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### Running command:
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### C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:lmdme.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings lmdme_1.36.0.tar.gz
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* using log directory 'C:/Users/biocbuild/bbs-3.14-bioc/meat/lmdme.Rcheck'
* using R version 4.1.3 (2022-03-10)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'lmdme/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'lmdme' version '1.36.0'
* 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 'lmdme' 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 'parallel' 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
biplot,lmdme : <anonymous>: no visible global function definition for
'X11'
biplot,lmdme : <anonymous>: no visible global function definition for
'par'
biplot,lmdme : <anonymous>: no visible global function definition for
'abline'
decomposition,lmdme : <anonymous>: no visible global function
definition for 'prcomp'
decomposition,lmdme : <anonymous>: no visible global function
definition for 'model.matrix'
decomposition,lmdme : <anonymous>: no visible global function
definition for 'plsr'
fitted.values,lmdme : <anonymous>: no visible global function
definition for 'model.matrix'
fitted.values,lmdme : <anonymous>: no visible global function
definition for 'as.formula'
leverage,lmdme: no visible global function definition for 'prcomp'
leverage,lmdme: no visible global function definition for 'quantile'
lmdme,formula-ANY-data.frame : printnow: no visible global function
definition for 'flush.console'
lmdme,formula-ANY-data.frame: no visible global function definition for
'terms'
lmdme,formula-ANY-data.frame: no visible binding for global variable
'as.formula'
lmdme,formula-ANY-data.frame : <anonymous>: no visible global function
definition for 'model.matrix'
lmdme,formula-ANY-data.frame : <anonymous>: no visible global function
definition for 'as.formula'
lmdme,formula-ANY-data.frame : <anonymous>: no visible global function
definition for 'pt'
lmdme,formula-ANY-data.frame : <anonymous>: no visible global function
definition for 'pchisq'
lmdme,formula-ANY-data.frame : <anonymous>: no visible global function
definition for 'pf'
lmdme,formula-ANY-data.frame : <anonymous>: no visible global function
definition for 'terms'
loadingplot,lmdme: no visible global function definition for 'loadings'
loadingplot,lmdme: no visible global function definition for 'matplot'
loadingplot,lmdme: no visible global function definition for 'box'
loadingplot,lmdme: no visible global function definition for 'axis'
loadingplot,lmdme: no visible global function definition for 'legend'
p.adjust,lmdme: no visible binding for global variable
'p.adjust.methods'
permutation,formula-data.frame-data.frame : printnow: no visible global
function definition for 'flush.console'
permutation,formula-data.frame-data.frame: no visible binding for
global variable 'mclapply'
permutation,formula-data.frame-data.frame: no visible global function
definition for 'detectCores'
print,lmdme: no visible global function definition for 'head'
print,lmdme: no visible global function definition for 'pvalues'
print,lmdme: no visible binding for global variable 'head'
screeplot,lmdme : <anonymous>: no visible global function definition
for 'X11'
screeplot,lmdme : <anonymous>: no visible global function definition
for 'par'
screeplot,lmdme : <anonymous>: no visible global function definition
for 'lines'
screeplot,lmdme: no visible global function definition for 'legend'
show,lmdme: no visible global function definition for 'head'
Undefined global functions or variables:
X11 abline as.formula axis box detectCores flush.console head legend
lines loadings matplot mclapply model.matrix p.adjust.methods par
pchisq pf plsr prcomp pt pvalues quantile terms
Consider adding
importFrom("grDevices", "X11")
importFrom("graphics", "abline", "axis", "box", "legend", "lines",
"matplot", "par")
importFrom("stats", "as.formula", "loadings", "model.matrix",
"p.adjust.methods", "pchisq", "pf", "prcomp", "pt",
"quantile", "terms")
importFrom("utils", "flush.console", "head")
to your NAMESPACE file.
* 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 ... WARNING
Documented arguments not in \usage in documentation object 'p.adjust':
'...'
Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
lmdme-permutation 7.04 0.7 7.75
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
lmdme-permutation 5.63 0.61 6.24
* 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
'C:/Users/biocbuild/bbs-3.14-bioc/meat/lmdme.Rcheck/00check.log'
for details.
