Cufflinks package fails to build on Launchpad PPA

[Carlos Borroto <carlos.borroto@gmail.com>]

Hi,

As a way of getting familiar with git-buildpackage and company. I have
been trying to clone several packages git repository and getting them
onto the PPA. I was able to do so for samtools, only for Oneiric as I
feel safer staying out of Lucid LTS until I gain more experience. I
created a new branch and tag on the samtools git repository to show
the source of the package.

Trying now to do the same for cufflinks, but the build if failing:

https://launchpadlibrarian.net/88726220/buildlog_ubuntu-oneiric-amd64.cufflinks_1.2.1-1~oneiric1_FAILEDTOBUILD.txt.gz

I think I can see the problem, on that log I see the package is been
build without the patches, so the BAM header files aren't been found:

dh_quilt_unpatch
Removing patch 0003-fix_includes_path.patch
Restoring src/hits.h

Removing patch 0002-bam2samtools.patch
Restoring ax_bam.m4

Removing patch 0001-fix_spelling.patch
Restoring src/locfit/arith.c
Restoring src/locfit/lfd.c

No patches applied
dh_clean
make[1]: Leaving directory `/build/buildd/cufflinks-1.2.1'
 debian/rules build
dh build --with autoreconf
   dh_testdir
   dh_autoreconf
...
...
checking for bamlib... configure: error: We could not detect the bam
libraries (version  or higher). If you have a staged bam library
(still not installed) please specify $BAM_ROOT in your environment and
do not give a PATH to --with-bam option.  If you are sure you have bam
installed, then check your version number looking in
<bam/version.hpp>. See http://randspringer.de/bam for more
documentation.




In my local environment using cowbuilder, the patches are applied:

dh_quilt_unpatch
Removing patch 0003-fix_includes_path.patch
Restoring src/hits.h

Removing patch 0002-bam2samtools.patch
Restoring ax_bam.m4

Removing patch 0001-fix_spelling.patch
Restoring src/locfit/lfd.c
Restoring src/locfit/arith.c

No patches applied
dh_clean
make[1]: Leaving directory `/tmp/buildd/cufflinks-1.2.1'
 dpkg-source -b cufflinks-1.2.1
dpkg-source: info: using source format `3.0 (quilt)'
dpkg-source: warning: patches have not been applied, applying them now
(use --no-preparation to override)
dpkg-source: info: applying 0001-fix_spelling.patch
dpkg-source: info: applying 0002-bam2samtools.patch
dpkg-source: info: applying 0003-fix_includes_path.patch
dpkg-source: info: building cufflinks using existing
./cufflinks_1.2.1.orig.tar.gz
dpkg-source: info: building cufflinks in
cufflinks_1.2.1-1~oneiric1.debian.tar.gz
dpkg-source: info: building cufflinks in cufflinks_1.2.1-1~oneiric1.dsc
 debian/rules build
dh build --with autoreconf
   dh_testdir
   dh_autoreconf
...
...
checking for bamlib... yes




Is there a reason why is this happening?
Thanks,
Carlos