[Bioc-devel] Coverage test badge not updating

Hervé Pagès hpages at fredhutch.org
Tue Nov 1 23:13:27 CET 2016

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!


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

Hervé Pagès

Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
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