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CHECK results for epiNEM on machv2

This page was generated on 2021-06-11 14:06:32 -0400 (Fri, 11 Jun 2021).

Package 585/2041HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
epiNEM 1.16.0  (landing page)
Martin Pirkl
Snapshot Date: 2021-06-10 06:50:12 -0400 (Thu, 10 Jun 2021)
URL: https://git.bioconductor.org/packages/epiNEM
Branch: RELEASE_3_13
Last Commit: 2383f66
Last Changed Date: 2021-05-19 12:26:21 -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
To the developers/maintainers of the epiNEM package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/epiNEM.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.

Summary

Package: epiNEM
Version: 1.16.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:epiNEM.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings epiNEM_1.16.0.tar.gz
StartedAt: 2021-06-10 18:34:44 -0400 (Thu, 10 Jun 2021)
EndedAt: 2021-06-10 18:38:14 -0400 (Thu, 10 Jun 2021)
EllapsedTime: 210.3 seconds
RetCode: 0
Status:   OK  
CheckDir: epiNEM.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:epiNEM.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings epiNEM_1.16.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.13-bioc/meat/epiNEM.Rcheck’
* using R version 4.1.0 (2021-05-18)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘epiNEM/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘epiNEM’ version ‘1.16.0’
* 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 ‘epiNEM’ 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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... NOTE
Foreign function call to a different package:
  .Call("getTruthTable_R", ..., PACKAGE = "BoolNet")
See chapter ‘System and foreign language interfaces’ in the ‘Writing R
Extensions’ manual.
* checking R code for possible problems ... NOTE
SimEpiNEM: no visible global function definition for ‘epiNEM2Bg’
SimEpiNEM: no visible global function definition for ‘dummyCNOlist’
SimEpiNEM: no visible global function definition for ‘readSIF’
SimEpiNEM: no visible global function definition for ‘preprocessing’
SimEpiNEM: no visible global function definition for ‘absorption’
SimEpiNEM: no visible global function definition for ‘bnem’
SimEpiNEM: no visible binding for global variable ‘popSize’
SimEpiNEM: no visible global function definition for ‘computeFc’
SimEpiNEM: no visible global function definition for
  ‘simulateStatesRecursive’
SimEpiNEM: no visible global function definition for ‘dnf2adj’
epiNEM: no visible binding for global variable ‘inference’
plot.epiSim: no visible binding for global variable ‘sim’
plot.epiSim: no visible global function definition for ‘layout’
plot.epiSim: no visible global function definition for ‘boxplot’
plot.epiSim: no visible global function definition for ‘abline’
plot.epiSim: no visible global function definition for ‘axis’
Undefined global functions or variables:
  abline absorption axis bnem boxplot computeFc dnf2adj dummyCNOlist
  epiNEM2Bg inference layout popSize preprocessing readSIF sim
  simulateStatesRecursive
Consider adding
  importFrom("graphics", "abline", "axis", "boxplot", "layout")
to your NAMESPACE file.
* 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 LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                 user system elapsed
plot.epiScreen 16.379  0.076  16.474
epiScreen      14.382  0.059  14.475
plot.epiSim    10.684  0.037  10.737
SimEpiNEM       9.348  0.106   9.473
* 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: 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.13-bioc/meat/epiNEM.Rcheck/00check.log’
for details.



Installation output

epiNEM.Rcheck/00install.out

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL epiNEM
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.1/Resources/library’
* installing *source* package ‘epiNEM’ ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** 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 (epiNEM)

Tests output

epiNEM.Rcheck/tests/runTests.Rout


R version 4.1.0 (2021-05-18) -- "Camp Pontanezen"
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("epiNEM")
[1] "Progress (of 1 iterations):"

1...


RUNIT TEST PROTOCOL -- Thu Jun 10 18:38:05 2021 
*********************************************** 
Number of test functions: 0 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
epiNEM 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 
  8.447   0.506   8.956 

Example timings

epiNEM.Rcheck/epiNEM-Ex.timings

nameusersystemelapsed
AddLogicGates0.0000.0010.001
CreateExtendedAdjacency0.4230.0050.429
CreateRandomGraph0.0000.0000.001
CreateTopology0.0740.0000.074
ExtendTopology0.0750.0000.077
GenerateData0.0780.0010.080
HeatmapOP0.1530.0140.167
Mll0.0020.0000.001
SimEpiNEM9.3480.1069.473
epiAnno0.2740.0030.278
epiNEM1.2460.0091.259
epiScreen14.382 0.05914.475
perm.rank.test0.5970.0080.605
plot.epiNEM1.4470.0031.452
plot.epiScreen16.379 0.07616.474
plot.epiSim10.684 0.03710.737
rank.enrichment0.4410.0080.450
sameith_GO0.0010.0000.002
sameith_string0.0000.0010.001
samscreen0.0010.0010.002
sim0.0010.0010.002
wageningen_GO0.0010.0010.001
wageningen_string0.0000.0010.002
wagscreen0.0010.0000.001