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### Running command:
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### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data scGPS
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* checking for file ‘scGPS/DESCRIPTION’ ... OK
* preparing ‘scGPS’:
* checking DESCRIPTION meta-information ... OK
* cleaning src
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘vignette.Rmd’ using rmarkdown
Loading required package: SummarizedExperiment
Loading required package: GenomicRanges
Loading required package: stats4
Loading required package: BiocGenerics
Loading required package: parallel
Attaching package: 'BiocGenerics'
The following objects are masked from 'package:parallel':
clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
clusterExport, clusterMap, parApply, parCapply, parLapply,
parLapplyLB, parRapply, parSapply, parSapplyLB
The following objects are masked from 'package:stats':
IQR, mad, sd, var, xtabs
The following objects are masked from 'package:base':
Filter, Find, Map, Position, Reduce, anyDuplicated, append,
as.data.frame, basename, cbind, colnames, dirname, do.call,
duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
tapply, union, unique, unsplit, which, which.max, which.min
Loading required package: S4Vectors
Attaching package: 'S4Vectors'
The following object is masked from 'package:base':
expand.grid
Loading required package: IRanges
Loading required package: GenomeInfoDb
Loading required package: Biobase
Welcome to Bioconductor
Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.
Loading required package: DelayedArray
Loading required package: matrixStats
Attaching package: 'matrixStats'
The following objects are masked from 'package:Biobase':
anyMissing, rowMedians
Loading required package: BiocParallel
Attaching package: 'DelayedArray'
The following objects are masked from 'package:matrixStats':
colMaxs, colMins, colRanges, rowMaxs, rowMins, rowRanges
The following objects are masked from 'package:base':
aperm, apply, rowsum
Loading required package: dynamicTreeCut
Loading required package: SingleCellExperiment
Warning in lda.default(x, grouping, ...) : variables are collinear
Warning in lda.default(x, grouping, ...) : variables are collinear
Warning in lda.default(x, grouping, ...) : variables are collinear
Warning in lda.default(x, grouping, ...) : variables are collinear
Warning in lda.default(x, grouping, ...) : variables are collinear
Warning in lda.default(x, grouping, ...) : variables are collinear
Warning in lda.default(x, grouping, ...) : variables are collinear
Warning in lda.default(x, grouping, ...) : variables are collinear
Warning in lda.default(x, grouping, ...) : variables are collinear
Warning in lda.default(x, grouping, ...) : variables are collinear
Warning in lda.default(x, grouping, ...) : variables are collinear
Warning in lda.default(x, grouping, ...) : variables are collinear
Warning in lda.default(x, grouping, ...) : variables are collinear
Warning in lda.default(x, grouping, ...) : variables are collinear
Warning in lda.default(x, grouping, ...) : variables are collinear
Warning in lda.default(x, grouping, ...) : variables are collinear
Warning in lda.default(x, grouping, ...) : variables are collinear
Warning in lda.default(x, grouping, ...) : variables are collinear
Warning in lda.default(x, grouping, ...) : variables are collinear
Warning in lda.default(x, grouping, ...) : variables are collinear
Warning in lda.default(x, grouping, ...) : variables are collinear
Warning in lda.default(x, grouping, ...) : variables are collinear
Warning in lda.default(x, grouping, ...) : variables are collinear
Warning in lda.default(x, grouping, ...) : variables are collinear
Warning in lda.default(x, grouping, ...) : variables are collinear
Warning in lda.default(x, grouping, ...) : variables are collinear
Warning in lda.default(x, grouping, ...) : variables are collinear
Warning in lda.default(x, grouping, ...) : variables are collinear
Warning in lda.default(x, grouping, ...) : variables are collinear
Warning in lda.default(x, grouping, ...) : variables are collinear
Warning in lda.default(x, grouping, ...) : variables are collinear
done training for bootstrap 1, moving to prediction...
Warning in lda.default(x, grouping, ...) : variables are collinear
Warning in lda.default(x, grouping, ...) : variables are collinear
Warning in lda.default(x, grouping, ...) : variables are collinear
Warning in lda.default(x, grouping, ...) : variables are collinear
Warning in lda.default(x, grouping, ...) : variables are collinear
Warning in lda.default(x, grouping, ...) : variables are collinear
Warning in lda.default(x, grouping, ...) : variables are collinear
Warning in lda.default(x, grouping, ...) : variables are collinear
Warning in lda.default(x, grouping, ...) : variables are collinear
Warning in lda.default(x, grouping, ...) : variables are collinear
Warning in lda.default(x, grouping, ...) : variables are collinear
Warning in lda.default(x, grouping, ...) : variables are collinear
Warning in lda.default(x, grouping, ...) : variables are collinear
Warning in lda.default(x, grouping, ...) : variables are collinear
Warning in lda.default(x, grouping, ...) : variables are collinear
Warning in lda.default(x, grouping, ...) : variables are collinear
Warning in lda.default(x, grouping, ...) : variables are collinear
Warning in lda.default(x, grouping, ...) : variables are collinear
Warning in lda.default(x, grouping, ...) : variables are collinear
Warning in lda.default(x, grouping, ...) : variables are collinear
Warning in lda.default(x, grouping, ...) : variables are collinear
Warning in lda.default(x, grouping, ...) : variables are collinear
Warning in lda.default(x, grouping, ...) : variables are collinear
Warning in lda.default(x, grouping, ...) : variables are collinear
Warning in lda.default(x, grouping, ...) : variables are collinear
Warning in lda.default(x, grouping, ...) : variables are collinear
Warning in lda.default(x, grouping, ...) : variables are collinear
Warning in lda.default(x, grouping, ...) : variables are collinear
Warning in lda.default(x, grouping, ...) : variables are collinear
Warning in lda.default(x, grouping, ...) : variables are collinear
Warning in lda.default(x, grouping, ...) : variables are collinear
done training for bootstrap 2, moving to prediction...
Warning in lda.default(x, grouping, ...) : variables are collinear
Warning in lda.default(x, grouping, ...) : variables are collinear
Warning in lda.default(x, grouping, ...) : variables are collinear
Warning in lda.default(x, grouping, ...) : variables are collinear
Warning in lda.default(x, grouping, ...) : variables are collinear
Warning in lda.default(x, grouping, ...) : variables are collinear
Warning in lda.default(x, grouping, ...) : variables are collinear
Warning in lda.default(x, grouping, ...) : variables are collinear
Warning in lda.default(x, grouping, ...) : variables are collinear
Warning in lda.default(x, grouping, ...) : variables are collinear
Warning in lda.default(x, grouping, ...) : variables are collinear
Warning in lda.default(x, grouping, ...) : variables are collinear
Warning in lda.default(x, grouping, ...) : variables are collinear
Warning in lda.default(x, grouping, ...) : variables are collinear
Warning in lda.default(x, grouping, ...) : variables are collinear
Warning in lda.default(x, grouping, ...) : variables are collinear
Warning in lda.default(x, grouping, ...) : variables are collinear
Warning in lda.default(x, grouping, ...) : variables are collinear
Warning in lda.default(x, grouping, ...) : variables are collinear
Warning in lda.default(x, grouping, ...) : variables are collinear
Warning in lda.default(x, grouping, ...) : variables are collinear
Warning in lda.default(x, grouping, ...) : variables are collinear
Warning in lda.default(x, grouping, ...) : variables are collinear
Warning in lda.default(x, grouping, ...) : variables are collinear
Warning in lda.default(x, grouping, ...) : variables are collinear
Warning in lda.default(x, grouping, ...) : variables are collinear
Warning in lda.default(x, grouping, ...) : variables are collinear
Warning in lda.default(x, grouping, ...) : variables are collinear
Warning in lda.default(x, grouping, ...) : variables are collinear
Warning in lda.default(x, grouping, ...) : variables are collinear
Warning in lda.default(x, grouping, ...) : variables are collinear
done training for bootstrap 3, moving to prediction...
Warning in FUN(newX[, i], ...) : NAs introduced by coercion
Performing 1 round of filtering
Identifying top variable genes
Calculating distance matrix
Performing hierarchical clustering
Finding clustering information
No more outliers detected in filtering round 1
Identifying top variable genes
Calculating distance matrix
Performing hierarchical clustering
Finding clustering information
Done clustering, moving to stability calculation...
Done calculating stability...
Start finding optimal clustering...
Done finding optimal clustering...
Performing 1 round of filtering
Identifying top variable genes
Calculating distance matrix
Performing hierarchical clustering
Finding clustering information
No more outliers detected in filtering round 1
Identifying top variable genes
Calculating distance matrix
Performing hierarchical clustering
Finding clustering information
500 cells left after filtering
Running 20 bagging runs, with 0.8 subsampling...
Done clustering, moving to stability calculation...
Done finding optimal clustering
Quitting from lines 204-208 (vignette.Rmd)
Error: processing vignette 'vignette.Rmd' failed with diagnostics:
Unknown colour name: 1
--- failed re-building ‘vignette.Rmd’
SUMMARY: processing the following file failed:
‘vignette.Rmd’
Error: Vignette re-building failed.
Execution halted