[med-svn] [cufflinks] 01/02: Force use boost_system, boost_thread when linking. Fixing FTBFS in ubuntu. Enable parallel build.

[Dmitrijs Ledkovs]

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

-- 
Alioth's /git/debian-med/git-commit-notice on /srv/git.debian.org/git/debian-med/cufflinks.git