On Sun, 25 Sep 2011, Henrik Bengtsson wrote:
On Sun, Sep 25, 2011 at 12:58 AM, Nick Sabbe <nick.sa...@ugent.be> wrote:
Here you go (though I doubt it will be actually helpful):
R version 2.13.1 (2011-07-08)
Platform: i386-pc-mingw32/i386 (32-bit)
It is useful, especially to know which version of R you are running
(at times when error report are posted it is only late in the
discussion it is found out it is for an old version of R).
FYI, checking the SVN log it seems that Brian Ripley has added some
protection/workarounds for your race condition in R rev 57047. So try
with a new R 2.13.2RC or R devel.
Actually, for the one I see, and only in R-devel.
/Henrik
locale:
[1] LC_COLLATE=Dutch_Belgium.1252 LC_CTYPE=Dutch_Belgium.1252
LC_MONETARY=Dutch_Belgium.1252 LC_NUMERIC=C
[5] LC_TIME=Dutch_Belgium.1252
attached base packages:
[1] grDevices datasets splines graphics stats tcltk utils
methods base
other attached packages:
[1] addendum_1.4 snowfall_1.84 snow_0.3-7 mgcv_1.7-6
rgl_0.92.798 glmnet_1.7
[7] Matrix_0.9996875-3 lattice_0.19-33 svSocket_0.9-51 TinnR_1.0.3
R2HTML_2.2 Hmisc_3.8-3
[13] survival_2.36-9
loaded via a namespace (and not attached):
[1] cluster_1.14.0 grid_2.13.1 nlme_3.1-102 svMisc_0.9-63 tools_2.13.1
Note that this is the sessionInfo from an interactive session. I don't know
of an obvious way to provide you the sessionInfo of the session that is
started by R CMD check (Assuming that at that point, an 'actual' R session
has actually been started - it appears the error occurs before any 'real
work' is started).
Nick Sabbe
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-- Do Not Disapprove
-----Original Message-----
From: henrik.bengts...@gmail.com [mailto:henrik.bengts...@gmail.com] On
Behalf Of Henrik Bengtsson
Sent: donderdag 22 september 2011 17:59
To: Duncan Murdoch
Cc: Nick Sabbe; r-devel@r-project.org
Subject: Re: [Rd] R CMD check file issues
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
--
ping: nick.sa...@ugent.be
link: http://biomath.ugent.be
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ring: 09/264.59.36
-- 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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Brian D. Ripley, rip...@stats.ox.ac.uk
Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/
University of Oxford, Tel: +44 1865 272861 (self)
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