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BUILD report for RforProteomics on malbec2

This page was generated on 2020-10-15 20:45:58 -0400 (Thu, 15 Oct 2020).

TO THE DEVELOPERS/MAINTAINERS OF THE RforProteomics PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 298/391HostnameOS / ArchINSTALLBUILDCHECK
RforProteomics 1.26.0
Laurent Gatto
Snapshot Date: 2020-10-15 07:30:17 -0400 (Thu, 15 Oct 2020)
URL: https://git.bioconductor.org/packages/RforProteomics
Branch: RELEASE_3_11
Last Commit: 5d70c79
Last Changed Date: 2020-04-27 15:15:40 -0400 (Mon, 27 Apr 2020)
malbec2 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK [ ERROR ] skipped 

Summary

Package: RforProteomics
Version: 1.26.0
Command: /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data RforProteomics
StartedAt: 2020-10-15 12:15:37 -0400 (Thu, 15 Oct 2020)
EndedAt: 2020-10-15 12:26:31 -0400 (Thu, 15 Oct 2020)
EllapsedTime: 653.7 seconds
RetCode: 1
Status:  ERROR 
PackageFile: None
PackageFileSize: NA

Command output

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### Running command:
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###   /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data RforProteomics
###
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* 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
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

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 object is masked from 'package:base':

    expand.grid

Loading required package: ProtGenerics

Attaching package: 'ProtGenerics'

The following object is masked from 'package:stats':

    smooth


This is MSnbase version 2.14.2 
  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 1.26.0.

  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

Bioconductor version 3.11 (BiocManager 1.30.10), ?BiocManager::install for help

This is MALDIquant version 1.19.3
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

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 1.28.0 
  Visit https://lgatto.github.io/pRoloc/ to get started.


This is pRolocdata version 1.26.0.
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:
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RNA-Seq, Differential Expression
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Bioinformatics
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HighThroughputSequencingData
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HighThroughputSequencing
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Bioinformatics
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HighThroughputSequencing
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NetworkAnalysis, GraphsAndNetworks
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Cancer, StemCells, HIV
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Experiment Data, Sequencing Data
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NoViewProvided
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Statistics
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Machine Learning, QC-RFSC, QC-RLSC, ComBat
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Regulation, HighThroughputSequencing, MultipleComparisons, Bioinformatics
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HighThroughputSequencing
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GO 
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NoViewProvided
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ConnectTools, HighThroughputSequencing
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Systems Biology, Pathway
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Bioinformatics
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Cancer
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Network Inference
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Statistics, Bioinformatics
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MultipleComparisons
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CopyNumber
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DataImport 
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SNPsAndGeneticVariability
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ImmunoOncologyGeneRegulation
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NoViewProvided
Warning: Dropping unknown biocViews terms:
CopyNumber, Mutations, Diagnosis, metastasis
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Bioinformatics
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Clustering.
Warning: Dropping unknown biocViews terms:
GeneticsCellBiology
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HighThroughputSequencing, HighThroughputSequencingData, Bioinformatics, MultipleComparisons
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NoViewProvided
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NoViewProvided
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Bioinformatics, Cancer, FlowCytData, DensityGating
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Gating
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GraphsAndNetworks
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NaturalLanguageProcessing
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Bioinformatics
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Bioinformatics
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HighThroughputSequencing
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Biological Question
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Bioinformatics, MultipleComparisons
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Statistical Method
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RNA-Seq, Differential Expression
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AMDIS, GCMS
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HighThroughputSequencingData
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R.utils
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MultipleComparisons
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Bioinformatics
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HighThroughputSequencing
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NetworkAnalysis, GraphsAndNetworks
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Cancer, StemCells, HIV
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Experiment Data, Sequencing Data
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Statistics
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Regulation, HighThroughputSequencing, MultipleComparisons, Bioinformatics
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GO 
trying URL 'ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2012/03/PXD000001/PXD000001_mztab.txt'
Content type 'unknown' length 864039 bytes (843 KB)
==================================================
Warning: Version 0.9 is deprecated. Please see '?readMzTabData' and '?MzTab' for details.
trying URL 'ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2012/03/PXD000001/TMT_Erwinia_1uLSike_Top10HCD_isol2_45stepped_60min_01-20141210.mzML'
Content type 'unknown' length 450032788 bytes (429.2 MB)
=
Quitting from lines 511-522 (RProtVis.Rmd) 
Error: processing vignette 'RProtVis.Rmd' failed with diagnostics:
cannot open URL 'ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2012/03/PXD000001/TMT_Erwinia_1uLSike_Top10HCD_isol2_45stepped_60min_01-20141210.mzML'
--- failed re-building ‘RProtVis.Rmd’

--- re-building ‘RforProteomics.Rmd’ using rmarkdown
Warning: Package 'IPPD' is deprecated and will be removed from Bioconductor
  version 3.12
starting worker pid=2241 on localhost:11432 at 12:24:47.569
starting worker pid=2240 on localhost:11432 at 12:24:47.585
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!
trying URL 'ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2012/03/PXD000001/TMT_Erwinia_1uLSike_Top10HCD_isol2_45stepped_60min_01.mzXML'
Content type 'unknown' length 243031280 bytes (231.8 MB)
===
Quitting from lines 519-523 (RforProteomics.Rmd) 
Error: processing vignette 'RforProteomics.Rmd' failed with diagnostics:
cannot open URL 'ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2012/03/PXD000001/TMT_Erwinia_1uLSike_Top10HCD_isol2_45stepped_60min_01.mzXML'
--- failed re-building ‘RforProteomics.Rmd’

SUMMARY: processing the following files failed:
  ‘RProtVis.Rmd’ ‘RforProteomics.Rmd’

Error: Vignette re-building failed.
Execution halted