src/gffread.cpp | 140 70 + 70 - 0 !
1 file changed, 70 insertions(+), 70 deletions(-)

 fix wrong usage indentation causing buffer overflow in gffread when 
 using -h, --help and other arguments.

configure.ac | 5 0 + 5 - 0 !
1 file changed, 5 deletions(-)

 update configure.ac to not force -m64.
Just because the compiler supports it, doesn't mean it can compile
natively to it (e.g. on powerpc, you can compile -m64, but there are
no headers for it plus it cannot run on 32-bit systems).

src/abundances.cpp | 2 1 + 1 - 0 !
src/locfit/arith.c | 2 1 + 1 - 0 !
src/locfit/lfd.c | 2 1 + 1 - 0 !
3 files changed, 3 insertions(+), 3 deletions(-)

 fix_spelling

ax_bam.m4 | 2 1 + 1 - 0 !
1 file changed, 1 insertion(+), 1 deletion(-)

 bam2samtools

ax_check_eigen.m4 | 2 1 + 1 - 0 !
configure | 2 1 + 1 - 0 !
src/abundances.cpp | 2 1 + 1 - 0 !
src/abundances.h | 2 1 + 1 - 0 !
src/hits.h | 2 1 + 1 - 0 !
src/jensen_shannon.h | 2 1 + 1 - 0 !
src/sampling.h | 2 1 + 1 - 0 !
7 files changed, 7 insertions(+), 7 deletions(-)

 fix_includes_path.patch

src/locfit/makecmd.c | 2 1 + 1 - 0 !
1 file changed, 1 insertion(+), 1 deletion(-)

 when building with --format-security (debhelper 9 hardening)
 this patch is needed to build successfully

src/abundances.cpp | 2 1 + 1 - 0 !
1 file changed, 1 insertion(+), 1 deletion(-)

 for some reason eigen thinks that v.colwise().sum() cannot be
 treated as a one-dimensional vector, which smells like a bug in Eigen.
Comment: Related upstream bug
 https://github.com/cole-trapnell-lab/cufflinks/issues/61

src/lemon/error.h | 4 2 + 2 - 0 !
1 file changed, 2 insertions(+), 2 deletions(-)

 fix a build issue caused by an unmaintained code copy
 of liblemon.
 Remark: Cufflinks does not build with the current Debian packaged liblemon.
         If you want to try you can use the branch use_debian_packaged_liblemon
         in the packaging Git