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CHECK report for HTSanalyzeR on merida1

This page was generated on 2020-04-15 12:36:27 -0400 (Wed, 15 Apr 2020).

Package 802/1823HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
HTSanalyzeR 2.38.0
Xin Wang
Snapshot Date: 2020-04-14 16:46:13 -0400 (Tue, 14 Apr 2020)
URL: https://git.bioconductor.org/packages/HTSanalyzeR
Branch: RELEASE_3_10
Last Commit: eec27b7
Last Changed Date: 2019-10-29 13:08:17 -0400 (Tue, 29 Oct 2019)
malbec1 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK  WARNINGS UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository
merida1 OS X 10.11.6 El Capitan / x86_64  OK  OK [ WARNINGS ] OK UNNEEDED, same version exists in internal repository

Summary

Package: HTSanalyzeR
Version: 2.38.0
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_2.38.0.tar.gz
StartedAt: 2020-04-15 03:04:46 -0400 (Wed, 15 Apr 2020)
EndedAt: 2020-04-15 03:08:43 -0400 (Wed, 15 Apr 2020)
EllapsedTime: 237.0 seconds
RetCode: 0
Status:  WARNINGS 
CheckDir: HTSanalyzeR.Rcheck
Warnings: 1

Command output

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### Running 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_2.38.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.10-bioc/meat/HTSanalyzeR.Rcheck’
* using R version 3.6.3 (2020-02-29)
* 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 ‘2.38.0’
* 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 ... WARNING
Found the following significant warnings:
  Warning: Package 'HTSanalyzeR' is deprecated and will be removed from
  Warning: replacing previous import ‘igraph::union’ by ‘GSEABase::union’ when loading ‘HTSanalyzeR’
See ‘/Users/biocbuild/bbs-3.10-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-3.10-bioc/meat/HTSanalyzeR.Rcheck/00check.log’
for details.



Installation output

HTSanalyzeR.Rcheck/00install.out

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL HTSanalyzeR
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library’
* installing *source* package ‘HTSanalyzeR’ ...
** using staged installation
** 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 from temporary location
Warning: replacing previous import ‘igraph::union’ by ‘GSEABase::union’ when loading ‘HTSanalyzeR’
Warning: Package 'HTSanalyzeR' is deprecated and will be removed from
  Bioconductor version 3.11
** testing if installed package can be loaded from final location
Warning: replacing previous import ‘igraph::union’ by ‘GSEABase::union’ when loading ‘HTSanalyzeR’
Warning: Package 'HTSanalyzeR' is deprecated and will be removed from
  Bioconductor version 3.11
** testing if installed package keeps a record of temporary installation path
* DONE (HTSanalyzeR)

Tests output


Example timings

HTSanalyzeR.Rcheck/HTSanalyzeR-Ex.timings

nameusersystemelapsed
FDRcollectionGsea0.6870.0230.713
GOGeneSets1.6600.1191.825
GSCA-class0.0000.0010.000
HTSanalyzeR4cellHTS2000
KeggGeneSets2.9570.0313.012
NWA-class0.0010.0000.000
aggregatePvals0.0030.0000.003
analyze0.0010.0000.000
analyzeGeneSetCollections0.0010.0000.001
annotationConvertor0.6370.0200.663
appendGSTerms0.0000.0010.001
biogridDataDownload000
celAnnotationConvertor1.3700.0551.446
cellHTS2OutputStatTests0.0000.0010.000
changes0.0010.0000.000
collectionGsea0.1750.0200.199
data-KcViab0.6860.0150.704
drosoAnnotationConvertor0.7300.0170.753
duplicateRemover0.0010.0000.001
getTopGeneSets000
gseaPlots0.0010.0010.000
gseaScores0.0120.0010.013
hyperGeoTest2.3520.0222.389
interactome000
mammalAnnotationConvertor1.6840.0461.741
multiHyperGeoTest0.0040.0000.003
networkAnalysis000
networkPlot000
pairwiseGsea0.5410.0320.575
pairwiseGseaPlot0.0000.0000.001
pairwisePhenoMannWhit0.0040.0000.004
permutationPvalueCollectionGsea0.1830.0170.200
plotEnrichMap0.0010.0000.000
plotGSEA000
plotSubNet000
preprocess000
report000
reportAll0.0010.0000.000
summarize0.0000.0010.001
viewEnrichMap0.0000.0000.001
viewGSEA0.0000.0000.001
viewSubNet0.0000.0000.001
writeReportHTSA0.0000.0000.001