Package: MCRestimate

Version: 2.38.0

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_2.38.0.tar.gz

StartedAt: 2019-04-16 01:03:25 -0400 (Tue, 16 Apr 2019)

EndedAt: 2019-04-16 01:04:48 -0400 (Tue, 16 Apr 2019)

EllapsedTime: 83.1 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_2.38.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.8-bioc/meat/MCRestimate.Rcheck’
* using R version 3.5.3 (2019-03-11)
* 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 ‘2.38.0’
* 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 ... 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 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 10.345  0.115  10.653
* 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
  ‘/Users/biocbuild/bbs-3.8-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/3.5/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	10.345	0.115	10.653
MCRconfusion	1.391	0.043	1.443
MCRestimate	2.254	0.075	2.354
PLR	1.163	0.082	1.258
SVM.OVA.wrap	0.000	0.000	0.001
class.factor.format	0.103	0.006	0.109
geneReduction	0.003	0.001	0.004
important.variable.names	3.139	0.318	3.508
indVotes	1.374	0.017	1.435
intersectList	0.000	0.001	0.002
plot.MCRestimate	0.018	0.001	0.019
wrapper.fkt	3.027	0.305	3.362