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Package 224/462HostnameOS / ArchBUILDCHECKBUILD BIN
HTSanalyzeR 2.5.0
Xin Wang
Snapshot Date: 2011-05-09 07:20:56 -0700 (Mon, 09 May 2011)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/HTSanalyzeR
Last Changed Rev: 54810 / Revision: 55359
Last Changed Date: 2011-04-13 18:14:51 -0700 (Wed, 13 Apr 2011)
wilson2 Linux (openSUSE 11.4) / 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 
pelham Mac OS X Leopard (10.5.8) / i386  OK  OK  OK 

Summary

Package: HTSanalyzeR
Version: 2.5.0
Command: E:\biocbld\bbs-2.9-bioc\R\bin\R.exe CMD check --no-vignettes --timings HTSanalyzeR_2.5.0.tar.gz
StartedAt: 2011-05-09 14:08:16 -0700 (Mon, 09 May 2011)
EndedAt: 2011-05-09 14:11:31 -0700 (Mon, 09 May 2011)
EllapsedTime: 195.4 seconds
RetCode: 0
Status:  OK  
CheckDir: HTSanalyzeR.Rcheck
Warnings: 0

Command output

* using log directory 'E:/biocbld/bbs-2.9-bioc/meat/HTSanalyzeR.Rcheck'
* using R version 2.14.0 Under development (unstable) (2011-04-17 r55484)
* using platform: i386-pc-mingw32 (32-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'HTSanalyzeR/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'HTSanalyzeR' version '2.5.0'
* 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 installed package size ... OK
* checking package directory ... OK
* checking for portable file names ... 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 contents of 'data' directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking examples ... OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in 'inst/doc' ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignettes ... 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
  'browseVignettes()'. 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 1.3-00)
** help
*** installing help indices
** building package indices ...
*** tangling vignette sources ...
   'HTSanalyzeR-Vignette.Rnw' 
** testing if installed package can be loaded
locfit 1.5-6 	 2010-01-20 
Scalable Robust Estimators with High Breakdown Point (version 1.3-00)

* DONE (HTSanalyzeR)

HTSanalyzeR.Rcheck/HTSanalyzeR-Ex.timings:

nameusersystemelapsed
FDRcollectionGsea1.000.021.02
GOGeneSets2.510.042.89
GSCA-class000
HTSanalyzeR4cellHTS20.020.000.02
KeggGeneSets4.670.085.04
NWA-class000
aggregatePvals000
analyze000
analyzeGeneSetCollections000
annotationConvertor1.010.031.17
appendGSTerms000
biogridDataDownload000
celAnnotationConvertor1.060.001.22
cellHTS2OutputStatTests000
collectionGsea0.430.000.42
data-KcViab1.000.021.02
drosoAnnotationConvertor0.840.000.84
duplicateRemover000
getTopGeneSets000
gseaPlots000
gseaScores0.010.000.01
hyperGeoTest3.80.03.8
interactome000
mammalAnnotationConvertor2.330.032.44
multiHyperGeoTest000
networkAnalysis000
networkPlot000
pairwiseGsea1.560.001.56
pairwiseGseaPlot000
pairwisePhenoMannWhit0.020.000.02
permutationPvalueCollectionGsea0.670.000.67
plotEnrichMap000
plotGSEA000
plotSubNet000
preprocess000
report000
reportAll000
summarize000
viewEnrichMap000
viewGSEA000
viewSubNet000
writeReportHTSA000