Re: [Rd] R-2.13.2 beta build for Windows

2011-09-22 Thread Duncan Murdoch 

On 11-09-22 8:00 PM, Dario Strbenac wrote:

Hello,

I've had a look at a number of CRAN servers and all of them give a similar 
error, like :

Not Found
The requested URL /bin/windows/base/R-2.13.2beta-win.exe was not found on this 
server.

Additionally, a 404 Not Found error was encountered while trying to use an 
ErrorDocument to handle the request.


Thank you.  We changed the scripts over the summer, and the new one 
still had an error in it.  Things should be fixed soon.


Duncan Murdoch

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[Rd] R-2.13.2 beta build for Windows

2011-09-22 Thread Dario Strbenac 
Hello,

I've had a look at a number of CRAN servers and all of them give a similar 
error, like :

Not Found
The requested URL /bin/windows/base/R-2.13.2beta-win.exe was not found on this 
server.

Additionally, a 404 Not Found error was encountered while trying to use an 
ErrorDocument to handle the request.

--
Dario Strbenac
Research Assistant
Cancer Epigenetics
Garvan Institute of Medical Research
Darlinghurst NSW 2010
Australia

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Re: [Rd] R CMD check file issues

2011-09-22 Thread Prof Brian Ripley 
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
 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

wink: A1.056, Coupure Links 653, 9000 Gent

ring: 09/264.59.36



-- Do Not Disapprove




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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)
1 South Parks Road, +44 1865 272866 (PA)
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[Rd] How to call an MPI-enabled program from R?

2011-09-22 Thread Alireza Mahani 
Conceptually, how is it possible to call an MPI-parallelized code in C from
R? My experience with MPI so far indicates that one has to launch an
MPI-enabled binary using a command like

mpiexec -n  

In other words, I'm not sure how to create an MPI 'library' and then call it
from a single-threaded application. In this sense, my question is perhaps
not strictly a R question but an MPI question. (Using a system call forces
one to use disk as intermediary between R and the MPI binary to pass data
between the two.)

I am also aware of packages such as Rmpi, but at this stage I want to be
able to understand the low-level capabilities rather than relying on an
abstraction layer.

Thank you,
Alireza


--
View this message in context: 
http://r.789695.n4.nabble.com/How-to-call-an-MPI-enabled-program-from-R-tp3834332p3834332.html
Sent from the R devel mailing list archive at Nabble.com.

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Re: [Rd] R CMD check file issues

2011-09-22 Thread Henrik Bengtsson 
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
 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

 wink: A1.056, Coupure Links 653, 9000 Gent

 ring: 09/264.59.36



 -- Do Not Disapprove




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 R-devel@r-project.org mailing list
 https://stat.ethz.ch/mailman/listinfo/r-devel
>>
>>
>
> __
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>

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Re: [Rd] using R as SHELL in gnu make

2011-09-22 Thread Cook, Malcolm 
OK,

I now have a working version of setting SHELL=R in a GNU make script, allowing 
make’s recipes to be written in R, that works out most of the complications.

I plan to clean it up a little more and blog about it soon here: 
http://malcook-gedanken.blogspot.com/ - I’ll follow up here  when I do.

The approach optionally allows evaluating the recipes using a running Rserve 
(http://rosuda.org/Rserve/), avoiding initialization time and allowing 
pre-loading of R libraries common to multiple recipes.

The approach however does NOT provide any special mechanism to preserve state 
between recipes, 
Rather, recipes may create the make rule’s target as a state dump by setting 
with `file=’$@’`  in a call to `save` (or `save.image`, `dump`, as desired).  
Other make rules may then call `load('$<')` when the previously saved dump is a 
pre-requisite to the rule.

I’m still not sure if it is not more of an amusement and am interested in all 
thoughts on this, and welcome any suggestions for example applications that I 
might include when I go to blog it up...

Cheers,

~Malcolm


-Original Message-
From: Paul Gilbert [mailto:pgilb...@bank-banque-canada.ca] 
Sent: Tuesday, September 20, 2011 8:32 AM
To: Cook, Malcolm; 'help-m...@gnu.org'; 'r-devel@r-project.org'
Subject: RE: using R as SHELL in gnu make

Other than the RServe part, I do this all the time. It works well. Perhaps we 
can put together some notes off-line and then bring it back to the list.

Paul

> -Original Message-
> From: r-devel-boun...@r-project.org [mailto:r-devel-bounces@r-
> project.org] On Behalf Of Cook, Malcolm
> Sent: September 19, 2011 6:35 PM
> To: 'help-m...@gnu.org'; 'r-devel@r-project.org'
> Subject: [Rd] using R as SHELL in gnu make
> 
> I am intrigued by the possibility of using R as the SHELL in a (Gnu)
> makefile (instead of /bin/sh).  (c.f.
> http://www.gnu.org/software/make/manual/make.html#Choosing-the-Shell)
> 
> Well, rather, I would like the makefile's SHELL to be a command which
> communicated with an R process.
> 
> The makefile targets/prerequistes would, as always, be OS files, which
> would be written/read using standard R file IO.
> 
> The makefile's "recipe"s would be written in R (instead of the usual
> shell).
> 
> The R process would be able to be initiated by `load`ing one or more R
> datasets, libraries or entire images.
> 
> The R process would be able to accumulate state as the makefile
> progressed.  The recipe's would be able to refer to that state,
> allowing conditional execution.
> 
> The R process would optionally be saved as an image of on job
> termination/completion.
> 
> The R process might be managed using the RServe package, and would need
> to be initiated once only, when the makefile was first invoked.
> 
> I would appreciate learning if anyone had any success, informative
> failures, or other lore that may help in (or dissuade me from)
> embarking on attempt this.
> 
> Thanks,
> 
> Malcolm Cook
> Stowers Institute for Medical Research
> 
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Re: [Rd] R CMD check file issues

2011-09-22 Thread Duncan Murdoch 

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

wink: A1.056, Coupure Links 653, 9000 Gent

ring: 09/264.59.36



-- Do Not Disapprove




[[alternative HTML version deleted]]

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Re: [Rd] R CMD check file issues

2011-09-22 Thread Nick Sabbe 
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 :-)


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
> >
> > 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

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Re: [Rd] R CMD check file issues

2011-09-22 Thread Duncan Murdoch 

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

wink: A1.056, Coupure Links 653, 9000 Gent

ring: 09/264.59.36



-- Do Not Disapprove




[[alternative HTML version deleted]]

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Re: [Rd] R CMD check file issues

2011-09-22 Thread Uwe Ligges 



On 22.09.2011 14:16, Nick Sabbe wrote:

Hello Uwe, and thanks for your interest in the issue.

There is most certainly not another process that stops working between the
two R CMD check calls (recently, I've made a habit out of being ready to
pressin the seconds after running my first R CMD check,
to rerun it if it fails).

At worst, there may ever have been an explorer window open, but this is
definitely not always the case, and I'm sure this window was not closed
then, between the calls.

I'm really quite afraid it is more of a windows issue than an R issue, but I
was hoping you wizards might have a workaround (apart from the obvious
suggestion to install Linux), as it is immensely annoying...



I have not seen this problem so far (but then, I am mostly under Windows 
XP and winbuilder is Windows Server 2003).


Uwe




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: Uwe Ligges [mailto:lig...@statistik.tu-dortmund.de]
Sent: donderdag 22 september 2011 13:58
To: Nick Sabbe
Cc: r-devel@r-project.org
Subject: Re: [Rd] R CMD check file issues

Are you sure there is no other check process or editor that locks the
file?

Uwe Ligges


On 22.09.2011 13:53, Nick Sabbe wrote:

This problem is likely to be specific to Windows, and particularly

Win7.




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

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Re: [Rd] R CMD check file issues

2011-09-22 Thread Nick Sabbe 
Hello Uwe, and thanks for your interest in the issue.

There is most certainly not another process that stops working between the
two R CMD check calls (recently, I've made a habit out of being ready to
press   in the seconds after running my first R CMD check,
to rerun it if it fails).

At worst, there may ever have been an explorer window open, but this is
definitely not always the case, and I'm sure this window was not closed
then, between the calls.

I'm really quite afraid it is more of a windows issue than an R issue, but I
was hoping you wizards might have a workaround (apart from the obvious
suggestion to install Linux), as it is immensely annoying...


Nick Sabbe
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link: http://biomath.ugent.be
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ring: 09/264.59.36

-- Do Not Disapprove




> -Original Message-
> From: Uwe Ligges [mailto:lig...@statistik.tu-dortmund.de]
> Sent: donderdag 22 september 2011 13:58
> To: Nick Sabbe
> Cc: r-devel@r-project.org
> Subject: Re: [Rd] R CMD check file issues
> 
> Are you sure there is no other check process or editor that locks the
> file?
> 
> Uwe Ligges
> 
> 
> On 22.09.2011 13:53, Nick Sabbe wrote:
> > This problem is likely to be specific to Windows, and particularly
> Win7.
> >
> >
> >
> > 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
> >
> > 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

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Re: [Rd] R CMD check file issues

2011-09-22 Thread Uwe Ligges 

Are you sure there is no other check process or editor that locks the file?

Uwe Ligges


On 22.09.2011 13:53, Nick Sabbe wrote:

This problem is likely to be specific to Windows, and particularly Win7.



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

wink: A1.056, Coupure Links 653, 9000 Gent

ring: 09/264.59.36



-- Do Not Disapprove




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Re: [Rd] R check error / update.packages

2011-09-22 Thread Uwe Ligges 
This is an infelicity in a recent glmnet release, I will follow up off 
list in a minute.


Best,
Uwe Ligges



On 22.09.2011 13:16, Nick Sabbe wrote:

While building/checking a package of mine that depends on glmnet, I got the
following message:



* checking whether the name space can be loaded with stated dependencies
...Warn

ing: running command
'"C:/Users/nisabbe/Documents/R/R-2.13.1/bin/i386/Rterm.exe"

  R_DEFAULT_PACKAGES=NULL --vanilla --slave -f
C:\Users\nisabbe\AppData\Local\Tem

p\RtmpZpjj07\Rin121ae93' had status 1

  WARNING

Error: .onLoad failed in loadNamespace() for 'glmnet', details:

   call: cat("Loaded glmnet", installed.packages()["glmnet", "Version"],

   error: could not find function "installed.packages"

Execution halted



A namespace must be able to be loaded with just the base namespace

loaded: otherwise if the namespace gets loaded by a saved object, the

session will be unable to start.



Probably some imports need to be declared in the NAMESPACE file.



I have not changed anything to my dependencies (since my last successful
build the day before yesterday), and to my knowledge, I have not changed
anything relevant. I am using R 2.13.1 (unchanged since the last successful
build) on Windows 7 32bit. When starting a vanilla R terminal, the function
installed.packages is present and can be run. Apart from this, I do not get
any warnings or errors (e.g. the examples run fine). Also, as far as I can
tell, I've never had the warning wrt status 1 (up to today), but it is
unclear whether one is just the consequence of the other. Note: the sources
for this package can be found on R-Forge:
https://r-forge.r-project.org/R/?group_id=1130

The namespace itself contains as its import statement: import(glmnet, rgl,
Matrix, snowfall)

Can someone please help me avoid this warning, as I prefer 0 errors 0
warnings.





On a related note, while trying to alleviate the problem, I ran
update.packages, which led me to another problem: apparently, packages that
are loaded at the time of update.packages are not updated and may end up
broken (this was the case for lattice and Hmisc, for me). Luckily my
colleague had gone through the same troubles and pointed me to the solution.
I can imagine it to be hard to define exactly which packages should or
shouldn't be updated, but it would be nice if the update.packages at least
issued a warning against this.





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




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[Rd] R CMD check file issues

2011-09-22 Thread Nick Sabbe 
This problem is likely to be specific to Windows, and particularly Win7.

 

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

wink: A1.056, Coupure Links 653, 9000 Gent

ring: 09/264.59.36

 

-- Do Not Disapprove

 


[[alternative HTML version deleted]]

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[Rd] R check error / update.packages

2011-09-22 Thread Nick Sabbe 
While building/checking a package of mine that depends on glmnet, I got the
following message:

 

* checking whether the name space can be loaded with stated dependencies
...Warn

ing: running command
'"C:/Users/nisabbe/Documents/R/R-2.13.1/bin/i386/Rterm.exe"

 R_DEFAULT_PACKAGES=NULL --vanilla --slave -f
C:\Users\nisabbe\AppData\Local\Tem

p\RtmpZpjj07\Rin121ae93' had status 1

 WARNING

Error: .onLoad failed in loadNamespace() for 'glmnet', details:

  call: cat("Loaded glmnet", installed.packages()["glmnet", "Version"],

  error: could not find function "installed.packages"

Execution halted

 

A namespace must be able to be loaded with just the base namespace

loaded: otherwise if the namespace gets loaded by a saved object, the

session will be unable to start.

 

Probably some imports need to be declared in the NAMESPACE file.

 

I have not changed anything to my dependencies (since my last successful
build the day before yesterday), and to my knowledge, I have not changed
anything relevant. I am using R 2.13.1 (unchanged since the last successful
build) on Windows 7 32bit. When starting a vanilla R terminal, the function
installed.packages is present and can be run. Apart from this, I do not get
any warnings or errors (e.g. the examples run fine). Also, as far as I can
tell, I've never had the warning wrt status 1 (up to today), but it is
unclear whether one is just the consequence of the other. Note: the sources
for this package can be found on R-Forge:
https://r-forge.r-project.org/R/?group_id=1130 

The namespace itself contains as its import statement: import(glmnet, rgl,
Matrix, snowfall)

Can someone please help me avoid this warning, as I prefer 0 errors 0
warnings.

 

 

On a related note, while trying to alleviate the problem, I ran
update.packages, which led me to another problem: apparently, packages that
are loaded at the time of update.packages are not updated and may end up
broken (this was the case for lattice and Hmisc, for me). Luckily my
colleague had gone through the same troubles and pointed me to the solution.
I can imagine it to be hard to define exactly which packages should or
shouldn't be updated, but it would be nice if the update.packages at least
issued a warning against this.

 

 

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

 


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[Rd] names Rd see Also{slotNames}

2011-09-22 Thread Timothy Bates 
Would anyone object to a suggestion that the names.Rd file could usefully point 
to seeAlso{slotNames}?

cheers,
tim
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Scotland, with registration number SC005336.

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