############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.14-bioc/R/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. 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 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 ... 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 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' 3: 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