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BioC 3.6: CHECK report for gage on tokay1

This page was generated on 2017-08-16 13:29:11 -0400 (Wed, 16 Aug 2017).

Package 496/1410HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
gage 2.27.1
Weijun Luo
Snapshot Date: 2017-08-15 17:18:21 -0400 (Tue, 15 Aug 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/gage
Last Changed Rev: 130661 / Revision: 131943
Last Changed Date: 2017-06-24 17:30:08 -0400 (Sat, 24 Jun 2017)
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 [ OK ] OK UNNEEDED, same version exists in internal repository
veracruz1 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: gage
Version: 2.27.1
Command: rm -rf gage.buildbin-libdir gage.Rcheck && mkdir gage.buildbin-libdir gage.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=gage.buildbin-libdir gage_2.27.1.tar.gz >gage.Rcheck\00install.out 2>&1 && cp gage.Rcheck\00install.out gage-install.out && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=gage.buildbin-libdir --install="check:gage-install.out" --force-multiarch --no-vignettes --timings gage_2.27.1.tar.gz
StartedAt: 2017-08-15 23:34:35 -0400 (Tue, 15 Aug 2017)
EndedAt: 2017-08-15 23:37:27 -0400 (Tue, 15 Aug 2017)
EllapsedTime: 171.9 seconds
RetCode: 0
Status:  OK  
CheckDir: gage.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf gage.buildbin-libdir gage.Rcheck && mkdir gage.buildbin-libdir gage.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=gage.buildbin-libdir gage_2.27.1.tar.gz >gage.Rcheck\00install.out 2>&1 && cp gage.Rcheck\00install.out gage-install.out  &&  C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=gage.buildbin-libdir --install="check:gage-install.out" --force-multiarch --no-vignettes --timings gage_2.27.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.6-bioc/meat/gage.Rcheck'
* using R version 3.4.1 (2017-06-30)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'gage/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'gage' version '2.27.1'
* 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 whether package 'gage' 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' call to 'GO.db' in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
colorpanel: no visible global function definition for 'col2rgb'
colorpanel: no visible global function definition for 'rgb'
deComp: no visible global function definition for 'annot.db'
deComp: no visible global function definition for 'write.table'
eg2sym: no visible binding for global variable 'egSymb'
essGene: no visible binding for global variable 'sd'
essGene: no visible global function definition for 'qchisq'
esset.grp: no visible global function definition for 'sd'
esset.grp : <anonymous>: no visible global function definition for
  'phyper'
esset.grp: no visible global function definition for 'as'
esset.grp: no visible global function definition for 'write.table'
esset.grp: no visible global function definition for 'nodes'
esset.grp: no visible global function definition for 'edgeNames'
esset.grp: no visible global function definition for 'pdf'
esset.grp: no visible global function definition for 'make.graph'
esset.grp : <anonymous>: no visible global function definition for
  'nodes'
esset.grp: no visible global function definition for 'points'
esset.grp: no visible global function definition for 'dev.off'
gageComp: no visible global function definition for 'pdf'
gageComp: no visible global function definition for 'dev.off'
gagePipe: no visible global function definition for 'write.table'
gagePipe: no visible global function definition for 'pdf'
gagePipe: no visible global function definition for 'dev.off'
gagePrep : <anonymous>: no visible global function definition for
  't.test'
gageSum: no visible global function definition for 'qnorm'
gageSum: no visible global function definition for 'pnorm'
gageSum: no visible global function definition for 'aggregate'
gageSum : <anonymous>: no visible global function definition for
  'pnorm'
gageSum: no visible global function definition for 'pgamma'
gageSum: no visible global function definition for 'p.adjust'
geneData: no visible global function definition for 'write.table'
geneData: no visible global function definition for 'pdf'
geneData: no visible global function definition for 'dev.off'
geneData: no visible global function definition for 'par'
geneData: no visible global function definition for 'plot'
geneData: no visible global function definition for 'abline'
geneData: no visible global function definition for 'points'
geneData: no visible global function definition for 'legend'
go.gsets: no visible global function definition for 'data'
go.gsets: no visible global function definition for 'biocLite'
go.gsets: no visible binding for global variable 'GOTERM'
gs.KSTest : <anonymous>: no visible global function definition for
  'ks.test'
gs.tTest: no visible binding for global variable 'sd'
gs.tTest: no visible global function definition for 'pt'
gs.zTest: no visible binding for global variable 'sd'
gs.zTest: no visible global function definition for 'pnorm'
heatmap2: no visible binding for global variable 'dist'
heatmap2: no visible binding for global variable 'hclust'
heatmap2: no visible global function definition for 'par'
heatmap2: no visible global function definition for 'median'
heatmap2: no visible binding for global variable 'sd'
heatmap2: no visible global function definition for 'order.dendrogram'
heatmap2: no visible global function definition for 'as.dendrogram'
heatmap2: no visible global function definition for 'reorder'
heatmap2: no visible global function definition for 'layout'
heatmap2: no visible global function definition for 'image'
heatmap2: no visible global function definition for 'axis'
heatmap2: no visible global function definition for 'mtext'
heatmap2: no visible global function definition for 'rect'
heatmap2: no visible global function definition for 'abline'
heatmap2: no visible global function definition for 'lines'
heatmap2: no visible global function definition for 'text'
heatmap2: no visible global function definition for 'plot'
heatmap2: no visible global function definition for 'plot.new'
heatmap2: no visible global function definition for 'title'
heatmap2: no visible global function definition for 'density'
heatmap2: no visible global function definition for 'hist'
kegg.gsets: no visible global function definition for 'read.delim'
kegg.gsets: no visible global function definition for 'data'
kegg.species.code: no visible global function definition for
  'read.delim'
kegg.species.code: no visible global function definition for 'data'
readExpData: no visible global function definition for 'read.delim'
rownorm : <anonymous>: no visible global function definition for 'sd'
sigGeneSet: no visible global function definition for 'pdf'
sigGeneSet: no visible global function definition for 'dev.off'
sym2eg: no visible binding for global variable 'egSymb'
vennDiagram2: no visible global function definition for 'is'
vennDiagram2: no visible global function definition for 'par'
vennDiagram2: no visible global function definition for 'plot'
vennDiagram2: no visible global function definition for 'lines'
vennDiagram2: no visible global function definition for 'text'
vennDiagram2: no visible global function definition for 'rect'
vennDiagram2 : printing: no visible global function definition for
  'text'
Undefined global functions or variables:
  GOTERM abline aggregate annot.db as as.dendrogram axis biocLite
  col2rgb data density dev.off dist edgeNames egSymb hclust hist image
  is ks.test layout legend lines make.graph median mtext nodes
  order.dendrogram p.adjust par pdf pgamma phyper plot plot.new pnorm
  points pt qchisq qnorm read.delim rect reorder rgb sd t.test text
  title write.table
Consider adding
  importFrom("grDevices", "col2rgb", "dev.off", "pdf", "rgb")
  importFrom("graphics", "abline", "axis", "hist", "image", "layout",
             "legend", "lines", "mtext", "par", "plot", "plot.new",
             "points", "rect", "text", "title")
  importFrom("methods", "as", "is")
  importFrom("stats", "aggregate", "as.dendrogram", "density", "dist",
             "hclust", "ks.test", "median", "order.dendrogram",
             "p.adjust", "pgamma", "phyper", "pnorm", "pt", "qchisq",
             "qnorm", "reorder", "sd", "t.test")
  importFrom("utils", "data", "read.delim", "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 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
kegg.gsets 4.17   0.04   14.21
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
           user system elapsed
kegg.gsets 2.75   0.05   11.05
* 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-3.6-bioc/meat/gage.Rcheck/00check.log'
for details.

gage.Rcheck/00install.out:


install for i386

* installing *source* package 'gage' ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded

install for x64

* installing *source* package 'gage' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'gage' as gage_2.27.1.zip
* DONE (gage)

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

nameusersystemelapsed
eg2sym1.090.021.11
egSymb0.800.010.81
essGene0.760.020.78
esset.grp1.110.021.12
gage1.910.001.91
gageComp1.330.043.83
gagePipe1.360.021.37
geneData0.370.030.41
go.gsets000
gs.tTest0.530.030.56
gse168730.330.000.33
heter.gage0.780.000.79
kegg.gs0.700.020.71
kegg.gsets 4.17 0.0414.21
readExpData0.020.000.01
readList0.200.000.21
sigGeneSet0.770.030.82

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

nameusersystemelapsed
eg2sym2.020.212.22
egSymb1.030.091.12
essGene0.960.020.96
esset.grp2.310.062.38
gage2.120.032.16
gageComp1.080.001.07
gagePipe0.850.030.88
geneData0.250.020.26
go.gsets000
gs.tTest0.420.000.43
gse168730.220.010.23
heter.gage0.750.030.78
kegg.gs0.950.020.97
kegg.gsets 2.75 0.0511.05
readExpData0.020.000.01
readList0.120.000.13
sigGeneSet0.500.010.51