Back to Multiple platform build/check report for BioC 3.14
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This page was generated on 2021-12-03 13:05:41 -0500 (Fri, 03 Dec 2021).

CHECK results for bnem on machv2

To the developers/maintainers of the bnem package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/bnem.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 207/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
bnem 1.2.0  (landing page)
Martin Pirkl
Snapshot Date: 2021-12-02 01:55:06 -0500 (Thu, 02 Dec 2021)
git_url: https://git.bioconductor.org/packages/bnem
git_branch: RELEASE_3_14
git_last_commit: 7189a51
git_last_commit_date: 2021-10-26 13:05:36 -0500 (Tue, 26 Oct 2021)
nebbiolo2Linux (Ubuntu 20.04.3 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: bnem
Version: 1.2.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:bnem.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings bnem_1.2.0.tar.gz
StartedAt: 2021-12-02 12:18:05 -0500 (Thu, 02 Dec 2021)
EndedAt: 2021-12-02 12:23:04 -0500 (Thu, 02 Dec 2021)
EllapsedTime: 298.8 seconds
RetCode: 0
Status:   OK  
CheckDir: bnem.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:bnem.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings bnem_1.2.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.14-bioc/meat/bnem.Rcheck’
* using R version 4.1.2 (2021-11-01)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘bnem/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘bnem’ version ‘1.2.0’
* 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 ‘bnem’ 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
Namespace in Imports field not imported from: ‘rmarkdown’
  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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.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-3.14-bioc/meat/bnem.Rcheck/00check.log’
for details.



Installation output

bnem.Rcheck/00install.out

##############################################################################
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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL bnem
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.1/Resources/library’
* installing *source* package ‘bnem’ ...
** using staged installation
** R
** data
** 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 (bnem)

Tests output

bnem.Rcheck/tests/runTests.Rout


R version 4.1.2 (2021-11-01) -- "Bird Hippie"
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("bnem")


RUNIT TEST PROTOCOL -- Thu Dec  2 12:22:56 2021 
*********************************************** 
Number of test functions: 0 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
bnem RUnit Tests - 0 test functions, 0 errors, 0 failures
Number of test functions: 0 
Number of errors: 0 
Number of failures: 0 
> 
> proc.time()
   user  system elapsed 
 12.238   0.558  12.796 

Example timings

bnem.Rcheck/bnem-Ex.timings

nameusersystemelapsed
absorption0.0010.0000.002
absorptionII0.0010.0010.003
addNoise1.3120.0321.346
bcr0.0110.0020.013
bnem0.0860.0020.089
bnemBs0.6580.0570.718
computeFc0.0150.0030.018
convertGraph0.0040.0010.004
dummyCNOlist0.0080.0020.010
epiNEM2Bg0.1090.0130.123
findResiduals0.2650.0300.295
plot.bnem0.7440.0510.796
plot.bnembs0.6330.0040.637
plot.bnemsim0.3000.0040.304
processDataBCR0.0090.0020.010
randomDnf0.0050.0010.005
reduceGraph0.0180.0010.020
scoreDnf0.0560.0020.058
simBoolGtn0.1200.0020.122
simulateStatesRecursive0.0120.0010.013
transClose0.0220.0000.022
transRed0.0260.0000.026
validateGraph0.2220.0140.237