[Bioc-devel] Identify Bioc build machines

[Thomas Lin Pedersen]

Gabes objections came to late for me filing a PR to testthat (and I don’t fully agree as well :-). skip_on_bioc() is now part of the development version of testthat available on Github for anyone interested…

best

Thomas

> On 08 Mar 2016, at 20:46, Gabe Becker <becker.gabe at gene.com> wrote:
> 
> 
> 
> On Fri, Mar 4, 2016 at 7:33 AM, Dan Tenenbaum <dtenenba at fredhutch.org <mailto:dtenenba at fredhutch.org>> wrote:
> There are a number of variables defined. You could check to see if the variable BBS_HOME is defined (it does not matter what the value is in your case, just whether it is defined or not).
> 
> Dan
> 
> 
> ----- Original Message -----
> > From: "Thomas Dybdal Pedersen" <thomasp85 at gmail.com <mailto:thomasp85 at gmail.com>>
> > To: "bioc-devel" <bioc-devel at r-project.org <mailto:bioc-devel at r-project.org>>
> > Sent: Friday, March 4, 2016 1:17:38 AM
> > Subject: [Bioc-devel] Identify Bioc build machines
> 
> > Hi
> >
> > Are there any environment variables set on the bloc build machines that unique
> > identify them as such? The reason I ask is that I’m planning to create a
> > testthat PR that adds a skip_on_bioc (similar to skip_on_cran) function. While
> > I know you generally shouldn’t skip unit tests on build machines, some tests
> > can be prohibitively heavy and cause the check to timeout - In these cases it
> > would be better to have the unit tests and run them locally but have them
> > automatically skipped on bio builds…
> 
> I would argue that tests like that, while valuable, belong in a different place, as they are unlikel to be run every time, even locally. IIRC testthat can take a directory in which to look for your tests, so putting them in inst/extra_tests (for example) and running that as needed locally would work. Basically, I'm saying that heavy unit-tests are (can) be good, but it's not clear they should be check tests.
> 
> Alternatively, you could simply modify your pkg/tests/test.R script (or whathaveyou) so that it checks for an enviroment variable to turn on/off certain tests. Build platforms won't have your package's special env variables set, so they won't be run in this case. This, if documented, would make it easy for users or build systems to run those tests if they want (our internal build system would not want to be skipping tests in a situation like this, for example, as correctness is more valuable than time to us).
> 
> Best,
> ~G
> 
>  
> >
> > best
> >
> > Thomas
> >
> > _______________________________________________
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> 
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> 
> 
> -- 
> Gabriel Becker, Ph.D
> Associate Scientist 
> Bioinformatics and Computational Biology
> Genentech Research


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