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

["Martin Mokrejs" <mmokrejs@fold.natur.cuni.cz>]

commit:     129e2c6e82a71b4ae4894081ce2384f302f2d096
Author:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Thu Mar 15 21:22:57 2012 +0000
Commit:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Thu Mar 15 21:22:57 2012 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=129e2c6e

sci-biology/sra_sdk-2.1.9: use EAPI=4 hoping it will handle symlinks in bin/ and lib/ directories properly (but it does not, bug #408199

(Portage version: 2.1.10.49/git/Linux x86_64, unsigned Manifest commit)

---
 sci-biology/sra_sdk/ChangeLog            |    5 +++++
 sci-biology/sra_sdk/sra_sdk-2.1.9.ebuild |   22 ++++++++++++++++++----
 2 files changed, 23 insertions(+), 4 deletions(-)

diff --git a/sci-biology/sra_sdk/ChangeLog b/sci-biology/sra_sdk/ChangeLog
index 1a3a884..9b86b3a 100644
--- a/sci-biology/sra_sdk/ChangeLog
+++ b/sci-biology/sra_sdk/ChangeLog
@@ -2,6 +2,11 @@
 # Copyright 1999-2012 Gentoo Foundation; Distributed under the GPL v2
 # $Header: $
 
+  15 Mar 2012; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
+  sra_sdk-2.1.9.ebuild:
+  use EAPI=4 hoping it will handle symlinks in bin/ and lib/ directories
+  properly (but it does not, bug #408199 sra_sdk-2.1.9.ebuild
+
 *sra_sdk-2.1.6 (17 Feb 2012)
 
   17 Feb 2012; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>

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 cf9c639..6baa61c 100644
--- a/sci-biology/sra_sdk/sra_sdk-2.1.9.ebuild
+++ b/sci-biology/sra_sdk/sra_sdk-2.1.9.ebuild
@@ -2,7 +2,7 @@
 # Distributed under the terms of the GNU General Public License v2
 # $Header: $
 
-EAPI=3
+EAPI=4
 
 inherit eutils
 
@@ -72,14 +72,28 @@ src_install(){
 	mkdir "${D}"/usr/bin
 	mkdir -p "${D}"/usr/lib/ncbi
 	mkdir -p "${D}"/usr/ncbi/schema
-	# dobin "${WORKDIR}"/objdir/linux/rel/gcc/"${builddir}"/bin/*
-	for f in "${WORKDIR}"/objdir/linux/rel/gcc/"${builddir}"/bin/*; do cp --preserve=links "$f" "${D}"/usr/bin || die "copy failed" ; done
-	dolib "${WORKDIR}"/objdir/linux/rel/gcc/"${builddir}"/lib/*
+
+	# BUG: neither 'doins -r' nor cp --preserve=all work
+	#insinto /usr/bin
+	#doins -r "${WORKDIR}"/objdir/linux/rel/gcc/"${builddir}"/bin/*
+	for f in "${WORKDIR}"/objdir/linux/rel/gcc/"${builddir}"/bin/*; do cp --preserve=all "$f" "${D}"/usr/bin/ || die "$f copying failed" ; done
+
+
 
 	# install the main libs and the ncbi/vdb-copy.kfg file
 	insinto /usr/lib/ncbi
 	doins "${WORKDIR}"/objdir/linux/rel/gcc/"${builddir}"/lib/ncbi/*
 
+	# zap the subdirectory so that copying below does not fail
+	rm -rf "${WORKDIR}"/objdir/linux/rel/gcc/"${builddir}"/lib/ncbi
+
+
+
+	# BUG: neither the dolib nor cp --preserve=all work
+	#dolib "${WORKDIR}"/objdir/linux/rel/gcc/"${builddir}"/lib/*
+	mkdir -p "${D}"/usr/lib64
+	for f in "${WORKDIR}"/objdir/linux/rel/gcc/"${builddir}"/lib/*; do cp --preserve=all "$f" "${D}"/usr/lib64/ || die "$f copying failed" ; done
+
 	insinto /usr/ncbi/schema
 	doins "${W}"/interfaces/align/*.vschema
 	doins "${W}"/interfaces/sra/*.vschema