[Bioc-devel] Unit Tests & Test Coverage

[Hervé Pagès]

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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