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, Hervé Pagès wrote:
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
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