From murdoch.duncan at gmail.com  Mon Sep 10 20:24:56 2012
From: murdoch.duncan at gmail.com (Duncan Murdoch)
Date: Mon, 10 Sep 2012 14:24:56 -0400
Subject: [Rd] problem building vignette
In-Reply-To: <504E2E34.3080605@gmail.com>
References: <504E2E34.3080605@gmail.com>
Message-ID: <504E3078.6040102@gmail.com>

On 10/09/2012 2:15 PM, Kevin R. Coombes wrote:
> Hi,
>
> I'm trying to get a package to pass through "R CMD check --as-cran" and
> have run into a problem that gives me no idea where to look to fix it.
> I'm running R version 15.1 on a Windows 7 64-bit machine, with the
> current set of Rtools.  An attempt to check the package dies at the
> following step:
>
> * checking running R code from vignettes ...
>      'SIBER.Rnw' ...Warning in file(con, "r") :
>     cannot open file 'SIBER.Rnw.log': Permission denied
> Error in file(con, "r") : cannot open the connection
> Execution halted
>
> The file "SIBER.Rnw.log" was successfully created.  All of the R code
> from the Sweave file was excuted; the last exceutable line was a call to
> sessionInfo().  The last lines of the log file are:
>
>   > sessionInfo()
> R version 2.15.1 (2012-06-22)
> Platform: x86_64-pc-mingw32/x64 (64-bit)
>
> locale:
> [1] LC_COLLATE=C
> [2] LC_CTYPE=English_United States.1252
> [3] LC_MONETARY=English_United States.1252
> [4] LC_NUMERIC=C
> [5] LC_TIME=English_United States.1252
>
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods   base
>
> other attached packages:
> [1] doSNOW_1.0.6    snow_0.3-9      iterators_1.0.6 foreach_1.4.0
> [5] edgeR_2.6.12    limma_3.10.2    SIBER_0.9.2     mclust_3.4.11
>
> loaded via a namespace (and not attached):
> [1] codetools_0.2-8 compiler_2.15.1 tools_2.15.1
>
>    *** Run successfully completed ***
>   > proc.time()
>      user  system elapsed
>      1.12    0.14    2.57
>
> We have about a dozen other packages that we maintain, and all of the
> others check, build, and install with no problems.
>
> Does anyone have any idea why this file permission issue would crop up
> here? Or what I can do to fix it?

Windows machines sometimes have permission problems when a virus checker 
opens a file in an exclusive mode for checking.  If this applies to you, 
you may be able to configure the checks to ignore the directory you're 
working in, or temporarily disable it completely.  Or you could switch 
virus checkers to one that is less hostile to your work.

Duncan Murdoch



[Rd] problem building vignette
Duncan Murdoch