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BioC 3.4: CHECK report for globaltest on moscato1

This page was generated on 2016-09-21 03:41:23 -0700 (Wed, 21 Sep 2016).

Package 521/1257HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
globaltest 5.27.0
Jelle Goeman
Snapshot Date: 2016-09-19 19:15:14 -0700 (Mon, 19 Sep 2016)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/globaltest
Last Changed Rev: 117081 / Revision: 121152
Last Changed Date: 2016-05-03 14:30:44 -0700 (Tue, 03 May 2016)
zin1 Linux (Ubuntu 16.04 LTS) / x86_64  OK  OK  WARNINGS UNNEEDED, same version exists in internal repository
moscato1 Windows Server 2008 R2 Standard (64-bit) / x64  OK  OK [ WARNINGS ] OK UNNEEDED, same version exists in internal repository
morelia Mac OS X Mavericks (10.9.5) / x86_64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository

Summary

Package: globaltest
Version: 5.27.0
Command: rm -rf globaltest.buildbin-libdir globaltest.Rcheck && mkdir globaltest.buildbin-libdir globaltest.Rcheck && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=globaltest.buildbin-libdir globaltest_5.27.0.tar.gz >globaltest.Rcheck\00install.out 2>&1 && cp globaltest.Rcheck\00install.out globaltest-install.out && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD check --library=globaltest.buildbin-libdir --install="check:globaltest-install.out" --force-multiarch --no-vignettes --timings globaltest_5.27.0.tar.gz
StartedAt: 2016-09-20 09:39:33 -0700 (Tue, 20 Sep 2016)
EndedAt: 2016-09-20 09:42:12 -0700 (Tue, 20 Sep 2016)
EllapsedTime: 159.1 seconds
RetCode: 0
Status:  WARNINGS  
CheckDir: globaltest.Rcheck
Warnings: 1

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf globaltest.buildbin-libdir globaltest.Rcheck && mkdir globaltest.buildbin-libdir globaltest.Rcheck && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=globaltest.buildbin-libdir globaltest_5.27.0.tar.gz >globaltest.Rcheck\00install.out 2>&1 && cp globaltest.Rcheck\00install.out globaltest-install.out  && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD check --library=globaltest.buildbin-libdir --install="check:globaltest-install.out" --force-multiarch --no-vignettes --timings globaltest_5.27.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'D:/biocbld/bbs-3.4-bioc/meat/globaltest.Rcheck'
* using R version 3.3.1 (2016-06-21)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'globaltest/DESCRIPTION' ... OK
* this is package 'globaltest' version '5.27.0'
* 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 'globaltest' 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 'Rgraphviz' 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
.coxtest: no visible global function definition for 'formula'
.coxtest : test: no visible global function definition for 'pnorm'
.coxtest : test: no visible global function definition for 'var'
.genF : <anonymous>: no visible global function definition for 'pf'
.getAlternative: no visible global function definition for
  'model.frame'
.getAlternative: no visible global function definition for 'terms'
.getNull: no visible global function definition for 'terms'
.getNull: no visible global function definition for 'model.offset'
.getNull: no visible global function definition for 'model.frame'
.glmtest: no visible global function definition for 'formula'
.glmtest: no visible global function definition for 'glm'
.glmtest : test: no visible global function definition for 'var'
.lineartest: no visible global function definition for 'formula'
.lineartest: no visible global function definition for 'lm'
.lineartest : test: no visible global function definition for 'var'
.multinomialtest: no visible global function definition for 'formula'
.multinomialtest : test: no visible global function definition for
  'var'
.multinomialtest : positive: no visible global function definition for
  'cor'
.pImhof: no visible global function definition for 'integrate'
comparative : <anonymous>: no visible global function definition for
  'flush.console'
comparative : <anonymous> : <anonymous>: no visible global function
  definition for 'flush.console'
covariates: no visible global function definition for 'flush.console'
covariates: no visible global function definition for 'par'
covariates: no visible global function definition for 'as.dist'
covariates: no visible global function definition for 'as.dendrogram'
covariates: no visible global function definition for 'hclust'
covariates: no visible global function definition for 'reorder'
covariates : sigcol: no visible global function definition for 'gray'
covariates : sigcol: no visible global function definition for
  'is.leaf'
covariates: no visible global function definition for 'layout'
covariates: no visible global function definition for 'axis'
covariates: no visible global function definition for 'strwidth'
covariates: no visible global function definition for 'rainbow'
covariates: no visible global function definition for 'barplot'
covariates: no visible global function definition for 'lines'
covariates: no visible global function definition for 'gray'
covariates : <anonymous>: no visible global function definition for
  'lines'
covariates : <anonymous> : <anonymous>: no visible global function
  definition for 'lines'
covariates: no visible global function definition for 'abline'
covariates: no visible global function definition for 'title'
covariates: no visible global function definition for 'dev.off'
dendro2sets : do.sets: no visible global function definition for
  'is.leaf'
dendro2sets: no visible global function definition for 'is.leaf'
draw: no visible global function definition for 'plot'
draw: no visible global function definition for 'flush.console'
draw: no visible global function definition for 'locator'
focusLevel : <anonymous>: no visible global function definition for
  'flush.console'
focusLevel: no visible global function definition for 'flush.console'
getK: no visible global function definition for 'dist'
getK: no visible global function definition for 'as.dist'
getK: no visible global function definition for 'cor'
getK: no visible global function definition for 'quantile'
getK : <anonymous>: no visible global function definition for
  'quantile'
getK : <anonymous>: no visible global function definition for 'dnorm'
gt: no visible global function definition for 'terms'
gt: no visible global function definition for 'formula'
gt : <anonymous>: no visible global function definition for 'lm'
gt : <anonymous>: no visible global function definition for 'coef'
gt: no visible binding for global variable 'var'
gt : <anonymous>: no visible global function definition for
  'flush.console'
gtKS: no visible global function definition for 'as.formula'
gtKS: no visible global function definition for 'terms'
gtKS: no visible global function definition for 'model.frame'
gtKS: no visible global function definition for 'formula'
gtKS: no visible global function definition for 'glm'
gtLI: no visible global function definition for 'as.formula'
gtLI: no visible global function definition for 'terms'
gtLI: no visible global function definition for 'formula'
gtLI: no visible global function definition for 'terms.formula'
gtPS: no visible global function definition for 'as.formula'
gtPS: no visible global function definition for 'terms'
gtPS: no visible global function definition for 'formula'
gtPS: no visible global function definition for 'glm'
gtPS: no visible global function definition for 'model.frame'
inheritance: no visible global function definition for 'as.dendrogram'
inheritance: no visible global function definition for 'flush.console'
inheritance : <anonymous>: no visible global function definition for
  'flush.console'
mlogit: no visible global function definition for 'glm.control'
similarity: no visible global function definition for 'as.dist'
similarity: no visible global function definition for 'as.dendrogram'
similarity: no visible global function definition for 'hclust'
similarity: no visible global function definition for 'rgb'
similarity: no visible global function definition for 'heatmap'
subjects: no visible global function definition for 'pnorm'
subjects: no visible global function definition for 'par'
subjects: no visible global function definition for 'as.dist'
subjects: no visible global function definition for 'as.dendrogram'
subjects: no visible global function definition for 'hclust'
subjects: no visible global function definition for 'reorder'
subjects: no visible global function definition for 'layout'
subjects: no visible global function definition for 'plot'
subjects: no visible global function definition for 'axis'
subjects: no visible global function definition for 'strwidth'
subjects: no visible global function definition for 'rainbow'
subjects: no visible global function definition for 'barplot'
subjects: no visible global function definition for 'lines'
subjects: no visible global function definition for 'gray'
subjects : <anonymous>: no visible global function definition for
  'lines'
subjects : <anonymous> : <anonymous>: no visible global function
  definition for 'lines'
subjects: no visible global function definition for 'abline'
subjects: no visible global function definition for 'title'
subjects: no visible global function definition for 'dev.off'
hist,gt.object : gt.hist: no visible global function definition for
  'arrows'
hist,gt.object : gt.hist: no visible global function definition for
  'text'
summary,mlogit: no visible binding for global variable 'quantile'
summary,mlogit: no visible global function definition for 'pnorm'
Undefined global functions or variables:
  abline arrows as.dendrogram as.dist as.formula axis barplot coef cor
  dev.off dist dnorm flush.console formula glm glm.control gray hclust
  heatmap integrate is.leaf layout lines lm locator model.frame
  model.offset par pf plot pnorm quantile rainbow reorder rgb strwidth
  terms terms.formula text title var
Consider adding
  importFrom("grDevices", "dev.off", "gray", "rainbow", "rgb")
  importFrom("graphics", "abline", "arrows", "axis", "barplot", "layout",
             "lines", "locator", "par", "plot", "strwidth", "text",
             "title")
  importFrom("stats", "as.dendrogram", "as.dist", "as.formula", "coef",
             "cor", "dist", "dnorm", "formula", "glm", "glm.control",
             "hclust", "heatmap", "integrate", "is.leaf", "lm",
             "model.frame", "model.offset", "pf", "pnorm", "quantile",
             "reorder", "terms", "terms.formula", "var")
  importFrom("utils", "flush.console")
to your NAMESPACE file.
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... WARNING
Undocumented S4 methods:
  generic '[' and siglist 'gt.object,ANY,ANY,ANY'
All user-level objects in a package (including S4 classes and methods)
should have documentation entries.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
** running examples for arch 'x64' ... OK
* 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, 2 NOTEs
See
  'D:/biocbld/bbs-3.4-bioc/meat/globaltest.Rcheck/00check.log'
for details.

globaltest.Rcheck/00install.out:


install for i386

* installing *source* package 'globaltest' ...
** R
** inst
** preparing package for lazy loading
Creating a generic function for 'sort' from package 'base' in package 'globaltest'
Creating a generic function for 'model.matrix' from package 'stats' in package 'globaltest'
Creating a generic function for 'coefficients' from package 'stats' in package 'globaltest'
Creating a generic function for 'fitted.values' from package 'stats' in package 'globaltest'
Creating a generic function for 'residuals' from package 'stats' in package 'globaltest'
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded

install for x64

* installing *source* package 'globaltest' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'globaltest' as globaltest_5.27.0.zip
* DONE (globaltest)

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

nameusersystemelapsed
comparative1.380.001.39
diagnostics0.550.000.55
genesettesting000
goodnessoffit0.640.010.65
gt0.230.000.24
gt.object-class0.440.020.56
gtoptions000
mlogit0.020.000.01
multtest0.250.000.25

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

nameusersystemelapsed
comparative1.530.001.53
diagnostics0.70.00.7
genesettesting000
goodnessoffit0.640.000.64
gt0.50.00.5
gt.object-class0.470.000.47
gtoptions000
mlogit000
multtest0.350.000.35