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
<lcoll...@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.hes...@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 <lcoll...@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@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel
_______________________________________________
Bioc-devel@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
1100 Fairview Ave. N, M1-B514
P.O. Box 19024
Seattle, WA 98109-1024
E-mail: hpa...@fredhutch.org
Phone: (206) 667-5791
Fax: (206) 667-1319
_______________________________________________
Bioc-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel
