci-biology/sra_sdk-2.0.1/work/sra_sdk-2.0.1/inter= faces/os/unix - # COMP env variable may have 'GCC' or 'ICC' values if use static; then emake static LIBDIR=3D/lib64 DESTDIR=3D"${D}" @@ -46,35 +48,19 @@ src_compile(){ } =20 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" ]; t= hen cp "$f" ${D}/usr/bin || die "copy failed" ; fi; done - - # looks the binaries have the folllowing libs statically linked in so w= e 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 }