Back to Multiple platform build/check report for BioC 3.18: simplified long |
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This page was generated on 2024-04-17 11:35:56 -0400 (Wed, 17 Apr 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.3.3 (2024-02-29) -- "Angel Food Cake" | 4676 |
palomino4 | Windows Server 2022 Datacenter | x64 | 4.3.3 (2024-02-29 ucrt) -- "Angel Food Cake" | 4414 |
merida1 | macOS 12.7.1 Monterey | x86_64 | 4.3.3 (2024-02-29) -- "Angel Food Cake" | 4437 |
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 655/2266 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
epiNEM 1.26.0 (landing page) Martin Pirkl
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | ![]() | ||||||||
palomino4 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | ![]() | ||||||||
merida1 | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | ![]() | ||||||||
kjohnson1 | macOS 13.6.1 Ventura / arm64 | see weekly results here | ||||||||||||
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. |
Package: epiNEM |
Version: 1.26.0 |
Command: /home/biocbuild/bbs-3.18-bioc/R/bin/R CMD check --install=check:epiNEM.install-out.txt --library=/home/biocbuild/bbs-3.18-bioc/R/site-library --timings epiNEM_1.26.0.tar.gz |
StartedAt: 2024-04-15 22:31:56 -0400 (Mon, 15 Apr 2024) |
EndedAt: 2024-04-15 22:35:52 -0400 (Mon, 15 Apr 2024) |
EllapsedTime: 236.4 seconds |
RetCode: 0 |
Status: OK |
CheckDir: epiNEM.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.18-bioc/R/bin/R CMD check --install=check:epiNEM.install-out.txt --library=/home/biocbuild/bbs-3.18-bioc/R/site-library --timings epiNEM_1.26.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.18-bioc/meat/epiNEM.Rcheck’ * using R version 4.3.3 (2024-02-29) * using platform: x86_64-pc-linux-gnu (64-bit) * 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 ‘1.26.0’ * 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 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 plot.epiScreen 8.981 0.103 9.085 epiScreen 8.796 0.216 9.011 SimEpiNEM 6.509 0.399 6.909 plot.epiSim 6.060 0.052 6.112 * 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 ... ‘epiNEM.Rmd’ using ‘UTF-8’... OK OK * checking re-building of vignette outputs ... OK * checking PDF version of manual ... OK * DONE Status: 2 NOTEs See ‘/home/biocbuild/bbs-3.18-bioc/meat/epiNEM.Rcheck/00check.log’ for details.
epiNEM.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.18-bioc/R/bin/R CMD INSTALL epiNEM ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.18-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)
epiNEM.Rcheck/tests/runTests.Rout
R version 4.3.3 (2024-02-29) -- "Angel Food Cake" Copyright (C) 2024 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 -- Mon Apr 15 22:34:18 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 5.605 0.236 5.827
epiNEM.Rcheck/epiNEM-Ex.timings
name | user | system | elapsed | |
AddLogicGates | 0 | 0 | 0 | |
CreateExtendedAdjacency | 0.055 | 0.000 | 0.056 | |
CreateRandomGraph | 0 | 0 | 0 | |
CreateTopology | 0.044 | 0.000 | 0.045 | |
ExtendTopology | 0.055 | 0.000 | 0.056 | |
GenerateData | 0.045 | 0.000 | 0.046 | |
HeatmapOP | 0.103 | 0.000 | 0.103 | |
Mll | 0.000 | 0.000 | 0.001 | |
SimEpiNEM | 6.509 | 0.399 | 6.909 | |
epiAnno | 0.223 | 0.016 | 0.243 | |
epiNEM | 1.185 | 0.021 | 1.205 | |
epiScreen | 8.796 | 0.216 | 9.011 | |
perm.rank.test | 0.283 | 0.011 | 0.295 | |
plot.epiNEM | 0.768 | 0.000 | 0.769 | |
plot.epiScreen | 8.981 | 0.103 | 9.085 | |
plot.epiSim | 6.060 | 0.052 | 6.112 | |
rank.enrichment | 0.326 | 0.008 | 0.335 | |
sameith_GO | 0.001 | 0.000 | 0.000 | |
sameith_string | 0.001 | 0.001 | 0.000 | |
samscreen | 0 | 0 | 0 | |
sim | 0 | 0 | 0 | |
wageningen_GO | 0 | 0 | 0 | |
wageningen_string | 0.000 | 0.000 | 0.001 | |
wagscreen | 0.000 | 0.000 | 0.001 | |