I do see this on Win7, and it is an antivirus issue (Sophos).
Excluding the R check area solves it for me, as does an earlier
delete.
I have considered adding a delay in check.R, but it is not clear how
long it would need to be.
On Thu, 22 Sep 2011, Henrik Bengtsson wrote:
I'm on Windows 7 (64-bit) and everything works perfectly. Obviously,
there is either another process locking down a file with the same name
or the directory doesn't exist at the time of the file() call.
Now to the most important question ...what's your sessionInfo()?
/Henrik
On Thu, Sep 22, 2011 at 5:33 AM, Duncan Murdoch
<murdoch.dun...@gmail.com> wrote:
On 11-09-22 8:30 AM, Nick Sabbe wrote:
Hi Duncan (and others).
I've just turned off my virus scanner (MS Forefront Endpoint Protection).
The issue persists. It appears that the first time I call R CMD check, it
deletes the previous rcheck folder, but tries to proceed before it is
actually gone. By the time I reissue the command, the folder is truly
gone,
and the R CMD check can safely do its work.
Is anyone else here using Win7 (32bit) and successfully building/checking
R
packages? Perhaps I'm the only one who has treaded this path :-)
I do use Win7 on one machine, and have seen odd things happen, but not what
you describe.
I imagine a simple workaround for you would be to delete the folder before
you call R CMD check (i.e. wrap R CMD check in a batch file to do that), but
it would be nice if that were not necessary.
Duncan Murdoch
Nick Sabbe
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link: http://biomath.ugent.be
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-- Do Not Disapprove
-----Original Message-----
From: Duncan Murdoch [mailto:murdoch.dun...@gmail.com]
Sent: donderdag 22 september 2011 14:20
To: Nick Sabbe
Cc: r-devel@r-project.org
Subject: Re: [Rd] R CMD check file issues
On 11-09-22 7:53 AM, Nick Sabbe wrote:
This problem is likely to be specific to Windows, and particularly
Win7.
The symptoms sound like interference from an anti-virus checker.
Duncan Murdoch
After a successful build of a package (R CMD build addendum), I
immediately
run an R CMD check for the same package.
Not always, but _very_ often, I get the following error:
C:\Users\nisabbe\Documents\@Doctoraat\R>R CMD check addendum
Loading required package: tcltk
Loading Tcl/Tk interface ... done
Loading required package: Hmisc
Loading required package: survival
Loading required package: stats
Loading required package: graphics
Loading required package: splines
Attaching package: 'Hmisc'
The following object(s) are masked from 'package:survival':
untangle.specials
The following object(s) are masked from 'package:base':
format.pval, round.POSIXt, trunc.POSIXt, units
Loading required package: R2HTML
Warning in file(filename, "wt") :
cannot open file
'C:/Users/nisabbe/Documents/@Doctoraat/R/addendum.Rcheck/00ch
eck.log': Permission denied
Error in file(filename, "wt") : cannot open the connection
Execution halted
If, after this, I immediately reissue the R CMD check command, it
works,
without the error.
I think this has something to do with how Win7 processes file
handling
(there are known issues even noticeable in windows explorer), but
perhaps
there is a way of circumventing this? It would be greatly
appreciated, as
this issue is preventing automation of build/check/install scripts.
Suggestions will be greatly appreciated.
Nick Sabbe
--
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link:<http://biomath.ugent.be/> http://biomath.ugent.be
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