Back to Multiple platform build/check report for BioC 3.13
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This page was generated on 2021-09-20 15:04:44 -0400 (Mon, 20 Sep 2021).

CHECK results for BioMM on nebbiolo1

To the developers/maintainers of the BioMM package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/BioMM.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 182/2041HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
BioMM 1.8.0  (landing page)
Junfang Chen
Snapshot Date: 2021-09-19 04:50:10 -0400 (Sun, 19 Sep 2021)
git_url: https://git.bioconductor.org/packages/BioMM
git_branch: RELEASE_3_13
git_last_commit: 765ffb7
git_last_commit_date: 2021-05-19 12:41:03 -0400 (Wed, 19 May 2021)
nebbiolo1Linux (Ubuntu 20.04.2 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: BioMM
Version: 1.8.0
Command: /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD check --install=check:BioMM.install-out.txt --library=/home/biocbuild/bbs-3.13-bioc/R/library --no-vignettes --timings BioMM_1.8.0.tar.gz
StartedAt: 2021-09-19 09:00:42 -0400 (Sun, 19 Sep 2021)
EndedAt: 2021-09-19 09:02:57 -0400 (Sun, 19 Sep 2021)
EllapsedTime: 135.4 seconds
RetCode: 0
Status:   OK  
CheckDir: BioMM.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD check --install=check:BioMM.install-out.txt --library=/home/biocbuild/bbs-3.13-bioc/R/library --no-vignettes --timings BioMM_1.8.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.13-bioc/meat/BioMM.Rcheck’
* using R version 4.1.1 (2021-08-10)
* using platform: x86_64-pc-linux-gnu (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 ‘1.8.0’
* 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     325.836  8.469  35.685
reconByUnsupervised  53.924  3.579  14.378
predByBS             22.878  9.265   2.621
predByCV             12.008  4.866   1.451
predByFS              7.439  2.004   0.812
reconBySupervised     8.680  0.195   8.876
* 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
  ‘/home/biocbuild/bbs-3.13-bioc/meat/BioMM.Rcheck/00check.log’
for details.



Installation output

BioMM.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD INSTALL BioMM
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.13-bioc/R/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 4.1.1 (2021-08-10) -- "Kick Things"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (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 -- Sun Sep 19 09:02:54 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 
> 
> proc.time()
   user  system elapsed 
  3.533   0.209   3.713 

Example timings

BioMM.Rcheck/BioMM-Ex.timings

nameusersystemelapsed
BioMM0.2560.0310.294
baseGLMnet0.4420.0400.483
baseModel0.3140.0170.316
baseRandForest0.5990.0130.595
baseSVM1.0930.0201.113
classifiACC0.9770.6610.427
getDataByFilter325.836 8.469 35.685
getMetrics1.9542.0010.775
omics2pathlist0.2670.0100.277
predByBS22.878 9.265 2.621
predByCV12.008 4.866 1.451
predByFS7.4392.0040.812
reconBySupervised8.6800.1958.876
reconByUnsupervised53.924 3.57914.378