BioC 3.5: CHECK report for epiNEM on veracruz2

Package: epiNEM

Version: 1.0.1

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings epiNEM_1.0.1.tar.gz

StartedAt: 2017-10-18 03:15:32 -0400 (Wed, 18 Oct 2017)

EndedAt: 2017-10-18 03:17:34 -0400 (Wed, 18 Oct 2017)

EllapsedTime: 121.4 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 --no-vignettes --timings epiNEM_1.0.1.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/epiNEM.Rcheck’
* using R version 3.4.2 (2017-09-28)
* 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 ‘1.0.1’
* 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 loading without being on the library search path ... 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’
SimEpiNEM : graph2adj: no visible global function definition for ‘adj’
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 adj 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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                 user system elapsed
plot.epiScreen 13.739  0.081  14.283
epiScreen      12.966  0.112  13.805
SimEpiNEM       7.971  0.070   8.390
plot.epiSim     7.330  0.036   7.732
* 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-3.5-bioc/meat/epiNEM.Rcheck/00check.log’
for details.

* installing *source* package ‘epiNEM’ ...
** R
** data
*** moving datasets to lazyload DB
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (epiNEM)

name	user	system	elapsed
AddLogicGates	0.001	0.000	0.001
CreateRandomGraph	0.001	0.000	0.000
CreateTopology	0.163	0.009	0.176
ExtendTopology	0.326	0.003	0.336
GenerateData	0.082	0.001	0.086
HeatmapOP	0.953	0.009	1.039
MLL	0.001	0.000	0.002
SimEpiNEM	7.971	0.070	8.390
createExtendedAdjacency	0.090	0.002	0.095
epiAnno	0.545	0.004	0.561
epiNEM	1.521	0.023	1.590
epiScreen	12.966	0.112	13.805
plot.epiNEM	1.847	0.009	1.932
plot.epiScreen	13.739	0.081	14.283
plot.epiSim	7.330	0.036	7.732
sameith_GO	0.001	0.001	0.001
sameith_string	0.001	0.000	0.002
samscreen	0.002	0.000	0.002
sim	0.002	0.000	0.002
wageningen_GO	0.002	0.001	0.002
wageningen_string	0.001	0.001	0.002
wagscreen	0.001	0.000	0.003