##############################################################################
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###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD check --install=check:OncoSimulR.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings OncoSimulR_4.10.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/OncoSimulR.Rcheck’
* using R Under development (unstable) (2025-02-19 r87757)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
    aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0
    GNU Fortran (GCC) 14.2.0
* running under: openEuler 24.03 (LTS-SP1)
* 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: ‘aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0’
* used C++ compiler: ‘aarch64-unknown-linux-gnu-g++ (GCC) 14.2.0’
* checking installed package size ... INFO
  installed size is 46.6Mb
  sub-directories of 1Mb or more:
    libs  44.9Mb
* 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 loading without being on the library search path ... OK
* checking whether startup messages can be suppressed ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking use of PKG_*FLAGS in Makefiles ... OK
* checking include directives in Makefiles ... OK
* checking compiled code ... NOTE
Note: information on .o files is not available
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.21-bioc/meat/OncoSimulR.Rcheck/00check.log’
for details.

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD INSTALL OncoSimulR
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/R/R-devel_2025-02-19/site-library’
* installing *source* package ‘OncoSimulR’ ...
** this is package ‘OncoSimulR’ version ‘4.10.0’
** using staged installation
** libs
using C compiler: ‘aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0’
using C++ compiler: ‘aarch64-unknown-linux-gnu-g++ (GCC) 14.2.0’
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -I"/home/biocbuild/R/R/include" -DNDEBUG  -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/Rcpp/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -Werror=format-security -c FitnessLandscape/gamma.c -o FitnessLandscape/gamma.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -I"/home/biocbuild/R/R/include" -DNDEBUG  -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/Rcpp/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -Werror=format-security -c FitnessLandscape/landscape.c -o FitnessLandscape/landscape.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -I"/home/biocbuild/R/R/include" -DNDEBUG  -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/Rcpp/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -Werror=format-security -c FitnessLandscape/random.c -o FitnessLandscape/random.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -I"/home/biocbuild/R/R/include" -DNDEBUG  -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/Rcpp/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -Werror=format-security -c FitnessLandscape/sort.c -o FitnessLandscape/sort.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -I"/home/biocbuild/R/R/include" -DNDEBUG  -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/Rcpp/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -Werror=format-security -c FitnessLandscape/chain.c -o FitnessLandscape/chain.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -I"/home/biocbuild/R/R/include" -DNDEBUG  -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/Rcpp/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -Werror=format-security -c FitnessLandscape/input.c -o FitnessLandscape/input.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -I"/home/biocbuild/R/R/include" -DNDEBUG  -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/Rcpp/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -Werror=format-security -c FitnessLandscape/genotypes.c -o FitnessLandscape/genotypes.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -I"/home/biocbuild/R/R/include" -DNDEBUG  -I'/home/biocbuild/R/R-devel_2025-02-19/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
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -I"/home/biocbuild/R/R/include" -DNDEBUG  -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/Rcpp/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -Werror=format-security -c FitnessLandscape/calculus.c -o FitnessLandscape/calculus.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -I"/home/biocbuild/R/R/include" -DNDEBUG  -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/Rcpp/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -Werror=format-security -c FitnessLandscape/vector.c -o FitnessLandscape/vector.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -I"/home/biocbuild/R/R/include" -DNDEBUG  -I'/home/biocbuild/R/R-devel_2025-02-19/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
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -I"/home/biocbuild/R/R/include" -DNDEBUG  -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/Rcpp/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -Werror=format-security -c FitnessLandscape/LinearAlgebra.c -o FitnessLandscape/LinearAlgebra.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -I"/home/biocbuild/R/R/include" -DNDEBUG  -I'/home/biocbuild/R/R-devel_2025-02-19/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
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -I"/home/biocbuild/R/R/include" -DNDEBUG  -I'/home/biocbuild/R/R-devel_2025-02-19/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
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -I"/home/biocbuild/R/R/include" -DNDEBUG  -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/Rcpp/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -Werror=format-security -c FitnessLandscape/decomposition.c -o FitnessLandscape/decomposition.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -I"/home/biocbuild/R/R/include" -DNDEBUG  -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/Rcpp/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -Werror=format-security -c FitnessLandscape/models.c -o FitnessLandscape/models.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -I"/home/biocbuild/R/R/include" -DNDEBUG  -I'/home/biocbuild/R/R-devel_2025-02-19/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;
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -O -Wall -o fl_statistics -I/FitnessLandscape/. -L. FitnessLandscape/main_fl_statistics.c -llandscape -lm;
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -O -Wall -o fl_generate -I/FitnessLandscape/. -L. FitnessLandscape/main_fl_generate.c -llandscape -lm;
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -I"/home/biocbuild/R/R/include" -DNDEBUG  -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/Rcpp/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -Werror=format-security -c OncoSimulR_init.c -o OncoSimulR_init.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++17 -I"/home/biocbuild/R/R/include" -DNDEBUG  -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/Rcpp/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -Werror=format-security  -c RcppExports.cpp -o RcppExports.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++17 -I"/home/biocbuild/R/R/include" -DNDEBUG  -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/Rcpp/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -Werror=format-security  -c unity_osimul.cpp -o unity_osimul.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++17 -shared -L/home/biocbuild/R/R/lib -L/usr/local/lib -o OncoSimulR.so OncoSimulR_init.o RcppExports.o unity_osimul.o -L/home/biocbuild/R/R/lib -lR
installing via 'install.libs.R' to /home/biocbuild/R/R-devel_2025-02-19/site-library/00LOCK-OncoSimulR/00new/OncoSimulR
[1] ""
Installing fl_statistics fl_generate to /home/biocbuild/R/R-devel_2025-02-19/site-library/00LOCK-OncoSimulR/00new/OncoSimulR/exec
Installing library OncoSimulR.so to /home/biocbuild/R/R-devel_2025-02-19/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 Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: aarch64-unknown-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 Fri Aug 15 12:30:03 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 Fri Aug 15 12:30:03 2025 
  Took  0.74 


 Starting LOD_POM at Fri Aug 15 12:30:03 2025 

 Ending LOD_POM at Fri Aug 15 12:30:16 2025 
  Took  12.58 


 Starting test.Z-all-fitness at Fri Aug 15 12:30:16 2025 

 Ending test.Z-all-fitness at Fri Aug 15 12:30:16 2025 
  Took  0.14 


 Starting test.Z-driver-counts at Fri Aug 15 12:30:16 2025 

 Ending test.Z-driver-counts at Fri Aug 15 12:30:16 2025 
  Took  0.17 


 Starting test.Z-fixation at Fri Aug 15 12:30:16 2025 

 Ending test.Z-fixation at Fri Aug 15 12:30:17 2025 
  Took  0.36 


 Starting test.Z-magellan at Fri Aug 15 12:30:17 2025 

 Ended test.Z-magellan at Fri Aug 15 12:30:18 2025 

 Starting test.Z-mutator at Fri Aug 15 12:30:18 2025 

 Ending test.Z-mutator at Fri Aug 15 12:30:19 2025 
  Took  0.45 


 Starting test.Z-mutatorFDF at Fri Aug 15 12:30:19 2025 

 Ending test.Z-mutatorFDF at Fri Aug 15 12:30:19 2025 
  Took  0.13 


 Starting test.Z-oncoSimulIndiv at Fri Aug 15 12:30:19 2025 

 Ending test.Z-oncoSimulIndiv at Fri Aug 15 12:30:20 2025 
  Took  0.72 


 Starting test.Z-oncoSimulIndivConstant at Fri Aug 15 12:30:20 2025 

 Ending test.Z-oncoSimulIndivConstant at Fri Aug 15 12:30:22 2025 
  Took  2.77 


 Starting test.Z-oncoSimulIndivDeath at Fri Aug 15 12:30:22 2025 


 Ending test.Z-oncoSimulIndivDeath at Fri Aug 15 12:30:24 2025 
  Took  1.3 


 Starting test.Z-oncoSimulIndivFDF at Fri Aug 15 12:30:24 2025 

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

 Ending test.Z-oncoSimulIndivFDF at Fri Aug 15 12:30:25 2025 
  Took  0.72 


 Starting test.Z-rfitness-landscape at Fri Aug 15 12:30:25 2025 

 Ending test.Z-rfitness-landscape at Fri Aug 15 12:30:25 2025 
  Took  0.29 


 Starting Z-sample-only-last tests Fri Aug 15 12:30:25 2025 

 Ending Z-sample-only-last tests Fri Aug 15 12:30:25 2025 
  Took  0 


 Starting Z-total-present-drivers tests Fri Aug 15 12:30:25 2025 

 Ending Z-total-present-drivers tests Fri Aug 15 12:30:26 2025 
  Took  0.96 


 Dummy empty test  Fri Aug 15 12:30:26 2025 

 Starting accessible_genotypes at Fri Aug 15 12:30:26 2025 

 Ending accessible_genotypes at Fri Aug 15 12:30:36 2025 
  Took  10.42 


 Starting all fitness at Fri Aug 15 12:30:36 2025
 Ending all-fitness at Fri Aug 15 12:30:43 2025 
  Took  6.78 


 Starting test.allFitnessEffectsFDF at Fri Aug 15 12:30:43 2025 

 Ending test.allFitnessEffectsFDF at Fri Aug 15 12:30:43 2025 
  Took  0.17 


 Starting test.allFitnessEffectsDeath at Fri Aug 15 12:30:43 2025 

 Ending test.allFitnessEffectsDeath at Fri Aug 15 12:30:44 2025 
  Took  0.52 


 Starting test.allFitnessEffectsFDF at Fri Aug 15 12:30:44 2025 

 Ending test.allFitnessEffectsFDF at Fri Aug 15 12:30:44 2025 
  Took  0.51 


 Starting driverCounts at Fri Aug 15 12:30:44 2025
 Ending driverCounts at Fri Aug 15 12:30:59 2025 
  Took  14.57 


 Starting epist-order-modules at Fri Aug 15 12:30:59 2025
 Ending epist-order-modules at Fri Aug 15 12:30:59 2025 
  Took  0.19 


 Starting test.evaluatingGenotypesDeath at Fri Aug 15 12:30:59 2025 

 Ending test.evaluatingGenotypesDeath at Fri Aug 15 12:30:59 2025 
  Took  0.3 


 Starting test.evaluatingGenotypesFDF at Fri Aug 15 12:30:59 2025 

 Ending test.evaluatingGenotypesFDF at Fri Aug 15 12:31:00 2025 
  Took  0.3 


 Starting exercise-plotting-code at Fri Aug 15 12:31:00 2025
 Ending exercise-plotting-code at Fri Aug 15 12:31:04 2025 
  Took  4.43 


 Starting exercise-rfitness at Fri Aug 15 12:31:04 2025 

 Ending exercise-rfitness at Fri Aug 15 12:31:17 2025 
  Took  12.64 


 Starting to_Magella at Fri Aug 15 12:31:17 2025 

 Ending to_Magella at Fri Aug 15 12:31:17 2025 
  Took  0.05 


 Starting fitness preds at Fri Aug 15 12:31:17 2025 

 Observed vs expected, case III

 T.not is 
[1] TRUE
 [1] 4.136458e-42 4.725024e-34 3.279573e-36 7.827397e-41 3.194190e-39
 [6] 1.141211e-38 0.000000e+00 0.000000e+00 9.649445e-36 1.678420e-40
[11] 9.699545e-35 6.740402e-35 8.863447e-30 3.844517e-42 1.792793e-25
[16] 3.905744e-23 2.117691e-35 2.763361e-18

 T.yest 
[1] TRUE
 [1] 0.71308172 0.14904218 0.07258238 0.41839518 0.08920144 0.23005495
 [7] 0.22609492 0.07077831 0.15296298 0.81547858 0.70861545 0.39684367
[13] 0.02954224 0.69647664 0.24040428 0.81200537 0.13115590 0.91166359
[19] 0.54421262 0.03211868 0.24788369 0.60178287 0.25621370 0.01159419
[25] 0.10746010 0.84819559 0.62930794 0.48830163 0.82418033 0.15549544

 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 
-0.027597 -0.001671  0.001017  0.005601  0.016462 

Coefficients:
               Estimate Std. Error  t value Pr(>|t|)    
(Intercept)   0.0155815  0.0070621    2.206   0.0357 *  
log(Expected) 0.9981748  0.0005937 1681.384   <2e-16 ***
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1

Residual standard error: 0.01068 on 28 degrees of freedom
Multiple R-squared:      1,	Adjusted R-squared:      1 
F-statistic: 2.827e+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 0.0051093                                
2     28 0.0031927  2 0.0019166 8.4045 0.001384 **
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1

 done tries 2 

 Ending fitness preds long at Fri Aug 15 12:31:37 2025 
  Took  20.29 


 Starting fixation  at Fri Aug 15 12:31:37 2025 

 Ending fixation  at Fri Aug 15 12:31:57 2025 
  Took  19.42 


 Starting test.flfast-additional.R test at Fri Aug 15 12:31:57 2025
 Ending test.flfast-additional.R test at Fri Aug 15 12:31:58 2025 
  Took  1.75 


 Starting test.flfast-mutator.R test at Fri Aug 15 12:31:58 2025
 Finished test.flfast-mutator.R test at Fri Aug 15 12:32:00 2025 
  Took  1.58 


 Starting genotFitness at Fri Aug 15 12:32:00 2025 

 Ending genotFitness at Fri Aug 15 12:32:00 2025 
  Took  0.23 


 Starting genot_fitness_to_epistasis at Fri Aug 15 12:32:00 2025 

 Ending genot_fitness_to_epistasis at Fri Aug 15 12:32:00 2025 
  Took  0.05 


 Starting init-mutant tests Fri Aug 15 12:32:00 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 Fri Aug 15 12:32:08 2025 
  Took  7.54 


 Starting interventions tests Fri Aug 15 12:32:08 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] 0.51 0.51 0.51
[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 Fri Aug 15 12:32:13 2025 
  Took  5.06 


 Starting test.magellan at Fri Aug 15 12:32:13 2025 

 Ending test.magellan at Fri Aug 15 12:32:13 2025 
  Took  0.15 


 Starting test.modules-root-no-root at Fri Aug 15 12:32:13 2025 

 Ending test.modules-root-no-root at Fri Aug 15 12:32:13 2025 
  Took  0.11 


 Starting at mutPropGrowth  Fri Aug 15 12:32:13 2025 

 Ended test.mutPropGrowth:  Fri Aug 15 12:32:23 2025 
  Took  9.52 


 Starting test.mutator-oncoSimulSample.R test at Fri Aug 15 12:32:23 2025 

 Finished test.mutator-oncoSimulSample.R test at Fri Aug 15 12:32:34 2025 
  Took  11.66 seconds 


 Starting test.mutator.R test at Fri Aug 15 12:32:34 2025[1] 5.97259e-09
[1] 8.046847e-13

 Finished test.mutator.R test at Fri Aug 15 12:32:52 2025 
  Took  18.11 


 Starting test.mutatorFDF.R test at Fri Aug 15 12:32:52 2025
 Starting test.no-v1 at Fri Aug 15 12:32:53 2025 

 Ending test.no-v1 at Fri Aug 15 12:32:53 2025 
  Took  0.01 


 Starting oncoSimulIndiv-miscell tests Fri Aug 15 12:32:53 2025 

 Ending oncoSimulIndiv-miscell tests Fri Aug 15 12:33:06 2025 
  Took  12.98 


 Starting oncoSimulSample-failures tests Fri Aug 15 12:33:06 2025 

 Ending oncoSimulSample-failures tests Fri Aug 15 12:33:11 2025 
  Took  4.37 


 Starting oncoSimulSample-limits tests Fri Aug 15 12:33:11 2025 

 Ending oncoSimulSample-limits tests Fri Aug 15 12:33:11 2025 
  Took  0.09 


 Starting per-gene-mutation rates at Fri Aug 15 12:33:11 2025 

 Ending per-gene-mutation rates at Fri Aug 15 12:33:47 2025 
  Took  36.18 


 Starting plotFitnessLandscape at Fri Aug 15 12:33:47 2025
 Ending plotFitnessLandscape at Fri Aug 15 12:33:51 2025 
  Took  4.64 


 Starting poset-transformations tests Fri Aug 15 12:33:51 2025 

 Ending poset-transformations tests Fri Aug 15 12:34:05 2025 
  Took  13.91 


 Starting sample-prob Fri Aug 15 12:34:05 2025 
[1] 2.859847e-31
[1] 1.057957e-10
[1] 1.225809e-08
[1] 1.260304e-11
[1] 9.28579e-13
[1] 2.981903e-16
[1] 1.231095e-10
[1] 3.252399e-12
[1] 2.169278e-10
[1] 1.249595e-10
[1] 4.871845e-08
[1] 8.141184e-10

 Ending sample-prob tests Fri Aug 15 12:34:15 2025 
 Took  9.28 



 Starting samplePop tests Fri Aug 15 12:34:15 2025 

 Ending samplePop tests Fri Aug 15 12:34:22 2025 
  Took  6.86 


 Starting simuls-runs-examples tests Fri Aug 15 12:34:22 2025 

 Ending simuls-runs-examples tests Fri Aug 15 12:34:35 2025 
  Took  13.6 


 Starting user variable tests Fri Aug 15 12:34:35 2025 
[1] "Checking user variable: user_var_1"
[1] "Checking rule: rule_1"

 Ending user variable tests Fri Aug 15 12:34:35 2025 
  Took  0.12 


 Starting warning-mutPropGrowth tests Fri Aug 15 12:34:35 2025 

 Ending warning-mutPropGrowth tests Fri Aug 15 12:34:36 2025 
  Took  0.46 


 Starting wide2long tests Fri Aug 15 12:34:36 2025 

 Ending wide2long tests Fri Aug 15 12:34:36 2025 
  Took  0.29 

[ FAIL 0 | WARN 19 | SKIP 5 | PASS 8409 ]

══ Skipped tests (5) ═══════════════════════════════════════════════════════════
• empty test (5): 'test.FDF-letter-fitness-order.R:376:1',
  'test.ZZ-dummy-skip-warn-test.R:8:1', 'test.ZZ-dummy-skip-warn-test.R:12:1',
  'test.fixation.R:4:1', 'test.init-mutant.R:1099:1'

[ FAIL 0 | WARN 19 | SKIP 5 | PASS 8409 ]
> 
> proc.time()
   user  system elapsed 
282.317  35.955 279.378