Issue:

When trying to execute filter.probes the following error occurs:

>ddFILT=filter.probes(ddNORM,control,wellaboveBG,isfound,wellaboveNEG,sa
t,PopnOL,NonUnifOL,nas,limWellAbove,limISF,limNEG,limSAT,limPopnOL,limNo
nUnifOL,limNAS,makePLOT=FALSE, annotation.package,flag.counts,targets)

FILTERING PROBES BY FLAGS

 

 

FILTERING BY ControlType FLAG

Error in sqliteFetch(rs, n = -1, ...) :

  RSQLite driver: (RS_SQLite_fetch: failed first step: disk I/O error)

 

 

This issue is reproducible on this particular Linux installation only
(craps out on all data sets, including sets known to work), so I've
tried uninstalling and reinstalling R, as well as the packages, several
times.  Utilizing the same data, I have been able to get results using
Windows installations and other Linux installs.  

 

Has anyone seen this error before and/or have ideas to remedy the
problem?

 

My session info:

> sessionInfo()

R version 2.11.1 (2010-05-31)

x86_64-unknown-linux-gnu

 

locale:

 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C

 [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8

 [5] LC_MONETARY=C              LC_MESSAGES=en_US.UTF-8

 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C

 [9] LC_ADDRESS=C               LC_TELEPHONE=C

[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C

 

attached base packages:

[1] stats     graphics  grDevices utils     datasets  methods   base

 

other attached packages:

 [1] vsn_3.16.0              mgug4122a.db_2.4.1      org.Mm.eg.db_2.4.1

 [4] RSQLite_0.9-2           DBI_0.2-5
Agi4x44PreProcess_1.8.0

 [7] genefilter_1.30.0       annotate_1.26.1
AnnotationDbi_1.10.2

[10] limma_3.4.4             Biobase_2.8.0

 

loaded via a namespace (and not attached):

[1] affy_1.26.1           affyio_1.16.0         grid_2.11.1

[4] lattice_0.18-8        preprocessCore_1.10.0 splines_2.11.1

[7] survival_2.35-8       xtable_1.5-6

 

 


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