Workflows build report for BioC 3.8 - BUILD report for recountWorkflow on tokay1

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### Running command:
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###   chmod a+r recountWorkflow -R && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD build --keep-empty-dirs --no-resave-data recountWorkflow
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* checking for file 'recountWorkflow/DESCRIPTION' ... OK
* preparing 'recountWorkflow':
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
Loading required package: SummarizedExperiment
Loading required package: GenomicRanges
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, lengths, 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

Loading required package: S4Vectors

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: GenomeInfoDb
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

Setting options('download.file.method.GEOquery'='auto')
Setting options('GEOquery.inmemory.gpl'=FALSE)

Attaching package: 'limma'

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

    plotMA


clusterProfiler v3.10.1  For help: https://guangchuangyu.github.io/software/clusterProfiler

If you use clusterProfiler in published research, please cite:
Guangchuang Yu, Li-Gen Wang, Yanyan Han, Qing-Yu He. clusterProfiler: an R package for comparing biological themes among gene clusters. OMICS: A Journal of Integrative Biology. 2012, 16(5):284-287.

Attaching package: 'clusterProfiler'

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

    simplify

Loading required package: AnnotationDbi


Attaching package: 'gplots'

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

    space

The following object is masked from 'package:S4Vectors':

    space

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

    lowess

Loading required package: foreach
Loading required package: iterators
Loading required package: locfit
locfit 1.5-9.1 	 2013-03-22
trying URL 'http://duffel.rail.bio/recount/v2/SRP045638/rse_gene.Rdata'
Content type 'application/octet-stream' length 12604886 bytes (12.0 MB)
==================================================
downloaded 12.0 MB

trying URL 'https://github.com/leekgroup/recount-website/blob/master/predictions/PredictedPhenotypes_v0.0.06.rda?raw=true'
Content type 'application/octet-stream' length 548129 bytes (535 KB)
==================================================
downloaded 535 KB

Invalid Parameter - -trim
Warning in shell(paste(c(cmd, args), collapse = " ")) :
  'convert "limmade1-1.png" -trim "limmade1-1.png"' execution failed with error code 4
Invalid Parameter - -trim
Warning in shell(paste(c(cmd, args), collapse = " ")) :
  'convert "limmade2-1.png" -trim "limmade2-1.png"' execution failed with error code 4
Invalid Parameter - -trim
Warning in shell(paste(c(cmd, args), collapse = " ")) :
  'convert "limmade3-1.png" -trim "limmade3-1.png"' execution failed with error code 4
Invalid Parameter - -trim
Warning in shell(paste(c(cmd, args), collapse = " ")) :
  'convert "limmaplots1-1.png" -trim "limmaplots1-1.png"' execution failed with error code 4
Invalid Parameter - -trim
Warning in shell(paste(c(cmd, args), collapse = " ")) :
  'convert "limmaplots2-1.png" -trim "limmaplots2-1.png"' execution failed with error code 4
Invalid Parameter - -trim
Warning in shell(paste(c(cmd, args), collapse = " ")) :
  'convert "goanalysis-1.png" -trim "goanalysis-1.png"' execution failed with error code 4
trying URL 'http://duffel.rail.bio/recount/v2/SRP045638/rse_exon.Rdata'
Content type 'application/octet-stream' length 110177449 bytes (105.1 MB)
==================================================
downloaded 105.1 MB

Invalid Parameter - -trim
Warning in shell(paste(c(cmd, args), collapse = " ")) :
  'convert "exondeanalysis1-1.png" -trim "exondeanalysis1-1.png"' execution failed with error code 4
Invalid Parameter - -trim
Warning in shell(paste(c(cmd, args), collapse = " ")) :
  'convert "exondeanalysis2-1.png" -trim "exondeanalysis2-1.png"' execution failed with error code 4
Invalid Parameter - -trim
Warning in shell(paste(c(cmd, args), collapse = " ")) :
  'convert "geneexon-1.png" -trim "geneexon-1.png"' execution failed with error code 4
Invalid Parameter - -trim
Warning in shell(paste(c(cmd, args), collapse = " ")) :
  'convert "geneexonmatch-1.png" -trim "geneexonmatch-1.png"' execution failed with error code 4
pandoc-citeproc: PandocHttpError "http://www.zotero.org/styles/vancouver" (HttpExceptionRequest Request {
  host                 = "www.zotero.org"
  port                 = 80
  secure               = False
  requestHeaders       = []
  path                 = "/styles/vancouver"
  queryString          = ""
  method               = "GET"
  proxy                = Nothing
  rawBody              = False
  redirectCount        = 10
  responseTimeout      = ResponseTimeoutDefault
  requestVersion       = HTTP/1.1
}
 ConnectionTimeout)
Error running filter pandoc-citeproc:
Filter returned error status 1
Error: processing vignette 'recount-workflow.Rmd' failed with diagnostics:
pandoc document conversion failed with error 83
Execution halted
BUILD report for recountWorkflow on tokay1

Summary

Command output
