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### Running command:
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###   /home/biocbuild/R/R-4.3.0/bin/R CMD build --keep-empty-dirs --no-resave-data appreci8R
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* checking for file ‘appreci8R/DESCRIPTION’ ... OK
* preparing ‘appreci8R’:
* checking DESCRIPTION meta-information ... OK
* installing the package to process help pages
* saving partial Rd database
* creating vignettes ... ERROR
--- re-building ‘appreci8R.Rnw’ using Sweave


Warning: replacing previous import ‘utils::findMatches’ by ‘S4Vectors::findMatches’ when loading ‘SNPlocs.Hsapiens.dbSNP144.GRCh37’
Warning: replacing previous import ‘utils::findMatches’ by ‘S4Vectors::findMatches’ when loading ‘XtraSNPlocs.Hsapiens.dbSNP144.GRCh37’
Warning: replacing previous import ‘utils::findMatches’ by ‘S4Vectors::findMatches’ when loading ‘MafDb.1Kgenomes.phase3.hs37d5’
Warning: replacing previous import ‘utils::findMatches’ by ‘S4Vectors::findMatches’ when loading ‘MafDb.ExAC.r1.0.hs37d5’
Warning: replacing previous import ‘utils::findMatches’ by ‘S4Vectors::findMatches’ when loading ‘MafDb.gnomADex.r2.1.hs37d5’
Warning: replacing previous import ‘utils::findMatches’ by ‘S4Vectors::findMatches’ when loading ‘appreci8R’
0. Reading input
1. Target filtration
2. Normalize
Loading required package: stats4
Loading required package: BiocGenerics

Attaching package: ‘BiocGenerics’

The following object is masked from ‘package:appreci8R’:

    normalize

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, aperm, 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.max, which.min

Loading required package: S4Vectors

Attaching package: ‘S4Vectors’

The following object is masked from ‘package:utils’:

    findMatches

The following objects are masked from ‘package:base’:

    I, expand.grid, unname

Loading required package: IRanges
Loading required package: GenomeInfoDb
Loading required package: AnnotationDbi
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: GenomicFeatures
Loading required package: XVector

Attaching package: ‘Biostrings’

The following object is masked from ‘package:base’:

    strsplit

3. Annotate
'select()' returned 1:1 mapping between keys and columns
Warning in valid.GenomicRanges.seqinfo(x, suggest.trim = TRUE) :
  GRanges object contains 11 out-of-bound ranges located on sequences 10808, 10809, 10810,
  and 18309. Note that ranges located on a sequence whose length is unknown (NA) or on a
  circular sequence are not considered out-of-bound (use seqlengths() and isCircular() to
  get the lengths and circularity flags of the underlying sequences). You can use trim() to
  trim these ranges. See ?`trim,GenomicRanges-method` for more information.
'select()' returned 1:1 mapping between keys and columns
'select()' returned 1:1 mapping between keys and columns
Warning in valid.GenomicRanges.seqinfo(x, suggest.trim = TRUE) :
  GRanges object contains 11 out-of-bound ranges located on sequences 10808, 10809, 10810,
  and 18309. Note that ranges located on a sequence whose length is unknown (NA) or on a
  circular sequence are not considered out-of-bound (use seqlengths() and isCircular() to
  get the lengths and circularity flags of the underlying sequences). You can use trim() to
  trim these ranges. See ?`trim,GenomicRanges-method` for more information.
4. Combine Output
5. Evaluate Coverage and BQ
6. Determine Extended Set of Characteristics (databases)
-> Downloading databases 
-> Pre-processing of the calls
-> Check databases
Getting info about the following rsIDs: rs2454206
6. Determine Extended Set of Characteristics (prediction)
7. Perform Final Filtration
->  Consider Frequency and Base Quality
->  Consider samples with the same call
->  Consider samples with a call at the same position
->  Consider background information
->  Consider nr of databases
->  Consider VAF when tolerated
->  Consider VAF when high nr of samples
->  Consider strand bias
->  Consider hotspot list
->  Perform final filtration
Calculate Artifact Score
Calculate Polymorphism Score
Correct Scores
->  Re-consider polymorphisms
Error: processing vignette 'appreci8R.Rnw' failed with diagnostics:
unable to run pdflatex on 'appreci8R.tex'
LaTeX errors:
! LaTeX Error: File `textpos.sty' not found.

Type X to quit or <RETURN> to proceed,
or enter new name. (Default extension: sty)

! Emergency stop.
<read *> 
         
l.9 \usepackage
               {amssymb}^^M
!  ==> Fatal error occurred, no output PDF file produced!
--- failed re-building ‘appreci8R.Rnw’

SUMMARY: processing the following file failed:
  ‘appreci8R.Rnw’

Error: Vignette re-building failed.
Execution halted