[BioC] Genominator error when calling syste.time

[Kasper Daniel Hansen]

Sounds reasonable, probably because the column names will start with numbers.

Kasper

On Wed, Apr 11, 2012 at 3:46 PM, Dan Tenenbaum <dtenenba at fhcrc.org> wrote:
> [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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