Back to Multiple platform build/check report for BioC 3.8
ABCDEFG[H]IJKLMNOPQRSTUVWXYZ

CHECK report for HTSanalyzeR on merida1

This page was generated on 2019-04-16 11:55:18 -0400 (Tue, 16 Apr 2019).

Package 736/1649HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
HTSanalyzeR 2.34.1
Xin Wang
Snapshot Date: 2019-04-15 17:01:12 -0400 (Mon, 15 Apr 2019)
URL: https://git.bioconductor.org/packages/HTSanalyzeR
Branch: RELEASE_3_8
Last Commit: 2e64a32
Last Changed Date: 2019-01-04 13:35:36 -0400 (Fri, 04 Jan 2019)
malbec1 Linux (Ubuntu 16.04.6 LTS) / x86_64  OK  OK  WARNINGS 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: 2.34.1
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_2.34.1.tar.gz
StartedAt: 2019-04-16 00:36:40 -0400 (Tue, 16 Apr 2019)
EndedAt: 2019-04-16 00:40:04 -0400 (Tue, 16 Apr 2019)
EllapsedTime: 204.0 seconds
RetCode: 0
Status:  WARNINGS 
CheckDir: HTSanalyzeR.Rcheck
Warnings: 1

Command output

##############################################################################
##############################################################################
###
### 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_2.34.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.8-bioc/meat/HTSanalyzeR.Rcheck’
* using R version 3.5.3 (2019-03-11)
* 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 ‘2.34.1’
* 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-3.8-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-3.8-bioc/meat/HTSanalyzeR.Rcheck/00check.log’
for details.



Installation output

HTSanalyzeR.Rcheck/00install.out

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


* installing to library ‘/Library/Frameworks/R.framework/Versions/3.5/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
FDRcollectionGsea0.5950.0190.618
GOGeneSets1.6460.1141.795
GSCA-class0.0000.0010.001
HTSanalyzeR4cellHTS20.0010.0000.001
KeggGeneSets3.0020.0373.055
NWA-class0.0000.0010.000
aggregatePvals0.0030.0000.004
analyze000
analyzeGeneSetCollections0.0000.0000.001
annotationConvertor0.6010.0190.624
appendGSTerms000
biogridDataDownload000
celAnnotationConvertor1.2620.0561.327
cellHTS2OutputStatTests000
changes0.0000.0000.001
collectionGsea0.1960.0200.218
data-KcViab0.8560.0150.886
drosoAnnotationConvertor0.6530.0180.677
duplicateRemover0.0010.0000.001
getTopGeneSets0.0010.0010.001
gseaPlots000
gseaScores0.0140.0010.014
hyperGeoTest2.4710.0252.519
interactome0.0010.0010.000
mammalAnnotationConvertor1.7630.0371.810
multiHyperGeoTest0.0030.0000.004
networkAnalysis000
networkPlot0.0000.0000.001
pairwiseGsea0.5290.0360.568
pairwiseGseaPlot0.0010.0000.001
pairwisePhenoMannWhit0.0060.0010.007
permutationPvalueCollectionGsea0.2360.0220.259
plotEnrichMap000
plotGSEA0.0010.0000.000
plotSubNet0.0000.0000.001
preprocess000
report0.0000.0000.001
reportAll0.0010.0000.001
summarize0.0000.0000.001
viewEnrichMap000
viewGSEA000
viewSubNet0.0010.0000.000
writeReportHTSA0.0010.0000.000