From kevin.r.coombes at gmail.com  Mon Sep 10 20:29:19 2012
From: kevin.r.coombes at gmail.com (Kevin R. Coombes)
Date: Mon, 10 Sep 2012 13:29:19 -0500
Subject: [Rd] problem building vignette
In-Reply-To: <504E3078.6040102@gmail.com>
References: <504E2E34.3080605@gmail.com> <504E3078.6040102@gmail.com>
Message-ID: <504E317F.1040308@gmail.com>

Why would the virus checker cause a problem with this package, and not 
any of the dozen other packaqes?

On 9/10/2012 1:24 PM, Duncan Murdoch wrote:
> 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
Kevin R. Coombes