In my particular case, the antivirus appears irrelevant (turning it off does not change anything ; admittedly, turning 'off' an antivirus program through its user interface may still involve some background meddling - stubborn creatures they are, these AVs)
Either way: since this is the only place I know of where R has problems with the slow filehandling in Win7, a solution may be to check repeatedly (with some delay and a timeout) after the delete calls whether the files are actually gone. Ugly, I admit, but since our Redmond friends don't provide it... Nick Sabbe -- ping: nick.sa...@ugent.be link: http://biomath.ugent.be wink: A1.056, Coupure Links 653, 9000 Gent ring: 09/264.59.36 -- Do Not Disapprove > -----Original Message----- > From: r-devel-boun...@r-project.org [mailto:r-devel-bounces@r- > project.org] On Behalf Of Prof Brian Ripley > Sent: donderdag 22 september 2011 22:04 > To: Henrik Bengtsson > Cc: r-devel@r-project.org > Subject: Re: [Rd] R CMD check file issues > > 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 > >>> -- > >>> ping: nick.sa...@ugent.be > >>> link: http://biomath.ugent.be > >>> wink: A1.056, Coupure Links 653, 9000 Gent > >>> 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 > >>>>> > >>>>> -- > >>>>> > >>>>> ping: nick.sa...@ugent.be > >>>>> > >>>>> link:<http://biomath.ugent.be/> http://biomath.ugent.be > >>>>> > >>>>> wink: A1.056, Coupure Links 653, 9000 Gent > >>>>> > >>>>> ring: 09/264.59.36 > >>>>> > >>>>> > >>>>> > >>>>> -- Do Not Disapprove > >>>>> > >>>>> > >>>>> > >>>>> > >>>>> [[alternative HTML version deleted]] > >>>>> > >>>>> ______________________________________________ > >>>>> R-devel@r-project.org mailing list > >>>>> https://stat.ethz.ch/mailman/listinfo/r-devel > >>> > >>> > >> > >> ______________________________________________ > >> R-devel@r-project.org mailing list > >> https://stat.ethz.ch/mailman/listinfo/r-devel > >> > > > > ______________________________________________ > > R-devel@r-project.org mailing list > > https://stat.ethz.ch/mailman/listinfo/r-devel > > > > -- > 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) > 1 South Parks Road, +44 1865 272866 (PA) > Oxford OX1 3TG, UK Fax: +44 1865 272595 ______________________________________________ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
