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BioC 3.4: BUILD report for shinyMethyl on morelia

This page was generated on 2016-09-21 03:53:26 -0700 (Wed, 21 Sep 2016).

Package 1106/1257HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
shinyMethyl 1.8.0
Jean-Philippe Fortin
Snapshot Date: 2016-09-19 19:15:14 -0700 (Mon, 19 Sep 2016)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/shinyMethyl
Last Changed Rev: 119994 / Revision: 121152
Last Changed Date: 2016-08-09 08:59:58 -0700 (Tue, 09 Aug 2016)
zin1 Linux (Ubuntu 16.04 LTS) / x86_64  NotNeeded  ERROR  skipped 
moscato1 Windows Server 2008 R2 Standard (64-bit) / x64  NotNeeded  ERROR  skipped  skipped 
morelia Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded [ ERROR ] skipped  skipped 

Summary

Package: shinyMethyl
Version: 1.8.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data shinyMethyl
StartedAt: 2016-09-20 00:03:13 -0700 (Tue, 20 Sep 2016)
EndedAt: 2016-09-20 00:03:47 -0700 (Tue, 20 Sep 2016)
EllapsedTime: 34.1 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 shinyMethyl
###
##############################################################################
##############################################################################


* checking for file ‘shinyMethyl/DESCRIPTION’ ... OK
* preparing ‘shinyMethyl’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
Loading required package: minfi
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

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: lattice
Loading required package: GenomicRanges
Loading required package: stats4
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
Loading required package: SummarizedExperiment
Loading required package: Biostrings
Loading required package: XVector
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: shiny
Loading required package: matrixStats
matrixStats v0.50.2 (2016-04-24) successfully loaded. See ?matrixStats for help.

Attaching package: 'matrixStats'

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

    rowRanges

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

    anyMissing, rowMedians

Quitting from lines 78-80 (shinyMethyl.Rnw) 
Error: processing vignette 'shinyMethyl.Rnw' failed with diagnostics:
subscript out of bounds
Execution halted