Re: [Rd] R CMD check file issues

From: Nick Sabbe <nick.sabbe_at_ugent.be>
Date: Thu, 22 Sep 2011 14:30:17 +0200

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 :-)

Nick Sabbe

--
ping: nick.sabbe_at_ugent.be
link: http://biomath.ugent.be
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ring: 09/264.59.36

-- Do Not Disapprove





> -----Original Message-----
> From: Duncan Murdoch [mailto:murdoch.duncan@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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Received on Thu 22 Sep 2011 - 12:33:00 GMT

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