Back to Multiple platform build/check report for BioC 3.9
ABCD[E]FGHIJKLMNOPQRSTUVWXYZ

BUILD report for epivizr on celaya2

This page was generated on 2019-10-16 12:52:08 -0400 (Wed, 16 Oct 2019).

Package 511/1741HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
epivizr 2.14.0
Hector Corrada Bravo
Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019)
URL: https://git.bioconductor.org/packages/epivizr
Branch: RELEASE_3_9
Last Commit: 612e74d
Last Changed Date: 2019-05-02 11:53:45 -0400 (Thu, 02 May 2019)
malbec2 Linux (Ubuntu 18.04.2 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository
celaya2 OS X 10.11.6 El Capitan / x86_64  OK [ ERROR ] skipped  skipped 

Summary

Package: epivizr
Version: 2.14.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data epivizr
StartedAt: 2019-10-15 21:00:23 -0400 (Tue, 15 Oct 2019)
EndedAt: 2019-10-15 21:01:59 -0400 (Tue, 15 Oct 2019)
EllapsedTime: 96.2 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 epivizr
###
##############################################################################
##############################################################################


* checking for file ‘epivizr/DESCRIPTION’ ... OK
* preparing ‘epivizr’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘IntroToEpivizr.Rmd’ using rmarkdown
Loading required package: Biobase
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

Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

Loading required package: GenomicRanges
Loading required package: stats4
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: 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

Warning in has_utility("convert", "ImageMagick") :
  ImageMagick not installed or not in PATH
Quitting from lines 132-133 (IntroToEpivizr.Rmd) 
Error: processing vignette 'IntroToEpivizr.Rmd' failed with diagnostics:
timespec_get failed
--- failed re-building ‘IntroToEpivizr.Rmd’

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

Error: Vignette re-building failed.
Execution halted