BioC 2.12: CHECK report for HTSanalyzeR on george2

Package: HTSanalyzeR

Version: 2.12.1

Command: /home/biocbuild/bbs-2.12-bioc/R/bin/R CMD check --no-vignettes --timings HTSanalyzeR_2.12.1.tar.gz

StartedAt: 2013-10-09 02:34:37 -0700 (Wed, 09 Oct 2013)

EndedAt: 2013-10-09 02:41:25 -0700 (Wed, 09 Oct 2013)

EllapsedTime: 408.0 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 3.0.1 (2013-05-16)
* 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 ‘2.12.1’
* 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 ----------------------//\n \n//------------please use function changes() to see new changes-------------//\n\n//------------please report any bug to [email protected]//\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 ... [56s/57s] OK
Examples with CPU or elapsed time > 5s
              user system elapsed
GOGeneSets   7.501  0.128   7.688
KeggGeneSets 6.348  0.068   6.639
hyperGeoTest 5.832  0.020   6.130
* 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
** testing if installed package can be loaded
* DONE (HTSanalyzeR)

name	user	system	elapsed
FDRcollectionGsea	2.288	0.024	2.314
GOGeneSets	7.501	0.128	7.688
GSCA-class	0.084	0.000	0.084
HTSanalyzeR4cellHTS2	0.072	0.000	0.074
KeggGeneSets	6.348	0.068	6.639
NWA-class	0.100	0.000	0.102
aggregatePvals	0.052	0.000	0.049
analyze	0.052	0.000	0.055
analyzeGeneSetCollections	0.06	0.00	0.06
annotationConvertor	2.088	0.020	2.130
appendGSTerms	0.040	0.000	0.038
biogridDataDownload	0.024	0.000	0.023
celAnnotationConvertor	3.297	0.056	3.357
cellHTS2OutputStatTests	0.044	0.004	0.047
changes	0.032	0.000	0.032
collectionGsea	0.568	0.000	0.607
data-KcViab	2.536	0.032	2.740
drosoAnnotationConvertor	2.592	0.024	2.622
duplicateRemover	0.008	0.000	0.008
getTopGeneSets	0.048	0.000	0.046
gseaPlots	0.036	0.000	0.036
gseaScores	0.104	0.000	0.106
hyperGeoTest	5.832	0.020	6.130
interactome	0.052	0.000	0.051
mammalAnnotationConvertor	3.921	0.036	3.963
multiHyperGeoTest	0.16	0.00	0.16
networkAnalysis	0.056	0.000	0.057
networkPlot	0.056	0.000	0.107
pairwiseGsea	1.244	0.008	1.257
pairwiseGseaPlot	0.060	0.000	0.058
pairwisePhenoMannWhit	0.068	0.000	0.069
permutationPvalueCollectionGsea	1.724	0.000	1.724
plotEnrichMap	0.056	0.004	0.057
plotGSEA	0.060	0.004	0.064
plotSubNet	0.064	0.000	0.064
preprocess	0.068	0.000	0.067
report	0.068	0.000	0.066
reportAll	0.068	0.000	0.069
summarize	0.108	0.000	0.109
viewEnrichMap	0.052	0.000	0.052
viewGSEA	0.080	0.000	0.077
viewSubNet	0.012	0.000	0.013
writeReportHTSA	0.064	0.000	0.063