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CHECK report for MLInterfaces on tokay1

This page was generated on 2019-04-13 11:19:28 -0400 (Sat, 13 Apr 2019).

Package 981/1649HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
MLInterfaces 1.62.1
V. Carey
Snapshot Date: 2019-04-12 17:01:30 -0400 (Fri, 12 Apr 2019)
URL: https://git.bioconductor.org/packages/MLInterfaces
Branch: RELEASE_3_8
Last Commit: 6cf59a9
Last Changed Date: 2019-04-03 12:26:22 -0400 (Wed, 03 Apr 2019)
malbec1 Linux (Ubuntu 16.04.6 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK [ WARNINGS ] OK UNNEEDED, same version exists in internal repository
merida1 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: MLInterfaces
Version: 1.62.1
Command: C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:MLInterfaces.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings MLInterfaces_1.62.1.tar.gz
StartedAt: 2019-04-13 03:55:30 -0400 (Sat, 13 Apr 2019)
EndedAt: 2019-04-13 04:00:17 -0400 (Sat, 13 Apr 2019)
EllapsedTime: 286.1 seconds
RetCode: 0
Status:  WARNINGS  
CheckDir: MLInterfaces.Rcheck
Warnings: 1

Command output

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:MLInterfaces.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings MLInterfaces_1.62.1.tar.gz
###
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##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.8-bioc/meat/MLInterfaces.Rcheck'
* using R version 3.5.3 (2019-03-11)
* 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 '1.62.1'
* checking package namespace information ... OK
* checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
  cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES'
 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:
  Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmp0qezcK/R.INSTALLd3c16af7fed/MLInterfaces/man/MLearn-new.Rd:163: file link 'mclapply' in package 'parallel' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmp0qezcK/R.INSTALLd3c16af7fed/MLInterfaces/man/hclustWidget.Rd:35: file link 'ExpressionSet-class' in package 'Biobase' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmp0qezcK/R.INSTALLd3c16af7fed/MLInterfaces/man/xvalSpec.Rd:43: file link 'mclapply' in package 'parallel' does not exist and so has been treated as a topic
See 'C:/Users/biocbuild/bbs-3.8-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 files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
            user system elapsed
MLearn-new 10.88   0.47    12.3
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
            user system elapsed
MLearn-new 15.54   0.37      16
* 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-3.8-bioc/meat/MLInterfaces.Rcheck/00check.log'
for details.



Installation output

MLInterfaces.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.8/bioc/src/contrib/MLInterfaces_1.62.1.tar.gz && rm -rf MLInterfaces.buildbin-libdir && mkdir MLInterfaces.buildbin-libdir && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=MLInterfaces.buildbin-libdir MLInterfaces_1.62.1.tar.gz && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL MLInterfaces_1.62.1.zip && rm MLInterfaces_1.62.1.tar.gz MLInterfaces_1.62.1.zip
###
##############################################################################
##############################################################################


  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100  205k  100  205k    0     0  4968k      0 --:--:-- --:--:-- --:--:-- 5412k

install for i386

* installing *source* package 'MLInterfaces' ...
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'MLInterfaces'
    finding HTML links ... done
    MLIntInternals                          html  
    MLearn-new                              html  
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmp0qezcK/R.INSTALLd3c16af7fed/MLInterfaces/man/MLearn-new.Rd:163: file link 'mclapply' in package 'parallel' does not exist and so has been treated as a topic
    RAB                                     html  
    balKfold.xvspec                         html  
    classifierOutput-class                  html  
    clusteringOutput-class                  html  
    confuMat-methods                        html  
    confuTab                                html  
    fs.absT                                 html  
    fsHistory                               html  
    hclustWidget                            html  
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmp0qezcK/R.INSTALLd3c16af7fed/MLInterfaces/man/hclustWidget.Rd:35: file link 'ExpressionSet-class' in package 'Biobase' does not exist and so has been treated as a topic
    learnerSchema-class                     html  
    performance-analytics                   html  
    planarPlot-methods                      html  
    plspinHcube                             html  
    predict.classifierOutput                html  
    projectLearnerToGrid                    html  
    projectedLearner-class                  html  
    raboostCont-class                       html  
    varImpStruct-class                      html  
    xvalLoop                                html  
    xvalSpec                                html  
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmp0qezcK/R.INSTALLd3c16af7fed/MLInterfaces/man/xvalSpec.Rd:43: file link 'mclapply' in package 'parallel' does not exist and so has been treated as a topic
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL

install for x64

* installing *source* package 'MLInterfaces' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'MLInterfaces' as MLInterfaces_1.62.1.zip
* DONE (MLInterfaces)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.8-bioc/R/library'
package 'MLInterfaces' successfully unpacked and MD5 sums checked
In R CMD INSTALL

Tests output

MLInterfaces.Rcheck/tests_i386/runTests.Rout


R version 3.5.3 (2019-03-11) -- "Great Truth"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> BiocGenerics:::testPackage("MLInterfaces")

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, basename, cbind, colMeans, colSums, colnames,
    dirname, do.call, duplicated, eval, evalq, get, grep, grepl,
    intersect, is.unsorted, lapply, lengths, mapply, match, mget,
    order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind,
    rowMeans, rowSums, rownames, sapply, setdiff, sort, table, tapply,
    union, unique, unsplit, which, which.max, which.min

Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.


Attaching package: 'S4Vectors'

The following object is masked from 'package:base':

    expand.grid


Attaching package: 'IRanges'

The following object is masked from 'package:grDevices':

    windows



RUNIT TEST PROTOCOL -- Sat Apr 13 04:00:05 2019 
*********************************************** 
Number of test functions: 0 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
MLInterfaces RUnit Tests - 0 test functions, 0 errors, 0 failures
Number of test functions: 0 
Number of errors: 0 
Number of failures: 0 
> 
> proc.time()
   user  system elapsed 
   5.18    0.42    5.62 

MLInterfaces.Rcheck/tests_x64/runTests.Rout


R version 3.5.3 (2019-03-11) -- "Great Truth"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> BiocGenerics:::testPackage("MLInterfaces")

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, basename, cbind, colMeans, colSums, colnames,
    dirname, do.call, duplicated, eval, evalq, get, grep, grepl,
    intersect, is.unsorted, lapply, lengths, mapply, match, mget,
    order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind,
    rowMeans, rowSums, rownames, sapply, setdiff, sort, table, tapply,
    union, unique, unsplit, which, which.max, which.min

Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.


Attaching package: 'S4Vectors'

The following object is masked from 'package:base':

    expand.grid


Attaching package: 'IRanges'

The following object is masked from 'package:grDevices':

    windows



RUNIT TEST PROTOCOL -- Sat Apr 13 04:00:12 2019 
*********************************************** 
Number of test functions: 0 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
MLInterfaces RUnit Tests - 0 test functions, 0 errors, 0 failures
Number of test functions: 0 
Number of errors: 0 
Number of failures: 0 
> 
> proc.time()
   user  system elapsed 
   5.59    0.25    5.84 

Example timings

MLInterfaces.Rcheck/examples_i386/MLInterfaces-Ex.timings

nameusersystemelapsed
MLearn-new10.88 0.4712.30
RAB0.110.000.11
balKfold.xvspec0.030.000.03
classifierOutput-class2.220.012.24
clusteringOutput-class000
confuMat-methods0.260.000.26
confuTab000
fs.absT0.040.000.03
fsHistory0.030.020.05
hclustWidget000
learnerSchema-class000
performance-analytics0.010.000.01
planarPlot-methods2.750.142.90
plspinHcube000
predict.classifierOutput2.020.022.03
projectLearnerToGrid0.800.030.82
projectedLearner-class000
raboostCont-class000
varImpStruct-class0.480.030.52
xvalLoop000
xvalSpec0.160.010.17

MLInterfaces.Rcheck/examples_x64/MLInterfaces-Ex.timings

nameusersystemelapsed
MLearn-new15.54 0.3716.00
RAB0.110.000.11
balKfold.xvspec0.040.000.05
classifierOutput-class2.240.022.25
clusteringOutput-class000
confuMat-methods0.320.030.35
confuTab000
fs.absT0.040.000.04
fsHistory0.080.000.08
hclustWidget000
learnerSchema-class000
performance-analytics000
planarPlot-methods3.090.083.17
plspinHcube000
predict.classifierOutput3.250.023.28
projectLearnerToGrid0.780.080.86
projectedLearner-class000
raboostCont-class000
varImpStruct-class0.560.010.57
xvalLoop000
xvalSpec0.180.000.18