[Rd] R CMD check file issues

Duncan Murdoch
Thu, 22 Sep 2011 12:33:03 -0000

On 11-09-22 8:30 AM, Nick Sabbe wrote:
> Hi Duncan (and others).
>
> I've just turned off my virus scanner (MS Forefront Endpoint
Protection).
>
> The issue persists. It appears that the first time I call R CMD check, it
> deletes the previous rcheck folder, but tries to proceed before it is
> actually gone. By the time I reissue the command, the folder is truly gone,
> and the R CMD check can safely do its work.
>
> Is anyone else here using Win7 (32bit) and successfully building/checking R
> packages? Perhaps I'm the only one who has treaded this path :-)

I do use Win7 on one machine, and have seen odd things happen, but not
what you describe.

I imagine a simple workaround for you would be to delete the folder
before you call R CMD check (i.e. wrap R CMD check in a batch file to do
that), but it would be nice if that were not necessary.

Duncan Murdoch

>
>
> Nick Sabbe
> --
> ping: nick.sabbe at ugent.be
> link: http://biomath.ugent.be
> wink: A1.056, Coupure Links 653, 9000 Gent
> ring: 09/264.59.36
>
> -- Do Not Disapprove
>
>
>
>
>> -----Original Message-----
>> From: Duncan Murdoch [mailto:murdoch.duncan at gmail.com]
>> Sent: donderdag 22 september 2011 14:20
>> To: Nick Sabbe
>> Cc: r-devel at r-project.org
>> Subject: Re: [Rd] R CMD check file issues
>>
>> On 11-09-22 7:53 AM, Nick Sabbe wrote:
>>> This problem is likely to be specific to Windows, and particularly
>> Win7.
>>
>> The symptoms sound like interference from an anti-virus checker.
>>
>> Duncan Murdoch
>>
>>>
>>>
>>> After a successful build of a package (R CMD build addendum), I
>> immediately
>>> run an R CMD check for the same package.
>>>
>>> Not always, but _very_ often, I get the following error:
>>>
>>> C:\Users\nisabbe\Documents\@Doctoraat\R>R CMD check addendum
>>>
>>> Loading required package: tcltk
>>>
>>> Loading Tcl/Tk interface ... done
>>>
>>> Loading required package: Hmisc
>>>
>>> Loading required package: survival
>>>
>>> Loading required package: stats
>>>
>>> Loading required package: graphics
>>>
>>> Loading required package: splines
>>>
>>>
>>>
>>> Attaching package: 'Hmisc'
>>>
>>>
>>>
>>> The following object(s) are masked from 'package:survival':
>>>
>>>
>>>
>>>       untangle.specials
>>>
>>>
>>>
>>> The following object(s) are masked from 'package:base':
>>>
>>>
>>>
>>>       format.pval, round.POSIXt, trunc.POSIXt, units
>>>
>>>
>>>
>>> Loading required package: R2HTML
>>>
>>> Warning in file(filename, "wt") :
>>>
>>>     cannot open file
>>> 'C:/Users/nisabbe/Documents/@Doctoraat/R/addendum.Rcheck/00ch
>>>
>>> eck.log': Permission denied
>>>
>>> Error in file(filename, "wt") : cannot open the
connection
>>>
>>> Execution halted
>>>
>>>
>>>
>>> If, after this, I immediately reissue the R CMD check command, it
>> works,
>>> without the error.
>>>
>>> I think this has something to do with how Win7 processes file
>> handling
>>> (there are known issues even noticeable in windows explorer), but
>> perhaps
>>> there is a way of circumventing this? It would be greatly
>> appreciated, as
>>> this issue is preventing automation of build/check/install scripts.
>>>
>>>
>>>
>>> Suggestions will be greatly appreciated.
>>>
>>>
>>>
>>> Nick Sabbe
>>>
>>> --
>>>
>>> ping: nick.sabbe at ugent.be
>>>
>>> link:<http://biomath.ugent.be/>   http://biomath.ugent.be
>>>
>>> wink: A1.056, Coupure Links 653, 9000 Gent
>>>
>>> ring: 09/264.59.36
>>>
>>>
>>>
>>> -- Do Not Disapprove
>>>
>>>
>>>
>>>
>>> 	[[alternative HTML version deleted]]
>>>
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>
>