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BioC 3.4: CHECK report for eisa on morelia

This page was generated on 2016-09-21 03:50:29 -0700 (Wed, 21 Sep 2016).

Package 363/1257HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
eisa 1.25.0
Gabor Csardi
Snapshot Date: 2016-09-19 19:15:14 -0700 (Mon, 19 Sep 2016)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/eisa
Last Changed Rev: 117081 / Revision: 121152
Last Changed Date: 2016-05-03 14:30:44 -0700 (Tue, 03 May 2016)
zin1 Linux (Ubuntu 16.04 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
moscato1 Windows Server 2008 R2 Standard (64-bit) / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
morelia Mac OS X Mavericks (10.9.5) / x86_64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: eisa
Version: 1.25.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings eisa_1.25.0.tar.gz
StartedAt: 2016-09-20 06:03:18 -0700 (Tue, 20 Sep 2016)
EndedAt: 2016-09-20 06:07:07 -0700 (Tue, 20 Sep 2016)
EllapsedTime: 229.1 seconds
RetCode: 0
Status:  OK 
CheckDir: eisa.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings eisa_1.25.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.4-bioc/meat/eisa.Rcheck’
* using R version 3.3.1 (2016-06-21)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘eisa/DESCRIPTION’ ... OK
* this is package ‘eisa’ version ‘1.25.0’
* 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 ‘eisa’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* 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:
  ‘GO.db’ ‘KEGG.db’ ‘MASS’ ‘biclust’ ‘igraph’ ‘xtable’
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Unexported objects imported by ':::' calls:
  ‘Category:::getDataEnv’ ‘Category:::getKeggToProbeMap’
  ‘Category:::probeToEntrezMapHelper’
  See the note in ?`:::` about the use of this operator.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
ISA : <anonymous>: no visible global function definition for ‘IQR’
ISA: no visible binding for global variable ‘var’
ISA2heatmap: no visible global function definition for ‘heatmap’
ISACHR: no visible global function definition for ‘p.adjust’
ISAEnrichment: no visible global function definition for ‘p.adjust’
ISAGO: no visible global function definition for ‘p.adjust’
ISAHTMLModules: no visible global function definition for ‘GO_dbconn’
ISAHTMLModules : go.graph: no visible global function definition for
  ‘graph.data.frame’
ISAHTMLTable: no visible global function definition for ‘GO_dbconn’
ISAHTMLTable : f: no visible binding for global variable
  ‘KEGGPATHID2NAME’
ISAKEGG: no visible global function definition for ‘p.adjust’
ISASweepGraph: no visible global function definition for ‘V’
ISASweepGraph: no visible global function definition for ‘V<-’
ISASweepGraph: no visible global function definition for
  ‘remove.vertex.attribute’
ISASweepGraphPlot: no visible global function definition for ‘V’
ISASweepGraphPlot: no visible global function definition for ‘axis’
ISASweepGraphPlot: no visible global function definition for ‘par’
ISASweepGraphPlot: no visible global function definition for ‘abline’
ISASweepGraphPlot: no visible global function definition for ‘text’
ISAmiRNA: no visible global function definition for ‘p.adjust’
cnvrt.coords: no visible global function definition for ‘xy.coords’
cnvrt.coords: no visible global function definition for ‘par’
condPlot: no visible global function definition for ‘sd’
condPlot: no visible global function definition for ‘par’
condPlot: no visible global function definition for ‘barplot’
condPlot: no visible global function definition for ‘abline’
condPlot: no visible global function definition for ‘text’
condPlot: no visible global function definition for ‘points’
convert.miRNA: no visible global function definition for ‘read.delim’
expPlot: no visible global function definition for ‘layout’
expPlot: no visible global function definition for ‘par’
expPlot: no visible global function definition for ‘image’
expPlot: no visible global function definition for ‘title’
expPlot: no visible global function definition for ‘axis’
expPlot: no visible global function definition for ‘abline’
expPlot: no visible global function definition for ‘lines’
expPlot: no visible global function definition for ‘text’
expPlot: no visible global function definition for ‘segments’
expPlotColbar: no visible global function definition for ‘par’
expPlotColbar: no visible global function definition for ‘image’
expPlotColbar: no visible global function definition for ‘axis’
expPlotColbar: no visible global function definition for ‘abline’
expPlotCreate: no visible global function definition for ‘hcl’
gograph: no visible binding for global variable ‘GOTERM’
gograph: no visible global function definition for ‘GO_dbconn’
gograph: no visible global function definition for ‘graph.data.frame’
gograph: no visible global function definition for ‘V’
gograph: no visible global function definition for ‘vcount’
gograph: no visible global function definition for ‘neighborhood’
gograph: no visible global function definition for ‘induced_subgraph’
gograph: no visible global function definition for ‘hcl’
gograph: no visible global function definition for ‘V<-’
gograph: no visible global function definition for ‘topological.sort’
gograph: no visible global function definition for ‘unfold.tree’
gograph: no visible global function definition for ‘E’
gograph: no visible global function definition for ‘E<-’
gograph: no visible global function definition for
  ‘layout.reingold.tilford’
gograph: no visible global function definition for ‘as_ids’
gographPlot: no visible global function definition for ‘dev.cur’
gographPlot: no visible global function definition for ‘par’
gographPlot: no visible global function definition for ‘V’
gographPlot: no visible global function definition for ‘text’
html.df: no visible global function definition for ‘xtable’
isa.autogen.module : tabulate: no visible binding for global variable
  ‘KEGGPATHID2NAME’
isa.autogen.module: no visible global function definition for ‘png’
isa.autogen.module: no visible global function definition for ‘dev.off’
isa.autogen.module : gp: no visible global function definition for
  ‘graph.empty’
isa.autogen.module : gp: no visible global function definition for
  ‘png’
isa.autogen.module : gp: no visible global function definition for
  ‘dev.off’
isa.autogen.module : ann: no visible global function definition for
  ‘vcount’
isa.autogen.module : ann: no visible global function definition for ‘V’
mnplot: no visible global function definition for ‘abline’
overlap: no visible global function definition for ‘cor’
overlap: no visible global function definition for ‘isoMDS’
overlap: no visible global function definition for ‘graph.adjacency’
overlap: no visible global function definition for ‘V’
overlap: no visible global function definition for ‘V<-’
overlap: no visible global function definition for ‘graph.empty’
overlap: no visible global function definition for ‘E’
overlap: no visible global function definition for ‘E<-’
overlap: no visible global function definition for
  ‘layout.fruchterman.reingold’
overlap: no visible global function definition for ‘layout.drl’
overlap: no visible global function definition for ‘ecount’
overlapPlot: no visible global function definition for ‘V’
overlapPlot: no visible global function definition for ‘layout.norm’
overlapPlot: no visible global function definition for ‘par’
profilePlot: no visible global function definition for ‘gray’
profilePlot : pp: no visible global function definition for ‘par’
profilePlot : pp: no visible global function definition for ‘title’
profilePlot : pp: no visible global function definition for ‘axis’
profilePlot : pp: no visible global function definition for ‘lines’
profilePlot: no visible global function definition for ‘par’
getFeatureMatrix,ISAModules: no visible global function definition for
  ‘Matrix’
getSampleMatrix,ISAModules: no visible global function definition for
  ‘Matrix’
htmlReport,GOListHyperGResult: no visible binding for global variable
  ‘GOTERM’
htmlReport,KEGGListHyperGResult: no visible binding for global variable
  ‘KEGGPATHID2NAME’
Undefined global functions or variables:
  E E<- GOTERM GO_dbconn IQR KEGGPATHID2NAME Matrix V V<- abline as_ids
  axis barplot cor dev.cur dev.off ecount graph.adjacency
  graph.data.frame graph.empty gray hcl heatmap image induced_subgraph
  isoMDS layout layout.drl layout.fruchterman.reingold layout.norm
  layout.reingold.tilford lines neighborhood p.adjust par png points
  read.delim remove.vertex.attribute sd segments text title
  topological.sort unfold.tree var vcount xtable xy.coords
Consider adding
  importFrom("grDevices", "dev.cur", "dev.off", "gray", "hcl", "png",
             "xy.coords")
  importFrom("graphics", "abline", "axis", "barplot", "image", "layout",
             "lines", "par", "points", "segments", "text", "title")
  importFrom("stats", "IQR", "cor", "heatmap", "p.adjust", "sd", "var")
  importFrom("utils", "read.delim")
to your NAMESPACE file.
* 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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
            user system elapsed
ISA       11.592  0.625  12.295
ISA.sweep  7.643  0.914   8.563
ISA.GO     5.776  0.440  35.591
gograph    5.255  0.320  11.920
* 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: 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.4-bioc/meat/eisa.Rcheck/00check.log’
for details.


eisa.Rcheck/00install.out:

* installing *source* package ‘eisa’ ...
** R
** data
** inst
** preparing package for lazy loading
in method for ‘coerce’ with signature ‘"Biclust","ISAModules"’: no definition for class “Biclust”
in method for ‘coerce’ with signature ‘"ISAModules","Biclust"’: no definition for class “Biclust”
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (eisa)

eisa.Rcheck/eisa-Ex.timings:

nameusersystemelapsed
ALLModules0.0290.0020.031
ISA.CHR0.6090.0170.686
ISA.GO 5.776 0.44035.591
ISA.KEGG1.5940.0411.661
ISA11.592 0.62512.295
ISA.html0.0010.0000.001
ISA.iterate4.3010.3824.685
ISA.miRNA0.7010.0360.896
ISA.normalize3.6640.2083.875
ISA.sweep7.6430.9148.563
ISA.unique4.3920.3524.745
ISA2heatmap1.1800.0451.226
ISAExpressionSet3.7910.1673.959
ISAModules-class0.0080.0010.009
ListHyperGParams-class4.3810.2464.627
ListHyperGResult-class4.3700.2724.644
cond.plot1.4790.1041.583
eisa.biclust2.3020.3593.989
enrichment0.2290.0050.235
exp.plot1.3300.0641.393
gograph 5.255 0.32011.920
mnplot1.6280.0661.696
overlap0.0620.0230.117
profilePlot1.2460.0421.290
robustness1.8560.0581.914