BioC 3.2: CHECK report for HTSanalyzeR on perceval

Package: HTSanalyzeR

Version: 2.21.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings HTSanalyzeR_2.21.0.tar.gz

StartedAt: 2015-06-26 01:53:23 -0700 (Fri, 26 Jun 2015)

EndedAt: 2015-06-26 01:57:50 -0700 (Fri, 26 Jun 2015)

EllapsedTime: 267.1 seconds

RetCode: 0

Status:  OK

CheckDir: HTSanalyzeR.Rcheck

Warnings: 0

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings HTSanalyzeR_2.21.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.2-bioc/meat/HTSanalyzeR.Rcheck’
* using R version 3.2.1 (2015-06-18)
* using platform: x86_64-apple-darwin10.8.0 (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 ‘2.21.0’
* 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 ... [22s/22s] 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
'library' or 'require' calls in package code:
  ‘org.Ce.eg.db’ ‘org.Dm.eg.db’ ‘org.Hs.eg.db’ ‘org.Mm.eg.db’
  ‘org.Rn.eg.db’
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
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.
* 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'.

cellHTS2OutputStatTests: no visible global function definition for
  ‘fData’
gseaScoresBatchParallel: no visible global function definition for
  ‘parSapply’
HTSanalyzeR4cellHTS2: no visible global function definition for ‘fData’
KeggGeneSets: no visible binding for global variable ‘KEGGPATHID2EXTID’
* 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 files in ‘vignettes’ ... OK
* checking examples ... [38s/38s] OK
Examples with CPU or elapsed time > 5s
                           user system elapsed
mammalAnnotationConvertor 5.054   0.06   5.132
* 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
* DONE

Status: 3 NOTEs
See
  ‘/Users/biocbuild/bbs-3.2-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	0.871	0.025	0.902
GOGeneSets	2.676	0.175	3.053
GSCA-class	0.002	0.000	0.002
HTSanalyzeR4cellHTS2	0.002	0.001	0.002
KeggGeneSets	3.630	0.101	3.823
NWA-class	0.001	0.001	0.002
aggregatePvals	0.005	0.001	0.006
analyze	0.001	0.000	0.001
analyzeGeneSetCollections	0.001	0.001	0.001
annotationConvertor	1.765	0.040	1.808
appendGSTerms	0.001	0.001	0.001
biogridDataDownload	0.001	0.000	0.001
celAnnotationConvertor	3.555	0.076	3.704
cellHTS2OutputStatTests	0.000	0.000	0.001
changes	0.001	0.000	0.001
collectionGsea	0.408	0.024	0.433
data-KcViab	1.000	0.053	1.053
drosoAnnotationConvertor	2.815	0.029	2.905
duplicateRemover	0.002	0.000	0.002
getTopGeneSets	0.001	0.001	0.002
gseaPlots	0.001	0.000	0.001
gseaScores	0.016	0.001	0.017
hyperGeoTest	3.296	0.044	3.341
interactome	0.001	0.001	0.001
mammalAnnotationConvertor	5.054	0.060	5.132
multiHyperGeoTest	0.007	0.000	0.008
networkAnalysis	0.001	0.000	0.001
networkPlot	0.001	0.000	0.001
pairwiseGsea	1.494	0.047	1.549
pairwiseGseaPlot	0.001	0.000	0.001
pairwisePhenoMannWhit	0.008	0.000	0.008
permutationPvalueCollectionGsea	0.396	0.017	0.413
plotEnrichMap	0.000	0.000	0.001
plotGSEA	0.001	0.000	0.002
plotSubNet	0.001	0.001	0.002
preprocess	0.001	0.000	0.001
report	0.002	0.001	0.002
reportAll	0.001	0.000	0.001
summarize	0.001	0.000	0.002
viewEnrichMap	0.001	0.000	0.001
viewGSEA	0.000	0.000	0.001
viewSubNet	0.001	0.000	0.001
writeReportHTSA	0.001	0.000	0.001