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BUILD report for cgdv17 on malbec2

This page was generated on 2021-01-14 15:58:58 -0500 (Thu, 14 Jan 2021).

TO THE DEVELOPERS/MAINTAINERS OF THE cgdv17 PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 55/385HostnameOS / ArchINSTALLBUILDCHECK
cgdv17 0.29.1
VJ Carey
Snapshot Date: 2021-01-14 09:00:13 -0500 (Thu, 14 Jan 2021)
URL: https://git.bioconductor.org/packages/cgdv17
Branch: master
Last Commit: 8e1b19a
Last Changed Date: 2020-11-30 08:21:37 -0500 (Mon, 30 Nov 2020)
malbec2 Linux (Ubuntu 20.04.1 LTS) / x86_64  OK [ ERROR ] skipped 
riesling1 Windows Server 2019 Standard / x64  OK  ERROR  skipped 

Summary

Package: cgdv17
Version: 0.29.1
Command: /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data cgdv17
StartedAt: 2021-01-14 10:23:58 -0500 (Thu, 14 Jan 2021)
EndedAt: 2021-01-14 10:24:56 -0500 (Thu, 14 Jan 2021)
EllapsedTime: 58.1 seconds
RetCode: 1
Status:  ERROR 
PackageFile: None
PackageFileSize: NA

Command output

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### Running command:
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###   /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data cgdv17
###
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* checking for file ‘cgdv17/DESCRIPTION’ ... OK
* preparing ‘cgdv17’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘cgdv.Rnw’ using Sweave
Loading required package: VariantAnnotation
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: MatrixGenerics
Loading required package: matrixStats

Attaching package: ‘MatrixGenerics’

The following objects are masked from ‘package:matrixStats’:

    colAlls, colAnyNAs, colAnys, colAvgsPerRowSet, colCollapse,
    colCounts, colCummaxs, colCummins, colCumprods, colCumsums,
    colDiffs, colIQRDiffs, colIQRs, colLogSumExps, colMadDiffs,
    colMads, colMaxs, colMeans2, colMedians, colMins, colOrderStats,
    colProds, colQuantiles, colRanges, colRanks, colSdDiffs, colSds,
    colSums2, colTabulates, colVarDiffs, colVars, colWeightedMads,
    colWeightedMeans, colWeightedMedians, colWeightedSds,
    colWeightedVars, rowAlls, rowAnyNAs, rowAnys, rowAvgsPerColSet,
    rowCollapse, rowCounts, rowCummaxs, rowCummins, rowCumprods,
    rowCumsums, rowDiffs, rowIQRDiffs, rowIQRs, rowLogSumExps,
    rowMadDiffs, rowMads, rowMaxs, rowMeans2, rowMedians, rowMins,
    rowOrderStats, rowProds, rowQuantiles, rowRanges, rowRanks,
    rowSdDiffs, rowSds, rowSums2, rowTabulates, rowVarDiffs, rowVars,
    rowWeightedMads, rowWeightedMeans, rowWeightedMedians,
    rowWeightedSds, rowWeightedVars

Loading required package: GenomeInfoDb
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: IRanges
Loading required package: GenomicRanges
Loading required package: SummarizedExperiment
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")'.


Attaching package: ‘Biobase’

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

    rowMedians

The following objects are masked from ‘package:matrixStats’:

    anyMissing, rowMedians

Loading required package: Rsamtools
Loading required package: Biostrings
Loading required package: XVector

Attaching package: ‘Biostrings’

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

    strsplit


Attaching package: ‘VariantAnnotation’

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

    tabulate

Warning: Package 'cgdv17' is deprecated and will be removed from Bioconductor
  version 3.14
Loading required package: GenomicFeatures
Loading required package: AnnotationDbi


Error: processing vignette 'cgdv.Rnw' failed with diagnostics:
 chunk 7 (label = getd) 
Error in library(GGtools) : there is no package called ‘GGtools’

--- failed re-building ‘cgdv.Rnw’

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

Error: Vignette re-building failed.
Execution halted