[Debian-med-packaging] ABySS version is out of date

[Anthony Raymond]

Hi Andreas,

Thanks so much for working on this!

I'll bring the matter of licensing up with my superiors, but I'm quite certain that the "for non-commercial use" clause is a hard requirement…

I agree that it would be nice to run the unit tests. I'm pretty sure we are calling gtest in some non-standard way. I'll see about sending you a patch this week (if not today) that addresses this.

Thanks!
Tony


On 2014-09-15, at 7:38 AM, Andreas Tille wrote:

> Hi Tony,
> 
> On Thu, Sep 11, 2014 at 11:39:20AM -0700, Anthony Raymond wrote:
>> Hi,
>> 
>> The latest version of ABySS listed in the debian-med packages overview is 1.3.7. There is a release 1.5.2, which was released earlier this summer and is downloadable from here:
>> https://github.com/bcgsc/abyss/releases/download/1.5.2/abyss-1.5.2.tar.gz
>> 
>> Let me know if there's anything I need to do to get the latest version of ABySS packaged in debian.
> 
> I commited the packaging for abyss 1.5.2 into our packaging git[1].
> Unfortunately it fails to run the unit tests since the build ended with
> 
> ...
> make[2]: Entering directory '/tmp/buildd/abyss-1.5.2/GapFiller'
> make[2]: Nothing to be done for 'check'.
> make[2]: Leaving directory '/tmp/buildd/abyss-1.5.2/GapFiller'
> make[2]: Entering directory '/tmp/buildd/abyss-1.5.2'
> make[2]: Nothing to be done for 'check-am'.
> make[2]: Leaving directory '/tmp/buildd/abyss-1.5.2'
> error: To use 'make check' command, please setup
>       gtest header&library as shown on the Wiki
> Makefile:860: recipe for target 'check' failed
> make[1]: *** [check] Error 1
> make[1]: Leaving directory '/tmp/buildd/abyss-1.5.2'
> dh_auto_test: make -j1 check returned exit code 2
> debian/rules:6: recipe for target 'build' failed
> make: *** [build] Error 2
> 
> 
> While I dadded libgtest-dev to the Build-Depends and the build log says:
> 
> 
> ...
> checking for boost/unordered_set.hpp... yes
> checking gtest/gtest.h usability... yes
> checking gtest/gtest.h presence... yes
> checking for gtest/gtest.h... yes
> checking for pthread_create in -lpthread... yes
> checking for main in -lgtest_main... no
> checking for g++ option to support OpenMP... -fopenmp
> checking that generated files are newer than configure... done
> ...
> 
> 
> I think the gtest headers are reasonably installed but I wonder what
> "-lgtest_main... no" might mean, whether this is connected to the
> problem and how to fix this (Steve as maintainer of libgtest-dev in
> CC).
> 
> While I could cowardly skip the unit tests I would really prefer to
> run them.
> 
> BTW, since you asked what you can do to get abyss packaged for Debian:
> while the package is technically packaged it does not belong to the
> Debian distribution since it is regarded as non-free due to its
> licensing restriction to non-commercial use.  I wonder whether you might
> consider with the people in charge to use a non-restricted license.
> This would be really appreciated and if you want me to be more verbose
> about the advantages I could go more into details.
> 
> Kind regards
> 
>        Andreas.
> 
> [1] git://anonscm.debian.org/debian-med/abyss.git
> 
> -- 
> http://fam-tille.de