Package: RefNet

Version: 1.20.0

Command: chmod a+r RefNet -R && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD build --keep-empty-dirs --no-resave-data RefNet

StartedAt: 2019-10-15 22:54:22 -0400 (Tue, 15 Oct 2019)

EndedAt: 2019-10-15 22:55:26 -0400 (Tue, 15 Oct 2019)

EllapsedTime: 63.4 seconds

RetCode: 1

Status:  ERROR

PackageFile: None

PackageFileSize: NA

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### Running command:
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###   chmod a+r RefNet -R && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD build --keep-empty-dirs --no-resave-data RefNet
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* checking for file 'RefNet/DESCRIPTION' ... OK
* preparing 'RefNet':
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building 'RefNet.Rnw' using Sweave
Loading required package: IRanges
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: S4Vectors
Loading required package: stats4

Attaching package: 'S4Vectors'

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    expand.grid


Attaching package: 'IRanges'

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Loading required package: PSICQUIC
Loading required package: biomaRt
Loading required package: httr
Loading required package: plyr

Attaching package: 'plyr'

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

    desc

The following object is masked from 'package:S4Vectors':

    rename

Warning: replacing previous import 'IRanges::desc' by 'plyr::desc' when loading 'PSICQUIC'
Loading required package: AnnotationHub
Loading required package: BiocFileCache
Loading required package: dbplyr
Loading required package: RCurl
Loading required package: bitops
Loading required package: shiny
snapshotDate(): 2019-05-02
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Loading required package: AnnotationDbi
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:AnnotationHub':

    cache

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

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Error: processing vignette 'RefNet.Rnw' failed with diagnostics:
 chunk 12 (label = eliminateDups) 
Error in addStandardNames(idMapper, tbl.8) : object 'idMapper' not found

--- failed re-building 'RefNet.Rnw'

SUMMARY: processing the following file failed:
  'RefNet.Rnw'

Error: Vignette re-building failed.
Execution halted