Ramon Diaz-Uriarte
| Snapshot Date: 2025-12-01 13:40 -0500 (Mon, 01 Dec 2025) |
| git_url: https://git.bioconductor.org/packages/OncoSimulR |
| git_branch: devel |
| git_last_commit: d241471 |
| git_last_commit_date: 2025-10-29 10:20:29 -0500 (Wed, 29 Oct 2025) |
| Back to Multiple platform build/check report for BioC 3.23: simplified long |
|
This page was generated on 2025-12-02 11:35 -0500 (Tue, 02 Dec 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | R Under development (unstable) (2025-10-20 r88955) -- "Unsuffered Consequences" | 4866 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | R Under development (unstable) (2025-11-04 r88984) -- "Unsuffered Consequences" | 4572 |
| 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 1494/2328 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| OncoSimulR 4.13.0 (landing page) Ramon Diaz-Uriarte
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
| kjohnson3 | macOS 13.7.7 Ventura / arm64 | ... NOT SUPPORTED ... | ||||||||||||
|
To the developers/maintainers of the OncoSimulR package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/OncoSimulR.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: OncoSimulR |
| Version: 4.13.0 |
| Command: /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD check --install=check:OncoSimulR.install-out.txt --library=/home/biocbuild/bbs-3.23-bioc/R/site-library --timings OncoSimulR_4.13.0.tar.gz |
| StartedAt: 2025-12-02 02:25:08 -0500 (Tue, 02 Dec 2025) |
| EndedAt: 2025-12-02 02:31:31 -0500 (Tue, 02 Dec 2025) |
| EllapsedTime: 383.7 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: OncoSimulR.Rcheck |
| Warnings: 0 |
##############################################################################
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###
### Running command:
###
### /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD check --install=check:OncoSimulR.install-out.txt --library=/home/biocbuild/bbs-3.23-bioc/R/site-library --timings OncoSimulR_4.13.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.23-bioc/meat/OncoSimulR.Rcheck’
* using R Under development (unstable) (2025-10-20 r88955)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.3 LTS
* using session charset: UTF-8
* checking for file ‘OncoSimulR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘OncoSimulR’ version ‘4.13.0’
* 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 ... NOTE
Found the following hidden files and directories:
.BBSoptions
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘OncoSimulR’ can be installed ... OK
* used C compiler: ‘gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’
* used C++ compiler: ‘g++ (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’
* checking installed package size ... INFO
installed size is 19.6Mb
sub-directories of 1Mb or more:
libs 18.2Mb
* 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 whether startup messages can be suppressed ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* 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 line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking use of PKG_*FLAGS in Makefiles ... OK
* checking include directives in Makefiles ... OK
* checking compiled code ... INFO
Note: information on .o files is not available
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.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: 1 NOTE
See
‘/home/biocbuild/bbs-3.23-bioc/meat/OncoSimulR.Rcheck/00check.log’
for details.
OncoSimulR.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD INSTALL OncoSimulR ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.23-bioc/R/site-library’ * installing *source* package ‘OncoSimulR’ ... ** this is package ‘OncoSimulR’ version ‘4.13.0’ ** using staged installation ** libs using C compiler: ‘gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’ using C++ compiler: ‘g++ (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’ gcc -std=gnu2x -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c FitnessLandscape/gamma.c -o FitnessLandscape/gamma.o gcc -std=gnu2x -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c FitnessLandscape/landscape.c -o FitnessLandscape/landscape.o gcc -std=gnu2x -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c FitnessLandscape/random.c -o FitnessLandscape/random.o gcc -std=gnu2x -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c FitnessLandscape/sort.c -o FitnessLandscape/sort.o gcc -std=gnu2x -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c FitnessLandscape/chain.c -o FitnessLandscape/chain.o gcc -std=gnu2x -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c FitnessLandscape/input.c -o FitnessLandscape/input.o gcc -std=gnu2x -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c FitnessLandscape/genotypes.c -o FitnessLandscape/genotypes.o gcc -std=gnu2x -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c FitnessLandscape/ordered_pairs.c -o FitnessLandscape/ordered_pairs.o gcc -std=gnu2x -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c FitnessLandscape/calculus.c -o FitnessLandscape/calculus.o gcc -std=gnu2x -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c FitnessLandscape/vector.c -o FitnessLandscape/vector.o gcc -std=gnu2x -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c FitnessLandscape/generalized_chain.c -o FitnessLandscape/generalized_chain.o gcc -std=gnu2x -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c FitnessLandscape/LinearAlgebra.c -o FitnessLandscape/LinearAlgebra.o gcc -std=gnu2x -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c FitnessLandscape/summary_statistics.c -o FitnessLandscape/summary_statistics.o gcc -std=gnu2x -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c FitnessLandscape/epistasis_type.c -o FitnessLandscape/epistasis_type.o gcc -std=gnu2x -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c FitnessLandscape/decomposition.c -o FitnessLandscape/decomposition.o gcc -std=gnu2x -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c FitnessLandscape/models.c -o FitnessLandscape/models.o gcc -std=gnu2x -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c FitnessLandscape/verbose.c -o FitnessLandscape/verbose.o ar -r liblandscape.a FitnessLandscape/gamma.o FitnessLandscape/landscape.o FitnessLandscape/random.o FitnessLandscape/sort.o FitnessLandscape/chain.o FitnessLandscape/input.o FitnessLandscape/genotypes.o FitnessLandscape/ordered_pairs.o FitnessLandscape/calculus.o FitnessLandscape/vector.o FitnessLandscape/generalized_chain.o FitnessLandscape/LinearAlgebra.o FitnessLandscape/summary_statistics.o FitnessLandscape/epistasis_type.o FitnessLandscape/decomposition.o FitnessLandscape/models.o FitnessLandscape/verbose.o ; ar: creating liblandscape.a ranlib liblandscape.a; gcc -std=gnu2x -O -Wall -o fl_statistics -I/FitnessLandscape/. -L. FitnessLandscape/main_fl_statistics.c -llandscape -lm; gcc -std=gnu2x -O -Wall -o fl_generate -I/FitnessLandscape/. -L. FitnessLandscape/main_fl_generate.c -llandscape -lm; gcc -std=gnu2x -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c OncoSimulR_init.c -o OncoSimulR_init.o g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c RcppExports.cpp -o RcppExports.o g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c unity_osimul.cpp -o unity_osimul.o g++ -std=gnu++17 -shared -L/home/biocbuild/bbs-3.23-bioc/R/lib -L/usr/local/lib -o OncoSimulR.so OncoSimulR_init.o RcppExports.o unity_osimul.o -L/home/biocbuild/bbs-3.23-bioc/R/lib -lR installing via 'install.libs.R' to /home/biocbuild/bbs-3.23-bioc/R/site-library/00LOCK-OncoSimulR/00new/OncoSimulR [1] "" Installing fl_statistics fl_generate to /home/biocbuild/bbs-3.23-bioc/R/site-library/00LOCK-OncoSimulR/00new/OncoSimulR/exec Installing library OncoSimulR.so to /home/biocbuild/bbs-3.23-bioc/R/site-library/00LOCK-OncoSimulR/00new/OncoSimulR/libs ** R ** data ** 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 ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (OncoSimulR)
OncoSimulR.Rcheck/tests/testthat.Rout
R Under development (unstable) (2025-10-20 r88955) -- "Unsuffered Consequences"
Copyright (C) 2025 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.
> library(testthat)
> library(OncoSimulR)
This is package OncoSimulR. If you are running it on an aarch64 (arm64) platform with a MacOS note that the package fails some tests in that platform + OS that I have no way of debugging. Please read file README_tests_kjohnson3_aarch64-apple-darwin20.txt in the tests directory. As of 2024-10-09, this platform is unsupported until we can properly debug it.
>
> test_check("OncoSimulR")
Starting FDF-letter-fitness-order Tue Dec 2 02:26:27 2025
exprtk parser error:
Error[00] Position: 00 Type: [ Syntax Error] Msg: ERR202 - Undefined symbol: 'n_2_3' Expression: n_2_3
exprtk parser error:
Error[00] Position: 00 Type: [ Syntax Error] Msg: ERR202 - Undefined symbol: 'f_2_3' Expression: f_2_3
Ending FDF-small-fitness-specs Tue Dec 2 02:26:27 2025
Took 0.43
Starting LOD_POM at Tue Dec 2 02:26:27 2025
Ending LOD_POM at Tue Dec 2 02:26:39 2025
Took 12.19
Starting test.Z-all-fitness at Tue Dec 2 02:26:39 2025
Ending test.Z-all-fitness at Tue Dec 2 02:26:39 2025
Took 0.1
Starting test.Z-driver-counts at Tue Dec 2 02:26:39 2025
Ending test.Z-driver-counts at Tue Dec 2 02:26:39 2025
Took 0.09
Starting test.Z-fixation at Tue Dec 2 02:26:39 2025
Ending test.Z-fixation at Tue Dec 2 02:26:40 2025
Took 0.22
Starting test.Z-magellan at Tue Dec 2 02:26:40 2025
Ended test.Z-magellan at Tue Dec 2 02:26:41 2025
Starting test.Z-mutator at Tue Dec 2 02:26:41 2025
Ending test.Z-mutator at Tue Dec 2 02:26:41 2025
Took 0.34
Starting test.Z-mutatorFDF at Tue Dec 2 02:26:41 2025
Ending test.Z-mutatorFDF at Tue Dec 2 02:26:42 2025
Took 0.1
Starting test.Z-oncoSimulIndiv at Tue Dec 2 02:26:42 2025
Ending test.Z-oncoSimulIndiv at Tue Dec 2 02:26:42 2025
Took 0.36
Starting test.Z-oncoSimulIndivConstant at Tue Dec 2 02:26:42 2025
Ending test.Z-oncoSimulIndivConstant at Tue Dec 2 02:26:44 2025
Took 2.21
Starting test.Z-oncoSimulIndivDeath at Tue Dec 2 02:26:44 2025
Ending test.Z-oncoSimulIndivDeath at Tue Dec 2 02:26:45 2025
Took 0.75
Starting test.Z-oncoSimulIndivFDF at Tue Dec 2 02:26:45 2025
Hitted wall time. Exiting.
Hitting wall time is regarded as an error.
Ending test.Z-oncoSimulIndivFDF at Tue Dec 2 02:26:46 2025
Took 0.6
Starting test.Z-rfitness-landscape at Tue Dec 2 02:26:46 2025
Ending test.Z-rfitness-landscape at Tue Dec 2 02:26:46 2025
Took 0.28
Starting Z-sample-only-last tests Tue Dec 2 02:26:46 2025
Ending Z-sample-only-last tests Tue Dec 2 02:26:46 2025
Took 0
Starting Z-total-present-drivers tests Tue Dec 2 02:26:46 2025
Ending Z-total-present-drivers tests Tue Dec 2 02:26:47 2025
Took 0.74
Dummy empty test Tue Dec 2 02:26:47 2025
Starting accessible_genotypes at Tue Dec 2 02:26:47 2025
Ending accessible_genotypes at Tue Dec 2 02:26:53 2025
Took 6.46
Starting all fitness at Tue Dec 2 02:26:53 2025
Ending all-fitness at Tue Dec 2 02:26:57 2025
Took 4.15
Starting test.allFitnessEffectsFDF at Tue Dec 2 02:26:57 2025
Ending test.allFitnessEffectsFDF at Tue Dec 2 02:26:57 2025
Took 0.12
Starting test.allFitnessEffectsDeath at Tue Dec 2 02:26:57 2025
Ending test.allFitnessEffectsDeath at Tue Dec 2 02:26:58 2025
Took 0.35
Starting test.allFitnessEffectsFDF at Tue Dec 2 02:26:58 2025
Ending test.allFitnessEffectsFDF at Tue Dec 2 02:26:58 2025
Took 0.36
Starting driverCounts at Tue Dec 2 02:26:58 2025
Ending driverCounts at Tue Dec 2 02:27:05 2025
Took 6.7
Starting epist-order-modules at Tue Dec 2 02:27:05 2025
Ending epist-order-modules at Tue Dec 2 02:27:05 2025
Took 0.05
Starting test.evaluatingGenotypesDeath at Tue Dec 2 02:27:05 2025
Ending test.evaluatingGenotypesDeath at Tue Dec 2 02:27:05 2025
Took 0.18
Starting test.evaluatingGenotypesFDF at Tue Dec 2 02:27:05 2025
Ending test.evaluatingGenotypesFDF at Tue Dec 2 02:27:05 2025
Took 0.17
Starting exercise-plotting-code at Tue Dec 2 02:27:05 2025
Ending exercise-plotting-code at Tue Dec 2 02:27:08 2025
Took 2.4
Starting exercise-rfitness at Tue Dec 2 02:27:08 2025
Ending exercise-rfitness at Tue Dec 2 02:27:16 2025
Took 8.27
Starting to_Magella at Tue Dec 2 02:27:16 2025
Ending to_Magella at Tue Dec 2 02:27:16 2025
Took 0.03
Starting fitness preds at Tue Dec 2 02:27:16 2025
Observed vs expected, case III
done tries 1
Ending fitness preds long at Tue Dec 2 02:27:20 2025
Took 4.58
Starting fixation at Tue Dec 2 02:27:20 2025
Ending fixation at Tue Dec 2 02:27:32 2025
Took 11.16
Starting test.flfast-additional.R test at Tue Dec 2 02:27:32 2025
Ending test.flfast-additional.R test at Tue Dec 2 02:27:33 2025
Took 1.44
Starting test.flfast-mutator.R test at Tue Dec 2 02:27:33 2025
Finished test.flfast-mutator.R test at Tue Dec 2 02:27:34 2025
Took 1.01
Starting genotFitness at Tue Dec 2 02:27:34 2025
Ending genotFitness at Tue Dec 2 02:27:34 2025
Took 0.2
Starting genot_fitness_to_epistasis at Tue Dec 2 02:27:34 2025
Ending genot_fitness_to_epistasis at Tue Dec 2 02:27:34 2025
Took 0.04
Starting init-mutant tests Tue Dec 2 02:27:34 2025
exprtk parser error:
Error[00] Position: 18 Type: [ Syntax Error] Msg: ERR202 - Undefined symbol: 'f_2' Expression: 1.1 + 0.7*((f_1 + f_2) > 0.3)
Ending init-mutant tests Tue Dec 2 02:27:40 2025
Took 5.47
Starting interventions tests Tue Dec 2 02:27:40 2025
[1] "Checking intervention: intOverA"
[1] "Checking intervention: intOverA"
[1] "Checking intervention: intOverA"
[1] "Checking intervention: intOverA"
[1] "Checking intervention: intOverMultiplicatesA"
In intervention:intOverMultiplicatesA with WhatHappens: n_1 = n_1 * 2. You cannot intervene to generate more population.[1] "Checking intervention: intOverA"
[1] "Checking intervention: intOverA"
[1] "Checking intervention: intOverTotPop"
[1] 0.78 0.78 0.78
[1] "Checking intervention: intOverTotPop"
[1] "Checking intervention: intOverA"
[1] "Checking intervention: intOverB"
[1] "Checking intervention: intOverC"
[1] "Checking intervention: intOverD"
Init Mutant with birth == 1.0
Init Mutant with birth == 1.0
[1] "Checking intervention: intOverA"
[1] "Checking intervention: intOverB"
[1] "Checking intervention: intOverC"
[1] "Checking intervention: intOverD"
Init Mutant with birth == 1.0
Init Mutant with birth == 1.0
[1] "Checking user variable: user_var_1"
[1] "Checking rule: rule_1"
[1] "Checking rule: rule_2"
[1] "Checking rule: rule_3"
[1] "Checking intervention: intOverTotPop"
[1] "Checking intervention: intOverTotPop2"
[1] "Checking intervention: intOverTotPop3"
[1] "Checking user variable: user_var_1"
[1] "Checking rule: rule_1"
[1] "Checking rule: rule_2"
[1] "Checking rule: rule_3"
[1] "Checking intervention: intOverTotPop"
Ending interventions tests Tue Dec 2 02:27:44 2025
Took 3.85
Starting test.magellan at Tue Dec 2 02:27:44 2025
Ending test.magellan at Tue Dec 2 02:27:44 2025
Took 0.14
Starting test.modules-root-no-root at Tue Dec 2 02:27:44 2025
Ending test.modules-root-no-root at Tue Dec 2 02:27:44 2025
Took 0.09
Starting at mutPropGrowth Tue Dec 2 02:27:44 2025
Ended test.mutPropGrowth: Tue Dec 2 02:27:49 2025
Took 5.4
Starting test.mutator-oncoSimulSample.R test at Tue Dec 2 02:27:49 2025
Finished test.mutator-oncoSimulSample.R test at Tue Dec 2 02:27:57 2025
Took 7.58 seconds
Starting test.mutator.R test at Tue Dec 2 02:27:57 2025[1] 1.92716e-07
[1] 1.735064e-11
Finished test.mutator.R test at Tue Dec 2 02:28:08 2025
Took 10.99
Starting test.mutatorFDF.R test at Tue Dec 2 02:28:08 2025
Starting oncoSimulIndiv-miscell tests Tue Dec 2 02:28:08 2025
Ending oncoSimulIndiv-miscell tests Tue Dec 2 02:28:16 2025
Took 7.9
Starting oncoSimulSample-failures tests Tue Dec 2 02:28:16 2025
Ending oncoSimulSample-failures tests Tue Dec 2 02:28:20 2025
Took 3.24
Starting oncoSimulSample-limits tests Tue Dec 2 02:28:20 2025
Ending oncoSimulSample-limits tests Tue Dec 2 02:28:20 2025
Took 0.06
Starting per-gene-mutation rates at Tue Dec 2 02:28:20 2025
Ending per-gene-mutation rates at Tue Dec 2 02:28:40 2025
Took 20.03
Starting plotFitnessLandscape at Tue Dec 2 02:28:40 2025
Ending plotFitnessLandscape at Tue Dec 2 02:28:43 2025
Took 3.43
Starting poset-transformations tests Tue Dec 2 02:28:43 2025
Ending poset-transformations tests Tue Dec 2 02:28:53 2025
Took 9.52
Starting sample-prob Tue Dec 2 02:28:53 2025
[1] 3.306107e-22
[1] 5.138094e-15
[1] 6.436269e-09
[1] -4.440892e-16
[1] 2.857435e-14
[1] 3.701849e-13
[1] 2.6022e-13
[1] 8.636256e-14
[1] 2.419731e-12
[1] 1.221245e-15
[1] 8.808951e-10
[1] 1.711886e-11
Ending sample-prob tests Tue Dec 2 02:28:57 2025
Took 4.49
Starting samplePop tests Tue Dec 2 02:28:57 2025
Ending samplePop tests Tue Dec 2 02:29:01 2025
Took 4.31
Starting simuls-runs-examples tests Tue Dec 2 02:29:01 2025
Ending simuls-runs-examples tests Tue Dec 2 02:29:09 2025
Took 7.78
Starting user variable tests Tue Dec 2 02:29:09 2025
[1] "Checking user variable: user_var_1"
[1] "Checking rule: rule_1"
Ending user variable tests Tue Dec 2 02:29:09 2025
Took 0.1
Starting warning-mutPropGrowth tests Tue Dec 2 02:29:09 2025
Ending warning-mutPropGrowth tests Tue Dec 2 02:29:10 2025
Took 0.25
Starting wide2long tests Tue Dec 2 02:29:10 2025
Ending wide2long tests Tue Dec 2 02:29:10 2025
Took 0.13
[ FAIL 0 | WARN 19 | SKIP 6 | PASS 8406 ]
══ Skipped tests (6) ═══════════════════════════════════════════════════════════
• empty test (6): 'test.FDF-letter-fitness-order.R:376:1', ,
'test.ZZ-dummy-skip-warn-test.R:8:1', 'test.ZZ-dummy-skip-warn-test.R:12:1',
'test.fixation.R:4:1', 'test.init-mutant.R:1099:1'
[ FAIL 0 | WARN 19 | SKIP 6 | PASS 8406 ]
>
> proc.time()
user system elapsed
182.213 29.373 167.502
OncoSimulR.Rcheck/OncoSimulR-Ex.timings
| name | user | system | elapsed | |
| OncoSimulWide2Long | 0.156 | 0.009 | 0.170 | |
| POM | 0.577 | 0.043 | 0.451 | |
| allFitnessEffects | 2.084 | 0.063 | 2.149 | |
| benchmarks | 0.013 | 0.004 | 0.018 | |
| createInterventions | 0.283 | 0.000 | 0.283 | |
| createUserVars | 0.425 | 0.001 | 0.426 | |
| evalAllGenotypes | 0.179 | 0.005 | 0.184 | |
| example-missing-drivers | 0.207 | 0.010 | 0.217 | |
| examplePosets | 0.255 | 0.002 | 0.257 | |
| examplesFitnessEffects | 0.078 | 0.001 | 0.079 | |
| freq-dep-simul-examples | 0.008 | 0.001 | 0.010 | |
| mcfLs | 0 | 0 | 0 | |
| oncoSimulIndiv | 0.981 | 0.176 | 1.088 | |
| plot.fitnessEffects | 0.258 | 0.021 | 0.279 | |
| plot.oncosimul | 0.405 | 0.008 | 0.415 | |
| plotClonePhylog | 1.238 | 0.042 | 1.282 | |
| plotFitnessLandscape | 1.425 | 0.134 | 1.559 | |
| plotPoset | 0.087 | 0.003 | 0.090 | |
| poset | 0.096 | 0.004 | 0.100 | |
| rfitness | 0.738 | 0.020 | 0.759 | |
| samplePop | 0.045 | 0.068 | 0.073 | |
| simOGraph | 0.049 | 0.020 | 0.070 | |
| to_Magellan | 0.170 | 0.026 | 0.197 | |
| vignette_pre_computed | 0.005 | 0.001 | 0.008 | |