[Bioc-devel] Coverage test badge not updating

[Leonardo Collado Torres]

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> 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> 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>
> 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>
> >>>> 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
> >>>>> 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
> >>>>> 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 mailing list
> >>>>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
> >>>>
> >> _______________________________________________
> >> Bioc-devel at r-project.org mailing list
> >> https://stat.ethz.ch/mailman/listinfo/bioc-devel
> >>
>
>
>
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