Package: CMA

Version: 1.41.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:CMA.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings CMA_1.41.0.tar.gz

StartedAt: 2019-04-09 00:47:22 -0400 (Tue, 09 Apr 2019)

EndedAt: 2019-04-09 00:48:57 -0400 (Tue, 09 Apr 2019)

EllapsedTime: 94.9 seconds

RetCode: 1

Status:  ERROR

CheckDir: CMA.Rcheck

Warnings: NA

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:CMA.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings CMA_1.41.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/CMA.Rcheck’
* using R Under development (unstable) (2019-03-18 r76245)
* using platform: x86_64-apple-darwin15.6.0 (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 sizes of PDF files under ‘inst/doc’ ... 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
  ‘/Users/biocbuild/bbs-3.9-bioc/meat/CMA.Rcheck/00check.log’
for details.

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL CMA
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library’
* installing *source* package ‘CMA’ ...
** using staged installation
** R
** data
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (CMA)

name	user	system	elapsed
ElasticNetCMA	1.898	0.202	2.102
GeneSelection	0.235	0.032	0.268
GenerateLearningsets	0.014	0.001	0.016
LassoCMA	0.543	0.075	0.618
Planarplot	0.203	0.028	0.231
classification	0.001	0.001	0.002
compBoostCMA	1.336	0.193	1.530
compare	0.001	0.001	0.001
dldaCMA	0.219	0.034	0.253
evaluation	0.183	0.015	0.197
fdaCMA	0.143	0.023	0.167
flexdaCMA	0.281	0.032	0.315
gbmCMA	3.390	0.097	3.508
golub	0.045	0.009	0.054
khan	0.062	0.009	0.070
knnCMA	0.228	0.028	0.256
ldaCMA	0.001	0.001	0.001
nnetCMA	0.102	0.016	0.119
pknnCMA	0.145	0.014	0.159
plrCMA	0.473	0.072	0.545
pls_ldaCMA	0.000	0.001	0.001