[BioC] foreach, doMC, and GOstats problems

[Benilton Carvalho]

I've seen errors like this when reading from SQLite dbs stored on
network devices (not running parallel jobs) and having them on local
disks seemed to address the issue. b

On 24 March 2011 17:39, Dan Tenenbaum <dtenenba at fhcrc.org> wrote:
> On Thu, Mar 24, 2011 at 9:29 AM, Tarca, Adi <atarca at med.wayne.edu> wrote:
>
>> Hi all,
>>
>> I am using foreach and doMC packages to do some parallel GO analyses with
>> GOstats.
>>
>> If I use 3 or less processors at the same time (i.e. the foreach loop goes
>> up to n=3) all works fine but when I want to use n>3 I get this error:
>>
>> "RSQLite driver: (RS_SQLite_fetch: failed: database disk image is
>> malformed)"
>> I assume that   the error comes from the multiple connections to the
>> annotation packages used by GOstats.  Is there a way to overcome this
>> problem?
>> Thanks
>>
>>
> Are you doing any writes to a SQLite database? SQLite is not so good at
> write concurrency but it should be able to handle multiple
> (near-)simultaneous reads.
>
> Also, how many processors do you have?
> Dan
>
>
>
>> Adi L. Tarca
>>
>> > sessionInfo()
>> R version 2.12.0 (2010-10-15)
>> Platform: x86_64-unknown-linux-gnu (64-bit)
>>
>> 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] doMC_1.2.1           multicore_0.1-3      foreach_1.3.0
>> [4] codetools_0.2-2      iterators_1.0.3      GOstats_2.16.0
>> [7] RSQLite_0.9-3        DBI_0.2-5            graph_1.28.0
>> [10] Category_2.16.0      AnnotationDbi_1.12.0 Biobase_2.10.0
>> [13] limma_3.6.6
>>
>> loaded via a namespace (and not attached):
>> [1] annotate_1.28.0   genefilter_1.32.0 GO.db_2.4.5       GSEABase_1.12.1
>> [5] RBGL_1.26.0       splines_2.12.0    survival_2.35-8   tools_2.12.0
>> [9] XML_3.2-0         xtable_1.5-6
>>
>>
>>
>>
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