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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 schex
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* checking for file ‘schex/DESCRIPTION’ ... OK
* preparing ‘schex’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘Seurat_schex.Rmd’ using rmarkdown
Loading required package: SingleCellExperiment
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
Loading required package: Seurat
Attaching SeuratObject
Attaching sp
Attaching package: 'Seurat'
The following object is masked from 'package:SummarizedExperiment':
Assays
Loading required package: shiny
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
Warning: The default method for RunUMAP has changed from calling Python UMAP via reticulate to the R-native UWOT using the cosine metric
To use Python UMAP via reticulate, set umap.method to 'umap-learn' and metric to 'correlation'
This message will be shown once per session
Warning: The vignette title specified in \VignetteIndexEntry{} is different from the title in the YAML metadata. The former is "Seurat_schex", and the latter is "Using schex with Seurat". If that is intentional, you may set options(rmarkdown.html_vignette.check_title = FALSE) to suppress this check.
--- finished re-building ‘Seurat_schex.Rmd’
--- re-building ‘multi_modal_schex.Rmd’ using rmarkdown
Warning: The vignette title specified in \VignetteIndexEntry{} is different from the title in the YAML metadata. The former is "multi_modal_schex", and the latter is "Exploring multi-modal single cell data with schex". If that is intentional, you may set options(rmarkdown.html_vignette.check_title = FALSE) to suppress this check.
--- finished re-building ‘multi_modal_schex.Rmd’
--- re-building ‘picking_the_right_resolution.Rmd’ using rmarkdown
Warning: The vignette title specified in \VignetteIndexEntry{} is different from the title in the YAML metadata. The former is "picking_the_right_resolution", and the latter is "Picking the right resolution". If that is intentional, you may set options(rmarkdown.html_vignette.check_title = FALSE) to suppress this check.
--- finished re-building ‘picking_the_right_resolution.Rmd’
--- re-building ‘shiny_schex.Rmd’ using rmarkdown
Warning: The vignette title specified in \VignetteIndexEntry{} is different from the title in the YAML metadata. The former is "shiny_schhex", and the latter is "Communicating results with schex and shinydashboard or iSEE". If that is intentional, you may set options(rmarkdown.html_vignette.check_title = FALSE) to suppress this check.
--- finished re-building ‘shiny_schex.Rmd’
--- re-building ‘using_schex.Rmd’ using rmarkdown
Attaching package: 'igraph'
The following objects are masked from 'package:dplyr':
as_data_frame, groups, union
The following object is masked from 'package:GenomicRanges':
union
The following object is masked from 'package:IRanges':
union
The following object is masked from 'package:S4Vectors':
union
The following objects are masked from 'package:BiocGenerics':
normalize, path, union
The following objects are masked from 'package:stats':
decompose, spectrum
The following object is masked from 'package:base':
union
Loading required package: HDF5Array
Loading required package: DelayedArray
Loading required package: Matrix
Attaching package: 'Matrix'
The following object is masked from 'package:S4Vectors':
expand
Attaching package: 'DelayedArray'
The following object is masked from 'package:igraph':
simplify
The following objects are masked from 'package:base':
aperm, apply, rowsum, scale, sweep
Loading required package: rhdf5
Attaching package: 'HDF5Array'
The following object is masked from 'package:rhdf5':
h5ls
Quitting from lines 35-41 (using_schex.Rmd)
Error: processing vignette 'using_schex.Rmd' failed with diagnostics:
there is no package called 'scater'
--- failed re-building ‘using_schex.Rmd’
SUMMARY: processing the following file failed:
‘using_schex.Rmd’
Error: Vignette re-building failed.
Execution halted
