I have seen this issue when the installation of the annotation package was
not 100% fine. Can you please try reinstalling it? (make sure you've got
enough free space on disk)

source("http://www.bioconductor.org/biocLite.R")
biocLite("pd.huex.1.0.st.v2")

The one other time I saw this happening was when the packages were being
installed a a remote disk (like NFS mounts) with low performance.

benilton


2014-05-18 17:52 GMT-03:00 Aaerp <al3n70rn@gmail.com>:

> Hi,
>
> I am having this error when I try to perform rma normalization in human
> exon affymetrix arrays.
>
> Here is my code:
>
>  library('oligo')
>  library('pd.huex.1.0.st.v2')
>
>  celFiles = list.celfiles("~/43107_status",full.name=T)
>
>  raw = read.celfiles (celFiles, pkgname = 'pd.huex.1.0.st.v2')
>
>  eset_core = rma(raw, target = "core")
>
> Error in sqliteFetch(rs, n = -1, ...) :
>   RSQLite driver: (RS_SQLite_fetch: failed first step: database disk image
> is malformed)
>
>  sessionInfo()
> R version 3.1.0 (2014-04-10)
> Platform: x86_64-apple-darwin10.8.0 (64-bit)
>
> locale:
> [1] fr_FR.UTF-8/fr_FR.UTF-8/fr_FR.UTF-8/C/fr_FR.UTF-8/fr_FR.UTF-8
>
> attached base packages:
> [1] parallel  stats     graphics  grDevices utils     datasets methods
> base
>
> other attached packages:
>  [1] pd.huex.1.0.st.v2_3.8.0 RSQLite_0.11.4 DBI_0.2-7
> oligo_1.28.1 Biostrings_2.32.0
>  [6] XVector_0.4.0           IRanges_1.22.6 Biobase_2.24.0
>  oligoClasses_1.26.0 BiocGenerics_0.10.0
>
> loaded via a namespace (and not attached):
>  [1] affxparser_1.36.0     affyio_1.32.0 BiocInstaller_1.14.2  bit_1.1-12
>            codetools_0.2-8 ff_2.2-13
>  [7] foreach_1.4.2         GenomeInfoDb_1.0.2 GenomicRanges_1.16.3
>  iterators_1.0.7       preprocessCore_1.26.1 splines_3.1.0
> [13] stats4_3.1.0          tools_3.1.0           zlibbioc_1.10.0
>
> Any clues to what is wrong?
>
> Agusti
>



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Benilton Carvalho
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