subject:"\[Bioc\-devel\] Coverage test badge not updating"

Re: [Bioc-devel] Coverage test badge not updating

2016-11-22 Thread Obenchain, Valerie

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
>  > 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
> >> > 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
> > 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
> >
>  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

Re: [Bioc-devel] Coverage test badge not updating

2016-11-18 Thread 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.obench...@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
> >>  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 
> 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
> >>
>
>
>
> 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.
>

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Re: [Bioc-devel] Coverage test badge not updating

2016-11-18 Thread Obenchain, Valerie

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
>>  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  
>>> 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 
 
 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
>>



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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 
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Re: [Bioc-devel] Coverage test badge not updating

2016-11-01 Thread Hervé Pagès


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
 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  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 
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

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--
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

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Re: [Bioc-devel] Coverage test badge not updating

2016-11-01 Thread Leonardo Collado Torres

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
 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  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 
> > 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
> >
> >

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Re: [Bioc-devel] Coverage test badge not updating

2015-11-23 Thread Leonardo Collado Torres

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  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 
> 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
>
>

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Re: [Bioc-devel] Coverage test badge not updating

2015-11-20 Thread Jim Hester

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 
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

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[Bioc-devel] Coverage test badge not updating

2015-11-17 Thread Leonardo Collado Torres

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

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Re: [Bioc-devel] Coverage test badge not updating

Re: [Bioc-devel] Coverage test badge not updating

Re: [Bioc-devel] Coverage test badge not updating

Re: [Bioc-devel] Coverage test badge not updating

Re: [Bioc-devel] Coverage test badge not updating

Re: [Bioc-devel] Coverage test badge not updating

Re: [Bioc-devel] Coverage test badge not updating

[Bioc-devel] Coverage test badge not updating

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