Hi Pranav,
On Thu, Feb 20, 2020 at 10:30:58PM +0530, Pranav Ballaney wrote:
> other day, and I've now added to loki
> <https://salsa.debian.org/med-team/loki> as well.
I had a look into loki now (please git pull). Besides minor issues
there is one remaining error in the test suite which is strange. I
added some debugging lines to track this down. If I run the script
directly on my machine with the installed loki package via
sh /usr/share/doc/loki/run-unit-test
everything is fine. However, I have configured my pbuilder
environment[1] where I do all my builds including the autopkgtest
hook[2]. This is executing the test inside a minimal chroot. If
I do this I get inside the build log:
autopkgtest [19:18:52]: test run-unit-test: [-----------------------
gzip: warning: GZIP environment variable is deprecated; use an alias or script
+ cp test_seedfile seedfile
+ echo '========= prep control_jv ========'
+ prep control_jv
========= prep control_jv ========
getseed(): Using stored state for mt19937b generator
Reading in data from file 'jvped'
15 records of 8 columns read in
Initializing and recoding pedigree
Recoding marker data
Pruning pedigree
No. components = 1
No. Full Sib Families = 7
No. loops = 3
Close inbreeding found - more details in logfile
3 first cousin marriages
Processing marker 'MARK1' (no. alleles = 4)
No. non-zero terms = 169, non-zero combinations = 558
Processing marker 'MARK2' (no. alleles = 3)
No. non-zero terms = 223, non-zero combinations = 634
Processing trait locus 'QTL'
[write_data.c:250] Error writing to file 'loki.dat'
loki: No such file or directory
Writing out data file...
autopkgtest [19:18:53]: test run-unit-test: -----------------------]
autopkgtest [19:18:53]: test run-unit-test: - - - - - - - - - - results - - -
- - - - - - -
run-unit-test FAIL non-zero exit status 1
autopkgtest [19:18:53]: @@@@@@@@@@@@@@@@@@@@ summary
run-unit-test FAIL non-zero exit status 1
This is strange and for the moment I have no solution for
this.
How are you running the test at your site?
Does anybody have an idea what might went wrong here?
Besides this issue you are perfectly on the right track and I repeat
that I'm absolutely happy about your performance right from the
beginning.
Kind regards
Andreas.
[1]
https://med-team.pages.debian.net/policy/#to-make-gbp-buildpackage-build-the-package-with-pdebuild
[2] /usr/share/doc/pbuilder/examples/B20autopkgtest
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