More strange R CMD build/check errors on Windows
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