schex 1.1.1
Saskia Freytag
| Snapshot Date: 2020-01-15 16:46:30 -0500 (Wed, 15 Jan 2020) |
| URL: https://git.bioconductor.org/packages/schex |
| Branch: master |
| Last Commit: c55bd41 |
| Last Changed Date: 2020-01-06 12:23:07 -0500 (Mon, 06 Jan 2020) |
| malbec2 | Linux (Ubuntu 18.04.3 LTS) / x86_64 | OK | ERROR | skipped | | |
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | ERROR | skipped | skipped | |
| celaya2 | OS X 10.11.6 El Capitan / x86_64 | OK | [ ERROR ] | skipped | skipped | |
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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 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: 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: Seurat
Attaching package: 'Seurat'
The following object is masked from 'package:SummarizedExperiment':
Assays
Warning: Package 'schex' is deprecated and will be removed from Bioconductor
version 3.12
Attaching package: 'dplyr'
The following object is masked from 'package:matrixStats':
count
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 objects are masked from 'package:stats':
filter, lag
The following objects are masked from 'package:base':
intersect, setdiff, setequal, union
Loading required package: HDF5Array
Loading required package: rhdf5
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
Quitting from lines 154-155 (Seurat_schex.Rmd)
Error: processing vignette 'Seurat_schex.Rmd' failed with diagnostics:
Column cannot be found in slot(sce, 'meta.data').
--- failed re-building ‘Seurat_schex.Rmd’
--- re-building ‘shiny_schex.Rmd’ using rmarkdown
--- finished re-building ‘shiny_schex.Rmd’
--- re-building ‘using_schex.Rmd’ using rmarkdown
Attaching package: 'igraph'
The following object is masked from 'package:HDF5Array':
path
The following object is masked from 'package:scater':
normalize
The following objects are masked from 'package:dplyr':
as_data_frame, groups, union
The following objects are masked from 'package:DelayedArray':
path, simplify
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
Quitting from lines 104-105 (using_schex.Rmd)
Error: processing vignette 'using_schex.Rmd' failed with diagnostics:
'normalize' is defunct.
Use ''normalize,SingleCellExperiment-method' is defunct.
Use 'logNormCounts' instead' instead.
See help("Defunct")
--- failed re-building ‘using_schex.Rmd’
SUMMARY: processing the following files failed:
‘Seurat_schex.Rmd’ ‘using_schex.Rmd’
Error: Vignette re-building failed.
Execution halted