[med-svn] [SCM] cufflinks branch, master, updated. debian/1.3.0-2-28-g76ea798

[Dmitrijs Ledkovs]

The following commit has been merged in the master branch:
commit d86155e906025b3663cc09663ad6665be72ee41f
Author: Dmitrijs Ledkovs <xnox at debian.org>
Date:   Thu May 23 01:04:10 2013 +0100

    Fix failing to build from source against boost1.53. (Closes: #709252)

diff --git a/debian/changelog b/debian/changelog
index c358c37..40046b6 100644
--- a/debian/changelog
+++ b/debian/changelog
@@ -1,3 +1,9 @@
+cufflinks (2.1.1-2) UNRELEASED; urgency=low
+
+  * Fix failing to build from source against boost1.53. (Closes: #709252)
+
+ -- Dmitrijs Ledkovs <xnox at debian.org>  Thu, 23 May 2013 00:30:51 +0100
+
 cufflinks (2.1.1-1) unstable; urgency=low
 
   [Carlos Borroto]
diff --git a/debian/control b/debian/control
index 0c2fa84..8767f7c 100644
--- a/debian/control
+++ b/debian/control
@@ -9,6 +9,7 @@ Build-Depends: debhelper (>= 9),
                autotools-dev,
                libboost-dev (>=1.47.0),
                libboost-thread-dev (>=1.47.0),
+	       libboost-system-dev (>=1.47.0),
                libbam-dev (>=0.1.16),
                zlib1g-dev,
                dh-autoreconf,
diff --git a/debian/patches/cufflinks-1.3.0-boost.patch b/debian/patches/cufflinks-1.3.0-boost.patch
new file mode 100644
index 0000000..8939952
--- /dev/null
+++ b/debian/patches/cufflinks-1.3.0-boost.patch
@@ -0,0 +1,47 @@
+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 805bdd1..7e782fa 100644
--- a/debian/patches/series
+++ b/debian/patches/series
@@ -3,3 +3,4 @@
 0002-bam2samtools.patch
 0003-fix_includes_path.patch
 format-security.patch
+cufflinks-1.3.0-boost.patch

-- 
Transcript assembly, differential expression, and differential regulation for RNA-Seq.