[BioC] oligo and pd.genomewidesnp.6_0

[Robert Gentleman]

Hi,
   Using biocLite (the recommended method), I had no problem, so I 
suspect that it is just fine, and that either issues due to incomplete 
downloading (check the size), or you are installing in some partition 
that is full.

  best wishes
   Robert


Morten Mattingsdal wrote:
> Hi,
> 
> Ive just intstalled a fresh version of R 2.7.0 and want to run CRLMM on 
> ~780 Affymetrix chips.
> When installing the subsequent platform design "pd.genomewidesnp.6_0" I 
> get the following errors:
> 
> R CMD INSTALL pd.genomewidesnp.6_0.4.2.tar.gz
> tar: pd.genomewidesnp.6/inst/extdata/pd.genomewidesnp.6.sqlite: Wrote 
> only 1024 of 10240 bytes
> tar: Skipping to next header
> tar: Archive contains obsolescent base-64 headers
> tar: pd.genomewidesnp.6/inst/UnitTests: Cannot mkdir: No space left on 
> device
> tar: pd.genomewidesnp.6/inst/UnitTests/crlmm_test.R: Cannot open: No 
> such file or directory
> tar: pd.genomewidesnp.6/inst/UnitTests/runfile.sh: Cannot open: No such 
> file or directory
> tar: pd.genomewidesnp.6/inst/UnitTests/Makefile: Cannot open: No such 
> file or directory
> tar: pd.genomewidesnp.6/inst/UnitTests/checkTables_test.R: Cannot open: 
> No such file or directory
> tar: pd.genomewidesnp.6/inst/UnitTests/runalltests.R: Cannot open: No 
> such file or directory
> tar: pd.genomewidesnp.6/inst/UnitTests/runall.sh: Cannot open: No such 
> file or directory
> tar: pd.genomewidesnp.6/R: Cannot mkdir: No space left on device
> tar: pd.genomewidesnp.6/R/all.R: Cannot open: No such file or directory
> tar: Error exit delayed from previous errors
> Fatal error: cannot mkdir R_TempDir
> * Installing to library ''
> ERROR: cannot write to or create directory '
> 
> My harddisk is not full, so I wounder if this version 
> pd.genomewidesnp.6_0 is broken. (pd.genomewidesnp.6_0.4.2.tar.gz)
> morten
> 
> 
> 
> 
>  > sessionInfo()
> R version 2.7.0 (2008-04-22)
> x86_64-unknown-linux-gnu
> 
> locale:
> LC_CTYPE=en_US;LC_NUMERIC=C;LC_TIME=en_US;LC_COLLATE=en_US;LC_MONETARY=C;LC_MESSAGES=en_US;LC_PAPER=en_US;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US;LC_IDENTIFICATION=C 
> 
> 
> attached base packages:
> [1] splines   tools     stats     graphics  grDevices utils     datasets
> [8] methods   base   
> other attached packages:
> [1] oligo_1.4.0          oligoClasses_1.2.0   affxparser_1.12.2  [4] 
> AnnotationDbi_1.2.1  preprocessCore_1.2.0 RSQLite_0.6-9      [7] DBI_0.2-4
> 
> _______________________________________________
> Bioconductor mailing list
> Bioconductor at stat.math.ethz.ch
> https://stat.ethz.ch/mailman/listinfo/bioconductor
> Search the archives: 
> http://news.gmane.org/gmane.science.biology.informatics.conductor
> 

-- 
Robert Gentleman, PhD
Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N, M2-B876
PO Box 19024
Seattle, Washington 98109-1024
206-667-7700
rgentlem at fhcrc.org