[Bioc-devel] Coverage test badge not updating

Obenchain, Valerie Valerie.Obenchain at roswellpark.org
Fri Nov 18 15:12:20 CET 2016

Coverage is now up and running for the release packages. I think all
looks well... let me know if you see any problems.


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

This email message may contain legally privileged and/or confidential information.  If you are not the intended recipient(s), or the employee or agent responsible for the delivery of this message to the intended recipient(s), you are hereby notified that any disclosure, copying, distribution, or use of this email message is prohibited.  If you have received this message in error, please notify the sender immediately by e-mail and delete this email message from your computer. Thank you.

More information about the Bioc-devel mailing list