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CHECK report for eisa on tokay2

This page was generated on 2019-10-16 12:23:10 -0400 (Wed, 16 Oct 2019).

Package 492/1741HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
eisa 1.36.0
Gabor Csardi
Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019)
URL: https://git.bioconductor.org/packages/eisa
Branch: RELEASE_3_9
Last Commit: 801a7d9
Last Changed Date: 2019-05-02 11:53:13 -0400 (Thu, 02 May 2019)
malbec2 Linux (Ubuntu 18.04.2 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository
celaya2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: eisa
Version: 1.36.0
Command: C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:eisa.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings eisa_1.36.0.tar.gz
StartedAt: 2019-10-16 03:28:47 -0400 (Wed, 16 Oct 2019)
EndedAt: 2019-10-16 04:03:25 -0400 (Wed, 16 Oct 2019)
EllapsedTime: 2077.7 seconds
RetCode: 0
Status:  OK  
CheckDir: eisa.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:eisa.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings eisa_1.36.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.9-bioc/meat/eisa.Rcheck'
* using R version 3.6.1 (2019-07-05)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'eisa/DESCRIPTION' ... OK
* this is package 'eisa' version '1.36.0'
* 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 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 : : 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 files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
                         user system elapsed
ISA                    581.33   0.71  582.19
ISA.iterate            428.72   0.44  429.51
ISA.unique             408.61   0.19  408.81
ISA.sweep              309.52   0.73  310.44
eisa.biclust             6.45   0.46    7.16
ListHyperGResult-class   4.92   0.64    5.56
gograph                  4.78   0.23    5.01
ISA.GO                   3.59   0.28    5.34
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                        user system elapsed
ISA                    17.70   0.93   18.67
ISA.sweep              14.74   0.81   15.55
ISA.iterate             8.33   0.34    8.69
ISA.unique              6.98   0.42    7.41
ISA.GO                  5.37   0.16    5.54
eisa.biclust            4.49   0.37    5.02
ListHyperGResult-class  4.45   0.17   12.72
* 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
  'C:/Users/biocbuild/bbs-3.9-bioc/meat/eisa.Rcheck/00check.log'
for details.

Installation output

eisa.Rcheck/00install.out

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.9/bioc/src/contrib/eisa_1.36.0.tar.gz && rm -rf eisa.buildbin-libdir && mkdir eisa.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=eisa.buildbin-libdir eisa_1.36.0.tar.gz && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL eisa_1.36.0.zip && rm eisa_1.36.0.tar.gz eisa_1.36.0.zip
###
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  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100 1197k  100 1197k    0     0  8348k      0 --:--:-- --:--:-- --:--:-- 8804k

install for i386

* 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
  converting help for package 'eisa'
    finding HTML links ... done
    ALLModules                              html  
    ISA.CHR                                 html  
    ISA.GO                                  html  
    ISA.KEGG                                html  
    ISA                                     html  
    ISA.html                                html  
    ISA.iterate                             html  
    ISA.miRNA                               html  
    ISA.normalize                           html  
    ISA.sweep                               html  
    ISA.unique                              html  
    ISA2heatmap                             html  
    ISAExpressionSet                        html  
    ISAModules-class                        html  
    ListHyperGParams-class                  html  
    ListHyperGResult-class                  html  
    cond.plot                               html  
    eisa.biclust                            html  
    enrichment                              html  
    exp.plot                                html  
    gograph                                 html  
    mnplot                                  html  
    overlap                                 html  
    profilePlot                             html  
    robustness                              html  
** 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

install for x64

* installing *source* package 'eisa' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'eisa' as eisa_1.36.0.zip
* DONE (eisa)
* installing to library 'C:/Users/biocbuild/bbs-3.9-bioc/R/library'
package 'eisa' successfully unpacked and MD5 sums checked

Tests output

Example timings

eisa.Rcheck/examples_i386/eisa-Ex.timings

nameusersystemelapsed
ALLModules0.020.010.03
ISA.CHR0.950.020.97
ISA.GO3.590.285.34
ISA.KEGG1.790.161.95
ISA581.33 0.71582.19
ISA.html000
ISA.iterate428.72 0.44429.51
ISA.miRNA0.780.050.85
ISA.normalize3.530.393.92
ISA.sweep309.52 0.73310.44
ISA.unique408.61 0.19408.81
ISA2heatmap1.720.061.78
ISAExpressionSet3.950.194.14
ISAModules-class0.010.000.02
ListHyperGParams-class4.660.244.89
ListHyperGResult-class4.920.645.56
cond.plot1.860.111.97
eisa.biclust6.450.467.16
enrichment0.460.020.46
exp.plot2.340.142.49
gograph4.780.235.01
mnplot1.990.072.05
overlap0.580.431.02
profilePlot1.700.051.75
robustness2.870.133.00

eisa.Rcheck/examples_x64/eisa-Ex.timings

nameusersystemelapsed
ALLModules0.040.000.05
ISA.CHR1.180.031.20
ISA.GO5.370.165.54
ISA.KEGG2.640.122.78
ISA17.70 0.9318.67
ISA.html000
ISA.iterate8.330.348.69
ISA.miRNA0.610.020.62
ISA.normalize3.780.143.92
ISA.sweep14.74 0.8115.55
ISA.unique6.980.427.41
ISA2heatmap1.140.061.20
ISAExpressionSet3.110.113.22
ISAModules-class0.020.000.01
ListHyperGParams-class4.300.224.52
ListHyperGResult-class 4.45 0.1712.72
cond.plot1.420.071.48
eisa.biclust4.490.375.02
enrichment0.280.020.30
exp.plot1.420.031.45
gograph4.170.204.50
mnplot1.840.111.95
overlap0.660.281.25
profilePlot1.630.041.67
robustness1.730.111.84