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BUILD report for a4 on malbec1

This page was generated on 2020-09-28 11:04:42 -0400 (Mon, 28 Sep 2020).

TO THE DEVELOPERS/MAINTAINERS OF THE a4 PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 1/1923HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
a4 1.37.0
Tobias Verbeke
Snapshot Date: 2020-09-27 14:41:58 -0400 (Sun, 27 Sep 2020)
URL: https://git.bioconductor.org/packages/a4
Branch: master
Last Commit: e86c9f6
Last Changed Date: 2020-04-27 14:25:31 -0400 (Mon, 27 Apr 2020)
malbec1 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK [ ERROR ] skipped 
nebbiolo1 Linux (Ubuntu 20.04.1 LTS) / x86_64  OK  ERROR  skipped 
tokay1 Windows Server 2012 R2 Standard / x64  OK  ERROR  skipped  skipped 
riesling1 Windows Server 2019 Standard / x64  OK  ERROR  skipped  skipped 
merida1 macOS 10.14.6 Mojave / x86_64  OK  ERROR  skipped  skipped 

Summary

Package: a4
Version: 1.37.0
Command: /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data a4
StartedAt: 2020-09-27 18:16:01 -0400 (Sun, 27 Sep 2020)
EndedAt: 2020-09-27 18:16:39 -0400 (Sun, 27 Sep 2020)
EllapsedTime: 38.6 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 a4
###
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* checking for file ‘a4/DESCRIPTION’ ... OK
* preparing ‘a4’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘a4vignette.Rnw’ using Sweave
Loading required package: a4Base
Loading required package: grid
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: AnnotationDbi
Loading required package: stats4
Loading required package: IRanges
Loading required package: S4Vectors

Attaching package: ‘S4Vectors’

The following object is masked from ‘package:base’:

    expand.grid

Loading required package: annaffy
Loading required package: GO.db

Loading required package: KEGG.db

KEGG.db contains mappings based on older
  data because the original resource was
  removed from the the public domain before
  the most recent update was produced. This
  package should now be considered
  deprecated and future versions of
  Bioconductor may not have it available.
  Users who want more current data are
  encouraged to look at the KEGGREST or
  reactome.db packages

Warning: Package 'KEGG.db' is deprecated and will be
  removed from Bioconductor version 3.12
Loading required package: mpm
Loading required package: MASS

Attaching package: ‘MASS’

The following object is masked from ‘package:AnnotationDbi’:

    select

Loading required package: KernSmooth
KernSmooth 2.23 loaded
Copyright M. P. Wand 1997-2009

mpm version 1.0-22

Loading required package: genefilter

Attaching package: ‘genefilter’

The following object is masked from ‘package:MASS’:

    area

Loading required package: limma

Attaching package: ‘limma’

The following object is masked from ‘package:BiocGenerics’:

    plotMA

Loading required package: multtest
Loading required package: glmnet
Loading required package: Matrix

Attaching package: ‘Matrix’

The following object is masked from ‘package:S4Vectors’:

    expand

Loaded glmnet 4.0-2
Loading required package: a4Preproc
Loading required package: a4Core

Attaching package: ‘a4Core’

The following object is masked from ‘package:limma’:

    topTable

Loading required package: gplots

Attaching package: ‘gplots’

The following object is masked from ‘package:multtest’:

    wapply

The following object is masked from ‘package:IRanges’:

    space

The following object is masked from ‘package:S4Vectors’:

    space

The following object is masked from ‘package:stats’:

    lowess


a4Base version 1.37.0

Loading required package: a4Classif
Loading required package: MLInterfaces
Loading required package: Rcpp
Loading required package: annotate
Loading required package: XML
Loading required package: cluster
Loading required package: ROCR
Loading required package: pamr
Loading required package: survival
Loading required package: varSelRF
Loading required package: randomForest
randomForest 4.6-14
Type rfNews() to see new features/changes/bug fixes.

Attaching package: ‘randomForest’

The following object is masked from ‘package:Biobase’:

    combine

The following object is masked from ‘package:BiocGenerics’:

    combine


a4Classif version 1.37.0

Loading required package: a4Reporting

a4 version 1.37.0

Loading required package: ALL
Loading required package: nlcv
Loading required package: xtable

Attaching package: ‘xtable’

The following object is masked from ‘package:a4Reporting’:

    xtable


nlcv version 0.3.5

Loading required package: hgu95av2.db
Loading required package: org.Hs.eg.db



Error: processing vignette 'a4vignette.Rnw' failed with diagnostics:
 chunk 15 (label = limma) 
Error in toptable(fit = fit[c("coefficients", "stdev.unscaled")], coef = coef,  : 
  could not find function "toptable"

--- failed re-building ‘a4vignette.Rnw’

SUMMARY: processing the following file failed:
  ‘a4vignette.Rnw’

Error: Vignette re-building failed.
Execution halted