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This page was generated on 2023-10-16 11:36:03 -0400 (Mon, 16 Oct 2023).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.2 LTS)x86_644.3.1 (2023-06-16) -- "Beagle Scouts" 4626
palomino3Windows Server 2022 Datacenterx644.3.1 (2023-06-16 ucrt) -- "Beagle Scouts" 4379
merida1macOS 12.6.4 Montereyx86_644.3.1 (2023-06-16) -- "Beagle Scouts" 4395
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

Package 496/2230HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
dasper 1.10.0  (landing page)
David Zhang
Snapshot Date: 2023-10-15 14:00:13 -0400 (Sun, 15 Oct 2023)
git_url: https://git.bioconductor.org/packages/dasper
git_branch: RELEASE_3_17
git_last_commit: 3a1d835
git_last_commit_date: 2023-04-25 11:24:39 -0400 (Tue, 25 Apr 2023)
nebbiolo1Linux (Ubuntu 22.04.2 LTS) / x86_64  OK    ERROR  skipped
palomino3Windows Server 2022 Datacenter / x64  OK    ERROR  skippedskipped
merida1macOS 12.6.4 Monterey / x86_64  OK    ERROR  skippedskipped
kjohnson2macOS 12.6.1 Monterey / arm64see weekly results here

BUILD results for dasper on palomino3


To the developers/maintainers of the dasper package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/dasper.git to reflect on this report. See Troubleshooting Build Report for more information.
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results

Summary

Package: dasper
Version: 1.10.0
Command: chmod a+r dasper -R && F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe --arch x64 CMD build --keep-empty-dirs --no-resave-data dasper
StartedAt: 2023-10-15 18:33:52 -0400 (Sun, 15 Oct 2023)
EndedAt: 2023-10-15 18:42:51 -0400 (Sun, 15 Oct 2023)
EllapsedTime: 538.2 seconds
RetCode: 1
Status:   ERROR  
PackageFile: None
PackageFileSize: NA

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   chmod a+r dasper -R && F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe --arch x64 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
building whole annotation region map done
2 chromosomes for annotated regions read
1 chromosomes for annotated regions read, collapsed
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.
total number of annotations in collapsed: 84
Processing C:\Users\biocbuild\AppData\Local/R/cache/R/BiocFileCache/42e41725936_SRR660824_SRS389722_SRX222703_male_lung.bw
building whole annotation region map done
2 chromosomes for annotated regions read
1 chromosomes for annotated regions read, collapsed
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.
total number of annotations in collapsed: 84
Processing C:\Users\biocbuild\AppData\Local/R/cache/R/BiocFileCache/42e41725936_SRR660824_SRS389722_SRX222703_male_lung.bw
building whole annotation region map done
2 chromosomes for annotated regions read
1 chromosomes for annotated regions read, collapsed
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.
total number of annotations in collapsed: 4
Processing C:\Users\biocbuild\AppData\Local/R/cache/R/BiocFileCache/42e41725936_SRR660824_SRS389722_SRX222703_male_lung.bw
building whole annotation region map done
2 chromosomes for annotated regions read
1 chromosomes for annotated regions read, collapsed
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.
total number of annotations in collapsed: 4
Processing C:\Users\biocbuild\AppData\Local/R/cache/R/BiocFileCache/42e41725936_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 C:\Users\biocbuild\AppData\Local/R/cache/R/BiocFileCache/42e41725936_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 C:\Users\biocbuild\AppData\Local/R/cache/R/BiocFileCache/42e41725936_SRR660824_SRS389722_SRX222703_male_lung.bw
building whole annotation region map done
2 chromosomes for annotated regions read
1 chromosomes for annotated regions read, collapsed
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.
total number of annotations in collapsed: 22
Processing C:\Users\biocbuild\AppData\Local/R/cache/R/BiocFileCache/42e41725936_SRR660824_SRS389722_SRX222703_male_lung.bw
building whole annotation region map done
2 chromosomes for annotated regions read
1 chromosomes for annotated regions read, collapsed
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.
total number of annotations in collapsed: 22
Processing C:\Users\biocbuild\AppData\Local/R/cache/R/BiocFileCache/42e41725936_SRR660824_SRS389722_SRX222703_male_lung.bw
building whole annotation region map done
2 chromosomes for annotated regions read
1 chromosomes for annotated regions read, collapsed
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.
total number of annotations in collapsed: 84
Processing C:\Users\biocbuild\AppData\Local/R/cache/R/BiocFileCache/42e41725936_SRR660824_SRS389722_SRX222703_male_lung.bw
building whole annotation region map done
2 chromosomes for annotated regions read
1 chromosomes for annotated regions read, collapsed
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.
total number of annotations in collapsed: 84
Processing C:\Users\biocbuild\AppData\Local/R/cache/R/BiocFileCache/42e41725936_SRR660824_SRS389722_SRX222703_male_lung.bw
building whole annotation region map done
2 chromosomes for annotated regions read
1 chromosomes for annotated regions read, collapsed
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.
total number of annotations in collapsed: 84
Processing C:\Users\biocbuild\AppData\Local/R/cache/R/BiocFileCache/42e41725936_SRR660824_SRS389722_SRX222703_male_lung.bw
building whole annotation region map done
2 chromosomes for annotated regions read
1 chromosomes for annotated regions read, collapsed
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.
total number of annotations in collapsed: 4
Processing C:\Users\biocbuild\AppData\Local/R/cache/R/BiocFileCache/42e41725936_SRR660824_SRS389722_SRX222703_male_lung.bw
building whole annotation region map done
2 chromosomes for annotated regions read
1 chromosomes for annotated regions read, collapsed
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.
total number of annotations in collapsed: 4
Processing C:\Users\biocbuild\AppData\Local/R/cache/R/BiocFileCache/42e41725936_SRR660824_SRS389722_SRX222703_male_lung.bw
building whole annotation region map done
2 chromosomes for annotated regions read
1 chromosomes for annotated regions read, collapsed
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.
total number of annotations in collapsed: 4
Processing C:\Users\biocbuild\AppData\Local/R/cache/R/BiocFileCache/42e41725936_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 C:\Users\biocbuild\AppData\Local/R/cache/R/BiocFileCache/42e41725936_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 C:\Users\biocbuild\AppData\Local/R/cache/R/BiocFileCache/42e41725936_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 C:\Users\biocbuild\AppData\Local/R/cache/R/BiocFileCache/42e41725936_SRR660824_SRS389722_SRX222703_male_lung.bw
building whole annotation region map done
2 chromosomes for annotated regions read
1 chromosomes for annotated regions read, collapsed
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.
total number of annotations in collapsed: 22
Processing C:\Users\biocbuild\AppData\Local/R/cache/R/BiocFileCache/42e41725936_SRR660824_SRS389722_SRX222703_male_lung.bw
building whole annotation region map done
2 chromosomes for annotated regions read
1 chromosomes for annotated regions read, collapsed
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.
total number of annotations in collapsed: 22
Processing C:\Users\biocbuild\AppData\Local/R/cache/R/BiocFileCache/42e41725936_SRR660824_SRS389722_SRX222703_male_lung.bw
building whole annotation region map done
2 chromosomes for annotated regions read
1 chromosomes for annotated regions read, collapsed
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.
total number of annotations in collapsed: 22
Processing C:\Users\biocbuild\AppData\Local/R/cache/R/BiocFileCache/42e41725936_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