Package: MCRestimate

Version: 2.39.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:MCRestimate.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings MCRestimate_2.39.0.tar.gz

StartedAt: 2019-04-09 02:00:09 -0400 (Tue, 09 Apr 2019)

EndedAt: 2019-04-09 02:01:37 -0400 (Tue, 09 Apr 2019)

EllapsedTime: 88.0 seconds

RetCode: 0

Status:  OK

CheckDir: MCRestimate.Rcheck

Warnings: 0

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:MCRestimate.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings MCRestimate_2.39.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/MCRestimate.Rcheck’
* using R Under development (unstable) (2018-11-27 r75683)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘MCRestimate/DESCRIPTION’ ... OK
* this is package ‘MCRestimate’ version ‘2.39.0’
* 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 ‘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
* 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 ... NOTE
Found the following apparent S3 methods exported but not registered:
  ClassifierBuild.default MCRestimate.default plot.MCRestimate
  predict.PLR
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
* 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                 user system elapsed
ClassifierBuild 9.411  0.107    9.61
* 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: 5 NOTEs
See
  ‘/Users/biocbuild/bbs-3.9-bioc/meat/MCRestimate.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 MCRestimate
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library’
* installing *source* package ‘MCRestimate’ ...
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (MCRestimate)

name	user	system	elapsed
ClassifierBuild	9.411	0.107	9.610
MCRconfusion	1.386	0.042	1.449
MCRestimate	2.113	0.073	2.211
PLR	1.123	0.089	1.223
SVM.OVA.wrap	0	0	0
class.factor.format	0.094	0.005	0.100
geneReduction	0.004	0.000	0.004
important.variable.names	3.012	0.315	3.375
indVotes	1.326	0.018	1.355
intersectList	0.001	0.001	0.001
plot.MCRestimate	0.023	0.001	0.025
wrapper.fkt	3.062	0.300	3.395