From hb at biostat.ucsf.edu  Thu Sep 22 17:59:14 2011
From: hb at biostat.ucsf.edu (Henrik Bengtsson)
Date: Thu, 22 Sep 2011 08:59:14 -0700
Subject: [Rd] R CMD check file issues
In-Reply-To: <4E7B2AFF.8010904@gmail.com>
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>
Message-ID: <CAFDcVCSaGSAL4jxvMWk2ftLAV-B3_Z2c9YhmrKvVB=TDzVeqQw@mail.gmail.com>

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
>



[Rd] R CMD check file issues
Henrik Bengtsson