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This page was generated on 2022-02-17 08:36:53 -0500 (Thu, 17 Feb 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_64R Under development (unstable) (2022-01-05 r81451) -- "Unsuffered Consequences" 1362
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BUILD results for RforProteomics on nebbiolo2


To the developers/maintainers of the RforProteomics package:
Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 305/406HostnameOS / ArchINSTALLBUILDCHECK
RforProteomics 1.33.0  (landing page)
Laurent Gatto
Snapshot Date: 2022-02-17 04:00:02 -0500 (Thu, 17 Feb 2022)
git_url: https://git.bioconductor.org/packages/RforProteomics
git_branch: master
git_last_commit: 5200bda
git_last_commit_date: 2021-10-26 11:58:00 -0500 (Tue, 26 Oct 2021)
nebbiolo2Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    ERROR  skipped

Summary

Package: RforProteomics
Version: 1.33.0
Command: /home/biocbuild/bbs-3.15-data-experiment/R/bin/R CMD build --keep-empty-dirs --no-resave-data RforProteomics
StartedAt: 2022-02-17 06:13:52 -0500 (Thu, 17 Feb 2022)
EndedAt: 2022-02-17 06:18:51 -0500 (Thu, 17 Feb 2022)
EllapsedTime: 299.1 seconds
RetCode: 1
Status:   ERROR  
PackageFile: None
PackageFileSize: NA

Command output

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.15-data-experiment/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

Attaching package: 'BiocGenerics'

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.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 objects are masked from 'package:base':

    I, expand.grid, unname

Loading required package: ProtGenerics

Attaching package: 'ProtGenerics'

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

    smooth


This is MSnbase version 2.21.5 
  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 1.33.0.

  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


This is MALDIquant version 1.21
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, transformIntensity

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 1.35.0 
  Visit https://lgatto.github.io/pRoloc/ to get started.


This is pRolocdata version 1.33.1.
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:
CopyNumberVariants
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Systems Biology, Pathway
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Bioinformatics
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Statistics, Bioinformatics
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CopyNumber
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SNPsAndGeneticVariability
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3' end sequencing, polyadenylation site, internal priming
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CopyNumber, Mutations, Diagnosis, metastasis
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Bioinformatics
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GeneticsCellBiology
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HighThroughputSequencing, HighThroughputSequencingData, Bioinformatics, MultipleComparisons
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Bioinformatics, Cancer, FlowCytData, DensityGating
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Bioinformatics
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HighThroughputSequencingData
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GraphsAndNetwork
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Statistics
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Infastructure
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PathBank, Panther
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HTA2.0
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MultipleComparisons
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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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Machine Learning, QC-RFSC, QC-RLSC, ComBat
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Regulation, HighThroughputSequencing, MultipleComparisons, Bioinformatics
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HighThroughputSequencing
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R.utils
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CopyNumberVariants
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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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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
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Clustering.
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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
Warning: Dropping unknown biocViews terms:
Gating
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NaturalLanguageProcessing
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Bioinformatics
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Bioinformatics
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NoViewProvided
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HighThroughputSequencing
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NoViewProvided
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Biological Question
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Bioinformatics, MultipleComparisons
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NoViewProvided
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Statistical Method
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Cancer
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RNA-Seq, Differential Expression
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Bioinformatics, Statistics, MultipleComparisons
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NoViewProvided
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AMDIS, GCMS
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Bioinformatics
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HighThroughputSequencingData
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NoViewProvided
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GraphsAndNetwork
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Statistics
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Infastructure
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PathBank, Panther
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NoViewProvided
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HTA2.0
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MultipleComparisons
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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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Machine Learning, QC-RFSC, QC-RLSC, ComBat
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Regulation, HighThroughputSequencing, MultipleComparisons, Bioinformatics
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HighThroughputSequencing
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R.utils
Warning: Version 0.9 is deprecated. Please see '?readMzTabData' and '?MzTab' for details.
Quitting from lines 518-522 (RProtVis.Rmd) 
Error: processing vignette 'RProtVis.Rmd' failed with diagnostics:
'from' must be a finite number
--- failed re-building ‘RProtVis.Rmd’

--- re-building ‘RforProteomics.Rmd’ using rmarkdown
starting worker pid=1255980 on localhost:11160 at 06:15:12.206
starting worker pid=1255981 on localhost:11160 at 06:15:12.299
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!
Error in x$.self$finalize() : attempt to apply non-function
Error in x$.self$finalize() : attempt to apply non-function
Warning: Removed 2 rows containing missing values (geom_bar).
Warning: Removed 2 rows containing missing values (geom_vline).
Warning: Removed 2 rows containing missing values (geom_text).
Warning in SpectrumSimilarity(as(simplottest[[1]], "data.frame"), as(simplottest[[2]],  :
  the m/z tolerance is set too high
trying URL 'http://www.uniprot.org/uniprot/P00924.fasta'
Content type 'text/plain' length 562 bytes
==================================================
downloaded 562 bytes

Quitting from lines 782-856 (RforProteomics.Rmd) 
Error: processing vignette 'RforProteomics.Rmd' failed with diagnostics:
package or namespace load failed for 'isobar':
 package slot missing from signature for generic 'coerce'
and classes IBSpectra, MSnSet
cannot use with duplicate class names (the package may need to be re-installed)
--- failed re-building ‘RforProteomics.Rmd’

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

Error: Vignette re-building failed.
Execution halted