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BUILD report for schex on celaya2

This page was generated on 2020-01-16 13:55:45 -0500 (Thu, 16 Jan 2020).

Package 1529/1818HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
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 

Summary

Package: schex
Version: 1.1.1
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data schex
StartedAt: 2020-01-16 01:01:08 -0500 (Thu, 16 Jan 2020)
EndedAt: 2020-01-16 01:05:27 -0500 (Thu, 16 Jan 2020)
EllapsedTime: 259.5 seconds
RetCode: 1
Status:  ERROR 
PackageFile: None
PackageFileSize: NA

Command output

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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