[Bioc-devel] Identify Bioc build machines

Gabe Becker becker.gabe at gene.com
Tue Mar 8 20:46:07 CET 2016

On Fri, Mar 4, 2016 at 7:33 AM, Dan Tenenbaum <dtenenba at fredhutch.org>

> 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>
> > To: "bioc-devel" <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
> >
> > 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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