##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD check --install=check:OncoSimulR.install-out.txt --library=/home/biocbuild/bbs-3.23-bioc/R/site-library --timings OncoSimulR_4.13.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.23-bioc/meat/OncoSimulR.Rcheck’
* using R version 4.6.0 alpha (2026-04-05 r89794)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.3.0-6ubuntu2~24.04.1) 13.3.0
    GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04.1) 13.3.0
* running under: Ubuntu 24.04.4 LTS
* using session charset: UTF-8
* current time: 2026-04-14 07:34:37 UTC
* checking for file ‘OncoSimulR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘OncoSimulR’ version ‘4.13.1’
* 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: ‘gcc (Ubuntu 13.3.0-6ubuntu2~24.04.1) 13.3.0’
* used C++ compiler: ‘g++ (Ubuntu 13.3.0-6ubuntu2~24.04.1) 13.3.0’
* checking installed package size ... INFO
  installed size is 19.3Mb
  sub-directories of 1Mb or more:
    libs  17.8Mb
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking whether startup messages can be suppressed ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking use of PKG_*FLAGS in Makefiles ... OK
* checking include directives in Makefiles ... OK
* checking compiled code ... INFO
Note: information on .o files is not available
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 1 NOTE
See
  ‘/home/biocbuild/bbs-3.23-bioc/meat/OncoSimulR.Rcheck/00check.log’
for details.

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD INSTALL OncoSimulR
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.23-bioc/R/site-library’
* installing *source* package ‘OncoSimulR’ ...
** this is package ‘OncoSimulR’ version ‘4.13.1’
** using staged installation
** libs
using C compiler: ‘gcc (Ubuntu 13.3.0-6ubuntu2~24.04.1) 13.3.0’
using C++ compiler: ‘g++ (Ubuntu 13.3.0-6ubuntu2~24.04.1) 13.3.0’
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rcpp/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security -c FitnessLandscape/gamma.c -o FitnessLandscape/gamma.o
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rcpp/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security -c FitnessLandscape/landscape.c -o FitnessLandscape/landscape.o
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rcpp/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security -c FitnessLandscape/random.c -o FitnessLandscape/random.o
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rcpp/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security -c FitnessLandscape/sort.c -o FitnessLandscape/sort.o
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rcpp/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security -c FitnessLandscape/chain.c -o FitnessLandscape/chain.o
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rcpp/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security -c FitnessLandscape/input.c -o FitnessLandscape/input.o
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rcpp/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security -c FitnessLandscape/genotypes.c -o FitnessLandscape/genotypes.o
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rcpp/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security -c FitnessLandscape/ordered_pairs.c -o FitnessLandscape/ordered_pairs.o
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rcpp/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security -c FitnessLandscape/calculus.c -o FitnessLandscape/calculus.o
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rcpp/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security -c FitnessLandscape/vector.c -o FitnessLandscape/vector.o
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rcpp/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security -c FitnessLandscape/generalized_chain.c -o FitnessLandscape/generalized_chain.o
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rcpp/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security -c FitnessLandscape/LinearAlgebra.c -o FitnessLandscape/LinearAlgebra.o
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rcpp/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security -c FitnessLandscape/summary_statistics.c -o FitnessLandscape/summary_statistics.o
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rcpp/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security -c FitnessLandscape/epistasis_type.c -o FitnessLandscape/epistasis_type.o
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rcpp/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security -c FitnessLandscape/decomposition.c -o FitnessLandscape/decomposition.o
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rcpp/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security -c FitnessLandscape/models.c -o FitnessLandscape/models.o
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rcpp/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security -c FitnessLandscape/verbose.c -o FitnessLandscape/verbose.o
ar -r liblandscape.a FitnessLandscape/gamma.o FitnessLandscape/landscape.o FitnessLandscape/random.o FitnessLandscape/sort.o FitnessLandscape/chain.o FitnessLandscape/input.o FitnessLandscape/genotypes.o FitnessLandscape/ordered_pairs.o FitnessLandscape/calculus.o FitnessLandscape/vector.o FitnessLandscape/generalized_chain.o FitnessLandscape/LinearAlgebra.o FitnessLandscape/summary_statistics.o FitnessLandscape/epistasis_type.o FitnessLandscape/decomposition.o FitnessLandscape/models.o FitnessLandscape/verbose.o ;
ar: creating liblandscape.a
ranlib liblandscape.a;
gcc -std=gnu2x -O -Wall -o fl_statistics -I/FitnessLandscape/. -L. FitnessLandscape/main_fl_statistics.c -llandscape -lm;
gcc -std=gnu2x -O -Wall -o fl_generate -I/FitnessLandscape/. -L. FitnessLandscape/main_fl_generate.c -llandscape -lm;
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rcpp/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security -c OncoSimulR_init.c -o OncoSimulR_init.o
g++ -std=gnu++20 -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rcpp/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++20 -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rcpp/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c unity_osimul.cpp -o unity_osimul.o
g++ -std=gnu++20 -shared -L/home/biocbuild/bbs-3.23-bioc/R/lib -L/usr/local/lib -o OncoSimulR.so OncoSimulR_init.o RcppExports.o unity_osimul.o -L/home/biocbuild/bbs-3.23-bioc/R/lib -lR
installing via 'install.libs.R' to /home/biocbuild/bbs-3.23-bioc/R/site-library/00LOCK-OncoSimulR/00new/OncoSimulR
[1] ""
Installing fl_statistics fl_generate to /home/biocbuild/bbs-3.23-bioc/R/site-library/00LOCK-OncoSimulR/00new/OncoSimulR/exec
Installing library OncoSimulR.so to /home/biocbuild/bbs-3.23-bioc/R/site-library/00LOCK-OncoSimulR/00new/OncoSimulR/libs
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (OncoSimulR)

R version 4.6.0 alpha (2026-04-05 r89794)
Copyright (C) 2026 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(testthat)
> library(OncoSimulR)
This is package OncoSimulR. If you are running it on an aarch64 (arm64) platform with a MacOS note that the package fails some tests in that platform + OS that I have no way of debugging. Please read file README_tests_kjohnson3_aarch64-apple-darwin20.txt in the tests directory. As of 2024-10-09, this platform is unsupported until we can properly debug it.
> 
> test_check("OncoSimulR")

 Starting FDF-letter-fitness-order Tue Apr 14 03:35:55 2026 

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 Apr 14 03:35:56 2026 
  Took  0.48 


 Starting LOD_POM at Tue Apr 14 03:35:56 2026 

 Ending LOD_POM at Tue Apr 14 03:36:05 2026 
  Took  9.16 


 Starting test.Z-all-fitness at Tue Apr 14 03:36:05 2026 

 Ending test.Z-all-fitness at Tue Apr 14 03:36:05 2026 
  Took  0.09 


 Starting test.Z-driver-counts at Tue Apr 14 03:36:05 2026 

 Ending test.Z-driver-counts at Tue Apr 14 03:36:05 2026 
  Took  0.09 


 Starting test.Z-fixation at Tue Apr 14 03:36:05 2026 

 Ending test.Z-fixation at Tue Apr 14 03:36:06 2026 
  Took  0.21 


 Starting test.Z-magellan at Tue Apr 14 03:36:06 2026 

 Ended test.Z-magellan at Tue Apr 14 03:36:07 2026 

 Starting test.Z-mutator at Tue Apr 14 03:36:07 2026 

 Ending test.Z-mutator at Tue Apr 14 03:36:07 2026 
  Took  0.3 


 Starting test.Z-mutatorFDF at Tue Apr 14 03:36:07 2026 

 Ending test.Z-mutatorFDF at Tue Apr 14 03:36:07 2026 
  Took  0.09 


 Starting test.Z-oncoSimulIndiv at Tue Apr 14 03:36:07 2026 

 Ending test.Z-oncoSimulIndiv at Tue Apr 14 03:36:08 2026 
  Took  0.34 


 Starting test.Z-oncoSimulIndivConstant at Tue Apr 14 03:36:08 2026 

 Ending test.Z-oncoSimulIndivConstant at Tue Apr 14 03:36:10 2026 
  Took  2.17 


 Starting test.Z-oncoSimulIndivDeath at Tue Apr 14 03:36:10 2026 


 Ending test.Z-oncoSimulIndivDeath at Tue Apr 14 03:36:11 2026 
  Took  0.77 


 Starting test.Z-oncoSimulIndivFDF at Tue Apr 14 03:36:11 2026 

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

 Ending test.Z-oncoSimulIndivFDF at Tue Apr 14 03:36:12 2026 
  Took  0.75 


 Starting test.Z-rfitness-landscape at Tue Apr 14 03:36:12 2026 

 Ending test.Z-rfitness-landscape at Tue Apr 14 03:36:12 2026 
  Took  0.28 


 Starting Z-sample-only-last tests Tue Apr 14 03:36:12 2026 

 Ending Z-sample-only-last tests Tue Apr 14 03:36:12 2026 
  Took  0 


 Starting Z-total-present-drivers tests Tue Apr 14 03:36:12 2026 

 Ending Z-total-present-drivers tests Tue Apr 14 03:36:13 2026 
  Took  0.73 


 Dummy empty test  Tue Apr 14 03:36:13 2026 

 Starting accessible_genotypes at Tue Apr 14 03:36:13 2026 

 Ending accessible_genotypes at Tue Apr 14 03:36:19 2026 
  Took  6.71 


 Starting all fitness at Tue Apr 14 03:36:19 2026
 Ending all-fitness at Tue Apr 14 03:36:23 2026 
  Took  4.03 


 Starting test.allFitnessEffectsFDF at Tue Apr 14 03:36:23 2026 

 Ending test.allFitnessEffectsFDF at Tue Apr 14 03:36:23 2026 
  Took  0.11 


 Starting test.allFitnessEffectsDeath at Tue Apr 14 03:36:23 2026 

 Ending test.allFitnessEffectsDeath at Tue Apr 14 03:36:24 2026 
  Took  0.32 


 Starting test.allFitnessEffectsFDF at Tue Apr 14 03:36:24 2026 

 Ending test.allFitnessEffectsFDF at Tue Apr 14 03:36:24 2026 
  Took  0.34 


 Starting driverCounts at Tue Apr 14 03:36:24 2026
 Ending driverCounts at Tue Apr 14 03:36:31 2026 
  Took  6.66 


 Starting epist-order-modules at Tue Apr 14 03:36:31 2026
 Ending epist-order-modules at Tue Apr 14 03:36:31 2026 
  Took  0.05 


 Starting test.evaluatingGenotypesDeath at Tue Apr 14 03:36:31 2026 

 Ending test.evaluatingGenotypesDeath at Tue Apr 14 03:36:31 2026 
  Took  0.18 


 Starting test.evaluatingGenotypesFDF at Tue Apr 14 03:36:31 2026 

 Ending test.evaluatingGenotypesFDF at Tue Apr 14 03:36:31 2026 
  Took  0.18 


 Starting exercise-plotting-code at Tue Apr 14 03:36:31 2026
 Ending exercise-plotting-code at Tue Apr 14 03:36:34 2026 
  Took  2.28 


 Starting exercise-rfitness at Tue Apr 14 03:36:34 2026 

 Ending exercise-rfitness at Tue Apr 14 03:36:42 2026 
  Took  7.99 


 Starting to_Magella at Tue Apr 14 03:36:42 2026 

 Ending to_Magella at Tue Apr 14 03:36:42 2026 
  Took  0.03 


 Starting fitness preds at Tue Apr 14 03:36:42 2026 

 Observed vs expected, case III

 T.not is 
[1] TRUE
 [1] 4.685359e-43 6.804776e-34 1.514720e-37 8.027842e-44 3.164287e-40
 [6] 4.310061e-40 0.000000e+00 0.000000e+00 1.742422e-36 2.217356e-39
[11] 1.561641e-29 2.940877e-34 2.491201e-25 1.381530e-47 3.989811e-26
[16] 1.079459e-22 1.098233e-36 2.019371e-15

 T.yest 
[1] TRUE
 [1] 0.67759118 0.95657706 0.68463864 0.58516451 0.93098146 0.20730442
 [7] 0.92600053 0.57930770 0.70239256 0.05113688 0.36231055 0.61868736
[13] 0.19625431 0.88458338 0.13798160 0.51061017 0.24478258 0.07371116
[19] 0.23394773 0.92529209 0.94593882 0.55200949 0.13287598 0.19587892
[25] 0.89842593 0.95769838 0.56612563 0.39030136 0.78740492 0.32796832

 larger values of T.yest 
integer(0)

 lm and plot

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

Residuals:
      Min        1Q    Median        3Q       Max 
-0.014786 -0.006115  0.002530  0.004969  0.013163 

Coefficients:
               Estimate Std. Error  t value Pr(>|t|)    
(Intercept)   0.0015233  0.0048024    0.317    0.753    
log(Expected) 0.9994983  0.0004037 2475.822   <2e-16 ***
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1

Residual standard error: 0.007261 on 28 degrees of freedom
Multiple R-squared:      1,	Adjusted R-squared:      1 
F-statistic: 6.13e+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 0.0020903                                 
2     28 0.0014764  2 0.00061391 5.8215 0.007689 **
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1

 done tries 2 

 Ending fitness preds long at Tue Apr 14 03:36:51 2026 
  Took  9.89 


 Starting fixation  at Tue Apr 14 03:36:51 2026 

 Ending fixation  at Tue Apr 14 03:37:02 2026 
  Took  10.77 


 Starting test.flfast-additional.R test at Tue Apr 14 03:37:02 2026
 Ending test.flfast-additional.R test at Tue Apr 14 03:37:03 2026 
  Took  1.04 


 Starting test.flfast-mutator.R test at Tue Apr 14 03:37:03 2026
 Finished test.flfast-mutator.R test at Tue Apr 14 03:37:04 2026 
  Took  0.96 


 Starting genotFitness at Tue Apr 14 03:37:04 2026 

 Ending genotFitness at Tue Apr 14 03:37:04 2026 
  Took  0.16 


 Starting genot_fitness_to_epistasis at Tue Apr 14 03:37:04 2026 

 Ending genot_fitness_to_epistasis at Tue Apr 14 03:37:04 2026 
  Took  0.03 


 Starting init-mutant tests Tue Apr 14 03:37:04 2026 

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 Apr 14 03:37:09 2026 
  Took  4.86 


 Starting interventions tests Tue Apr 14 03:37:09 2026 
[1] "Checking intervention: intOverA"
[1] "Checking intervention: intOverA"
[1] "Checking intervention: intOverA"
[1] "Checking intervention: intOverA"
[1] "Checking intervention: intOverMultiplicatesA"
In intervention:intOverMultiplicatesA with WhatHappens: n_1 = n_1 * 2. You cannot intervene to generate more population.[1] "Checking intervention: intOverA"
[1] "Checking intervention: intOverA"
[1] "Checking intervention: intOverTotPop"
[1] 0.78 0.78 0.78
[1] "Checking intervention: intOverTotPop"
[1] "Checking intervention: intOverA"
[1] "Checking intervention: intOverB"
[1] "Checking intervention: intOverC"
[1] "Checking intervention: intOverD"
Init Mutant with birth == 1.0
Init Mutant with birth == 1.0
[1] "Checking intervention: intOverA"
[1] "Checking intervention: intOverB"
[1] "Checking intervention: intOverC"
[1] "Checking intervention: intOverD"
Init Mutant with birth == 1.0
Init Mutant with birth == 1.0
[1] "Checking user variable: user_var_1"
[1] "Checking rule: rule_1"
[1] "Checking rule: rule_2"
[1] "Checking rule: rule_3"
[1] "Checking intervention: intOverTotPop"
[1] "Checking intervention: intOverTotPop2"
[1] "Checking intervention: intOverTotPop3"
[1] "Checking user variable: user_var_1"
[1] "Checking rule: rule_1"
[1] "Checking rule: rule_2"
[1] "Checking rule: rule_3"
[1] "Checking intervention: intOverTotPop"

 Ending interventions tests Tue Apr 14 03:37:13 2026 
  Took  3.71 


 Starting test.magellan at Tue Apr 14 03:37:13 2026 

 Ending test.magellan at Tue Apr 14 03:37:13 2026 
  Took  0.13 


 Starting test.modules-root-no-root at Tue Apr 14 03:37:13 2026 

 Ending test.modules-root-no-root at Tue Apr 14 03:37:13 2026 
  Took  0.07 


 Starting at mutPropGrowth  Tue Apr 14 03:37:13 2026 

 Ended test.mutPropGrowth:  Tue Apr 14 03:37:18 2026 
  Took  5.1 


 Starting test.mutator-oncoSimulSample.R test at Tue Apr 14 03:37:18 2026 

 Finished test.mutator-oncoSimulSample.R test at Tue Apr 14 03:37:26 2026 
  Took  7.39 seconds 


 Starting test.mutator.R test at Tue Apr 14 03:37:26 2026[1] 1.437744e-06
[1] 1.847937e-11

 Finished test.mutator.R test at Tue Apr 14 03:37:36 2026 
  Took  10.6 


 Starting test.mutatorFDF.R test at Tue Apr 14 03:37:36 2026
 Starting oncoSimulIndiv-miscell tests Tue Apr 14 03:37:37 2026 

 Ending oncoSimulIndiv-miscell tests Tue Apr 14 03:37:45 2026 
  Took  7.86 


 Starting oncoSimulSample-failures tests Tue Apr 14 03:37:45 2026 

 Ending oncoSimulSample-failures tests Tue Apr 14 03:37:49 2026 
  Took  3.82 


 Starting oncoSimulSample-limits tests Tue Apr 14 03:37:49 2026 

 Ending oncoSimulSample-limits tests Tue Apr 14 03:37:49 2026 
  Took  0.06 


 Starting per-gene-mutation rates at Tue Apr 14 03:37:49 2026 

 Ending per-gene-mutation rates at Tue Apr 14 03:38:09 2026 
  Took  20.85 


 Starting plotFitnessLandscape at Tue Apr 14 03:38:09 2026
 Ending plotFitnessLandscape at Tue Apr 14 03:38:13 2026 
  Took  3.43 


 Starting poset-transformations tests Tue Apr 14 03:38:13 2026 

 Ending poset-transformations tests Tue Apr 14 03:38:22 2026 
  Took  8.89 


 Starting sample-prob Tue Apr 14 03:38:22 2026 
[1] 3.013953e-26
[1] 3.307137e-14
[1] 2.527367e-11
[1] -1.110223e-15
[1] 7.832685e-14
[1] 1.12606e-15
[1] 5.967783e-16
[1] 2.420386e-13
[1] 6.223227e-10
[1] 2.50216e-10
[1] 1.713889e-09
[1] 1.853484e-11

 Ending sample-prob tests Tue Apr 14 03:38:27 2026 
 Took  5.04 



 Starting samplePop tests Tue Apr 14 03:38:27 2026 

 Ending samplePop tests Tue Apr 14 03:38:31 2026 
  Took  4.22 


 Starting simuls-runs-examples tests Tue Apr 14 03:38:31 2026 

 Ending simuls-runs-examples tests Tue Apr 14 03:38:37 2026 
  Took  6.33 


 Starting user variable tests Tue Apr 14 03:38:37 2026 
[1] "Checking user variable: user_var_1"
[1] "Checking rule: rule_1"

 Ending user variable tests Tue Apr 14 03:38:37 2026 
  Took  0.09 


 Starting warning-mutPropGrowth tests Tue Apr 14 03:38:37 2026 

 Ending warning-mutPropGrowth tests Tue Apr 14 03:38:38 2026 
  Took  0.21 


 Starting wide2long tests Tue Apr 14 03:38:38 2026 

 Ending wide2long tests Tue Apr 14 03:38:38 2026 
  Took  0.11 

[ FAIL 0 | WARN 19 | SKIP 6 | PASS 8387 ]

══ Skipped tests (6) ═══════════════════════════════════════════════════════════
• empty test (6): 'test.FDF-letter-fitness-order.R:376:1', ,
  'test.ZZ-dummy-skip-warn-test.R:8:1', 'test.ZZ-dummy-skip-warn-test.R:12:1',
  'test.fixation.R:4:1', 'test.init-mutant.R:1099:1'

[ FAIL 0 | WARN 19 | SKIP 6 | PASS 8387 ]
> 
> proc.time()
   user  system elapsed 
183.149  33.655 166.502