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BioC 3.3: BUILD report for customProDB on zin2

This page was generated on 2016-10-13 12:43:58 -0700 (Thu, 13 Oct 2016).

Package 265/1210HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
customProDB 1.12.1
xiaojing wang
Snapshot Date: 2016-10-12 17:20:15 -0700 (Wed, 12 Oct 2016)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_3/madman/Rpacks/customProDB
Last Changed Rev: 122247 / Revision: 122332
Last Changed Date: 2016-10-12 07:16:49 -0700 (Wed, 12 Oct 2016)
zin2 Linux (Ubuntu 14.04.2 LTS) / x86_64  OK [ ERROR ] skipped 
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  OK  OK  OK YES, new version is higher than in internal repository
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  OK  OK  ERROR  OK 

Summary

Package: customProDB
Version: 1.12.1
Command: /home/biocbuild/bbs-3.3-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data customProDB
StartedAt: 2016-10-12 20:52:25 -0700 (Wed, 12 Oct 2016)
EndedAt: 2016-10-12 20:52:49 -0700 (Wed, 12 Oct 2016)
EllapsedTime: 24.3 seconds
RetCode: 1
Status:  ERROR 
PackageFile: None
PackageFileSize: NA

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.3-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data customProDB
###
##############################################################################
##############################################################################


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

Loading required package: S4Vectors
Loading required package: stats4

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: AnnotationDbi
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: biomaRt
Build TranscriptDB object (txdb.sqlite) ... 

Error: processing vignette 'customProDB.Rnw' failed with diagnostics:
 chunk 4 (label = PrepareAnnoRef) 
Error in `genome<-`(`*tmp*`, value = "hg19") : 
  Failed to set session genome to 'hg19'
Execution halted