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CHECK report for BioMM on merida1

This page was generated on 2020-08-10 12:43:52 -0400 (Mon, 10 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: 2020-08-09 14:51:29 -0400 (Sun, 09 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
nebbiolo1 Linux (Ubuntu 20.04.1 LTS) / x86_64  OK  OK  OK 
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: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:BioMM.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings BioMM_1.5.2.tar.gz
StartedAt: 2020-08-10 04:16:42 -0400 (Mon, 10 Aug 2020)
EndedAt: 2020-08-10 04:20:29 -0400 (Mon, 10 Aug 2020)
EllapsedTime: 226.9 seconds
RetCode: 0
Status:  OK 
CheckDir: BioMM.Rcheck
Warnings: 0

Command output

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:BioMM.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings BioMM_1.5.2.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.12-bioc/meat/BioMM.Rcheck’
* using R version 4.0.2 (2020-06-22)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* 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 for sufficient/correct file permissions ... 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
* 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 ... OK
Examples with CPU (user + system) or elapsed time > 5s
                      user system elapsed
getDataByFilter     87.613  9.299  12.329
reconByUnsupervised 48.514  6.241  24.870
predByBS            25.038  7.106   3.229
reconBySupervised   19.240  1.201  20.438
predByCV             8.083  3.621   1.460
classifiACC          4.084  1.978   0.910
getMetrics           4.080  1.328   1.220
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  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:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL BioMM
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.0/Resources/library’
* installing *source* package ‘BioMM’ ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** 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
* DONE (BioMM)

Tests output

BioMM.Rcheck/tests/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-apple-darwin17.0 (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 -- Mon Aug 10 04:20:15 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 
  6.488   0.483   6.910 

Example timings

BioMM.Rcheck/BioMM-Ex.timings

nameusersystemelapsed
BioMM0.3670.0410.408
baseGLMnet1.2980.1021.399
baseModel0.7080.0490.700
baseRandForest0.6710.0430.657
baseSVM2.4280.2692.679
classifiACC4.0841.9780.910
getDataByFilter87.613 9.29912.329
getMetrics4.0801.3281.220
omics2pathlist0.4370.0240.462
predByBS25.038 7.106 3.229
predByCV8.0833.6211.460
predByFS0.7400.3960.415
reconBySupervised19.240 1.20120.438
reconByUnsupervised48.514 6.24124.870