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CHECK report for HTSanalyzeR on merida2

This page was generated on 2019-04-09 13:25:22 -0400 (Tue, 09 Apr 2019).

Package 759/1703HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
HTSanalyzeR 2.35.1
Xin Wang
Snapshot Date: 2019-04-08 17:01:18 -0400 (Mon, 08 Apr 2019)
URL: https://git.bioconductor.org/packages/HTSanalyzeR
Branch: master
Last Commit: 2ae206c
Last Changed Date: 2019-01-04 13:35:31 -0400 (Fri, 04 Jan 2019)
malbec2 Linux (Ubuntu 18.04.2 LTS) / x86_64  OK  OK  WARNINGS UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository
celaya2 OS X 10.11.6 El Capitan / x86_64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository
merida2 OS X 10.11.6 El Capitan / x86_64  OK  OK [ WARNINGS ] OK 

Summary

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

Command output

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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.



Installation output

HTSanalyzeR.Rcheck/00install.out

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### Running command:
###
###   /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)

Tests output


Example timings

HTSanalyzeR.Rcheck/HTSanalyzeR-Ex.timings

nameusersystemelapsed
FDRcollectionGsea0.6200.0230.650
GOGeneSets1.6150.1324.802
GSCA-class0.0010.0000.059
HTSanalyzeR4cellHTS20.0000.0010.001
KeggGeneSets2.6390.0422.876
NWA-class000
aggregatePvals0.0020.0000.003
analyze0.0010.0010.001
analyzeGeneSetCollections0.0000.0000.001
annotationConvertor0.7120.0180.954
appendGSTerms0.0000.0000.065
biogridDataDownload0.0000.0010.000
celAnnotationConvertor1.4470.0422.202
cellHTS2OutputStatTests000
changes000
collectionGsea0.2080.0160.320
data-KcViab0.8030.0561.089
drosoAnnotationConvertor0.6700.0140.687
duplicateRemover0.0010.0000.002
getTopGeneSets0.0010.0000.000
gseaPlots000
gseaScores0.0160.0020.018
hyperGeoTest2.5150.0322.607
interactome0.0000.0010.001
mammalAnnotationConvertor2.3040.0452.413
multiHyperGeoTest0.0040.0000.004
networkAnalysis0.0000.0000.001
networkPlot000
pairwiseGsea0.3280.0380.383
pairwiseGseaPlot0.0000.0000.001
pairwisePhenoMannWhit0.0050.0010.005
permutationPvalueCollectionGsea0.2180.0150.286
plotEnrichMap0.0000.0000.001
plotGSEA0.0000.0000.001
plotSubNet0.0010.0010.001
preprocess000
report0.0000.0000.001
reportAll0.0010.0000.001
summarize0.0000.0000.001
viewEnrichMap0.0000.0000.002
viewGSEA0.0000.0000.001
viewSubNet000
writeReportHTSA000