From nick.sabbe at ugent.be  Sun Sep 25 10:04:55 2011
From: nick.sabbe at ugent.be (Nick Sabbe)
Date: Sun, 25 Sep 2011 10:04:55 +0200
Subject: [Rd] R CMD check file issues
In-Reply-To: <alpine.LFD.2.02.1109222102180.13324@gannet.stats.ox.ac.uk>
References: <4e7b2236.9a58df0a.3724.7ee5SMTPIN_ADDED@mx.google.com>	<4E7B27FE.6050804@gmail.com>	<4e7b2a5a.d1c9e30a.0f61.ffffa3c8SMTPIN_ADDED@mx.google.com>	<4E7B2AFF.8010904@gmail.com>	<CAFDcVCSaGSAL4jxvMWk2ftLAV-B3_Z2c9YhmrKvVB=TDzVeqQw@mail.gmail.com>
	<alpine.LFD.2.02.1109222102180.13324@gannet.stats.ox.ac.uk>
Message-ID: <036b01cc7b59$d0228210$70678630$@sabbe@ugent.be>

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.sabbe at 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-bounces at r-project.org [mailto:r-devel-bounces at r-
> project.org] On Behalf Of Prof Brian Ripley
> Sent: donderdag 22 september 2011 22:04
> To: Henrik Bengtsson
> Cc: r-devel at 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.duncan at 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.sabbe at 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.duncan at gmail.com]
> >>>> Sent: donderdag 22 september 2011 14:20
> >>>> To: Nick Sabbe
> >>>> Cc: r-devel at 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.sabbe at 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 at r-project.org mailing list
> >>>>> https://stat.ethz.ch/mailman/listinfo/r-devel
> >>>
> >>>
> >>
> >> ______________________________________________
> >> R-devel at r-project.org mailing list
> >> https://stat.ethz.ch/mailman/listinfo/r-devel
> >>
> >
> > ______________________________________________
> > R-devel at r-project.org mailing list
> > https://stat.ethz.ch/mailman/listinfo/r-devel
> >
> 
> --
> Brian D. Ripley,                  ripley at 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



[Rd] R CMD check file issues
Nick Sabbe