Package: MCRestimate

Version: 2.38.0

Command: C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:MCRestimate.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings MCRestimate_2.38.0.tar.gz

StartedAt: 2019-04-13 03:34:53 -0400 (Sat, 13 Apr 2019)

EndedAt: 2019-04-13 03:37:37 -0400 (Sat, 13 Apr 2019)

EllapsedTime: 164.5 seconds

RetCode: 0

Status:  OK

CheckDir: MCRestimate.Rcheck

Warnings: 0

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### Running command:
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###   C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:MCRestimate.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings MCRestimate_2.38.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.8-bioc/meat/MCRestimate.Rcheck'
* using R version 3.5.3 (2019-03-11)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'MCRestimate/DESCRIPTION' ... OK
* this is package 'MCRestimate' version '2.38.0'
* checking package namespace information ... OK
* checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
  cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES'
 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 'MCRestimate' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Description field: should contain one or more complete sentences.
* 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:
  'ROC' 'genefilter' 'gpls'
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Package in Depends field not imported from: 'golubEsets'
  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
MCRestimate.default : my.balanced.folds: warning in
  get("balanced.folds", en = asNamespace("pamr")): partial argument
  match of 'en' to 'envir'
important.variable.names : <anonymous>: warning in median(x, na =
  TRUE): partial argument match of 'na' to 'na.rm'
important.variable.names : <anonymous>: warning in var(x, na = TRUE):
  partial argument match of 'na' to 'na.rm'
plot.MCRestimate: warning in layout(c(1, 2), height = c(5, 1)): partial
  argument match of 'height' to 'heights'
GPLS.wrap: no visible global function definition for 'glpls1a'
varSel.AUC : AUC.rfc: no visible global function definition for 'AUC'
varSel.AUC : AUC.rfc: no visible global function definition for
  'rocdemo.sca'
varSel.AUC : AUC.rfc: no visible binding for global variable
  'dxrule.sca'
varSel.highest.t.stat: no visible global function definition for
  'rowttests'
varSel.highest.t.stat.eSRG: no visible global function definition for
  'rowttests'
Undefined global functions or variables:
  AUC dxrule.sca glpls1a rocdemo.sca rowttests
* checking Rd files ... NOTE
prepare_Rd: PLR.Rd:19: Dropping empty section \details
* 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 files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
                user system elapsed
ClassifierBuild 6.24   0.08    6.31
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                user system elapsed
ClassifierBuild 9.63   0.05    9.67
* 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: 4 NOTEs
See
  'C:/Users/biocbuild/bbs-3.8-bioc/meat/MCRestimate.Rcheck/00check.log'
for details.

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.8/bioc/src/contrib/MCRestimate_2.38.0.tar.gz && rm -rf MCRestimate.buildbin-libdir && mkdir MCRestimate.buildbin-libdir && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=MCRestimate.buildbin-libdir MCRestimate_2.38.0.tar.gz && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL MCRestimate_2.38.0.zip && rm MCRestimate_2.38.0.tar.gz MCRestimate_2.38.0.zip
###
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install for i386

* installing *source* package 'MCRestimate' ...
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'MCRestimate'
    finding HTML links ... done
    ClassifierBuild                         html  
    MCRconfusion                            html  
    MCRestimate                             html  
    MCRestimateMerge                        html  
    PLR                                     html  
    SVM.OVA.wrap                            html  
    class.factor.format                     html  
    geneReduction                           html  
    important.variable.names                html  
    indVotes                                html  
    intersectList                           html  
    plot.MCRestimate                        html  
    replace.NA                              html  
    select.NA.elements                      html  
    wrapper.fkt                             html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL

install for x64

* installing *source* package 'MCRestimate' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'MCRestimate' as MCRestimate_2.38.0.zip
* DONE (MCRestimate)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.8-bioc/R/library'
package 'MCRestimate' successfully unpacked and MD5 sums checked
In R CMD INSTALL