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

* 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

* 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)

name	user	system	elapsed
FDRcollectionGsea	1.492	0.008	1.501
GOGeneSets	4.096	0.084	4.391
GSCA-class	0	0	0
HTSanalyzeR4cellHTS2	0.000	0.000	0.001
KeggGeneSets	4.805	0.028	4.877
NWA-class	0.004	0.000	0.000
aggregatePvals	0.004	0.000	0.005
analyze	0	0	0
analyzeGeneSetCollections	0	0	0
annotationConvertor	0.908	0.016	0.962
appendGSTerms	0	0	0
biogridDataDownload	0	0	0
celAnnotationConvertor	1.484	0.020	1.554
cellHTS2OutputStatTests	0	0	0
collectionGsea	0.368	0.024	0.391
data-KcViab	0.540	0.012	0.557
drosoAnnotationConvertor	0.916	0.000	0.918
duplicateRemover	0.000	0.000	0.001
getTopGeneSets	0.000	0.000	0.001
gseaPlots	0	0	0
gseaScores	0.024	0.000	0.024
hyperGeoTest	5.348	0.016	5.367
interactome	0	0	0
mammalAnnotationConvertor	3.208	0.028	3.246
multiHyperGeoTest	0.008	0.000	0.008
networkAnalysis	0	0	0
networkPlot	0	0	0
pairwiseGsea	0.764	0.012	0.774
pairwiseGseaPlot	0	0	0
pairwisePhenoMannWhit	0.008	0.000	0.007
permutationPvalueCollectionGsea	0.429	0.000	0.433
plotEnrichMap	0	0	0
plotGSEA	0	0	0
plotSubNet	0	0	0
preprocess	0	0	0
report	0.000	0.000	0.001
reportAll	0.000	0.004	0.000
summarize	0	0	0
viewEnrichMap	0.000	0.000	0.001
viewGSEA	0	0	0
viewSubNet	0	0	0
writeReportHTSA	0.000	0.000	0.001