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CHECK report for BioMM on merida1

This page was generated on 2021-05-06 12:34:26 -0400 (Thu, 06 May 2021).

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 179/1974HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
BioMM 1.6.0  (landing page)
Junfang Chen
Snapshot Date: 2021-05-05 14:51:38 -0400 (Wed, 05 May 2021)
URL: https://git.bioconductor.org/packages/BioMM
Branch: RELEASE_3_12
Last Commit: bb432b4
Last Changed Date: 2020-10-27 11:42:47 -0400 (Tue, 27 Oct 2020)
malbec1Linux (Ubuntu 18.04.5 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version exists in internal repository
tokay1Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version exists in internal repository
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version exists in internal repository

Summary

Package: BioMM
Version: 1.6.0
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_1.6.0.tar.gz
StartedAt: 2021-05-05 23:42:37 -0400 (Wed, 05 May 2021)
EndedAt: 2021-05-05 23:45:55 -0400 (Wed, 05 May 2021)
EllapsedTime: 198.2 seconds
RetCode: 0
Status:   OK  
CheckDir: BioMM.Rcheck
Warnings: 0

Command output

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### Running 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_1.6.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.12-bioc/meat/BioMM.Rcheck’
* using R version 4.0.5 (2021-03-31)
* 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 ‘1.6.0’
* 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 ... NOTE
Namespaces in Imports field not imported from:
  ‘imager’ ‘topGO’ ‘xlsx’
  All declared Imports should be used.
* 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     399.898  8.025  49.336
reconByUnsupervised  68.845  6.746  19.092
getMetrics           48.182  3.236   1.074
predByBS             29.473  9.098   3.304
reconBySupervised    14.311  1.797  13.825
predByCV              7.084  3.806   1.481
predByFS              6.425  3.019   1.475
* 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: 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.12-bioc/meat/BioMM.Rcheck/00check.log’
for details.



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
Warning in .recacheSubclasses(def@className, def, env) :
  undefined subclass "numericVector" of class "Mnumeric"; definition not updated
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
Warning in .recacheSubclasses(def@className, def, env) :
  undefined subclass "numericVector" of class "Mnumeric"; definition not updated
** testing if installed package can be loaded from final location
Warning in .recacheSubclasses(def@className, def, env) :
  undefined subclass "numericVector" of class "Mnumeric"; definition not updated
** testing if installed package keeps a record of temporary installation path
* DONE (BioMM)

Tests output

BioMM.Rcheck/tests/runTest.Rout


R version 4.0.5 (2021-03-31) -- "Shake and Throw"
Copyright (C) 2021 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 -- Wed May  5 23:45:47 2021 
*********************************************** 
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 
Warning message:
In .recacheSubclasses(def@className, def, env) :
  undefined subclass "numericVector" of class "Mnumeric"; definition not updated
> 
> proc.time()
   user  system elapsed 
  4.816   0.401   5.186 

Example timings

BioMM.Rcheck/BioMM-Ex.timings

nameusersystemelapsed
BioMM0.4000.0420.442
baseGLMnet0.7190.1010.820
baseModel0.5680.0560.597
baseRandForest0.7560.0470.783
baseSVM1.7810.2522.021
classifiACC3.3401.6140.673
getDataByFilter399.898 8.025 49.336
getMetrics48.182 3.236 1.074
omics2pathlist0.2910.0200.310
predByBS29.473 9.098 3.304
predByCV7.0843.8061.481
predByFS6.4253.0191.475
reconBySupervised14.311 1.79713.825
reconByUnsupervised68.845 6.74619.092