[Debian-med-packaging] ABySS version is out of date

[Anthony Raymond]

Hi Andreas, Steve,

I had to follow the instructions on this post to build libgtest.a and libgtest_main.a:
http://askubuntu.com/questions/145887/why-no-library-files-installed-for-google-test

Then I also had to add a check for libgtest in order to include -lgtest when compiling the tests (see attached patch). I haven't had to do this when I compile the gtest library myself, but it's not a big deal to add.

Cheers,
Tony


On 2014-09-15, at 10:10 AM, Tony Raymond wrote:

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


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