Package: a4Classif

Version: 1.26.0

Command: rm -rf a4Classif.buildbin-libdir a4Classif.Rcheck && mkdir a4Classif.buildbin-libdir a4Classif.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=a4Classif.buildbin-libdir a4Classif_1.26.0.tar.gz >a4Classif.Rcheck\00install.out 2>&1 && cp a4Classif.Rcheck\00install.out a4Classif-install.out && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=a4Classif.buildbin-libdir --install="check:a4Classif-install.out" --force-multiarch --no-vignettes --timings a4Classif_1.26.0.tar.gz

StartedAt: 2018-04-11 22:04:49 -0400 (Wed, 11 Apr 2018)

EndedAt: 2018-04-11 22:09:19 -0400 (Wed, 11 Apr 2018)

EllapsedTime: 270.3 seconds

RetCode: 0

Status:  OK

CheckDir: a4Classif.Rcheck

Warnings: 0

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### Running command:
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###   rm -rf a4Classif.buildbin-libdir a4Classif.Rcheck && mkdir a4Classif.buildbin-libdir a4Classif.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=a4Classif.buildbin-libdir a4Classif_1.26.0.tar.gz >a4Classif.Rcheck\00install.out 2>&1 && cp a4Classif.Rcheck\00install.out a4Classif-install.out  &&  C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=a4Classif.buildbin-libdir --install="check:a4Classif-install.out" --force-multiarch --no-vignettes --timings a4Classif_1.26.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.6-bioc/meat/a4Classif.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 'a4Classif/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'a4Classif' version '1.26.0'
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Depends: includes the non-default packages:
  'a4Core' 'a4Preproc' 'MLInterfaces' 'ROCR' 'pamr' 'glmnet' 'varSelRF'
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 'a4Classif' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Description field: should contain one or more complete sentences.
Package listed in more than one of Depends, Imports, Suggests, Enhances:
  'a4Core'
A package should be listed in only one of these fields.
* 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
Packages in Depends field not imported from:
  'MLInterfaces' 'ROCR' 'a4Preproc' 'glmnet' 'methods' 'pamr'
  'varSelRF'
  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
.onAttach: no visible global function definition for
  'packageDescription'
ROCcurve: no visible global function definition for 'exprs'
ROCcurve: no visible global function definition for 'featureData'
ROCcurve: no visible global function definition for 'featureNames'
ROCcurve: no visible global function definition for 'pData'
ROCcurve: no visible global function definition for 'prediction'
ROCcurve: no visible global function definition for 'performance'
ROCcurve: no visible global function definition for 'plot'
confusionMatrix.pamClass: no visible global function definition for
  'pamr.confusion'
lassoClass: no visible global function definition for 'pData'
lassoClass: no visible global function definition for 'glmnet'
lassoClass: no visible global function definition for 'exprs'
lassoClass: no visible global function definition for 'featureData'
pamClass: no visible global function definition for 'pData'
pamClass: no visible global function definition for 'featureNames'
pamClass: no visible global function definition for 'exprs'
pamClass: no visible global function definition for 'capture.output'
pamClass: no visible global function definition for 'pamr.train'
pamClass: no visible global function definition for 'pamr.cv'
pamClass: no visible global function definition for 'featureData'
plot.pamClass: no visible binding for global variable 'var'
plot.pamClass: no visible global function definition for 'par'
plot.pamClass: no visible global function definition for 'plot'
plot.pamClass: no visible global function definition for 'lines'
plot.pamClass: no visible global function definition for 'segments'
plot.pamClass: no visible global function definition for 'axis'
plot.pamClass: no visible global function definition for 'points'
plot.rfClass: no visible global function definition for 'par'
plot.rfClass: no visible global function definition for 'plot'
plot.rfClass: no visible global function definition for 'lines'
plot.rfClass: no visible global function definition for 'segments'
plot.rfClass: no visible global function definition for 'axis'
plot.rfClass: no visible global function definition for 'points'
rfClass: no visible global function definition for 'pData'
rfClass: no visible global function definition for 'varSelRF'
rfClass: no visible global function definition for 'exprs'
rfClass: no visible global function definition for 'featureData'
rfClass: no visible global function definition for 'featureNames'
topTable,pamClass: no visible global function definition for
  'capture.output'
topTable,pamClass: no visible global function definition for
  'pamr.listgenes'
Undefined global functions or variables:
  axis capture.output exprs featureData featureNames glmnet lines pData
  packageDescription pamr.confusion pamr.cv pamr.listgenes pamr.train
  par performance plot points prediction segments var varSelRF
Consider adding
  importFrom("graphics", "axis", "lines", "par", "plot", "points",
             "segments")
  importFrom("stats", "var")
  importFrom("utils", "capture.output", "packageDescription")
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 examples ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
           user system elapsed
lassoClass 3.29   0.05    5.17
** running examples for arch 'x64' ... OK
* checking PDF version of manual ... OK
* DONE

Status: 4 NOTEs
See
  'C:/Users/biocbuild/bbs-3.6-bioc/meat/a4Classif.Rcheck/00check.log'
for details.

install for i386

* installing *source* package 'a4Classif' ...
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
  converting help for package 'a4Classif'
    finding HTML links ... done
    ROCcurve                                html  
    lassoClass                              html  
    pamClass                                html  
    rfClass                                 html  
** building package indices
** testing if installed package can be loaded
In R CMD INSTALL

install for x64

* installing *source* package 'a4Classif' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'a4Classif' as a4Classif_1.26.0.zip
* DONE (a4Classif)
In R CMD INSTALL
In R CMD INSTALL