[BioC] Looks like a bug in GenomicRanges::.breakTie

[Valerie Obenchain]

Now fixed in devel version 1.7.42.

Valerie

On 03/27/2012 08:59 AM, Valerie Obenchain wrote:
> Hi Paul,
>
> Thanks for the bug report. I'll look into it.
>
> Valerie
>
> On 03/27/2012 08:20 AM, Paul Theodor Pyl wrote:
>> Hi,
>>
>> I encountered (during a call to VariantAnnotation::locateVariants) an 
>> error that originated from GenomicRanges::.breakTie. From the source 
>> code of that function (svn revision 64480) it looks like equivalue 
>> can only ever have a length of 1 while equidist can be longer which 
>> breaks the call to DataFrame because the column lengths do not match.
>>
>> Error in DataFrame(idx = c(mindist, eqidist), value = c(minvalue, 
>> eqivalue)) :
>>   different row counts implied by arguments
>>
>> Enter a frame number, or 0 to exit
>>  1: locateVariants(insertions_granges, txdb19)
>>  2: locateVariants(insertions_granges, txdb19)
>>  3: .locateVariants(query, subject, ...)
>>  4: .intergenic(txCO, query, cache, map)
>>  5: follow(query, rng)
>>  6: follow(query, rng)
>>  7: .local(x, subject, ...)
>>  8: .findRanges(x, subject, ignore.strand, type = "follow", ...)
>>  9: .breakTie(sub1, res1, k1, dist1, sub2, res2, k2, dist2, type)
>> 10: DataFrame(idx = c(mindist, eqidist), value = c(minvalue, eqivalue))
>>
>> Kind Regards,
>> Paul
>>
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>
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