problem building vignette

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