Back to Multiple platform build/check report for BioC 3.11
ABCDEFGHIJKLMNOPQR[S]TUVWXYZ

BUILD report for SingleR on machv2

This page was generated on 2020-10-17 11:59:38 -0400 (Sat, 17 Oct 2020).

TO THE DEVELOPERS/MAINTAINERS OF THE SingleR PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 1674/1905HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
SingleR 1.2.4
Aaron Lun
Snapshot Date: 2020-10-16 14:40:19 -0400 (Fri, 16 Oct 2020)
URL: https://git.bioconductor.org/packages/SingleR
Branch: RELEASE_3_11
Last Commit: 4653a3c
Last Changed Date: 2020-05-24 18:13:10 -0400 (Sun, 24 May 2020)
malbec2 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  WARNINGS  NA 
machv2 macOS 10.14.6 Mojave / x86_64  OK [ ERROR ] skipped  skipped 

Summary

Package: SingleR
Version: 1.2.4
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data SingleR
StartedAt: 2020-10-16 21:20:58 -0400 (Fri, 16 Oct 2020)
EndedAt: 2020-10-16 21:23:49 -0400 (Fri, 16 Oct 2020)
EllapsedTime: 171.0 seconds
RetCode: 1
Status:  ERROR 
PackageFile: None
PackageFileSize: NA

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data SingleR
###
##############################################################################
##############################################################################


* checking for file ‘SingleR/DESCRIPTION’ ... OK
* preparing ‘SingleR’:
* checking DESCRIPTION meta-information ... OK
* cleaning src
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘SingleR.Rmd’ using rmarkdown
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


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

snapshotDate(): 2020-04-27
see ?SingleR and browseVignettes('SingleR') for documentation
loading from cache
see ?SingleR and browseVignettes('SingleR') for documentation
loading from cache
Loading required package: SingleCellExperiment
snapshotDate(): 2020-04-27
see ?scRNAseq and browseVignettes('scRNAseq') for documentation
loading from cache
see ?scRNAseq and browseVignettes('scRNAseq') for documentation
loading from cache
Loading required package: ggplot2
snapshotDate(): 2020-04-27
see ?scRNAseq and browseVignettes('scRNAseq') for documentation
loading from cache
see ?scRNAseq and browseVignettes('scRNAseq') for documentation
loading from cache
snapshotDate(): 2020-04-27
see ?scRNAseq and browseVignettes('scRNAseq') for documentation
loading from cache
snapshotDate(): 2020-04-27
see ?SingleR and browseVignettes('SingleR') for documentation
loading from cache
Quitting from lines 253-259 (SingleR.Rmd) 
Error: processing vignette 'SingleR.Rmd' failed with diagnostics:
operation not supported on matrices of type character
--- failed re-building ‘SingleR.Rmd’

SUMMARY: processing the following file failed:
  ‘SingleR.Rmd’

Error: Vignette re-building failed.
Execution halted