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: 2013-03-25 03:05:57 -0700 (Mon, 25 Mar 2013)

EndedAt: 2013-03-25 03:10:58 -0700 (Mon, 25 Mar 2013)

EllapsedTime: 301.0 seconds

RetCode: 0

Status:  OK

CheckDir: HTSanalyzeR.Rcheck

Warnings: 0

* using log directory '/Users/biocbuild/bbs-2.12-bioc/meat/HTSanalyzeR.Rcheck'
* using R Under development (unstable) (2013-02-26 r62077)
* using platform: i386-apple-darwin9.8.0 (32-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 ... [25s/25s] 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 sizes of PDF files under 'inst/doc' ... OK
* checking installed files from 'inst/doc' ... OK
* checking examples ... [43s/43s] 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
  '/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	1.145	0.053	1.199
GOGeneSets	3.059	0.283	3.447
GSCA-class	0.032	0.016	0.048
HTSanalyzeR4cellHTS2	0.034	0.018	0.053
KeggGeneSets	4.486	0.167	4.670
NWA-class	0.254	0.014	0.268
aggregatePvals	0.021	0.011	0.032
analyze	0.026	0.017	0.043
analyzeGeneSetCollections	0.021	0.014	0.037
annotationConvertor	1.212	0.071	1.300
appendGSTerms	0.027	0.012	0.043
biogridDataDownload	0.010	0.006	0.016
celAnnotationConvertor	3.056	0.158	3.321
cellHTS2OutputStatTests	0.025	0.007	0.031
changes	0.013	0.004	0.017
collectionGsea	1.059	0.047	1.108
data-KcViab	2.291	0.068	2.361
drosoAnnotationConvertor	1.822	0.064	1.893
duplicateRemover	0.024	0.007	0.032
getTopGeneSets	0.061	0.017	0.079
gseaPlots	0.042	0.009	0.052
gseaScores	0.093	0.028	0.122
hyperGeoTest	4.485	0.120	4.613
interactome	0.037	0.011	0.049
mammalAnnotationConvertor	3.328	0.134	3.470
multiHyperGeoTest	0.087	0.015	0.101
networkAnalysis	0.036	0.008	0.044
networkPlot	0.053	0.010	0.063
pairwiseGsea	1.623	0.079	1.711
pairwiseGseaPlot	0.327	0.011	0.339
pairwisePhenoMannWhit	0.045	0.012	0.056
permutationPvalueCollectionGsea	0.557	0.046	0.604
plotEnrichMap	0.055	0.010	0.066
plotGSEA	0.056	0.013	0.069
plotSubNet	0.082	0.015	0.098
preprocess	0.038	0.011	0.049
report	0.038	0.010	0.048
reportAll	0.037	0.010	0.046
summarize	0.054	0.013	0.067
viewEnrichMap	0.020	0.008	0.028
viewGSEA	0.037	0.008	0.045
viewSubNet	0.019	0.006	0.025
writeReportHTSA	0.039	0.011	0.049