[med-svn] [cufflinks] 01/02: Force use boost_system, boost_thread when linking. Fixing FTBFS in ubuntu. Enable parallel build.
Dmitrijs Ledkovs
xnox at alioth.debian.org
Wed Oct 23 15:31:05 UTC 2013
This is an automated email from the git hooks/post-receive script.
xnox pushed a commit to branch master
in repository cufflinks.
commit d1be7a9f667868aa49627a46e0f5232ce0879f49
Author: Dmitrijs Ledkovs <dmitrij.ledkov at ubuntu.com>
Date: Wed Oct 23 16:26:42 2013 +0100
Force use boost_system, boost_thread when linking. Fixing FTBFS in ubuntu.
Enable parallel build.
---
debian/changelog | 8 +++++
debian/patches/cufflinks-1.3.0-boost.patch | 47 ----------------------------
debian/patches/series | 1 -
debian/rules | 5 ++-
4 files changed, 12 insertions(+), 49 deletions(-)
diff --git a/debian/changelog b/debian/changelog
index fc906c9..7aac6a2 100644
--- a/debian/changelog
+++ b/debian/changelog
@@ -1,3 +1,11 @@
+cufflinks (2.1.1-4) UNRELEASED; urgency=low
+
+ * Force use boost_system, boost_thread when linking. Fixing FTBFS in
+ ubuntu.
+ * Enable parallel build.
+
+ -- Dmitrijs Ledkovs <xnox at ubuntu.com> Tue, 22 Oct 2013 18:08:35 +0100
+
cufflinks (2.1.1-3) unstable; urgency=low
* Rebuild against boost1.54.
diff --git a/debian/patches/cufflinks-1.3.0-boost.patch b/debian/patches/cufflinks-1.3.0-boost.patch
deleted file mode 100644
index 8939952..0000000
--- a/debian/patches/cufflinks-1.3.0-boost.patch
+++ /dev/null
@@ -1,47 +0,0 @@
-Description: boost 1.50+ fixes from Gentoo
- ax_boost_thread.m4 | 6 +++---
- src/abundances.cpp | 56 +++++++++++++++++++++++++-------------------------
- src/biascorrection.cpp | 2 +-
- src/bundles.cpp | 10 ++++-----
- src/bundles.h | 10 ++++-----
- src/common.h | 4 ++--
- src/compress_gtf.cpp | 12 +++++------
- src/cuffdiff.cpp | 30 +++++++++++++--------------
- src/cufflinks.cpp | 34 +++++++++++++++---------------
- src/differential.cpp | 38 +++++++++++++++++-----------------
- src/filters.cpp | 8 ++++----
- src/genes.h | 6 +++---
- src/gtf_to_sam.cpp | 8 ++++----
- src/hits.cpp | 4 ++--
- src/replicates.cpp | 6 +++---
- src/replicates.h | 18 ++++++++--------
- src/scaffolds.cpp | 28 ++++++++++++-------------
- src/scaffolds.h | 2 +-
- 18 files changed, 141 insertions(+), 141 deletions(-)
-
---- a/ax_boost_thread.m4
-+++ b/ax_boost_thread.m4
-@@ -107,20 +107,20 @@
- for libextension in `ls $BOOSTLIBDIR/libboost_thread*.so* 2>/dev/null | sed 's,.*/,,' | sed -e 's;^lib\(boost_thread.*\)\.so.*$;\1;'` `ls $BOOSTLIBDIR/libboost_thread*.a* 2>/dev/null | sed 's,.*/,,' | sed -e 's;^lib\(boost_thread.*\)\.a*$;\1;'`; do
- ax_lib=${libextension}
- AC_CHECK_LIB($ax_lib, exit,
-- [BOOST_THREAD_LIB="-l$ax_lib"; AC_SUBST(BOOST_THREAD_LIB) link_thread="yes"; break],
-+ [BOOST_THREAD_LIB="-l$ax_lib -lboost_system"; AC_SUBST(BOOST_THREAD_LIB) link_thread="yes"; break],
- [link_thread="no"])
- done
- if test "x$link_thread" != "xyes"; then
- for libextension in `ls $BOOSTLIBDIR/boost_thread*.dll* 2>/dev/null | sed 's,.*/,,' | sed -e 's;^\(boost_thread.*\)\.dll.*$;\1;'` `ls $BOOSTLIBDIR/libboost_thread*.a* 2>/dev/null | sed 's,.*/,,' | sed -e 's;^\(boost_thread.*\)\.a*$;\1;'` ; do
- ax_lib=${libextension}
- AC_CHECK_LIB($ax_lib, exit,
-- [BOOST_THREAD_LIB="-l$ax_lib"; AC_SUBST(BOOST_THREAD_LIB) link_thread="yes"; break],
-+ [BOOST_THREAD_LIB="-l$ax_lib -lboost_system"; AC_SUBST(BOOST_THREAD_LIB) link_thread="yes"; break],
- [link_thread="no"])
- done
- fi
-
- else
-- BOOST_THREAD_LIB="$ax_boost_user_thread_lib";
-+ BOOST_THREAD_LIB="$ax_boost_user_thread_lib -lboost_system";
- AC_SUBST(BOOST_THREAD_LIB)
- link_thread="yes";
-
diff --git a/debian/patches/series b/debian/patches/series
index 7e782fa..805bdd1 100644
--- a/debian/patches/series
+++ b/debian/patches/series
@@ -3,4 +3,3 @@
0002-bam2samtools.patch
0003-fix_includes_path.patch
format-security.patch
-cufflinks-1.3.0-boost.patch
diff --git a/debian/rules b/debian/rules
index cbf1211..3b54c00 100755
--- a/debian/rules
+++ b/debian/rules
@@ -4,7 +4,10 @@
#export DH_VERBOSE=1
%:
- dh $@ --with autoreconf
+ dh $@ --with autoreconf --parallel
+
+override_dh_auto_configure:
+ dh_auto_configure -- LIBS="-lboost_system -lboost_thread"
override_dh_auto_clean:
dh_auto_clean
--
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