[gentoo-commits] proj/sci:master commit in: sci-biology/sra_sdk/files/, sci-biology/sra_sdk/

[Martin Mokrejs]

commit:     73c1e487f0d8fc8c14f39c83e729c95acaf6be0d
Author:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Mon Feb  6 18:21:43 2012 +0000
Commit:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Mon Feb  6 18:21:43 2012 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=73c1e487

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(-)

diff --git a/sci-biology/sra_sdk/ChangeLog b/sci-biology/sra_sdk/ChangeLog
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: $
 
+  06 Feb 2012; Martin Mokrejs <mmokrejs@×××××××××××××××.cz>
+  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 <mmokrejs@×××××××××××××××.cz>

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 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))
+ 
+ $(LIBDIR)/libsrapath.$(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 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 
+ 
+ $(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 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="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
 }