Thanks Robert, that is a great idea indeed. I like doing checks before submitting a new release to the tracker. Avoids bad surprises.
Just to be clear, in this case, I wasn't expecting to see any change in the build report (I had OKs everywhere, even when the bug existed). The bug only occurred when using my package with microarray data, which I forgot to test since I did relevant changes in my code. The only data I provide at the moment with the package for testing is RNA-Seq, which I use in the examples and the vignette. I occasionally test the package with an in-house microarray dataset. >From this experience, I believe it is best if I include a subset of my microarray dataset as well. But at this stage I think it's better to wait until the release is out. The package is now is a good working state, and I'd rather not take risks just before the big day :) Cheers Kevin On 10 October 2014 16:38, Robert M. Flight <rfligh...@gmail.com> wrote: > If you want to be really sure that the changes fixed the problem without > pushing to Bioconductor master (and seeing a build report), you can set up > a Travis CI on a bugfix branch and see what happens there. The r-travis > wiki has some good documentation > https://github.com/craigcitro/r-travis/wiki, and my own package uses it, > as well as others. > https://github.com/rmflight/categoryCompare/blob/master/.travis.yml > > -Robert > > Robert M Flight, PhD > Bioinformatics PostDoctoral Scholar > Resource Center for Stable Isotope Resolved Metabolomics > Markey Cancer Center > University of Kentucky > Lexington, KY > > Twitter: @rmflight <https://twitter.com/rmflight> > Web: rmflight.github.io > EM rfligh...@gmail.com > PH 502-509-1827 > > The most exciting phrase to hear in science, the one that heralds new > discoveries, is not "Eureka!" (I found it!) but "That's funny ..." - Isaac > Asimov > > > > > On Fri, Oct 10, 2014 at 11:15 AM, Dan Tenenbaum <dtene...@fhcrc.org> > wrote: > >> >> >> ----- Original Message ----- >> > From: "Kevin Rue-Albrecht" <kevin....@ucdconnect.ie> >> > To: "Dan Tenenbaum" <dtene...@fhcrc.org> >> > Cc: bioc-devel@r-project.org >> > Sent: Friday, October 10, 2014 8:03:25 AM >> > Subject: Re: [Bioc-devel] no more commits allowed before release ? >> > >> > >> > Hi Dan, >> > >> > >> > Ok good, you have just given me the most recent commit that I did >> > today, so the ones I was most concerned about (from yesterday) >> > should be there too, that's good for me. The changes should show up >> > in the next build report. >> >> I do see a commit with the commit message "Bug fix...". >> >> > Maybe the build system just started the checks just before I pushed >> > those changes yesterday morning (10am, Irish time.. so around 2am >> > Seattle time, I believe), which could have left them out of the >> > build report. >> > >> >> Changes need to be committed by 4:20 PM Seattle time in order to show up >> in the following day's build report. >> >> >> > >> > >> > I always run CMD check locally before submitting. That wasn't the >> > problem, it was just a scenario that I hadn't tested in a while. I >> > am considering throwing some unit tests in the package soon, but I >> > won't have time before the release.. I'll have to spend some time to >> > do it correctly as it'd be my first time writing unit tests for an R >> > package (did it in other languages before). >> > >> > >> > * Are the unit tests run by the BiocCheck ? In which case, I >> > would need to add another testing dataset corresponding to the >> > scenario that I fixed yesterday. >> >> >> Yes, unit tests are run by BiocCheck, our howto page shows you how to >> make this happen: >> http://www.bioconductor.org/developers/how-to/unitTesting-guidelines/ >> >> Dan >> >> > >> > >> > Cheers >> > Kevin >> > >> > >> > >> > >> > >> > >> > >> > >> > >> > >> > On 10 October 2014 15:40, Dan Tenenbaum < dtene...@fhcrc.org > wrote: >> > >> > >> > >> > >> > ----- Original Message ----- >> > > From: "Kevin Rue-Albrecht" < kevin....@ucdconnect.ie > >> > > To: bioc-devel@r-project.org >> > > Sent: Friday, October 10, 2014 7:31:36 AM >> > > Subject: [Bioc-devel] no more commits allowed before release ? >> > > >> > > Dear all, >> > > >> > > I fixed a bug affecting one particular situation in my package >> > > (GOexpress) >> > > yesterday, and pushed the changes to GitHub. However, the webhook >> > > did >> > > not >> > > trigger to update the page, due to the feature freeze if I >> > > understand >> > > the >> > > schedule correctly >> > > ( http://www.bioconductor.org/developers/release-schedule/ >> > > ). >> > > >> > >> > I see a commit at 2014-10-10 13:13:54 +0100 (your time) / 2014-10-10 >> > 05:11:29 -0700 (Seattle time). >> > >> > Is that the one? The commit message is " Little addition of details >> > to the description of DAM and NCN participation in the project." >> > >> > We do not disable commits to trunk. We have disabled commits to the >> > current release branch (Bioconductor 2.14) because 2.14 builds have >> > stopped. >> > >> > > I suppose I need to wait the release is out to push these changes >> > > again to >> > > update the SVN ? Or is it still possible to include those changes >> > > in >> > > the >> > > release? From the schedule, it still sounds possible "Package >> > > maintainers >> > > should limit changes to "show-stopper" bugs and documentation >> > > improvements." >> > > >> > >> > It is possible, but there are very few build cycles left till the >> > release, so please build and check your package locally before >> > committing changes and then keep an eye on the build report to make >> > sure that the package built ok. >> > >> > Dan >> > >> > >> > > Sincerely, >> > > Kevin >> > > >> > > -- >> > > Kévin RUE-ALBRECHT >> > > Wellcome Trust Computational Infection Biology PhD Programme >> > > University College Dublin >> > > Ireland >> > > http://fr.linkedin.com/pub/k%C3%A9vin-rue/28/a45/149/en >> > > >> > > [[alternative HTML version deleted]] >> > > >> > > _______________________________________________ >> > > Bioc-devel@r-project.org mailing list >> > > https://stat.ethz.ch/mailman/listinfo/bioc-devel >> > > >> > >> > >> > >> > >> > -- >> > >> > Kévin RUE-ALBRECHT >> > Wellcome Trust Computational Infection Biology PhD Programme >> > University College Dublin >> > Ireland >> > http://fr.linkedin.com/pub/k%C3%A9vin-rue/28/a45/149/en >> > >> >> _______________________________________________ >> Bioc-devel@r-project.org mailing list >> https://stat.ethz.ch/mailman/listinfo/bioc-devel >> > > -- Kévin RUE-ALBRECHT Wellcome Trust Computational Infection Biology PhD Programme University College Dublin Ireland http://fr.linkedin.com/pub/k%C3%A9vin-rue/28/a45/149/en [[alternative HTML version deleted]] _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel