[Bioc-devel] palomino4 CHECK error "permission denied" msqrob2

Hervé Pagès hp@ge@@on@g|thub @end|ng |rom gm@||@com
Fri Oct 28 19:00:16 CEST 2022

Hi Stijn,

Note that today the error is gone.

This is a race condition in 'R CMD check' that affects some packages on 
Windows. What 'R CMD check' is trying to do here is open the 
msqrob2-Ex.Rout file but that file is still being written to by another 
process. Windows (unlike Linux or macOS) doesn't like that: it won't let 
a process open a file if the file is being hold by another process.

More precisely here is what is happening here:

- One of the checks that 'R CMD check' performs is to run all the 
examples in a package, and to capture the output produced by the 
examples in a file (the msqrob2-Ex.Rout in your case).

- Once it's done running the examples, 'R CMD check' wants to know if 
the examples produced errors. It does this by parsing the 
msqrob2-Ex.Rout file. That's when it tries to open the file in read-only 

- But sometimes, when 'R CMD check' tries to open msqrob2-Ex.Rout in 
read-only mode, other processes are still holding on the msqrob2-Ex.Rout 
file. This typically happens when the examples in the package spawn 
subprocesses. For example these spawned processes can be the workers 
spawned by BiocParallel or by other parallel evaluation mechanism (e.g. 
doParallel/foreach). Note that there can be a very small lag between the 
moment the main worker and the spawned workers are done. If one of the 
spawned workers takes a fraction of an extra second to finish writing 
some output to msqrob2-Ex.Rout, then 'R CMD check' won't be able to open 
the file.

One could argue that this is an issue with 'R CMD check'. Maybe on 
Windows it should wait a couple of seconds before trying to open 
msqrob2-Ex.Rout, I don't know.

Maybe there's something that could be done in BiocParallel too. I don't 
know how hard that would be, or if that's even feasible, but maybe 
there's a way that the main worker could wait and make sure that all the 
spawn processes are dead before returning. I guess that kind of feature 
would only make sense for some parallel back-ends.

Does some of the examples in msqrob2 use parallelization? If so maybe 
you can try to add a call to Sys.sleep(2) at the end of those examples 
and see if that helps.

In any case there's nothing that can really be done on our Windows 
builders to prevent this, sorry.

Hope this helps,


On 28/10/2022 06:29, vandenbulcke stijn wrote:
> Dear All,
> On the palomino4 host the check for msqrob2 returns the following error (
> http://bioconductor.org/checkResults/devel/bioc-LATEST/msqrob2/palomino4-checksrc.html
> )
> * checking examples ...Warning in file(con, "r") :
>    cannot open file 'msqrob2-Ex.Rout': Permission denied
> Error in file(con, "r") : cannot open the connection
> Execution halted
> I am however not able to reproduce this, and it works on the other hosts.
> Would anyone know the cause of this issue?
> Thanks in advance
> Stijn
> 	[[alternative HTML version deleted]]
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Hervé Pagès

Bioconductor Core Team
hpages.on.github using gmail.com

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