[Bioc-devel] Error during CHECK on Windows (tokay1)

Hervé Pagès hpages at fredhutch.org
Thu Mar 22 17:08:24 CET 2018

Hi Matthias,

Not sure what's causing this but I just wanted to mention a couple
of things:

Even though you didn't modify your package, it can start failing
for many reasons. The most common reason is that R or another package
that your package depends on was modified. It turns out that a few
days ago we updated R from 3.4.3 to 3.4.4 on the release build
machines. Not sure that's related to the error you're seeing on
tokay1 but this cannot completely be discarded.

Unlike Unix-like system, Windows doesn't let a process open a file
if the file is currently in use (by the same or another process).
The "cannot open file 'foo': Permission denied" error is typically
the result of such situation. This type of error can be hard to
reproduce because it won't necessarily happen each time one runs
'R CMD check' on Windows. It only happens if one process is still
holding on file 'foo' when another process tries to access 'foo'.
But sometimes the process holding on 'foo' finishes a little bit
earlier (and releases the file) or the process trying to access
'foo' does it a little bit later, and everything is fine.
Because of this, troubleshooting this kind of error (called a
race condition) can be tricky.

The first thing you could do is disable parallel execution in
your examples and see if that eliminates the issue. If you still
see the error, then you can remove doParallel/foreach from the
equation. If you don't see the error anymore (but you'll have
to wait several build iterations to be sure because you could
just be lucky that the race condition doesn't happen for a few
days in a row), then you can fairly suspect that the problem
has something to do with doParallel/foreach and contact the
doParallel/foreach folks.

Hope this helps,

On 03/22/2018 07:31 AM, Matthias Döring wrote:
> Although I didn't make any changes to my package openPrimeR, it is
> currently not passing the checks on tokay1 due to the following error
> while running the examples:
> * checking examples ...
> ** running examples for arch 'i386' ...Warning in file(con, "r") :
>     cannot open file '../openPrimeR-Ex_i386.Rout': Permission denied
> Error in file(con, "r") : cannot open the connection
> Execution halted
> https://urldefense.proofpoint.com/v2/url?u=http-3A__bioconductor.org_checkResults_release_bioc-2DLATEST_openPrimeR_tokay1-2Dchecksrc.html&d=DwIDaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=HjFin7ZZwuYWdlO8wvE3KmoPwjRiq-bV_UKHWdKLLP4&m=SZhlV-e7h7S6Ndf9G2qUGp37kMZHgjDPmkvI7cCtGDA&s=eK8w8Wfg-rPx9HSrExZjtAqbHQSDmYOxNJvdltvzCTM&e=
> I've just searched for this type of error and found that it can be
> caused by the parallel backend if it isn't explicitly closed. However,
> I'm not creating clusters manually but rather using the foreach package
> for this purpose, so this shouldn't be the root of the problem.
> Interestingly, there are no problems for the development version on
> tokay2
> (https://urldefense.proofpoint.com/v2/url?u=http-3A__bioconductor.org_checkResults_devel_bioc-2DLATEST_openPrimeR_tokay2-2Dchecksrc.html&d=DwIDaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=HjFin7ZZwuYWdlO8wvE3KmoPwjRiq-bV_UKHWdKLLP4&m=SZhlV-e7h7S6Ndf9G2qUGp37kMZHgjDPmkvI7cCtGDA&s=zAWDhUHJG5jAGFu2WUc1K_uSBXN1daXMN5VVObIUjEk&e=).
> Should I just ignore this problem? Any pointers?
> Best
>    Matthias

Hervé Pagès

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