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This page was generated on 2022-01-17 13:06:17 -0500 (Mon, 17 Jan 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_644.1.2 (2021-11-01) -- "Bird Hippie" 4328
tokay2Windows Server 2012 R2 Standardx644.1.2 (2021-11-01) -- "Bird Hippie" 4077
machv2macOS 10.14.6 Mojavex86_644.1.2 (2021-11-01) -- "Bird Hippie" 4138
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 tokay2


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? here 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 704/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
gCrisprTools 2.0.0  (landing page)
Russell Bainer
Snapshot Date: 2022-01-16 01:55:05 -0500 (Sun, 16 Jan 2022)
git_url: https://git.bioconductor.org/packages/gCrisprTools
git_branch: RELEASE_3_14
git_last_commit: 4783d8f
git_last_commit_date: 2021-10-26 12:29:53 -0500 (Tue, 26 Oct 2021)
nebbiolo2Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    ERROR  skipped
tokay2Windows Server 2012 R2 Standard / x64  OK    ERROR  skippedskipped
machv2macOS 10.14.6 Mojave / x86_64  OK    ERROR  skippedskipped

Summary

Package: gCrisprTools
Version: 2.0.0
Command: chmod a+r gCrisprTools -R && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD build --keep-empty-dirs --no-resave-data gCrisprTools
StartedAt: 2022-01-16 10:56:34 -0500 (Sun, 16 Jan 2022)
EndedAt: 2022-01-16 11:00:35 -0500 (Sun, 16 Jan 2022)
EllapsedTime: 240.7 seconds
RetCode: 1
Status:   ERROR  
PackageFile: None
PackageFileSize: NA

Command output

##############################################################################
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###
### Running command:
###
###   chmod a+r gCrisprTools -R && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe 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.
GeneSetDb feature_ids coded as geneIDs.
Depending on the composition of your library, you might consider switching to a target-level analysis; see ?ct.GREATdb() for details.
Removed genes absent from the provided GeneSetDb.
Warning in fn(gsd, x, design, contrast, logFC = logFC, use.treat = use.treat,  :
  logical column to identify enriched genes not found: selectedsetting `significant` column manually
Warning in ora(logFC, gsd, selected = selected, groups = groups, feature.bias = feature.bias,  :
  Only 0 / 1features found in 'dat'

Quitting from lines 212-228 (Contrast_Comparisons.Rmd) 
Error: processing vignette 'Contrast_Comparisons.Rmd' failed with diagnostics:
attempt to set an attribute on NULL
--- 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.
GeneSetDb feature_ids coded as geneIDs.
Depending on the composition of your library, you might consider switching to a target-level analysis; see ?ct.GREATdb() for details.
Removed genes absent from the provided GeneSetDb.
Quitting from lines 225-238 (Crispr_example_workflow.Rmd) 
Warning in sparrow::seas(x = ipt, gsd = gdb, methods = c("ora", "fgsea"),  :
  An error in `seas` stopped it from finishing ...
Warning messages:
1: In fn(gsd, x, design, contrast, logFC = logFC, use.treat = use.treat,  :
  logical column to identify enriched genes not found: selectedsetting `significant` column manually
2: In ora(logFC, gsd, selected = selected, groups = groups, feature.bias = feature.bias,  :
  Only 0 / 1features found in 'dat'
Error: processing vignette 'Crispr_example_workflow.Rmd' failed with diagnostics:
attempt to set an attribute on NULL
--- 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.
In addition: Warning message:
In sparrow::seas(x = ipt, gsd = gdb, methods = c("ora", "fgsea"),  :
  The following GSEA methods failed and are removed from the downstream result: ora,fgsea

Execution halted