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BioC 3.4: BUILD report for goseq on zin1

This page was generated on 2016-09-21 03:36:58 -0700 (Wed, 21 Sep 2016).

Package 529/1257HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
goseq 1.25.0
Nadia Davidson , Anthony Hawkins
Snapshot Date: 2016-09-19 19:15:14 -0700 (Mon, 19 Sep 2016)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/goseq
Last Changed Rev: 117081 / Revision: 121152
Last Changed Date: 2016-05-03 14:30:44 -0700 (Tue, 03 May 2016)
zin1 Linux (Ubuntu 16.04 LTS) / x86_64  OK [ ERROR ] skipped 
moscato1 Windows Server 2008 R2 Standard (64-bit) / x64  OK  ERROR  skipped  skipped 
morelia Mac OS X Mavericks (10.9.5) / x86_64  OK  ERROR  skipped  skipped 

Summary

Package: goseq
Version: 1.25.0
Command: /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data goseq
StartedAt: 2016-09-19 21:43:31 -0700 (Mon, 19 Sep 2016)
EndedAt: 2016-09-19 21:44:23 -0700 (Mon, 19 Sep 2016)
EllapsedTime: 52.1 seconds
RetCode: 1
Status:  ERROR 
PackageFile: None
PackageFileSize: NA

Command output

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data goseq
###
##############################################################################
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* checking for file ‘goseq/DESCRIPTION’ ... OK
* preparing ‘goseq’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
Loading required package: BiasedUrn
Loading required package: geneLenDataBase

Loading required package: limma
Loading required package: rtracklayer
Loading required package: GenomicRanges
Loading required package: stats4
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 object is masked from ‘package:limma’:

    plotMA

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

    IQR, mad, xtabs

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

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, cbind, colnames, do.call, duplicated, eval, evalq, get,
    grep, grepl, intersect, is.unsorted, lapply, lengths, 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

Attaching package: ‘S4Vectors’

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

    colMeans, colSums, expand.grid, rowMeans, rowSums

Loading required package: IRanges
Loading required package: GenomeInfoDb

Error: processing vignette 'goseq.Rnw' failed with diagnostics:
 chunk 9 (label = head_organisms) 
Error in `[<-.data.frame`(`*tmp*`, nrow(base) + 1, , value = c("geneSymbol",  : 
  replacement has 4 items, need 5
Execution halted