[Rd] R CMD check file issues

Prof Brian Ripley ripley at stats.ox.ac.uk
Sun Sep 25 17:43:43 CEST 2011 

On Sun, 25 Sep 2011, Henrik Bengtsson wrote:

> On Sun, Sep 25, 2011 at 12:58 AM, Nick Sabbe <nick.sabbe at ugent.be> wrote:
>> Here you go (though I doubt it will be actually helpful):
>>
>> R version 2.13.1 (2011-07-08)
>> Platform: i386-pc-mingw32/i386 (32-bit)
>
> It is useful, especially to know which version of R you are running
> (at times when error report are posted it is only late in the
> discussion it is found out it is for an old version of R).
>
> FYI, checking the SVN log it seems that Brian Ripley has added some
> protection/workarounds for your race condition in R rev 57047.  So try
> with a new R 2.13.2RC or R devel.

Actually, for the one I see, and only in R-devel.

>
> /Henrik
>
>>
>> locale:
>> [1] LC_COLLATE=Dutch_Belgium.1252  LC_CTYPE=Dutch_Belgium.1252
>> LC_MONETARY=Dutch_Belgium.1252 LC_NUMERIC=C
>> [5] LC_TIME=Dutch_Belgium.1252
>>
>> attached base packages:
>> [1] grDevices datasets  splines   graphics  stats     tcltk     utils
>> methods   base
>>
>> other attached packages:
>>  [1] addendum_1.4       snowfall_1.84      snow_0.3-7         mgcv_1.7-6
>> rgl_0.92.798       glmnet_1.7
>>  [7] Matrix_0.9996875-3 lattice_0.19-33    svSocket_0.9-51    TinnR_1.0.3
>> R2HTML_2.2         Hmisc_3.8-3
>> [13] survival_2.36-9
>>
>> loaded via a namespace (and not attached):
>> [1] cluster_1.14.0 grid_2.13.1    nlme_3.1-102   svMisc_0.9-63  tools_2.13.1
>>
>> Note that this is the sessionInfo from an interactive session. I don't know
>> of an obvious way to provide you the sessionInfo of the session that is
>> started by R CMD check (Assuming that at that point, an 'actual' R session
>> has actually been started - it appears the error occurs before any 'real
>> work' is started).
>>
>>
>> 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: henrik.bengtsson at gmail.com [mailto:henrik.bengtsson at gmail.com] On
>>> Behalf Of Henrik Bengtsson
>>> Sent: donderdag 22 september 2011 17:59
>>> To: Duncan Murdoch
>>> Cc: Nick Sabbe; r-devel at r-project.org
>>> Subject: Re: [Rd] R CMD check file issues
>>>
>>> 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
>>>>>
>>>>>
>>>>
>>>> ______________________________________________
>>>> 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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