This page was generated on 2022-07-07 11:11:58 -0400 (Thu, 07 Jul 2022).
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### Running command:
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### /Library/Frameworks/R.framework/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data scp
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* checking for file ‘scp/DESCRIPTION’ ... OK
* preparing ‘scp’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘QFeatures_nutshell.Rmd’ using rmarkdown
Loading required package: QFeatures
Loading required package: MultiAssayExperiment
Loading required package: SummarizedExperiment
Loading required package: MatrixGenerics
Loading required package: matrixStats
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
Attaching package: 'BiocGenerics'
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 objects are masked from 'package:base':
I, expand.grid, unname
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")'.
Attaching package: 'Biobase'
The following object is masked from 'package:MatrixGenerics':
rowMedians
The following objects are masked from 'package:matrixStats':
anyMissing, rowMedians
Attaching package: 'QFeatures'
The following object is masked from 'package:MultiAssayExperiment':
longFormat
The following object is masked from 'package:base':
sweep
Failed with error: 'there is no package called 'impute''
Quitting from lines 309-312 (QFeatures_nutshell.Rmd)
Error: processing vignette 'QFeatures_nutshell.Rmd' failed with diagnostics:
there is no package called 'impute'
--- failed re-building ‘QFeatures_nutshell.Rmd’
--- re-building ‘advanced.Rmd’ using rmarkdown
--- finished re-building ‘advanced.Rmd’
--- re-building ‘read_scp.Rmd’ using rmarkdown
--- finished re-building ‘read_scp.Rmd’
--- re-building ‘scp.Rmd’ using rmarkdown
Attaching package: 'magrittr'
The following object is masked from 'package:GenomicRanges':
subtract
Attaching package: 'dplyr'
The following object is masked from 'package:Biobase':
combine
The following objects are masked from 'package:GenomicRanges':
intersect, setdiff, union
The following object is masked from 'package:GenomeInfoDb':
intersect
The following objects are masked from 'package:IRanges':
collapse, desc, intersect, setdiff, slice, union
The following objects are masked from 'package:S4Vectors':
first, intersect, rename, setdiff, setequal, union
The following objects are masked from 'package:BiocGenerics':
combine, intersect, setdiff, union
The following object is masked from 'package:matrixStats':
count
The following objects are masked from 'package:stats':
filter, lag
The following objects are masked from 'package:base':
intersect, setdiff, setequal, union
`stat_bin()` using `bins = 30`. Pick better value with `binwidth`.
Warning: Removed 15 rows containing non-finite values (stat_bin).
Aggregated: 1/3
Aggregated: 2/3
Aggregated: 3/3
Warning: 'experiments' dropped; see 'metadata'
Failed with error: 'there is no package called 'impute''
Quitting from lines 812-817 (scp.Rmd)
Error: processing vignette 'scp.Rmd' failed with diagnostics:
there is no package called 'impute'
--- failed re-building ‘scp.Rmd’
SUMMARY: processing the following files failed:
‘QFeatures_nutshell.Rmd’ ‘scp.Rmd’
Error: Vignette re-building failed.
Execution halted