Package: maPredictDSC

Version: 1.16.0

Command: rm -rf maPredictDSC.buildbin-libdir maPredictDSC.Rcheck && mkdir maPredictDSC.buildbin-libdir maPredictDSC.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=maPredictDSC.buildbin-libdir maPredictDSC_1.16.0.tar.gz >maPredictDSC.Rcheck\00install.out 2>&1 && cp maPredictDSC.Rcheck\00install.out maPredictDSC-install.out && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=maPredictDSC.buildbin-libdir --install="check:maPredictDSC-install.out" --force-multiarch --no-vignettes --timings maPredictDSC_1.16.0.tar.gz

StartedAt: 2018-04-12 01:07:31 -0400 (Thu, 12 Apr 2018)

EndedAt: 2018-04-12 01:19:15 -0400 (Thu, 12 Apr 2018)

EllapsedTime: 704.1 seconds

RetCode: 0

Status:  OK

CheckDir: maPredictDSC.Rcheck

Warnings: 0

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf maPredictDSC.buildbin-libdir maPredictDSC.Rcheck && mkdir maPredictDSC.buildbin-libdir maPredictDSC.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=maPredictDSC.buildbin-libdir maPredictDSC_1.16.0.tar.gz >maPredictDSC.Rcheck\00install.out 2>&1 && cp maPredictDSC.Rcheck\00install.out maPredictDSC-install.out  &&  C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=maPredictDSC.buildbin-libdir --install="check:maPredictDSC-install.out" --force-multiarch --no-vignettes --timings maPredictDSC_1.16.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.6-bioc/meat/maPredictDSC.Rcheck'
* using R version 3.4.4 (2018-03-15)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'maPredictDSC/DESCRIPTION' ... OK
* this is package 'maPredictDSC' version '1.16.0'
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Depends: includes the non-default packages:
  'MASS' 'affy' 'limma' 'gcrma' 'ROC' 'class' 'e1071' 'caret'
  'hgu133plus2.db' 'ROCR' 'AnnotationDbi' 'LungCancerACvsSCCGEO'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
* 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 'maPredictDSC' 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
** checking loading without being on the library search path ... 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 loading without being on the library search path ... OK
* checking dependencies in R code ... NOTE
'library' or 'require' calls to packages already attached by Depends:
  'ROC' 'ROCR' 'affy' 'caret' 'class' 'e1071' 'gcrma' 'limma'
  Please remove these calls from your code.
'library' or 'require' call to 'parallel' in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Packages in Depends field not imported from:
  'LungCancerACvsSCCGEO' 'ROC' 'ROCR' 'affy' 'caret' 'class' 'e1071'
  'gcrma' 'hgu133plus2.db' 'limma'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
maPredictDSC: no visible global function definition for
  'installed.packages'
maPredictDSC: no visible global function definition for 'ReadAffy'
maPredictDSC: no visible global function definition for 'rma'
maPredictDSC: no visible global function definition for 'mas5'
maPredictDSC: no visible global function definition for 'gcrma'
maPredictDSC: no visible global function definition for 'exprs'
maPredictDSC: no visible global function definition for 'mas5calls'
maPredictDSC: no visible global function definition for 'createFolds'
maPredictDSC : mff: no visible global function definition for
  'model.matrix'
maPredictDSC : mff: no visible global function definition for 'formula'
maPredictDSC : mff: no visible global function definition for 'lmFit'
maPredictDSC : mff: no visible global function definition for
  'makeContrasts'
maPredictDSC : mff: no visible global function definition for
  'contrasts.fit'
maPredictDSC : mff: no visible global function definition for 'eBayes'
maPredictDSC : mff: no visible global function definition for
  'topTable'
maPredictDSC : mff: no visible global function definition for 'pt'
maPredictDSC : mff : wf: no visible global function definition for
  'wilcox.test'
maPredictDSC : mff: no visible global function definition for 'predict'
maPredictDSC : mff: no visible global function definition for 'knn'
maPredictDSC : mff: no visible global function definition for 'svm'
maPredictDSC : mff: no visible global function definition for
  'rocdemo.sca'
maPredictDSC : mff: no visible binding for global variable 'dxrule.sca'
maPredictDSC : mff: no visible global function definition for 'AUC'
maPredictDSC: no visible global function definition for 'mclapply'
maPredictDSC: no visible global function definition for 'sd'
maPredictDSC: no visible global function definition for 'model.matrix'
maPredictDSC: no visible global function definition for 'formula'
maPredictDSC: no visible global function definition for 'lmFit'
maPredictDSC: no visible global function definition for 'makeContrasts'
maPredictDSC: no visible global function definition for 'contrasts.fit'
maPredictDSC: no visible global function definition for 'eBayes'
maPredictDSC: no visible global function definition for 'topTable'
maPredictDSC: no visible global function definition for 'pt'
maPredictDSC : wf: no visible global function definition for
  'wilcox.test'
maPredictDSC: no visible global function definition for 'predict'
maPredictDSC: no visible global function definition for 'knn'
maPredictDSC: no visible global function definition for 'svm'
perfDSC: no visible global function definition for 'prediction'
perfDSC: no visible global function definition for 'performance'
perfDSC: no visible global function definition for 'na.omit'
perfDSC: no visible global function definition for 'trapezint'
perfDSC: no visible global function definition for 'rocdemo.sca'
perfDSC: no visible binding for global variable 'dxrule.sca'
perfDSC: no visible global function definition for 'AUC'
Undefined global functions or variables:
  AUC ReadAffy contrasts.fit createFolds dxrule.sca eBayes exprs
  formula gcrma installed.packages knn lmFit makeContrasts mas5
  mas5calls mclapply model.matrix na.omit performance predict
  prediction pt rma rocdemo.sca sd svm topTable trapezint wilcox.test
Consider adding
  importFrom("stats", "formula", "model.matrix", "na.omit", "predict",
             "pt", "sd", "wilcox.test")
  importFrom("utils", "installed.packages")
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 installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
           user system elapsed
predictDSC  215   4.11     231
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
             user system elapsed
predictDSC 234.62   2.88  238.36
* 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: 3 NOTEs
See
  'C:/Users/biocbuild/bbs-3.6-bioc/meat/maPredictDSC.Rcheck/00check.log'
for details.

install for i386

* installing *source* package 'maPredictDSC' ...
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
  converting help for package 'maPredictDSC'
    finding HTML links ... done
    aggregateDSC                            html  
    maPredictDSC-internal                   html  
    perfDSC                                 html  
    predictDSC                              html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL

install for x64

* installing *source* package 'maPredictDSC' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'maPredictDSC' as maPredictDSC_1.16.0.zip
* DONE (maPredictDSC)
In R CMD INSTALL
In R CMD INSTALL