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BioC 3.5: BUILD report for conumee on oaxaca

This page was generated on 2017-03-04 16:49:39 -0500 (Sat, 04 Mar 2017).

Package 261/1339HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
conumee 1.9.0
Volker Hovestadt
Snapshot Date: 2017-03-03 17:15:47 -0500 (Fri, 03 Mar 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/conumee
Last Changed Rev: 122712 / Revision: 127142
Last Changed Date: 2016-10-17 15:10:43 -0400 (Mon, 17 Oct 2016)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  NotNeeded  ERROR  skipped 
tokay2 Windows Server 2012 R2 Standard / x64  NotNeeded  ERROR  skipped  skipped 
toluca2 Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  ERROR  skipped  skipped 
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded [ ERROR ] skipped  skipped 

Summary

Package: conumee
Version: 1.9.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data conumee
StartedAt: 2017-03-03 20:03:25 -0800 (Fri, 03 Mar 2017)
EndedAt: 2017-03-03 20:08:16 -0800 (Fri, 03 Mar 2017)
EllapsedTime: 290.2 seconds
RetCode: 1
Status:  ERROR 
PackageFile: None
PackageFileSize: NA

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data conumee
###
##############################################################################
##############################################################################


* checking for file ‘conumee/DESCRIPTION’ ... OK
* preparing ‘conumee’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
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, cbind, colMeans, colSums, 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, rowMeans,
    rowSums, rownames, sapply, setdiff, sort, table, tapply,
    union, unique, unsplit, which, which.max, which.min

Loading required package: GenomicRanges
Loading required package: stats4
Loading required package: S4Vectors

Attaching package: 'S4Vectors'

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

    expand.grid

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

Loading required package: DelayedArray
Loading required package: matrixStats
matrixStats v0.51.0 (2016-10-08) successfully loaded. See ?matrixStats for help.

Attaching package: 'matrixStats'

The following objects are masked from 'package:Biobase':

    anyMissing, rowMedians


Attaching package: 'DelayedArray'

The following objects are masked from 'package:matrixStats':

    colMaxs, rowMaxs

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

    apply


Attaching package: 'SummarizedExperiment'

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

    rowRanges

Loading required package: Biostrings
Loading required package: XVector

Attaching package: 'Biostrings'

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

    type

Loading required package: bumphunter
Loading required package: foreach
Loading required package: iterators
Loading required package: locfit
locfit 1.5-9.1 	 2013-03-22
Setting options('download.file.method.GEOquery'='auto')
Setting options('GEOquery.inmemory.gpl'=FALSE)
Loading required package: IlluminaHumanMethylation450kmanifest
Loading required package: IlluminaHumanMethylation450kanno.ilmn12.hg19
Loading required package: IlluminaHumanMethylationEPICmanifest
Loading required package: IlluminaHumanMethylationEPICanno.ilm10b2.hg19

Attaching package: 'IlluminaHumanMethylationEPICanno.ilm10b2.hg19'

The following objects are masked from 'package:IlluminaHumanMethylation450kanno.ilmn12.hg19':

    Islands.UCSC, Locations, Manifest, Other,
    SNPs.132CommonSingle, SNPs.135CommonSingle,
    SNPs.137CommonSingle, SNPs.138CommonSingle,
    SNPs.141CommonSingle, SNPs.142CommonSingle,
    SNPs.144CommonSingle, SNPs.146CommonSingle,
    SNPs.147CommonSingle, SNPs.Illumina

downloading 6042324037_R05C02_Grn.idat - done.
downloading 6042324037_R05C02_Red.idat - done.
downloading 6042324037_R06C01_Grn.idat - done.
downloading 6042324037_R06C01_Red.idat - done.
Quitting from lines 59-62 (conumee.Rmd) 
Error: processing vignette 'conumee.Rmd' failed with diagnostics:
'assay(<RGChannelSet>, i="character", ...)' invalid subscript 'i'
no slot of name "assays" for this object of class "RGChannelSet"
Execution halted