BioC 3.2: CHECK report for HTSanalyzeR on moscato1

Package: HTSanalyzeR

Version: 2.22.0

Command: rm -rf HTSanalyzeR.buildbin-libdir HTSanalyzeR.Rcheck && mkdir HTSanalyzeR.buildbin-libdir HTSanalyzeR.Rcheck && D:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=HTSanalyzeR.buildbin-libdir HTSanalyzeR_2.22.0.tar.gz >HTSanalyzeR.Rcheck\00install.out 2>&1 && cp HTSanalyzeR.Rcheck\00install.out HTSanalyzeR-install.out && D:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD check --library=HTSanalyzeR.buildbin-libdir --install="check:HTSanalyzeR-install.out" --force-multiarch --no-vignettes --timings HTSanalyzeR_2.22.0.tar.gz

StartedAt: 2016-04-23 03:40:47 -0700 (Sat, 23 Apr 2016)

EndedAt: 2016-04-23 03:47:29 -0700 (Sat, 23 Apr 2016)

EllapsedTime: 401.7 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: HTSanalyzeR.Rcheck

Warnings: 1

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### Running command:
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###   rm -rf HTSanalyzeR.buildbin-libdir HTSanalyzeR.Rcheck && mkdir HTSanalyzeR.buildbin-libdir HTSanalyzeR.Rcheck && D:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=HTSanalyzeR.buildbin-libdir HTSanalyzeR_2.22.0.tar.gz >HTSanalyzeR.Rcheck\00install.out 2>&1 && cp HTSanalyzeR.Rcheck\00install.out HTSanalyzeR-install.out  && D:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD check --library=HTSanalyzeR.buildbin-libdir --install="check:HTSanalyzeR-install.out" --force-multiarch --no-vignettes --timings HTSanalyzeR_2.22.0.tar.gz
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* using log directory 'D:/biocbld/bbs-3.2-bioc/meat/HTSanalyzeR.Rcheck'
* using R version 3.2.4 (2016-03-10)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'HTSanalyzeR/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'HTSanalyzeR' version '2.22.0'
* 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 whether package 'HTSanalyzeR' can be installed ... WARNING
Found the following significant warnings:
  Warning: replacing previous import 'igraph::union' by 'GSEABase::union' when loading 'HTSanalyzeR'
See 'D:/biocbld/bbs-3.2-bioc/meat/HTSanalyzeR.Rcheck/00install.out' for details.
* 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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'.

appendGSTerms,GSCA : .local : appendKEGGTerm: warning in mget(gsKEGG,
  env = KEGGPATHID2NAME, ifnotfound = NA): partial argument match of
  'env' to 'envir'
HTSanalyzeR4cellHTS2: no visible global function definition for 'fData'
KeggGeneSets: no visible binding for global variable 'KEGGPATHID2EXTID'
cellHTS2OutputStatTests: no visible global function definition for
  'fData'
gseaScoresBatchParallel: no visible global function definition for
  'parSapply'
appendGSTerms,GSCA : .local : appendKEGGTerm: no visible binding for
  global variable 'KEGGPATHID2NAME'
* 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 files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... [42s] OK
Examples with CPU or elapsed time > 5s
           user system elapsed
GOGeneSets 2.31   0.07    7.63
** running examples for arch 'x64' ... [37s] 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
* DONE

Status: 1 WARNING, 3 NOTEs
See
  'D:/biocbld/bbs-3.2-bioc/meat/HTSanalyzeR.Rcheck/00check.log'
for details.

install for i386

* installing *source* package 'HTSanalyzeR' ...
** R
** data
** inst
** preparing package for lazy loading
Warning: replacing previous import 'igraph::union' by 'GSEABase::union' when loading 'HTSanalyzeR'
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Warning: replacing previous import 'igraph::union' by 'GSEABase::union' when loading 'HTSanalyzeR'

install for x64

* installing *source* package 'HTSanalyzeR' ...
** testing if installed package can be loaded
Warning: replacing previous import 'igraph::union' by 'GSEABase::union' when loading 'HTSanalyzeR'
* MD5 sums
packaged installation of 'HTSanalyzeR' as HTSanalyzeR_2.22.0.zip
* DONE (HTSanalyzeR)

name	user	system	elapsed
FDRcollectionGsea	0.78	0.03	0.81
GOGeneSets	2.31	0.07	7.63
GSCA-class	0	0	0
HTSanalyzeR4cellHTS2	0	0	0
KeggGeneSets	3.85	0.02	4.32
NWA-class	0	0	0
aggregatePvals	0	0	0
analyze	0	0	0
analyzeGeneSetCollections	0	0	0
annotationConvertor	1.37	0.02	1.45
appendGSTerms	0	0	0
biogridDataDownload	0	0	0
celAnnotationConvertor	2.56	0.03	3.29
cellHTS2OutputStatTests	0	0	0
changes	0	0	0
collectionGsea	0.41	0.00	0.40
data-KcViab	1.46	0.01	1.46
drosoAnnotationConvertor	2.12	0.02	2.14
duplicateRemover	0	0	0
getTopGeneSets	0	0	0
gseaPlots	0	0	0
gseaScores	0.01	0.00	0.02
hyperGeoTest	3.83	0.03	3.85
interactome	0	0	0
mammalAnnotationConvertor	3.73	0.03	4.32
multiHyperGeoTest	0	0	0
networkAnalysis	0	0	0
networkPlot	0	0	0
pairwiseGsea	0.59	0.00	0.60
pairwiseGseaPlot	0	0	0
pairwisePhenoMannWhit	0.01	0.00	0.01
permutationPvalueCollectionGsea	0.66	0.00	0.66
plotEnrichMap	0	0	0
plotGSEA	0	0	0
plotSubNet	0	0	0
preprocess	0	0	0
report	0.02	0.00	0.02
reportAll	0	0	0
summarize	0	0	0
viewEnrichMap	0	0	0
viewGSEA	0	0	0
viewSubNet	0	0	0
writeReportHTSA	0	0	0

name	user	system	elapsed
FDRcollectionGsea	0.48	0.02	0.50
GOGeneSets	2.79	0.05	2.86
GSCA-class	0	0	0
HTSanalyzeR4cellHTS2	0	0	0
KeggGeneSets	4.07	0.03	4.11
NWA-class	0	0	0
aggregatePvals	0	0	0
analyze	0	0	0
analyzeGeneSetCollections	0	0	0
annotationConvertor	1.37	0.05	1.42
appendGSTerms	0	0	0
biogridDataDownload	0	0	0
celAnnotationConvertor	3.37	0.00	3.37
cellHTS2OutputStatTests	0	0	0
changes	0	0	0
collectionGsea	0.31	0.02	0.32
data-KcViab	1.17	0.01	1.19
drosoAnnotationConvertor	1.45	0.02	1.46
duplicateRemover	0	0	0
getTopGeneSets	0	0	0
gseaPlots	0	0	0
gseaScores	0.00	0.01	0.01
hyperGeoTest	4.19	0.03	4.23
interactome	0	0	0
mammalAnnotationConvertor	3.52	0.05	3.57
multiHyperGeoTest	0.01	0.00	0.02
networkAnalysis	0	0	0
networkPlot	0	0	0
pairwiseGsea	1.27	0.00	1.26
pairwiseGseaPlot	0	0	0
pairwisePhenoMannWhit	0.02	0.00	0.01
permutationPvalueCollectionGsea	0.48	0.00	0.49
plotEnrichMap	0	0	0
plotGSEA	0	0	0
plotSubNet	0	0	0
preprocess	0	0	0
report	0	0	0
reportAll	0	0	0
summarize	0	0	0
viewEnrichMap	0	0	0
viewGSEA	0	0	0
viewSubNet	0	0	0
writeReportHTSA	0	0	0