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### Running command:
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### chmod a+r progeny -R && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD build --keep-empty-dirs --no-resave-data progeny
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* checking for file 'progeny/DESCRIPTION' ... OK
* preparing 'progeny':
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building 'ProgenySingleCell.Rmd' using rmarkdown
Attaching package: 'dplyr'
The following objects are masked from 'package:stats':
filter, lag
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intersect, setdiff, setequal, union
Attaching SeuratObject
Performing log-normalization
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Performing log-normalization
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Calculating gene variances
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Calculating feature variances of standardized and clipped values
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Centering and scaling data matrix
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Quitting from lines 148-153 (ProgenySingleCell.Rmd)
Error: processing vignette 'ProgenySingleCell.Rmd' failed with diagnostics:
invalid class "Graph" object: superclass "Mnumeric" not defined in the environment of the object's class
--- failed re-building 'ProgenySingleCell.Rmd'
--- re-building 'progenyBulk.Rmd' using rmarkdown
Loading required package: SummarizedExperiment
Loading required package: MatrixGenerics
Loading required package: matrixStats
Attaching package: 'matrixStats'
The following object is masked from 'package:dplyr':
count
Attaching package: 'MatrixGenerics'
The following objects are masked from 'package:matrixStats':
colAlls, colAnyNAs, colAnys, colAvgsPerRowSet, colCollapse,
colCounts, colCummaxs, colCummins, colCumprods, colCumsums,
colDiffs, colIQRDiffs, colIQRs, colLogSumExps, colMadDiffs,
colMads, colMaxs, colMeans2, colMedians, colMins, colOrderStats,
colProds, colQuantiles, colRanges, colRanks, colSdDiffs, colSds,
colSums2, colTabulates, colVarDiffs, colVars, colWeightedMads,
colWeightedMeans, colWeightedMedians, colWeightedSds,
colWeightedVars, rowAlls, rowAnyNAs, rowAnys, rowAvgsPerColSet,
rowCollapse, rowCounts, rowCummaxs, rowCummins, rowCumprods,
rowCumsums, rowDiffs, rowIQRDiffs, rowIQRs, rowLogSumExps,
rowMadDiffs, rowMads, rowMaxs, rowMeans2, rowMedians, rowMins,
rowOrderStats, rowProds, rowQuantiles, rowRanges, rowRanks,
rowSdDiffs, rowSds, rowSums2, rowTabulates, rowVarDiffs, rowVars,
rowWeightedMads, rowWeightedMeans, rowWeightedMedians,
rowWeightedSds, rowWeightedVars
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:dplyr':
combine, intersect, setdiff, union
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.max, which.min
Loading required package: S4Vectors
Attaching package: 'S4Vectors'
The following object is masked from 'package:tidyr':
expand
The following objects are masked from 'package:dplyr':
first, rename
The following object is masked from 'package:base':
expand.grid
Loading required package: IRanges
Attaching package: 'IRanges'
The following objects are masked from 'package:dplyr':
collapse, desc, slice
The following object is masked from 'package:grDevices':
windows
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")'.
Attaching package: 'Biobase'
The following object is masked from 'package:MatrixGenerics':
rowMedians
The following objects are masked from 'package:matrixStats':
anyMissing, rowMedians
Attaching package: 'SummarizedExperiment'
The following object is masked from 'package:SeuratObject':
Assays
The following object is masked from 'package:Seurat':
Assays
gene-wise dispersion estimates
mean-dispersion relationship
final dispersion estimates
Registered S3 method overwritten by 'cli':
method from
print.boxx spatstat.geom
Loading required package: dbplyr
Attaching package: 'dbplyr'
The following objects are masked from 'package:dplyr':
ident, sql
adding rname 'http://www.cancerrxgene.org/gdsc1000/GDSC1000_WebResources/Data/suppData/TableS4A.xlsx'
adding rname 'http://www.cancerrxgene.org/gdsc1000/GDSC1000_WebResources/Data/preprocessed/Cell_line_RMA_proc_basalExp.txt.zip'
New names:
* `` -> ...1
* `` -> ...2
* `BMS-708163` -> `BMS-708163...15`
* UNC0638 -> UNC0638...70
* UNC0638 -> UNC0638...71
* ...
-- Column specification --------------------------------------------------------
cols(
.default = col_double(),
GENE_SYMBOLS = col_character(),
GENE_title = col_character()
)
i Use `spec()` for the full column specifications.
--- finished re-building 'progenyBulk.Rmd'
SUMMARY: processing the following file failed:
'ProgenySingleCell.Rmd'
Error: Vignette re-building failed.
Execution halted