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BUILD report for proFIA on malbec1

This page was generated on 2021-03-03 12:10:43 -0500 (Wed, 03 Mar 2021).

To the developers/maintainers of the proFIA package:
Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 1392/1974HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
proFIA 1.16.0
Alexis Delabriere
Snapshot Date: 2021-03-02 14:50:31 -0500 (Tue, 02 Mar 2021)
URL: https://git.bioconductor.org/packages/proFIA
Branch: RELEASE_3_12
Last Commit: 18a3bec
Last Changed Date: 2020-10-27 11:19:13 -0500 (Tue, 27 Oct 2020)
malbec1Linux (Ubuntu 18.04.5 LTS) / x86_64  OK    ERROR  skipped
nebbiolo1Linux (Ubuntu 20.04.2 LTS) / x86_64  OK    ERROR  skipped
tokay1Windows Server 2012 R2 Standard / x64  OK    ERROR  skippedskipped
merida1macOS 10.14.6 Mojave / x86_64  OK    ERROR  skippedskipped

Summary

Package: proFIA
Version: 1.16.0
Command: /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data proFIA
StartedAt: 2021-03-02 21:27:38 -0500 (Tue, 02 Mar 2021)
EndedAt: 2021-03-02 21:29:01 -0500 (Tue, 02 Mar 2021)
EllapsedTime: 82.9 seconds
RetCode: 1
Status:   ERROR  
PackageFile: None
PackageFileSize: NA

Command output

##############################################################################
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### Running command:
###
###   /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data proFIA
###
##############################################################################
##############################################################################


* checking for file ‘proFIA/DESCRIPTION’ ... OK
* preparing ‘proFIA’:
* checking DESCRIPTION meta-information ... OK
* cleaning src
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘proFIA-vignette.Rmd’ using rmarkdown
Loading required package: xcms
Loading required package: Biobase
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

Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

Loading required package: BiocParallel
Loading required package: MSnbase
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


This is xcms version 3.12.0 


Attaching package: 'xcms'

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

    sigma

1 directories have been found : mzML

6 files found in directories mzML
 
Create profile matrix with method 'bin' and step 1 ... OK
Create profile matrix with method 'bin' and step 1 ... OK
Create profile matrix with method 'bin' and step 1 ... OK
Beginning band detection for C100A

Create profile matrix with method 'bin' and step 1 ... OK
Beginning band detection for C100B

Create profile matrix with method 'bin' and step 1 ... OK
Beginning band detection for C10A

Create profile matrix with method 'bin' and step 1 ... OK
Beginning band detection for C10B

Create profile matrix with method 'bin' and step 1 ... OK
Beginning band detection for C1A

Create profile matrix with method 'bin' and step 1 ... OK
Beginning band detection for C1B

Create profile matrix with method 'bin' and step 1 ... OK
processing: /home/biocbuild/bbs-3.12-bioc/R/library/plasFIA/mzML/C100A.mzML

Quitting from lines 94-99 (proFIA-vignette.Rmd) 
Error: processing vignette 'proFIA-vignette.Rmd' failed with diagnostics:
argument "f" is missing, with no default
--- failed re-building ‘proFIA-vignette.Rmd’

SUMMARY: processing the following file failed:
  ‘proFIA-vignette.Rmd’

Error: Vignette re-building failed.
Execution halted