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Package 203/419HostnameOS / ArchBUILDCHECKBUILD BIN
HTSanalyzeR 2.3.5
Xin Wang
Snapshot Date: 2011-04-06 23:24:01 -0700 (Wed, 06 Apr 2011)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_7/madman/Rpacks/HTSanalyzeR
Last Changed Rev: 53612 / Revision: 54588
Last Changed Date: 2011-03-11 07:35:16 -0800 (Fri, 11 Mar 2011)
lamb2 Linux (openSUSE 11.2) / x86_64  OK [ OK ]
liverpool Windows Server 2003 R2 (32-bit) / x64  OK  OK  OK 
gewurz Windows Server 2008 R2 Enterprise (64-bit) / x64  OK  OK  OK 

Summary

Package: HTSanalyzeR
Version: 2.3.5
Command: /home/biocbuild/bbs-2.7-bioc/R/bin/R CMD check --no-vignettes --timings HTSanalyzeR_2.3.5.tar.gz
StartedAt: 2011-04-07 07:04:58 -0700 (Thu, 07 Apr 2011)
EndedAt: 2011-04-07 07:08:06 -0700 (Thu, 07 Apr 2011)
EllapsedTime: 188.1 seconds
RetCode: 0
Status:  OK 
CheckDir: HTSanalyzeR.Rcheck
Warnings: 0

Command output

* using log directory ‘/loc/home/biocbuild/bbs-2.7-bioc/meat/HTSanalyzeR.Rcheck’
* using R version 2.12.2 (2011-02-25)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘HTSanalyzeR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘HTSanalyzeR’ version ‘2.3.5’
* checking package name space information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking whether package ‘HTSanalyzeR’ can be installed ... OK
* checking package directory ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the name space can be loaded with stated dependencies ... OK
* checking whether the name space can be unloaded cleanly ... OK
* checking for unstated dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
GOGeneSets: no visible binding for global variable ‘org.Rn.egGo2EG’
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking data for non-ASCII characters ... OK
* checking examples ... OK
* checking package vignettes in ‘inst/doc’ ... SKIPPED
* checking PDF version of manual ... OK

HTSanalyzeR.Rcheck/00install.out:

* installing *source* package ‘HTSanalyzeR’ ...
** R
** data
** inst
** preparing package for lazy loading
Loading required package: Biobase

Welcome to Bioconductor

  Vignettes contain introductory material. To view, type
  'openVignette()'. To cite Bioconductor, see
  'citation("Biobase")' and for packages 'citation(pkgname)'.

Loading required package: annotate
Loading required package: AnnotationDbi
Loading required package: graph

Attaching package: 'graph'

The following object(s) are masked from 'package:igraph':

    degree

Loading required package: RBGL

Attaching package: 'RBGL'

The following object(s) are masked from 'package:igraph':

    transitivity

Loading required package: RColorBrewer
Loading required package: genefilter
Loading required package: splots
Loading required package: vsn
Loading required package: hwriter
Loading required package: locfit
Loading required package: akima
Loading required package: lattice
locfit 1.5-6 	 2010-01-20 
Loading required package: grid
Scalable Robust Estimators with High Breakdown Point (version 1.2-01)
** help
*** installing help indices
** building package indices ...
** testing if installed package can be loaded

* DONE (HTSanalyzeR)

HTSanalyzeR.Rcheck/HTSanalyzeR-Ex.timings:

nameusersystemelapsed
FDRcollectionGsea1.4400.0201.462
GOGeneSets3.0040.0763.166
GSCA-class000
HTSanalyzeR4cellHTS20.0000.0000.001
KeggGeneSets4.8280.0444.914
NWA-class0.0000.0000.001
aggregatePvals0.0040.0000.004
analyze0.0040.0000.001
analyzeGeneSetCollections0.0000.0000.001
annotationConvertor1.1290.0081.156
appendGSTerms000
biogridDataDownload000
celAnnotationConvertor1.1560.0161.196
cellHTS2OutputStatTests000
collectionGsea0.4040.0040.410
data-KcViab0.7560.0040.760
drosoAnnotationConvertor0.9240.0120.936
duplicateRemover0.0000.0000.001
getTopGeneSets000
gseaPlots000
gseaScores0.0680.0000.070
hyperGeoTest4.4280.0084.437
interactome000
mammalAnnotationConvertor2.8000.0162.824
multiHyperGeoTest0.0080.0000.007
networkAnalysis0.0000.0000.001
networkPlot0.0000.0000.001
pairwiseGsea1.5240.0001.522
pairwiseGseaPlot000
pairwisePhenoMannWhit0.0080.0000.007
permutationPvalueCollectionGsea0.780.000.78
plotEnrichMap0.0000.0000.001
plotGSEA000
plotSubNet000
preprocess000
report000
reportAll0.0000.0000.001
summarize0.0000.0000.001
viewEnrichMap000
viewGSEA0.0000.0000.001
viewSubNet000
writeReportHTSA000