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

[Martin Mokrejs]

commit:     ed89336ce84a769dcc2c43c85596590e2112dd74
Author:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Mon Feb  6 03:35:44 2012 +0000
Commit:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Mon Feb  6 03:35:44 2012 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=ed89336c

sci-biology/sra_sdk-2.1.9: version bump and almost correct DESTDIR patch

(Portage version: 2.1.10.45/git/Linux x86_64, unsigned Manifest commit)

---
 sci-biology/sra_sdk/ChangeLog                      |    8 ++-
 sci-biology/sra_sdk/files/sra_sdk-destdir.patch    |   76 ++++++++++++++++++++
 sci-biology/sra_sdk/sra_sdk-2.1.6.ebuild           |   14 ++--
 .../{sra_sdk-2.1.6.ebuild => sra_sdk-2.1.9.ebuild} |   21 ++++--
 4 files changed, 104 insertions(+), 15 deletions(-)

diff --git a/sci-biology/sra_sdk/ChangeLog b/sci-biology/sra_sdk/ChangeLog
index 994dd91..0b2163f 100644
--- a/sci-biology/sra_sdk/ChangeLog
+++ b/sci-biology/sra_sdk/ChangeLog
@@ -1,7 +1,13 @@
 # ChangeLog for sci-biology/sra_sdk
-# Copyright 1999-2011 Gentoo Foundation; Distributed under the GPL v2
+# Copyright 1999-2012 Gentoo Foundation; Distributed under the GPL v2
 # $Header: $
 
+*sra_sdk-2.1.9 (06 Feb 2012)
+
+  06 Feb 2012; Martin Mokrejs <mmokrejs@×××××××××××××××.cz>
+  sra_sdk-2.1.6.ebuild, +sra_sdk-2.1.9.ebuild, +files/sra_sdk-destdir.patch:
+  version bump and almost correct DESTDIR patch
+
   22 Sep 2011; Martin Mokrejs <mmokrejs@×××××××××××××××.cz>
   sra_sdk-2.1.6.ebuild:
   adjust to altered source tree strcuture, add weird ncbi/ subdirs to be

diff --git a/sci-biology/sra_sdk/files/sra_sdk-destdir.patch b/sci-biology/sra_sdk/files/sra_sdk-destdir.patch
new file mode 100644
index 0000000..bf66c6e
--- /dev/null
+++ b/sci-biology/sra_sdk/files/sra_sdk-destdir.patch
@@ -0,0 +1,76 @@
+diff -r -u -w sra_sdk-2.1.9/work/sra_sdk-2.1.9/build/Makefile.env sra_sdk-2.1.9-/work/sra_sdk-2.1.9/build/Makefile.env
+--- sra_sdk-2.1.9/work/sra_sdk-2.1.9/build/Makefile.env	2011-08-31 21:46:21.000000000 +0200
++++ sra_sdk-2.1.9-/work/sra_sdk-2.1.9/build/Makefile.env	2012-02-06 02:02:38.000000000 +0100
+@@ -141,7 +141,7 @@
+ 
+ # create all required output directories
+ makedirs:
+-	@ mkdir -p $(addprefix $(TARGDIR)/,$(SUBDIRS) obj/$(MODULE)) $(NCBIDIR)
++	@ mkdir -p $(addprefix $(TARGDIR)/,$(SUBDIRS) obj/$(MODULE)) $(DESTDIR)/$(NCBIDIR)
+ 
+ ifeq (win,$(OS))
+ 
+diff -r -u -w sra_sdk-2.1.9/work/sra_sdk-2.1.9/build/ld.linux.gcc.sh sra_sdk-2.1.9-/work/sra_sdk-2.1.9/build/ld.linux.gcc.sh
+--- sra_sdk-2.1.9/work/sra_sdk-2.1.9/build/ld.linux.gcc.sh	2010-12-28 22:46:39.000000000 +0100
++++ sra_sdk-2.1.9-/work/sra_sdk-2.1.9/build/ld.linux.gcc.sh	2012-02-06 02:23:07.000000000 +0100
+@@ -38,10 +38,10 @@
+ # versioned output
+ if [ "$VERS" = "" ]
+ then
+-    DLIB_CMD="$DLIB_CMD -o $TARG"
+-    EXE_CMD="$EXE_CMD -o $TARG"
++    DLIB_CMD="$DLIB_CMD -o $DESTDIR$TARG"
++    EXE_CMD="$EXE_CMD -o $TARG"
+ else
+     set-vers $(echo $VERS | tr '.' ' ')
+-    DLIB_CMD="$DLIB_CMD -o $OUTDIR/$NAME$DBGAP.so.$VERS -Wl,-soname,$NAME.so.$MAJ"
+-    EXE_CMD="$EXE_CMD -o $OUTDIR/$NAME$DBGAP.$VERS"
++    DLIB_CMD="$DLIB_CMD -o $DESTDIR$OUTDIR/$NAME$DBGAP.so.$VERS -Wl,-soname,$NAME.so.$MAJ"
++    EXE_CMD="$EXE_CMD -o $DESTDIR$OUTDIR/$NAME$DBGAP.$VERS"
+ fi
+diff -r -u -w sra_sdk-2.1.9/work/sra_sdk-2.1.9/build/ld.linux.ln.sh sra_sdk-2.1.9-/work/sra_sdk-2.1.9/build/ld.linux.ln.sh
+--- sra_sdk-2.1.9/work/sra_sdk-2.1.9/build/ld.linux.ln.sh	2010-12-28 22:46:39.000000000 +0100
++++ sra_sdk-2.1.9-/work/sra_sdk-2.1.9/build/ld.linux.ln.sh	2012-02-06 02:34:46.000000000 +0100
+@@ -52,12 +52,12 @@
+ 
+ set-vers $(echo $VERS | tr '.' ' ')
+ 
+-cd "$OUTDIR" || exit 5
++cd $DESTDIR$OUTDIR || exit 5
+ 
+ # create link
+ create-link ()
+ {
+-    rm -f "$2"
++    rm -f $DESTDIR"$2"
+     local CMD="ln -s $1 $2"
+     echo $CMD
+     $CMD
+--- sra_sdk-2.1.9/work/sra_sdk-2.1.9/build/ld.linux.slib.sh        2012-02-06 04:05:16.000000000 +0100
++++ sra_sdk-2.1.9-/work/sra_sdk-2.1.9/build/ld.linux.slib.sh	2012-02-06 04:05:29.000000000 +0100
+@@ -77,7 +77,7 @@
+     CMD="$CMD $TARG"
+ else
+     set-vers $(echo $VERS | tr '.' ' ')
+-    CMD="$CMD $OUTDIR/$NAME$DBGAP.a.$VERS"
++    CMD="$CMD $DESTDIR/$OUTDIR/$NAME$DBGAP.a.$VERS"
+ fi
+ 
+ # tack on object files
+--- sra_sdk-2.1.9/work/sra_sdk-2.1.9/build/Makefile.gcc.ori	2012-02-06 04:24:39.000000000 +0100
++++ sra_sdk-2.1.9/work/sra_sdk-2.1.9/build/Makefile.gcc	2012-02-06 04:22:57.000000000 +0100
+@@ -36,12 +36,12 @@
+ LD = @ $(TOP)/build/ld.sh $(OS) $(ARCH) gcc \
+ 	--build $(BUILD) --ldflags "$(LDFLAGS)" $(STATIC) \
+ 	$(STATICSYSLIBS) $(CHECKSUM) --objx $(OBJX) --shlx $(SHLX) --libx $(LIBX) \
+-	-MD --srcdir $(SRCDIR) --bindir $(BINDIR) -L$(LIBDIR):$(ILIBDIR)
++	-MD --srcdir $(SRCDIR) --bindir $(BINDIR) -L$(DESTDIR)$(LIBDIR):$(ILIBDIR)
+ 
+ LP = @ $(TOP)/build/ld.sh $(OS) $(ARCH) g++ \
+ 	--build $(BUILD) --ldflags "$(LDFLAGS)" $(STATIC) \
+ 	$(STATICSYSLIBS) $(CHECKSUM) --objx $(OBJX) --shlx $(SHLX) --libx $(LIBX) \
+-	-MD --srcdir $(SRCDIR) --bindir $(BINDIR) -L$(LIBDIR):$(ILIBDIR)
++	-MD --srcdir $(SRCDIR) --bindir $(BINDIR) -L$(DESTDIR)$(LIBDIR):$(ILIBDIR)
+ 
+ # tool options
+ WARN = -Wall -Wno-variadic-macros # -Wconversion

diff --git a/sci-biology/sra_sdk/sra_sdk-2.1.6.ebuild b/sci-biology/sra_sdk/sra_sdk-2.1.6.ebuild
index 8e964bd..4e08fb3 100644
--- a/sci-biology/sra_sdk/sra_sdk-2.1.6.ebuild
+++ b/sci-biology/sra_sdk/sra_sdk-2.1.6.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2011 Gentoo Foundation
+# Copyright 1999-2012 Gentoo Foundation
 # Distributed under the terms of the GNU General Public License v2
 # $Header: $
 
@@ -11,8 +11,8 @@ 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=""
+KEYWORDS="~amd64 ~x86"
 IUSE="static"
 
 DEPEND="app-shells/bash
@@ -27,14 +27,14 @@ RDEPEND="${DEPEND}"
 src_compile(){
 	# -I/usr/include/libxml2
 	# -I/var/tmp/portage/sci-biology/sra_sdk-2.0.1/work/sra_sdk-2.0.1/interfaces/os/unix
-	LIBXML_INCLUDES="/usr/include/libxml2" make -j1 OUTDIR="${WORKDIR}"/objdir out || die
-	LIBXML_INCLUDES="/usr/include/libxml2" make -j1 OUTDIR="${WORKDIR}"/objdir || die
+	LIBXML_INCLUDES="/usr/include/libxml2" make -j1 OUTDIR="${WORKDIR}"/objdir out LIBDIR=/usr/lib64 DESTDIR="${D}" || die
+	LIBXML_INCLUDES="/usr/include/libxml2" make -j1 OUTDIR="${WORKDIR}"/objdir LIBDIR=/usr/lib64 DESTDIR="${D}" || die
 
 	# COMP env variable may have 'GCC' or 'ICC' values
 	if use static; then
-		emake static
+		emake static LIBDIR=/usr/lib64 DESTDIR="${D}"
 	else
-		emake dynamic
+		emake dynamic LIBDIR=/usr/lib64 DESTDIR="${D}"
 	fi
 }
 

diff --git a/sci-biology/sra_sdk/sra_sdk-2.1.6.ebuild b/sci-biology/sra_sdk/sra_sdk-2.1.9.ebuild
similarity index 86%
copy from sci-biology/sra_sdk/sra_sdk-2.1.6.ebuild
copy to sci-biology/sra_sdk/sra_sdk-2.1.9.ebuild
index 8e964bd..92d51bf 100644
--- a/sci-biology/sra_sdk/sra_sdk-2.1.6.ebuild
+++ b/sci-biology/sra_sdk/sra_sdk-2.1.9.ebuild
@@ -1,9 +1,11 @@
-# Copyright 1999-2011 Gentoo Foundation
+# Copyright 1999-2012 Gentoo Foundation
 # Distributed under the terms of the GNU General Public License v2
 # $Header: $
 
 EAPI=3
 
+inherit eutils
+
 DESCRIPTION="NCBI Sequence Read Archive (SRA) sratoolkit"
 HOMEPAGE="http://trace.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?cmd=show&f=faspftp_runs_v1&m=downloads&s=download_sra"
 SRC_URI="http://trace.ncbi.nlm.nih.gov/Traces/sra/static/sra_sdk-"${PV}".tar.gz"
@@ -11,8 +13,8 @@ SRC_URI="http://trace.ncbi.nlm.nih.gov/Traces/sra/static/sra_sdk-"${PV}".tar.gz"
 
 LICENSE="public-domain"
 SLOT="0"
-KEYWORDS=""
-#KEYWORDS="~amd64 ~x86"
+#KEYWORDS=""
+KEYWORDS="~amd64 ~x86"
 IUSE="static"
 
 DEPEND="app-shells/bash
@@ -24,18 +26,23 @@ RDEPEND="${DEPEND}"
 # upstream says:
 # icc, icpc are supported: tested with 11.0 (64-bit) and 10.1 (32-bit), 32-bit 11.0 does not work
 
+src_prepare(){
+	epatch "${FILESDIR}"/sra_sdk-destdir.patch || die
+}
+
 src_compile(){
 	# -I/usr/include/libxml2
 	# -I/var/tmp/portage/sci-biology/sra_sdk-2.0.1/work/sra_sdk-2.0.1/interfaces/os/unix
-	LIBXML_INCLUDES="/usr/include/libxml2" make -j1 OUTDIR="${WORKDIR}"/objdir out || die
-	LIBXML_INCLUDES="/usr/include/libxml2" make -j1 OUTDIR="${WORKDIR}"/objdir || die
 
 	# COMP env variable may have 'GCC' or 'ICC' values
 	if use static; then
-		emake static
+		emake static LIBDIR=/lib64 DESTDIR="${D}"
 	else
-		emake dynamic
+		emake dynamic LIBDIR=/lib64 DESTDIR="${D}"
 	fi
+
+	LIBXML_INCLUDES="/usr/include/libxml2" make -j1 OUTDIR="${WORKDIR}"/objdir out LIBDIR=/lib64 DESTDIR="${D}" || die
+	LIBXML_INCLUDES="/usr/include/libxml2" make -j1 OUTDIR="${WORKDIR}"/objdir LIBDIR=/lib64 DESTDIR="${D}" || die
 }
 
 src_install(){