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This page was generated on 2023-04-19 11:01:54 -0400 (Wed, 19 Apr 2023).

HostnameOSArch (*)R versionInstalled pkgs
kjohnsonmacOS 13.0 Venturaarm644.2.2 (2022-10-31) -- "Innocent and Trusting" 4256
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BUILD results for dasper on kjohnson


To the developers/maintainers of the dasper package:
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 / ArchINSTALLBUILDBUILD BIN
dasper 1.8.0  (landing page)
David Zhang
Snapshot Date: 2023-04-12 13:00:02 -0400 (Wed, 12 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)
kjohnsonmacOS 13.0 Ventura / arm64  OK    ERROR  skipped

Summary

Package: dasper
Version: 1.8.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data dasper
StartedAt: 2023-04-17 02:40:25 -0400 (Mon, 17 Apr 2023)
EndedAt: 2023-04-17 02:44:21 -0400 (Mon, 17 Apr 2023)
EllapsedTime: 235.1 seconds
RetCode: 1
Status:   ERROR  
PackageFile: None
PackageFileSize: NA

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/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 /Users/biocbuild/Library/Caches/org.R-project.R/R/BiocFileCache/17d2039c1e1ef_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 /Users/biocbuild/Library/Caches/org.R-project.R/R/BiocFileCache/17d2039c1e1ef_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 /Users/biocbuild/Library/Caches/org.R-project.R/R/BiocFileCache/17d2039c1e1ef_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 /Users/biocbuild/Library/Caches/org.R-project.R/R/BiocFileCache/17d2039c1e1ef_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 /Users/biocbuild/Library/Caches/org.R-project.R/R/BiocFileCache/17d2039c1e1ef_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 /Users/biocbuild/Library/Caches/org.R-project.R/R/BiocFileCache/17d2039c1e1ef_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 /Users/biocbuild/Library/Caches/org.R-project.R/R/BiocFileCache/17d2039c1e1ef_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 /Users/biocbuild/Library/Caches/org.R-project.R/R/BiocFileCache/17d2039c1e1ef_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 /Users/biocbuild/Library/Caches/org.R-project.R/R/BiocFileCache/17d2039c1e1ef_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 /Users/biocbuild/Library/Caches/org.R-project.R/R/BiocFileCache/17d2039c1e1ef_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 /Users/biocbuild/Library/Caches/org.R-project.R/R/BiocFileCache/17d2039c1e1ef_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 /Users/biocbuild/Library/Caches/org.R-project.R/R/BiocFileCache/17d2039c1e1ef_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 /Users/biocbuild/Library/Caches/org.R-project.R/R/BiocFileCache/17d2039c1e1ef_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 /Users/biocbuild/Library/Caches/org.R-project.R/R/BiocFileCache/17d2039c1e1ef_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 /Users/biocbuild/Library/Caches/org.R-project.R/R/BiocFileCache/17d2039c1e1ef_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 /Users/biocbuild/Library/Caches/org.R-project.R/R/BiocFileCache/17d2039c1e1ef_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 /Users/biocbuild/Library/Caches/org.R-project.R/R/BiocFileCache/17d2039c1e1ef_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 /Users/biocbuild/Library/Caches/org.R-project.R/R/BiocFileCache/17d2039c1e1ef_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 /Users/biocbuild/Library/Caches/org.R-project.R/R/BiocFileCache/17d2039c1e1ef_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 /Users/biocbuild/Library/Caches/org.R-project.R/R/BiocFileCache/17d2039c1e1ef_SRR660824_SRS389722_SRX222703_male_lung.bw
Collecting package metadata (current_repodata.json): ...working... done
Solving environment: ...working... failed with repodata from current_repodata.json, will retry with next repodata source.
Collecting package metadata (repodata.json): ...working... done
Solving environment: ...working... done

## Package Plan ##

  environment location: /Users/biocbuild/Library/Caches/org.R-project.R/R/basilisk/1.10.2/dasper/1.8.0/env_sklearn

  added / updated specs:
    - python=3.8.13


The following NEW packages will be INSTALLED:

  bzip2              conda-forge/osx-arm64::bzip2-1.0.8-h3422bc3_4
  ca-certificates    conda-forge/osx-arm64::ca-certificates-2022.12.7-h4653dfc_0
  libffi             conda-forge/osx-arm64::libffi-3.4.2-h3422bc3_5
  libsqlite          conda-forge/osx-arm64::libsqlite-3.40.0-h76d750c_0
  libzlib            conda-forge/osx-arm64::libzlib-1.2.13-h03a7124_4
  ncurses            conda-forge/osx-arm64::ncurses-6.3-h07bb92c_1
  openssl            conda-forge/osx-arm64::openssl-3.1.0-h03a7124_0
  pip                conda-forge/noarch::pip-23.1-pyhd8ed1ab_0
  python             conda-forge/osx-arm64::python-3.8.13-hd3575e6_0_cpython
  readline           conda-forge/osx-arm64::readline-8.2-h92ec313_1
  setuptools         conda-forge/noarch::setuptools-67.6.1-pyhd8ed1ab_0
  sqlite             conda-forge/osx-arm64::sqlite-3.40.0-h2229b38_0
  tk                 conda-forge/osx-arm64::tk-8.6.12-he1e0b03_0
  wheel              conda-forge/noarch::wheel-0.40.0-pyhd8ed1ab_0
  xz                 conda-forge/osx-arm64::xz-5.2.6-h57fd34a_0


Preparing transaction: ...working... done
Verifying transaction: ...working... done
Executing transaction: ...working... done
Collecting package metadata (current_repodata.json): ...working... done
Solving environment: ...working... done

## Package Plan ##

  environment location: /Users/biocbuild/Library/Caches/org.R-project.R/R/basilisk/1.10.2/dasper/1.8.0/env_sklearn

  added / updated specs:
    - python=3.8.13


The following packages will be UPDATED:

  ca-certificates    conda-forge::ca-certificates-2022.12.~ --> pkgs/main::ca-certificates-2023.01.10-hca03da5_0


Preparing transaction: ...working... done
Verifying transaction: ...working... done
Executing transaction: ...working... done


==> WARNING: A newer version of conda exists. <==
  current version: 4.12.0
  latest version: 23.3.1

Please update conda by running

    $ conda update -n base -c defaults conda


Collecting package metadata (current_repodata.json): ...working... done
Solving environment: ...working... failed with initial frozen solve. Retrying with flexible solve.
Collecting package metadata (repodata.json): ...working... done
Solving environment: ...working... failed with initial frozen solve. Retrying with flexible solve.

PackagesNotFoundError: The following packages are not available from current channels:

  - pandas=0.25.3

Current channels:

  - https://conda.anaconda.org/conda-forge/osx-arm64
  - https://conda.anaconda.org/conda-forge/noarch
  - https://repo.anaconda.com/pkgs/main/osx-arm64
  - https://repo.anaconda.com/pkgs/main/noarch
  - https://repo.anaconda.com/pkgs/r/osx-arm64
  - https://repo.anaconda.com/pkgs/r/noarch

To search for alternate channels that may provide the conda package you're
looking for, navigate to

    https://anaconda.org

and use the search bar at the top of the page.


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: one or more Python packages failed to install [error code 1]

--- failed re-building ‘dasper.Rmd’

SUMMARY: processing the following file failed:
  ‘dasper.Rmd’

Error: Vignette re-building failed.
Execution halted