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CHECK report for BioMM on tokay1

This page was generated on 2020-08-07 12:16:41 -0400 (Fri, 07 Aug 2020).

TO THE DEVELOPERS/MAINTAINERS OF THE BioMM PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 169/1882HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
BioMM 1.5.2
Junfang Chen
Snapshot Date: 2020-08-06 14:50:46 -0400 (Thu, 06 Aug 2020)
URL: https://git.bioconductor.org/packages/BioMM
Branch: master
Last Commit: de6c715
Last Changed Date: 2020-05-28 10:38:53 -0400 (Thu, 28 May 2020)
malbec1 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository
merida1 macOS 10.14.6 Mojave / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: BioMM
Version: 1.5.2
Command: C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:BioMM.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings BioMM_1.5.2.tar.gz
StartedAt: 2020-08-07 05:13:28 -0400 (Fri, 07 Aug 2020)
EndedAt: 2020-08-07 05:19:46 -0400 (Fri, 07 Aug 2020)
EllapsedTime: 378.4 seconds
RetCode: 0
Status:  OK  
CheckDir: BioMM.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:BioMM.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings BioMM_1.5.2.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.12-bioc/meat/BioMM.Rcheck'
* using R version 4.0.2 (2020-06-22)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'BioMM/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'BioMM' version '1.5.2'
* package encoding: UTF-8
* 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 'BioMM' 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 files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                     user system elapsed
getDataByFilter     50.55   0.72   51.33
reconByUnsupervised 23.13   0.21   23.35
predByBS            15.35   0.95   13.41
reconBySupervised   11.87   0.06   11.94
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                     user system elapsed
getDataByFilter     39.99   0.48   40.92
reconByUnsupervised 31.82   0.10   31.90
reconBySupervised   15.70   0.04   16.86
predByBS            13.12   0.76   12.21
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'runTest.R'
 OK
** running tests for arch 'x64' ...
  Running 'runTest.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

BioMM.Rcheck/00install.out

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.12/bioc/src/contrib/BioMM_1.5.2.tar.gz && rm -rf BioMM.buildbin-libdir && mkdir BioMM.buildbin-libdir && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=BioMM.buildbin-libdir BioMM_1.5.2.tar.gz && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL BioMM_1.5.2.zip && rm BioMM_1.5.2.tar.gz BioMM_1.5.2.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 4246k  100 4246k    0     0  35.4M      0 --:--:-- --:--:-- --:--:-- 36.7M

install for i386

* installing *source* package 'BioMM' ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'BioMM'
    finding HTML links ... done
    BioMM                                   html  
    BioMMstage2pred                         html  
    baseGLMnet                              html  
    baseModel                               html  
    baseRandForest                          html  
    baseSVM                                 html  
    cirPlot4pathway                         html  
    classifiACC                             html  
    getDataByFilter                         html  
    getMetrics                              html  
    omics2pathlist                          html  
    plotRankedFeature                       html  
    plotVarExplained                        html  
    predByBS                                html  
    predByCV                                html  
    predByFS                                html  
    reconBySupervised                       html  
    reconByUnsupervised                     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 'BioMM' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'BioMM' as BioMM_1.5.2.zip
* DONE (BioMM)
* installing to library 'C:/Users/biocbuild/bbs-3.12-bioc/R/library'
package 'BioMM' successfully unpacked and MD5 sums checked

Tests output

BioMM.Rcheck/tests_i386/runTest.Rout


R version 4.0.2 (2020-06-22) -- "Taking Off Again"
Copyright (C) 2020 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("BioMM")


RUNIT TEST PROTOCOL -- Fri Aug 07 05:19:35 2020 
*********************************************** 
Number of test functions: 2 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
BioMM RUnit Tests - 2 test functions, 0 errors, 0 failures
Number of test functions: 2 
Number of errors: 0 
Number of failures: 0 
> 
> proc.time()
   user  system elapsed 
   4.78    0.43    5.20 

BioMM.Rcheck/tests_x64/runTest.Rout


R version 4.0.2 (2020-06-22) -- "Taking Off Again"
Copyright (C) 2020 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("BioMM")


RUNIT TEST PROTOCOL -- Fri Aug 07 05:19:41 2020 
*********************************************** 
Number of test functions: 2 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
BioMM RUnit Tests - 2 test functions, 0 errors, 0 failures
Number of test functions: 2 
Number of errors: 0 
Number of failures: 0 
> 
> proc.time()
   user  system elapsed 
   5.53    0.54    6.00 

Example timings

BioMM.Rcheck/examples_i386/BioMM-Ex.timings

nameusersystemelapsed
BioMM0.360.000.41
baseGLMnet0.860.141.00
baseModel0.950.000.95
baseRandForest0.610.010.53
baseSVM1.640.101.74
classifiACC2.510.142.56
getDataByFilter50.55 0.7251.33
getMetrics2.230.141.76
omics2pathlist0.630.000.64
predByBS15.35 0.9513.41
predByCV3.900.143.98
predByFS0.340.000.34
reconBySupervised11.87 0.0611.94
reconByUnsupervised23.13 0.2123.35

BioMM.Rcheck/examples_x64/BioMM-Ex.timings

nameusersystemelapsed
BioMM0.220.000.22
baseGLMnet0.920.030.96
baseModel0.570.010.57
baseRandForest0.340.030.38
baseSVM1.590.051.64
classifiACC1.640.081.69
getDataByFilter39.99 0.4840.92
getMetrics1.950.131.47
omics2pathlist0.350.000.34
predByBS13.12 0.7612.21
predByCV3.330.073.35
predByFS0.280.000.29
reconBySupervised15.70 0.0416.86
reconByUnsupervised31.82 0.1031.90