From hpages at fhcrc.org  Thu Sep 16 02:21:53 2010
From: hpages at fhcrc.org (=?windows-1252?Q?Herv=E9_Pag=E8s?=)
Date: Wed, 15 Sep 2010 17:21:53 -0700
Subject: [Rd] More strange R CMD build/check errors on Windows
In-Reply-To: <4C8FBDB0.4060106@fhcrc.org>
References: <4C8C6ECB.5080705@fhcrc.org>
	<4C8C94A3.3080600@gmail.com>	<4C8CA70C.40109@fhcrc.org>	<4C8F613E.8070407@statistik.tu-dortmund.de>
	<4C8FBDB0.4060106@fhcrc.org>
Message-ID: <4C916321.9050108@fhcrc.org>

On 09/14/2010 11:23 AM, Herv? Pag?s wrote:
> Hi Uwe,
>
> On 09/14/2010 04:49 AM, Uwe Ligges wrote:
...
>> Brian had some ideas that the problems are related to the shell that is
>> used. Is the problem still apparent in a very recent R-devel from few
>> days ago? I am just back from vacations and have not updated yet.
>> I experienced the same problems and I am just iterating automatically if
>> typical problems are apparent from the log files. I hope some if not all
>> parts are solved now and will do some new test runs shortly.
>
> Sounds good. I just upgraded to R-2.12 (2010-09-13 r52905) on our 32-bit
> Windows machine and I'll report here tomorrow after the next build run
> has completed. I can already see that this new R solves the issue I
> reported here:
>
> https://stat.ethz.ch/pipermail/r-devel/2010-September/058460.html

Not true sorry 
(https://stat.ethz.ch/pipermail/r-devel/2010-September/058530.html)

As for the strange R CMD build/check errors on Windows I still see them.
A sample of Today's Victims:

   R\bin\R.exe CMD build AffyCompatible
   * checking for file 'AffyCompatible/DESCRIPTION' ... OK
   * preparing 'AffyCompatible':
   * checking DESCRIPTION meta-information ... OK
   * installing the package to re-build vignettes
   * creating vignettes ... ERROR
   Error: ERROR: no packages specified

   R\bin\R.exe CMD build ArrayTools
   * checking for file 'ArrayTools/DESCRIPTION' ... OK
   * preparing 'ArrayTools':
   * checking DESCRIPTION meta-information ... OK
   * installing the package to re-build vignettes
         -----------------------------------
   Warning: unknown option '-l'
   * checking for file 
'E:\biocbld\bbs-2.7-bioc\tmpdir\Rtmpbtur24\Rinst494950ff/DESCRIPTION' ... NO
         -----------------------------------
   ERROR: Installation failed
   Removing installation dir

   R\bin\R.exe CMD build baySeq
   * checking for file 'baySeq/DESCRIPTION' ... OK
   * preparing 'baySeq':
   * checking DESCRIPTION meta-information ... OK
   * installing the package to re-build vignettes
   * creating vignettes ...Warning in file(con, "r") :
     cannot open file 
'E:\biocbld\bbs-2.7-bioc\tmpdir\RtmpKRrdst\xshell4d4a5c70': Permission 
denied
   Error in file(con, "r") : cannot open the connection
   Execution halted

   R\bin\R.exe CMD build beadarray
   --> produces no output at all and returns code 0.

etc...

Cheers,
H.


>
> Thanks!
> H.
>
>
>>
>> Best,
>> Uwe
>>
>>
>>
>>
>>
>>
>>>>> Thanks,
>>>>> H.
>>>>>
>>>>
>>>> Antivirus software? I suspect you already ruled that out, but it has
>>>> been the culprit for problems with mysteriously disappearing
>>>> intermediate files in several cases, so I thought I'd mention it.
>>>>
>>>
>>> Actually I didn't try that yet because we still build BioC release
>>> (using R-2.11.1) on these 2 Windows boxes and we don't see any of
>>> those problems for the release builds. But I will. Could it be that
>>> the fact that 'R CMD build' and 'R CMD check' are R-based in R-2.12
>>> (and not Perl-based anymore) make them more fragile when something
>>> like an antivirus is messing around with the filesystem?
>>>
>>> Thanks for the suggestion,
>>> H.
>>>
>
>


-- 
Herv? Pag?s

Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N, M2-B876
P.O. Box 19024
Seattle, WA 98109-1024

E-mail: hpages at fhcrc.org
Phone:  (206) 667-5791
Fax:    (206) 667-1319



[Rd] More strange R CMD build/check errors on Windows
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