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 _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
