From hb at biostat.ucsf.edu  Sun Sep 25 14:57:51 2011
From: hb at biostat.ucsf.edu (Henrik Bengtsson)
Date: Sun, 25 Sep 2011 05:57:51 -0700
Subject: [Rd] R CMD check file issues
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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.

/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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> https://stat.ethz.ch/mailman/listinfo/r-devel
>



[Rd] R CMD check file issues
Henrik Bengtsson