Package: HTSanalyzeR

Version: 2.5.1

Command: /home/biocbuild/bbs-2.9-bioc/R/bin/R CMD check --no-vignettes --timings HTSanalyzeR_2.5.1.tar.gz

StartedAt: 2011-07-07 01:00:19 -0700 (Thu, 07 Jul 2011)

EndedAt: 2011-07-07 01:03:45 -0700 (Thu, 07 Jul 2011)

EllapsedTime: 205.8 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) (2011-06-15 r56138)
* 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 ‘2.5.1’
* 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 1.3-01)
** 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 1.3-01)

* DONE (HTSanalyzeR)

name	user	system	elapsed
FDRcollectionGsea	1.200	0.008	1.211
GOGeneSets	4.184	0.124	4.336
GSCA-class	0.000	0.004	0.000
HTSanalyzeR4cellHTS2	0	0	0
KeggGeneSets	4.781	0.036	4.824
NWA-class	0	0	0
aggregatePvals	0.008	0.000	0.004
analyze	0	0	0
analyzeGeneSetCollections	0	0	0
annotationConvertor	1.280	0.008	1.294
appendGSTerms	0	0	0
biogridDataDownload	0	0	0
celAnnotationConvertor	1.148	0.012	1.193
cellHTS2OutputStatTests	0.000	0.000	0.001
collectionGsea	0.452	0.004	0.457
data-KcViab	1.052	0.016	1.078
drosoAnnotationConvertor	1.228	0.024	1.254
duplicateRemover	0.004	0.000	0.001
getTopGeneSets	0	0	0
gseaPlots	0	0	0
gseaScores	0.04	0.00	0.04
hyperGeoTest	4.892	0.048	4.947
interactome	0	0	0
mammalAnnotationConvertor	3.268	0.048	3.322
multiHyperGeoTest	0.004	0.000	0.006
networkAnalysis	0	0	0
networkPlot	0	0	0
pairwiseGsea	1.269	0.012	1.285
pairwiseGseaPlot	0	0	0
pairwisePhenoMannWhit	0.008	0.000	0.006
permutationPvalueCollectionGsea	0.488	0.000	0.492
plotEnrichMap	0.004	0.000	0.000
plotGSEA	0	0	0
plotSubNet	0.000	0.000	0.001
preprocess	0	0	0
report	0	0	0
reportAll	0	0	0
summarize	0.000	0.000	0.001
viewEnrichMap	0	0	0
viewGSEA	0.000	0.000	0.001
viewSubNet	0	0	0
writeReportHTSA	0	0	0