Re: [Rd] R CMD check file issues

From: Nick Sabbe <nick.sabbe_at_ugent.be>
Date: Sun, 25 Sep 2011 09:58:52 +0200

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)

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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Received on Sun 25 Sep 2011 - 08:01:14 GMT

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