Hello Andreas, > 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.
I'll notify them. I agree, even this particular release candidate has been out for a while. Anything useful or any replies I will also CC or forward to this mailing list. Kind regards, Shayan Doust On 05/09/2019 06:27, Andreas Tille wrote: > 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 > >
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