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BUILD report for RforProteomics on malbec2

This page was generated on 2019-10-17 16:51:26 -0400 (Thu, 17 Oct 2019).

Package 288/371HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
RforProteomics 1.22.0
Laurent Gatto
Snapshot Date: 2019-10-17 09:00:12 -0400 (Thu, 17 Oct 2019)
URL: https://git.bioconductor.org/packages/RforProteomics
Branch: RELEASE_3_9
Last Commit: 44f65d0
Last Changed Date: 2019-05-02 11:56:30 -0400 (Thu, 02 May 2019)
malbec2 Linux (Ubuntu 18.04.2 LTS) / x86_64  OK [ ERROR ] skipped 

Summary

Package: RforProteomics
Version: 1.22.0
Command: /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data RforProteomics
StartedAt: 2019-10-17 11:40:28 -0400 (Thu, 17 Oct 2019)
EndedAt: 2019-10-17 11:42:05 -0400 (Thu, 17 Oct 2019)
EllapsedTime: 96.7 seconds
RetCode: 1
Status:  ERROR 
PackageFile: None
PackageFileSize: NA

Command output

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### Running command:
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###   /home/biocbuild/bbs-3.9-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,
    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

This is MSnbase version 2.10.1 
  Visit https://lgatto.github.io/MSnbase/ to get started.


Attaching package: 'MSnbase'

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

    smooth

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

    trimws

Registered S3 method overwritten by 'R.oo':
  method        from       
  throw.default R.methodsS3
Warning: replacing previous import 'MSnbase::plot' by 'graphics::plot' when loading 'RforProteomics'

This is the 'RforProteomics' version 1.22.0.

  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 1.19.3
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, 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'

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    trim

Loading required package: XML

Attaching package: 'annotate'

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Loading required package: cluster
Loading required package: BiocParallel
Warning: replacing previous import 'mclust::dmvnorm' by 'mvtnorm::dmvnorm' when loading 'pRoloc'

This is pRoloc version 1.24.1 
  Visit https://lgatto.github.io/pRoloc/ to get started.


This is pRolocdata version 1.22.0.
Use 'pRolocdata()' to list available data sets.
Loading required package: msmsEDA

Attaching package: 'e1071'

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    impute

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Quitting from lines 166-196 (RProtVis.Rmd) 
Error: processing vignette 'RProtVis.Rmd' failed with diagnostics:
Recv failure: Connection reset by peer
--- failed re-building ‘RProtVis.Rmd’

--- re-building ‘RforProteomics.Rmd’ using rmarkdown

Attaching package: 'reshape2'

The following objects are masked from 'package:data.table':

    dcast, melt

starting worker pid=1479 on localhost:11544 at 11:41:55.994
starting worker pid=1494 on localhost:11544 at 11:41:56.230
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!
Quitting from lines 380-388 (RforProteomics.Rmd) 
Error: processing vignette 'RforProteomics.Rmd' failed with diagnostics:
Recv failure: Connection reset by peer
--- failed re-building ‘RforProteomics.Rmd’

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

Error: Vignette re-building failed.
Execution halted