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BioC 3.4: CHECK report for MCRestimate on zin1

This page was generated on 2016-09-21 03:36:41 -0700 (Wed, 21 Sep 2016).

Package 703/1257HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
MCRestimate 2.29.0
Marc Johannes
Snapshot Date: 2016-09-19 19:15:14 -0700 (Mon, 19 Sep 2016)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/MCRestimate
Last Changed Rev: 117081 / Revision: 121152
Last Changed Date: 2016-05-03 14:30:44 -0700 (Tue, 03 May 2016)
zin1 Linux (Ubuntu 16.04 LTS) / x86_64  NotNeeded  OK [ OK ]UNNEEDED, same version exists in internal repository
moscato1 Windows Server 2008 R2 Standard (64-bit) / x64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository
morelia Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: MCRestimate
Version: 2.29.0
Command: /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings MCRestimate_2.29.0.tar.gz
StartedAt: 2016-09-20 08:56:51 -0700 (Tue, 20 Sep 2016)
EndedAt: 2016-09-20 08:57:47 -0700 (Tue, 20 Sep 2016)
EllapsedTime: 56.9 seconds
RetCode: 0
Status:  OK 
CheckDir: MCRestimate.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings MCRestimate_2.29.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.4-bioc/meat/MCRestimate.Rcheck’
* using R version 3.3.1 (2016-06-21)
* 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 ‘2.29.0’
* 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 loading without being on the library search path ... 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 installed files from ‘inst/doc’ ... 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: 4 NOTEs
See
  ‘/home/biocbuild/bbs-3.4-bioc/meat/MCRestimate.Rcheck/00check.log’
for details.


MCRestimate.Rcheck/00install.out:

* installing *source* package ‘MCRestimate’ ...
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (MCRestimate)

MCRestimate.Rcheck/MCRestimate-Ex.timings:

nameusersystemelapsed
ClassifierBuild4.4920.0244.514
MCRconfusion1.2480.0041.251
MCRestimate1.8040.0161.826
PLR0.9520.0160.976
SVM.OVA.wrap0.0000.0040.000
class.factor.format0.0640.0040.068
geneReduction0.0000.0000.003
important.variable.names3.1520.0363.187
indVotes1.1440.0001.147
intersectList000
plot.MCRestimate0.0160.0000.015
wrapper.fkt3.1640.0123.175