On 09/14/2010 11:23 AM, Hervé Pagès 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.
--
Hervé Pagès
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: hpa...@fhcrc.org
Phone: (206) 667-5791
Fax: (206) 667-1319
______________________________________________
R-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-devel
