Package: gage

Version: 2.33.1

Command: /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:gage.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings gage_2.33.1.tar.gz

StartedAt: 2019-04-09 00:36:05 -0400 (Tue, 09 Apr 2019)

EndedAt: 2019-04-09 00:38:02 -0400 (Tue, 09 Apr 2019)

EllapsedTime: 116.2 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: gage.Rcheck

Warnings: 1

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### Running command:
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###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:gage.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings gage_2.33.1.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.9-bioc/meat/gage.Rcheck’
* using R Under development (unstable) (2019-03-18 r76245)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘gage/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘gage’ version ‘2.33.1’
* 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 for sufficient/correct file permissions ... 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
* 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 ... WARNING
'::' or ':::' import not declared from: ‘BiocManager’
'loadNamespace' or 'requireNamespace' call not declared from: ‘BiocManager’
'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 ‘install.packages’
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 col2rgb data
  density dev.off dist edgeNames egSymb hclust hist image
  install.packages 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", "install.packages", "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 ... OK
Examples with CPU or elapsed time > 5s
            user system elapsed
kegg.gsets 0.849  0.017   8.913
* 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: 1 WARNING, 1 NOTE
See
  ‘/home/biocbuild/bbs-3.9-bioc/meat/gage.Rcheck/00check.log’
for details.

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### Running command:
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###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD INSTALL gage
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* installing to library ‘/home/biocbuild/bbs-3.9-bioc/R/library’
* installing *source* package ‘gage’ ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** 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 (gage)

name	user	system	elapsed
eg2sym	0.779	0.008	0.787
egSymb	0.615	0.000	0.615
essGene	0.274	0.000	0.274
esset.grp	1.795	0.005	1.800
gage	1.814	0.038	1.852
gageComp	0.656	0.016	0.703
gagePipe	0.611	0.004	0.615
geneData	0.191	0.004	0.195
go.gsets	0.001	0.000	0.001
gs.tTest	0.161	0.000	0.160
gse16873	0.195	0.000	0.195
heter.gage	0.377	0.004	0.381
kegg.gs	0.734	0.000	0.734
kegg.gsets	0.849	0.017	8.913
readExpData	0.004	0.003	0.019
readList	0.188	0.000	0.197
sigGeneSet	0.63	0.00	0.63