############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data proteomics ### ############################################################################## ############################################################################## * checking for file ‘proteomics/DESCRIPTION’ ... OK * preparing ‘proteomics’: * checking DESCRIPTION meta-information ... OK * installing the package to build vignettes * creating vignettes ... ERROR --- re-building ‘proteomics.Rmd’ using rmarkdown Warning: replacing previous import 'MSnbase::plot' by 'graphics::plot' when loading 'RforProteomics' This is the 'RforProteomics' version 1.32.0. 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 Warning: Dropping unknown biocViews terms: CopyNumberVariants Warning: Dropping unknown biocViews terms: NoViewProvided 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: GraphsAndNetworks 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: R.utils 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: CopyNumberVariants Warning: Dropping unknown biocViews terms: NoViewProvided 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: GraphsAndNetworks 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: R.utils 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: Colorectal, Cancer, TCGA, RNAExpressionData Warning: Dropping unknown biocViews terms: Cancer Warning: Dropping unknown biocViews terms: Cancer, Breast Warning: Dropping unknown biocViews terms: Phaeodactylum_tricornutum_data Warning: Dropping unknown biocViews terms: NoViewProvided Warning: Dropping unknown biocViews terms: NoViewProvided Warning: Dropping unknown biocViews terms: NoViewProvided Warning: Dropping unknown biocViews terms: NoViewProvided Warning: Dropping unknown biocViews terms: NoViewProvided Warning: Dropping unknown biocViews terms: Annotation Data Warning: Dropping unknown biocViews terms: Annotation Data Warning: Dropping unknown biocViews terms: Annotation Data Quitting from lines 209-212 (proteomics.Rmd) Error: processing vignette 'proteomics.Rmd' failed with diagnostics: Can not open file /Users/biocbuild/Library/Caches/org.R-project.R/R/rpx/fe872d9f90f7_TMT_Erwinia_1uLSike_Top10HCD_isol2_45stepped_60min_01-20141210.mzML! Original error was: Error in pwizModule$open(filename): [SpectrumList_mzML::create()] Bad istream. --- failed re-building ‘proteomics.Rmd’ SUMMARY: processing the following file failed: ‘proteomics.Rmd’ Error: Vignette re-building failed. Execution halted