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BioC experimental data: BUILD report for RforProteomics on malbec1

This page was generated on 2017年04月15日 16:49:34 -0400 (2017年4月15日).

Package 241/310 Hostname OS / Arch INSTALL BUILD CHECK BUILD BIN
RforProteomics 1.12.0
Laurent Gatto
Snapshot Date: 2017年04月15日 09:20:05 -0400 (Sat, 15 Apr 2017)
URL: https://hedgehog.fhcrc.org/bioc-data/branches/RELEASE_3_4/experiment/pkgs/RforProteomics
Last Changed Rev: 3958 / Revision: 4141
Last Changed Date: 2016年10月17日 14:47:53 -0400 (Mon, 17 Oct 2016)
malbec1 Linux (Ubuntu 16.04.1 LTS) / x86_64 NotNeeded [ ERROR ] skipped

Summary

Package: RforProteomics
Version: 1.12.0
Command: /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data RforProteomics
StartedAt: 2017年04月15日 10:10:52 -0400 (2017年4月15日)
EndedAt: 2017年04月15日 10:13:03 -0400 (2017年4月15日)
EllapsedTime: 130.8 seconds
RetCode: 1
Status: ERROR
PackageFile: None
PackageFileSize: NA

Command output

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### Running command:
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### /home/biocbuild/bbs-3.4-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, xtabs
The following objects are masked from 'package:base':
 Filter, Find, Map, Position, Reduce, anyDuplicated, append,
 as.data.frame, cbind, colnames, do.call, duplicated, eval,
 evalq, get, grep, grepl, intersect, is.unsorted, lapply,
 lengths, 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: BiocParallel
Loading required package: ProtGenerics
This is MSnbase version 2.0.2 
 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
The following object is masked from 'package:base':
 trimws
This is the 'RforProteomics' version 1.12.0.
 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')
Bioconductor version 3.4 (BiocInstaller 1.24.0), ?biocLite for help
Attaching package: 'xtable'
The following object is masked from 'package:RforProteomics':
 display
This is MALDIquant version 1.16.2
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, mass, mz, mz<-
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
The following objects are masked from 'package:base':
 colMeans, colSums, expand.grid, rowMeans, rowSums
Attaching package: 'IRanges'
The following object is masked from 'package:MALDIquant':
 trim
Loading required package: XML
Loading required package: cluster
This is pRoloc version 1.14.6 
 Read '?pRoloc' and references therein for information
 about the package and how to get started.
This is pRolocdata version 1.12.0.
Use 'pRolocdata()' to list available data sets.
Loading required package: msmsEDA
Warning: Dropping unknown biocViews terms:
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HTA2.0
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Bioinformatics
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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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NetworkAnalysis
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Cancer, StemCells, HIV
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NoViewProvided
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Statistics
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Statistical Method
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Regulation, HighThroughputSequencing, MultipleComparisons, Bioinformatics
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HighThroughputSequencing
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CopyNumberVariants
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NoViewProvided
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NoViewProvided
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Bioinformatics
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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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Statistics, Bioinformatics
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MultipleComparisons
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CopyNumber
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Bioinformatics, Enrichment
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SNPsAndGeneticVariability
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NoViewProvided
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Bioinformatics
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Bioinformatics
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Clustering.
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HighThroughputSequencing, HighThroughputSequencingData, Bioinformatics, MultipleComparisons
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NoViewProvided
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NoViewProvided
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HighThroughputSequencing
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Bioinformatics, Cancer, FlowCytData, StemCells, DensityGating
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Gating
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GraphsAndNetworks
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Bioinformatics
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Bioinformatics
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NoViewProvided
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HighThroughputSequencing
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Biological Question
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Bioinformatics, MultipleComparisons
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Cancer
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RNA-Seq, Differential Expression
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Bioinformatics, Statistics, MultipleComparisons
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AMDIS, GCMS
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Bioinformatics
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HighThroughputSequencingData
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GO 
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HTA2.0
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MultipleComparisons
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Bioinformatics
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Bioinformatics
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Statistics
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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
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/README.txt'
ftp data connection made, file length 1645 bytes
==================================================
downloaded 1645 bytes
Quitting from lines 511-521 (RProtVis.Rmd) 
Error: processing vignette 'RProtVis.Rmd' failed with diagnostics:
Unable to create valid cRamp object.
Execution halted

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