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This page was generated on 2023-04-12 11:05:02 -0400 (Wed, 12 Apr 2023).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.5 LTS)x86_644.2.3 (2023-03-15) -- "Shortstop Beagle" 4502
palomino4Windows Server 2022 Datacenterx644.2.3 (2023-03-15 ucrt) -- "Shortstop Beagle" 4282
lconwaymacOS 12.5.1 Montereyx86_644.2.3 (2023-03-15) -- "Shortstop Beagle" 4310
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

BUILD results for dasper on nebbiolo2


To the developers/maintainers of the dasper package:
- Please 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 How and When does the builder pull? When will my changes propagate? for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 478/2183HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
dasper 1.8.0  (landing page)
David Zhang
Snapshot Date: 2023-04-10 14:00:05 -0400 (Mon, 10 Apr 2023)
git_url: https://git.bioconductor.org/packages/dasper
git_branch: RELEASE_3_16
git_last_commit: 0bb89af
git_last_commit_date: 2022-11-01 11:23:22 -0400 (Tue, 01 Nov 2022)
nebbiolo2Linux (Ubuntu 20.04.5 LTS) / x86_64  OK    ERROR  skipped
palomino4Windows Server 2022 Datacenter / x64  OK    ERROR  skippedskipped
lconwaymacOS 12.5.1 Monterey / x86_64  OK    ERROR  skippedskipped

Summary

Package: dasper
Version: 1.8.0
Command: /home/biocbuild/bbs-3.16-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data dasper
StartedAt: 2023-04-10 16:31:30 -0400 (Mon, 10 Apr 2023)
EndedAt: 2023-04-10 16:33:29 -0400 (Mon, 10 Apr 2023)
EllapsedTime: 119.4 seconds
RetCode: 1
Status:   ERROR  
PackageFile: None
PackageFileSize: NA

Command output

##############################################################################
##############################################################################
###
### 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