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BUILD report for cellbaseR on celaya2

This page was generated on 2019-04-09 13:18:14 -0400 (Tue, 09 Apr 2019).

Package 221/1703HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
cellbaseR 1.7.2
Mohammed OE Abdallah
Snapshot Date: 2019-04-08 17:01:18 -0400 (Mon, 08 Apr 2019)
URL: https://git.bioconductor.org/packages/cellbaseR
Branch: master
Last Commit: d074bcb7
Last Changed Date: 2019-04-08 15:36:02 -0400 (Mon, 08 Apr 2019)
malbec2 Linux (Ubuntu 18.04.2 LTS) / x86_64  OK  OK  OK YES, new version is higher than in internal repository
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 
merida2 OS X 10.11.6 El Capitan / x86_64  OK  ERROR  skipped  skipped 

Summary

Package: cellbaseR
Version: 1.7.2
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data cellbaseR
StartedAt: 2019-04-08 22:29:43 -0400 (Mon, 08 Apr 2019)
EndedAt: 2019-04-08 22:31:26 -0400 (Mon, 08 Apr 2019)
EllapsedTime: 103.5 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 cellbaseR
###
##############################################################################
##############################################################################


* checking for file ‘cellbaseR/DESCRIPTION’ ... OK
* preparing ‘cellbaseR’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘cellbaseR.Rmd’ using rmarkdown
Registered S3 method overwritten by 'R.oo':
  method        from       
  throw.default R.methodsS3
Loading required package: Gviz
Loading required package: S4Vectors
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, colMeans, colSums, 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, rowMeans,
    rowSums, rownames, sapply, setdiff, sort, table, tapply, union,
    unique, unsplit, which, which.max, which.min


Attaching package: 'S4Vectors'

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

    expand.grid

Loading required package: IRanges
Loading required package: GenomicRanges
Loading required package: GenomeInfoDb
Loading required package: grid
Registered S3 methods overwritten by 'ggplot2':
  method         from 
  [.quosures     rlang
  c.quosures     rlang
  print.quosures rlang
Warning in has_utility("convert", "ImageMagick") :
  ImageMagick not installed or not in PATH
Loading required package: SummarizedExperiment
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: Rsamtools
Loading required package: Biostrings
Loading required package: XVector

Attaching package: 'Biostrings'

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

    type

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

    strsplit


Attaching package: 'VariantAnnotation'

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

    tabulate

Quitting from lines 153-163 (cellbaseR.Rmd) 
Error: processing vignette 'cellbaseR.Rmd' failed with diagnostics:
error writing to connection
--- failed re-building ‘cellbaseR.Rmd’

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

Error: Vignette re-building failed.
Execution halted