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 ] | |  |
| moscato1 | Windows Server 2008 R2 Standard (64-bit) / x64 | OK | OK | WARNINGS | OK | |
| morelia | Mac OS X Mavericks (10.9.5) / x86_64 | OK | OK | WARNINGS | OK | |
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### Running command:
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### /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings globaltest_5.27.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.4-bioc/meat/globaltest.Rcheck’
* using R version 3.3.1 (2016-06-21)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* 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 for sufficient/correct file permissions ... 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
* 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... 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
‘/home/biocbuild/bbs-3.4-bioc/meat/globaltest.Rcheck/00check.log’
for details.