Hi Shayan, On Thu, Sep 05, 2019 at 01:45:36AM +0100, Shayan Doust wrote: > Some investigative work. I also compiled a clean copy directly from the > upstream website to prevent any sort of contamination and to rule out > possible upstream fault and then a packaging build attempt (debhelper 11).
Thanks a lot for diving into this. > > I have some gut feeling that the test files for comparison do not > > really fit the proper result. > > This may be the case, but I am having a hard time getting the same > output as > https://buildd.debian.org/status/fetch.php?pkg=tree-puzzle&arch=all&ver=5.2-11&stamp=1539685923&raw=0 > > I have just ran qp-pure-prot.test as an example: > > 113,114c86,87 > < WARNING: Result of chi-square test may not be valid because of > < small maximum likelihood frequencies and short sequence length! > --- > > WARNING: Result of chi-square test may not be valid because of small > > maximum likelihood frequencies and short sequence length! > > * Diffs like this indicate formatting faults which are easy to rectify, > or remove as a whole. > > * The first line of the test output file contains TEST-PUZZLE and the > version number. This version number (5.3.rc16) is not visible in the > upstream expected output file, so diff will of course display this as a > delta. > > * There is a higher verbosity of paragraphed description / output in the > test's newly-generated results file compared to what upstream has. Maybe > upstream is running an older / more obselete version of the program? > > * From what I can see, the numbers seem to match for the most part, but > upstream has introduced chi2-value column which is not present in the > expected results file. > > For instance, running qp-pure-bin.test. Here is a small slice of my output: > > 194c169 > < (bipartition with sequences in input order : number of times seen (and > ratio)) > --- > > (bipartition with sequences in input order : number of times seen) > 196,197c171,172 > < *..** : 1000 (1.000) > < *...* : 1000 (1.000) > --- > > *..** : 1000 > > *...* : 1000 > 201c176 > < (bipartition with sequences in input order : number of times seen (and > ratio)) > --- > > (bipartition with sequences in input order : number of times seen) > > Ratios seem to have been added to the test. Scanning through all the > other test binaries and their outputs, my values seem to match up to > what is expected regardless of the issues above. > > So next I decided to see when the tests directory was added. This > happened to be version 5.2. Quickly testing a couple of test binaries, > they run successfully. It seems like to me that the expected test > results file introduced in 5.2 were just never updated to 5.3~rc16. This matches perfectly my suspicion after a way less deep inspection. Thanks for confirming. > I am > not sure why your build log is different in terms of value. Maybe > upstream modified the current release candidate and version (some do > this). I will keep this updated with anything else that I spot or comes > to mind. Would you mind pinging upstream about this? I have no idea about their release schedule. Version 5.3~rc16 is out for quite some while but may be its the right moment to approach them. > Kind regards, Thanks again for your very valuable contribution Andreas. > On Mon, 8 Jul 2019 21:26:02 +0200 Andreas Tille <andr...@an3as.eu> wrote: > > Hi, > > > > after switching tree-puzzle debhelper level to 9 I was cheating around > > the build time test suite via > > > > override_dh_auto_test: > > # unfortunately most tests are failing for the moment > > # the issue is documented in > > # debian/patches/patch_test_results.patch > > # and needs to be discussed with upstream > > dh_auto_test || true > > > > The rationale was that just by switching the debhelper level the build > > time test suite was run at all. Most probably it was failing all the > > time before and simply nobody realised this. To sort this out we need > > to talk to upstream. The issue is documented in bug #806214 (bug in > > CC). > > > > I now bumped the upstream source in Git to the latest upstream release > > candidate. Since this had not changed quite some time I assume upstream > > is not very rapidly pushing a final release. However, this might be the > > right point in time to sort things out. > > > > If you check the build log of 5.2-11 at > > > > > > https://buildd.debian.org/status/fetch.php?pkg=tree-puzzle&arch=all&ver=5.2-11&stamp=1539685923&raw=0 > > > > you can find > > > > ... > > dh_auto_test || true > > make -j1 check VERBOSE=1 > > make[2]: Entering directory '/<<PKGBUILDDIR>>' > > Making check in src > > make[3]: Entering directory '/<<PKGBUILDDIR>>/src' > > make[3]: Leaving directory '/<<PKGBUILDDIR>>/src' > > Making check in doc > > make[3]: Entering directory '/<<PKGBUILDDIR>>/doc' > > make[4]: Entering directory '/<<PKGBUILDDIR>>/doc' > > make[4]: Nothing to be done for 'check-am'. > > make[4]: Leaving directory '/<<PKGBUILDDIR>>/doc' > > make[3]: Leaving directory '/<<PKGBUILDDIR>>/doc' > > Making check in data > > make[3]: Entering directory '/<<PKGBUILDDIR>>/data' > > make[3]: Nothing to be done for 'check'. > > make[3]: Leaving directory '/<<PKGBUILDDIR>>/data' > > Making check in tests > > make[3]: Entering directory '/<<PKGBUILDDIR>>/tests' > > make check-TESTS > > make[4]: Entering directory '/<<PKGBUILDDIR>>/tests' > > make[5]: Entering directory '/<<PKGBUILDDIR>>/tests' > > SKIP: build-puzzle > > FAIL: qp-pure-bin.test > > FAIL: qp-pure-nucl.test > > FAIL: qp-tn-nucl.test > > FAIL: qp-hky-clock-nucl.test > > FAIL: qp-hky-rhet-nucl.test > > FAIL: qp-hky-rhet-clock-nucl.test > > FAIL: qp-pure-prot.test > > FAIL: qp-mtrev-prot.test > > _______________________________________________ > Debian-med-packaging mailing list > debian-med-packag...@alioth-lists.debian.net > https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-packaging -- http://fam-tille.de