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BUILD report for regionReport on veracruz1

This page was generated on 2018-04-12 13:39:30 -0400 (Thu, 12 Apr 2018).

Package 1156/1472HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
regionReport 1.12.2
Leonardo Collado-Torres
Snapshot Date: 2018-04-11 16:45:18 -0400 (Wed, 11 Apr 2018)
URL: https://git.bioconductor.org/packages/regionReport
Branch: RELEASE_3_6
Last Commit: 67c95c2
Last Changed Date: 2018-01-19 19:32:50 -0400 (Fri, 19 Jan 2018)
malbec1 Linux (Ubuntu 16.04.1 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
veracruz1 OS X 10.11.6 El Capitan / x86_64  OK [ ERROR ] skipped  skipped 

Summary

Package: regionReport
Version: 1.12.2
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data regionReport
StartedAt: 2018-04-11 21:05:33 -0400 (Wed, 11 Apr 2018)
EndedAt: 2018-04-11 21:11:16 -0400 (Wed, 11 Apr 2018)
EllapsedTime: 342.4 seconds
RetCode: 1
Status:  ERROR 
PackageFile: None
PackageFileSize: NA

Command output

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data regionReport
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* checking for file ‘regionReport/DESCRIPTION’ ... OK
* preparing ‘regionReport’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
sh: line 1: 87409 Abort trap: 6           'convert' 'bumphunterExampleOutput_files/figure-html/regLen2-1.png' -trim 'bumphunterExampleOutput_files/figure-html/regLen2-1.png' > /dev/null
sh: line 1: 87825 Abort trap: 6           'convert' 'bumphunterExampleOutput_files/figure-html/density-solo-area-1.png' -trim 'bumphunterExampleOutput_files/figure-html/density-solo-area-1.png' > /dev/null
sh: line 1: 87894 Abort trap: 6           'convert' 'bumphunterExampleOutput_files/figure-html/density-solo-value-1.png' -trim 'bumphunterExampleOutput_files/figure-html/density-solo-value-1.png' > /dev/null
sh: line 1: 87898 Abort trap: 6           'convert' 'bumphunterExampleOutput_files/figure-html/density-solo-clusterL-1.png' -trim 'bumphunterExampleOutput_files/figure-html/density-solo-clusterL-1.png' > /dev/null
sh: line 1: 88535 Abort trap: 6           'convert' 'bumphunterExampleOutput_files/figure-html/genomeOverview2-1.png' -trim 'bumphunterExampleOutput_files/figure-html/genomeOverview2-1.png' > /dev/null
sh: line 1: 91184 Abort trap: 6           'convert' 'bumphunterExampleOutput_files/figure-html/vennDiagram-1.png' -trim 'bumphunterExampleOutput_files/figure-html/vennDiagram-1.png' > /dev/null
[WARNING] This document format requires a nonempty <title> element.
  Please specify either 'title' or 'pagetitle' in the metadata.
  Falling back to 'bumphunterExampleOutput.utf8'
Warning in citation("BiocStyle") :
  no date field in DESCRIPTION file of package 'BiocStyle'
Warning in citation("BiocStyle") :
  could not determine year for 'BiocStyle' from package DESCRIPTION file
Warning in citation("biovizBase") :
  no date field in DESCRIPTION file of package 'biovizBase'
Warning in citation("biovizBase") :
  could not determine year for 'biovizBase' from package DESCRIPTION file
Warning in citation("TxDb.Hsapiens.UCSC.hg19.knownGene") :
  no date field in DESCRIPTION file of package 'TxDb.Hsapiens.UCSC.hg19.knownGene'
Warning in citation("DEFormats") :
  no date field in DESCRIPTION file of package 'DEFormats'
Warning in citation("DEFormats") :
  could not determine year for 'DEFormats' from package DESCRIPTION file
Writing 34 Bibtex entries ... OK
Results written to file 'regionReportRef.bib'
sh: line 1: 91271 Abort trap: 6           'convert' 'basicExploration_files/figure-html/pvals-1.png' -trim 'basicExploration_files/figure-html/pvals-1.png' > /dev/null
sh: line 1: 91274 Abort trap: 6           'convert' 'basicExploration_files/figure-html/regLen-1.png' -trim 'basicExploration_files/figure-html/regLen-1.png' > /dev/null
sh: line 1: 91279 Abort trap: 6           'convert' 'basicExploration_files/figure-html/regArea-1.png' -trim 'basicExploration_files/figure-html/regArea-1.png' > /dev/null
sh: line 1: 91297 Abort trap: 6           'convert' 'basicExploration_files/figure-html/nullLengthArea-1.png' -trim 'basicExploration_files/figure-html/nullLengthArea-1.png' > /dev/null
sh: line 1: 91299 Abort trap: 6           'convert' 'basicExploration_files/figure-html/meanCov-1.png' -trim 'basicExploration_files/figure-html/meanCov-1.png' > /dev/null
sh: line 1: 91303 Abort trap: 6           'convert' 'basicExploration_files/figure-html/MAstyle-1.png' -trim 'basicExploration_files/figure-html/MAstyle-1.png' > /dev/null
sh: line 1: 91315 Abort trap: 6           'convert' 'basicExploration_files/figure-html/genomeOverview1-1.png' -trim 'basicExploration_files/figure-html/genomeOverview1-1.png' > /dev/null
sh: line 1: 91317 Abort trap: 6           'convert' 'basicExploration_files/figure-html/genomeOverview2-1.png' -trim 'basicExploration_files/figure-html/genomeOverview2-1.png' > /dev/null
sh: line 1: 91691 Abort trap: 6           'convert' 'basicExploration_files/figure-html/genomeOverview3-1.png' -trim 'basicExploration_files/figure-html/genomeOverview3-1.png' > /dev/null
sh: line 1: 91891 Abort trap: 6           'convert' 'basicExploration_files/figure-html/plotRegions-1.png' -trim 'basicExploration_files/figure-html/plotRegions-1.png' > /dev/null
sh: line 1: 91893 Abort trap: 6           'convert' 'basicExploration_files/figure-html/plotRegions-2.png' -trim 'basicExploration_files/figure-html/plotRegions-2.png' > /dev/null
sh: line 1: 91895 Abort trap: 6           'convert' 'basicExploration_files/figure-html/plotRegions-3.png' -trim 'basicExploration_files/figure-html/plotRegions-3.png' > /dev/null
sh: line 1: 91897 Abort trap: 6           'convert' 'basicExploration_files/figure-html/plotRegions-4.png' -trim 'basicExploration_files/figure-html/plotRegions-4.png' > /dev/null
sh: line 1: 91899 Abort trap: 6           'convert' 'basicExploration_files/figure-html/plotRegions-5.png' -trim 'basicExploration_files/figure-html/plotRegions-5.png' > /dev/null
sh: line 1: 91901 Abort trap: 6           'convert' 'basicExploration_files/figure-html/plotRegions-6.png' -trim 'basicExploration_files/figure-html/plotRegions-6.png' > /dev/null
sh: line 1: 91903 Abort trap: 6           'convert' 'basicExploration_files/figure-html/plotRegions-7.png' -trim 'basicExploration_files/figure-html/plotRegions-7.png' > /dev/null
sh: line 1: 91905 Abort trap: 6           'convert' 'basicExploration_files/figure-html/plotRegions-8.png' -trim 'basicExploration_files/figure-html/plotRegions-8.png' > /dev/null
sh: line 1: 91907 Abort trap: 6           'convert' 'basicExploration_files/figure-html/plotRegions-9.png' -trim 'basicExploration_files/figure-html/plotRegions-9.png' > /dev/null
sh: line 1: 91909 Abort trap: 6           'convert' 'basicExploration_files/figure-html/plotRegions-10.png' -trim 'basicExploration_files/figure-html/plotRegions-10.png' > /dev/null
sh: line 1: 91911 Abort trap: 6           'convert' 'basicExploration_files/figure-html/plotRegions-11.png' -trim 'basicExploration_files/figure-html/plotRegions-11.png' > /dev/null
sh: line 1: 91913 Abort trap: 6           'convert' 'basicExploration_files/figure-html/plotRegions-12.png' -trim 'basicExploration_files/figure-html/plotRegions-12.png' > /dev/null
sh: line 1: 91915 Abort trap: 6           'convert' 'basicExploration_files/figure-html/plotRegions-13.png' -trim 'basicExploration_files/figure-html/plotRegions-13.png' > /dev/null
sh: line 1: 91917 Abort trap: 6           'convert' 'basicExploration_files/figure-html/plotRegions-14.png' -trim 'basicExploration_files/figure-html/plotRegions-14.png' > /dev/null
sh: line 1: 91919 Abort trap: 6           'convert' 'basicExploration_files/figure-html/plotRegions-15.png' -trim 'basicExploration_files/figure-html/plotRegions-15.png' > /dev/null
sh: line 1: 91921 Abort trap: 6           'convert' 'basicExploration_files/figure-html/plotRegions-16.png' -trim 'basicExploration_files/figure-html/plotRegions-16.png' > /dev/null
sh: line 1: 91923 Abort trap: 6           'convert' 'basicExploration_files/figure-html/plotRegions-17.png' -trim 'basicExploration_files/figure-html/plotRegions-17.png' > /dev/null
sh: line 1: 91927 Abort trap: 6           'convert' 'basicExploration_files/figure-html/vennDiagram-1.png' -trim 'basicExploration_files/figure-html/vennDiagram-1.png' > /dev/null
sh: line 1: 91931 Abort trap: 6           'convert' 'basicExploration_files/figure-html/vennDiagramSignificant-1.png' -trim 'basicExploration_files/figure-html/vennDiagramSignificant-1.png' > /dev/null
Warning: `panel.margin` is deprecated. Please use `panel.spacing` property instead
Warning: `panel.margin` is deprecated. Please use `panel.spacing` property instead
Warning: `panel.margin` is deprecated. Please use `panel.spacing` property instead
Warning: `panel.margin` is deprecated. Please use `panel.spacing` property instead
Warning: `panel.margin` is deprecated. Please use `panel.spacing` property instead
Warning: `panel.margin` is deprecated. Please use `panel.spacing` property instead
Warning: `panel.margin` is deprecated. Please use `panel.spacing` property instead
Warning: `panel.margin` is deprecated. Please use `panel.spacing` property instead
Warning: `panel.margin` is deprecated. Please use `panel.spacing` property instead
Warning: `panel.margin` is deprecated. Please use `panel.spacing` property instead
Warning: `panel.margin` is deprecated. Please use `panel.spacing` property instead
Warning: Transformation introduced infinite values in continuous y-axis
Warning: Transformation introduced infinite values in continuous y-axis
Warning: `panel.margin` is deprecated. Please use `panel.spacing` property instead
Warning: `panel.margin` is deprecated. Please use `panel.spacing` property instead
Warning: `panel.margin` is deprecated. Please use `panel.spacing` property instead
Warning: `panel.margin` is deprecated. Please use `panel.spacing` property instead
Warning: `panel.margin` is deprecated. Please use `panel.spacing` property instead
Warning: `panel.margin` is deprecated. Please use `panel.spacing` property instead
Warning: `panel.margin` is deprecated. Please use `panel.spacing` property instead
Warning: `panel.margin` is deprecated. Please use `panel.spacing` property instead
Warning: `panel.margin` is deprecated. Please use `panel.spacing` property instead
Warning: Transformation introduced infinite values in continuous y-axis
Warning: Transformation introduced infinite values in continuous y-axis
sh: line 1: 92011 Abort trap: 6           'convert' 'basicExploration_files/figure-html/bestClusters-1.png' -trim 'basicExploration_files/figure-html/bestClusters-1.png' > /dev/null
sh: line 1: 92013 Abort trap: 6           'convert' 'basicExploration_files/figure-html/bestClusters-2.png' -trim 'basicExploration_files/figure-html/bestClusters-2.png' > /dev/null
[WARNING] This document format requires a nonempty <title> element.
  Please specify either 'title' or 'pagetitle' in the metadata.
  Falling back to 'basicExploration.utf8'
Warning in `[[.bibentry`(bib, "mgcv") : subscript out of bounds
Warning in `[[.bibentry`(bib, "whisker") : subscript out of bounds
No encoding supplied: defaulting to UTF-8.
Quitting from lines 412-414 (regionReport.Rmd) 
Error: processing vignette 'regionReport.Rmd' failed with diagnostics:
argument is of length zero
Execution halted