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

[Andreas Tille]

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