Re: Failure in autopkgtest for loki (Was: Working tests seem to exist for epcr)

Hi Andreas,

Thanks for taking the time out to look into my work.

On Fri, Feb 21, 2020 at 1:54 AM Andreas Tille <tille@debian.org> wrote:

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?

I run the tests inside a chroot I made using sbuild-debian-developer-setup [1], and everything seems to be fine there as well.

From the output, it seems that loki is trying to create a file called loki.dat, but failing.

Just off the top of my head, could it be an issue with permissions? Does the chroot allow programs to create files?
I will try building a pbuilder environment on my machine as well, and look into this at the earliest.

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.

Thank you so much!

[1]: https://wiki.debian.org/sbuild#Using_sbuild-debian-developer-setup

Regards,

Pranav