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This page was generated on 2025-04-22 13:16 -0400 (Tue, 22 Apr 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.1 LTS)x86_644.5.0 RC (2025-04-04 r88126) -- "How About a Twenty-Six" 4831
palomino7Windows Server 2022 Datacenterx644.5.0 RC (2025-04-04 r88126 ucrt) -- "How About a Twenty-Six" 4573
lconwaymacOS 12.7.1 Montereyx86_644.5.0 RC (2025-04-04 r88126) -- "How About a Twenty-Six" 4599
kjohnson3macOS 13.7.1 Venturaarm644.5.0 RC (2025-04-04 r88126) -- "How About a Twenty-Six" 4553
kunpeng2Linux (openEuler 24.03 LTS)aarch64R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" 4570
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: 2025-04-21 13:40 -0400 (Mon, 21 Apr 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 24.04.1 LTS) / x86_64  OK    OK    OK  YES
palomino7Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  YES
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  YES
kjohnson3macOS 13.7.1 Ventura / arm64... NOT SUPPORTED ...
kunpeng2Linux (openEuler 24.03 LTS) / aarch64  OK    OK    OK  

CHECK results for OncoSimulR on lconway

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: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:OncoSimulR.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings OncoSimulR_4.10.0.tar.gz
StartedAt: 2025-04-21 22:24:19 -0400 (Mon, 21 Apr 2025)
EndedAt: 2025-04-21 22:30:53 -0400 (Mon, 21 Apr 2025)
EllapsedTime: 394.9 seconds
RetCode: 0
Status:   OK  
CheckDir: OncoSimulR.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:OncoSimulR.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings OncoSimulR_4.10.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/OncoSimulR.Rcheck’
* using R version 4.5.0 RC (2025-04-04 r88126)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 14.2.0
* running under: macOS Monterey 12.7.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* 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: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
* used C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
* used SDK: ‘MacOSX11.3.sdk’
* checking installed package size ... INFO
  installed size is  9.4Mb
  sub-directories of 1Mb or more:
    libs   7.9Mb
* 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 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 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-3.21-bioc/meat/OncoSimulR.Rcheck/00check.log’
for details.

Installation output

OncoSimulR.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL OncoSimulR
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library’
* installing *source* package ‘OncoSimulR’ ...
** this is package ‘OncoSimulR’ version ‘4.10.0’
** using staged installation
** libs
using C compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
using C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
using SDK: ‘MacOSX11.3.sdk’
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c FitnessLandscape/gamma.c -o FitnessLandscape/gamma.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c FitnessLandscape/landscape.c -o FitnessLandscape/landscape.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c FitnessLandscape/random.c -o FitnessLandscape/random.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c FitnessLandscape/sort.c -o FitnessLandscape/sort.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c FitnessLandscape/chain.c -o FitnessLandscape/chain.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c FitnessLandscape/input.c -o FitnessLandscape/input.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c FitnessLandscape/genotypes.c -o FitnessLandscape/genotypes.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c FitnessLandscape/ordered_pairs.c -o FitnessLandscape/ordered_pairs.o
FitnessLandscape/ordered_pairs.c:138:6: warning: variable 'tot_pairs' set but not used [-Wunused-but-set-variable]
        int tot_pairs=0;
            ^
1 warning generated.
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c FitnessLandscape/calculus.c -o FitnessLandscape/calculus.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c FitnessLandscape/vector.c -o FitnessLandscape/vector.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c FitnessLandscape/generalized_chain.c -o FitnessLandscape/generalized_chain.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c FitnessLandscape/LinearAlgebra.c -o FitnessLandscape/LinearAlgebra.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c FitnessLandscape/summary_statistics.c -o FitnessLandscape/summary_statistics.o
FitnessLandscape/summary_statistics.c:515:9: warning: variable 'meanVarianceNumberOfStepsFL' set but not used [-Wunused-but-set-variable]
        double meanVarianceNumberOfStepsFL = 0;
               ^
1 warning generated.
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c FitnessLandscape/epistasis_type.c -o FitnessLandscape/epistasis_type.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c FitnessLandscape/decomposition.c -o FitnessLandscape/decomposition.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c FitnessLandscape/models.c -o FitnessLandscape/models.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -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 archive liblandscape.a
ranlib liblandscape.a;
clang -arch x86_64 -O -Wall -o fl_statistics -I/FitnessLandscape/. -L. FitnessLandscape/main_fl_statistics.c -llandscape -lm;
clang -arch x86_64 -O -Wall -o fl_generate -I/FitnessLandscape/. -L. FitnessLandscape/main_fl_generate.c -llandscape -lm;
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c OncoSimulR_init.c -o OncoSimulR_init.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c RcppExports.cpp -o RcppExports.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c unity_osimul.cpp -o unity_osimul.o
In file included from unity_osimul.cpp:10:
./UnityOncoSimul/intervention_private_2.cpp:17:10: warning: variable 'totalPop' set but not used [-Wunused-but-set-variable]
  double totalPop = 0.0;
         ^
1 warning generated.
clang++ -arch x86_64 -std=gnu++17 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/x86_64/lib -o OncoSimulR.so OncoSimulR_init.o RcppExports.o unity_osimul.o -F/Library/Frameworks/R.framework/.. -framework R
installing via 'install.libs.R' to /Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/00LOCK-OncoSimulR/00new/OncoSimulR
[1] ""
Installing fl_statistics fl_generate to /Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/00LOCK-OncoSimulR/00new/OncoSimulR/exec
Installing library OncoSimulR.so to /Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/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 4.5.0 RC (2025-04-04 r88126) -- "How About a Twenty-Six"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20

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 Mon Apr 21 22:25:50 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 Mon Apr 21 22:25:51 2025 
  Took  0.48 


 Starting LOD_POM at Mon Apr 21 22:25:51 2025 

 Ending LOD_POM at Mon Apr 21 22:26:02 2025 
  Took  11.08 


 Starting test.Z-all-fitness at Mon Apr 21 22:26:02 2025 

 Ending test.Z-all-fitness at Mon Apr 21 22:26:02 2025 
  Took  0.14 


 Starting test.Z-driver-counts at Mon Apr 21 22:26:02 2025 

 Ending test.Z-driver-counts at Mon Apr 21 22:26:02 2025 
  Took  0.12 


 Starting test.Z-fixation at Mon Apr 21 22:26:02 2025 

 Ending test.Z-fixation at Mon Apr 21 22:26:02 2025 
  Took  0.31 


 Starting test.Z-magellan at Mon Apr 21 22:26:02 2025 

 Ended test.Z-magellan at Mon Apr 21 22:26:04 2025 

 Starting test.Z-mutator at Mon Apr 21 22:26:04 2025 

 Ending test.Z-mutator at Mon Apr 21 22:26:05 2025 
  Took  0.42 


 Starting test.Z-mutatorFDF at Mon Apr 21 22:26:05 2025 

 Ending test.Z-mutatorFDF at Mon Apr 21 22:26:05 2025 
  Took  0.14 


 Starting test.Z-oncoSimulIndiv at Mon Apr 21 22:26:05 2025 

 Ending test.Z-oncoSimulIndiv at Mon Apr 21 22:26:05 2025 
  Took  0.49 


 Starting test.Z-oncoSimulIndivConstant at Mon Apr 21 22:26:05 2025 

 Ending test.Z-oncoSimulIndivConstant at Mon Apr 21 22:26:08 2025 
  Took  2.7 


 Starting test.Z-oncoSimulIndivDeath at Mon Apr 21 22:26:08 2025 


 Ending test.Z-oncoSimulIndivDeath at Mon Apr 21 22:26:09 2025 
  Took  0.91 


 Starting test.Z-oncoSimulIndivFDF at Mon Apr 21 22:26:09 2025 

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

 Ending test.Z-oncoSimulIndivFDF at Mon Apr 21 22:26:10 2025 
  Took  0.51 


 Starting test.Z-rfitness-landscape at Mon Apr 21 22:26:10 2025 

 Ending test.Z-rfitness-landscape at Mon Apr 21 22:26:10 2025 
  Took  0.25 


 Starting Z-sample-only-last tests Mon Apr 21 22:26:10 2025 

 Ending Z-sample-only-last tests Mon Apr 21 22:26:10 2025 
  Took  0 


 Starting Z-total-present-drivers tests Mon Apr 21 22:26:10 2025 

 Ending Z-total-present-drivers tests Mon Apr 21 22:26:11 2025 
  Took  0.86 


 Dummy empty test  Mon Apr 21 22:26:11 2025 

 Starting accessible_genotypes at Mon Apr 21 22:26:11 2025 

 Ending accessible_genotypes at Mon Apr 21 22:26:20 2025 
  Took  8.83 


 Starting all fitness at Mon Apr 21 22:26:20 2025
 Ending all-fitness at Mon Apr 21 22:26:25 2025 
  Took  5.46 


 Starting test.allFitnessEffectsFDF at Mon Apr 21 22:26:25 2025 

 Ending test.allFitnessEffectsFDF at Mon Apr 21 22:26:25 2025 
  Took  0.15 


 Starting test.allFitnessEffectsDeath at Mon Apr 21 22:26:25 2025 

 Ending test.allFitnessEffectsDeath at Mon Apr 21 22:26:26 2025 
  Took  0.54 


 Starting test.allFitnessEffectsFDF at Mon Apr 21 22:26:26 2025 

 Ending test.allFitnessEffectsFDF at Mon Apr 21 22:26:26 2025 
  Took  0.45 


 Starting driverCounts at Mon Apr 21 22:26:26 2025
 Ending driverCounts at Mon Apr 21 22:26:37 2025 
  Took  10.86 


 Starting epist-order-modules at Mon Apr 21 22:26:37 2025
 Ending epist-order-modules at Mon Apr 21 22:26:37 2025 
  Took  0.06 


 Starting test.evaluatingGenotypesDeath at Mon Apr 21 22:26:37 2025 

 Ending test.evaluatingGenotypesDeath at Mon Apr 21 22:26:37 2025 
  Took  0.21 


 Starting test.evaluatingGenotypesFDF at Mon Apr 21 22:26:37 2025 

 Ending test.evaluatingGenotypesFDF at Mon Apr 21 22:26:37 2025 
  Took  0.21 


 Starting exercise-plotting-code at Mon Apr 21 22:26:37 2025
 Ending exercise-plotting-code at Mon Apr 21 22:26:40 2025 
  Took  2.99 


 Starting exercise-rfitness at Mon Apr 21 22:26:40 2025 

 Ending exercise-rfitness at Mon Apr 21 22:26:52 2025 
  Took  11.69 


 Starting to_Magella at Mon Apr 21 22:26:52 2025 

 Ending to_Magella at Mon Apr 21 22:26:52 2025 
  Took  0.05 


 Starting fitness preds at Mon Apr 21 22:26:52 2025 

 Observed vs expected, case III

 done tries 1 

 Ending fitness preds long at Mon Apr 21 22:27:00 2025 
  Took  8.1 


 Starting fixation  at Mon Apr 21 22:27:00 2025 

 Ending fixation  at Mon Apr 21 22:27:18 2025 
  Took  17.39 


 Starting test.flfast-additional.R test at Mon Apr 21 22:27:18 2025
 Ending test.flfast-additional.R test at Mon Apr 21 22:27:19 2025 
  Took  1.29 


 Starting test.flfast-mutator.R test at Mon Apr 21 22:27:19 2025
 Finished test.flfast-mutator.R test at Mon Apr 21 22:27:20 2025 
  Took  1.33 


 Starting genotFitness at Mon Apr 21 22:27:20 2025 

 Ending genotFitness at Mon Apr 21 22:27:21 2025 
  Took  0.24 


 Starting genot_fitness_to_epistasis at Mon Apr 21 22:27:21 2025 

 Ending genot_fitness_to_epistasis at Mon Apr 21 22:27:21 2025 
  Took  0.05 


 Starting init-mutant tests Mon Apr 21 22:27:21 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 Mon Apr 21 22:27:28 2025 
  Took  6.87 


 Starting interventions tests Mon Apr 21 22:27:28 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] 0.62 0.62 0.62
[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 Mon Apr 21 22:27:32 2025 
  Took  4.88 


 Starting test.magellan at Mon Apr 21 22:27:32 2025 

 Ending test.magellan at Mon Apr 21 22:27:33 2025 
  Took  0.25 


 Starting test.modules-root-no-root at Mon Apr 21 22:27:33 2025 

 Ending test.modules-root-no-root at Mon Apr 21 22:27:33 2025 
  Took  0.1 


 Starting at mutPropGrowth  Mon Apr 21 22:27:33 2025 

 Ended test.mutPropGrowth:  Mon Apr 21 22:27:39 2025 
  Took  6.4 


 Starting test.mutator-oncoSimulSample.R test at Mon Apr 21 22:27:39 2025 

 Finished test.mutator-oncoSimulSample.R test at Mon Apr 21 22:27:48 2025 
  Took  8.41 seconds 


 Starting test.mutator.R test at Mon Apr 21 22:27:48 2025[1] 1.760323e-09
[1] 5.495058e-13

 Finished test.mutator.R test at Mon Apr 21 22:28:11 2025 
  Took  22.96 


 Starting test.mutatorFDF.R test at Mon Apr 21 22:28:11 2025
 Starting test.no-v1 at Mon Apr 21 22:28:11 2025 

 Ending test.no-v1 at Mon Apr 21 22:28:11 2025 
  Took  0.01 


 Starting oncoSimulIndiv-miscell tests Mon Apr 21 22:28:11 2025 

 Ending oncoSimulIndiv-miscell tests Mon Apr 21 22:28:17 2025 
  Took  6.06 


 Starting oncoSimulSample-failures tests Mon Apr 21 22:28:17 2025 

 Ending oncoSimulSample-failures tests Mon Apr 21 22:28:22 2025 
  Took  4.06 


 Starting oncoSimulSample-limits tests Mon Apr 21 22:28:22 2025 

 Ending oncoSimulSample-limits tests Mon Apr 21 22:28:22 2025 
  Took  0.1 


 Starting per-gene-mutation rates at Mon Apr 21 22:28:22 2025 

 Ending per-gene-mutation rates at Mon Apr 21 22:29:12 2025 
  Took  50.21 


 Starting plotFitnessLandscape at Mon Apr 21 22:29:12 2025
 Ending plotFitnessLandscape at Mon Apr 21 22:29:17 2025 
  Took  4.66 


 Starting poset-transformations tests Mon Apr 21 22:29:17 2025 

 Ending poset-transformations tests Mon Apr 21 22:29:32 2025 
  Took  15.05 


 Starting sample-prob Mon Apr 21 22:29:32 2025 
[1] 2.737904e-24
[1] 1.92527e-16
[1] 3.820732e-10
[1] 1.251503e-11
[1] 2.695768e-13
[1] 7.229567e-16
[1] 1.189297e-08
[1] 2.231413e-15
[1] 8.605355e-10
[1] 2.214005e-09
[1] 1.134405e-07
[1] 7.338183e-09

 Ending sample-prob tests Mon Apr 21 22:29:51 2025 
 Took  19.5 



 Starting samplePop tests Mon Apr 21 22:29:51 2025 

 Ending samplePop tests Mon Apr 21 22:29:58 2025 
  Took  7.27 


 Starting simuls-runs-examples tests Mon Apr 21 22:29:58 2025 

 Ending simuls-runs-examples tests Mon Apr 21 22:30:06 2025 
  Took  7.59 


 Starting user variable tests Mon Apr 21 22:30:06 2025 
[1] "Checking user variable: user_var_1"
[1] "Checking rule: rule_1"

 Ending user variable tests Mon Apr 21 22:30:06 2025 
  Took  0.21 


 Starting warning-mutPropGrowth tests Mon Apr 21 22:30:06 2025 

 Ending warning-mutPropGrowth tests Mon Apr 21 22:30:07 2025 
  Took  1.2 


 Starting wide2long tests Mon Apr 21 22:30:07 2025 

 Ending wide2long tests Mon Apr 21 22:30:08 2025 
  Took  0.35 

[ FAIL 0 | WARN 19 | SKIP 7 | PASS 8385 ]

══ Skipped tests (7) ═══════════════════════════════════════════════════════════
• On Mac (2): 'test.Z-magellan.R:664:5', 'test.Z-oncoSimulIndivFDF.R:125:3'
• 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 7 | PASS 8385 ]
> 
> proc.time()
   user  system elapsed 
245.298  76.139 266.372

Example timings

OncoSimulR.Rcheck/OncoSimulR-Ex.timings

nameusersystemelapsed
OncoSimulWide2Long0.1620.0030.168
POM0.8220.0750.540
allFitnessEffects2.0910.0722.182
benchmarks0.0100.0070.017
createInterventions0.3710.0130.387
createUserVars0.4830.0180.503
evalAllGenotypes0.2280.0150.245
example-missing-drivers0.2190.0160.236
examplePosets0.2940.0100.306
examplesFitnessEffects0.0900.0050.095
freq-dep-simul-examples0.0090.0030.012
mcfLs000
oncoSimulIndiv1.1400.1861.301
plot.fitnessEffects0.2400.0240.268
plot.oncosimul0.4060.0220.431
plotClonePhylog1.6060.0701.688
plotFitnessLandscape1.1870.0421.236
plotPoset0.0930.0060.101
poset0.1100.0060.118
rfitness0.6020.0120.656
samplePop0.1390.2170.222
simOGraph0.0900.0160.107
to_Magellan0.2040.0630.385
vignette_pre_computed0.0070.0030.010