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This page was generated on 2024-06-11 14:39 -0400 (Tue, 11 Jun 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_644.4.0 (2024-04-24) -- "Puppy Cup" 4757
palomino3Windows Server 2022 Datacenterx644.4.0 (2024-04-24 ucrt) -- "Puppy Cup" 4491
lconwaymacOS 12.7.1 Montereyx86_644.4.0 (2024-04-24) -- "Puppy Cup" 4522
kjohnson3macOS 13.6.5 Venturaarm644.4.0 (2024-04-24) -- "Puppy Cup" 4468
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

Package 665/2300HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
epiNEM 1.28.0  (landing page)
Martin Pirkl
Snapshot Date: 2024-06-09 14:00 -0400 (Sun, 09 Jun 2024)
git_url: https://git.bioconductor.org/packages/epiNEM
git_branch: RELEASE_3_19
git_last_commit: d210c36
git_last_commit_date: 2024-04-30 10:56:41 -0400 (Tue, 30 Apr 2024)
nebbiolo1Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino3Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson3macOS 13.6.5 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published


CHECK results for epiNEM on nebbiolo1

To the developers/maintainers of the epiNEM package:
- 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 Troubleshooting Build Report for more information.
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results


Summary

Package: epiNEM
Version: 1.28.0
Command: /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:epiNEM.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings epiNEM_1.28.0.tar.gz
StartedAt: 2024-06-09 22:45:02 -0400 (Sun, 09 Jun 2024)
EndedAt: 2024-06-09 22:48:21 -0400 (Sun, 09 Jun 2024)
EllapsedTime: 199.3 seconds
RetCode: 0
Status:   OK  
CheckDir: epiNEM.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:epiNEM.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings epiNEM_1.28.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/epiNEM.Rcheck’
* using R version 4.4.0 (2024-04-24)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
    GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
* running under: Ubuntu 22.04.4 LTS
* using session charset: UTF-8
* checking for file ‘epiNEM/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘epiNEM’ version ‘1.28.0’
* 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 code 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’
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
epiScreen      9.181  0.143   9.325
plot.epiScreen 8.649  0.077   8.726
SimEpiNEM      5.934  0.184   6.119
plot.epiSim    5.921  0.027   5.948
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.19-bioc/meat/epiNEM.Rcheck/00check.log’
for details.


Installation output

epiNEM.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD INSTALL epiNEM
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.19-bioc/R/site-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 4.4.0 (2024-04-24) -- "Puppy Cup"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu

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 -- Sun Jun  9 22:47:26 2024 
*********************************************** 
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 
  5.758   0.291   6.040 

Example timings

epiNEM.Rcheck/epiNEM-Ex.timings

nameusersystemelapsed
AddLogicGates0.0000.0000.001
CreateExtendedAdjacency0.1210.0000.122
CreateRandomGraph0.0010.0000.000
CreateTopology0.0440.0000.044
ExtendTopology0.3450.0000.345
GenerateData0.0430.0000.042
HeatmapOP0.1020.0000.102
Mll0.0010.0000.001
SimEpiNEM5.9340.1846.119
epiAnno0.2220.0030.225
epiNEM0.8680.0000.868
epiScreen9.1810.1439.325
perm.rank.test0.2870.0080.295
plot.epiNEM0.7190.0000.720
plot.epiScreen8.6490.0778.726
plot.epiSim5.9210.0275.948
rank.enrichment0.3380.0090.346
sameith_GO0.0010.0000.001
sameith_string0.0000.0000.001
samscreen0.0010.0000.001
sim0.0010.0000.001
wageningen_GO0.0010.0000.000
wageningen_string0.0010.0000.000
wagscreen0.0010.0000.001