############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.17-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/3768704b46bc0b_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/3768704b46bc0b_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/3768704b46bc0b_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/3768704b46bc0b_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/3768704b46bc0b_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/3768704b46bc0b_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/3768704b46bc0b_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/3768704b46bc0b_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/3768704b46bc0b_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/3768704b46bc0b_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/3768704b46bc0b_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/3768704b46bc0b_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/3768704b46bc0b_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/3768704b46bc0b_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/3768704b46bc0b_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/3768704b46bc0b_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/3768704b46bc0b_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/3768704b46bc0b_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/3768704b46bc0b_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/3768704b46bc0b_SRR660824_SRS389722_SRX222703_male_lung.bw Quitting from lines 284-291 [outlier_detect] (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: --- failed re-building ‘dasper.Rmd’ SUMMARY: processing the following file failed: ‘dasper.Rmd’ Error: Vignette re-building failed. Execution halted