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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 manta
###
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* 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