R CMD check file issues

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]]

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]]

-----Original Message-----
From: henrik.bengtsson at gmail.com [mailto:henrik.bengtsson at gmail.com] On
Behalf Of Henrik Bengtsson
Sent: donderdag 22 september 2011 17:59
To: Duncan Murdoch
Cc: Nick Sabbe; r-devel at 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.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]]

-----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]]

--
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