Package: CMA

Version: 1.41.0

Command: C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:CMA.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings CMA_1.41.0.tar.gz

StartedAt: 2019-04-09 01:51:02 -0400 (Tue, 09 Apr 2019)

EndedAt: 2019-04-09 01:52:35 -0400 (Tue, 09 Apr 2019)

EllapsedTime: 93.0 seconds

RetCode: 1

Status:  ERROR

CheckDir: CMA.Rcheck

Warnings: NA

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:CMA.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings CMA_1.41.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.9-bioc/meat/CMA.Rcheck'
* using R Under development (unstable) (2019-03-09 r76216)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* 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 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
* 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' 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 ...
** running examples for arch 'i386' ... 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
** running examples for arch 'x64' ... 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: 2 ERRORs, 2 NOTEs
See
  'C:/Users/biocbuild/bbs-3.9-bioc/meat/CMA.Rcheck/00check.log'
for details.

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.9/bioc/src/contrib/CMA_1.41.0.tar.gz && rm -rf CMA.buildbin-libdir && mkdir CMA.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=CMA.buildbin-libdir CMA_1.41.0.tar.gz && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL CMA_1.41.0.zip && rm CMA_1.41.0.tar.gz CMA_1.41.0.zip
###
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100  816k  100  816k    0     0  5544k      0 --:--:-- --:--:-- --:--:-- 5833k

install for i386

* installing *source* package 'CMA' ...
** R
** data
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'CMA'
    finding HTML links ... done
    CMA-package                             html  
    ElasticNetCMA-methods                   html  
    ElasticNetCMA                           html  
    GeneSelection-methods                   html  
    GeneSelection                           html  
    GenerateLearningsets                    html  
    LassoCMA-methods                        html  
    LassoCMA                                html  
    Planarplot-methods                      html  
    Planarplot                              html  
    best                                    html  
    boxplot                                 html  
    classification-methods                  html  
    classification                          html  
    cloutput-class                          html  
    clvarseloutput-class                    html  
    compBoostCMA-methods                    html  
    compBoostCMA                            html  
    compare-methods                         html  
    compare                                 html  
    dldaCMA-methods                         html  
    dldaCMA                                 html  
    evaloutput-class                        html  
    evaluation-methods                      html  
    evaluation                              html  
    fdaCMA-methods                          html  
    fdaCMA                                  html  
    filter                                  html  
    flexdaCMA-methods                       html  
    flexdaCMA                               html  
    ftable                                  html  
    gbmCMA-methods                          html  
    gbmCMA                                  html  
    genesel-class                           html  
    golub                                   html  
    internals                               html  
    join-methods                            html  
    join                                    html  
    khan                                    html  
    knnCMA-methods                          html  
    knnCMA                                  html  
    ldaCMA-methods                          html  
    ldaCMA                                  html  
    learningsets-class                      html  
    nnetCMA-methods                         html  
    nnetCMA                                 html  
    obsinfo                                 html  
    pknnCMA-methods                         html  
    pknnCMA                                 html  
    plot,cloutput-method                    html  
    plot,genesel-method                     html  
    plot,tuningresult-method                html  
    plrCMA-methods                          html  
    plrCMA                                  html  
    pls_ldaCMA-methods                      html  
    pls_ldaCMA                              html  
    pls_lrCMA-methods                       html  
    pls_lrCMA                               html  
    pls_rfCMA-methods                       html  
    pls_rfCMA                               html  
    pnnCMA-methods                          html  
    pnnCMA                                  html  
    prediction-methods                      html  
    prediction                              html  
    predoutput-class                        html  
    qdaCMA-methods                          html  
    qdaCMA                                  html  
    rfCMA-methods                           html  
    rfCMA                                   html  
    roc                                     html  
    scdaCMA-methods                         html  
    scdaCMA                                 html  
    shrinkldaCMA-methods                    html  
    shrinkldaCMA                            html  
    summary                                 html  
    svmCMA-methods                          html  
    svmCMA                                  html  
    toplist                                 html  
    tune-methods                            html  
    tune                                    html  
    tuningresult-class                      html  
    varseloutput-class                      html  
    weighted_mcr-methods                    html  
    weighted_mcr                            html  
    wmc-methods                             html  
    wmc                                     html  
    wmcr_result-class                       html  
** 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

install for x64

* installing *source* package 'CMA' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'CMA' as CMA_1.41.0.zip
* DONE (CMA)
* installing to library 'C:/Users/biocbuild/bbs-3.9-bioc/R/library'
package 'CMA' successfully unpacked and MD5 sums checked