Package: InterMineR

Version: 1.6.1

Command: chmod a+r InterMineR -R && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD build --keep-empty-dirs --no-resave-data InterMineR

StartedAt: 2019-10-16 00:42:22 -0400 (Wed, 16 Oct 2019)

EndedAt: 2019-10-16 00:46:53 -0400 (Wed, 16 Oct 2019)

EllapsedTime: 271.5 seconds

RetCode: 1

Status:  ERROR

PackageFile: None

PackageFileSize: NA

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### Running command:
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###   chmod a+r InterMineR -R && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe 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


Attaching package: 'IRanges'

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

    windows

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

Invalid Parameter - /figure-html
Warning in shell(paste(c(cmd, args), collapse = " ")) :
  'convert "Enrichment_Analysis_and_Visualization_files/figure-html/geneAnswersHeatmap-1.png" -trim "Enrichment_Analysis_and_Visualization_files/figure-html/geneAnswersHeatmap-1.png"' execution failed with error code 4
--- 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'
Invalid Parameter - /figure-html
Warning in shell(paste(c(cmd, args), collapse = " ")) :
  'convert "InterMineR_files/figure-html/plottracks-1.png" -trim "InterMineR_files/figure-html/plottracks-1.png"' execution failed with error code 4
--- finished re-building 'InterMineR.Rmd'

SUMMARY: processing the following file failed:
  'FlyMine_Genomic_Visualizations.Rmd'

Error: Vignette re-building failed.
Execution halted