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BUILD report for InterMineR on malbec2

This page was generated on 2019-10-16 12:11:58 -0400 (Wed, 16 Oct 2019).

Package 823/1741HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
InterMineR 1.6.1
InterMine Team
Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019)
URL: https://git.bioconductor.org/packages/InterMineR
Branch: RELEASE_3_9
Last Commit: d2f1a3b
Last Changed Date: 2019-07-08 07:35:51 -0400 (Mon, 08 Jul 2019)
malbec2 Linux (Ubuntu 18.04.2 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: InterMineR
Version: 1.6.1
Command: /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data InterMineR
StartedAt: 2019-10-15 22:37:03 -0400 (Tue, 15 Oct 2019)
EndedAt: 2019-10-15 22:40:31 -0400 (Tue, 15 Oct 2019)
EllapsedTime: 208.7 seconds
RetCode: 1
Status:  ERROR 
PackageFile: None
PackageFileSize: NA

Command output

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### Running command:
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###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data InterMineR
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* checking for file ‘InterMineR/DESCRIPTION’ ... OK
* preparing ‘InterMineR’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘Enrichment_Analysis_and_Visualization.Rmd’ using rmarkdown
Loading required package: igraph

Attaching package: 'igraph'

The following objects are masked from 'package:stats':

    decompose, spectrum

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

    union

Loading required package: RCurl
Loading required package: bitops
Loading required package: annotate
Loading required package: AnnotationDbi
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:igraph':

    normalize, path, union

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: 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: IRanges
Loading required package: S4Vectors

Attaching package: 'S4Vectors'

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

    expand.grid

Loading required package: XML
Loading required package: RSQLite
Loading required package: MASS

Attaching package: 'MASS'

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

    select

Loading required package: Heatplus
Loading required package: RColorBrewer
Warning: replacing previous import 'stats::decompose' by 'igraph::decompose' when loading 'GeneAnswers'
Warning: replacing previous import 'stats::spectrum' by 'igraph::spectrum' when loading 'GeneAnswers'
Loading required package: GO.db

Loading required package: org.Hs.eg.db

--- finished re-building ‘Enrichment_Analysis_and_Visualization.Rmd’

--- re-building ‘FlyMine_Genomic_Visualizations.Rmd’ using rmarkdown
Loading required package: GenomicRanges
Loading required package: GenomeInfoDb
Loading required package: grid
Quitting from lines 156-174 (FlyMine_Genomic_Visualizations.Rmd) 
Error: processing vignette 'FlyMine_Genomic_Visualizations.Rmd' failed with diagnostics:
Internal Server Error (HTTP 500).
--- failed re-building ‘FlyMine_Genomic_Visualizations.Rmd’

--- re-building ‘InterMineR.Rmd’ using rmarkdown
Found more than one class "file" in cache; using the first, from namespace 'BiocGenerics'
Also defined by 'RJSONIO'
Found more than one class "file" in cache; using the first, from namespace 'BiocGenerics'
Also defined by 'RJSONIO'
--- finished re-building ‘InterMineR.Rmd’

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

Error: Vignette re-building failed.
Execution halted