Back to Multiple platform build/check report for BioC 3.14
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This page was generated on 2021-10-21 12:05:13 -0400 (Thu, 21 Oct 2021).

CHECK results for bnem on merida1

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 205/2075HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
bnem 1.1.3  (landing page)
Martin Pirkl
Snapshot Date: 2021-10-20 14:50:05 -0400 (Wed, 20 Oct 2021)
git_url: https://git.bioconductor.org/packages/bnem
git_branch: master
git_last_commit: 43cf9d2
git_last_commit_date: 2021-10-08 05:12:44 -0400 (Fri, 08 Oct 2021)
nebbiolo2Linux (Ubuntu 20.04.2 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
riesling1Windows Server 2019 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: bnem
Version: 1.1.3
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_1.1.3.tar.gz
StartedAt: 2021-10-21 01:21:32 -0400 (Thu, 21 Oct 2021)
EndedAt: 2021-10-21 01:26:25 -0400 (Thu, 21 Oct 2021)
EllapsedTime: 292.4 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_1.1.3.tar.gz
###
##############################################################################
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* using log directory ‘/Users/biocbuild/bbs-3.14-bioc/meat/bnem.Rcheck’
* using R version 4.1.1 Patched (2021-08-22 r80813)
* 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 ‘1.1.3’
* 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 4.1.1 Patched (2021-08-22 r80813) -- "Kick Things"
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 Oct 21 01:26:16 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 
 11.715   0.647  12.334 

Example timings

bnem.Rcheck/bnem-Ex.timings

nameusersystemelapsed
absorption0.0010.0000.001
absorptionII0.0010.0010.001
addNoise1.3930.0331.428
bcr0.0100.0020.013
bnem0.1230.0030.126
bnemBs1.3480.0441.394
computeFc0.0170.0010.018
convertGraph0.0030.0000.004
dummyCNOlist0.0080.0010.008
epiNEM2Bg0.0840.0030.088
findResiduals0.2790.0050.285
plot.bnem0.7980.0690.869
plot.bnembs0.6950.0700.765
plot.bnemsim0.2480.0140.263
processDataBCR0.0070.0010.008
randomDnf0.0030.0000.003
reduceGraph0.0170.0010.017
scoreDnf0.0460.0000.046
simBoolGtn0.1360.0010.138
simulateStatesRecursive0.0140.0030.018
transClose0.0300.0010.030
transRed0.0370.0000.037
validateGraph0.1900.0030.193