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CHECK report for OmicsMarkeR on tokay2

This page was generated on 2019-10-16 12:32:58 -0400 (Wed, 16 Oct 2019).

Package 1133/1741HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
OmicsMarkeR 1.16.0
Charles E. Determan Jr.
Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019)
URL: https://git.bioconductor.org/packages/OmicsMarkeR
Branch: RELEASE_3_9
Last Commit: 8410584
Last Changed Date: 2019-05-02 11:53:54 -0400 (Thu, 02 May 2019)
malbec2 Linux (Ubuntu 18.04.2 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository
celaya2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: OmicsMarkeR
Version: 1.16.0
Command: C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:OmicsMarkeR.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings OmicsMarkeR_1.16.0.tar.gz
StartedAt: 2019-10-16 05:41:43 -0400 (Wed, 16 Oct 2019)
EndedAt: 2019-10-16 05:47:54 -0400 (Wed, 16 Oct 2019)
EllapsedTime: 371.0 seconds
RetCode: 0
Status:  OK  
CheckDir: OmicsMarkeR.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:OmicsMarkeR.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings OmicsMarkeR_1.16.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.9-bioc/meat/OmicsMarkeR.Rcheck'
* using R version 3.6.1 (2019-07-05)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'OmicsMarkeR/DESCRIPTION' ... OK
* this is package 'OmicsMarkeR' version '1.16.0'
* 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 'OmicsMarkeR' can be installed ... OK
* 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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* 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
perm.class          13.00   0.08   13.08
feature.table       11.89   0.18   12.08
performance.metrics 10.92   0.02   10.93
perm.features       10.55   0.09   10.64
predictNewClasses    9.96   0.06   10.03
fs.stability         9.57   0.08    9.66
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                     user system elapsed
perm.class          12.52   0.02   13.47
perm.features       10.42   0.00   10.42
performance.metrics 10.01   0.01   10.94
feature.table        9.86   0.09    9.96
predictNewClasses    9.89   0.00    9.91
fs.stability         9.44   0.02    9.77
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'testthat.R'
 OK
** running tests for arch 'x64' ...
  Running 'testthat.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: OK


Installation output

OmicsMarkeR.Rcheck/00install.out

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.9/bioc/src/contrib/OmicsMarkeR_1.16.0.tar.gz && rm -rf OmicsMarkeR.buildbin-libdir && mkdir OmicsMarkeR.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=OmicsMarkeR.buildbin-libdir OmicsMarkeR_1.16.0.tar.gz && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL OmicsMarkeR_1.16.0.zip && rm OmicsMarkeR_1.16.0.tar.gz OmicsMarkeR_1.16.0.zip
###
##############################################################################
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  % 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  236k  100  236k    0     0  2576k      0 --:--:-- --:--:-- --:--:-- 2780k

install for i386

* installing *source* package 'OmicsMarkeR' ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'OmicsMarkeR'
    finding HTML links ... done
    CLA                                     html  
    EE                                      html  
    EM                                      html  
    ES                                      html  
    RPT                                     html  
    aggregation                             html  
    bagging.wrapper                         html  
    canberra                                html  
    canberra_stability                      html  
    create.corr.matrix                      html  
    create.discr.matrix                     html  
    create.random.matrix                    html  
    denovo.grid                             html  
    extract.args                            html  
    extract.features                        html  
    feature.table                           html  
    fit.only.model                          html  
    fs.ensembl.stability                    html  
    fs.stability                            html  
    jaccard                                 html  
    kuncheva                                html  
    modelList                               html  
    modelTuner                              html  
    modelTuner_loo                          html  
    noise.matrix                            html  
    ochiai                                  html  
    optimize.model                          html  
    pairwise.model.stability                html  
    pairwise.stability                      html  
    params                                  html  
    perf.calc                               html  
    finding level-2 HTML links ... done

    performance.metrics                     html  
    performance.stats                       html  
    perm.class                              html  
    perm.features                           html  
    pof                                     html  
    predictNewClasses                       html  
    predicting                              html  
    prediction.metrics                      html  
    sequester                               html  
    sorensen                                html  
    spearman                                html  
    svm.weights                             html  
    svmrfeFeatureRanking                    html  
    svmrfeFeatureRankingForMulticlass       html  
    training                                html  
    tune.instructions                       html  
** 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

install for x64

* installing *source* package 'OmicsMarkeR' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'OmicsMarkeR' as OmicsMarkeR_1.16.0.zip
* DONE (OmicsMarkeR)
* installing to library 'C:/Users/biocbuild/bbs-3.9-bioc/R/library'
package 'OmicsMarkeR' successfully unpacked and MD5 sums checked

Tests output

OmicsMarkeR.Rcheck/tests_i386/testthat.Rout


R version 3.6.1 (2019-07-05) -- "Action of the Toes"
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.

> library(testthat)
> library(OmicsMarkeR)
> 
> test_check("OmicsMarkeR")
== testthat results  ===========================================================
[ OK: 100 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
  53.81    0.57   55.76 

OmicsMarkeR.Rcheck/tests_x64/testthat.Rout


R version 3.6.1 (2019-07-05) -- "Action of the Toes"
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.

> library(testthat)
> library(OmicsMarkeR)
> 
> test_check("OmicsMarkeR")
== testthat results  ===========================================================
[ OK: 100 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
  59.12    0.42   59.53 

Example timings

OmicsMarkeR.Rcheck/examples_i386/OmicsMarkeR-Ex.timings

nameusersystemelapsed
RPT0.000.000.08
aggregation000
canberra000
canberra_stability000
create.corr.matrix000
create.discr.matrix0.010.000.01
create.random.matrix000
denovo.grid0.010.000.01
feature.table11.89 0.1812.08
fit.only.model4.070.074.14
fs.ensembl.stability000
fs.stability9.570.089.66
jaccard000
kuncheva000
modelList000
ochiai000
pairwise.model.stability0.020.000.02
pairwise.stability0.010.000.02
params000
performance.metrics10.92 0.0210.93
perm.class13.00 0.0813.08
perm.features10.55 0.0910.64
pof000
predictNewClasses 9.96 0.0610.03
sorensen000
spearman000
svmrfeFeatureRanking0.070.000.06
svmrfeFeatureRankingForMulticlass0.110.000.11

OmicsMarkeR.Rcheck/examples_x64/OmicsMarkeR-Ex.timings

nameusersystemelapsed
RPT0.010.000.01
aggregation000
canberra000
canberra_stability000
create.corr.matrix0.020.000.01
create.discr.matrix000
create.random.matrix000
denovo.grid0.020.000.01
feature.table9.860.099.96
fit.only.model3.260.083.34
fs.ensembl.stability000
fs.stability9.440.029.77
jaccard000
kuncheva000
modelList000
ochiai000
pairwise.model.stability0.010.000.02
pairwise.stability000
params0.020.000.01
performance.metrics10.01 0.0110.94
perm.class12.52 0.0213.47
perm.features10.42 0.0010.42
pof000
predictNewClasses9.890.009.91
sorensen000
spearman000
svmrfeFeatureRanking0.080.000.08
svmrfeFeatureRankingForMulticlass0.190.000.18