[Debian-med-packaging] Bug#687968: Upstream now at v2.1.1

[David Eccles (gringer)]

The upstream source has been updated again to v2.1.1 (as of
2013-Apr-11), which is a minor bugfix release from v2.1.0. The 2.1.x
release is a substantial improvement over previous releases according
to the cufflinks page:

http://cufflinks.cbcb.umd.edu/

I don't see any easily accessible source repository, but here's the
source code link from that page:

http://cufflinks.cbcb.umd.edu/downloads/cufflinks-2.1.1.tar.gz

Previous versions are downloadable from the directory, but there is no
-latest symlink:

http://cufflinks.cbcb.umd.edu/downloads/

I get an error when trying to compile 2.1.1 from source on Debian at
the configure stage:

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.

autoreconf suggests there is probably other modernisation work to do
as well (which is beyond my current abilities unfortunately -- I'm not
familiar with the autotools):

configure.ac:38: the top level
configure.ac:39: warning: AC_LANG_CONFTEST: no AC_LANG_SOURCE call
detected in body
../../lib/autoconf/lang.m4:193: AC_LANG_CONFTEST is expanded from...
../../lib/autoconf/general.m4:2590: _AC_COMPILE_IFELSE is expanded from...
../../lib/autoconf/general.m4:2606: AC_COMPILE_IFELSE is expanded from...
../../lib/m4sugar/m4sh.m4:639: AS_IF is expanded from...
../../lib/autoconf/general.m4:2031: AC_CACHE_VAL is expanded from...
../../lib/autoconf/general.m4:2052: AC_CACHE_CHECK is expanded from...
ax_boost_thread.m4:33: AX_BOOST_THREAD is expanded from...
configure.ac:39: the top level
configure.ac:34: required file `build-aux/ar-lib' not found
configure.ac:34:   `automake --add-missing' can install `ar-lib'
autoreconf: automake failed with exit status: 1

 - David Eccles (gringer)