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BioC 3.5: CHECK report for MCRestimate on tokay2

This page was generated on 2017-08-16 13:20:08 -0400 (Wed, 16 Aug 2017).

Package 770/1382HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
MCRestimate 2.32.0
Marc Johannes
Snapshot Date: 2017-08-15 17:17:57 -0400 (Tue, 15 Aug 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_5/madman/Rpacks/MCRestimate
Last Changed Rev: 129126 / Revision: 131943
Last Changed Date: 2017-04-24 15:25:24 -0400 (Mon, 24 Apr 2017)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  NotNeeded  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  NotNeeded  OK [ OK ] OK UNNEEDED, same version exists in internal repository
veracruz2 OS X 10.11.6 El Capitan / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: MCRestimate
Version: 2.32.0
Command: rm -rf MCRestimate.buildbin-libdir MCRestimate.Rcheck && mkdir MCRestimate.buildbin-libdir MCRestimate.Rcheck && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=MCRestimate.buildbin-libdir MCRestimate_2.32.0.tar.gz >MCRestimate.Rcheck\00install.out 2>&1 && cp MCRestimate.Rcheck\00install.out MCRestimate-install.out && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD check --library=MCRestimate.buildbin-libdir --install="check:MCRestimate-install.out" --force-multiarch --no-vignettes --timings MCRestimate_2.32.0.tar.gz
StartedAt: 2017-08-16 01:00:40 -0400 (Wed, 16 Aug 2017)
EndedAt: 2017-08-16 01:03:00 -0400 (Wed, 16 Aug 2017)
EllapsedTime: 140.1 seconds
RetCode: 0
Status:  OK  
CheckDir: MCRestimate.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf MCRestimate.buildbin-libdir MCRestimate.Rcheck && mkdir MCRestimate.buildbin-libdir MCRestimate.Rcheck && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=MCRestimate.buildbin-libdir MCRestimate_2.32.0.tar.gz >MCRestimate.Rcheck\00install.out 2>&1 && cp MCRestimate.Rcheck\00install.out MCRestimate-install.out  &&  C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD check --library=MCRestimate.buildbin-libdir --install="check:MCRestimate-install.out" --force-multiarch --no-vignettes --timings MCRestimate_2.32.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.5-bioc/meat/MCRestimate.Rcheck'
* using R version 3.4.1 (2017-06-30)
* 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 '2.32.0'
* 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 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
** checking loading without being on the library search path ... 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 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 installed files from 'inst/doc' ... 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  5.3   0.04    5.33
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                user system elapsed
ClassifierBuild 5.13   0.08     5.2
* 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-3.5-bioc/meat/MCRestimate.Rcheck/00check.log'
for details.


MCRestimate.Rcheck/00install.out:


install for i386

* 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

install for x64

* installing *source* package 'MCRestimate' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'MCRestimate' as MCRestimate_2.32.0.zip
* DONE (MCRestimate)

MCRestimate.Rcheck/examples_i386/MCRestimate-Ex.timings:

nameusersystemelapsed
ClassifierBuild5.300.045.33
MCRconfusion1.920.001.92
MCRestimate3.080.053.14
PLR1.630.011.71
SVM.OVA.wrap000
class.factor.format0.080.020.10
geneReduction000
important.variable.names3.960.444.44
indVotes1.860.001.86
intersectList000
plot.MCRestimate0.140.000.14
wrapper.fkt4.690.204.89

MCRestimate.Rcheck/examples_x64/MCRestimate-Ex.timings:

nameusersystemelapsed
ClassifierBuild5.130.085.20
MCRconfusion1.590.021.61
MCRestimate2.470.032.50
PLR1.250.041.30
SVM.OVA.wrap000
class.factor.format0.050.020.06
geneReduction0.010.000.02
important.variable.names3.930.204.12
indVotes1.070.011.10
intersectList000
plot.MCRestimate0.080.000.08
wrapper.fkt4.210.164.36