############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.16-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data dasper ### ############################################################################## ############################################################################## * checking for file ‘dasper/DESCRIPTION’ ... OK * preparing ‘dasper’: * checking DESCRIPTION meta-information ... OK * installing the package to build vignettes * creating vignettes ... ERROR --- re-building ‘dasper.Rmd’ using rmarkdown unsorted interval: chr21 26021921 26022042 , falling back to slower matching (doesn't affect BAM processing) For potentially faster BigWig reading performance, please sort your argument to --annotations (BED) file via sort -k1,1 -k2,2n and re-run megadepth. building whole annotation region map done 2 chromosomes for annotated regions read 1 chromosomes for annotated regions read, collapsed total number of annotations in collapsed: 84 Processing /home/biocbuild/.cache/R/BiocFileCache/35dafa364cd476_SRR660824_SRS389722_SRX222703_male_lung.bw unsorted interval: chr21 26021921 26022042 , falling back to slower matching (doesn't affect BAM processing) For potentially faster BigWig reading performance, please sort your argument to --annotations (BED) file via sort -k1,1 -k2,2n and re-run megadepth. building whole annotation region map done 2 chromosomes for annotated regions read 1 chromosomes for annotated regions read, collapsed total number of annotations in collapsed: 84 Processing /home/biocbuild/.cache/R/BiocFileCache/35dafa364cd476_SRR660824_SRS389722_SRX222703_male_lung.bw unsorted interval: chr21 6456880 6456950 , falling back to slower matching (doesn't affect BAM processing) For potentially faster BigWig reading performance, please sort your argument to --annotations (BED) file via sort -k1,1 -k2,2n and re-run megadepth. building whole annotation region map done 2 chromosomes for annotated regions read 1 chromosomes for annotated regions read, collapsed total number of annotations in collapsed: 4 Processing /home/biocbuild/.cache/R/BiocFileCache/35dafa364cd476_SRR660824_SRS389722_SRX222703_male_lung.bw unsorted interval: chr21 6456880 6456950 , falling back to slower matching (doesn't affect BAM processing) For potentially faster BigWig reading performance, please sort your argument to --annotations (BED) file via sort -k1,1 -k2,2n and re-run megadepth. building whole annotation region map done 2 chromosomes for annotated regions read 1 chromosomes for annotated regions read, collapsed total number of annotations in collapsed: 4 Processing /home/biocbuild/.cache/R/BiocFileCache/35dafa364cd476_SRR660824_SRS389722_SRX222703_male_lung.bw building whole annotation region map done 2 chromosomes for annotated regions read 2 chromosomes for annotated regions read, collapsed total number of annotations in collapsed: 624 Processing /home/biocbuild/.cache/R/BiocFileCache/35dafa364cd476_SRR660824_SRS389722_SRX222703_male_lung.bw building whole annotation region map done 2 chromosomes for annotated regions read 2 chromosomes for annotated regions read, collapsed total number of annotations in collapsed: 624 Processing /home/biocbuild/.cache/R/BiocFileCache/35dafa364cd476_SRR660824_SRS389722_SRX222703_male_lung.bw unsorted interval: chr21 25880549 26171128 , falling back to slower matching (doesn't affect BAM processing) For potentially faster BigWig reading performance, please sort your argument to --annotations (BED) file via sort -k1,1 -k2,2n and re-run megadepth. building whole annotation region map done 2 chromosomes for annotated regions read 1 chromosomes for annotated regions read, collapsed total number of annotations in collapsed: 22 Processing /home/biocbuild/.cache/R/BiocFileCache/35dafa364cd476_SRR660824_SRS389722_SRX222703_male_lung.bw unsorted interval: chr21 25880549 26171128 , falling back to slower matching (doesn't affect BAM processing) For potentially faster BigWig reading performance, please sort your argument to --annotations (BED) file via sort -k1,1 -k2,2n and re-run megadepth. building whole annotation region map done 2 chromosomes for annotated regions read 1 chromosomes for annotated regions read, collapsed total number of annotations in collapsed: 22 Processing /home/biocbuild/.cache/R/BiocFileCache/35dafa364cd476_SRR660824_SRS389722_SRX222703_male_lung.bw unsorted interval: chr21 26021921 26022042 , falling back to slower matching (doesn't affect BAM processing) For potentially faster BigWig reading performance, please sort your argument to --annotations (BED) file via sort -k1,1 -k2,2n and re-run megadepth. building whole annotation region map done 2 chromosomes for annotated regions read 1 chromosomes for annotated regions read, collapsed total number of annotations in collapsed: 84 Processing /home/biocbuild/.cache/R/BiocFileCache/35dafa364cd476_SRR660824_SRS389722_SRX222703_male_lung.bw unsorted interval: chr21 26021921 26022042 , falling back to slower matching (doesn't affect BAM processing) For potentially faster BigWig reading performance, please sort your argument to --annotations (BED) file via sort -k1,1 -k2,2n and re-run megadepth. building whole annotation region map done 2 chromosomes for annotated regions read 1 chromosomes for annotated regions read, collapsed total number of annotations in collapsed: 84 Processing /home/biocbuild/.cache/R/BiocFileCache/35dafa364cd476_SRR660824_SRS389722_SRX222703_male_lung.bw unsorted interval: chr21 26021921 26022042 , falling back to slower matching (doesn't affect BAM processing) For potentially faster BigWig reading performance, please sort your argument to --annotations (BED) file via sort -k1,1 -k2,2n and re-run megadepth. building whole annotation region map done 2 chromosomes for annotated regions read 1 chromosomes for annotated regions read, collapsed total number of annotations in collapsed: 84 Processing /home/biocbuild/.cache/R/BiocFileCache/35dafa364cd476_SRR660824_SRS389722_SRX222703_male_lung.bw unsorted interval: chr21 6456880 6456950 , falling back to slower matching (doesn't affect BAM processing) For potentially faster BigWig reading performance, please sort your argument to --annotations (BED) file via sort -k1,1 -k2,2n and re-run megadepth. building whole annotation region map done 2 chromosomes for annotated regions read 1 chromosomes for annotated regions read, collapsed total number of annotations in collapsed: 4 Processing /home/biocbuild/.cache/R/BiocFileCache/35dafa364cd476_SRR660824_SRS389722_SRX222703_male_lung.bw unsorted interval: chr21 6456880 6456950 , falling back to slower matching (doesn't affect BAM processing) For potentially faster BigWig reading performance, please sort your argument to --annotations (BED) file via sort -k1,1 -k2,2n and re-run megadepth. building whole annotation region map done 2 chromosomes for annotated regions read 1 chromosomes for annotated regions read, collapsed total number of annotations in collapsed: 4 Processing /home/biocbuild/.cache/R/BiocFileCache/35dafa364cd476_SRR660824_SRS389722_SRX222703_male_lung.bw unsorted interval: chr21 6456880 6456950 , falling back to slower matching (doesn't affect BAM processing) For potentially faster BigWig reading performance, please sort your argument to --annotations (BED) file via sort -k1,1 -k2,2n and re-run megadepth. building whole annotation region map done 2 chromosomes for annotated regions read 1 chromosomes for annotated regions read, collapsed total number of annotations in collapsed: 4 Processing /home/biocbuild/.cache/R/BiocFileCache/35dafa364cd476_SRR660824_SRS389722_SRX222703_male_lung.bw building whole annotation region map done 2 chromosomes for annotated regions read 2 chromosomes for annotated regions read, collapsed total number of annotations in collapsed: 624 Processing /home/biocbuild/.cache/R/BiocFileCache/35dafa364cd476_SRR660824_SRS389722_SRX222703_male_lung.bw building whole annotation region map done 2 chromosomes for annotated regions read 2 chromosomes for annotated regions read, collapsed total number of annotations in collapsed: 624 Processing /home/biocbuild/.cache/R/BiocFileCache/35dafa364cd476_SRR660824_SRS389722_SRX222703_male_lung.bw building whole annotation region map done 2 chromosomes for annotated regions read 2 chromosomes for annotated regions read, collapsed total number of annotations in collapsed: 624 Processing /home/biocbuild/.cache/R/BiocFileCache/35dafa364cd476_SRR660824_SRS389722_SRX222703_male_lung.bw unsorted interval: chr21 25880549 26171128 , falling back to slower matching (doesn't affect BAM processing) For potentially faster BigWig reading performance, please sort your argument to --annotations (BED) file via sort -k1,1 -k2,2n and re-run megadepth. building whole annotation region map done 2 chromosomes for annotated regions read 1 chromosomes for annotated regions read, collapsed total number of annotations in collapsed: 22 Processing /home/biocbuild/.cache/R/BiocFileCache/35dafa364cd476_SRR660824_SRS389722_SRX222703_male_lung.bw unsorted interval: chr21 25880549 26171128 , falling back to slower matching (doesn't affect BAM processing) For potentially faster BigWig reading performance, please sort your argument to --annotations (BED) file via sort -k1,1 -k2,2n and re-run megadepth. building whole annotation region map done 2 chromosomes for annotated regions read 1 chromosomes for annotated regions read, collapsed total number of annotations in collapsed: 22 Processing /home/biocbuild/.cache/R/BiocFileCache/35dafa364cd476_SRR660824_SRS389722_SRX222703_male_lung.bw unsorted interval: chr21 25880549 26171128 , falling back to slower matching (doesn't affect BAM processing) For potentially faster BigWig reading performance, please sort your argument to --annotations (BED) file via sort -k1,1 -k2,2n and re-run megadepth. building whole annotation region map done 2 chromosomes for annotated regions read 1 chromosomes for annotated regions read, collapsed total number of annotations in collapsed: 22 Processing /home/biocbuild/.cache/R/BiocFileCache/35dafa364cd476_SRR660824_SRS389722_SRX222703_male_lung.bw Quitting from lines 284-291 (dasper.Rmd) Error: processing vignette 'dasper.Rmd' failed with diagnostics: BiocParallel errors 1 remote errors, element index: 1 1 unevaluated and other errors first remote error: Error in eval(expr, envir, enclos): ImportError: /usr/lib/x86_64-linux-gnu/libstdc++.so.6: version `GLIBCXX_3.4.30' not found (required by /home/biocbuild/.cache/R/basilisk/1.10.2/dasper/1.8.0/env_sklearn/lib/python3.8/site-packages/scipy/optimize/_highs/_highs_wrapper.cpython-38-x86_64-linux-gnu.so) --- failed re-building ‘dasper.Rmd’ SUMMARY: processing the following file failed: ‘dasper.Rmd’ Error: Vignette re-building failed. Execution halted