Package: HTSanalyzeR

Version: 2.11.0

Command: /home/biocbuild/bbs-2.12-bioc/R/bin/R CMD check --no-vignettes --timings HTSanalyzeR_2.11.0.tar.gz

StartedAt: 2013-03-25 02:24:13 -0700 (Mon, 25 Mar 2013)

EndedAt: 2013-03-25 02:31:07 -0700 (Mon, 25 Mar 2013)

EllapsedTime: 414.7 seconds

RetCode: 0

Status:  OK

CheckDir: HTSanalyzeR.Rcheck

Warnings: 0

* using log directory ‘/home/biocbuild/bbs-2.12-bioc/meat/HTSanalyzeR.Rcheck’
* using R version 3.0.0 beta (2013-03-19 r62328)
* 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 ‘2.11.0’
* 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 ... [32s/33s] 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 ... [57s/58s] OK
Examples with CPU or elapsed time > 5s
                           user system elapsed
GOGeneSets                7.001  0.096   7.133
mammalAnnotationConvertor 5.573  0.028   6.236
KeggGeneSets              4.904  0.064   5.035
* 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
  ‘/home/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	2.012	0.048	2.081
GOGeneSets	7.001	0.096	7.133
GSCA-class	0.044	0.000	0.046
HTSanalyzeR4cellHTS2	0.044	0.000	0.047
KeggGeneSets	4.904	0.064	5.035
NWA-class	0.120	0.004	0.125
aggregatePvals	0.036	0.000	0.034
analyze	0.056	0.000	0.055
analyzeGeneSetCollections	0.052	0.000	0.054
annotationConvertor	1.344	0.012	1.400
appendGSTerms	0.064	0.004	0.064
biogridDataDownload	0.032	0.000	0.034
celAnnotationConvertor	4.497	0.072	4.632
cellHTS2OutputStatTests	0.040	0.000	0.043
changes	0.044	0.000	0.042
collectionGsea	0.624	0.004	0.655
data-KcViab	1.028	0.028	1.058
drosoAnnotationConvertor	1.968	0.016	2.045
duplicateRemover	0.048	0.004	0.054
getTopGeneSets	0.164	0.000	0.252
gseaPlots	0.052	0.000	0.055
gseaScores	0.288	0.000	0.286
hyperGeoTest	4.772	0.024	4.807
interactome	0.096	0.000	0.099
mammalAnnotationConvertor	5.573	0.028	6.236
multiHyperGeoTest	0.132	0.000	0.133
networkAnalysis	0.064	0.000	0.063
networkPlot	0.064	0.000	0.061
pairwiseGsea	1.336	0.000	1.336
pairwiseGseaPlot	0.980	0.008	0.992
pairwisePhenoMannWhit	0.068	0.000	0.067
permutationPvalueCollectionGsea	1.504	0.012	1.517
plotEnrichMap	0.004	0.000	0.005
plotGSEA	0.056	0.000	0.055
plotSubNet	0.044	0.004	0.048
preprocess	0.056	0.000	0.055
report	0.052	0.000	0.051
reportAll	0.060	0.000	0.058
summarize	0.128	0.000	0.125
viewEnrichMap	0.076	0.000	0.076
viewGSEA	0.064	0.000	0.065
viewSubNet	0.004	0.000	0.005
writeReportHTSA	0.048	0.000	0.048