From murdoch.duncan at gmail.com  Thu Sep 22 14:20:14 2011
From: murdoch.duncan at gmail.com (Duncan Murdoch)
Date: Thu, 22 Sep 2011 08:20:14 -0400
Subject: [Rd] R CMD check file issues
In-Reply-To: <4e7b2236.9a58df0a.3724.7ee5SMTPIN_ADDED@mx.google.com>
References: <4e7b2236.9a58df0a.3724.7ee5SMTPIN_ADDED@mx.google.com>
Message-ID: <4E7B27FE.6050804@gmail.com>

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]]
>
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[Rd] R CMD check file issues
Duncan Murdoch