Package: epiNEM

Version: 1.10.0

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_1.10.0.tar.gz

StartedAt: 2020-04-15 02:08:02 -0400 (Wed, 15 Apr 2020)

EndedAt: 2020-04-15 02:10:14 -0400 (Wed, 15 Apr 2020)

EllapsedTime: 132.5 seconds

RetCode: 0

Status:  OK

CheckDir: epiNEM.Rcheck

Warnings: 0

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### Running command:
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###   /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_1.10.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.10-bioc/meat/epiNEM.Rcheck’
* using R version 3.6.3 (2020-02-29)
* using platform: x86_64-apple-darwin15.6.0 (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 ‘1.10.0’
* 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 ‘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’
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 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 data for ASCII and uncompressed saves ... OK
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                 user system elapsed
epiScreen      16.320  0.063  16.585
plot.epiScreen 16.031  0.049  16.232
SimEpiNEM      10.820  0.048  11.007
plot.epiSim    10.795  0.038  10.974
* 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-3.10-bioc/meat/epiNEM.Rcheck/00check.log’
for details.

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL epiNEM
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/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)

R version 3.6.3 (2020-02-29) -- "Holding the Windsock"
Copyright (C) 2020 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin15.6.0 (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 -- Wed Apr 15 02:10:09 2020 
*********************************************** 
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 
  4.394   0.211   4.632 

name	user	system	elapsed
AddLogicGates	0.001	0.001	0.002
CreateRandomGraph	0.001	0.000	0.000
CreateTopology	0.087	0.006	0.094
ExtendTopology	0.082	0.009	0.094
GenerateData	0.082	0.009	0.092
HeatmapOP	0.173	0.016	0.189
MLL	0.001	0.000	0.001
SimEpiNEM	10.820	0.048	11.007
createExtendedAdjacency	0.115	0.004	0.121
epiAnno	0.435	0.002	0.441
epiNEM	1.448	0.006	1.467
epiScreen	16.320	0.063	16.585
plot.epiNEM	1.422	0.003	1.438
plot.epiScreen	16.031	0.049	16.232
plot.epiSim	10.795	0.038	10.974
sameith_GO	0.001	0.001	0.001
sameith_string	0.001	0.001	0.002
samscreen	0.001	0.001	0.002
sim	0.002	0.001	0.002
wageningen_GO	0.001	0.000	0.002
wageningen_string	0.002	0.000	0.002
wagscreen	0.001	0.001	0.003