[Debian-med-packaging] We are basically through libbpp* upgrade

[Julien Yann Dutheil]

Dear Andreas,

Would you mind giving it another try? I made some more changes, hopefully
for good.

Best,

Julien.

On Tue, May 1, 2018 at 8:29 AM, Andreas Tille <tille at debian.org> wrote:

> Hi Julien,
>
> thanks for your work on the Debian packaging.
>
> On Mon, Apr 30, 2018 at 05:57:16PM +0200, Julien Yann Dutheil wrote:
> > I have committed a patch for libbpp-phyl, I hope it will solve the
> failing
> > test on the remaining architectures.
>
> Hmmm, I've build the package the first time successfully.  Than I've
> fixed some minor things (added a DEP3 header and bumped
> Standards-Version - please git pull) and tried to build again ... than it
> failed.
>
> ...
> /usr/bin/ctest --force-new-ctest-process -j4
> ...
>       Start 11: test_simulations
>  8/14 Test  #5: test_likelihood_nh ...............***Failed   19.45 sec
> ^M/ 1^M- 2^M\ 3^M- 4^M/ 5^M- 6^M\ 7^M- 8^M/ 9^M- 10^M\ 11 nodes loaded.
> Theta0 set to 0.872938
> Theta1 set to 0.676144
> Theta2 set to 0.464858
> Theta3 set to 0.917092
> Theta4 set to 0.504837
> Theta5 set to 0.192247
> Theta6 set to 0.195117
> Theta7 set to 0.79673
> Theta8 set to 0.574392
> Theta9 set to 0.842239
> Initializing data structure............: Done.
> Number of distinct sites...............: 376
> Initializing data structure............: Done.
> Number of distinct sites...............: 376
> ^MOptimizing... / 1^MOptimizing... - 2^MOptimizing... \ 3^MOptimizing... -
> 4^MOptimizing... / 5^MOptimizing... - 6^MOptimizing... \ 7^MOptimizing... -
> 8^MOptimizing... / 9^MOptimizing... - 10
>
> ^MOptimizing... / 1^MOptimizing... - 2^MOptimizing... \ 3^MOptimizing... -
> 4^MOptimizing... / 5^MOptimizing... - 6^MOptimizing... \ 7^MOptimizing... -
> 8^MOptimizing... / 9^MOptimizing... - 10
> /usr/bin/ctest --force-new-ctest-process -j4
> Test project /build/libbpp-phyl-2.4.0/obj-x86_64-linux-gnu
>       Start  1: test_bowker
> ...
> 93% tests passed, 1 tests failed out of 14
>
> Total Test time (real) = 138.22 sec
>
> The following tests FAILED:
>           5 - test_likelihood_nh (Failed)
> Errors while running CTest
>
>
> I admit I have no idea why this failed the second time.  The only
> observation I made is that my laptop fan was working quite heavily
> since I have build another package in parallel.  So the only idea
> is that the test somehow might depend from some random process that
> might not be initialised correctly.  But you might know better.
>
> > I have also made an update for maffilter. Some notes regarding that one:
> > - There are 3 lintian warnings about linked but unused libraries. One
> > (boost regex) is included automatically by the inclusion of
> boost-iostream
> > in cmake, I do not know how to get rid of it. The two others (gzip and
> > bzip) are required for the program to link properly. I I do not include
> > them it fails (and I actually need them, I do not use them directly but
> via
> > some wrappers in boost-iostream).
>
> Hmmm, I do not get the said warnings.  Are you using the latest lintian
> from unstable?  The only thing that might deserve some attention is
>
>   maffilter: spelling-error-in-binary usr/bin/maffilter Ouput Output
>
> > - I have read that BUILD_TYPE should be set to "None" when building a
> cmake
> > project. If I do so, however, I get a warning about missing debug
> symbols.
> > For me it only works if I set BUILD_TYPE=RelWithDebInfos (applies to
> > maffilter, bppsuite, bppphyview and physamp). If there is a better
> solution
> > I'd be happy to implement it.
>
> May be you check this thread on the Debian Med mailing list:
>
>    https://lists.debian.org/debian-med/2018/04/msg00132.html
>
> Kind regards
>
>        Andreas.
>
> --
> http://fam-tille.de
>



-- 
Julien Y. Dutheil, Ph-D
0 (+49) 6421 178 986

§ Max Planck Institute for Evolutionary Biology
Molecular Systems Evolution
Department of Evolutionary Genetics
Plön -- GERMANY

§ Institute of Evolutionary Sciences - Montpellier
University of Montpellier 2 -- FRANCE
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