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BUILD report for manta on machv2

This page was generated on 2020-10-17 11:58:50 -0400 (Sat, 17 Oct 2020).

TO THE DEVELOPERS/MAINTAINERS OF THE manta PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 981/1905HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
manta 1.34.0
Chris Berthiaume , Adrian Marchetti
Snapshot Date: 2020-10-16 14:40:19 -0400 (Fri, 16 Oct 2020)
URL: https://git.bioconductor.org/packages/manta
Branch: RELEASE_3_11
Last Commit: ca7ddbf
Last Changed Date: 2020-04-27 14:28:19 -0400 (Mon, 27 Apr 2020)
malbec2 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  ERROR  skipped 
tokay2 Windows Server 2012 R2 Standard / x64  OK  ERROR  skipped  skipped 
machv2 macOS 10.14.6 Mojave / x86_64  OK [ ERROR ] skipped  skipped 

Summary

Package: manta
Version: 1.34.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data manta
StartedAt: 2020-10-16 19:47:45 -0400 (Fri, 16 Oct 2020)
EndedAt: 2020-10-16 19:48:27 -0400 (Fri, 16 Oct 2020)
EllapsedTime: 42.0 seconds
RetCode: 1
Status:  ERROR 
PackageFile: None
PackageFileSize: NA

Command output

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


* checking for file ‘manta/DESCRIPTION’ ... OK
* preparing ‘manta’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘manta.Rnw’ using Sweave
Loading required package: edgeR
Loading required package: limma
Warning: Package 'manta' is deprecated and will be removed
  from Bioconductor version 3.12
Warning in estimateCommonDisp.DGEList(obj) :
  There is no replication, setting dispersion to NA.
Warning in estimateCommonDisp.DGEList(obj) :
  There is no replication, setting dispersion to NA.
Warning in estimateCommonDisp.DGEList(obj) :
  There is no replication, setting dispersion to NA.
Loading required package: RSQLite
Reading pplacer taxtable databases:

Warning in sstable(genetree.sub, idx.clmns = c("tax_name", "group")) :
  some or all of your index columns are not factors. coercing them...
Warning in sstable(genetree.sub, idx.clmns = c("tax_name", "group")) :
  some or all of your index columns are not factors. coercing them...
Warning in sstable(genetree.sub, idx.clmns = c("tax_name", "group")) :
  some or all of your index columns are not factors. coercing them...
Warning in sstable(genetree.sub, idx.clmns = c("tax_name", "group")) :
  some or all of your index columns are not factors. coercing them...
Warning in sstable(genetree.sub, idx.clmns = c("tax_name", "group")) :
  some or all of your index columns are not factors. coercing them...
Warning in sstable(genetree.sub, idx.clmns = c("tax_name", "group")) :
  some or all of your index columns are not factors. coercing them...
Warning in sstable(genetree.sub, idx.clmns = c("tax_name", "group")) :
  some or all of your index columns are not factors. coercing them...
Warning in sstable(genetree.sub, idx.clmns = c("tax_name", "group")) :
  some or all of your index columns are not factors. coercing them...
Warning in sstable(genetree.sub, idx.clmns = c("tax_name", "group")) :
  some or all of your index columns are not factors. coercing them...
Warning in sstable(genetree.sub, idx.clmns = c("tax_name", "group")) :
  some or all of your index columns are not factors. coercing them...
Warning in sstable(genetree.sub, idx.clmns = c("tax_name", "group")) :
  some or all of your index columns are not factors. coercing them...
Warning in sstable(genetree.sub, idx.clmns = c("tax_name", "group")) :
  some or all of your index columns are not factors. coercing them...
Warning in sstable(genetree.sub, idx.clmns = c("tax_name", "group")) :
  some or all of your index columns are not factors. coercing them...
Warning in sstable(genetree.sub, idx.clmns = c("tax_name", "group")) :
  some or all of your index columns are not factors. coercing them...
Warning in sstable(genetree.sub, idx.clmns = c("tax_name", "group")) :
  some or all of your index columns are not factors. coercing them...
Warning in sstable(genetree.sub, idx.clmns = c("tax_name", "group")) :
  some or all of your index columns are not factors. coercing them...
Warning in sstable(genetree.sub, idx.clmns = c("tax_name", "group")) :
  some or all of your index columns are not factors. coercing them...
Warning in sstable(genetree.sub, idx.clmns = c("tax_name", "group")) :
  some or all of your index columns are not factors. coercing them...
Warning in sstable(genetree.sub, idx.clmns = c("tax_name", "group")) :
  some or all of your index columns are not factors. coercing them...
Warning in sstable(genetree.sub, idx.clmns = c("tax_name", "group")) :
  some or all of your index columns are not factors. coercing them...
Warning in sstable(genetree.sub, idx.clmns = c("tax_name", "group")) :
  some or all of your index columns are not factors. coercing them...
Warning in sstable(genetree.sub, idx.clmns = c("tax_name", "group")) :
  some or all of your index columns are not factors. coercing them...
Warning in sstable(genetree.sub, idx.clmns = c("tax_name", "group")) :
  some or all of your index columns are not factors. coercing them...
Warning in sstable(genetree.sub, idx.clmns = c("tax_name", "group")) :
  some or all of your index columns are not factors. coercing them...
Warning in sstable(genetree.sub, idx.clmns = c("tax_name", "group")) :
  some or all of your index columns are not factors. coercing them...
Warning in sstable(genetree.sub, idx.clmns = c("tax_name", "group")) :
  some or all of your index columns are not factors. coercing them...
Warning in sstable(genetree.sub, idx.clmns = c("tax_name", "group")) :
  some or all of your index columns are not factors. coercing them...
Warning in sstable(genetree.sub, idx.clmns = c("tax_name", "group")) :
  some or all of your index columns are not factors. coercing them...
Warning in sstable(genetree.sub, idx.clmns = c("tax_name", "group")) :
  some or all of your index columns are not factors. coercing them...
Warning in sstable(genetree.sub, idx.clmns = c("tax_name", "group")) :
  some or all of your index columns are not factors. coercing them...
Warning in sstable(genetree.sub, idx.clmns = c("tax_name", "group")) :
  some or all of your index columns are not factors. coercing them...
Warning in sstable(genetree.sub, idx.clmns = c("tax_name", "group")) :
  some or all of your index columns are not factors. coercing them...
Warning in sstable(genetree.sub, idx.clmns = c("tax_name", "group")) :
  some or all of your index columns are not factors. coercing them...
Warning in sstable(genetree.sub, idx.clmns = c("tax_name", "group")) :
  some or all of your index columns are not factors. coercing them...
Warning in sstable(genetree.sub, idx.clmns = c("tax_name", "group")) :
  some or all of your index columns are not factors. coercing them...
Warning in sstable(genetree.sub, idx.clmns = c("tax_name", "group")) :
  some or all of your index columns are not factors. coercing them...
Warning in sstable(genetree.sub, idx.clmns = c("tax_name", "group")) :
  some or all of your index columns are not factors. coercing them...
Warning in sstable(genetree.sub, idx.clmns = c("tax_name", "group")) :
  some or all of your index columns are not factors. coercing them...
Warning in sstable(genetree.sub, idx.clmns = c("tax_name", "group")) :
  some or all of your index columns are not factors. coercing them...
Warning in sstable(genetree.sub, idx.clmns = c("tax_name", "group")) :
  some or all of your index columns are not factors. coercing them...
Warning in sstable(genetree.sub, idx.clmns = c("tax_name", "group")) :
  some or all of your index columns are not factors. coercing them...
Warning in sstable(genetree.sub, idx.clmns = c("tax_name", "group")) :
  some or all of your index columns are not factors. coercing them...
Warning in estimateCommonDisp.DGEList(obj) :
  There is no replication, setting dispersion to NA.
Warning in estimateCommonDisp.DGEList(obj.sub) :
  There is no replication, setting dispersion to NA.

Error: processing vignette 'manta.Rnw' failed with diagnostics:
 chunk 16 (label = plotmanta) 
Error in xy.coords(x, y, xlabel, ylabel, log) : 
  'x' is a list, but does not have components 'x' and 'y'

--- failed re-building ‘manta.Rnw’

SUMMARY: processing the following file failed:
  ‘manta.Rnw’

Error: Vignette re-building failed.
Execution halted