From hpages at fhcrc.org  Mon Sep 27 19:47:20 2010
From: hpages at fhcrc.org (=?windows-1252?Q?Herv=E9_Pag=E8s?=)
Date: Mon, 27 Sep 2010 10:47:20 -0700
Subject: [Rd] More strange R CMD build/check errors on Windows
In-Reply-To: <4C916321.9050108@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>
	<4C916321.9050108@fhcrc.org>
Message-ID: <4CA0D8A8.6000505@fhcrc.org>

Hi,

Something I should mention too, and I don't know whether it is
related to the "'R CMD' confusion" issue I described previously,
is that with the migration from Perl-based to R-based 'R CMD build',
we also started to see the following 'R CMD build' error on Windows:

R\bin\R.exe CMD build cosmoGUI
* checking for file 'cosmoGUI/DESCRIPTION' ... OK
* preparing 'cosmoGUI':
* checking DESCRIPTION meta-information ... OK
/cygdrive/c/RTOOLS?1/bin/tar: cosmoGUI/DESCRIPTION: Cannot change 
ownership to uid 0, gid 401: Invalid argument
/cygdrive/c/RTOOLS?1/bin/tar: cosmoGUI/man/constraintBuilder.Rd: Cannot 
change ownership to uid 0, gid 401: Invalid argument
/cygdrive/c/RTOOLS?1/bin/tar: cosmoGUI/man: Cannot change ownership to 
uid 0, gid 401: Invalid argument
/cygdrive/c/RTOOLS?1/bin/tar: cosmoGUI/NAMESPACE: Cannot change 
ownership to uid 0, gid 401: Invalid argument
/cygdrive/c/RTOOLS?1/bin/tar: cosmoGUI/R/gui.R: Cannot change ownership 
to uid 0, gid 401: Invalid argument
/cygdrive/c/RTOOLS?1/bin/tar: cosmoGUI/R: Cannot change ownership to uid 
0, gid 401: Invalid argument
/cygdrive/c/RTOOLS?1/bin/tar: cosmoGUI: Cannot change ownership to uid 
0, gid 401: Invalid argument
/cygdrive/c/RTOOLS?1/bin/tar: Exiting with failure status due to 
previous errors
  ERROR
copying to build directory failed

Like for the "'R CMD' confusion" issue, this error will show up
randomly everyday on our build report for around 10% of the
Bioconductor packages.

This is with 2.12.0 alpha (2010-09-24 r52991) on Windows Server 2003 R2
(32-bit). The tar command used is from current Rtools212.

Cheers,
H.


On 09/15/2010 05:21 PM, Herv? Pag?s wrote:
> 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
=?windows-1252?Q?Herv=E9_Pag=E8s?=