Back to Multiple platform build/check report for BioC 3.11
ABCD[E]FGHIJKLMNOPQRSTUVWXYZ

CHECK report for eisa on machv2

This page was generated on 2020-10-17 11:58:25 -0400 (Sat, 17 Oct 2020).

TO THE DEVELOPERS/MAINTAINERS OF THE eisa PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 534/1905HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
eisa 1.40.0
Gabor Csardi
Snapshot Date: 2020-10-16 14:40:19 -0400 (Fri, 16 Oct 2020)
URL: https://git.bioconductor.org/packages/eisa
Branch: RELEASE_3_11
Last Commit: 5f3dd5e
Last Changed Date: 2020-04-27 14:20:46 -0400 (Mon, 27 Apr 2020)
malbec2 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK  OK 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
machv2 macOS 10.14.6 Mojave / x86_64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: eisa
Version: 1.40.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:eisa.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings eisa_1.40.0.tar.gz
StartedAt: 2020-10-17 00:48:45 -0400 (Sat, 17 Oct 2020)
EndedAt: 2020-10-17 00:53:45 -0400 (Sat, 17 Oct 2020)
EllapsedTime: 300.1 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 --install=check:eisa.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings eisa_1.40.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.11-bioc/meat/eisa.Rcheck’
* using R version 4.0.3 (2020-10-10)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘eisa/DESCRIPTION’ ... OK
* this is package ‘eisa’ version ‘1.40.0’
* 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                         user system elapsed
ISA                    18.814  0.578  19.405
ISA.sweep              14.321  1.157  15.502
ISA.iterate             8.368  0.390   8.763
ISA.unique              8.076  0.272   8.363
gograph                 6.525  0.305   6.841
ISA.GO                  6.245  0.348   6.600
ListHyperGResult-class  5.750  0.306   6.063
ListHyperGParams-class  5.087  0.265   5.356
* 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-3.11-bioc/meat/eisa.Rcheck/00check.log’
for details.



Installation output

eisa.Rcheck/00install.out

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


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.0/Resources/library’
* installing *source* package ‘eisa’ ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare 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 from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (eisa)

Tests output


Example timings

eisa.Rcheck/eisa-Ex.timings

nameusersystemelapsed
ALLModules0.0480.0060.054
ISA.CHR0.8800.0650.946
ISA.GO6.2450.3486.600
ISA.KEGG2.7930.0442.840
ISA18.814 0.57819.405
ISA.html0.0000.0010.001
ISA.iterate8.3680.3908.763
ISA.miRNA0.8430.0410.894
ISA.normalize3.6710.2593.936
ISA.sweep14.321 1.15715.502
ISA.unique8.0760.2728.363
ISA2heatmap1.3910.0541.448
ISAExpressionSet3.6890.1423.837
ISAModules-class0.0140.0050.020
ListHyperGParams-class5.0870.2655.356
ListHyperGResult-class5.7500.3066.063
cond.plot1.7920.0541.849
eisa.biclust4.2880.4544.757
enrichment0.4800.0120.494
exp.plot2.2590.0612.327
gograph6.5250.3056.841
mnplot1.8510.0641.920
overlap0.0840.0130.099
profilePlot1.4190.0271.448
robustness2.5140.0762.594