Thanks! I patched my local copy on my own, so I'll be fine until the next
release.
On Mar 25, 2014 3:04 AM, "Julian Gehring" <julian.gehring@embl.de> wrote:

> 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
>

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