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BioC 2.14: BUILD report for categoryCompare on zin2

This page was generated on 2014-10-08 08:49:30 -0700 (Wed, 08 Oct 2014).

Package 122/824HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
categoryCompare 1.8.0
Robert M. Flight
Snapshot Date: 2014-10-07 17:20:37 -0700 (Tue, 07 Oct 2014)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_14/madman/Rpacks/categoryCompare
Last Changed Rev: 88838 / Revision: 95116
Last Changed Date: 2014-04-11 14:07:21 -0700 (Fri, 11 Apr 2014)
zin2 Linux (Ubuntu 12.04.4 LTS) / x86_64  NotNeeded [ ERROR ] skipped 
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  NotNeeded  OK  OK  OK 
petty Mac OS X Snow Leopard (10.6.8) / x86_64  NotNeeded  OK  OK  OK 
morelia Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK  OK  OK 

Summary

Package: categoryCompare
Version: 1.8.0
Command: /home/biocbuild/bbs-2.14-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data categoryCompare
StartedAt: 2014-10-07 20:15:59 -0700 (Tue, 07 Oct 2014)
EndedAt: 2014-10-07 20:18:15 -0700 (Tue, 07 Oct 2014)
EllapsedTime: 135.5 seconds
RetCode: 1
Status:  ERROR 
PackageFile: None
PackageFileSize: NA

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-2.14-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data categoryCompare
###
##############################################################################
##############################################################################


* checking for file ‘categoryCompare/DESCRIPTION’ ... OK
* preparing ‘categoryCompare’:
* 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 object is masked from ‘package:stats’:

    xtabs

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

    Filter, Find, Map, Position, Reduce,
    anyDuplicated, append, as.data.frame, as.vector,
    cbind, colnames, do.call, duplicated, eval,
    evalq, get, intersect, is.unsorted, lapply,
    mapply, match, mget, order, paste, pmax,
    pmax.int, pmin, pmin.int, rank, rbind, rep.int,
    rownames, sapply, setdiff, sort, table, tapply,
    union, unique, unlist

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: AnnotationDbi
Loading required package: GenomeInfoDb
Loading required package: org.Hs.eg.db
Loading required package: DBI



Attaching package: ‘genefilter’

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

    anyNA


Attaching package: ‘limma’

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

    plotMA

Warning: replacing previous import by ‘utils::head’ when loading ‘hgu95av2cdf’
Warning: replacing previous import by ‘utils::tail’ when loading ‘hgu95av2cdf’


Note: the specification for S3 class “AsIs” in package ‘XMLRPC’ seems equivalent to one from package ‘BiocGenerics’: not turning on duplicate class definitions for this class.

KEGG.db contains mappings based on older data because
  the original resource was removed from the the
  public domain before the most recent update was
  produced. This package should now be considered
  deprecated and future versions of Bioconductor may
  not have it available.  Users who want more current
  data are encouraged to look at the KEGGREST or
  reactome.db packages

Warning in makeValidccLists(.Object) : NAs introduced by coercion

Error: processing vignette 'categoryCompare_vignette.Rnw' failed with diagnostics:
 chunk 14 (label = ExamineResultsBP) 
Error in function (type, msg, asError = TRUE)  : couldn't connect to host
Execution halted