[BioC] oligo and pd.genomewidesnp.6_0

[Morten Mattingsdal]

Hi,
Yes, indeed. The /tmp partition was full. Ive changed it using TMPDIR
export TMPDIR=/new/tmp
thanks
morten


> your hard disk may not be full but your temp space seems to be full.
> perhaps you need to reset the path where R writes temporary files --
> check the administrator's manual
>
> ---
> Vince Carey, PhD
> Assoc. Prof Med (Biostatistics)
> Harvard Medical School
> Channing Laboratory - ph 6175252265 fa 6177311541
> 181 Longwood Ave Boston MA 02115 USA
> stvjc at channing.harvard.edu
>
> On Tue, 17 Jun 2008, 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
>>
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>>
>>     
>
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