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BioC 3.5: CHECK report for MLInterfaces on tokay2

This page was generated on 2017-08-16 13:18:47 -0400 (Wed, 16 Aug 2017).

Package 835/1382HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
MLInterfaces 1.56.0
V. Carey
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/MLInterfaces
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  OK  OK  WARNINGS UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK [ WARNINGS ] OK UNNEEDED, same version exists in internal repository
veracruz2 OS X 10.11.6 El Capitan / x86_64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository

Summary

Package: MLInterfaces
Version: 1.56.0
Command: rm -rf MLInterfaces.buildbin-libdir MLInterfaces.Rcheck && mkdir MLInterfaces.buildbin-libdir MLInterfaces.Rcheck && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=MLInterfaces.buildbin-libdir MLInterfaces_1.56.0.tar.gz >MLInterfaces.Rcheck\00install.out 2>&1 && cp MLInterfaces.Rcheck\00install.out MLInterfaces-install.out && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD check --library=MLInterfaces.buildbin-libdir --install="check:MLInterfaces-install.out" --force-multiarch --no-vignettes --timings MLInterfaces_1.56.0.tar.gz
StartedAt: 2017-08-16 01:20:58 -0400 (Wed, 16 Aug 2017)
EndedAt: 2017-08-16 01:25:54 -0400 (Wed, 16 Aug 2017)
EllapsedTime: 296.1 seconds
RetCode: 0
Status:  WARNINGS  
CheckDir: MLInterfaces.Rcheck
Warnings: 1

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf MLInterfaces.buildbin-libdir MLInterfaces.Rcheck && mkdir MLInterfaces.buildbin-libdir MLInterfaces.Rcheck && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=MLInterfaces.buildbin-libdir MLInterfaces_1.56.0.tar.gz >MLInterfaces.Rcheck\00install.out 2>&1 && cp MLInterfaces.Rcheck\00install.out MLInterfaces-install.out  &&  C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD check --library=MLInterfaces.buildbin-libdir --install="check:MLInterfaces-install.out" --force-multiarch --no-vignettes --timings MLInterfaces_1.56.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.5-bioc/meat/MLInterfaces.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 'MLInterfaces/DESCRIPTION' ... OK
* this is package 'MLInterfaces' version '1.56.0'
* 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 'MLInterfaces' can be installed ... WARNING
Found the following significant warnings:
  Warning: replacing previous import 'BiocGenerics::var' by 'stats::var' when loading 'MLInterfaces'
See 'C:/Users/biocbuild/bbs-3.5-bioc/meat/MLInterfaces.Rcheck/00install.out' for details.
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... OK
* 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
* 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 dependencies in R code ... NOTE
Unexported objects imported by ':::' calls:
  'MASS:::predict.lda' 'ada:::predict.ada' 'e1071:::predict.svm'
  'rpart:::predict.rpart' 'stats:::plot.hclust'
  See the note in ?`:::` about the use of this operator.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
hclustWidget : <anonymous>: no visible global function definition for
  ':='
hclustWidget : <anonymous>: no visible binding for global variable
  'key'
Undefined global functions or variables:
  := key
* checking Rd files ... NOTE
prepare_Rd: plspinHcube.Rd:17-19: 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
MLearn-new 14.81   0.38   17.48
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
            user system elapsed
MLearn-new 17.92   0.25   18.64
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'runTests.R'
 OK
** running tests for arch 'x64' ...
  Running 'runTests.R'
 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: 1 WARNING, 3 NOTEs
See
  'C:/Users/biocbuild/bbs-3.5-bioc/meat/MLInterfaces.Rcheck/00check.log'
for details.


MLInterfaces.Rcheck/00install.out:


install for i386

* installing *source* package 'MLInterfaces' ...
** R
** inst
** preparing package for lazy loading
Warning: replacing previous import 'BiocGenerics::var' by 'stats::var' when loading 'MLInterfaces'
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Warning: replacing previous import 'BiocGenerics::var' by 'stats::var' when loading 'MLInterfaces'

install for x64

* installing *source* package 'MLInterfaces' ...
** testing if installed package can be loaded
Warning: replacing previous import 'BiocGenerics::var' by 'stats::var' when loading 'MLInterfaces'
* MD5 sums
packaged installation of 'MLInterfaces' as MLInterfaces_1.56.0.zip
* DONE (MLInterfaces)

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

nameusersystemelapsed
MLearn-new14.81 0.3817.48
RAB0.120.010.14
balKfold.xvspec0.020.020.04
classifierOutput-class2.260.022.28
clusteringOutput-class000
confuMat-methods0.250.030.28
confuTab000
fs.absT0.050.000.05
fsHistory0.040.010.06
hclustWidget000
learnerSchema-class000
performance-analytics000
planarPlot-methods3.820.163.97
plspinHcube000
predict.classifierOutput2.270.002.26
projectLearnerToGrid0.920.111.05
projectedLearner-class000
raboostCont-class0.000.010.02
varImpStruct-class0.620.040.65
xvalLoop000
xvalSpec0.320.000.31

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

nameusersystemelapsed
MLearn-new17.92 0.2518.64
RAB0.140.000.14
balKfold.xvspec0.050.000.05
classifierOutput-class2.480.022.50
clusteringOutput-class000
confuMat-methods0.30.00.3
confuTab000
fs.absT0.030.010.04
fsHistory0.060.020.08
hclustWidget0.020.000.02
learnerSchema-class000
performance-analytics000
planarPlot-methods3.330.093.42
plspinHcube000
predict.classifierOutput3.440.003.87
projectLearnerToGrid1.010.071.11
projectedLearner-class000
raboostCont-class0.020.000.02
varImpStruct-class0.790.030.83
xvalLoop000
xvalSpec0.210.010.22