[BioC] Agi4x44PreProcess- RSQLite driver: (RS_SQLite_fetch: failed first step: disk I/O error)

[Benilton Carvalho]

I have seen something similar (with RSQLite alone)... and, back in the
day, it appeared to have an association with the fact that the library
directory was on a network drive (and the connection of the machine
with the storage system was not that great)...

Installing the RSQLite-dependent package on a local disk always solved
the problem for me...

b

On 25 August 2010 21:10, Brown, Joseph <BrownJo at njhealth.org> wrote:
> 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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