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BUILD report for RforProteomics on malbec1

This page was generated on 2019-04-16 15:26:06 -0400 (Tue, 16 Apr 2019).

Package 277/360HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
RforProteomics 1.20.0
Laurent Gatto
Snapshot Date: 2019-04-16 11:00:05 -0400 (Tue, 16 Apr 2019)
URL: https://git.bioconductor.org/packages/RforProteomics
Branch: RELEASE_3_8
Last Commit: e4de488
Last Changed Date: 2018-10-30 11:36:22 -0400 (Tue, 30 Oct 2018)
malbec1 Linux (Ubuntu 16.04.6 LTS) / x86_64  OK [ ERROR ] skipped 

Summary

Package: RforProteomics
Version: 1.20.0
Command: /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data RforProteomics
StartedAt: 2019-04-16 12:24:58 -0400 (Tue, 16 Apr 2019)
EndedAt: 2019-04-16 12:39:40 -0400 (Tue, 16 Apr 2019)
EllapsedTime: 881.6 seconds
RetCode: 1
Status:  ERROR 
PackageFile: None
PackageFileSize: NA

Command output

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### Running command:
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###   /home/biocbuild/bbs-3.8-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
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

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    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
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    intersect, is.unsorted, lapply, lengths, mapply, match, mget,
    order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind,
    rowMeans, rowSums, 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'

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Loading required package: ProtGenerics

This is MSnbase version 2.8.3 
  Visit https://lgatto.github.io/MSnbase/ to get started.


Attaching package: 'MSnbase'

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

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Warning: replacing previous import 'MSnbase::plot' by 'graphics::plot' when loading 'RforProteomics'

This is the 'RforProteomics' version 1.20.0.

  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':

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This is MALDIquant version 1.19.2
Quantitative Analysis of Mass Spectrometry Data
 See '?MALDIquant' for more information about this package.


Attaching package: 'MALDIquant'

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    estimateNoise, intensity, isEmpty, mz

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Loading required package: MLInterfaces
Loading required package: annotate
Loading required package: AnnotationDbi
Loading required package: IRanges

Attaching package: 'IRanges'

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Loading required package: XML

Attaching package: 'annotate'

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Loading required package: cluster
Loading required package: BiocParallel

This is pRoloc version 1.22.2 
  Visit https://lgatto.github.io/pRoloc/ to get started.


This is pRolocdata version 1.20.0.
Use 'pRolocdata()' to list available data sets.
Loading required package: msmsEDA

Attaching package: 'e1071'

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trying URL 'ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2012/03/PXD000001/PXD000001_mztab.txt'
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trying URL 'ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2012/03/PXD000001/TMT_Erwinia_1uLSike_Top10HCD_isol2_45stepped_60min_01-20141210.mzML'
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Attaching package: 'reshape2'

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starting worker pid=303 on localhost:11095 at 12:31:23.829
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55merge_omssa.mzid DONE!
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trying URL 'http://www.uniprot.org/uniprot/P00924.fasta'
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Quitting from lines 1490-1494 (RforProteomics.Rmd) 
Error: processing vignette 'RforProteomics.Rmd' failed with diagnostics:
cannot open the connection to 'http://cran.r-project.org/web/views/ChemPhys.html'
Execution halted