##############################################################################
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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_4.9.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/OncoSimulR.Rcheck’
* using R Under development (unstable) (2025-01-22 r87618)
* 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 ‘4.9.0’
* 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 ... NOTE
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  plot.oncosimul.Rd: brewer.pal
  plotClonePhylog.Rd: get.adjacency
  plotFitnessLandscape.Rd: ggrepel
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
* 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: 3 NOTEs
See
  ‘/Users/biocbuild/bbs-3.21-bioc/meat/OncoSimulR.Rcheck/00check.log’
for details.

##############################################################################
##############################################################################
###
### 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 ‘4.9.0’
** 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  -DR_NO_REMAP -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  -DR_NO_REMAP -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 -Wl,-framework -Wl,CoreFoundation
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)

R Under development (unstable) (2025-01-22 r87618) -- "Unsuffered Consequences"
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 Tue Feb 25 22:09:11 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 Feb 25 22:09:11 2025 
  Took  0.51 


 Starting LOD_POM at Tue Feb 25 22:09:11 2025 

 Ending LOD_POM at Tue Feb 25 22:09:25 2025 
  Took  13.85 


 Starting test.Z-all-fitness at Tue Feb 25 22:09:25 2025 

 Ending test.Z-all-fitness at Tue Feb 25 22:09:25 2025 
  Took  0.16 


 Starting test.Z-driver-counts at Tue Feb 25 22:09:25 2025 

 Ending test.Z-driver-counts at Tue Feb 25 22:09:25 2025 
  Took  0.14 


 Starting test.Z-fixation at Tue Feb 25 22:09:25 2025 

 Ending test.Z-fixation at Tue Feb 25 22:09:26 2025 
  Took  0.32 


 Starting test.Z-magellan at Tue Feb 25 22:09:26 2025 

 Ended test.Z-magellan at Tue Feb 25 22:09:28 2025 

 Starting test.Z-mutator at Tue Feb 25 22:09:28 2025 

 Ending test.Z-mutator at Tue Feb 25 22:09:28 2025 
  Took  0.44 


 Starting test.Z-mutatorFDF at Tue Feb 25 22:09:28 2025 

 Ending test.Z-mutatorFDF at Tue Feb 25 22:09:28 2025 
  Took  0.14 


 Starting test.Z-oncoSimulIndiv at Tue Feb 25 22:09:28 2025 

 Ending test.Z-oncoSimulIndiv at Tue Feb 25 22:09:29 2025 
  Took  0.49 


 Starting test.Z-oncoSimulIndivConstant at Tue Feb 25 22:09:29 2025 

 Ending test.Z-oncoSimulIndivConstant at Tue Feb 25 22:09:32 2025 
  Took  2.98 


 Starting test.Z-oncoSimulIndivDeath at Tue Feb 25 22:09:32 2025 


 Ending test.Z-oncoSimulIndivDeath at Tue Feb 25 22:09:33 2025 
  Took  0.98 


 Starting test.Z-oncoSimulIndivFDF at Tue Feb 25 22:09:33 2025 

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

 Ending test.Z-oncoSimulIndivFDF at Tue Feb 25 22:09:34 2025 
  Took  0.91 


 Starting test.Z-rfitness-landscape at Tue Feb 25 22:09:34 2025 

 Ending test.Z-rfitness-landscape at Tue Feb 25 22:09:34 2025 
  Took  0.24 


 Starting Z-sample-only-last tests Tue Feb 25 22:09:34 2025 

 Ending Z-sample-only-last tests Tue Feb 25 22:09:34 2025 
  Took  0 


 Starting Z-total-present-drivers tests Tue Feb 25 22:09:34 2025 

 Ending Z-total-present-drivers tests Tue Feb 25 22:09:35 2025 
  Took  0.88 


 Dummy empty test  Tue Feb 25 22:09:35 2025 

 Starting accessible_genotypes at Tue Feb 25 22:09:35 2025 

 Ending accessible_genotypes at Tue Feb 25 22:09:43 2025 
  Took  8.77 


 Starting all fitness at Tue Feb 25 22:09:43 2025
 Ending all-fitness at Tue Feb 25 22:09:49 2025 
  Took  5.05 


 Starting test.allFitnessEffectsFDF at Tue Feb 25 22:09:49 2025 

 Ending test.allFitnessEffectsFDF at Tue Feb 25 22:09:49 2025 
  Took  0.13 


 Starting test.allFitnessEffectsDeath at Tue Feb 25 22:09:49 2025 

 Ending test.allFitnessEffectsDeath at Tue Feb 25 22:09:49 2025 
  Took  0.47 


 Starting test.allFitnessEffectsFDF at Tue Feb 25 22:09:49 2025 

 Ending test.allFitnessEffectsFDF at Tue Feb 25 22:09:50 2025 
  Took  0.45 


 Starting driverCounts at Tue Feb 25 22:09:50 2025
 Ending driverCounts at Tue Feb 25 22:10:00 2025 
  Took  10.52 


 Starting epist-order-modules at Tue Feb 25 22:10:00 2025
 Ending epist-order-modules at Tue Feb 25 22:10:00 2025 
  Took  0.07 


 Starting test.evaluatingGenotypesDeath at Tue Feb 25 22:10:00 2025 

 Ending test.evaluatingGenotypesDeath at Tue Feb 25 22:10:00 2025 
  Took  0.21 


 Starting test.evaluatingGenotypesFDF at Tue Feb 25 22:10:00 2025 

 Ending test.evaluatingGenotypesFDF at Tue Feb 25 22:10:01 2025 
  Took  0.22 


 Starting exercise-plotting-code at Tue Feb 25 22:10:01 2025
 Ending exercise-plotting-code at Tue Feb 25 22:10:04 2025 
  Took  3.1 


 Starting exercise-rfitness at Tue Feb 25 22:10:04 2025 

 Ending exercise-rfitness at Tue Feb 25 22:10:16 2025 
  Took  11.95 


 Starting to_Magella at Tue Feb 25 22:10:16 2025 

 Ending to_Magella at Tue Feb 25 22:10:16 2025 
  Took  0.04 


 Starting fitness preds at Tue Feb 25 22:10:16 2025 

 Observed vs expected, case III

 done tries 1 

 Ending fitness preds long at Tue Feb 25 22:10:24 2025 
  Took  8.31 


 Starting fixation  at Tue Feb 25 22:10:24 2025 

 Ending fixation  at Tue Feb 25 22:10:42 2025 
  Took  17.79 


 Starting test.flfast-additional.R test at Tue Feb 25 22:10:42 2025
 DEBUG2: Value of rnb = nan

 DEBUG2: Value of m = 1

 DEBUG2: Value of pe = 0

 DEBUG2: Value of pm = 0.999997

 this is spP

 popSize = 1
 birth = 1
 death = 0
 W = 1.00001
 R = 1.00001
 mutation = 6e-06
 timeLastUpdate = 2.58193
 absfitness = -inf
 numMutablePos = 6

 Unrecoverable exception: Algo 2: retval not finite. Aborting. 

 Ending test.flfast-additional.R test at Tue Feb 25 22:10:43 2025 
  Took  1.31 


 Starting test.flfast-mutator.R test at Tue Feb 25 22:10:43 2025
 Finished test.flfast-mutator.R test at Tue Feb 25 22:10:44 2025 
  Took  1.18 


 Starting genotFitness at Tue Feb 25 22:10:44 2025 

 Ending genotFitness at Tue Feb 25 22:10:45 2025 
  Took  0.22 


 Starting genot_fitness_to_epistasis at Tue Feb 25 22:10:45 2025 

 Ending genot_fitness_to_epistasis at Tue Feb 25 22:10:45 2025 
  Took  0.05 


 Starting init-mutant tests Tue Feb 25 22:10:45 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 Feb 25 22:10:52 2025 
  Took  7.58 


 Starting interventions tests Tue Feb 25 22:10:52 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] 0.68 0.68 0.68
[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 Feb 25 22:10:57 2025 
  Took  5.01 


 Starting test.magellan at Tue Feb 25 22:10:57 2025 

 Ending test.magellan at Tue Feb 25 22:10:58 2025 
  Took  0.26 


 Starting test.modules-root-no-root at Tue Feb 25 22:10:58 2025 

 Ending test.modules-root-no-root at Tue Feb 25 22:10:58 2025 
  Took  0.11 


 Starting at mutPropGrowth  Tue Feb 25 22:10:58 2025 

 Ended test.mutPropGrowth:  Tue Feb 25 22:11:04 2025 
  Took  6.86 


 Starting test.mutator-oncoSimulSample.R test at Tue Feb 25 22:11:05 2025 

 Finished test.mutator-oncoSimulSample.R test at Tue Feb 25 22:11:13 2025 
  Took  8.11 seconds 


 Starting test.mutator.R test at Tue Feb 25 22:11:13 2025[1] 1.626015e-08
[1] 4.949118e-12

 Finished test.mutator.R test at Tue Feb 25 22:11:28 2025 
  Took  15.87 


 Starting test.mutatorFDF.R test at Tue Feb 25 22:11:29 2025
 Starting test.no-v1 at Tue Feb 25 22:11:29 2025 

 Ending test.no-v1 at Tue Feb 25 22:11:29 2025 
  Took  0.01 


 Starting oncoSimulIndiv-miscell tests Tue Feb 25 22:11:29 2025 

 Ending oncoSimulIndiv-miscell tests Tue Feb 25 22:11:34 2025 
  Took  5.2 


 Starting oncoSimulSample-failures tests Tue Feb 25 22:11:34 2025 

 Ending oncoSimulSample-failures tests Tue Feb 25 22:11:39 2025 
  Took  4.21 


 Starting oncoSimulSample-limits tests Tue Feb 25 22:11:39 2025 

 Ending oncoSimulSample-limits tests Tue Feb 25 22:11:39 2025 
  Took  0.09 


 Starting per-gene-mutation rates at Tue Feb 25 22:11:39 2025 

 Ending per-gene-mutation rates at Tue Feb 25 22:12:40 2025 
  Took  60.98 


 Starting plotFitnessLandscape at Tue Feb 25 22:12:40 2025
 Ending plotFitnessLandscape at Tue Feb 25 22:12:44 2025 
  Took  4.46 


 Starting poset-transformations tests Tue Feb 25 22:12:44 2025 

 Ending poset-transformations tests Tue Feb 25 22:12:59 2025 
  Took  14.88 


 Starting sample-prob Tue Feb 25 22:12:59 2025 
[1] 1.353202e-28
[1] 5.786074e-13
[1] 4.393451e-10
[1] 1.571751e-11
[1] 1.14109e-13
[1] 2.571817e-14
[1] 3.604651e-10
[1] 9.538859e-16
[1] 8.026096e-09
[1] 7.338645e-12
[1] 2.286635e-08
[1] 2.54081e-09

 Ending sample-prob tests Tue Feb 25 22:13:26 2025 
 Took  26.86 



 Starting samplePop tests Tue Feb 25 22:13:26 2025 

 Ending samplePop tests Tue Feb 25 22:13:30 2025 
  Took  4.41 


 Starting simuls-runs-examples tests Tue Feb 25 22:13:30 2025 

 Ending simuls-runs-examples tests Tue Feb 25 22:13:34 2025 
  Took  3.8 


 Starting user variable tests Tue Feb 25 22:13:34 2025 
[1] "Checking user variable: user_var_1"
[1] "Checking rule: rule_1"

 Ending user variable tests Tue Feb 25 22:13:34 2025 
  Took  0.14 


 Starting warning-mutPropGrowth tests Tue Feb 25 22:13:34 2025 

 Ending warning-mutPropGrowth tests Tue Feb 25 22:13:35 2025 
  Took  0.28 


 Starting wide2long tests Tue Feb 25 22:13:35 2025 

 Ending wide2long tests Tue Feb 25 22:13:35 2025 
  Took  0.17 

[ FAIL 0 | WARN 19 | SKIP 7 | PASS 8419 ]

══ 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 8419 ]
> 
> proc.time()
   user  system elapsed 
241.020  90.109 268.879