BioC 2.13: CHECK report for HTSanalyzeR on zin1

Package: HTSanalyzeR

Version: 2.14.0

Command: /home/biocbuild/bbs-2.13-bioc/R/bin/R CMD check --no-vignettes --timings HTSanalyzeR_2.14.0.tar.gz

StartedAt: 2014-04-05 01:52:54 -0700 (Sat, 05 Apr 2014)

EndedAt: 2014-04-05 01:56:51 -0700 (Sat, 05 Apr 2014)

EllapsedTime: 237.3 seconds

RetCode: 0

Status:  OK

CheckDir: HTSanalyzeR.Rcheck

Warnings: 0

* using log directory ‘/home/biocbuild/bbs-2.13-bioc/meat/HTSanalyzeR.Rcheck’
* using R version 3.0.3 (2014-03-06)
* 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 ‘2.14.0’
* 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 ... [20s/21s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Package listed in more than one of Depends, Imports, Suggests, Enhances:
  ‘igraph’
A package should be listed in only one of these fields.
* 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 dependencies in R code ... NOTE
Package in Depends field not imported from: ‘methods’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
See the information on DESCRIPTION files in the chapter ‘Creating R
packages’ of the ‘Writing R Extensions’ manual.
* 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 xinwang2hms@gmail.com---------------//\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 for old-style vignette sources ... NOTE
Vignette sources only in ‘inst/doc’:
  ‘HTSanalyzeR-Vignette.Rnw’
A ‘vignettes’ directory will be required as from R 3.1.0
* checking examples ... [28s/28s] 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 vignette outputs ... SKIPPED
* checking PDF version of manual ... OK

NOTE: There were 4 notes.
See
  ‘/home/biocbuild/bbs-2.13-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	0.728	0.000	0.730
GOGeneSets	2.952	0.052	3.052
GSCA-class	0.008	0.000	0.007
HTSanalyzeR4cellHTS2	0.008	0.000	0.006
KeggGeneSets	2.492	0.036	2.544
NWA-class	0.008	0.000	0.009
aggregatePvals	0.012	0.000	0.013
analyze	0.008	0.000	0.009
analyzeGeneSetCollections	0.008	0.000	0.008
annotationConvertor	0.801	0.012	0.824
appendGSTerms	0.008	0.000	0.011
biogridDataDownload	0.004	0.000	0.001
celAnnotationConvertor	1.852	0.032	1.887
cellHTS2OutputStatTests	0.000	0.000	0.002
changes	0.000	0.000	0.001
collectionGsea	0.544	0.000	0.544
data-KcViab	0.752	0.008	0.759
drosoAnnotationConvertor	0.920	0.012	0.965
duplicateRemover	0.016	0.000	0.014
getTopGeneSets	0.024	0.000	0.025
gseaPlots	0.012	0.000	0.013
gseaScores	0.048	0.000	0.050
hyperGeoTest	3.064	0.028	3.098
interactome	0.012	0.000	0.012
mammalAnnotationConvertor	2.228	0.012	2.243
multiHyperGeoTest	0.032	0.000	0.030
networkAnalysis	0.016	0.000	0.013
networkPlot	0.012	0.000	0.012
pairwiseGsea	0.496	0.000	0.498
pairwiseGseaPlot	0.012	0.000	0.012
pairwisePhenoMannWhit	0.020	0.000	0.018
permutationPvalueCollectionGsea	0.276	0.000	0.276
plotEnrichMap	0.012	0.000	0.012
plotGSEA	0.032	0.000	0.035
plotSubNet	0.344	0.000	0.344
preprocess	0.012	0.000	0.014
report	0.000	0.000	0.002
reportAll	0.012	0.000	0.012
summarize	0.016	0.000	0.013
viewEnrichMap	0.012	0.000	0.013
viewGSEA	0.004	0.000	0.002
viewSubNet	0.000	0.000	0.001
writeReportHTSA	0.012	0.000	0.012