Package: epiNEM

Version: 1.7.0

Command: /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:epiNEM.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings epiNEM_1.7.0.tar.gz

StartedAt: 2019-04-09 00:20:51 -0400 (Tue, 09 Apr 2019)

EndedAt: 2019-04-09 00:22:40 -0400 (Tue, 09 Apr 2019)

EllapsedTime: 109.5 seconds

RetCode: 0

Status:  OK

CheckDir: epiNEM.Rcheck

Warnings: 0

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:epiNEM.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings epiNEM_1.7.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.9-bioc/meat/epiNEM.Rcheck’
* using R Under development (unstable) (2019-03-18 r76245)
* using platform: x86_64-pc-linux-gnu (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 ‘1.7.0’
* 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 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                 user system elapsed
epiScreen      12.618  0.000  12.623
plot.epiScreen 12.187  0.000  12.196
plot.epiSim     9.815  0.000   9.815
SimEpiNEM       8.607  0.005   8.612
* 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
  ‘/home/biocbuild/bbs-3.9-bioc/meat/epiNEM.Rcheck/00check.log’
for details.

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD INSTALL epiNEM
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.9-bioc/R/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 Under development (unstable) (2019-03-18 r76245) -- "Unsuffered Consequences"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (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 -- Tue Apr  9 00:22:37 2019 
*********************************************** 
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 
  3.367   0.135   3.504 

name	user	system	elapsed
AddLogicGates	0.001	0.000	0.001
CreateRandomGraph	0.001	0.000	0.000
CreateTopology	0.083	0.000	0.097
ExtendTopology	0.063	0.016	0.078
GenerateData	0.078	0.000	0.079
HeatmapOP	0.168	0.020	0.188
MLL	0.000	0.001	0.001
SimEpiNEM	8.607	0.005	8.612
createExtendedAdjacency	0.066	0.000	0.075
epiAnno	0.285	0.000	0.285
epiNEM	0.884	0.000	0.884
epiScreen	12.618	0.000	12.623
plot.epiNEM	0.990	0.000	0.998
plot.epiScreen	12.187	0.000	12.196
plot.epiSim	9.815	0.000	9.815
sameith_GO	0.001	0.000	0.001
sameith_string	0.000	0.001	0.002
samscreen	0.000	0.001	0.002
sim	0.001	0.000	0.001
wageningen_GO	0.002	0.000	0.001
wageningen_string	0.002	0.000	0.002
wagscreen	0.000	0.001	0.001