CMA 1.29.0
Christoph Bernau
| Snapshot Date: 2015-10-26 20:20:04 -0400 (Mon, 26 Oct 2015) | | URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/CMA | | Last Changed Rev: 109592 / Revision: 109948 | | Last Changed Date: 2015-10-13 15:59:53 -0400 (Tue, 13 Oct 2015) |
| linux2.bioconductor.org | Linux (Ubuntu 14.04.2 LTS) / x86_64 | NotNeeded | OK | [ OK ] | |  |
| windows2.bioconductor.org | Windows Server 2012 R2 Enterprise SP1 (64-bit) / x64 | NotNeeded | OK | OK | OK | |
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### Running command:
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### /home/biocbuild/bbs-3.3-bioc/R/bin/R CMD check --no-vignettes --timings CMA_1.29.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.3-bioc/meat/CMA.Rcheck’
* using R Under development (unstable) (2015-09-09 r69333)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘CMA/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘CMA’ version ‘1.29.0’
* 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 ... [3s/3s] 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 loading without being on the library search path ... OK
* checking dependencies in R code ... NOTE
'library' or 'require' calls in package code:
‘MASS’ ‘class’ ‘corpcor’ ‘e1071’ ‘gbm’ ‘glmnet’ ‘limma’ ‘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
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’
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’
rfe: no visible binding for global variable ‘cost’
rfe: no visible binding for global variable ‘svm’
boxplot,evaloutput: no visible binding for global variable ‘main’
compare,list: no visible binding for global variable ‘main’
flexdaCMA,matrix-numeric-missing: no visible global function definition
for ‘gam’
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’
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,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’
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:
MaxNWts bag.fraction cex.lab class.ind classifyTestsF contrasts.fit
cost cov.shrink eBayes gam gbm.fit knn lda lmFit lwd main
make.positive.definite n.minobsinnode n.trees pls.regression pmvnorm
predicition qda randomForest rmvnorm size svm transformy verbose xlab
ylab ylim
* 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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [13s/13s] 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: 2 NOTEs
See
‘/home/biocbuild/bbs-3.3-bioc/meat/CMA.Rcheck/00check.log’
for details.