Package: cellbaseR

Version: 1.7.2

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

StartedAt: 2019-04-08 23:55:11 -0400 (Mon, 08 Apr 2019)

EndedAt: 2019-04-08 23:58:22 -0400 (Mon, 08 Apr 2019)

EllapsedTime: 191.3 seconds

RetCode: 1

Status:  ERROR

PackageFile: None

PackageFileSize: NA

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### Running command:
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###   chmod a+r cellbaseR -R && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD build --keep-empty-dirs --no-resave-data cellbaseR
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* 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

Attaching package: 'IRanges'

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

    windows

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
Invalid Parameter - /figure-html
Warning in shell(paste(c(cmd, args), collapse = " ")) :
  'convert "cellbaseR_files/figure-html/unnamed-chunk-6-1.png" -trim "cellbaseR_files/figure-html/unnamed-chunk-6-1.png"' execution failed with error code 4
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

Registered S3 method overwritten by 'R.oo':
  method        from       
  throw.default R.methodsS3
Registered S3 method overwritten by 'R.oo':
  method        from       
  throw.default R.methodsS3
Registered S3 method overwritten by 'R.oo':
  method        from       
  throw.default R.methodsS3
Registered S3 method overwritten by 'R.oo':
  method        from       
  throw.default R.methodsS3
Registered S3 method overwritten by 'R.oo':
  method        from       
  throw.default R.methodsS3
Registered S3 method overwritten by 'R.oo':
  method        from       
  throw.default R.methodsS3