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BioC 3.4: BUILD report for phenoTest on morelia

This page was generated on 2016-09-21 03:50:54 -0700 (Wed, 21 Sep 2016).

Package 892/1257HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
phenoTest 1.21.0
Evarist Planet
Snapshot Date: 2016-09-19 19:15:14 -0700 (Mon, 19 Sep 2016)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/phenoTest
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: phenoTest
Version: 1.21.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data phenoTest
StartedAt: 2016-09-19 22:11:11 -0700 (Mon, 19 Sep 2016)
EndedAt: 2016-09-19 22:11:49 -0700 (Mon, 19 Sep 2016)
EllapsedTime: 38.2 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 phenoTest
###
##############################################################################
##############################################################################


* checking for file ‘phenoTest/DESCRIPTION’ ... OK
* preparing ‘phenoTest’:
* checking DESCRIPTION meta-information ... OK
* 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")'.

Loading required package: annotate
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: Heatplus
Loading required package: BMA
Loading required package: survival
Loading required package: leaps
Loading required package: robustbase

Attaching package: ‘robustbase’

The following object is masked from ‘package:survival’:

    heart

The following object is masked from ‘package:Biobase’:

    rowMedians

Loading required package: inline
Loading required package: rrcov
Scalable Robust Estimators with High Breakdown Point (version 1.4-3)

Loading required package: ggplot2

Warning: replacing previous import ‘igraph::union’ by ‘GSEABase::union’ when loading ‘HTSanalyzeR’
/////////////////////////////////////////////////////////////////////////////

//------------------    Thanks for using HTSanalyzeR    -------------------//
 
//------------please use function changes() to see new changes-------------//

//------------please report any bug to xinwang2hms@gmail.com---------------//

/////////////////////////////////////////////////////////////////////////////

Error: processing vignette 'phenoTest.Rnw' failed with diagnostics:
 chunk 5 (label = pValueAdjust) 
Error in .validate_assayDataElementReplace(obj, value) : 
  object and replacement value have different dimensions
Execution halted