############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.15-data-experiment/R/bin/R CMD build --keep-empty-dirs --no-resave-data RforProteomics ### ############################################################################## ############################################################################## * checking for file ‘RforProteomics/DESCRIPTION’ ... OK * preparing ‘RforProteomics’: * checking DESCRIPTION meta-information ... OK * installing the package to build vignettes * creating vignettes ... ERROR --- re-building ‘RProtVis.Rmd’ using rmarkdown Loading required package: MSnbase Loading required package: BiocGenerics 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, 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: 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: mzR Loading required package: Rcpp Loading required package: S4Vectors Loading required package: stats4 Attaching package: 'S4Vectors' The following objects are masked from 'package:base': I, expand.grid, unname Loading required package: ProtGenerics Attaching package: 'ProtGenerics' The following object is masked from 'package:stats': smooth This is MSnbase version 2.21.5 Visit https://lgatto.github.io/MSnbase/ to get started. Attaching package: 'MSnbase' The following object is masked from 'package:base': trimws Warning: replacing previous import 'MSnbase::plot' by 'graphics::plot' when loading 'RforProteomics' This is the 'RforProteomics' version 1.33.0. To get started, visit http://lgatto.github.com/RforProteomics/ or, in R, open package vignettes by typing RforProteomics() # R/Bioc for proteomics overview RProtVis() # R/Bioc for proteomics visualisation For a full list of available documents: vignette(package='RforProteomics') Attaching package: 'RforProteomics' The following object is masked from 'package:stats': spectrum This is MALDIquant version 1.21 Quantitative Analysis of Mass Spectrometry Data See '?MALDIquant' for more information about this package. Attaching package: 'MALDIquant' The following objects are masked from 'package:MSnbase': estimateNoise, intensity, isEmpty, mz, transformIntensity The following objects are masked from 'package:ProtGenerics': intensity, intensity<-, mass, mz, mz<- The following object is masked from 'package:S4Vectors': isEmpty Loading required package: MLInterfaces Loading required package: annotate Loading required package: AnnotationDbi Loading required package: IRanges Attaching package: 'IRanges' The following object is masked from 'package:MALDIquant': trim Loading required package: XML Attaching package: 'annotate' The following object is masked from 'package:mzR': nChrom Loading required package: cluster Loading required package: BiocParallel This is pRoloc version 1.35.0 Visit https://lgatto.github.io/pRoloc/ to get started. This is pRolocdata version 1.33.1. Use 'pRolocdata()' to list available data sets. Loading required package: msmsEDA Attaching package: 'e1071' The following object is masked from 'package:MSnbase': impute The following object is masked from 'package:ProtGenerics': impute Warning: Dropping unknown biocViews terms: CopyNumberVariants Warning: Dropping unknown biocViews terms: NoViewProvided Warning: Dropping unknown biocViews terms: ConnectTools, HighThroughputSequencing Warning: Dropping unknown biocViews terms: Systems Biology, Pathway Warning: Dropping unknown biocViews terms: Bioinformatics Warning: Dropping unknown biocViews terms: Cancer Warning: Dropping unknown biocViews terms: Network Inference Warning: Dropping unknown biocViews terms: Statistics, Bioinformatics Warning: Dropping unknown biocViews terms: CopyNumber Warning: Dropping unknown biocViews terms: DataImport Warning: Dropping unknown biocViews terms: SNPsAndGeneticVariability Warning: Dropping unknown biocViews terms: 3' end sequencing, polyadenylation site, internal priming Warning: Dropping unknown biocViews terms: NoViewProvided Warning: Dropping unknown biocViews terms: CopyNumber, Mutations, Diagnosis, metastasis Warning: Dropping unknown biocViews terms: Bioinformatics Warning: Dropping unknown biocViews terms: Clustering. Warning: Dropping unknown biocViews terms: GeneticsCellBiology Warning: Dropping unknown biocViews terms: HighThroughputSequencing, HighThroughputSequencingData, Bioinformatics, MultipleComparisons Warning: Dropping unknown biocViews terms: NoViewProvided Warning: Dropping unknown biocViews terms: NoViewProvided Warning: Dropping unknown biocViews terms: Bioinformatics, Cancer, FlowCytData, DensityGating Warning: Dropping unknown biocViews terms: Gating Warning: Dropping unknown biocViews terms: NaturalLanguageProcessing Warning: Dropping unknown biocViews terms: Bioinformatics Warning: Dropping unknown biocViews terms: Bioinformatics Warning: Dropping unknown biocViews terms: NoViewProvided Warning: Dropping unknown biocViews terms: HighThroughputSequencing Warning: Dropping unknown biocViews terms: NoViewProvided Warning: Dropping unknown biocViews terms: Biological Question Warning: Dropping unknown biocViews terms: Bioinformatics, MultipleComparisons Warning: Dropping unknown biocViews terms: NoViewProvided Warning: Dropping unknown biocViews terms: Statistical Method Warning: Dropping unknown biocViews terms: Cancer Warning: Dropping unknown biocViews terms: RNA-Seq, Differential Expression Warning: Dropping unknown biocViews terms: Bioinformatics, Statistics, MultipleComparisons Warning: Dropping unknown biocViews terms: NoViewProvided Warning: Dropping unknown biocViews terms: AMDIS, GCMS Warning: Dropping unknown biocViews terms: Bioinformatics Warning: Dropping unknown biocViews terms: HighThroughputSequencingData Warning: Dropping unknown biocViews terms: NoViewProvided Warning: Dropping unknown biocViews terms: GraphsAndNetwork Warning: Dropping unknown biocViews terms: Statistics Warning: Dropping unknown biocViews terms: NoViewProvided Warning: Dropping unknown biocViews terms: Infastructure Warning: Dropping unknown biocViews terms: PathBank, Panther Warning: Dropping unknown biocViews terms: NoViewProvided Warning: Dropping unknown biocViews terms: HTA2.0 Warning: Dropping unknown biocViews terms: MultipleComparisons Warning: Dropping unknown biocViews terms: HighThroughputSequencing Warning: Dropping unknown biocViews terms: Bioinformatics Warning: Dropping unknown biocViews terms: HighThroughputSequencing Warning: Dropping unknown biocViews terms: NetworkAnalysis, GraphsAndNetworks Warning: Dropping unknown biocViews terms: Cancer, StemCells, HIV Warning: Dropping unknown biocViews terms: Experiment Data, Sequencing Data Warning: Dropping unknown biocViews terms: NoViewProvided Warning: Dropping unknown biocViews terms: Machine Learning, QC-RFSC, QC-RLSC, ComBat Warning: Dropping unknown biocViews terms: Regulation, HighThroughputSequencing, MultipleComparisons, Bioinformatics Warning: Dropping unknown biocViews terms: HighThroughputSequencing Warning: Dropping unknown biocViews terms: R.utils Warning: Dropping unknown biocViews terms: CopyNumberVariants Warning: Dropping unknown biocViews terms: NoViewProvided Warning: Dropping unknown biocViews terms: ConnectTools, HighThroughputSequencing Warning: Dropping unknown biocViews terms: Systems Biology, Pathway Warning: Dropping unknown biocViews terms: Bioinformatics Warning: Dropping unknown biocViews terms: Cancer Warning: Dropping unknown biocViews terms: Network Inference Warning: Dropping unknown biocViews terms: Statistics, Bioinformatics Warning: Dropping unknown biocViews terms: CopyNumber Warning: Dropping unknown biocViews terms: DataImport Warning: Dropping unknown biocViews terms: SNPsAndGeneticVariability Warning: Dropping unknown biocViews terms: 3' end sequencing, polyadenylation site, internal priming Warning: Dropping unknown biocViews terms: NoViewProvided Warning: Dropping unknown biocViews terms: CopyNumber, Mutations, Diagnosis, metastasis Warning: Dropping unknown biocViews terms: Bioinformatics Warning: Dropping unknown biocViews terms: Clustering. Warning: Dropping unknown biocViews terms: GeneticsCellBiology Warning: Dropping unknown biocViews terms: HighThroughputSequencing, HighThroughputSequencingData, Bioinformatics, MultipleComparisons Warning: Dropping unknown biocViews terms: NoViewProvided Warning: Dropping unknown biocViews terms: NoViewProvided Warning: Dropping unknown biocViews terms: Bioinformatics, Cancer, FlowCytData, DensityGating Warning: Dropping unknown biocViews terms: Gating Warning: Dropping unknown biocViews terms: NaturalLanguageProcessing Warning: Dropping unknown biocViews terms: Bioinformatics Warning: Dropping unknown biocViews terms: Bioinformatics Warning: Dropping unknown biocViews terms: NoViewProvided Warning: Dropping unknown biocViews terms: HighThroughputSequencing Warning: Dropping unknown biocViews terms: NoViewProvided Warning: Dropping unknown biocViews terms: Biological Question Warning: Dropping unknown biocViews terms: Bioinformatics, MultipleComparisons Warning: Dropping unknown biocViews terms: NoViewProvided Warning: Dropping unknown biocViews terms: Statistical Method Warning: Dropping unknown biocViews terms: Cancer Warning: Dropping unknown biocViews terms: RNA-Seq, Differential Expression Warning: Dropping unknown biocViews terms: Bioinformatics, Statistics, MultipleComparisons Warning: Dropping unknown biocViews terms: NoViewProvided Warning: Dropping unknown biocViews terms: AMDIS, GCMS Warning: Dropping unknown biocViews terms: Bioinformatics Warning: Dropping unknown biocViews terms: HighThroughputSequencingData Warning: Dropping unknown biocViews terms: NoViewProvided Warning: Dropping unknown biocViews terms: GraphsAndNetwork Warning: Dropping unknown biocViews terms: Statistics Warning: Dropping unknown biocViews terms: NoViewProvided Warning: Dropping unknown biocViews terms: Infastructure Warning: Dropping unknown biocViews terms: PathBank, Panther Warning: Dropping unknown biocViews terms: NoViewProvided Warning: Dropping unknown biocViews terms: HTA2.0 Warning: Dropping unknown biocViews terms: MultipleComparisons Warning: Dropping unknown biocViews terms: HighThroughputSequencing Warning: Dropping unknown biocViews terms: Bioinformatics Warning: Dropping unknown biocViews terms: HighThroughputSequencing Warning: Dropping unknown biocViews terms: NetworkAnalysis, GraphsAndNetworks Warning: Dropping unknown biocViews terms: Cancer, StemCells, HIV Warning: Dropping unknown biocViews terms: Experiment Data, Sequencing Data Warning: Dropping unknown biocViews terms: NoViewProvided Warning: Dropping unknown biocViews terms: Machine Learning, QC-RFSC, QC-RLSC, ComBat Warning: Dropping unknown biocViews terms: Regulation, HighThroughputSequencing, MultipleComparisons, Bioinformatics Warning: Dropping unknown biocViews terms: HighThroughputSequencing Warning: Dropping unknown biocViews terms: R.utils Warning: Version 0.9 is deprecated. Please see '?readMzTabData' and '?MzTab' for details. Quitting from lines 518-522 (RProtVis.Rmd) Error: processing vignette 'RProtVis.Rmd' failed with diagnostics: 'from' must be a finite number --- failed re-building ‘RProtVis.Rmd’ --- re-building ‘RforProteomics.Rmd’ using rmarkdown starting worker pid=1255980 on localhost:11160 at 06:15:12.206 starting worker pid=1255981 on localhost:11160 at 06:15:12.299 Loading required package: mzID Loading required package: mzID loaded mzID and set parent environment loaded mzID and set parent environment reading 55merge_omssa.mzid... reading 55merge_tandem.mzid... 55merge_omssa.mzid DONE! 55merge_tandem.mzid DONE! Error in x$.self$finalize() : attempt to apply non-function Error in x$.self$finalize() : attempt to apply non-function Warning: Removed 2 rows containing missing values (geom_bar). Warning: Removed 2 rows containing missing values (geom_vline). Warning: Removed 2 rows containing missing values (geom_text). Warning in SpectrumSimilarity(as(simplottest[[1]], "data.frame"), as(simplottest[[2]], : the m/z tolerance is set too high trying URL 'http://www.uniprot.org/uniprot/P00924.fasta' Content type 'text/plain' length 562 bytes ================================================== downloaded 562 bytes Quitting from lines 782-856 (RforProteomics.Rmd) Error: processing vignette 'RforProteomics.Rmd' failed with diagnostics: package or namespace load failed for 'isobar': package slot missing from signature for generic 'coerce' and classes IBSpectra, MSnSet cannot use with duplicate class names (the package may need to be re-installed) --- failed re-building ‘RforProteomics.Rmd’ SUMMARY: processing the following files failed: ‘RProtVis.Rmd’ ‘RforProteomics.Rmd’ Error: Vignette re-building failed. Execution halted