Package: HTSanalyzeR

Version: 2.35.1

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:HTSanalyzeR.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings HTSanalyzeR_2.35.1.tar.gz

StartedAt: 2019-04-09 01:33:00 -0400 (Tue, 09 Apr 2019)

EndedAt: 2019-04-09 01:37:02 -0400 (Tue, 09 Apr 2019)

EllapsedTime: 242.0 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: HTSanalyzeR.Rcheck

Warnings: 1

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:HTSanalyzeR.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings HTSanalyzeR_2.35.1.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/HTSanalyzeR.Rcheck’
* using R Under development (unstable) (2018-11-27 r75683)
* using platform: x86_64-apple-darwin15.6.0 (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 ‘2.35.1’
* 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 ... WARNING
Found the following significant warnings:
  Warning: replacing previous import ‘igraph::union’ by ‘GSEABase::union’ when loading ‘HTSanalyzeR’
See ‘/Users/biocbuild/bbs-3.9-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
* 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 : appendKEGGTerm: warning in mget(gsKEGG, env =
  KEGGPATHID2NAME, ifnotfound = NA): partial argument match of 'env' to
  'envir'
HTSanalyzeR4cellHTS2: no visible global function definition for ‘fData’
HTSanalyzeR4cellHTS2: no visible global function definition for ‘new’
KeggGeneSets: no visible binding for global variable ‘KEGGPATHID2EXTID’
aggregatePvals: no visible global function definition for ‘is’
aggregatePvals: no visible global function definition for ‘pchisq’
aggregatePvals : <anonymous>: no visible global function definition for
  ‘pnorm’
aggregatePvals : <anonymous>: no visible global function definition for
  ‘qnorm’
aggregatePvals: no visible global function definition for ‘p.adjust’
analyzeGeneSetCollections: no visible global function definition for
  ‘p.adjust’
biogridDataDownload: no visible global function definition for
  ‘download.file’
biogridDataDownload: no visible global function definition for ‘unzip’
biogridDataDownload: no visible global function definition for
  ‘read.table’
cellHTS2OutputStatTests: no visible global function definition for
  ‘fData’
cellHTS2OutputStatTests: no visible global function definition for
  ‘median’
cellHTS2OutputStatTests : <anonymous>: no visible global function
  definition for ‘t.test’
cellHTS2OutputStatTests : <anonymous>: no visible global function
  definition for ‘wilcox.test’
collectionGsea: no visible global function definition for ‘is’
collectionGsea: no visible global function definition for
  ‘txtProgressBar’
collectionGsea: no visible global function definition for
  ‘setTxtProgressBar’
drosoAnnotationConvertor: no visible global function definition for
  ‘is’
gseaPlots: no visible global function definition for ‘par’
gseaPlots: no visible global function definition for ‘plot’
gseaPlots: no visible global function definition for ‘abline’
gseaPlots: no visible global function definition for ‘lines’
gseaScoresBatchParallel: no visible global function definition for
  ‘parSapply’
hyperGeoTest: no visible global function definition for ‘phyper’
makeGSEAplots: no visible global function definition for ‘pdf’
makeGSEAplots: no visible global function definition for ‘png’
makeGSEAplots: no visible global function definition for ‘dev.off’
makeOverlapTable: no visible global function definition for
  ‘write.table’
mammalAnnotationConvertor: no visible global function definition for
  ‘is’
multiHyperGeoTest: no visible global function definition for
  ‘txtProgressBar’
multiHyperGeoTest : <anonymous>: no visible global function definition
  for ‘setTxtProgressBar’
multiHyperGeoTest: no visible global function definition for ‘p.adjust’
networkPlot: no visible global function definition for ‘is’
networkPlot: no visible global function definition for
  ‘colorRampPalette’
networkPlot: no visible global function definition for ‘points’
networkPlot: no visible global function definition for ‘text’
pairwiseGsea: no visible global function definition for ‘p.adjust’
pairwiseGseaPlot: no visible global function definition for ‘pdf’
pairwiseGseaPlot: no visible global function definition for ‘png’
pairwiseGseaPlot: no visible global function definition for ‘par’
pairwiseGseaPlot: no visible global function definition for ‘plot’
pairwiseGseaPlot: no visible global function definition for ‘abline’
pairwiseGseaPlot: no visible global function definition for ‘dev.off’
pairwisePhenoMannWhit : <anonymous>: no visible global function
  definition for ‘wilcox.test’
pairwisePhenoMannWhit: no visible global function definition for
  ‘p.adjust’
paraCheck: no visible global function definition for ‘is’
writeReportHTSA: no visible global function definition for ‘is’
writeReportHTSA: no visible global function definition for
  ‘write.table’
appendGSTerms,GSCA : appendKEGGTerm: no visible binding for global
  variable ‘KEGGPATHID2NAME’
plotEnrichMap,GSCA: no visible global function definition for ‘pdf’
plotEnrichMap,GSCA: no visible global function definition for ‘png’
plotEnrichMap,GSCA: no visible global function definition for ‘dev.off’
plotSubNet,NWA: no visible global function definition for ‘pdf’
plotSubNet,NWA: no visible global function definition for ‘png’
plotSubNet,NWA: no visible global function definition for ‘dev.off’
viewEnrichMap,GSCA: no visible global function definition for
  ‘colorRampPalette’
viewEnrichMap,GSCA: no visible global function definition for ‘grey’
viewEnrichMap,GSCA: no visible global function definition for ‘title’
viewEnrichMap,GSCA: no visible global function definition for ‘points’
viewEnrichMap,GSCA: no visible global function definition for ‘text’
Undefined global functions or variables:
  KEGGPATHID2EXTID KEGGPATHID2NAME abline colorRampPalette dev.off
  download.file fData grey is lines median new p.adjust par parSapply
  pchisq pdf phyper plot png pnorm points qnorm read.table
  setTxtProgressBar t.test text title txtProgressBar unzip wilcox.test
  write.table
Consider adding
  importFrom("grDevices", "colorRampPalette", "dev.off", "grey", "pdf",
             "png")
  importFrom("graphics", "abline", "lines", "par", "plot", "points",
             "text", "title")
  importFrom("methods", "is", "new")
  importFrom("stats", "median", "p.adjust", "pchisq", "phyper", "pnorm",
             "qnorm", "t.test", "wilcox.test")
  importFrom("utils", "download.file", "read.table", "setTxtProgressBar",
             "txtProgressBar", "unzip", "write.table")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* 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 files in ‘vignettes’ ... OK
* checking examples ... 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
  ‘/Users/biocbuild/bbs-3.9-bioc/meat/HTSanalyzeR.Rcheck/00check.log’
for details.

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL HTSanalyzeR
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library’
* installing *source* package ‘HTSanalyzeR’ ...
** R
** data
** inst
** byte-compile and prepare 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’
* DONE (HTSanalyzeR)

name	user	system	elapsed
FDRcollectionGsea	0.620	0.023	0.650
GOGeneSets	1.615	0.132	4.802
GSCA-class	0.001	0.000	0.059
HTSanalyzeR4cellHTS2	0.000	0.001	0.001
KeggGeneSets	2.639	0.042	2.876
NWA-class	0	0	0
aggregatePvals	0.002	0.000	0.003
analyze	0.001	0.001	0.001
analyzeGeneSetCollections	0.000	0.000	0.001
annotationConvertor	0.712	0.018	0.954
appendGSTerms	0.000	0.000	0.065
biogridDataDownload	0.000	0.001	0.000
celAnnotationConvertor	1.447	0.042	2.202
cellHTS2OutputStatTests	0	0	0
changes	0	0	0
collectionGsea	0.208	0.016	0.320
data-KcViab	0.803	0.056	1.089
drosoAnnotationConvertor	0.670	0.014	0.687
duplicateRemover	0.001	0.000	0.002
getTopGeneSets	0.001	0.000	0.000
gseaPlots	0	0	0
gseaScores	0.016	0.002	0.018
hyperGeoTest	2.515	0.032	2.607
interactome	0.000	0.001	0.001
mammalAnnotationConvertor	2.304	0.045	2.413
multiHyperGeoTest	0.004	0.000	0.004
networkAnalysis	0.000	0.000	0.001
networkPlot	0	0	0
pairwiseGsea	0.328	0.038	0.383
pairwiseGseaPlot	0.000	0.000	0.001
pairwisePhenoMannWhit	0.005	0.001	0.005
permutationPvalueCollectionGsea	0.218	0.015	0.286
plotEnrichMap	0.000	0.000	0.001
plotGSEA	0.000	0.000	0.001
plotSubNet	0.001	0.001	0.001
preprocess	0	0	0
report	0.000	0.000	0.001
reportAll	0.001	0.000	0.001
summarize	0.000	0.000	0.001
viewEnrichMap	0.000	0.000	0.002
viewGSEA	0.000	0.000	0.001
viewSubNet	0	0	0
writeReportHTSA	0	0	0