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This page was generated on 2022-07-07 11:11:10 -0400 (Thu, 07 Jul 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_644.2.0 Patched (2022-06-02 r82447) -- "Vigorous Calisthenics" 4343
palomino4Windows Server 2022 Datacenterx644.2.0 Patched (2022-06-02 r82447 ucrt) -- "Vigorous Calisthenics" 4148
lconwaymacOS 12.2.1 Montereyx86_644.2.0 Patched (2022-05-29 r82424) -- "Vigorous Calisthenics" 4160
kjohnsonmacOS 12.4 Montereyarm644.2.0 Patched (2022-06-09 r82473) -- "Vigorous Calisthenics" 3115
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 gCrisprTools on kjohnson


To the developers/maintainers of the gCrisprTools package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/gCrisprTools.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 721/2124HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
gCrisprTools 2.3.1  (landing page)
Russell Bainer
Snapshot Date: 2022-07-06 14:00:06 -0400 (Wed, 06 Jul 2022)
git_url: https://git.bioconductor.org/packages/gCrisprTools
git_branch: master
git_last_commit: 2e49f6f
git_last_commit_date: 2022-04-26 14:53:07 -0400 (Tue, 26 Apr 2022)
nebbiolo2Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino4Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.2.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnsonmacOS 12.4 Monterey / arm64  OK    ERROR  skippedskipped

Summary

Package: gCrisprTools
Version: 2.3.1
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data gCrisprTools
StartedAt: 2022-07-06 21:20:56 -0400 (Wed, 06 Jul 2022)
EndedAt: 2022-07-06 21:24:23 -0400 (Wed, 06 Jul 2022)
EllapsedTime: 207.5 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 gCrisprTools
###
##############################################################################
##############################################################################


* checking for file ‘gCrisprTools/DESCRIPTION’ ... OK
* preparing ‘gCrisprTools’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘Contrast_Comparisons.Rmd’ using knitr
1500 targets in common. Omitting others.

Attaching package: 'limma'

The following object is masked from 'package:BiocGenerics':

    plotMA

Permuting 1000 times, this may take a minute ...
Making Rho null distribution for3guides per gene.
Making Rho null distribution for4guides per gene.
Making Rho null distribution for5guides per gene.
Making Rho null distribution for6guides per gene.
Making Rho null distribution for7guides per gene.
Making Rho null distribution for8guides per gene.
Making Rho null distribution for12guides per gene.
Making Rho null distribution for47guides per gene.
Permuting 1000 times, this may take a minute ...
Making Rho null distribution for3guides per gene.
Making Rho null distribution for4guides per gene.
Making Rho null distribution for5guides per gene.
Making Rho null distribution for6guides per gene.
Making Rho null distribution for7guides per gene.
Making Rho null distribution for8guides per gene.
Making Rho null distribution for12guides per gene.
Making Rho null distribution for47guides per gene.
Permuting 1000 times, this may take a minute ...
Making Rho null distribution for3guides per gene.
Making Rho null distribution for4guides per gene.
Making Rho null distribution for5guides per gene.
Making Rho null distribution for6guides per gene.
Making Rho null distribution for7guides per gene.
Making Rho null distribution for8guides per gene.
Making Rho null distribution for12guides per gene.
Making Rho null distribution for47guides per gene.
Permuting 1000 times, this may take a minute ...
Making Rho null distribution for3guides per gene.
Making Rho null distribution for4guides per gene.
Making Rho null distribution for5guides per gene.
Making Rho null distribution for6guides per gene.
Making Rho null distribution for7guides per gene.
Making Rho null distribution for8guides per gene.
Making Rho null distribution for12guides per gene.
Making Rho null distribution for47guides per gene.
Permuting 1000 times, this may take a minute ...
Making Rho null distribution for3guides per gene.
Making Rho null distribution for4guides per gene.
Making Rho null distribution for5guides per gene.
Making Rho null distribution for6guides per gene.
Making Rho null distribution for7guides per gene.
Making Rho null distribution for8guides per gene.
Making Rho null distribution for12guides per gene.
Making Rho null distribution for47guides per gene.
Permuting 1000 times, this may take a minute ...
Making Rho null distribution for3guides per gene.
Making Rho null distribution for4guides per gene.
Making Rho null distribution for5guides per gene.
Making Rho null distribution for6guides per gene.
Making Rho null distribution for7guides per gene.
Making Rho null distribution for8guides per gene.
Making Rho null distribution for12guides per gene.
Making Rho null distribution for47guides per gene.
Quitting from lines 212-228 (Contrast_Comparisons.Rmd) 
Error: processing vignette 'Contrast_Comparisons.Rmd' failed with diagnostics:
there is no package called 'sparrow'
--- failed re-building ‘Contrast_Comparisons.Rmd’

--- re-building ‘Crispr_example_workflow.Rmd’ using knitr
sampleKey must be supplied for plotting normalization effects.
307 elements defined in the annotation file are not present in row names of the specified object. Omitting.
Permuting 1000 times, this may take a minute ...
Making Rho null distribution for3guides per gene.
Making Rho null distribution for4guides per gene.
Making Rho null distribution for5guides per gene.
Making Rho null distribution for6guides per gene.
Making Rho null distribution for7guides per gene.
Making Rho null distribution for8guides per gene.
Making Rho null distribution for10guides per gene.
Making Rho null distribution for11guides per gene.
Making Rho null distribution for12guides per gene.
Making Rho null distribution for47guides per gene.
Permuting 1000 times, this may take a minute ...
Making Rho null distribution for3guides per gene.
Making Rho null distribution for4guides per gene.
Making Rho null distribution for5guides per gene.
Making Rho null distribution for6guides per gene.
Making Rho null distribution for7guides per gene.
Making Rho null distribution for8guides per gene.
Making Rho null distribution for10guides per gene.
Making Rho null distribution for11guides per gene.
Making Rho null distribution for12guides per gene.
Making Rho null distribution for47guides per gene.
Permuting 1000 times, this may take a minute ...
Making Rho null distribution for3guides per gene.
Making Rho null distribution for4guides per gene.
Making Rho null distribution for5guides per gene.
Making Rho null distribution for6guides per gene.
Making Rho null distribution for7guides per gene.
Making Rho null distribution for8guides per gene.
Making Rho null distribution for9guides per gene.
Making Rho null distribution for10guides per gene.
Making Rho null distribution for11guides per gene.
Making Rho null distribution for12guides per gene.
Making Rho null distribution for13guides per gene.
Making Rho null distribution for49guides per gene.
Permuting 1000 times, this may take a minute ...
Making Rho null distribution for3guides per gene.
Making Rho null distribution for4guides per gene.
Making Rho null distribution for5guides per gene.
Making Rho null distribution for6guides per gene.
Making Rho null distribution for7guides per gene.
Making Rho null distribution for8guides per gene.
Making Rho null distribution for9guides per gene.
Making Rho null distribution for10guides per gene.
Making Rho null distribution for11guides per gene.
Making Rho null distribution for12guides per gene.
Making Rho null distribution for13guides per gene.
Making Rho null distribution for49guides per gene.
No control geneSymbol supplied, so I'll use the default of 'NoTarget'.
No control geneSymbol supplied, so I'll use the default of 'NoTarget'.
Normalizing gRNAs by median scaling.
Warning in regularize.values(x, y, ties, missing(ties)) :
  collapsing to unique 'x' values
Warning in regularize.values(x, y, ties, missing(ties)) :
  collapsing to unique 'x' values
Warning in regularize.values(x, y, ties, missing(ties)) :
  collapsing to unique 'x' values
Warning in regularize.values(x, y, ties, missing(ties)) :
  collapsing to unique 'x' values
Warning in regularize.values(x, y, ties, missing(ties)) :
  collapsing to unique 'x' values
Warning in regularize.values(x, y, ties, missing(ties)) :
  collapsing to unique 'x' values
Warning in regularize.values(x, y, ties, missing(ties)) :
  collapsing to unique 'x' values
Warning in regularize.values(x, y, ties, missing(ties)) :
  collapsing to unique 'x' values
Warning in regularize.values(x, y, ties, missing(ties)) :
  collapsing to unique 'x' values
Warning in regularize.values(x, y, ties, missing(ties)) :
  collapsing to unique 'x' values
Warning in regularize.values(x, y, ties, missing(ties)) :
  collapsing to unique 'x' values
Warning in regularize.values(x, y, ties, missing(ties)) :
  collapsing to unique 'x' values
Summarizing gRNA counts into targets.
Summarizing gRNA counts into targets.
Summarizing gRNA counts into targets.
Quitting from lines 225-238 (Crispr_example_workflow.Rmd) 
Error: processing vignette 'Crispr_example_workflow.Rmd' failed with diagnostics:
there is no package called 'sparrow'
--- failed re-building ‘Crispr_example_workflow.Rmd’

--- re-building ‘gCrisprTools_Vignette.Rmd’ using knitr
Permuting 1000 times, this may take a minute ...
Making Rho null distribution for3guides per gene.
Making Rho null distribution for4guides per gene.
Making Rho null distribution for5guides per gene.
Making Rho null distribution for6guides per gene.
Making Rho null distribution for7guides per gene.
Making Rho null distribution for8guides per gene.
Making Rho null distribution for10guides per gene.
Making Rho null distribution for11guides per gene.
Making Rho null distribution for12guides per gene.
Making Rho null distribution for47guides per gene.
Permuting 1000 times, this may take a minute ...
Making Rho null distribution for3guides per gene.
Making Rho null distribution for4guides per gene.
Making Rho null distribution for5guides per gene.
Making Rho null distribution for6guides per gene.
Making Rho null distribution for7guides per gene.
Making Rho null distribution for8guides per gene.
Making Rho null distribution for10guides per gene.
Making Rho null distribution for11guides per gene.
Making Rho null distribution for12guides per gene.
Making Rho null distribution for47guides per gene.
--- finished re-building ‘gCrisprTools_Vignette.Rmd’

SUMMARY: processing the following files failed:
  ‘Contrast_Comparisons.Rmd’ ‘Crispr_example_workflow.Rmd’

Error: Vignette re-building failed.
Execution halted