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BioC 3.5: BUILD report for hiAnnotator on oaxaca

This page was generated on 2017-03-04 16:47:30 -0500 (Sat, 04 Mar 2017).

Package 603/1339HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
hiAnnotator 1.9.0
Nirav V Malani
Snapshot Date: 2017-03-03 17:15:47 -0500 (Fri, 03 Mar 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/hiAnnotator
Last Changed Rev: 122712 / Revision: 127142
Last Changed Date: 2016-10-17 15:10:43 -0400 (Mon, 17 Oct 2016)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  OK  ERROR  skipped 
tokay2 Windows Server 2012 R2 Standard / x64  NotNeeded  ERROR  skipped  skipped 
toluca2 Mac OS X Mavericks (10.9.5) / x86_64  OK  ERROR  skipped  skipped 
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  OK [ ERROR ] skipped  skipped 

Summary

Package: hiAnnotator
Version: 1.9.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data hiAnnotator
StartedAt: 2017-03-03 19:04:06 -0800 (Fri, 03 Mar 2017)
EndedAt: 2017-03-03 19:04:54 -0800 (Fri, 03 Mar 2017)
EllapsedTime: 48.6 seconds
RetCode: 1
Status:  ERROR 
PackageFile: None
PackageFileSize: NA

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data hiAnnotator
###
##############################################################################
##############################################################################


* checking for file ‘hiAnnotator/DESCRIPTION’ ... OK
* preparing ‘hiAnnotator’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
Quitting from lines 48-68 (Intro.Rmd) 
Error: processing vignette 'Intro.Rmd' failed with diagnostics:
The following seqlevels are to be dropped but are currently in use
  (i.e. have ranges on them): chrM, chr1_random, chr2_random,
  chr3_random, chr4_random, chr5_h2_hap1, chr5_random,
  chr6_cox_hap1, chr6_qbl_hap2, chr6_random, chr8_random,
  chr9_random, chr13_random, chr15_random, chr19_random,
  chr21_random, chr22_h2_hap1, chr22_random, chrX_random. Please use
  the 'pruning.mode' argument to control how to prune 'x', that is,
  how to remove the ranges in 'x' that are on these sequences. For
  example, do something like:
  
  seqlevels(x, pruning.mode="coarse") <- new_seqlevels
  
  or
  
  keepSeqlevels(x, new_seqlevels, pruning.mode="coarse")
  
  See ?seqinfo for a description of the pruning modes.
Execution halted