Re: [Rd] R CMD check file issues

From: Prof Brian Ripley <ripley_at_stats.ox.ac.uk>
Date: Thu, 22 Sep 2011 21:04:04 +0100 (BST)

I do see this on Win7, and it is an antivirus issue (Sophos). Excluding the R check area solves it for me, as does an earlier delete.

I have considered adding a delay in check.R, but it is not clear how long it would need to be.

On Thu, 22 Sep 2011, Henrik Bengtsson wrote:

> I'm on Windows 7 (64-bit) and everything works perfectly. Obviously,
> there is either another process locking down a file with the same name
> or the directory doesn't exist at the time of the file() call.
>
> Now to the most important question ...what's your sessionInfo()?
>
> /Henrik
>
> On Thu, Sep 22, 2011 at 5:33 AM, Duncan Murdoch
> <murdoch.duncan_at_gmail.com> wrote:
>> 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]]
>>>>>
>>>>> ______________________________________________
>>>>> R-devel_at_r-project.org mailing list
>>>>> https://stat.ethz.ch/mailman/listinfo/r-devel
>>>
>>>
>>
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>
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-- 
Brian D. Ripley,                  ripley_at_stats.ox.ac.uk
Professor of Applied Statistics,  http://www.stats.ox.ac.uk/~ripley/
University of Oxford,             Tel:  +44 1865 272861 (self)
1 South Parks Road,                     +44 1865 272866 (PA)
Oxford OX1 3TG, UK                Fax:  +44 1865 272595


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