Back to Multiple platform build/check report for BioC 3.14
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This page was generated on 2022-04-13 12:05:07 -0400 (Wed, 13 Apr 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_644.1.3 (2022-03-10) -- "One Push-Up" 4324
tokay2Windows Server 2012 R2 Standardx644.1.3 (2022-03-10) -- "One Push-Up" 4077
machv2macOS 10.14.6 Mojavex86_644.1.3 (2022-03-10) -- "One Push-Up" 4137
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

CHECK results for BioMM on nebbiolo2


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? 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 184/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
BioMM 1.10.0  (landing page)
Junfang Chen
Snapshot Date: 2022-04-12 01:55:07 -0400 (Tue, 12 Apr 2022)
git_url: https://git.bioconductor.org/packages/BioMM
git_branch: RELEASE_3_14
git_last_commit: 861a791
git_last_commit_date: 2021-10-26 12:49:29 -0400 (Tue, 26 Oct 2021)
nebbiolo2Linux (Ubuntu 20.04.4 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: 1.10.0
Command: /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD check --install=check:BioMM.install-out.txt --library=/home/biocbuild/bbs-3.14-bioc/R/library --no-vignettes --timings BioMM_1.10.0.tar.gz
StartedAt: 2022-04-12 06:34:49 -0400 (Tue, 12 Apr 2022)
EndedAt: 2022-04-12 06:36:56 -0400 (Tue, 12 Apr 2022)
EllapsedTime: 127.3 seconds
RetCode: 0
Status:   OK  
CheckDir: BioMM.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD check --install=check:BioMM.install-out.txt --library=/home/biocbuild/bbs-3.14-bioc/R/library --no-vignettes --timings BioMM_1.10.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.14-bioc/meat/BioMM.Rcheck’
* using R version 4.1.3 (2022-03-10)
* 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 ‘1.10.0’
* 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     338.988  4.569  35.402
reconByUnsupervised  50.330  3.403  12.441
predByBS             27.775  8.760   2.381
predByFS              7.737  2.799   0.618
reconBySupervised     7.976  0.108   8.085
predByCV              4.722  1.992   1.205
* 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-3.14-bioc/meat/BioMM.Rcheck/00check.log’
for details.



Installation output

BioMM.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD INSTALL BioMM
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.14-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 4.1.3 (2022-03-10) -- "One Push-Up"
Copyright (C) 2022 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 -- Tue Apr 12 06:36:53 2022 
*********************************************** 
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 
  2.962   0.279   3.203 

Example timings

BioMM.Rcheck/BioMM-Ex.timings

nameusersystemelapsed
BioMM0.2150.0040.220
baseGLMnet0.3570.0160.373
baseModel0.3350.0410.349
baseRandForest0.5370.0130.528
baseSVM0.8990.0160.916
classifiACC1.3120.7990.390
getDataByFilter338.988 4.569 35.402
getMetrics1.8080.9350.485
omics2pathlist0.2070.0040.212
predByBS27.775 8.760 2.381
predByCV4.7221.9921.205
predByFS7.7372.7990.618
reconBySupervised7.9760.1088.085
reconByUnsupervised50.330 3.40312.441