Bug squashing in December (Was: December)
Hi Debian Med fans, may be the subject of the original mail was not catchy enough and people did not realised that we are doing a 24 day internet wide bug squashing party. Believers in different tradition than advent are welcome to join as well, for sure. I admit I have not realised a dramatic bump in bug fixing activity. It would be *really*, *really* nice if everybody who thinks that Debian Med is helpful for personal work and who wants to contribute tries to squash at least one bug in this time period, better one per week. We really need to get our bug count done and there are low hanging fruits on our list. You can also ask for help here if you have no idea how to squash a bug. Thanks for your contribution Andreas. On Fri, Dec 01, 2017 at 08:39:56AM +0100, Andreas Tille wrote: > Hi everybody, > > its really that simple to close a bug which I'm doing here without a line > of code closing my first bug in this mail after having checked that zstd > has hit backports and adding "882244-d...@bugs.debian.org" to the list of > receivers of this mail. > > Not all bugs are *that* simple to solve but **everybody** is kindly > invited to head for the simple ones right now. > > On Thu, Nov 30, 2017 at 12:44:39PM +0100, Thorsten Alteholz wrote: > > Hi everybody, > > > > this time of the year has come again and in order to carry on a tradition > > (it is the seventh time this year), I want to remind everybody of our > > combined efforts to take care of some poor souls. > > > > The days are closing in, the year is drawing to an end and we should think > > of all those, that are not around with their own kind. Again, during the > > last few months, lots of volunteers all around the world tracked down those > > poor souls and put their cases in the database. We should take care of those > > needy. This year, there are about 180 cases which are relevant to Debian > > Med[1] (this time 21 are serious[2]). So please feel pity for them and allow > > the transition of as many as possible poor souls to their final destination, > > the retirement community in the Archive. Maybe some of the "won't fix" can > > be resolved as well. > > We should definitely try to fix the serious ones - even if they are mostly > not that simple. > > > Furthermore I would like to mention another page[3] with lots of information > > about Debian Med packages. Besides the list of RC bugs you can also see > > packages that can not be built on a Debian architecture, packages that are > > not allowed to migrate from unstable to testing (and thus won't be included > > in the next release) and packages with a new upstream version. I think those > > packages need some care as well. > > Definitely. > > > As soon as I get the notice of a closed case I will record that in our > > Advent calendar[4]. In contrast to normal calendars, let us fill this > > special one with lot s of good deeds. Maybe we can hide at least one number > > of a closed case behind every door. > > > > I would like to mention #225651 [5] here, as this seems to be the oldest one > > that needs some help (at least a proper closing). > > Pinging Aaron explicitly to refresh his statement given several years ago. > > > Have fun, > > Thorsten > > Thanks for the fun and all your work > > Andreas. > > > [1]http://bugs.debian.org/cgi-bin/pkgreport.cgi?which=maint&data=debian-med-packaging%40lists.alioth.debian.org&archive=no&raw=yes&bug-rev=yes&pend-exc=fixed&pend-exc=done > > [2]http://bugs.debian.org/cgi-bin/pkgreport.cgi?which=maint&data=debian-med-packaging%40lists.alioth.debian.org&archive=no&pend-exc=done&sev-inc=critical&sev-inc=grave&sev-inc=serious > > [3]http://udd.debian.org/dmd.cgi?email=debian-med-packag...@lists.alioth.debian.org > > [4]http://debian-med.alteholz.de/advent-2017 > > [5]https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=225651 > > > > -- > http://fam-tille.de > > -- http://fam-tille.de
Re: December: tophat
Hi Andreas, On 04.12.2017 17:33, Andreas Tille wrote: > On Mon, Dec 04, 2017 at 02:09:48PM +0100, Fabian Klötzl wrote: >> I just pushed some changes to build tophat with our version of libbam. >> Not sure if the previously mentioned issue in [1] is fixed; can't test, > > Thanks to the test suite we now know that the issue is not solved yet: > > $ sh run-unit-test That should be done with my recent commit; The new samtools version used a different set of arguments. That's an old one down for the advent calendar. ☺ Best Fabian
Re: December: tophat
Hi Fabian, On Wed, Dec 06, 2017 at 03:53:09PM +0100, Fabian Klötzl wrote: > On 04.12.2017 17:33, Andreas Tille wrote: > > > > Thanks to the test suite we now know that the issue is not solved yet: > > > > $ sh run-unit-test > > That should be done with my recent commit; The new samtools version used > a different set of arguments. I repackaged the upstream tarball to get really rid of the code copy and did some according polishing as well. I also added a versioned Dependency from samtools. It seems we need this versioning since if I install the package on a stretch system the run-unit-test script fails. Since we have samtools 1.3 on stretch it seems to be the reason for the failure. > That's an old one down for the advent calendar. ☺ That's a really nice one. :-) Please keep on with the bug squashing (as well as hopefully others will do!) Kind regards Andreas. -- http://fam-tille.de
Re: December: tophat
On 06.12.2017 16:20, Andreas Tille wrote: > Hi Fabian, > > On Wed, Dec 06, 2017 at 03:53:09PM +0100, Fabian Klötzl wrote: >> On 04.12.2017 17:33, Andreas Tille wrote: >>> >>> Thanks to the test suite we now know that the issue is not solved yet: >>> >>> $ sh run-unit-test >> >> That should be done with my recent commit; The new samtools version used >> a different set of arguments. > > I repackaged the upstream tarball to get really rid of the code copy and > did some according polishing as well. I also added a versioned > Dependency from samtools. It seems we need this versioning since if I > install the package on a stretch system the run-unit-test script fails. > Since we have samtools 1.3 on stretch it seems to be the reason for the > failure. I was testing on sid with samtools 1.5. So yeah, versioning seems like the way to go.
bug squashing target: Probably bowtie 1.2.1.1 issue (Was: Bug#880347: bioperl-run: FTBFS: Test failures)
Hi, this bug report has a time correlation to the upload of the new version of bowtie (1.2.1.1): On Mon, Oct 30, 2017 at 09:08:15PM +0100, Lucas Nussbaum wrote: > Source: bioperl-run > Version: 1.7.2-1 > Severity: serious > ... > > Relevant part (hopefully): > > ok 9 # skip Required executable for Bio::Tools::Run::tRNAscanSE is not > > present > > ok 10 # skip Required executable for Bio::Tools::Run::tRNAscanSE is not > > present > > ok 11 # skip Required executable for Bio::Tools::Run::tRNAscanSE is not > > present > > ok 12 # skip Required executable for Bio::Tools::Run::tRNAscanSE is not > > present > > ok > > > > Test Summary Report > > --- > > t/Bowtie.t (Wstat: 512 Tests: 61 Failed: 2) > > Failed tests: 43, 45 > > Non-zero exit status: 2 > > Files=72, Tests=1690, 156 wallclock secs ( 0.24 usr 0.07 sys + 133.72 cusr > > 6.41 csys = 140.44 CPU) > > Result: FAIL > > Failed 1/72 test programs. 2/1690 subtests failed. > > dh_auto_test: perl Build test --verbose 1 returned exit code 255 > > debian/rules:32: recipe for target 'override_dh_auto_test' failed Earlier in the log: ... # Failed test 'bowtie success' # at t/Bowtie.t line 188. # '# reads processed: 2000 # # reads with at least one reported alignment: 2000 (100.00%) # # reads that failed to align: 0 (0.00%) # Reported 1000 paired-end alignments to 1 output stream(s) # ' # doesn't match '(?^:reads processed: 1000)' # Failed test 'bowtie success' # at t/Bowtie.t line 195. # '# reads processed: 2000 # # reads with at least one reported alignment: 2000 (100.00%) # # reads that failed to align: 0 (0.00%) # Reported 1000 paired-end alignments to 1 output stream(s) # ' # doesn't match '(?^:reads processed: 1000)' # Looks like you failed 2 tests of 61. t/Bowtie.t . ... I suspect that some change between bowtie 1.2.0 and bowtie 1.2.1.1 is responsible for the issue in bioperl-run. I wonder whether tracking down this issue sounds interesting for somebody who knows (and uses) bowtie a bit. Kind regards Andreas. -- http://fam-tille.de
