R devel - Sep 2012 - problem building vignette

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?

Thanks,
     Kevin

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