useNames = NA is defunct

[gevro]

Hi, DROP 1.3.4 is crashing in the aberrantExpression analysis per below. Can you please advise?

I suspect a bug in DROP's code.

Wed May 29 13:35:57 2024: P-value calculation ...
Wed May 29 13:37:01 2024: Zscore calculation ...
[Wed May 29 13:37:11 2024]
Finished job 298.
148 of 154 steps (96%) done
Select jobs to execute...

[Wed May 29 13:37:12 2024]
rule AberrantExpression_pipeline_OUTRIDER_results_R:
    input: /gpfs/scratch/g01/drop/.drop/helpers/add_HPO_cols.R, /gpfs/scratch/g01/drop/root/processed_results/aberrant_expression/v32/outrider/GTEX100/ods.Rds, /gpfs/scratch/g01/drop/root/processed_data/preprocess/v32/g
ene_name_mapping_v32.tsv, /gpfs/scratch/g01/drop/root/processed_data/aberrant_expression/v32/params/results/GTEX100_resultParams.csv, Scripts/AberrantExpression/pipeline/OUTRIDER/results.R
    output: /gpfs/scratch/g01/drop/root/processed_results/aberrant_expression/v32/outrider/GTEX100/OUTRIDER_results.tsv, /gpfs/scratch/g01/drop/root/processed_results/aberrant_expression/v32/outrider/GTEX100/OUTRIDER_results
_all.Rds
    log: /gpfs/scratch/g01/drop/.drop/tmp/AE/v32/GTEX100/OUTRIDER_results.Rds
    jobid: 300
    wildcards: annotation=v32, dataset=GTEX100
    resources: tmpdir=/tmp

[Wed May 29 13:37:12 2024]
rule AberrantExpression_pipeline_Counting_Summary_R:
    input: /gpfs/scratch/g01/drop/root/processed_results/aberrant_expression/v32/outrider/GTEX100/ods_unfitted.Rds, /gpfs/scratch/g01/drop/root/processed_data/aberrant_expression/bam_stats/GTEX100.tsv, Scripts/AberrantExpres
sion/pipeline/Counting/Summary.R
    output: /gpfs/scratch/g01/drop/htmlOutput/AberrantExpression/Counting/v32/Summary_GTEX100.html
    log: /gpfs/scratch/g01/drop/.drop/tmp/AE/v32/GTEX100/count_summary.Rds
    jobid: 2
    wildcards: annotation=v32, dataset=GTEX100
    resources: tmpdir=/tmp

Loading required package: knitr
Loading required package: rmarkdown
[1] TRUE

processing file: /tmp/RtmpL0BafB/file307ec740880409/Summary.spin.Rmd
1/13                  
2/13 [unnamed-chunk-1]
3/13                  
4/13 [unnamed-chunk-2]
5/13                  
6/13 [unnamed-chunk-3]
Error:
! [matrixStats (>= 1.2.0)] useNames = NA is defunct. Instead, specify either useNames = TRUE or useNames = FALSE. See also ?matrixStats::matrixStats.options
Backtrace:
 1. MatrixGenerics::rowQuantiles(cnts_mtx, probs = quant)
 2. MatrixGenerics::rowQuantiles(cnts_mtx, probs = quant)
 3. matrixStats::rowQuantiles(...)
 4. matrixStats:::deprecatedUseNamesNA()
 5. base::.Defunct(...)

Quitting from lines 114-165 [unnamed-chunk-3] (/tmp/RtmpL0BafB/file307ec740880409/Summary.spin.Rmd)
Execution halted
[Wed May 29 13:37:36 2024]
Error in rule AberrantExpression_pipeline_Counting_Summary_R:
    jobid: 2
    output: /gpfs/scratch/g01/drop/htmlOutput/AberrantExpression/Counting/v32/Summary_GTEX100.html
    log: /gpfs/scratch/g01/drop/.drop/tmp/AE/v32/GTEX100/count_summary.Rds (check log file(s) for error message)

RuleException:
CalledProcessError in line 25 of /tmp/tmpou6it0lx:
Command 'Rscript --vanilla /gpfs/scratch/g01/drop/.snakemake/scripts/tmp_law3jao.wBRender.R' returned non-zero exit status 1.
  File "/tmp/tmpou6it0lx", line 25, in __rule_AberrantExpression_pipeline_Counting_Summary_R
  File "/gpfs/home/g01/ylab/bin/drop-conda/lib/python3.9/concurrent/futures/thread.py", line 52, in run
[Wed May 29 13:37:55 2024]
Finished job 300.
149 of 154 steps (97%) done
Shutting down, this might take some time.
Exiting because a job execution failed. Look above for error message
Complete log: /gpfs/scratch/g01/drop/.snakemake/log/2024-05-26T163909.048116.snakemake.log

[gevro]

In the meantime I will try a new installation using your conda yaml configuration.

[vyepez88]

Hi, consider using 1.4.0 which we released on Wednesday

[vyepez88]

Hi @gevro, was this solved with the new conda yaml installation?

[gevro]

Yes!