From kevin.r.coombes at gmail.com  Mon Sep 10 20:15:16 2012
From: kevin.r.coombes at gmail.com (Kevin R. Coombes)
Date: Mon, 10 Sep 2012 13:15:16 -0500
Subject: [Rd] problem building vignette
Message-ID: <504E2E34.3080605@gmail.com>

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



[Rd] problem building vignette
Kevin R. Coombes