package or namespace load failed for ‘UpSetR’

[Nicobouch]

Description of the bug

I keep getting the following error using nextflow version 22.10.4 and chipseq v2.0.0
Does anyone has any idea what's going on ?
Thanks.

Command error:
Error: package or namespace load failed for ‘UpSetR’ in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]):
namespace ‘scales’ 1.1.1 is being loaded, but >= 1.2.0 is required
Execution halted

Command used and terminal output

nextflow run nf-core/chipseq --input sample.csv --outdir test --fasta Arabidopsis_thaliana.TAIR10.dna.toplevel56.fa.gz --gff Arabidopsis_thaliana.TAIR10.56.gff.gz --macs_gsize 119667750 --read_length 150 --save_macs_pileup TRUE -profile ifb_core

Relevant files

No response

System information

No response

[Jose Espinosa-Carrasco]

Could you provide the whole error message or the .nextflow.log. Also, are you using Conda to run the pipeline?

[Nicobouch]

I'm not using conda. Here is the whole error message:

---

Error executing process > 'NFCORE_CHIPSEQ:CHIPSEQ:MACS2_CONSENSUS (H3K9)'

Caused by:
Process NFCORE_CHIPSEQ:CHIPSEQ:MACS2_CONSENSUS (H3K9) terminated with an error exit status (1)

Command executed:

sort -T '.' -k1,1 -k2,2n CONTR1_H3K9_peaks.broadPeak CONTR2_H3K9_peaks.broadPeak CONTR3_H3K9_peaks.broadPeak frim7_1_H3K9_peaks.broadPeak frim7_2_H3K9_peaks.broadPeak frim7_3_H3K9_peaks.broadPeak pom_1_H3K9_peaks.broadPeak pom_2_H3K9_peaks.broadPeak pom_3_H3K9_peaks.broadPeak
| mergeBed -c 2,3,4,5,6,7,8,9 -o collapse,collapse,collapse,collapse,collapse,collapse,collapse,collapse > H3K9.consensus_peaks.txt

macs2_merged_expand.py
H3K9.consensus_peaks.txt
CONTR1_H3K9,CONTR2_H3K9,CONTR3_H3K9,frim7_1_H3K9,frim7_2_H3K9,frim7_3_H3K9,pom_1_H3K9,pom_2_H3K9,pom_3_H3K9
H3K9.consensus_peaks.boolean.txt
--min_replicates 1 \

awk -v FS=' ' -v OFS=' ' 'FNR > 1 { print $1, $2, $3, $4, "0", "+" }' H3K9.consensus_peaks.boolean.txt > H3K9.consensus_peaks.bed

echo -e "GeneID Chr Start End Strand" > H3K9.consensus_peaks.saf
awk -v FS=' ' -v OFS=' ' 'FNR > 1 { print $4, $1, $2, $3, "+" }' H3K9.consensus_peaks.boolean.txt >> H3K9.consensus_peaks.saf

plot_peak_intersect.r -i H3K9.consensus_peaks.boolean.intersect.txt -o H3K9.consensus_peaks.boolean.intersect.plot.pdf

echo "H3K9.consensus_peaks.bed H3K9/H3K9.consensus_peaks.bed" > H3K9.consensus_peaks.antibody.txt

cat <<-END_VERSIONS > versions.yml
"NFCORE_CHIPSEQ:CHIPSEQ:MACS2_CONSENSUS":
python: $(python --version | sed 's/Python //g')
r-base: $(echo $(R --version 2>&1) | sed 's/^.R version //; s/ .$//')
END_VERSIONS

Command exit status:
1

Command output:
(empty)

Command error:
Error: package or namespace load failed for ‘UpSetR’ in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]):
namespace ‘scales’ 1.1.1 is being loaded, but >= 1.2.0 is required
Execution halted

Work dir:
/shared/ifbstor1/projects/project_nbouche/frim7_ChIP_CONTR/work/d0/c9bf0fd655e9a11bbae24e711026ab

Tip: view the complete command output by changing to the process work dir and entering the command cat .command.out

[Jose Espinosa-Carrasco]

I think that it could be that you have a local version of the R package installed in your environment which overwrites the one in the image (which actually meets the requirements since is 1.14). If this is the case, maybe it will be worth to remove the local version of the UpSetR package.