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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_4.11.1.tar.gz
###
##############################################################################
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* using log directory ‘/Users/biocbuild/bbs-3.22-bioc/meat/OncoSimulR.Rcheck’
* using R version 4.5.1 Patched (2025-09-10 r88807)
* 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 ‘4.11.1’
* 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: ‘MacOSX11.3.1.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-3.22-bioc/meat/OncoSimulR.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL OncoSimulR
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library’
* installing *source* package ‘OncoSimulR’ ...
** this is package ‘OncoSimulR’ version ‘4.11.1’
** 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: ‘MacOSX11.3.1.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)

R version 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root"
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 Thu Sep 25 23:00:20 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 23:00:20 2025 
  Took  0.54 


 Starting LOD_POM at Thu Sep 25 23:00:20 2025 

 Ending LOD_POM at Thu Sep 25 23:00:34 2025 
  Took  13.51 


 Starting test.Z-all-fitness at Thu Sep 25 23:00:34 2025 

 Ending test.Z-all-fitness at Thu Sep 25 23:00:34 2025 
  Took  0.15 


 Starting test.Z-driver-counts at Thu Sep 25 23:00:34 2025 

 Ending test.Z-driver-counts at Thu Sep 25 23:00:34 2025 
  Took  0.15 


 Starting test.Z-fixation at Thu Sep 25 23:00:34 2025 

 Ending test.Z-fixation at Thu Sep 25 23:00:35 2025 
  Took  0.3 


 Starting test.Z-magellan at Thu Sep 25 23:00:35 2025 

 Ended test.Z-magellan at Thu Sep 25 23:00:37 2025 

 Starting test.Z-mutator at Thu Sep 25 23:00:37 2025 

 Ending test.Z-mutator at Thu Sep 25 23:00:37 2025 
  Took  0.43 


 Starting test.Z-mutatorFDF at Thu Sep 25 23:00:37 2025 

 Ending test.Z-mutatorFDF at Thu Sep 25 23:00:37 2025 
  Took  0.13 


 Starting test.Z-oncoSimulIndiv at Thu Sep 25 23:00:37 2025 

 Ending test.Z-oncoSimulIndiv at Thu Sep 25 23:00:38 2025 
  Took  0.49 


 Starting test.Z-oncoSimulIndivConstant at Thu Sep 25 23:00:38 2025 

 Ending test.Z-oncoSimulIndivConstant at Thu Sep 25 23:00:40 2025 
  Took  2.78 


 Starting test.Z-oncoSimulIndivDeath at Thu Sep 25 23:00:40 2025 


 Ending test.Z-oncoSimulIndivDeath at Thu Sep 25 23:00:41 2025 
  Took  0.97 


 Starting test.Z-oncoSimulIndivFDF at Thu Sep 25 23:00:41 2025 

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

 Ending test.Z-oncoSimulIndivFDF at Thu Sep 25 23:00:43 2025 
  Took  1.05 


 Starting test.Z-rfitness-landscape at Thu Sep 25 23:00:43 2025 

 Ending test.Z-rfitness-landscape at Thu Sep 25 23:00:43 2025 
  Took  0.38 


 Starting Z-sample-only-last tests Thu Sep 25 23:00:43 2025 

 Ending Z-sample-only-last tests Thu Sep 25 23:00:43 2025 
  Took  0 


 Starting Z-total-present-drivers tests Thu Sep 25 23:00:43 2025 

 Ending Z-total-present-drivers tests Thu Sep 25 23:00:44 2025 
  Took  0.92 


 Dummy empty test  Thu Sep 25 23:00:44 2025 

 Starting accessible_genotypes at Thu Sep 25 23:00:44 2025 

 Ending accessible_genotypes at Thu Sep 25 23:00:53 2025 
  Took  9.13 


 Starting all fitness at Thu Sep 25 23:00:53 2025
 Ending all-fitness at Thu Sep 25 23:00:58 2025 
  Took  5.05 


 Starting test.allFitnessEffectsFDF at Thu Sep 25 23:00:58 2025 

 Ending test.allFitnessEffectsFDF at Thu Sep 25 23:00:58 2025 
  Took  0.13 


 Starting test.allFitnessEffectsDeath at Thu Sep 25 23:00:58 2025 

 Ending test.allFitnessEffectsDeath at Thu Sep 25 23:00:59 2025 
  Took  0.47 


 Starting test.allFitnessEffectsFDF at Thu Sep 25 23:00:59 2025 

 Ending test.allFitnessEffectsFDF at Thu Sep 25 23:00:59 2025 
  Took  0.41 


 Starting driverCounts at Thu Sep 25 23:00:59 2025
 Ending driverCounts at Thu Sep 25 23:01:11 2025 
  Took  12.29 


 Starting epist-order-modules at Thu Sep 25 23:01:11 2025
 Ending epist-order-modules at Thu Sep 25 23:01:11 2025 
  Took  0.07 


 Starting test.evaluatingGenotypesDeath at Thu Sep 25 23:01:11 2025 

 Ending test.evaluatingGenotypesDeath at Thu Sep 25 23:01:12 2025 
  Took  0.25 


 Starting test.evaluatingGenotypesFDF at Thu Sep 25 23:01:12 2025 

 Ending test.evaluatingGenotypesFDF at Thu Sep 25 23:01:12 2025 
  Took  0.23 


 Starting exercise-plotting-code at Thu Sep 25 23:01:12 2025
 Ending exercise-plotting-code at Thu Sep 25 23:01:15 2025 
  Took  3.29 


 Starting exercise-rfitness at Thu Sep 25 23:01:15 2025 

 Ending exercise-rfitness at Thu Sep 25 23:01:28 2025 
  Took  12.42 


 Starting to_Magella at Thu Sep 25 23:01:28 2025 

 Ending to_Magella at Thu Sep 25 23:01:28 2025 
  Took  0.06 


 Starting fitness preds at Thu Sep 25 23:01:28 2025 

 Observed vs expected, case III

 T.not is 
[1] TRUE
 [1] 9.339847e-41 6.134482e-35 3.268011e-37 2.478665e-42 2.691338e-41
 [6] 9.388950e-37 0.000000e+00 0.000000e+00 2.307349e-36 2.793877e-40
[11] 1.448520e-32 9.562112e-34 1.446766e-26 9.788638e-45 3.769677e-24
[16] 3.489086e-25 9.624038e-38 2.154777e-13

 T.yest 
[1] FALSE
 [1] 0.5062083780 0.8541434599 0.3857453301 0.6715746118 0.0126102161
 [6] 0.0777511299 0.5420607454 0.0001186703 0.9434455212 0.7963506557
[11] 0.9465299196 0.4148703710 0.4446954016 0.2128724335 0.5088376700
[16] 0.6855850067 0.5163231359 0.7000142295 0.5107986095 0.0578658734
[21] 0.2846980362 0.0709291505 0.9201175280 0.6898337443 0.2118793970
[26] 0.6111494090 0.0173325343 0.7521824997 0.8147969777 0.3519647563

 larger values of T.yest 
[1] 8

 lm and plot

Call:
lm(formula = log(Observed) ~ log(Expected), data = d1)

Residuals:
       Min         1Q     Median         3Q        Max 
-0.0225053 -0.0025201  0.0009215  0.0043353  0.0129112 

Coefficients:
                Estimate Std. Error  t value Pr(>|t|)    
(Intercept)   -0.0049038  0.0050243   -0.976    0.337    
log(Expected)  1.0005325  0.0004224 2368.906   <2e-16 ***
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1

Residual standard error: 0.007597 on 28 degrees of freedom
Multiple R-squared:      1,	Adjusted R-squared:      1 
F-statistic: 5.612e+06 on 1 and 28 DF,  p-value: < 2.2e-16


Linear hypothesis test:
(Intercept) = 0
log(Expected) = 1

Model 1: restricted model
Model 2: log(Observed) ~ log(Expected)

  Res.Df       RSS Df  Sum of Sq      F Pr(>F)
1     30 0.0017498                            
2     28 0.0016160  2 0.00013381 1.1592 0.3283

 done tries 2 

 Ending fitness preds long at Thu Sep 25 23:01:44 2025 
  Took  16.64 


 Starting fixation  at Thu Sep 25 23:01:44 2025 

 Ending fixation  at Thu Sep 25 23:02:03 2025 
  Took  18.9 


 Starting test.flfast-additional.R test at Thu Sep 25 23:02:03 2025
 Ending test.flfast-additional.R test at Thu Sep 25 23:02:05 2025 
  Took  1.36 


 Starting test.flfast-mutator.R test at Thu Sep 25 23:02:05 2025
 Finished test.flfast-mutator.R test at Thu Sep 25 23:02:06 2025 
  Took  1.46 


 Starting genotFitness at Thu Sep 25 23:02:06 2025 

 Ending genotFitness at Thu Sep 25 23:02:06 2025 
  Took  0.24 


 Starting genot_fitness_to_epistasis at Thu Sep 25 23:02:06 2025 

 Ending genot_fitness_to_epistasis at Thu Sep 25 23:02:06 2025 
  Took  0.05 


 Starting init-mutant tests Thu Sep 25 23:02:06 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 23:02:14 2025 
  Took  7.27 


 Starting interventions tests Thu Sep 25 23:02:14 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] 0.66 0.66 0.66
[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 23:02:19 2025 
  Took  4.94 


 Starting test.magellan at Thu Sep 25 23:02:19 2025 

 Ending test.magellan at Thu Sep 25 23:02:19 2025 
  Took  0.27 


 Starting test.modules-root-no-root at Thu Sep 25 23:02:19 2025 

 Ending test.modules-root-no-root at Thu Sep 25 23:02:19 2025 
  Took  0.11 


 Starting at mutPropGrowth  Thu Sep 25 23:02:19 2025 

 Ended test.mutPropGrowth:  Thu Sep 25 23:02:36 2025 
  Took  17.42 


 Starting test.mutator-oncoSimulSample.R test at Thu Sep 25 23:02:37 2025 

 Finished test.mutator-oncoSimulSample.R test at Thu Sep 25 23:02:53 2025 
  Took  16.73 seconds 


 Starting test.mutator.R test at Thu Sep 25 23:02:53 2025[1] 2.043526e-12
[1] 4.931631e-14

 Finished test.mutator.R test at Thu Sep 25 23:04:11 2025 
  Took  77.74 


 Starting test.mutatorFDF.R test at Thu Sep 25 23:04:11 2025
 Starting oncoSimulIndiv-miscell tests Thu Sep 25 23:04:12 2025 

 Ending oncoSimulIndiv-miscell tests Thu Sep 25 23:04:23 2025 
  Took  11.09 


 Starting oncoSimulSample-failures tests Thu Sep 25 23:04:23 2025 

 Ending oncoSimulSample-failures tests Thu Sep 25 23:04:27 2025 
  Took  3.79 


 Starting oncoSimulSample-limits tests Thu Sep 25 23:04:27 2025 

 Ending oncoSimulSample-limits tests Thu Sep 25 23:04:27 2025 
  Took  0.09 


 Starting per-gene-mutation rates at Thu Sep 25 23:04:27 2025 

 Ending per-gene-mutation rates at Thu Sep 25 23:05:00 2025 
  Took  33.16 


 Starting plotFitnessLandscape at Thu Sep 25 23:05:00 2025
 Ending plotFitnessLandscape at Thu Sep 25 23:05:04 2025 
  Took  4.35 


 Starting poset-transformations tests Thu Sep 25 23:05:04 2025 

 Ending poset-transformations tests Thu Sep 25 23:05:17 2025 
  Took  13.17 


 Starting sample-prob Thu Sep 25 23:05:17 2025 
[1] 6.364246e-20
[1] 1.654597e-09
[1] 1.55689e-10
[1] 1.337001e-11
[1] 1.848708e-11
[1] 1.160289e-12
[1] 3.416702e-15
[1] 1.298293e-14
[1] 7.552051e-10
[1] 2.611141e-11
[1] 2.601676e-08
[1] 2.001124e-08

 Ending sample-prob tests Thu Sep 25 23:05:40 2025 
 Took  23.11 



 Starting samplePop tests Thu Sep 25 23:05:41 2025 

 Ending samplePop tests Thu Sep 25 23:05:58 2025 
  Took  17.29 


 Starting simuls-runs-examples tests Thu Sep 25 23:05:58 2025 

 Ending simuls-runs-examples tests Thu Sep 25 23:06:08 2025 
  Took  9.81 


 Starting user variable tests Thu Sep 25 23:06:08 2025 
[1] "Checking user variable: user_var_1"
[1] "Checking rule: rule_1"

 Ending user variable tests Thu Sep 25 23:06:08 2025 
  Took  0.13 


 Starting warning-mutPropGrowth tests Thu Sep 25 23:06:08 2025 

 Ending warning-mutPropGrowth tests Thu Sep 25 23:06:08 2025 
  Took  0.43 


 Starting wide2long tests Thu Sep 25 23:06:08 2025 

 Ending wide2long tests Thu Sep 25 23:06:08 2025 
  Took  0.23 

[ FAIL 0 | WARN 19 | SKIP 7 | PASS 8376 ]

══ 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 8376 ]
> 
> proc.time()
   user  system elapsed 
265.726 108.977 356.110