Re: GenomeTester4 (Was: (Bug#890993) primer3 FTBFS on big endian: test failure)
On Wed, Jun 06, 2018 at 01:18:09PM +0200, Liubov Chuprikova wrote: > > I think it is OK to test only part of the tools. May be you can inform > > upstream by opening an issue that the hard coded memory could create > > trouble in practical applications. > > Thanks for the idea! I have checked and they are already appeared to have > one issue opened [1]. Except it is stated to be about compressed input > files, not about memory, I got the same error and the problem was > definitely with running out of memory. I'll write a bit later to this > issue, too. Fine. > > Not really critical but please add some information about the test data > > sets in README.source - preferably some "wget ..." or so. > > I put info about test data files in d/copyright. Should I transfer it to > README.source instead? No, that's fine. I should have checked there as well. I'll upload as is. > PS: Once you have added this do you know with which package you want to > > continue or should I make some suggestions? > > I thought about these packages: ncbi-entrez-direct, sra-sdk, rsem, > soapdenovo, soapdenovo2, kmer, treeview, fastdnaml. All sound pretty useful. So just go for it and keep us updated about any issue. > Not sure about artemis. As far as I can see its a GUI application. If you find sensible ways to do some CLI checks that would be perfect. BTW, if you have some Java background - will you be able to get the latest version build? > All are familiar to me to some extent. I'll be happy to have any > suggestions or recommendations from you! :-) I'll come up with further suggestions once you are done with these. Kind regards Andreas. > [1] https://github.com/bioinfo-ut/GenomeTester4/issues/4 -- http://fam-tille.de
Re: GenomeTester4 (Was: (Bug#890993) primer3 FTBFS on big endian: test failure)
On Wed, 6 Jun 2018 at 08:06 Andreas Tille wrote: > Hi Liubov, > > On Wed, Jun 06, 2018 at 12:16:38AM +0200, Liubov Chuprikova wrote: > > > > I have just added tests. Unfortunately, I could not test gmer_counter and > > gmer_caller, as they require a lot of memory to allocate (it is > hardcoded). > > I think it is OK to test only part of the tools. May be you can inform > upstream by opening an issue that the hard coded memory could create > trouble in practical applications. > Thanks for the idea! I have checked and they are already appeared to have one issue opened [1]. Except it is stated to be about compressed input files, not about memory, I got the same error and the problem was definitely with running out of memory. I'll write a bit later to this issue, too. > Please, take a look at the package! I think that it could be uploaded if I > > have not missed something critical. > > Not really critical but please add some information about the test data > sets in README.source - preferably some "wget ..." or so. > I put info about test data files in d/copyright. Should I transfer it to README.source instead? PS: Once you have added this do you know with which package you want to > continue or should I make some suggestions? > I thought about these packages: ncbi-entrez-direct, sra-sdk, rsem, soapdenovo, soapdenovo2, kmer, treeview, fastdnaml. Not sure about artemis. All are familiar to me to some extent. I'll be happy to have any suggestions or recommendations from you! :-) With regards, Liubov [1] https://github.com/bioinfo-ut/GenomeTester4/issues/4
Re: GenomeTester4 (Was: (Bug#890993) primer3 FTBFS on big endian: test failure)
Hi Liubov, On Wed, Jun 06, 2018 at 12:16:38AM +0200, Liubov Chuprikova wrote: > > I have just added tests. Unfortunately, I could not test gmer_counter and > gmer_caller, as they require a lot of memory to allocate (it is hardcoded). I think it is OK to test only part of the tools. May be you can inform upstream by opening an issue that the hard coded memory could create trouble in practical applications. > Please, take a look at the package! I think that it could be uploaded if I > have not missed something critical. Not really critical but please add some information about the test data sets in README.source - preferably some "wget ..." or so. Thank for your work Andreas. PS: Once you have added this do you know with which package you want to continue or should I make some suggestions? -- http://fam-tille.de
Re: GenomeTester4 (Was: (Bug#890993) primer3 FTBFS on big endian: test failure)
Hi Andreas, On Mon, 4 Jun 2018 at 18:23 Liubov Chuprikova wrote: > On Mon, 4 Jun 2018 at 16:42 Andreas Tille wrote: > >> >> I think the package is ready for upload but you probably want to add a >> test for the scripts. Please let me know if you consider the package >> ready. >> > > Yes, of course! > I have just added tests. Unfortunately, I could not test gmer_counter and gmer_caller, as they require a lot of memory to allocate (it is hardcoded). Please, take a look at the package! I think that it could be uploaded if I have not missed something critical. Thank you, Liubov
Re: GenomeTester4 (Was: (Bug#890993) primer3 FTBFS on big endian: test failure)
On Mon, 4 Jun 2018 at 16:42 Andreas Tille wrote: > > On Mon, Jun 04, 2018 at 01:37:13PM +0200, Liubov Chuprikova wrote: > > > Apropos ITP bug: Since I'm pretty lazy > > > > I do not believe in it! :-D > > So you do not believe it is lazy to make others work on autopkgtests > rather than doing it myself? :-P > You still didn't convince me since I can guess about how many tasks on you by looking at the activity panel :-P > > I have finally succeeded in reporting an ITP bug [1]! Not from the first > > try: some packages that had to be installed by default were absent on my > > system (my fault) (exim4 is one of them). It took time to understand the > > problem, as the reportbug was not providing any error message in this > case. > Oh, I wrote it wrong — it worked out actually after I reconfigured repotbug. Anyway, I hope that I could not confuse you with this exim4.. Its good in general to have a working setup for reportbug. BTW, you can > even copy the text of the bug report into GMail interface and send it to > cont...@bugs.debian.org. > I've now added you as Uploader to the package and also made the > changelog entry "yours" since this is what matches the ITP. > Thank you! I have also changed the ITP's "Owned by" field to Debian Med mailing list as it is recommended. Sorry for this mess! I think the package is ready for upload but you probably want to add a > test for the scripts. Please let me know if you consider the package > ready. > Yes, of course! With regards, Liubov > [1] https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=900752 >
Re: GenomeTester4 (Was: (Bug#890993) primer3 FTBFS on big endian: test failure)
Dear Liubov, On Mon, Jun 04, 2018 at 01:37:13PM +0200, Liubov Chuprikova wrote: > > Yes, and an ITP bug. > > > > Apropos ITP bug: Since I'm pretty lazy > > I do not believe in it! :-D So you do not believe it is lazy to make others work on autopkgtests rather than doing it myself? :-P > Thanks a lot for the instructions! > > I have finally succeeded in reporting an ITP bug [1]! Not from the first > try: some packages that had to be installed by default were absent on my > system (my fault) (exim4 is one of them). It took time to understand the > problem, as the reportbug was not providing any error message in this case. Its good in general to have a working setup for reportbug. BTW, you can even copy the text of the bug report into GMail interface and send it to cont...@bugs.debian.org. I've now added you as Uploader to the package and also made the changelog entry "yours" since this is what matches the ITP. I think the package is ready for upload but you probably want to add a test for the scripts. Please let me know if you consider the package ready. Thanks for your work on this Andreas. > [1] https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=900752 -- http://fam-tille.de
Re: GenomeTester4 (Was: (Bug#890993) primer3 FTBFS on big endian: test failure)
Dear Andreas, On Fri, 1 Jun 2018 at 14:00 Andreas Tille wrote: > > On Fri, Jun 01, 2018 at 11:49:09AM +0200, Liubov Chuprikova wrote: > > Has something remained to be done except for testsuite? > > Yes, and an ITP bug. > > Apropos ITP bug: Since I'm pretty lazy I do not believe in it! :-D > I wrote a small script which is > in the dh-r git repository[1]. So you do the following: Go to your > the repository with your prepared packaging stuff and call > > /itp_from_debian_dir > > which generates the output you need to paste. Then you do: > > > $ reportbug --no-check wnpp > > 1 (for ITP) > anything (package name comes later) > anything (package description comes later > first_line_of_script_output (the team that maintains the package > > Remove all text and copy everything else from the script after > the second empty line. (First line should be "Subject ...") > Thanks a lot for the instructions! I have finally succeeded in reporting an ITP bug [1]! Not from the first try: some packages that had to be installed by default were absent on my system (my fault) (exim4 is one of them). It took time to understand the problem, as the reportbug was not providing any error message in this case. With regards, Liubov [1] https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=900752
Re: GenomeTester4 (Was: (Bug#890993) primer3 FTBFS on big endian: test failure)
Hi Liubov, On Fri, Jun 01, 2018 at 11:49:09AM +0200, Liubov Chuprikova wrote: > > Ok, I'll try to do it! Thank you! :-) > > > > Please, check out my last commits! I have changed d/rules, added install > files, manpages, and two patches to fix lintian warnings. I haven't fixed > all hardenings, as I don't understand them fully yet. Sometimes lintian just finds false positives. Since its just info I'd recommend to leave this as is. For a test I added $(LDFLAGS) but these seem to be duplicated then so I droped this again. > Has something remained to be done except for testsuite? Yes, and an ITP bug. Apropos ITP bug: Since I'm pretty lazy I wrote a small script which is in the dh-r git repository[1]. So you do the following: Go to your the repository with your prepared packaging stuff and call /itp_from_debian_dir which generates the output you need to paste. Then you do: $ reportbug --no-check wnpp 1 (for ITP) anything (package name comes later) anything (package description comes later first_line_of_script_output (the team that maintains the package Remove all text and copy everything else from the script after the second empty line. (First line should be "Subject ...") For sure you can pick all the information manually ... but recently I needed to file lots of ITPs (18 on one day :-P ). Hope this helps Andreas. [1] https://salsa.debian.org/r-pkg-team/dh-r/blob/master/scripts/itp_from_debian_dir -- http://fam-tille.de
Re: GenomeTester4 (Was: (Bug#890993) primer3 FTBFS on big endian: test failure)
Hi Andreas, On Tue, 29 May 2018 at 16:40 Liubov Chuprikova wrote: > On Tue, 29 May 2018 at 16:28 Andreas Tille wrote: > >> >> BTW, that looks easy. I've prepared it[1] and if you like you can add >> >> override_dh_build >> >> after reading install instructions and implement these in debian/rules, >> install files and add a test. >> > > Ok, I'll try to do it! Thank you! :-) > Please, check out my last commits! I have changed d/rules, added install files, manpages, and two patches to fix lintian warnings. I haven't fixed all hardenings, as I don't understand them fully yet. Has something remained to be done except for testsuite? With regards, Liubov
Re: GenomeTester4 (Was: (Bug#890993) primer3 FTBFS on big endian: test failure)
On Tue, 29 May 2018 at 16:28 Andreas Tille wrote: > On Tue, May 29, 2018 at 03:15:29PM +0200, Liubov Chuprikova wrote: > > > > > > 2. Since you have saved time to work out proper tests on rarely > > > used architectures you have time to package > > >https://github.com/bioinfo-ut/GenomeTester4 > > > > > > While the later is half joking this could be quite useful. You would > > > have need the tool for your original plan - may be for other things as > > > well and you could learn packaging. > > > > > > > I am not sure that I could get through packaging process at the moment. I > > would prefer to put this package on my list of cases so that I could > return > > to it when I feel more confidently. :-) > > BTW, that looks easy. I've prepared it[1] and if you like you can add > > override_dh_build > > after reading install instructions and implement these in debian/rules, > install files and add a test. > Ok, I'll try to do it! Thank you! :-) With regards, Liubov
