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### Running command:
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### /Library/Frameworks/R.framework/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data R453Plus1Toolbox
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* checking for file ‘R453Plus1Toolbox/DESCRIPTION’ ... OK
* preparing ‘R453Plus1Toolbox’:
* checking DESCRIPTION meta-information ... OK
* cleaning src
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘vignette.Rnw’ using Sweave
Loading required package: VariantAnnotation
Loading required package: BiocGenerics
Loading required package: generics
Attaching package: ‘generics’
The following objects are masked from ‘package:base’:
as.difftime, as.factor, as.ordered, intersect,
is.element, setdiff, setequal, union
Attaching package: ‘BiocGenerics’
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,
is.unsorted, lapply, mapply, match, mget, order,
paste, pmax, pmax.int, pmin, pmin.int, rank,
rbind, rownames, sapply, saveRDS, table, tapply,
unique, unsplit, which.max, which.min
Loading required package: MatrixGenerics
Loading required package: matrixStats
Attaching package: ‘MatrixGenerics’
The following objects are masked from ‘package:matrixStats’:
colAlls, colAnyNAs, colAnys, colAvgsPerRowSet,
colCollapse, colCounts, colCummaxs, colCummins,
colCumprods, colCumsums, colDiffs, colIQRDiffs,
colIQRs, colLogSumExps, colMadDiffs, colMads,
colMaxs, colMeans2, colMedians, colMins,
colOrderStats, colProds, colQuantiles, colRanges,
colRanks, colSdDiffs, colSds, colSums2,
colTabulates, colVarDiffs, colVars,
colWeightedMads, colWeightedMeans,
colWeightedMedians, colWeightedSds,
colWeightedVars, rowAlls, rowAnyNAs, rowAnys,
rowAvgsPerColSet, rowCollapse, rowCounts,
rowCummaxs, rowCummins, rowCumprods, rowCumsums,
rowDiffs, rowIQRDiffs, rowIQRs, rowLogSumExps,
rowMadDiffs, rowMads, rowMaxs, rowMeans2,
rowMedians, rowMins, rowOrderStats, rowProds,
rowQuantiles, rowRanges, rowRanks, rowSdDiffs,
rowSds, rowSums2, rowTabulates, rowVarDiffs,
rowVars, rowWeightedMads, rowWeightedMeans,
rowWeightedMedians, rowWeightedSds,
rowWeightedVars
Loading required package: GenomeInfoDb
Loading required package: S4Vectors
Loading required package: stats4
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: GenomicRanges
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")'.
Attaching package: ‘Biobase’
The following object is masked from ‘package:MatrixGenerics’:
rowMedians
The following objects are masked from ‘package:matrixStats’:
anyMissing, rowMedians
Loading required package: Rsamtools
Loading required package: Biostrings
Loading required package: XVector
Attaching package: ‘Biostrings’
The following object is masked from ‘package:base’:
strsplit
Attaching package: ‘VariantAnnotation’
The following object is masked from ‘package:base’:
tabulate
Loading required package: pwalign
Attaching package: ‘pwalign’
The following objects are masked from ‘package:Biostrings’:
PairwiseAlignments,
PairwiseAlignmentsSingleSubject, aligned,
alignedPattern, alignedSubject, compareStrings,
deletion, errorSubstitutionMatrices, indel,
insertion, mismatchSummary, mismatchTable, nedit,
nindel, nucleotideSubstitutionMatrix,
pairwiseAlignment, pattern, pid,
qualitySubstitutionMatrices, stringDist,
unaligned, writePairwiseAlignments
Warning in .local(dirname) : 'AVASet(dirname)' is deprecated.
Use 'AVASet(dirname, avaBin)' instead.
See help("Deprecated")
Reading sample data ... done
Reading reference sequences ... done
Reading variant data ... done
Reading amplicon data ... done
Variants:
Amplicons:
assayDataAmp:4 features, 6 samples
element names:forwCountrevCount
featureDataAmp:
Reference sequences:
Loading required package: BiocParallel
Loading required package: GenomicAlignments
combined forward & reverse filter set to 0.05
forward filter set to 0.1
reverse filter set to 0.05
combined forward & reverse filter set to 0
combined forward & reverse filter set to 0
Warning: Ensembl will soon enforce the use of https.
Ensure the 'host' argument includes "https://"
Reading data ...
... from /private/tmp/RtmpGyhSbt/Rinstedd014e0c3f8/R453Plus1Toolbox/extdata/MapperSet/N01
... from /private/tmp/RtmpGyhSbt/Rinstedd014e0c3f8/R453Plus1Toolbox/extdata/MapperSet/N03
... from /private/tmp/RtmpGyhSbt/Rinstedd014e0c3f8/R453Plus1Toolbox/extdata/MapperSet/N04
done
Error: processing vignette 'vignette.Rnw' failed with diagnostics:
chunk 45 (label = demultiplex)
Error in unlist(substitutionMatrix, substitutionMatrix) :
'recursive' must be a length-1 vector
--- failed re-building ‘vignette.Rnw’
SUMMARY: processing the following file failed:
‘vignette.Rnw’
Error: Vignette re-building failed.
Execution halted