manta 1.33.1
Chris Berthiaume , Adrian Marchetti
| Snapshot Date: 2020-01-15 16:46:30 -0500 (Wed, 15 Jan 2020) |
| URL: https://git.bioconductor.org/packages/manta |
| Branch: master |
| Last Commit: 39c8f96 |
| Last Changed Date: 2020-01-06 11:06:09 -0500 (Mon, 06 Jan 2020) |
| malbec2 | Linux (Ubuntu 18.04.3 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 | |
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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