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BUILD report for Harman on tokay2

This page was generated on 2019-04-09 12:26:33 -0400 (Tue, 09 Apr 2019).

Package 730/1703HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
Harman 1.11.0
Jason Ross
Snapshot Date: 2019-04-08 17:01:18 -0400 (Mon, 08 Apr 2019)
URL: https://git.bioconductor.org/packages/Harman
Branch: master
Last Commit: 61ae188
Last Changed Date: 2018-10-30 11:54:36 -0400 (Tue, 30 Oct 2018)
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 
merida2 OS X 10.11.6 El Capitan / x86_64  OK  ERROR  skipped  skipped 

Summary

Package: Harman
Version: 1.11.0
Command: chmod a+r Harman -R && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD build --keep-empty-dirs --no-resave-data Harman
StartedAt: 2019-04-08 23:21:56 -0400 (Mon, 08 Apr 2019)
EndedAt: 2019-04-08 23:23:05 -0400 (Mon, 08 Apr 2019)
EllapsedTime: 69.0 seconds
RetCode: 1
Status:  ERROR  
PackageFile: None
PackageFileSize: NA

Command output

##############################################################################
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###
### Running command:
###
###   chmod a+r Harman -R && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD build --keep-empty-dirs --no-resave-data Harman
###
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* checking for file 'Harman/DESCRIPTION' ... OK
* preparing 'Harman':
* checking DESCRIPTION meta-information ... OK
* cleaning src
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building 'IntroductionToHarman.Rmd' using rmarkdown
Invalid Parameter - /figure-html
Warning in shell(paste(c(cmd, args), collapse = " ")) :
  'convert "IntroductionToHarman_files/figure-html/unnamed-chunk-7-1.png" -trim "IntroductionToHarman_files/figure-html/unnamed-chunk-7-1.png"' execution failed with error code 4
Invalid Parameter - /figure-html
Warning in shell(paste(c(cmd, args), collapse = " ")) :
  'convert "IntroductionToHarman_files/figure-html/unnamed-chunk-8-1.png" -trim "IntroductionToHarman_files/figure-html/unnamed-chunk-8-1.png"' execution failed with error code 4
Invalid Parameter - /figure-html
Warning in shell(paste(c(cmd, args), collapse = " ")) :
  'convert "IntroductionToHarman_files/figure-html/unnamed-chunk-11-1.png" -trim "IntroductionToHarman_files/figure-html/unnamed-chunk-11-1.png"' execution failed with error code 4
Invalid Parameter - /figure-html
Warning in shell(paste(c(cmd, args), collapse = " ")) :
  'convert "IntroductionToHarman_files/figure-html/unnamed-chunk-12-1.png" -trim "IntroductionToHarman_files/figure-html/unnamed-chunk-12-1.png"' execution failed with error code 4
Invalid Parameter - /figure-html
Warning in shell(paste(c(cmd, args), collapse = " ")) :
  'convert "IntroductionToHarman_files/figure-html/unnamed-chunk-13-1.png" -trim "IntroductionToHarman_files/figure-html/unnamed-chunk-13-1.png"' execution failed with error code 4
Invalid Parameter - /figure-html
Warning in shell(paste(c(cmd, args), collapse = " ")) :
  'convert "IntroductionToHarman_files/figure-html/unnamed-chunk-16-1.png" -trim "IntroductionToHarman_files/figure-html/unnamed-chunk-16-1.png"' execution failed with error code 4
Invalid Parameter - /figure-html
Warning in shell(paste(c(cmd, args), collapse = " ")) :
  'convert "IntroductionToHarman_files/figure-html/unnamed-chunk-20-1.png" -trim "IntroductionToHarman_files/figure-html/unnamed-chunk-20-1.png"' execution failed with error code 4
Invalid Parameter - /figure-html
Warning in shell(paste(c(cmd, args), collapse = " ")) :
  'convert "IntroductionToHarman_files/figure-html/unnamed-chunk-23-1.png" -trim "IntroductionToHarman_files/figure-html/unnamed-chunk-23-1.png"' execution failed with error code 4
Invalid Parameter - /figure-html
Warning in shell(paste(c(cmd, args), collapse = " ")) :
  'convert "IntroductionToHarman_files/figure-html/unnamed-chunk-23-2.png" -trim "IntroductionToHarman_files/figure-html/unnamed-chunk-23-2.png"' execution failed with error code 4
Invalid Parameter - /figure-html
Warning in shell(paste(c(cmd, args), collapse = " ")) :
  'convert "IntroductionToHarman_files/figure-html/unnamed-chunk-24-1.png" -trim "IntroductionToHarman_files/figure-html/unnamed-chunk-24-1.png"' execution failed with error code 4
Invalid Parameter - /figure-html
Warning in shell(paste(c(cmd, args), collapse = " ")) :
  'convert "IntroductionToHarman_files/figure-html/unnamed-chunk-25-1.png" -trim "IntroductionToHarman_files/figure-html/unnamed-chunk-25-1.png"' execution failed with error code 4
Invalid Parameter - /figure-html
Warning in shell(paste(c(cmd, args), collapse = " ")) :
  'convert "IntroductionToHarman_files/figure-html/unnamed-chunk-27-1.png" -trim "IntroductionToHarman_files/figure-html/unnamed-chunk-27-1.png"' execution failed with error code 4

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

Welcome to Bioconductor

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

Invalid Parameter - /figure-html
Warning in shell(paste(c(cmd, args), collapse = " ")) :
  'convert "IntroductionToHarman_files/figure-html/unnamed-chunk-29-1.png" -trim "IntroductionToHarman_files/figure-html/unnamed-chunk-29-1.png"' execution failed with error code 4
Invalid Parameter - /figure-html
Warning in shell(paste(c(cmd, args), collapse = " ")) :
  'convert "IntroductionToHarman_files/figure-html/normalize-1.png" -trim "IntroductionToHarman_files/figure-html/normalize-1.png"' execution failed with error code 4
Invalid Parameter - /figure-html
Warning in shell(paste(c(cmd, args), collapse = " ")) :
  'convert "IntroductionToHarman_files/figure-html/normalize-2.png" -trim "IntroductionToHarman_files/figure-html/normalize-2.png"' execution failed with error code 4
Invalid Parameter - /figure-html
Warning in shell(paste(c(cmd, args), collapse = " ")) :
  'convert "IntroductionToHarman_files/figure-html/unnamed-chunk-34-1.png" -trim "IntroductionToHarman_files/figure-html/unnamed-chunk-34-1.png"' execution failed with error code 4
Invalid Parameter - /figure-html
Warning in shell(paste(c(cmd, args), collapse = " ")) :
  'convert "IntroductionToHarman_files/figure-html/unnamed-chunk-34-2.png" -trim "IntroductionToHarman_files/figure-html/unnamed-chunk-34-2.png"' execution failed with error code 4
Invalid Parameter - /figure-html
Warning in shell(paste(c(cmd, args), collapse = " ")) :
  'convert "IntroductionToHarman_files/figure-html/unnamed-chunk-39-1.png" -trim "IntroductionToHarman_files/figure-html/unnamed-chunk-39-1.png"' execution failed with error code 4
Invalid Parameter - /figure-html
Warning in shell(paste(c(cmd, args), collapse = " ")) :
  'convert "IntroductionToHarman_files/figure-html/unnamed-chunk-42-1.png" -trim "IntroductionToHarman_files/figure-html/unnamed-chunk-42-1.png"' execution failed with error code 4
Invalid Parameter - /figure-html
Warning in shell(paste(c(cmd, args), collapse = " ")) :
  'convert "IntroductionToHarman_files/figure-html/unnamed-chunk-43-1.png" -trim "IntroductionToHarman_files/figure-html/unnamed-chunk-43-1.png"' execution failed with error code 4
Invalid Parameter - /figure-html
Warning in shell(paste(c(cmd, args), collapse = " ")) :
  'convert "IntroductionToHarman_files/figure-html/unnamed-chunk-44-1.png" -trim "IntroductionToHarman_files/figure-html/unnamed-chunk-44-1.png"' execution failed with error code 4

Attaching package: 'limma'

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

    plotMA

Quitting from lines 466-477 (IntroductionToHarman.Rmd) 
Error: processing vignette 'IntroductionToHarman.Rmd' failed with diagnostics:
could not find function "classifyTestsT"
--- failed re-building 'IntroductionToHarman.Rmd'

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

Error: Vignette re-building failed.
Execution halted