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This page was generated on 2025-09-25 11:38 -0400 (Thu, 25 Sep 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 (2025-06-13) -- "Great Square Root" 4827
merida1macOS 12.7.5 Montereyx86_644.5.1 RC (2025-06-05 r88288) -- "Great Square Root" 4608
kjohnson1macOS 13.6.6 Venturaarm644.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" 4549
kunpeng2Linux (openEuler 24.03 LTS)aarch64R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" 4581
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 1490/2341HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
OncoSimulR 4.10.0  (landing page)
Ramon Diaz-Uriarte
Snapshot Date: 2025-09-22 13:40 -0400 (Mon, 22 Sep 2025)
git_url: https://git.bioconductor.org/packages/OncoSimulR
git_branch: RELEASE_3_21
git_last_commit: 165d213
git_last_commit_date: 2025-04-15 10:32:39 -0400 (Tue, 15 Apr 2025)
nebbiolo1Linux (Ubuntu 24.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 12.7.5 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.6.6 Ventura / arm64... NOT SUPPORTED ...
kunpeng2Linux (openEuler 24.03 LTS) / aarch64  OK    TIMEOUT  skipped

CHECK results for OncoSimulR on nebbiolo1

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.

raw results


Summary

Package: OncoSimulR
Version: 4.10.0
Command: /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:OncoSimulR.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings OncoSimulR_4.10.0.tar.gz
StartedAt: 2025-09-25 02:13:40 -0400 (Thu, 25 Sep 2025)
EndedAt: 2025-09-25 02:20:39 -0400 (Thu, 25 Sep 2025)
EllapsedTime: 418.8 seconds
RetCode: 0
Status:   OK  
CheckDir: OncoSimulR.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:OncoSimulR.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings OncoSimulR_4.10.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/OncoSimulR.Rcheck’
* using R version 4.5.1 (2025-06-13)
* 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 ‘4.10.0’
* 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 ... NOTE
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: 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.21-bioc/meat/OncoSimulR.Rcheck/00check.log’
for details.

Installation output

OncoSimulR.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD INSTALL OncoSimulR
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.21-bioc/R/site-library’
* installing *source* package ‘OncoSimulR’ ...
** this is package ‘OncoSimulR’ version ‘4.10.0’
** 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-3.21-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.21-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-3.21-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.21-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-3.21-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.21-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-3.21-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.21-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-3.21-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.21-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-3.21-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.21-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-3.21-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.21-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-3.21-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.21-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-3.21-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.21-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-3.21-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.21-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-3.21-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.21-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-3.21-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.21-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-3.21-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.21-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-3.21-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.21-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-3.21-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.21-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-3.21-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.21-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-3.21-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.21-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-3.21-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.21-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-3.21-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.21-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-3.21-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.21-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-3.21-bioc/R/lib -L/usr/local/lib -o OncoSimulR.so OncoSimulR_init.o RcppExports.o unity_osimul.o -L/home/biocbuild/bbs-3.21-bioc/R/lib -lR
installing via 'install.libs.R' to /home/biocbuild/bbs-3.21-bioc/R/site-library/00LOCK-OncoSimulR/00new/OncoSimulR
[1] ""
Installing fl_statistics fl_generate to /home/biocbuild/bbs-3.21-bioc/R/site-library/00LOCK-OncoSimulR/00new/OncoSimulR/exec
Installing library OncoSimulR.so to /home/biocbuild/bbs-3.21-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)

Tests output

OncoSimulR.Rcheck/tests/testthat.Rout


R version 4.5.1 (2025-06-13) -- "Great Square Root"
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 Thu Sep 25 02:14:57 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 Thu Sep 25 02:14:58 2025 
  Took  0.43 


 Starting LOD_POM at Thu Sep 25 02:14:58 2025 

 Ending LOD_POM at Thu Sep 25 02:15:07 2025 
  Took  9.3 


 Starting test.Z-all-fitness at Thu Sep 25 02:15:07 2025 

 Ending test.Z-all-fitness at Thu Sep 25 02:15:07 2025 
  Took  0.09 


 Starting test.Z-driver-counts at Thu Sep 25 02:15:07 2025 

 Ending test.Z-driver-counts at Thu Sep 25 02:15:07 2025 
  Took  0.11 


 Starting test.Z-fixation at Thu Sep 25 02:15:07 2025 

 Ending test.Z-fixation at Thu Sep 25 02:15:07 2025 
  Took  0.21 


 Starting test.Z-magellan at Thu Sep 25 02:15:07 2025 

 Ended test.Z-magellan at Thu Sep 25 02:15:09 2025 

 Starting test.Z-mutator at Thu Sep 25 02:15:09 2025 

 Ending test.Z-mutator at Thu Sep 25 02:15:09 2025 
  Took  0.31 


 Starting test.Z-mutatorFDF at Thu Sep 25 02:15:09 2025 

 Ending test.Z-mutatorFDF at Thu Sep 25 02:15:09 2025 
  Took  0.09 


 Starting test.Z-oncoSimulIndiv at Thu Sep 25 02:15:09 2025 

 Ending test.Z-oncoSimulIndiv at Thu Sep 25 02:15:10 2025 
  Took  0.36 


 Starting test.Z-oncoSimulIndivConstant at Thu Sep 25 02:15:10 2025 

 Ending test.Z-oncoSimulIndivConstant at Thu Sep 25 02:15:12 2025 
  Took  2.18 


 Starting test.Z-oncoSimulIndivDeath at Thu Sep 25 02:15:12 2025 


 Ending test.Z-oncoSimulIndivDeath at Thu Sep 25 02:15:12 2025 
  Took  0.72 


 Starting test.Z-oncoSimulIndivFDF at Thu Sep 25 02:15:13 2025 

 Hitted wall time. Exiting.
 Hitting wall time is regarded as an error. 

 Ending test.Z-oncoSimulIndivFDF at Thu Sep 25 02:15:14 2025 
  Took  1.01 


 Starting test.Z-rfitness-landscape at Thu Sep 25 02:15:14 2025 

 Ending test.Z-rfitness-landscape at Thu Sep 25 02:15:14 2025 
  Took  0.27 


 Starting Z-sample-only-last tests Thu Sep 25 02:15:14 2025 

 Ending Z-sample-only-last tests Thu Sep 25 02:15:14 2025 
  Took  0 


 Starting Z-total-present-drivers tests Thu Sep 25 02:15:14 2025 

 Ending Z-total-present-drivers tests Thu Sep 25 02:15:15 2025 
  Took  0.75 


 Dummy empty test  Thu Sep 25 02:15:15 2025 

 Starting accessible_genotypes at Thu Sep 25 02:15:15 2025 

 Ending accessible_genotypes at Thu Sep 25 02:15:21 2025 
  Took  6.34 


 Starting all fitness at Thu Sep 25 02:15:21 2025
 Ending all-fitness at Thu Sep 25 02:15:25 2025 
  Took  4.24 


 Starting test.allFitnessEffectsFDF at Thu Sep 25 02:15:25 2025 

 Ending test.allFitnessEffectsFDF at Thu Sep 25 02:15:25 2025 
  Took  0.12 


 Starting test.allFitnessEffectsDeath at Thu Sep 25 02:15:25 2025 

 Ending test.allFitnessEffectsDeath at Thu Sep 25 02:15:26 2025 
  Took  0.33 


 Starting test.allFitnessEffectsFDF at Thu Sep 25 02:15:26 2025 

 Ending test.allFitnessEffectsFDF at Thu Sep 25 02:15:26 2025 
  Took  0.33 


 Starting driverCounts at Thu Sep 25 02:15:26 2025
 Ending driverCounts at Thu Sep 25 02:15:33 2025 
  Took  6.64 


 Starting epist-order-modules at Thu Sep 25 02:15:33 2025
 Ending epist-order-modules at Thu Sep 25 02:15:33 2025 
  Took  0.05 


 Starting test.evaluatingGenotypesDeath at Thu Sep 25 02:15:33 2025 

 Ending test.evaluatingGenotypesDeath at Thu Sep 25 02:15:33 2025 
  Took  0.16 


 Starting test.evaluatingGenotypesFDF at Thu Sep 25 02:15:33 2025 

 Ending test.evaluatingGenotypesFDF at Thu Sep 25 02:15:33 2025 
  Took  0.18 


 Starting exercise-plotting-code at Thu Sep 25 02:15:33 2025
 Ending exercise-plotting-code at Thu Sep 25 02:15:36 2025 
  Took  2.5 


 Starting exercise-rfitness at Thu Sep 25 02:15:36 2025 

 Ending exercise-rfitness at Thu Sep 25 02:15:44 2025 
  Took  8.83 


 Starting to_Magella at Thu Sep 25 02:15:44 2025 

 Ending to_Magella at Thu Sep 25 02:15:44 2025 
  Took  0.05 


 Starting fitness preds at Thu Sep 25 02:15:44 2025 

 Observed vs expected, case III

 done tries 1 

 Ending fitness preds long at Thu Sep 25 02:15:50 2025 
  Took  5.3 


 Starting fixation  at Thu Sep 25 02:15:50 2025 

 Ending fixation  at Thu Sep 25 02:16:01 2025 
  Took  11.17 


 Starting test.flfast-additional.R test at Thu Sep 25 02:16:01 2025
 Ending test.flfast-additional.R test at Thu Sep 25 02:16:02 2025 
  Took  1.25 


 Starting test.flfast-mutator.R test at Thu Sep 25 02:16:02 2025
 Finished test.flfast-mutator.R test at Thu Sep 25 02:16:03 2025 
  Took  1.05 


 Starting genotFitness at Thu Sep 25 02:16:03 2025 

 Ending genotFitness at Thu Sep 25 02:16:03 2025 
  Took  0.18 


 Starting genot_fitness_to_epistasis at Thu Sep 25 02:16:03 2025 

 Ending genot_fitness_to_epistasis at Thu Sep 25 02:16:03 2025 
  Took  0.03 


 Starting init-mutant tests Thu Sep 25 02:16:03 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 Thu Sep 25 02:16:09 2025 
  Took  5.11 


 Starting interventions tests Thu Sep 25 02:16:09 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] 0.53 0.53 0.53
[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 Thu Sep 25 02:16:12 2025 
  Took  3.59 


 Starting test.magellan at Thu Sep 25 02:16:12 2025 

 Ending test.magellan at Thu Sep 25 02:16:12 2025 
  Took  0.13 


 Starting test.modules-root-no-root at Thu Sep 25 02:16:12 2025 

 Ending test.modules-root-no-root at Thu Sep 25 02:16:12 2025 
  Took  0.08 


 Starting at mutPropGrowth  Thu Sep 25 02:16:12 2025 

 Ended test.mutPropGrowth:  Thu Sep 25 02:16:18 2025 
  Took  5.49 


 Starting test.mutator-oncoSimulSample.R test at Thu Sep 25 02:16:18 2025 

 Finished test.mutator-oncoSimulSample.R test at Thu Sep 25 02:16:25 2025 
  Took  7.57 seconds 


 Starting test.mutator.R test at Thu Sep 25 02:16:25 2025[1] 6.001712e-07
[1] 1.366675e-10

 Finished test.mutator.R test at Thu Sep 25 02:16:36 2025 
  Took  10.54 


 Starting test.mutatorFDF.R test at Thu Sep 25 02:16:36 2025
 Starting test.no-v1 at Thu Sep 25 02:16:37 2025 

 Ending test.no-v1 at Thu Sep 25 02:16:37 2025 
  Took  0.01 


 Starting oncoSimulIndiv-miscell tests Thu Sep 25 02:16:37 2025 

 Ending oncoSimulIndiv-miscell tests Thu Sep 25 02:16:43 2025 
  Took  6.59 


 Starting oncoSimulSample-failures tests Thu Sep 25 02:16:43 2025 

 Ending oncoSimulSample-failures tests Thu Sep 25 02:16:47 2025 
  Took  3.4 


 Starting oncoSimulSample-limits tests Thu Sep 25 02:16:47 2025 

 Ending oncoSimulSample-limits tests Thu Sep 25 02:16:47 2025 
  Took  0.06 


 Starting per-gene-mutation rates at Thu Sep 25 02:16:47 2025 

 Ending per-gene-mutation rates at Thu Sep 25 02:17:10 2025 
  Took  23.02 


 Starting plotFitnessLandscape at Thu Sep 25 02:17:10 2025
 Ending plotFitnessLandscape at Thu Sep 25 02:17:13 2025 
  Took  3.58 


 Starting poset-transformations tests Thu Sep 25 02:17:13 2025 

 Ending poset-transformations tests Thu Sep 25 02:17:22 2025 
  Took  8.98 


 Starting sample-prob Thu Sep 25 02:17:22 2025 
[1] 2.189544e-25
[1] 6.612703e-12
[1] 1.253321e-09
[1] 1.261107e-11
[1] 5.443956e-15
[1] 3.937564e-13
[1] 1.406243e-10
[1] 1.109282e-15
[1] 1.68769e-10
[1] 1.365588e-07
[1] 2.170795e-09
[1] 1.442551e-09

 Ending sample-prob tests Thu Sep 25 02:17:27 2025 
 Took  4.92 



 Starting samplePop tests Thu Sep 25 02:17:27 2025 

 Ending samplePop tests Thu Sep 25 02:17:30 2025 
  Took  3.15 


 Starting simuls-runs-examples tests Thu Sep 25 02:17:30 2025 

 Ending simuls-runs-examples tests Thu Sep 25 02:17:36 2025 
  Took  5.78 


 Starting user variable tests Thu Sep 25 02:17:36 2025 
[1] "Checking user variable: user_var_1"
[1] "Checking rule: rule_1"

 Ending user variable tests Thu Sep 25 02:17:36 2025 
  Took  0.11 


 Starting warning-mutPropGrowth tests Thu Sep 25 02:17:36 2025 

 Ending warning-mutPropGrowth tests Thu Sep 25 02:17:37 2025 
  Took  0.31 


 Starting wide2long tests Thu Sep 25 02:17:37 2025 

 Ending wide2long tests Thu Sep 25 02:17:37 2025 
  Took  0.18 

[ FAIL 0 | WARN 19 | SKIP 5 | PASS 8397 ]

══ Skipped tests (5) ═══════════════════════════════════════════════════════════
• empty test (5): '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 5 | PASS 8397 ]
> 
> proc.time()
   user  system elapsed 
178.208  31.622 163.832

Example timings

OncoSimulR.Rcheck/OncoSimulR-Ex.timings

nameusersystemelapsed
OncoSimulWide2Long0.1250.0010.131
POM0.5420.0610.438
allFitnessEffects1.9890.0642.056
benchmarks0.0080.0020.011
createInterventions0.2720.0020.274
createUserVars0.4170.0010.419
evalAllGenotypes0.1850.0390.225
example-missing-drivers0.2020.0350.238
examplePosets0.2390.0000.239
examplesFitnessEffects0.0760.0010.077
freq-dep-simul-examples0.0090.0010.009
mcfLs0.0010.0000.000
oncoSimulIndiv0.9120.1360.993
plot.fitnessEffects0.2070.0240.233
plot.oncosimul0.3980.0130.411
plotClonePhylog1.2220.0991.323
plotFitnessLandscape1.4240.1121.536
plotPoset0.0870.0060.093
poset0.1020.0020.103
rfitness0.7140.0060.721
samplePop0.0710.0790.090
simOGraph0.0600.0110.070
to_Magellan0.1700.0350.206
vignette_pre_computed0.0040.0020.008