[Bioc-devel] Coverage test badge not updating
Obenchain, Valerie
Valerie.Obenchain at roswellpark.org
Wed Nov 23 00:02:45 CET 2016
Thanks Leo. This should be fixed now - the url format needed to be updated.
Valerie
On 11/18/2016 08:17 AM, Leonardo Collado Torres wrote:
> Hi Valerie,
>
> Thanks! I do see the badges now but the percent reported seems off.
> Particularly:
>
> * http://bioconductor.org/packages/release/bioc/html/recount.html
> shows a 65% badge with a link
> to https://codecov.io/github/Bioconductor-mirror/recount?branch=release-3.4
> which has a 97% coverage
> * http://bioconductor.org/packages/devel/bioc/html/recount.html shows
> the correct percent in the badge
> (matching https://codecov.io/github/Bioconductor-mirror/recount?branch=master
> )
>
> It could be related to recount failing the latest build report on
> release. Or maybe it's another alphabetical bug because the derfinder*
> packages look ok.
>
> Best,
> Leo
>
> On Fri, Nov 18, 2016 at 9:12 AM, Obenchain, Valerie
> <Valerie.Obenchain at roswellpark.org
> <mailto:Valerie.Obenchain at roswellpark.org>> wrote:
>
> Coverage is now up and running for the release packages. I think all
> looks well... let me know if you see any problems.
>
> Valerie
>
>
> On 11/01/2016 03:14 PM, Hervé Pagès wrote:
> > Hi Leo,
> >
> > I can confirm that while Bioc 3.4 was in devel, package coverage was
> > computed only for the devel version of packages. When we released
> > BioC 3.4, I moved the compute_coverage script that used to run on
> > zin1 (which used to be the central build node for BioC 3.4 for
> months)
> > to malbec2, which is the central build node for BioC 3.5.
> >
> > So yes, package coverage is still only computed for devel packages
> > at the moment. We'll see if we can restore package coverage for
> > release. If, for whatever reason, this is not possible or is too
> > complicated, we'll remove the badges from the release landing pages.
> >
> > Thanks for the reminder!
> >
> > Cheers,
> > H.
> >
> > On 11/01/2016 12:18 PM, Leonardo Collado Torres wrote:
> >> Hi,
> >>
> >> I know that there are several old threads about the coverage badges
> >> including this thread. Basically, while Bioc 3.4 was in devel, the
> >> coverage badges didn't work for Bioc release (3.3). However,
> now that
> >> 3.4 has been released, the badges for Bioc-release (3.4) are
> still not
> >> working and they only work for Bioc-devel (3.5).
> >>
> >> In one of the threads, Dan mentioned that something at codecov had
> >> changed and that he was going to ask for advice on how to
> proceed. I'm
> >> just curious if there are any updates on this issue. If it's only
> >> possible to have the coverage badges work for one branch, then it
> >> might be best to leave them in Bioc-devel (given Jim's arguments
> >> earlier) and remove them from Bioc-release.
> >>
> >> Best,
> >> Leo
> >>
> >> On Mon, Nov 23, 2015 at 4:25 PM, Leonardo Collado Torres
> >> <lcollado at jhu.edu <mailto:lcollado at jhu.edu>> wrote:
> >>> Thank you for fixing this Jim! I noticed it working now on devel.
> >>> However, I believe that is still not working for the release
> branch.
> >>>
> >>> Cheers,
> >>> Leo
> >>>
> >>> On Fri, Nov 20, 2015 at 3:37 PM, Jim Hester
> <james.f.hester at gmail.com <mailto:james.f.hester at gmail.com>> wrote:
> >>>> The coverage tests were inadvertently not running, but they
> are now
> >>>> re-enabled.
> >>>>
> >>>> Please let us know if you notice any other problems
> >>>>
> >>>> Jim
> >>>>
> >>>> On Tue, Nov 17, 2015 at 12:16 PM, Leonardo Collado Torres
> <lcollado at jhu.edu <mailto:lcollado at jhu.edu>>
> >>>> wrote:
> >>>>> Hi,
> >>>>>
> >>>>> In my packages I enabled testing (via testthat) a few weeks
> ago. I did
> >>>>> so as can be seen in
> >>>>>
> >>>>>
> https://github.com/leekgroup/derfinderHelper/commit/26d9d5543d9082f85bbb2d0ae9f02c5c309b9a48
> <https://github.com/leekgroup/derfinderHelper/commit/26d9d5543d9082f85bbb2d0ae9f02c5c309b9a48>
> >>>>> for the changes to tests/test-all.R You can see that the
> tests are
> >>>>> actually being run at
> >>>>>
> >>>>>
> http://bioconductor.org/checkResults/devel/bioc-LATEST/derfinderHelper/zin2-checksrc.html
> <http://bioconductor.org/checkResults/devel/bioc-LATEST/derfinderHelper/zin2-checksrc.html>
> >>>>> Specifically at the lines:
> >>>>>
> >>>>> * checking tests ...
> >>>>> Running ‘test-all.R’ [3s/13s]
> >>>>> [3s/14s] OK
> >>>>>
> >>>>> I'm wondering if the coverage tests are only run at a less
> frequent
> >>>>> pace (say once per month) or if my tests/test-all.R file is
> still
> >>>>> posing problems to covr.
> >>>>>
> >>>>> Thanks,
> >>>>> Leo
> >>>>>
> >>>>> _______________________________________________
> >>>>> Bioc-devel at r-project.org <mailto:Bioc-devel at r-project.org>
> mailing list
> >>>>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
> <https://stat.ethz.ch/mailman/listinfo/bioc-devel>
> >>>>
> >> _______________________________________________
> >> Bioc-devel at r-project.org <mailto:Bioc-devel at r-project.org>
> mailing list
> >> https://stat.ethz.ch/mailman/listinfo/bioc-devel
> <https://stat.ethz.ch/mailman/listinfo/bioc-devel>
> >>
>
>
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