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BioC experimental data: BUILD report for RforProteomics on zin1

This page was generated on 2015-08-22 17:43:46 -0700 (Sat, 22 Aug 2015).

Package 194/246HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
RforProteomics 1.7.1
Laurent Gatto
Snapshot Date: 2015-08-22 06:15:25 -0700 (Sat, 22 Aug 2015)
URL: https://hedgehog.fhcrc.org/bioc-data/trunk/experiment/pkgs/RforProteomics
Last Changed Rev: 3313 / Revision: 3391
Last Changed Date: 2015-06-11 16:54:28 -0700 (Thu, 11 Jun 2015)
zin1 Linux (Ubuntu 14.04.2 LTS) / x86_64  NotNeeded [ ERROR ] skipped 
moscato1 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  NotNeeded  ERROR  skipped  skipped 
perceval Mac OS X Snow Leopard (10.6.8) / x86_64  NotNeeded  ERROR  skipped  skipped 

Summary

Package: RforProteomics
Version: 1.7.1
Command: /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data RforProteomics
StartedAt: 2015-08-22 07:15:52 -0700 (Sat, 22 Aug 2015)
EndedAt: 2015-08-22 07:17:04 -0700 (Sat, 22 Aug 2015)
EllapsedTime: 72.6 seconds
RetCode: 1
Status:  ERROR 
PackageFile: None
PackageFileSize: NA

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.2-bioc/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
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, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, as.vector, cbind, colnames, 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, rep.int, rownames,
    sapply, setdiff, sort, table, tapply, union, unique, unlist,
    unsplit

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: BiocParallel
Loading required package: ProtGenerics

This is MSnbase version 1.17.14 
  Read '?MSnbase' and references therein for information
  about the package and how to get started.


Attaching package: 'MSnbase'

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

    smooth

Note: the specification for S3 class "AsIs" in package 'RJSONIO' seems equivalent to one from package 'BiocGenerics': not turning on duplicate class definitions for this class.

This is the 'RforProteomics' version 1.7.1.

  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')


Bioconductor version 3.2 (BiocInstaller 1.19.13), ?biocLite for help

Attaching package: 'xtable'

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

    display


This is MALDIquant version 1.12
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':

    intensity, isEmpty

The following objects are masked from 'package:ProtGenerics':

    intensity, mass

Loading required package: MLInterfaces
Loading required package: annotate
Loading required package: AnnotationDbi
Loading required package: stats4
Loading required package: IRanges
Loading required package: S4Vectors

Attaching package: 'S4Vectors'

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

    isEmpty


Attaching package: 'IRanges'

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

    trim

Loading required package: XML
Loading required package: cluster
Note: the specification for S3 class "family" in package 'MatrixModels' seems equivalent to one from package 'lme4': not turning on duplicate class definitions for this class.

This is MSnbase version 1.9.6 
  Read '?pRoloc' and references therein for information
  about the package and how to get started.


This is pRolocdata version 1.7.2.
Use 'pRolocdata()' to list available data sets.
Loading required package: msmsEDA
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Bioinformatics
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Regulation, HighThroughputSequencing, MultipleComparisons, Bioinformatics
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Cancer
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HighThroughputSequencing
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HighThroughputSequencing
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CopyNumberVariants
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NoViewProvided
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Cancer
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AMDIS, GCMS
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GraphsAndNetwork
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Bioinformatics
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HighThroughputSequencingData
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Bioinformatics, GraphsAndNetworks
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NoViewProvided
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Bioinformatics, Visualisation
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Warning: Dropping unknown biocViews terms:
NetworkAnalysis, GraphsAndNetworks
Warning: Dropping unknown biocViews terms:
NetworkAnalysis
Warning: Dropping unknown biocViews terms:
Cancer, StemCells, HIV
Warning: Dropping unknown biocViews terms:
NoViewProvided
Warning: Dropping unknown biocViews terms:
Statistics
Warning: Dropping unknown biocViews terms:
Bioinformatics
Warning: Dropping unknown biocViews terms:
Regulation, HighThroughputSequencing, MultipleComparisons, Bioinformatics
Warning: Dropping unknown biocViews terms:
Cancer
Warning: Dropping unknown biocViews terms:
HighThroughputSequencing
Warning: Dropping unknown biocViews terms:
HighThroughputSequencing
Warning in extractPath(nodeind(thiss), nodeind(thisf[j]), curdi) :
  NAs introduced by coercion
Warning in extractPath(nodeind(thiss), nodeind(thisf[j]), curdi) :
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Warning in extractPath(nodeind(thiss), nodeind(thisf[j]), curdi) :
  NAs introduced by coercion
Warning in extractPath(nodeind(thiss), nodeind(thisf[j]), curdi) :
  NAs introduced by coercion
Warning in extractPath(nodeind(thiss), nodeind(thisf[j]), curdi) :
  NAs introduced by coercion
Warning in extractPath(nodeind(thiss), nodeind(thisf[j]), curdi) :
  NAs introduced by coercion
Warning in extractPath(nodeind(thiss), nodeind(thisf[j]), curdi) :
  NAs introduced by coercion
Warning in extractPath(nodeind(thiss), nodeind(thisf[j]), curdi) :
  NAs introduced by coercion
Warning in extractPath(nodeind(thiss), nodeind(thisf[j]), curdi) :
  NAs introduced by coercion
Warning in extractPath(nodeind(thiss), nodeind(thisf[j]), curdi) :
  NAs introduced by coercion
Warning in extractPath(nodeind(thiss), nodeind(thisf[j]), curdi) :
  NAs introduced by coercion
Warning in extractPath(nodeind(thiss), nodeind(thisf[j]), curdi) :
  NAs introduced by coercion
Warning in extractPath(nodeind(thiss), nodeind(thisf[j]), curdi) :
  NAs introduced by coercion
Warning in extractPath(nodeind(thiss), nodeind(thisf[j]), curdi) :
  NAs introduced by coercion
Warning in extractPath(nodeind(thiss), nodeind(thisf[j]), curdi) :
  NAs introduced by coercion
Warning in extractPath(nodeind(thiss), nodeind(thisf[j]), curdi) :
  NAs introduced by coercion
Warning in extractPath(nodeind(thiss), nodeind(thisf[j]), curdi) :
  NAs introduced by coercion
Warning in extractPath(nodeind(thiss), nodeind(thisf[j]), curdi) :
  NAs introduced by coercion
Warning in extractPath(nodeind(thiss), nodeind(thisf[j]), curdi) :
  NAs introduced by coercion
Warning in extractPath(nodeind(thiss), nodeind(thisf[j]), curdi) :
  NAs introduced by coercion
Warning in extractPath(nodeind(thiss), nodeind(thisf[j]), curdi) :
  NAs introduced by coercion
Warning in extractPath(nodeind(thiss), nodeind(thisf[j]), curdi) :
  NAs introduced by coercion
Warning in extractPath(nodeind(thiss), nodeind(thisf[j]), curdi) :
  NAs introduced by coercion
Warning in extractPath(nodeind(thiss), nodeind(thisf[j]), curdi) :
  NAs introduced by coercion
Warning in extractPath(nodeind(thiss), nodeind(thisf[j]), curdi) :
  NAs introduced by coercion
Warning in extractPath(nodeind(thiss), nodeind(thisf[j]), curdi) :
  NAs introduced by coercion
Warning in extractPath(nodeind(thiss), nodeind(thisf[j]), curdi) :
  NAs introduced by coercion
Warning in extractPath(nodeind(thiss), nodeind(thisf[j]), curdi) :
  NAs introduced by coercion
Warning in extractPath(nodeind(thiss), nodeind(thisf[j]), curdi) :
  NAs introduced by coercion
Warning in extractPath(nodeind(thiss), nodeind(thisf[j]), curdi) :
  NAs introduced by coercion
Warning in extractPath(nodeind(thiss), nodeind(thisf[j]), curdi) :
  NAs introduced by coercion
Warning in extractPath(nodeind(thiss), nodeind(thisf[j]), curdi) :
  NAs introduced by coercion
Warning in extractPath(nodeind(thiss), nodeind(thisf[j]), curdi) :
  NAs introduced by coercion
Warning in extractPath(nodeind(thiss), nodeind(thisf[j]), curdi) :
  NAs introduced by coercion
Warning in extractPath(nodeind(thiss), nodeind(thisf[j]), curdi) :
  NAs introduced by coercion
Warning in extractPath(nodeind(thiss), nodeind(thisf[j]), curdi) :
  NAs introduced by coercion
Warning in extractPath(nodeind(thiss), nodeind(thisf[j]), curdi) :
  NAs introduced by coercion
Warning in extractPath(nodeind(thiss), nodeind(thisf[j]), curdi) :
  NAs introduced by coercion
Warning in extractPath(nodeind(thiss), nodeind(thisf[j]), curdi) :
  NAs introduced by coercion
Warning in extractPath(nodeind(thiss), nodeind(thisf[j]), curdi) :
  NAs introduced by coercion
Warning in extractPath(nodeind(thiss), nodeind(thisf[j]), curdi) :
  NAs introduced by coercion
Warning in extractPath(nodeind(thiss), nodeind(thisf[j]), curdi) :
  NAs introduced by coercion
Warning in extractPath(nodeind(thiss), nodeind(thisf[j]), curdi) :
  NAs introduced by coercion
Warning in extractPath(nodeind(thiss), nodeind(thisf[j]), curdi) :
  NAs introduced by coercion
Warning in extractPath(nodeind(thiss), nodeind(thisf[j]), curdi) :
  NAs introduced by coercion
Warning in extractPath(nodeind(thiss), nodeind(thisf[j]), curdi) :
  NAs introduced by coercion
Warning in extractPath(nodeind(thiss), nodeind(thisf[j]), curdi) :
  NAs introduced by coercion
Warning in extractPath(nodeind(thiss), nodeind(thisf[j]), curdi) :
  NAs introduced by coercion
Warning in extractPath(nodeind(thiss), nodeind(thisf[j]), curdi) :
  NAs introduced by coercion
Warning in extractPath(nodeind(thiss), nodeind(thisf[j]), curdi) :
  NAs introduced by coercion
Warning in extractPath(nodeind(thiss), nodeind(thisf[j]), curdi) :
  NAs introduced by coercion
Warning in extractPath(nodeind(thiss), nodeind(thisf[j]), curdi) :
  NAs introduced by coercion
Warning in extractPath(nodeind(thiss), nodeind(thisf[j]), curdi) :
  NAs introduced by coercion
Warning in extractPath(nodeind(thiss), nodeind(thisf[j]), curdi) :
  NAs introduced by coercion
Warning in extractPath(nodeind(thiss), nodeind(thisf[j]), curdi) :
  NAs introduced by coercion
Warning in extractPath(nodeind(thiss), nodeind(thisf[j]), curdi) :
  NAs introduced by coercion
Warning in extractPath(nodeind(thiss), nodeind(thisf[j]), curdi) :
  NAs introduced by coercion
Warning in extractPath(nodeind(thiss), nodeind(thisf[j]), curdi) :
  NAs introduced by coercion
Warning in extractPath(nodeind(thiss), nodeind(thisf[j]), curdi) :
  NAs introduced by coercion
Warning in extractPath(nodeind(thiss), nodeind(thisf[j]), curdi) :
  NAs introduced by coercion
Warning in extractPath(nodeind(thiss), nodeind(thisf[j]), curdi) :
  NAs introduced by coercion
Warning in extractPath(nodeind(thiss), nodeind(thisf[j]), curdi) :
  NAs introduced by coercion
Warning in extractPath(nodeind(thiss), nodeind(thisf[j]), curdi) :
  NAs introduced by coercion
Warning in extractPath(nodeind(thiss), nodeind(thisf[j]), curdi) :
  NAs introduced by coercion
Warning in extractPath(nodeind(thiss), nodeind(thisf[j]), curdi) :
  NAs introduced by coercion
Warning in extractPath(nodeind(thiss), nodeind(thisf[j]), curdi) :
  NAs introduced by coercion
Warning in extractPath(nodeind(thiss), nodeind(thisf[j]), curdi) :
  NAs introduced by coercion
Warning in extractPath(nodeind(thiss), nodeind(thisf[j]), curdi) :
  NAs introduced by coercion
Warning in extractPath(nodeind(thiss), nodeind(thisf[j]), curdi) :
  NAs introduced by coercion
Warning in extractPath(nodeind(thiss), nodeind(thisf[j]), curdi) :
  NAs introduced by coercion
Warning in extractPath(nodeind(thiss), nodeind(thisf[j]), curdi) :
  NAs introduced by coercion
Warning in extractPath(nodeind(thiss), nodeind(thisf[j]), curdi) :
  NAs introduced by coercion
Warning in extractPath(nodeind(thiss), nodeind(thisf[j]), curdi) :
  NAs introduced by coercion
Warning in extractPath(nodeind(thiss), nodeind(thisf[j]), curdi) :
  NAs introduced by coercion
Warning in extractPath(nodeind(thiss), nodeind(thisf[j]), curdi) :
  NAs introduced by coercion
Warning in extractPath(nodeind(thiss), nodeind(thisf[j]), curdi) :
  NAs introduced by coercion
Warning in extractPath(nodeind(thiss), nodeind(thisf[j]), curdi) :
  NAs introduced by coercion
Warning in extractPath(nodeind(thiss), nodeind(thisf[j]), curdi) :
  NAs introduced by coercion
Warning in extractPath(nodeind(thiss), nodeind(thisf[j]), curdi) :
  NAs introduced by coercion
Warning in extractPath(nodeind(thiss), nodeind(thisf[j]), curdi) :
  NAs introduced by coercion
Warning in extractPath(nodeind(thiss), nodeind(thisf[j]), curdi) :
  NAs introduced by coercion
Warning in extractPath(nodeind(thiss), nodeind(thisf[j]), curdi) :
  NAs introduced by coercion
Warning in extractPath(nodeind(thiss), nodeind(thisf[j]), curdi) :
  NAs introduced by coercion
Warning in extractPath(nodeind(thiss), nodeind(thisf[j]), curdi) :
  NAs introduced by coercion
Warning in extractPath(nodeind(thiss), nodeind(thisf[j]), curdi) :
  NAs introduced by coercion
Warning in extractPath(nodeind(thiss), nodeind(thisf[j]), curdi) :
  NAs introduced by coercion
Warning in extractPath(nodeind(thiss), nodeind(thisf[j]), curdi) :
  NAs introduced by coercion
Warning in extractPath(nodeind(thiss), nodeind(thisf[j]), curdi) :
  NAs introduced by coercion
Warning in extractPath(nodeind(thiss), nodeind(thisf[j]), curdi) :
  NAs introduced by coercion
Warning in extractPath(nodeind(thiss), nodeind(thisf[j]), curdi) :
  NAs introduced by coercion
Warning in extractPath(nodeind(thiss), nodeind(thisf[j]), curdi) :
  NAs introduced by coercion
Warning in extractPath(nodeind(thiss), nodeind(thisf[j]), curdi) :
  NAs introduced by coercion
Warning in extractPath(nodeind(thiss), nodeind(thisf[j]), curdi) :
  NAs introduced by coercion
Warning in extractPath(nodeind(thiss), nodeind(thisf[j]), curdi) :
  NAs introduced by coercion
Warning in extractPath(nodeind(thiss), nodeind(thisf[j]), curdi) :
  NAs introduced by coercion
Warning in extractPath(nodeind(thiss), nodeind(thisf[j]), curdi) :
  NAs introduced by coercion
Warning in extractPath(nodeind(thiss), nodeind(thisf[j]), curdi) :
  NAs introduced by coercion
Warning in extractPath(nodeind(thiss), nodeind(thisf[j]), curdi) :
  NAs introduced by coercion
Warning in extractPath(nodeind(thiss), nodeind(thisf[j]), curdi) :
  NAs introduced by coercion
Warning in extractPath(nodeind(thiss), nodeind(thisf[j]), curdi) :
  NAs introduced by coercion
Warning in extractPath(nodeind(thiss), nodeind(thisf[j]), curdi) :
  NAs introduced by coercion
Warning in extractPath(nodeind(thiss), nodeind(thisf[j]), curdi) :
  NAs introduced by coercion
Warning in extractPath(nodeind(thiss), nodeind(thisf[j]), curdi) :
  NAs introduced by coercion
Warning in extractPath(nodeind(thiss), nodeind(thisf[j]), curdi) :
  NAs introduced by coercion
Warning in extractPath(nodeind(thiss), nodeind(thisf[j]), curdi) :
  NAs introduced by coercion
Warning in extractPath(nodeind(thiss), nodeind(thisf[j]), curdi) :
  NAs introduced by coercion
Warning in extractPath(nodeind(thiss), nodeind(thisf[j]), curdi) :
  NAs introduced by coercion
Warning in extractPath(nodeind(thiss), nodeind(thisf[j]), curdi) :
  NAs introduced by coercion
Warning in extractPath(nodeind(thiss), nodeind(thisf[j]), curdi) :
  NAs introduced by coercion
Warning in extractPath(nodeind(thiss), nodeind(thisf[j]), curdi) :
  NAs introduced by coercion
Warning in extractPath(nodeind(thiss), nodeind(thisf[j]), curdi) :
  NAs introduced by coercion
Warning in extractPath(nodeind(thiss), nodeind(thisf[j]), curdi) :
  NAs introduced by coercion
Warning in extractPath(nodeind(thiss), nodeind(thisf[j]), curdi) :
  NAs introduced by coercion
Warning in extractPath(nodeind(thiss), nodeind(thisf[j]), curdi) :
  NAs introduced by coercion
Warning in extractPath(nodeind(thiss), nodeind(thisf[j]), curdi) :
  NAs introduced by coercion
Warning in extractPath(nodeind(thiss), nodeind(thisf[j]), curdi) :
  NAs introduced by coercion
Warning in extractPath(nodeind(thiss), nodeind(thisf[j]), curdi) :
  NAs introduced by coercion
Warning in extractPath(nodeind(thiss), nodeind(thisf[j]), curdi) :
  NAs introduced by coercion
Warning in extractPath(nodeind(thiss), nodeind(thisf[j]), curdi) :
  NAs introduced by coercion
Warning in extractPath(nodeind(thiss), nodeind(thisf[j]), curdi) :
  NAs introduced by coercion
Warning in extractPath(nodeind(thiss), nodeind(thisf[j]), curdi) :
  NAs introduced by coercion
Warning in extractPath(nodeind(thiss), nodeind(thisf[j]), curdi) :
  NAs introduced by coercion
Warning in extractPath(nodeind(thiss), nodeind(thisf[j]), curdi) :
  NAs introduced by coercion
Warning in extractPath(nodeind(thiss), nodeind(thisf[j]), curdi) :
  NAs introduced by coercion
Warning in extractPath(nodeind(thiss), nodeind(thisf[j]), curdi) :
  NAs introduced by coercion
Warning in extractPath(nodeind(thiss), nodeind(thisf[j]), curdi) :
  NAs introduced by coercion
Warning in extractPath(nodeind(thiss), nodeind(thisf[j]), curdi) :
  NAs introduced by coercion
Warning in extractPath(nodeind(thiss), nodeind(thisf[j]), curdi) :
  NAs introduced by coercion
Warning in extractPath(nodeind(thiss), nodeind(thisf[j]), curdi) :
  NAs introduced by coercion
Warning in extractPath(nodeind(thiss), nodeind(thisf[j]), curdi) :
  NAs introduced by coercion
Warning in extractPath(nodeind(thiss), nodeind(thisf[j]), curdi) :
  NAs introduced by coercion
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trying URL 'ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2012/03/PXD000001/PXD000001_mztab.txt'
ftp data connection made, file length 864039 bytes
==================================================
downloaded 843 KB

Quitting from lines 159-188 (RProtVis.Rmd) 
Error: processing vignette 'RProtVis.Rmd' failed with diagnostics:
number of new names (6) should equal number of rows in AnnotatedDataFrame (0)
Execution halted