[Bioc-devel] Unit Tests & Test Coverage

Hervé Pagès hpages at fredhutch.org
Thu Mar 23 21:32:04 CET 2017

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:


but the package is still at commit 127616 on Bioconductor-mirror:


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://github.com/Bioconductor-mirror/) 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.


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:


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.


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
1100 Fairview Ave. N, M1-B514
P.O. Box 19024
Seattle, WA 98109-1024

E-mail: hpages at fredhutch.org
Phone:  (206) 667-5791
Fax:    (206) 667-1319

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