OTUbase 1.37.0
Daniel Beck
| Snapshot Date: 2020-01-15 16:46:30 -0500 (Wed, 15 Jan 2020) |
| URL: https://git.bioconductor.org/packages/OTUbase |
| Branch: master |
| Last Commit: 9effc0c |
| Last Changed Date: 2019-10-29 13:35:19 -0500 (Tue, 29 Oct 2019) |
| malbec2 | Linux (Ubuntu 18.04.3 LTS) / x86_64 | OK | OK | OK | |  |
| 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 | |
##############################################################################
##############################################################################
###
### Running command:
###
### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data OTUbase
###
##############################################################################
##############################################################################
* checking for file ‘OTUbase/DESCRIPTION’ ... OK
* preparing ‘OTUbase’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘Introduction_to_OTUbase.Rnw’ using Sweave
Loading required package: S4Vectors
Loading required package: stats4
Loading required package: BiocGenerics
Loading required package: parallel
Attaching package: ‘BiocGenerics’
The following objects are masked from ‘package:parallel’:
clusterApply, clusterApplyLB, clusterCall,
clusterEvalQ, clusterExport, clusterMap,
parApply, parCapply, parLapply, parLapplyLB,
parRapply, parSapply, parSapplyLB
The following objects are masked from ‘package:stats’:
IQR, mad, sd, var, xtabs
The following objects are masked from ‘package:base’:
Filter, Find, Map, Position, Reduce,
anyDuplicated, append, as.data.frame, basename,
cbind, colnames, dirname, do.call, duplicated,
eval, evalq, get, grep, grepl, intersect,
is.unsorted, lapply, mapply, match, mget, order,
paste, pmax, pmax.int, pmin, pmin.int, rank,
rbind, rownames, sapply, setdiff, sort, table,
tapply, union, unique, unsplit, which, which.max,
which.min
Attaching package: ‘S4Vectors’
The following object is masked from ‘package:base’:
expand.grid
Loading required package: IRanges
Loading required package: ShortRead
Loading required package: BiocParallel
Loading required package: Biostrings
Loading required package: XVector
Attaching package: ‘Biostrings’
The following object is masked from ‘package:base’:
strsplit
Loading required package: Rsamtools
Loading required package: GenomeInfoDb
Loading required package: GenomicRanges
Loading required package: GenomicAlignments
Loading required package: SummarizedExperiment
Loading required package: Biobase
Welcome to Bioconductor
Vignettes contain introductory material; view
with 'browseVignettes()'. To cite Bioconductor,
see 'citation("Biobase")', and for packages
'citation("pkgname")'.
Loading required package: DelayedArray
Loading required package: matrixStats
Attaching package: ‘matrixStats’
The following objects are masked from ‘package:Biobase’:
anyMissing, rowMedians
Attaching package: ‘DelayedArray’
The following objects are masked from ‘package:matrixStats’:
colMaxs, colMins, colRanges, rowMaxs, rowMins,
rowRanges
The following objects are masked from ‘package:base’:
aperm, apply, rowsum
Loading required package: vegan
Loading required package: permute
Loading required package: lattice
This is vegan 2.5-6
============================================================
Welcome to OTUbase version 1.37.0
Attaching package: ‘OTUbase’
The following object is masked from ‘package:GenomicAlignments’:
seqnames
The following object is masked from ‘package:SummarizedExperiment’:
seqnames
The following object is masked from ‘package:GenomicRanges’:
seqnames
The following object is masked from ‘package:GenomeInfoDb’:
seqnames
Looking for column with names
Note: Classification file must be RDP's fixed taxonomy.
Warning: If fastafile has fewer sequences then are in the taxfile, the extra taxfile names will be left out.
Looking for column with names
Error: processing vignette 'Introduction_to_OTUbase.Rnw' failed with diagnostics:
Running 'texi2dvi' on 'Introduction_to_OTUbase.tex' failed.
LaTeX errors:
! Package inputenc Error: Unicode character − (U+2212)
(inputenc) not set up for use with LaTeX.
See the inputenc package documentation for explanation.
Type H <return> for immediate help.
! Package inputenc Error: Unicode character − (U+2212)
(inputenc) not set up for use with LaTeX.
See the inputenc package documentation for explanation.
Type H <return> for immediate help.
! Package inputenc Error: Unicode character − (U+2212)
(inputenc) not set up for use with LaTeX.
See the inputenc package documentation for explanation.
Type H <return> for immediate help.
! Package inputenc Error: Unicode character − (U+2212)
(inputenc) not set up for use with LaTeX.
See the inputenc package documentation for explanation.
Type H <return> for immediate help.
! Package inputenc Error: Unicode character − (U+2212)
(inputenc) not set up for use with LaTeX.
See the inputenc package documentation for explanation.
Type H <return> for immediate help.
! Package inputenc Error: Unicode character − (U+2212)
(inputenc) not set up for use with LaTeX.
See the inputenc package documentation for explanation.
Type H <return> for immediate help.
--- failed re-building ‘Introduction_to_OTUbase.Rnw’
SUMMARY: processing the following file failed:
‘Introduction_to_OTUbase.Rnw’
Error: Vignette re-building failed.
Execution halted