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BioC 3.4: BUILD report for lumi on zin1

This page was generated on 2016-09-21 03:36:11 -0700 (Wed, 21 Sep 2016).

Package 671/1257HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
lumi 2.25.0
Pan Du
Snapshot Date: 2016-09-19 19:15:14 -0700 (Mon, 19 Sep 2016)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/lumi
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: lumi
Version: 2.25.0
Command: /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data lumi
StartedAt: 2016-09-19 20:59:50 -0700 (Mon, 19 Sep 2016)
EndedAt: 2016-09-19 21:00:36 -0700 (Mon, 19 Sep 2016)
EllapsedTime: 46.2 seconds
RetCode: 1
Status:  ERROR 
PackageFile: None
PackageFileSize: NA

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data lumi
###
##############################################################################
##############################################################################


* checking for file ‘lumi/DESCRIPTION’ ... OK
* preparing ‘lumi’:
* checking DESCRIPTION meta-information ... OK
Warning: bad markup (extra space?) at lumiMethyR.Rd:18:16
Warning: bad markup (extra space?) at lumiMethyR.Rd:19:28
Warning: bad markup (extra space?) at lumiMethyR.Rd:20:13
* installing the package to build vignettes
* creating vignettes ... ERROR
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, 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

Welcome to Bioconductor

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

Setting options('download.file.method.GEOquery'='auto')
Setting options('GEOquery.inmemory.gpl'=FALSE)
Loading required package: AnnotationDbi
Loading required package: stats4
Loading required package: IRanges
Loading required package: S4Vectors

Attaching package: ‘S4Vectors’

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

    colMeans, colSums, expand.grid, rowMeans, rowSums

Loading required package: XML
Loading required package: lumiHumanIDMapping
Loading required package: lumiHumanAll.db
Loading required package: org.Hs.eg.db


lumiHumanAll.db is using or is likely to need access to special nuID
  identifiers.  Users can learn about these identifiers from vignette
  documentation provided with the lumi package.


Error: processing vignette 'lumi.Rnw' failed with diagnostics:
 chunk 14 (label = VST transform) 
Error in (function (od, vd)  : 
  object and replacement value dimnames differ
Execution halted