Workflow Error: xfun R dependency mismatch in DESeq2

[kee007ney]

Following instructions with correct Ubuntu and Nextflow versions produces this (excerpted) error:

  Error: package or namespace load failed for ‘DESeq2’ in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]):
   namespace ‘xfun’ 0.15 is being loaded, but >= 0.19 is required
  In addition: Warning message:
  package ‘matrixStats’ was built under R version 3.6.3 
  Execution halted

(Full error is below):

Pipeline completed with errors-
WARN: To render the execution DAG in the required format it is required to install Graphviz -- See http://www.graphviz.org for more info.
Error executing process > 'CONSENSUS_PEAKS_DESEQ2 (SPT5)'

Caused by:
  Process `CONSENSUS_PEAKS_DESEQ2 (SPT5)` terminated with an error exit status (1)

Command executed:

  featurecounts_deseq2.r \
      --featurecount_file SPT5.consensus_peaks.featureCounts.txt \
      --bam_suffix '.mLb.clN.bam' \
      --outdir ./ \
      --outprefix SPT5.consensus_peaks \
      --outsuffix '' \
      --cores 2 \
  
  
  sed 's/deseq2_pca/deseq2_pca_1/g' <deseq2_pca_header.txt >tmp.txt
  sed -i -e 's/DESeq2 /SPT5 DESeq2 /g' tmp.txt
  cat tmp.txt SPT5.consensus_peaks.pca.vals.txt > SPT5.consensus_peaks.pca.vals_mqc.tsv
  
  sed 's/deseq2_clustering/deseq2_clustering_1/g' <deseq2_clustering_header.txt >tmp.txt
  sed -i -e 's/DESeq2 /SPT5 DESeq2 /g' tmp.txt
  cat tmp.txt SPT5.consensus_peaks.sample.dists.txt > SPT5.consensus_peaks.sample.dists_mqc.tsv
  
  find * -type f -name "*.FDR0.05.results.bed" -exec echo -e "bwa/mergedLibrary/macs/broadPeak/consensus/SPT5/deseq2/"{}"\t255,0,0" \; > SPT5.consensus_peaks.igv.txt

Command exit status:
  1

Command output:
  (empty)

Command error:
      dirname, do.call, duplicated, eval, evalq, Filter, Find, get, grep,
      grepl, intersect, is.unsorted, lapply, Map, mapply, match, mget,
      order, paste, pmax, pmax.int, pmin, pmin.int, Position, rank,
      rbind, Reduce, rownames, sapply, setdiff, sort, table, tapply,
      union, unique, unsplit, which, which.max, which.min
  
  
  Attaching package: ‘S4Vectors’
  
  The following object is masked from ‘package:base’:
  
      expand.grid
  
  Loading required package: IRanges
  Loading required package: GenomicRanges
  Loading required package: GenomeInfoDb
  Loading required package: SummarizedExperiment
  Loading required package: Biobase
  Welcome to Bioconductor
  
      Vignettes contain introductory material; view with
      'browseVignettes()'. To cite Bioconductor, see
      'citation("Biobase")', and for packages 'citation("pkgname")'.
  
  Loading required package: DelayedArray
  Loading required package: matrixStats
  
  Attaching package: ‘matrixStats’
  
  The following objects are masked from ‘package:Biobase’:
  
      anyMissing, rowMedians
  
  Loading required package: BiocParallel
  
  Attaching package: ‘DelayedArray’
  
  The following objects are masked from ‘package:matrixStats’:
  
      colMaxs, colMins, colRanges, rowMaxs, rowMins, rowRanges
  
  The following objects are masked from ‘package:base’:
  
      aperm, apply, rowsum
  
  Error: package or namespace load failed for ‘DESeq2’ in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]):
   namespace ‘xfun’ 0.15 is being loaded, but >= 0.19 is required
  In addition: Warning message:
  package ‘matrixStats’ was built under R version 3.6.3 
  Execution halted

Work dir:
  /home/j/chipseq_20210330/data/work/4e/c7a9b7394c7760781354adda99f45c

Tip: when you have fixed the problem you can continue the execution adding the option `-resume` to the run command line

[stain]

This error seems to be related to nf-core/chipseq/issues/206 and the fact that R is not following semantic versioning.

I get a different error by running in a fresh Docker container of ubuntu:20.04 after installing curl, miniconda and the nextflow environment according to this guide.

(bco-ro) root@5ba894f413ba:/chipseq_20200924# nextflow run nf-core/chipseq -revision 1.2.1 -profile test,conda
N E X T F L O W  ~  version 20.07.1
Pulling nf-core/chipseq ...
downloaded from https://github.com/nf-core/chipseq.git
Launching `nf-core/chipseq` [grave_morse] - revision: 0f487ed76d [1.2.1]
----------------------------------------------------
                                        ,--./,-.
        ___     __   __   __   ___     /,-._.--~'
  |\ | |__  __ /  ` /  \ |__) |__         }  {
  | \| |       \__, \__/ |  \ |___     \`-._,-`-,
                                        `._,._,'
  nf-core/chipseq v1.2.1
----------------------------------------------------
Run Name            : grave_morse
Data Type           : Paired-End
Design File         : https://raw.githubusercontent.com/nf-core/test-datasets/chipseq/design.csv
Genome              : Not supplied
Fasta File          : https://raw.githubusercontent.com/nf-core/test-datasets/atacseq/reference/genome.fa
GTF File            : https://raw.githubusercontent.com/nf-core/test-datasets/atacseq/reference/genes.gtf
MACS2 Genome Size   : 1.2E+7
Min Consensus Reps  : 1
MACS2 Narrow Peaks  : No
MACS2 Broad Cutoff  : 0.1
Trim R1             : 0 bp
Trim R2             : 0 bp
Trim 3' R1          : 0 bp
Trim 3' R2          : 0 bp
NextSeq Trim        : 0 bp
Fingerprint Bins    : 100
Save Genome Index   : No
Max Resources       : 6 GB memory, 2 cpus, 12h time per job
Output Dir          : ./results
Launch Dir          : /chipseq_20200924
Working Dir         : /chipseq_20200924/work
Script Dir          : /root/.nextflow/assets/nf-core/chipseq
User                : root
Config Profile      : test,conda
Config Description  : Minimal test dataset to check pipeline function
----------------------------------------------------
[-        ] process > CHECK_DESIGN             -
[-        ] process > BWA_INDEX                -
[-        ] process > MAKE_GENE_BED            -
[-        ] process > MAKE_GENOME_FILTER       -
[-        ] process > FASTQC                   -
[-        ] process > TRIMGALORE               -
[-        ] process > BWA_MEM                  -
[-        ] process > SORT_BAM                 -
[-        ] process > MERGED_BAM               -
[-        ] process > MERGED_BAM_FILTER        -
[-        ] process > MERGED_BAM_REMOVE_ORPHAN -
[-        ] process > PRESEQ                   -
[-        ] process > PICARD_METRICS           -
[-        ] process > BIGWIG                   -
[-        ] process > PLOTPROFILE              -
[-        ] process > PHANTOMPEAKQUALTOOLS     -
[-        ] process > PLOTFINGERPRINT          -
[-        ] process > MACS2                    -
[-        ] process > MACS2_ANNOTATE           -
[-        ] process > MACS2_QC                 -
[-        ] process > CONSENSUS_PEAKS          -
[-        ] process > CONSENSUS_PEAKS_ANNOTATE -
[-        ] process > CONSENSUS_PEAKS_COUNTS   -
[-        ] process > CONSENSUS_PEAKS_DESEQ2   -
[-        ] process > IGV                      -
[-        ] process > get_software_versions    -
[-        ] process > MULTIQC                  -
[-        ] process > output_documentation     -
Error executing process > 'MAKE_GENE_BED (genes.gtf)'

Caused by:
  Failed to create Conda environment
  command: conda env create --prefix /chipseq_20200924/work/conda/nf-core-chipseq-1.2.1-124f0f8d69d9dfbfcea852493605e617 --file /root/.nextflow/assets/nf-core/chipseq/environment.yml
  status : 137
  message:



-[nf-core/chipseq] Pipeline completed with errors-
WARN: To render the execution DAG in the required format it is required to install Graphviz -- See http://www.graphviz.org for more info.

(bco-ro) root@5ba894f413ba:/chipseq_20200924# 

[stain]

Reproduced original error also with older 1.2.0 version of workflow:

Error executing process > 'CONSENSUS_PEAKS_DESEQ2 (SPT5)'

Caused by:
  Process `CONSENSUS_PEAKS_DESEQ2 (SPT5)` terminated with an error exit status (1)

Command executed:

  featurecounts_deseq2.r \
      --featurecount_file SPT5.consensus_peaks.featureCounts.txt \
      --bam_suffix '.mLb.clN.bam' \
      --outdir ./ \
      --outprefix SPT5.consensus_peaks \
      --outsuffix '' \
      --cores 2 \
  
  
  sed 's/deseq2_pca/deseq2_pca_1/g' <deseq2_pca_header.txt >tmp.txt
  sed -i -e 's/DESeq2 /SPT5 DESeq2 /g' tmp.txt
  cat tmp.txt SPT5.consensus_peaks.pca.vals.txt > SPT5.consensus_peaks.pca.vals_mqc.tsv
  
  sed 's/deseq2_clustering/deseq2_clustering_1/g' <deseq2_clustering_header.txt >tmp.txt
  sed -i -e 's/DESeq2 /SPT5 DESeq2 /g' tmp.txt
  cat tmp.txt SPT5.consensus_peaks.sample.dists.txt > SPT5.consensus_peaks.sample.dists_mqc.tsv
  
  find * -type f -name "*.FDR0.05.results.bed" -exec echo -e "bwa/mergedLibrary/macs/broadPeak/consensus/SPT5/deseq2/"{}"\t255,0,0" \; > SPT5.consensus_peaks.igv.txt

Command exit status:
  1

Command output:
  (empty)

Command error:
      as.data.frame, basename, cbind, colnames, dirname, do.call,
      duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
      lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
      pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
      tapply, union, unique, unsplit, which, which.max, which.min
  
  
  Attaching package: 'S4Vectors'
  
  The following object is masked from 'package:base':
  
      expand.grid
  
  Loading required package: IRanges
  Loading required package: GenomicRanges
  Loading required package: GenomeInfoDb
  Loading required package: SummarizedExperiment
  Loading required package: Biobase
  Welcome to Bioconductor
  
      Vignettes contain introductory material; view with
      'browseVignettes()'. To cite Bioconductor, see
      'citation("Biobase")', and for packages 'citation("pkgname")'.
  
  Loading required package: DelayedArray
  Loading required package: matrixStats
  
  Attaching package: 'matrixStats'
  
  The following objects are masked from 'package:Biobase':
  
      anyMissing, rowMedians
  
  Loading required package: BiocParallel
  
  Attaching package: 'DelayedArray'
  
  The following objects are masked from 'package:matrixStats':
  
      colMaxs, colMins, colRanges, rowMaxs, rowMins, rowRanges
  
  The following objects are masked from 'package:base':
  
      aperm, apply, rowsum
  
  Error: package or namespace load failed for 'DESeq2' in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]):
   namespace 'xfun' 0.15 is being loaded, but >= 0.19 is required
  In addition: Warning message:
  package 'matrixStats' was built under R version 3.6.3 
  Execution halted

Work dir:
  /work/ba/e59a76de2b41b2ffa2fbd83c3fef1d

Tip: you can try to figure out what's wrong by changing to the process work dir and showing the script file named `.command.sh`

Alternatives:

• Patch the workflow as part of the tutorial (confusing)
• download patched version from our repo (confuses argument of URLs and authors),
• await new workflow release of 1.2.1
• switch to a different nf-core workflow (update example, screenshots etc) e.g. https://nf-co.re/rnaseq/2.0
• switch to run workflow with Docker (more things to install, memory configuration of VM etc)
• switch tutorial to NOT run the workflow, but download pre-baked non-BCO results as starting point

[stain]

Fixed in nf-core/chipseq#206 - thanks to @drpatelh for rolling an updated 1.2.2.