CMA 1.41.0
Christoph Bernau
| Snapshot Date: 2019-04-08 17:01:18 -0400 (Mon, 08 Apr 2019) |
| URL: https://git.bioconductor.org/packages/CMA |
| Branch: master |
| Last Commit: daaa124 |
| Last Changed Date: 2018-10-30 11:54:28 -0400 (Tue, 30 Oct 2018) |
| malbec2 | Linux (Ubuntu 18.04.2 LTS) / x86_64 | OK | OK | [ ERROR ] | | |
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | ERROR | OK | |
| celaya2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | ERROR | OK | |
| merida2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | |
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### Running command:
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### /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:CMA.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings CMA_1.41.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.9-bioc/meat/CMA.Rcheck’
* using R Under development (unstable) (2019-03-18 r76245)
* 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 ‘1.41.0’
* 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 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' 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’
ROCinternal: no visible global function definition for ‘box’
ROCinternal: no visible global function definition for ‘text’
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’
Planarplot,matrix-numeric-missing: no visible global function
definition for ‘points’
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’
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:
MaxNWts 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 n.minobsinnode n.trees par pls.regression
pmvnorm points predicition qda randomForest rmvnorm size svm text
transformy verbose xlab ylab ylim
Consider adding
importFrom("grDevices", "dev.interactive")
importFrom("graphics", "abline", "axis", "barplot", "box", "contour",
"lines", "par", "points", "text")
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 ... 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 files in ‘vignettes’ ... OK
* checking examples ... ERROR
Running examples in ‘CMA-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: pls_lrCMA
> ### Title: Partial Least Squares followed by logistic regression
> ### Aliases: pls_lrCMA
> ### Keywords: multivariate
>
> ### ** Examples
>
> ### load Golub AML/ALL data
> data(golub)
> ### extract class labels
> golubY <- golub[,1]
> ### extract gene expression
> golubX <- as.matrix(golub[,-1])
> ### select learningset
> ratio <- 2/3
> set.seed(111)
> learnind <- sample(length(golubY), size=floor(ratio*length(golubY)))
> ### run PLS, combined with logistic regression
> result <- pls_lrCMA(X=golubX, y=golubY, learnind=learnind)
For any news related to the 'plsgenomics' package (update, corrected bugs), please check http://thoth.inrialpes.fr/people/gdurif/
C++ based sparse PLS routines will soon be available on the CRAN in the new 'fastPLS' package.
Error in penlogitfit(design, y = Ylearn, lambda = lambda) :
Convergence failure in penalized logistic regression
Calls: pls_lrCMA ... pls_lrCMA -> .local -> pls_lrCMA -> pls_lrCMA -> penlogitfit
Execution halted
* 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 ERROR, 2 NOTEs
See
‘/home/biocbuild/bbs-3.9-bioc/meat/CMA.Rcheck/00check.log’
for details.