Package: MCRestimate

Version: 2.40.0

Command: /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:MCRestimate.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings MCRestimate_2.40.0.tar.gz

StartedAt: 2019-10-16 02:55:58 -0400 (Wed, 16 Oct 2019)

EndedAt: 2019-10-16 02:57:13 -0400 (Wed, 16 Oct 2019)

EllapsedTime: 75.2 seconds

RetCode: 0

Status:  OK

CheckDir: MCRestimate.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:MCRestimate.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings MCRestimate_2.40.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.9-bioc/meat/MCRestimate.Rcheck’
* using R version 3.6.1 (2019-07-05)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘MCRestimate/DESCRIPTION’ ... OK
* this is package ‘MCRestimate’ version ‘2.40.0’
* 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 : : warning in median(x, na =
  TRUE): partial argument match of 'na' to 'na.rm'
important.variable.names : : 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 ... OK
* 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
  ‘/home/biocbuild/bbs-3.9-bioc/meat/MCRestimate.Rcheck/00check.log’
for details.

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### Running command:
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###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD INSTALL MCRestimate
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* installing to library ‘/home/biocbuild/bbs-3.9-bioc/R/library’
* installing *source* package ‘MCRestimate’ ...
** using staged installation
** 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 from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (MCRestimate)

name	user	system	elapsed
ClassifierBuild	4.049	0.023	4.074
MCRconfusion	1.347	0.000	1.346
MCRestimate	2.300	0.023	2.338
PLR	1.041	0.024	1.082
SVM.OVA.wrap	0	0	0
class.factor.format	0.104	0.000	0.104
geneReduction	0.004	0.000	0.004
important.variable.names	2.996	0.028	3.024
indVotes	1.435	0.008	1.443
intersectList	0.001	0.000	0.001
plot.MCRestimate	0.021	0.000	0.021
wrapper.fkt	2.480	0.028	2.508