Package: HTSanalyzeR

Version: 2.8.0

Command: /home/hpages/test-puck5/bbs-2.10-bioc/R/bin/R CMD check --no-vignettes --timings HTSanalyzeR_2.8.0.tar.gz

StartedAt: 2012-04-01 01:38:42 -0700 (Sun, 01 Apr 2012)

EndedAt: 2012-04-01 01:42:12 -0700 (Sun, 01 Apr 2012)

EllapsedTime: 209.6 seconds

RetCode: 0

Status:  OK

CheckDir: HTSanalyzeR.Rcheck

Warnings: 0

* using log directory '/loc/home/hpages/test-puck5/bbs-2.10-bioc/meat/HTSanalyzeR.Rcheck'
* using R version 2.15.0 RC (2012-03-22 r58802)
* using platform: x86_64-unknown-linux-gnu (64-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 '2.8.0'
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... 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 namespace can be loaded with stated dependencies ... OK
* checking whether the namespace 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'
pairwiseGseaPlot: warning in png(file = file.path(filepath,
  paste("pairwiseGsea_plots", filename, sep = "")), ... = ...): partial
  argument match of 'file' to 'filename'
writeReportHTSA: warning in dir(system.file("templates", package =
  "HTSanalyzeR"), full = TRUE): partial argument match of 'full' to
  'full.names'
* 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 installed files from 'inst/doc' ... 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

NOTE: There was 1 note.
See
  '/loc/home/hpages/test-puck5/bbs-2.10-bioc/meat/HTSanalyzeR.Rcheck/00check.log'
for details.

* installing *source* package 'HTSanalyzeR' ...
** R
** data
** inst
** preparing package for lazy loading
Scalable Robust Estimators with High Breakdown Point (version 1.3-01)
Warning: replacing previous import 'coerce' when loading 'cellHTS2'
Warning: replacing previous import 'initialize' when loading 'cellHTS2'
** help
*** installing help indices
** building package indices
** installing vignettes
   'HTSanalyzeR-Vignette.Rnw' 
** testing if installed package can be loaded
Scalable Robust Estimators with High Breakdown Point (version 1.3-01)
Warning: replacing previous import 'coerce' when loading 'cellHTS2'
Warning: replacing previous import 'initialize' when loading 'cellHTS2'

* DONE (HTSanalyzeR)

name	user	system	elapsed
FDRcollectionGsea	0.736	0.004	0.740
GOGeneSets	2.432	0.060	2.547
GSCA-class	0	0	0
HTSanalyzeR4cellHTS2	0	0	0
KeggGeneSets	2.736	0.040	2.830
NWA-class	0	0	0
aggregatePvals	0.004	0.000	0.004
analyze	0.000	0.000	0.001
analyzeGeneSetCollections	0.000	0.000	0.001
annotationConvertor	0.660	0.004	0.679
appendGSTerms	0	0	0
biogridDataDownload	0	0	0
celAnnotationConvertor	0.860	0.020	0.921
cellHTS2OutputStatTests	0	0	0
collectionGsea	0.264	0.004	0.267
data-KcViab	0.845	0.024	1.025
drosoAnnotationConvertor	0.640	0.000	0.649
duplicateRemover	0.000	0.000	0.001
getTopGeneSets	0	0	0
gseaPlots	0.004	0.000	0.000
gseaScores	0.016	0.000	0.019
hyperGeoTest	2.688	0.020	2.765
interactome	0	0	0
mammalAnnotationConvertor	1.780	0.012	1.830
multiHyperGeoTest	0.000	0.004	0.005
networkAnalysis	0.004	0.000	0.000
networkPlot	0	0	0
pairwiseGsea	0.536	0.004	0.539
pairwiseGseaPlot	0	0	0
pairwisePhenoMannWhit	0.008	0.000	0.005
permutationPvalueCollectionGsea	0.480	0.004	0.485
plotEnrichMap	0	0	0
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	0	0
viewSubNet	0	0	0
writeReportHTSA	0	0	0