Package: HTSanalyzeR

Version: 2.12.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch HTSanalyzeR_2.12.0.tar.gz

StartedAt: 2013-05-01 06:53:17 -0700 (Wed, 01 May 2013)

EndedAt: 2013-05-01 06:59:12 -0700 (Wed, 01 May 2013)

EllapsedTime: 355.1 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 Patched (2013-04-08 r62531)
* 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 '2.12.0'
* 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/30s] 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/52s] OK
Examples with CPU or elapsed time > 5s
              user system elapsed
GOGeneSets   5.666  0.326   6.280
hyperGeoTest 4.891  0.127   5.226
KeggGeneSets 4.784  0.147   5.339
* 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
** testing if installed package can be loaded
* DONE (HTSanalyzeR)

name	user	system	elapsed
FDRcollectionGsea	1.117	0.053	1.187
GOGeneSets	5.666	0.326	6.280
GSCA-class	0.042	0.013	0.072
HTSanalyzeR4cellHTS2	0.041	0.011	0.077
KeggGeneSets	4.784	0.147	5.339
NWA-class	0.017	0.016	0.034
aggregatePvals	0.422	0.011	0.492
analyze	0.016	0.013	0.030
analyzeGeneSetCollections	0.015	0.012	0.027
annotationConvertor	1.611	0.072	1.783
appendGSTerms	0.017	0.010	0.027
biogridDataDownload	0.013	0.004	0.017
celAnnotationConvertor	3.664	0.160	4.160
cellHTS2OutputStatTests	0.018	0.005	0.023
changes	0.003	0.004	0.007
collectionGsea	0.481	0.052	0.547
data-KcViab	1.425	0.079	1.558
drosoAnnotationConvertor	2.329	0.073	2.462
duplicateRemover	0.005	0.007	0.011
getTopGeneSets	0.029	0.013	0.049
gseaPlots	0.027	0.010	0.038
gseaScores	0.071	0.022	0.095
hyperGeoTest	4.891	0.127	5.226
interactome	0.028	0.009	0.038
mammalAnnotationConvertor	4.436	0.141	4.818
multiHyperGeoTest	0.041	0.014	0.055
networkAnalysis	0.029	0.007	0.036
networkPlot	0.004	0.006	0.011
pairwiseGsea	0.985	0.084	1.109
pairwiseGseaPlot	0.031	0.010	0.044
pairwisePhenoMannWhit	0.039	0.008	0.050
permutationPvalueCollectionGsea	0.486	0.051	0.537
plotEnrichMap	0.030	0.006	0.037
plotGSEA	0.059	0.011	0.072
plotSubNet	0.035	0.009	0.044
preprocess	0.055	0.008	0.066
report	0.028	0.007	0.036
reportAll	0.029	0.007	0.036
summarize	0.057	0.010	0.080
viewEnrichMap	0.004	0.007	0.012
viewGSEA	0.004	0.006	0.010
viewSubNet	0.003	0.005	0.008
writeReportHTSA	0.004	0.006	0.011