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This page was generated on 2022-06-30 14:50:10 -0400 (Thu, 30 Jun 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 20.04.4 LTS)x86_644.2.0 (2022-04-22) -- "Vigorous Calisthenics" 4380
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BUILD results for RforProteomics on nebbiolo1


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 306/410HostnameOS / ArchINSTALLBUILDCHECK
RforProteomics 1.34.0  (landing page)
Laurent Gatto
Snapshot Date: 2022-06-30 07:30:02 -0400 (Thu, 30 Jun 2022)
git_url: https://git.bioconductor.org/packages/RforProteomics
git_branch: RELEASE_3_15
git_last_commit: e58866e
git_last_commit_date: 2022-04-26 13:07:16 -0400 (Tue, 26 Apr 2022)
nebbiolo1Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    ERROR  skipped

Summary

Package: RforProteomics
Version: 1.34.0
Command: /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data RforProteomics
StartedAt: 2022-06-30 10:36:26 -0400 (Thu, 30 Jun 2022)
EndedAt: 2022-06-30 10:41:40 -0400 (Thu, 30 Jun 2022)
EllapsedTime: 314.9 seconds
RetCode: 1
Status:   ERROR  
PackageFile: None
PackageFileSize: NA

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.15-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
--- 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 2.22.0 
  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 1.34.0.

  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 1.36.0 
  Visit https://lgatto.github.io/pRoloc/ to get started.


This is pRolocdata version 1.34.0.
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

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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=481081 on localhost:11514 at 10:37:36.597
starting worker pid=481080 on localhost:11514 at 10:37:36.597
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
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; format=fasta' length 562 bytes
==================================================
downloaded 562 bytes

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Quitting from lines 1232-1236 (RforProteomics.Rmd) 
Error: processing vignette 'RforProteomics.Rmd' failed with diagnostics:
error in evaluating the argument 'x' in selecting a method for function 'grep': argument of length 0
--- failed re-building ‘RforProteomics.Rmd’

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

Error: Vignette re-building failed.
Execution halted