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BUILD report for RforProteomics on malbec1

This page was generated on 2021-05-06 14:10:13 -0400 (Thu, 06 May 2021).

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 303/398HostnameOS / ArchINSTALLBUILDCHECK
RforProteomics 1.28.1  (landing page)
Laurent Gatto
Snapshot Date: 2021-05-06 09:00:13 -0400 (Thu, 06 May 2021)
URL: https://git.bioconductor.org/packages/RforProteomics
Branch: RELEASE_3_12
Last Commit: 96a57e3
Last Changed Date: 2021-01-15 12:17:32 -0400 (Fri, 15 Jan 2021)
malbec1Linux (Ubuntu 18.04.5 LTS) / x86_64  OK    ERROR  skipped

Summary

Package: RforProteomics
Version: 1.28.1
Command: /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data RforProteomics
StartedAt: 2021-05-06 11:14:45 -0400 (Thu, 06 May 2021)
EndedAt: 2021-05-06 11:20:17 -0400 (Thu, 06 May 2021)
EllapsedTime: 331.6 seconds
RetCode: 1
Status:   ERROR  
PackageFile: None
PackageFileSize: NA

Command output

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### Running command:
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###   /home/biocbuild/bbs-3.12-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.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 2.16.1 
  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 1.28.1.

  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')



Attaching package: 'RforProteomics'

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

    spectrum


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 1.30.0 
  Visit https://lgatto.github.io/pRoloc/ to get started.


This is pRolocdata version 1.28.0.
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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Machine Learning, QC-RFSC, QC-RLSC, ComBat
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Regulation, HighThroughputSequencing, MultipleComparisons, Bioinformatics
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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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NoViewProvided
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Bioinformatics
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Warning: Version 0.9 is deprecated. Please see '?readMzTabData' and '?MzTab' for details.
--- finished re-building ‘RProtVis.Rmd’

--- re-building ‘RforProteomics.Rmd’ using rmarkdown
starting worker pid=30189 on localhost:11767 at 11:16:30.494
starting worker pid=30188 on localhost:11767 at 11:16:30.498
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!
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
Warning in min(nchar(exppep)) :
  no non-missing arguments to min; returning Inf
trying URL 'http://www.uniprot.org/uniprot/P00924.fasta'
Warning in download.file("http://www.uniprot.org/uniprot/P00924.fasta",  :
  URL 'http://www.uniprot.org/uniprot/P00924.fasta': status was 'Failure when receiving data from the peer'
Quitting from lines 652-707 (RforProteomics.Rmd) 
Error: processing vignette 'RforProteomics.Rmd' failed with diagnostics:
cannot open URL 'http://www.uniprot.org/uniprot/P00924.fasta'
--- failed re-building ‘RforProteomics.Rmd’

SUMMARY: processing the following file failed:
  ‘RforProteomics.Rmd’

Error: Vignette re-building failed.
Execution halted