Package: HTSanalyzeR

Version: 2.11.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch HTSanalyzeR_2.11.0.tar.gz

StartedAt: 2013-03-24 06:35:36 -0700 (Sun, 24 Mar 2013)

EndedAt: 2013-03-24 06:41:25 -0700 (Sun, 24 Mar 2013)

EllapsedTime: 349.5 seconds

RetCode: 0

Status:  OK

CheckDir: HTSanalyzeR.Rcheck

Warnings: 0

* using log directory '/Users/biocbuild/bbs-2.12-bioc/meat/HTSanalyzeR.Rcheck'
* using R version 3.0.0 beta (2013-03-21 r62346)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: ASCII
* using option '--no-vignettes'
* checking for file 'HTSanalyzeR/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'HTSanalyzeR' version '2.11.0'
* 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 for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package 'HTSanalyzeR' can be installed ... [28s/29s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over 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
File 'HTSanalyzeR/R/zzz.R':
  .onLoad calls:
    packageStartupMessage("/////////////////////////////////////////////////////////////////////////////\n\n//------------------Thanks for using HTSanalyzeR v 2.9.4-------------------//\n \n//------------please use function changes() to see new changes-------------//\n\n//------------please report any bug to xin.wang@cancer.org.uk--------------//\n\n/////////////////////////////////////////////////////////////////////////////\n",     appendLF = FALSE)

See section 'Good practice' in '?.onAttach'.
* 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 ... [49s/51s] OK
Examples with CPU or elapsed time > 5s
              user system elapsed
GOGeneSets   5.455  0.293   6.200
hyperGeoTest 5.186  0.120   5.417
* 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
  '/Users/biocbuild/bbs-2.12-bioc/meat/HTSanalyzeR.Rcheck/00check.log'
for details.

* installing *source* package 'HTSanalyzeR' ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
   'HTSanalyzeR-Vignette.Rnw' 
** testing if installed package can be loaded
* DONE (HTSanalyzeR)

name	user	system	elapsed
FDRcollectionGsea	1.601	0.062	1.678
GOGeneSets	5.455	0.293	6.200
GSCA-class	0.014	0.017	0.031
HTSanalyzeR4cellHTS2	0.016	0.015	0.032
KeggGeneSets	4.485	0.144	4.867
NWA-class	0.016	0.014	0.029
aggregatePvals	0.020	0.008	0.029
analyze	0.028	0.016	0.046
analyzeGeneSetCollections	0.016	0.013	0.029
annotationConvertor	1.407	0.061	1.481
appendGSTerms	0.017	0.014	0.033
biogridDataDownload	0.016	0.009	0.025
celAnnotationConvertor	3.323	0.156	3.728
cellHTS2OutputStatTests	0.019	0.006	0.024
changes	0.003	0.005	0.009
collectionGsea	0.505	0.052	0.570
data-KcViab	1.898	0.077	2.017
drosoAnnotationConvertor	1.623	0.056	1.785
duplicateRemover	0.039	0.006	0.047
getTopGeneSets	0.068	0.010	0.079
gseaPlots	0.035	0.007	0.043
gseaScores	0.193	0.016	0.221
hyperGeoTest	5.186	0.120	5.417
interactome	0.025	0.011	0.036
mammalAnnotationConvertor	3.472	0.134	3.708
multiHyperGeoTest	0.039	0.012	0.052
networkAnalysis	0.027	0.008	0.037
networkPlot	0.030	0.011	0.041
pairwiseGsea	1.032	0.081	1.126
pairwiseGseaPlot	0.579	0.017	0.622
pairwisePhenoMannWhit	0.039	0.009	0.050
permutationPvalueCollectionGsea	0.518	0.047	0.646
plotEnrichMap	0.054	0.007	0.099
plotGSEA	0.056	0.010	0.097
plotSubNet	0.056	0.009	0.066
preprocess	0.055	0.009	0.070
report	0.055	0.008	0.064
reportAll	0.035	0.013	0.048
summarize	0.031	0.013	0.044
viewEnrichMap	0.004	0.008	0.013
viewGSEA	0.004	0.008	0.012
viewSubNet	0.004	0.006	0.008
writeReportHTSA	0.028	0.011	0.039