[Bioc-devel] Unit Tests & Test Coverage

[Romero, Juan Pablo]

Hi Hervé,


Thanks for all the clarifications related to the tests and the coverage for packages.


Yes, I've just checked EventPointer landing page and the coverage bad is working great at

this moment. It seems that it was just a matter of time before it was displayed.


Again, thanks for all.


Best regards,


Juan Pablo

________________________________
From: Hervé Pagès <hpages at fredhutch.org>
Sent: Friday, March 24, 2017 8:29:08 AM
To: Romero, Juan Pablo; bioc-devel at r-project.org
Subject: Re: [Bioc-devel] Unit Tests & Test Coverage

The coverage badge finally got updated:

   https://bioconductor.org/packages/3.5/bioc/html/EventPointer.html

I didn't do anything. Looks like for some reason it took a long time
for the coverage result on codecov.io to propagate to the package
landing page.

Cheers,
H.


On 03/23/2017 01:32 PM, Hervé Pagès wrote:
> Hi Juan Pablo,
>
> Thanks for adding unit tests to your package. We really encourage
> developers to do this. I'm sorry that this is not reflected on
> EventPointer's landing page.
>
> I investigated this a bit (I'm not familiar with how the coverage
> badges are generated on the package landing pages) and here is
> what I found so far.
>
> One possible reason for this is that some packages on
> Bioconductor-mirror are lagging behind their latest svn revision.
> This is actually the case right now for EventPointer. Latest svn
> commit is 127626:
>
>   https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/EventPointer
>
> but the package is still at commit 127616 on Bioconductor-mirror:
>
>
> https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_Bioconductor-2Dmirror_EventPointer&d=DwIGaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=QY4w9Io4Cx1vbUkb-sjYFCC4fp88dTA9tPfm7O_ueSQ&s=O1j0kLptbtmlzKItTODgtPNL9X7OXDteiR7Sn7zCgMg&e=
>
> This is a known issue. We'll try to remedy this ASAP.
>
> This can be a reason why coverage is not updated on a package
> landing page. That's because the script we use for computing
> the coverage interacts with our svn repo (on hedgehog.fhcrc.org)
> in order to get the latest revision of the package, but also with
> the Bioconductor-mirror account on github
> (https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_Bioconductor-2Dmirror_&d=DwIGaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=QY4w9Io4Cx1vbUkb-sjYFCC4fp88dTA9tPfm7O_ueSQ&s=7KRBTOWvXmA76VMkUfMzdWDh-_KsXNXV8K2qWDirx6o&e=
> ) in order to map the
> latest svn revision of a package to the corresponding git commit
> on Bioconductor-mirror. This seems to be needed in order to upload
> the coverage results to codecov.io where the coverage history is
> kept e.g.
>
>
> https://urldefense.proofpoint.com/v2/url?u=https-3A__codecov.io_github_Bioconductor-2Dmirror_VariantAnnotation_branch_master&d=DwIGaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=QY4w9Io4Cx1vbUkb-sjYFCC4fp88dTA9tPfm7O_ueSQ&s=ANws4fvdvik6ga1hynXgSPss0Jrix_9wdl5_tl_0IIo&e=
>
> The coverage information displayed on a package landing page is coming
> from there.
>
> When a package is lagging behind on Bioconductor-mirror, the mapping
> between last svn revision and git commit fails and so uploading the
> coverage results to codecov.io also fails.
>
> However, in the case of EventPointer, there seems to be already 1 point
> in the coverage history at codecov.io:
>
>
> https://urldefense.proofpoint.com/v2/url?u=https-3A__codecov.io_github_Bioconductor-2Dmirror_EventPointer_branch_master&d=DwIGaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=QY4w9Io4Cx1vbUkb-sjYFCC4fp88dTA9tPfm7O_ueSQ&s=dDjRgkJSvMLudzs009l-1rcMyEWa3psee7CK90enRk0&e=
>
> It shows a coverage of about 30%. For some reason, this doesn't show
> up on EventPointer's landing page. I'll investigate more and will
> let you know.
>
> H.
>
>
> On 03/23/2017 04:58 AM, Romero, Juan Pablo wrote:
>> Hi,
>>
>>
>> I'm currently doing the last updates to my package EventPointer before
>> the deadline for next BioC release.
>>
>>
>> I've added unit tests according to the guide lines in
>> https://urldefense.proofpoint.com/v2/url?u=http-3A__bioconductor.org_developers_unitTesting-2Dguidelines_&d=DwIFaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=4xEe7s13qw8OtBMzGMqJ0vk6PIoU68FR0RJ88otY0yg&s=47DUypCrCnkcv9C1Mlybb0QHi3RLMZh57Q35XoIXkBU&e=
>> and the package
>>
>> build report shows no problems for both build and check in all
>> systems. However, the test coverage tab at top of the package page
>>
>> still displays "unknown" and im not sure if there is any problem with
>> the tests or how to find possible errors.
>>
>>
>> Here is what the build report shows in all OS:
>>
>> * checking examples ... OK
>> * checking for unstated dependencies in �tests� ... OK
>> * checking tests ...
>>   Running �runTests.R�
>>  OK
>> * checking for unstated dependencies in vignettes ... OK
>> * checking package vignettes in �inst/doc� ... OK
>>
>> Thanks!
>>
>>
>> Best regards,
>>
>>
>> Juan Pablo Romero
>>
>>
>>
>>     [[alternative HTML version deleted]]
>>
>>
>>
>> _______________________________________________
>> Bioc-devel at r-project.org mailing list
>> https://urldefense.proofpoint.com/v2/url?u=https-3A__stat.ethz.ch_mailman_listinfo_bioc-2Ddevel&d=DwICAg&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=4xEe7s13qw8OtBMzGMqJ0vk6PIoU68FR0RJ88otY0yg&s=cT2EjT9BIxY3Q8Nmikk0rGfWteNuwuaDEpwNFwpjL2g&e=
>>
>>
>

--
Hervé Pagès

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