Back to Build/check report for BioC 3.17
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This page was generated on 2023-01-02 09:00:21 -0500 (Mon, 02 Jan 2023).

HostnameOSArch (*)R versionInstalled pkgs
palomino5Windows Server 2022 Datacenterx64R Under development (unstable) (2022-12-25 r83502 ucrt) -- "Unsuffered Consequences" 4165
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CHECK results for bnem on palomino5


To the developers/maintainers of the bnem package:
Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 212/2158HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
bnem 1.7.0  (landing page)
Martin Pirkl
Snapshot Date: 2022-12-28 11:00:06 -0500 (Wed, 28 Dec 2022)
git_url: https://git.bioconductor.org/packages/bnem
git_branch: master
git_last_commit: c3803ae
git_last_commit_date: 2022-12-02 05:16:11 -0500 (Fri, 02 Dec 2022)
palomino5Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  

Summary

Package: bnem
Version: 1.7.0
Command: F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:bnem.install-out.txt --library=F:\biocbuild\bbs-3.17-bioc\R\library --no-vignettes --timings bnem_1.7.0.tar.gz
StartedAt: 2022-12-28 22:05:41 -0500 (Wed, 28 Dec 2022)
EndedAt: 2022-12-28 22:08:49 -0500 (Wed, 28 Dec 2022)
EllapsedTime: 188.2 seconds
RetCode: 0
Status:   OK  
CheckDir: bnem.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:bnem.install-out.txt --library=F:\biocbuild\bbs-3.17-bioc\R\library --no-vignettes --timings bnem_1.7.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'F:/biocbuild/bbs-3.17-bioc-rtools43/meat/bnem.Rcheck'
* using R Under development (unstable) (2022-12-25 r83502 ucrt)
* using platform: x86_64-w64-mingw32 (64-bit)
* R was compiled by
    gcc.exe (GCC) 10.4.0
    GNU Fortran (GCC) 10.4.0
* running under: Windows Server x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'bnem/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'bnem' version '1.7.0'
* 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 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
  'F:/biocbuild/bbs-3.17-bioc-rtools43/meat/bnem.Rcheck/00check.log'
for details.



Installation output

bnem.Rcheck/00install.out

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###
### Running command:
###
###   F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD INSTALL bnem
###
##############################################################################
##############################################################################


* installing to library 'F:/biocbuild/bbs-3.17-bioc/R/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 Under development (unstable) (2022-12-25 r83502 ucrt) -- "Unsuffered Consequences"
Copyright (C) 2022 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (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 -- Wed Dec 28 22:08:39 2022 
*********************************************** 
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 
   7.59    0.68    8.25 

Example timings

bnem.Rcheck/bnem-Ex.timings

nameusersystemelapsed
absorption000
absorptionII000
addNoise0.930.000.94
bcr0.010.000.01
bnem0.060.000.07
bnemBs0.410.010.43
computeFc0.020.000.02
convertGraph000
dummyCNOlist0.010.000.02
epiNEM2Bg0.080.000.09
findResiduals0.160.000.16
plot.bnem0.390.030.42
plot.bnembs0.430.000.44
plot.bnemsim0.160.020.17
processDataBCR0.020.000.01
randomDnf000
reduceGraph0.010.000.02
scoreDnf0.030.000.03
simBoolGtn0.060.010.08
simulateStatesRecursive0.020.000.01
transClose0.020.000.02
transRed0.020.000.02
validateGraph0.180.000.19