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### Running command:
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### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:CMA.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings CMA_1.62.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.19-bioc-mac-arm64/meat/CMA.Rcheck’
* using R version 4.4.0 (2024-04-24)
* using platform: aarch64-apple-darwin20
* R was compiled by
Apple clang version 14.0.0 (clang-1400.0.29.202)
GNU Fortran (GCC) 12.2.0
* running under: macOS Ventura 13.6.5
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘CMA/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘CMA’ version ‘1.62.0’
* 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 ‘CMA’ 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 code 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' calls in package code:
‘class’ ‘corpcor’ ‘e1071’ ‘gbm’ ‘glmnet’ ‘limma’ ‘MASS’ ‘mgcv’
‘mvtnorm’ ‘nnet’ ‘plsgenomics’ ‘randomForest’ ‘st’
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
characterplot: no visible global function definition for ‘points’
limmatest: no visible global function definition for ‘lmFit’
limmatest: no visible global function definition for ‘contrasts.fit’
limmatest: no visible global function definition for ‘eBayes’
limmatest: no visible global function definition for ‘classifyTestsF’
plotprob: no visible global function definition for ‘axis’
plotprob: no visible global function definition for ‘points’
plotprob: no visible global function definition for ‘abline’
plotprob: no visible global function definition for ‘text’
rfe: no visible binding for global variable ‘cost’
rfe: no visible binding for global variable ‘svm’
ROCinternal: no visible binding for global variable ‘xlab’
ROCinternal: no visible binding for global variable ‘ylab’
ROCinternal: no visible binding for global variable ‘main’
ROCinternal: no visible binding for global variable ‘lwd’
ROCinternal: no visible global function definition for ‘box’
ROCinternal: no visible global function definition for ‘text’
boxplot,evaloutput: no visible binding for global variable ‘main’
compare,list: no visible global function definition for ‘par’
compare,list: no visible global function definition for
‘dev.interactive’
compare,list: no visible binding for global variable ‘main’
fdaCMA,matrix-numeric-missing: no visible global function definition
for ‘points’
flexdaCMA,matrix-numeric-missing: no visible global function definition
for ‘gam’
flexdaCMA,matrix-numeric-missing: no visible global function definition
for ‘points’
gbmCMA,matrix-numeric-missing: no visible binding for global variable
‘n.minobsinnode’
gbmCMA,matrix-numeric-missing: no visible binding for global variable
‘bag.fraction’
gbmCMA,matrix-numeric-missing: no visible binding for global variable
‘n.trees’
gbmCMA,matrix-numeric-missing: no visible binding for global variable
‘verbose’
gbmCMA,matrix-numeric-missing: no visible binding for global variable
‘gbm.fit’
knnCMA,matrix-numeric-missing: no visible global function definition
for ‘knn’
ldaCMA,matrix-numeric-missing: no visible global function definition
for ‘lda’
nnetCMA,matrix-numeric-missing: no visible binding for global variable
‘size’
nnetCMA,matrix-numeric-missing: no visible binding for global variable
‘MaxNWts’
nnetCMA,matrix-numeric-missing: no visible global function definition
for ‘class.ind’
Planarplot,matrix-numeric-missing: no visible global function
definition for ‘points’
plot,genesel-missing: no visible binding for global variable ‘xlab’
plot,genesel-missing: no visible binding for global variable ‘ylab’
plot,genesel-missing: no visible binding for global variable ‘main’
plot,genesel-missing: no visible binding for global variable ‘cex.lab’
plot,genesel-missing: no visible binding for global variable ‘ylim’
plot,genesel-missing: no visible binding for global variable ‘barplot’
plot,genesel-missing: no visible global function definition for ‘par’
plot,genesel-missing: no visible global function definition for
‘dev.interactive’
plot,tuningresult-missing: no visible binding for global variable
‘main’
plot,tuningresult-missing: no visible binding for global variable
‘xlab’
plot,tuningresult-missing: no visible binding for global variable
‘ylab’
plot,tuningresult-missing: no visible binding for global variable
‘ylim’
plot,tuningresult-missing: no visible binding for global variable
‘lines’
plot,tuningresult-missing: no visible global function definition for
‘abline’
plot,tuningresult-missing: no visible binding for global variable
‘contour’
plot,tuningresult-missing: no visible global function definition for
‘points’
pls_ldaCMA,matrix-numeric-missing: no visible global function
definition for ‘pls.regression’
pls_ldaCMA,matrix-numeric-missing: no visible global function
definition for ‘transformy’
pls_ldaCMA,matrix-numeric-missing: no visible global function
definition for ‘lda’
pls_lrCMA,matrix-numeric-missing: no visible global function definition
for ‘pls.regression’
pls_lrCMA,matrix-numeric-missing: no visible global function definition
for ‘transformy’
pls_rfCMA,matrix-numeric-missing: no visible global function definition
for ‘pls.regression’
pls_rfCMA,matrix-numeric-missing: no visible global function definition
for ‘transformy’
pls_rfCMA,matrix-numeric-missing: no visible global function definition
for ‘randomForest’
prediction,data.frame-missing-data.frame-formula: no visible global
function definition for ‘predicition’
qdaCMA,matrix-numeric-missing: no visible global function definition
for ‘qda’
rfCMA,matrix-numeric-missing: no visible global function definition for
‘randomForest’
shrinkldaCMA,matrix-numeric-missing: no visible global function
definition for ‘cov.shrink’
svmCMA,matrix-numeric-missing: no visible binding for global variable
‘cost’
weighted.mcr,character-character-numeric-character-matrix-numeric: no
visible global function definition for ‘make.positive.definite’
weighted.mcr,character-character-numeric-character-matrix-numeric: no
visible global function definition for ‘pmvnorm’
weighted.mcr,character-character-numeric-character-matrix-numeric: no
visible global function definition for ‘rmvnorm’
wmc,matrix-numeric-numeric: no visible global function definition for
‘make.positive.definite’
wmc,matrix-numeric-numeric: no visible global function definition for
‘pmvnorm’
wmc,matrix-numeric-numeric: no visible global function definition for
‘rmvnorm’
Undefined global functions or variables:
abline axis bag.fraction barplot box cex.lab class.ind classifyTestsF
contour contrasts.fit cost cov.shrink dev.interactive eBayes gam
gbm.fit knn lda lines lmFit lwd main make.positive.definite MaxNWts
n.minobsinnode n.trees par pls.regression pmvnorm points predicition
qda randomForest rmvnorm size svm text transformy verbose xlab ylab
ylim
Consider adding
importFrom("graphics", "abline", "axis", "barplot", "box", "contour",
"lines", "par", "points", "text")
importFrom("grDevices", "dev.interactive")
to your NAMESPACE file.
* checking Rd files ... NOTE
checkRd: (-1) learningsets-class.Rd:28: Lost braces in \itemize; meant \describe ?
* 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: 3 NOTEs
See
‘/Users/biocbuild/bbs-3.19-bioc-mac-arm64/meat/CMA.Rcheck/00check.log’
for details.
