featurecounts_deseq2.r fails

[mestia]

While running atacseq pipeline we get the following error when it comes to MergedLibConsensusPeakSetDESeq
featurecounts_deseq2.r -i consensus_peaks.mLb.clN.featureCounts.txt -b '.mLb.clN.bam' -o ./ -p consensus_peaks.mLb.clN -s .mLb

Warning messages:
1: package ‘S4Vectors’ was built under R version 3.4.4
2: package ‘BiocGenerics’ was built under R version 3.4.4
3: package ‘IRanges’ was built under R version 3.4.4
4: package ‘GenomicRanges’ was built under R version 3.4.4
5: package ‘GenomeInfoDb’ was built under R version 3.4.4
6: package ‘SummarizedExperiment’ was built under R version 3.4.4
7: package ‘Biobase’ was built under R version 3.4.4
8: package ‘DelayedArray’ was built under R version 3.4.4
9: package ‘matrixStats’ was built under R version 3.4.4
converting counts to integer mode
estimating size factors
estimating dispersions
gene-wise dispersion estimates
mean-dispersion relationship
final dispersion estimates
fitting model and testing
Error in validObject(.Object) :
invalid class “DESeqResults” object: superclass "list_OR_List" not defined in the environment of the object's class
Calls: results ... DESeqResults -> new -> initialize -> initialize -> validObject
Execution halted

Any hint is appreciated.
@ktrns, please feel free to provide more details.

[drpatelh]

Hi @mestia My suspicion is that this has something to do with a local installation of R conflicting with the version in the container.

Please see the issue thread below and see if that solves the problem:
nf-core/tools#541

Be interested to hear back.

Have a great weekend!

[mestia]

Thanks for the hint, I'll check it. For now I run the dev singularity image with atacsec from dev branch and it successfully went through. Are there plans to release a new stable version any time soon?
Thanks!

[drpatelh]

No worries! Yep. I've already created a PR for the release:
#87

Need a couple of reviews and then should be ready to go. I'm planning on releasing it during the nf-core Hackathon next week but will try and close a couple of issues first. Hopefully soon ⏳