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CHECK report for gage on tokay2

This page was generated on 2018-10-17 08:34:59 -0400 (Wed, 17 Oct 2018).

Package 538/1561HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
gage 2.30.0
Weijun Luo
Snapshot Date: 2018-10-15 16:45:08 -0400 (Mon, 15 Oct 2018)
URL: https://git.bioconductor.org/packages/gage
Branch: RELEASE_3_7
Last Commit: 0168af3
Last Changed Date: 2018-04-30 10:35:15 -0400 (Mon, 30 Apr 2018)
malbec2 Linux (Ubuntu 16.04.1 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
merida2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: gage
Version: 2.30.0
Command: C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:gage.install-out.txt --library=C:\Users\biocbuild\bbs-3.7-bioc\R\library --no-vignettes --timings gage_2.30.0.tar.gz
StartedAt: 2018-10-17 02:05:35 -0400 (Wed, 17 Oct 2018)
EndedAt: 2018-10-17 02:08:23 -0400 (Wed, 17 Oct 2018)
EllapsedTime: 168.5 seconds
RetCode: 0
Status:  OK  
CheckDir: gage.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:gage.install-out.txt --library=C:\Users\biocbuild\bbs-3.7-bioc\R\library --no-vignettes --timings gage_2.30.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.7-bioc/meat/gage.Rcheck'
* using R version 3.5.1 Patched (2018-07-24 r75005)
* 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 '2.30.0'
* 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 '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 'data'
kegg.gsets: no visible binding for global variable 'khier'
kegg.species.code: no visible global function definition for 'data'
kegg.species.code: no visible binding for global variable 'korg.1'
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 khier korg.1 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 files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
           user system elapsed
kegg.gsets 1.06   0.02   10.41
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
           user system elapsed
kegg.gsets 1.67   0.01   10.08
* 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-3.7-bioc/meat/gage.Rcheck/00check.log'
for details.

Installation output

gage.Rcheck/00install.out

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.7/bioc/src/contrib/gage_2.30.0.tar.gz && rm -rf gage.buildbin-libdir && mkdir gage.buildbin-libdir && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=gage.buildbin-libdir gage_2.30.0.tar.gz && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL gage_2.30.0.zip && rm gage_2.30.0.tar.gz gage_2.30.0.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 1642k  100 1642k    0     0  16.4M      0 --:--:-- --:--:-- --:--:-- 17.8M

install for i386

* installing *source* package 'gage' ...
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'gage'
    finding HTML links ... done
    eg2sym                                  html  
    egSymb                                  html  
    essGene                                 html  
    esset.grp                               html  
    gage-internal                           html  
    gage                                    html  
    gageComp                                html  
    gagePipe                                html  
    geneData                                html  
    go.gsets                                html  
    gs.tTest                                html  
    gse16873                                html  
    heter.gage                              html  
    kegg.gs                                 html  
    kegg.gsets                              html  
    readExpData                             html  
    readList                                html  
    sigGeneSet                              html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL

install for x64

* installing *source* package 'gage' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'gage' as gage_2.30.0.zip
* DONE (gage)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.7-bioc/R/library'
package 'gage' successfully unpacked and MD5 sums checked
In R CMD INSTALL

Tests output

Example timings

gage.Rcheck/examples_i386/gage-Ex.timings

nameusersystemelapsed
eg2sym0.890.070.97
egSymb0.700.040.74
essGene0.460.040.50
esset.grp1.670.001.67
gage2.50.02.5
gageComp1.160.051.21
gagePipe1.040.011.05
geneData0.310.050.36
go.gsets000
gs.tTest0.400.020.42
gse168730.300.010.31
heter.gage0.690.030.72
kegg.gs0.940.000.94
kegg.gsets 1.06 0.0210.41
readExpData0.030.000.06
readList0.220.000.30
sigGeneSet0.620.050.67

gage.Rcheck/examples_x64/gage-Ex.timings

nameusersystemelapsed
eg2sym1.060.141.20
egSymb0.890.030.92
essGene0.330.000.33
esset.grp1.110.001.11
gage2.530.042.56
gageComp1.500.031.53
gagePipe1.490.031.52
geneData0.440.000.44
go.gsets0.000.010.01
gs.tTest0.420.000.43
gse168730.460.020.47
heter.gage1.110.001.10
kegg.gs1.000.051.07
kegg.gsets 1.67 0.0110.08
readExpData0.010.000.01
readList0.140.000.14
sigGeneSet0.640.020.66