[BioC] Genominator error when calling syste.time

[Dan Tenenbaum]

[CC'ing Genominator maintainer]

On Wed, Apr 11, 2012 at 12:41 PM, Kasper Daniel Hansen
<kasperdanielhansen at gmail.com> wrote:
> On Wed, Apr 11, 2012 at 3:32 PM, Boel Brynedal <Boel.Brynedal at ki.se> wrote:
>>> eData <- importFromAlignedReads(aligned, chrMap=chroms, dbFilename='test.db', tablename='raw', type="BAM", verbose=FALSE)
>> Error in system.time(exp) :
>>  Unable to write the table, delete table or specify overwrite.
>> In addition: Warning message:
>> In value[[3L]](cond) :
>>  RS-DBI driver: (error in statement: near "20417.6": syntax error)
>> Timing stopped at: 0.076 0 0.081
>> Timing stopped at: 12.851 0.74 13.631
>
> The system.time is a red herring I think.  Note that it says
>  >  Unable to write the table, delete table or specify overwrite.
> I suggest you have too little disk space, or permission issues.
>

It seems that the warning is significant as well. Looks like the
package is trying to use the names of your BAM files in a SQL query
but that query is malformed.

Dan


> Kasper
>
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