Hi Andreas, Thanks for taking the time out to look into my work. On Fri, Feb 21, 2020 at 1:54 AM Andreas Tille <ti...@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 ᐧ
