[Bioc-devel] no more commits allowed before release ?

[Robert M. Flight]

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 rflight79 at 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 <dtenenba at fhcrc.org> wrote:

>
>
> ----- Original Message -----
> > From: "Kevin Rue-Albrecht" <kevin.rue at ucdconnect.ie>
> > To: "Dan Tenenbaum" <dtenenba at fhcrc.org>
> > Cc: bioc-devel at 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 < dtenenba at fhcrc.org > wrote:
> >
> >
> >
> >
> > ----- Original Message -----
> > > From: "Kevin Rue-Albrecht" < kevin.rue at ucdconnect.ie >
> > > To: bioc-devel at 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 at 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
> >
>
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