[Bioc-devel] Bug in les:::cdfDuplicates

[Julian Gehring]

Hi Ryan,

Thank you for the detailed bug report and already providing a fix for
this.  I have added your patch to 'les_1.13.2' and pushed it to
bioc-devel, the updated build should become available soon.

I'll do some more tests within the next days, and then also update
bioc-release.  If you need a patched version of the package now, let me
know.

Best wishes
Julian


On 24/03/14 19:14, Ryan C. Thompson wrote:
> Hello,
> 
> I have discovered a bug in the cdfDuplicates function in the les
> package. This function is used indirectly by the GSRI package, and I was
> attempting to use this package when I encountered an error. The error
> appears to occur because both rle and table are used to deduplicate a
> (sorted) vector, and these two functions apparently fail to use the same
> definition of equality for floating point values. This results in two
> different length vectors, which raises an error when they are passed to
> rep.int, which requires vectors of the same length. Replacing
> rle(pvalSort)$length with table(pvalSort) seems to solve the problem. I
> have compiled my test case into an RDS file that you can download and
> use to reproduce the bug:
> 
> https://www.dropbox.com/s/k7k1m3s28aa4ajb/GSRI-les-cdfDuplicates-error-case.RDS
> 
> 
> This RDS file contains the full argument list that I pass to the "gsri"
> function to reproduce the error. Just download it, then execute the
> following R code:
> 
> library(GSRI)
> do.call(gsri, readRDS("GSRI-les-cdfDuplicates-error-case.RDS"))
> 
> After making the suggested change, this test case now works properly.
> The expression data is my own, and the gene set is MSigDB ID
> "AAAYRNCTG_UNKNOWN", with the gene IDs converted to my organism
> (cynomolgus monkey, whose genes are annotated with orthologous Ensembl
> Peptide IDs from human & rhesus).
> 
> -Ryan