##############################################################################
##############################################################################
###
### 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 1.38.0

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