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BUILD report for CATALYST on merida1

This page was generated on 2020-08-07 12:36:21 -0400 (Fri, 07 Aug 2020).

TO THE DEVELOPERS/MAINTAINERS OF THE CATALYST PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 227/1882HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
CATALYST 1.13.1
Helena L. Crowell
Snapshot Date: 2020-08-06 14:50:46 -0400 (Thu, 06 Aug 2020)
URL: https://git.bioconductor.org/packages/CATALYST
Branch: master
Last Commit: 78d76eb
Last Changed Date: 2020-05-06 03:40:47 -0400 (Wed, 06 May 2020)
malbec1 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  ERROR  skipped 
tokay1 Windows Server 2012 R2 Standard / x64  OK  ERROR  skipped  skipped 
merida1 macOS 10.14.6 Mojave / x86_64  OK [ ERROR ] skipped  skipped 

Summary

Package: CATALYST
Version: 1.13.1
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data CATALYST
StartedAt: 2020-08-06 20:30:51 -0400 (Thu, 06 Aug 2020)
EndedAt: 2020-08-06 20:31:53 -0400 (Thu, 06 Aug 2020)
EllapsedTime: 62.5 seconds
RetCode: 1
Status:  ERROR 
PackageFile: None
PackageFileSize: NA

Command output

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


* checking for file ‘CATALYST/DESCRIPTION’ ... OK
* preparing ‘CATALYST’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘differential.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.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: Matrix

Attaching package: 'Matrix'

The following object is masked from 'package:S4Vectors':

    expand

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


********************************************************
Note: As of version 1.0.0, cowplot does not change the
  default ggplot2 theme anymore. To recover the previous
  behavior, execute:
  theme_set(theme_cowplot())
********************************************************


Attaching package: 'flowCore'

The following object is masked from 'package:Matrix':

    %&%

The following object is masked from 'package:BiocGenerics':

    normalize

Registered S3 methods overwritten by 'lme4':
  method                          from
  cooks.distance.influence.merMod car 
  influence.merMod                car 
  dfbeta.influence.merMod         car 
  dfbetas.influence.merMod        car 
Loading required package: ggplot2

Attaching package: 'scater'

The following object is masked from 'package:diffcyt':

    plotHeatmap

Quitting from lines 86-87 (differential.Rmd) 
Error: processing vignette 'differential.Rmd' failed with diagnostics:
invalid class "SingleCellExperiment" object: 
    no 'colPairs' field in 'int_colData'
--- failed re-building ‘differential.Rmd’

--- re-building ‘preprocessing.Rmd’ using rmarkdown
Quitting from lines 75-81 (preprocessing.Rmd) 
Error: processing vignette 'preprocessing.Rmd' failed with diagnostics:
invalid class "SingleCellExperiment" object: 
    no 'colPairs' field in 'int_colData'
--- failed re-building ‘preprocessing.Rmd’

SUMMARY: processing the following files failed:
  ‘differential.Rmd’ ‘preprocessing.Rmd’

Error: Vignette re-building failed.
Execution halted