I am using 'derfinder' to find differentially expressed regions using RNA-seq data. The tool works until some point and gets stuck after calculating p-values. Some of the intermediate files are created but it doesn't finish the analysis. Here is the log:

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Error in tools:::httpdPort <= 0L : 
  comparison (4) is possible only for atomic and list types
> library(derfinder)
Find out what's changed in derfinder with
news(Version == "1.2.0", package = "derfinder")
> library(GenomicRanges)

> library(BiocParallel)

> setwd("~/Research/Ring/rnaSeq/bams/");
> 
> files <- Sys.glob(file.path(".","*chr20*.bam"))
> fullCov <- fullCoverage(files=files,chrs='20')
2015-06-12 14:07:26 fullCoverage: processing chromosome 20
2015-06-12 14:07:26 loadCoverage: finding chromosome lengths
2015-06-12 14:07:26 loadCoverage: loading BAM file ./E11-1.chr20.sorted.bam
2015-06-12 14:07:31 loadCoverage: loading BAM file ./E11-2.chr20.sorted.bam
2015-06-12 14:07:33 loadCoverage: loading BAM file ./E8-1.chr20.sorted.bam
2015-06-12 14:07:36 loadCoverage: loading BAM file ./E8-2.chr20.sorted.bam
2015-06-12 14:07:39 loadCoverage: applying the cutoff to the merged data
2015-06-12 14:07:39 filterData: originally there were 63025520 rows, now there are 63025520 rows. Meaning that 0 percent was filtered.
extendedMapSeqlevels: sequence names mapped from NCBI to UCSC for species homo_sapiens
> filteredCov <- lapply(fullCov, filterData, cutoff = 2)
2015-06-12 14:07:40 filterData: originally there were 63025520 rows, now there are 3580364 rows. Meaning that 94.32 percent was filtered.
> sampleDepths <- sampleDepth(collapseFullCoverage(fullCov), 1)
2015-06-12 14:07:40 sampleDepth: Calculating sample quantiles
2015-06-12 14:07:40 sampleDepth: Calculating sample adjustments
> pheno <- data.frame(group = c("Ring","Ring","WT","WT"))
> 
> models <- makeModels(sampleDepths, testvars = pheno$group)
> originalWd <- getwd()
> setwd(file.path(originalWd, 'analysisResults'))
> 
> results <- analyzeChr(chr = '20', filteredCov$chr20, models, cutoffType='manual', mc.cores=6, method = 'regular', runAnnotation = 'false', BPPARAM.custom = MulticoreParam(workers = 6),
+                       groupInfo = pheno$group, writeOutput = FALSE, cutoffFstat = 5e-02, nPermute = 5, seeds = 20140923 + seq_len(5), returnOutput = TRUE)
extendedMapSeqlevels: sequence names mapped from NCBI to UCSC for species homo_sapiens
2015-06-12 14:09:07 analyzeChr: Pre-processing the coverage data
2015-06-12 14:09:18 analyzeChr: Calculating statistics
2015-06-12 14:09:18 calculateStats: calculating the F-statistics
2015-06-12 14:09:21 analyzeChr: Calculating pvalues
2015-06-12 14:09:21 analyzeChr: Using the following manual cutoff for the F-statistics 0.05
2015-06-12 14:09:21 calculatePvalues: identifying data segments
2015-06-12 14:09:21 findRegions: segmenting F-stats information
2015-06-12 14:09:21 findRegions: identifying candidate regions
2015-06-12 14:09:21 findRegions: identifying region clusters
2015-06-12 14:09:48 calculatePvalues: calculating F-statistics for permutation 1 and seed 20140924
2015-06-12 14:09:51 findRegions: segmenting F-stats information
2015-06-12 14:09:51 findRegions: identifying candidate regions
2015-06-12 14:09:51 calculatePvalues: calculating F-statistics for permutation 2 and seed 20140925
2015-06-12 14:09:53 findRegions: segmenting F-stats information
2015-06-12 14:09:53 findRegions: identifying candidate regions
2015-06-12 14:09:54 calculatePvalues: calculating F-statistics for permutation 3 and seed 20140926
2015-06-12 14:09:56 findRegions: segmenting F-stats information
2015-06-12 14:09:56 findRegions: identifying candidate regions
2015-06-12 14:09:56 calculatePvalues: calculating F-statistics for permutation 4 and seed 20140927
2015-06-12 14:09:58 findRegions: segmenting F-stats information
2015-06-12 14:09:59 findRegions: identifying candidate regions
2015-06-12 14:09:59 calculatePvalues: calculating F-statistics for permutation 5 and seed 20140928
2015-06-12 14:10:01 findRegions: segmenting F-stats information
2015-06-12 14:10:01 findRegions: identifying candidate regions
2015-06-12 14:10:01 calculatePvalues: calculating the p-values

It just gets stuck here. Any suggestions to fix?

Hi,

This issue has been addressed in derfinder Bioconductor-release version 1.2.1 (and Bioconductor-devel version 1.3.1) as explained in further detail at https://github.com/lcolladotor/derfinder/issues/29.

The user has not gotten back to me with the session information they had, but it's fair to assume that they were not using this version given that it has only been available from biocLite() since today.

I originally asked for the session information for completeness and also because the above github issue got resolved 5 days ago, 1 day before the user posted this question. The delay in derfinder 1.2.1's availability via biocLite() happened because the derfinder Bioconductor-release git-svn bridge was not properly setup, my bad.

Best,

Leonardo

Sorry for not providing the session info. However, I upgraded the package to the latest version and it is working fine.

Thanks for the support.