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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: /home/biocbuild/bbs-2.9-bioc/R/bin/R CMD check --no-vignettes --timings HTSanalyzeR_2.5.0.tar.gz
StartedAt: 2011-05-09 12:53:04 -0700 (Mon, 09 May 2011)
EndedAt: 2011-05-09 12:56:35 -0700 (Mon, 09 May 2011)
EllapsedTime: 211.0 seconds
RetCode: 0
Status:  OK 
CheckDir: HTSanalyzeR.Rcheck
Warnings: 0

Command output

* using log directory ‘/loc/home/biocbuild/bbs-2.9-bioc/meat/HTSanalyzeR.Rcheck’
* using R version 2.14.0 Under development (unstable) (2011-04-18 r55504)
* 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 ‘2.5.0’
* 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 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 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
FDRcollectionGsea1.4920.0081.501
GOGeneSets4.0960.0844.391
GSCA-class000
HTSanalyzeR4cellHTS20.0000.0000.001
KeggGeneSets4.8050.0284.877
NWA-class0.0040.0000.000
aggregatePvals0.0040.0000.005
analyze000
analyzeGeneSetCollections000
annotationConvertor0.9080.0160.962
appendGSTerms000
biogridDataDownload000
celAnnotationConvertor1.4840.0201.554
cellHTS2OutputStatTests000
collectionGsea0.3680.0240.391
data-KcViab0.5400.0120.557
drosoAnnotationConvertor0.9160.0000.918
duplicateRemover0.0000.0000.001
getTopGeneSets0.0000.0000.001
gseaPlots000
gseaScores0.0240.0000.024
hyperGeoTest5.3480.0165.367
interactome000
mammalAnnotationConvertor3.2080.0283.246
multiHyperGeoTest0.0080.0000.008
networkAnalysis000
networkPlot000
pairwiseGsea0.7640.0120.774
pairwiseGseaPlot000
pairwisePhenoMannWhit0.0080.0000.007
permutationPvalueCollectionGsea0.4290.0000.433
plotEnrichMap000
plotGSEA000
plotSubNet000
preprocess000
report0.0000.0000.001
reportAll0.0000.0040.000
summarize000
viewEnrichMap0.0000.0000.001
viewGSEA000
viewSubNet000
writeReportHTSA0.0000.0000.001