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BioC 3.4: CHECK report for eisa on tokay1

This page was generated on 2017-04-15 16:16:05 -0400 (Sat, 15 Apr 2017).

Package 372/1296HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
eisa 1.26.0
Gabor Csardi
Snapshot Date: 2017-04-14 17:17:13 -0400 (Fri, 14 Apr 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_4/madman/Rpacks/eisa
Last Changed Rev: 122710 / Revision: 128728
Last Changed Date: 2016-10-17 14:45:06 -0400 (Mon, 17 Oct 2016)
malbec1 Linux (Ubuntu 16.04.1 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK [ TIMEOUT ] OK 
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: 1.26.0
Command: rm -rf eisa.buildbin-libdir eisa.Rcheck && mkdir eisa.buildbin-libdir eisa.Rcheck && C:\Users\biocbuild\bbs-3.4-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=eisa.buildbin-libdir eisa_1.26.0.tar.gz >eisa.Rcheck\00install.out 2>&1 && cp eisa.Rcheck\00install.out eisa-install.out && C:\Users\biocbuild\bbs-3.4-bioc\R\bin\R.exe CMD check --library=eisa.buildbin-libdir --install="check:eisa-install.out" --force-multiarch --no-vignettes --timings eisa_1.26.0.tar.gz
StartedAt: 2017-04-14 22:07:00 -0400 (Fri, 14 Apr 2017)
EndedAt: 2017-04-14 22:47:02 -0400 (Fri, 14 Apr 2017)
EllapsedTime: 2402.1 seconds
RetCode: None
Status:  TIMEOUT  
CheckDir: eisa.Rcheck
Warnings: NA

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf eisa.buildbin-libdir eisa.Rcheck && mkdir eisa.buildbin-libdir eisa.Rcheck && C:\Users\biocbuild\bbs-3.4-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=eisa.buildbin-libdir eisa_1.26.0.tar.gz >eisa.Rcheck\00install.out 2>&1 && cp eisa.Rcheck\00install.out eisa-install.out  && C:\Users\biocbuild\bbs-3.4-bioc\R\bin\R.exe CMD check --library=eisa.buildbin-libdir --install="check:eisa-install.out" --force-multiarch --no-vignettes --timings eisa_1.26.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.4-bioc/meat/eisa.Rcheck'
* using R version 3.3.3 (2017-03-06)
* 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 '1.26.0'
* 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 : <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 installed files from 'inst/doc' ... 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         375.36   0.56  375.92
ISA.iterate 368.78   0.52  369.31
ISA.unique  364.03   0.09  364.13
ISA.sweep   259.60   0.30  259.90
ISA.GO        7.70   0.23   12.16
gograph       5.67   0.23    5.90
** running examples for arch 'x64' ...

eisa.Rcheck/00install.out:


install for i386

* 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

install for x64

* installing *source* package 'eisa' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'eisa' as eisa_1.26.0.zip
* DONE (eisa)

eisa.Rcheck/examples_i386/eisa-Ex.timings:

nameusersystemelapsed
ALLModules0.030.000.03
ISA.CHR0.990.011.00
ISA.GO 7.70 0.2312.16
ISA.KEGG1.620.021.64
ISA375.36 0.56375.92
ISA.html000
ISA.iterate368.78 0.52369.31
ISA.miRNA0.810.012.47
ISA.normalize3.510.173.69
ISA.sweep259.6 0.3259.9
ISA.unique364.03 0.09364.13
ISA2heatmap1.700.041.73
ISAExpressionSet4.050.114.16
ISAModules-class0.020.000.02
ListHyperGParams-class4.670.294.96
ListHyperGResult-class4.610.164.77
cond.plot1.610.051.66
eisa.biclust4.170.354.84
enrichment0.310.020.33
exp.plot1.870.081.96
gograph5.670.235.90
mnplot1.940.102.03
overlap0.560.360.93
profilePlot1.570.031.59
robustness2.400.082.48

eisa.Rcheck/examples_x64/eisa-Ex.timings:

nameusersystemelapsed
ALLModules0.030.000.03
ISA.CHR0.810.030.84
ISA.GO5.940.206.14
ISA.KEGG2.420.052.47
ISA247.30 0.56247.87
ISA.html000
ISA.iterate250.19 0.48250.67
ISA.miRNA0.710.100.79
ISA.normalize3.900.314.22
ISA.sweep181.64 0.30181.96