##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.16-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:OncoSimulR.install-out.txt --library=F:\biocbuild\bbs-3.16-bioc\R\library --no-vignettes --timings OncoSimulR_4.0.2.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'F:/biocbuild/bbs-3.16-bioc/meat/OncoSimulR.Rcheck'
* using R version 4.2.3 (2023-03-15 ucrt)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'OncoSimulR/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'OncoSimulR' version '4.0.2'
* 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 ... OK
* checking for portable file names ... OK
* checking whether package 'OncoSimulR' can be installed ... OK
* checking installed package size ... NOTE
  installed size is  8.4Mb
  sub-directories of 1Mb or more:
    libs   6.6Mb
* 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 R 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 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 for x64 is not available
File 'F:/biocbuild/bbs-3.16-bioc/R/library/OncoSimulR/libs/x64/OncoSimulR.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
  Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs. The detected symbols are linked into the code but
might come from libraries and not actually be called.

See 'Writing portable packages' in the 'Writing R Extensions' manual.
* 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 in 'inst/doc' ... 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
  'F:/biocbuild/bbs-3.16-bioc/meat/OncoSimulR.Rcheck/00check.log'
for details.

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.16-bioc\R\bin\R.exe CMD INSTALL OncoSimulR
###
##############################################################################
##############################################################################


* installing to library 'F:/biocbuild/bbs-3.16-bioc/R/library'
* installing *source* package 'OncoSimulR' ...
** using staged installation
** libs
gcc  -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include'   -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c FitnessLandscape/gamma.c -o FitnessLandscape/gamma.o
gcc  -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include'   -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c FitnessLandscape/landscape.c -o FitnessLandscape/landscape.o
gcc  -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include'   -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c FitnessLandscape/random.c -o FitnessLandscape/random.o
gcc  -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include'   -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c FitnessLandscape/sort.c -o FitnessLandscape/sort.o
gcc  -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include'   -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c FitnessLandscape/chain.c -o FitnessLandscape/chain.o
gcc  -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include'   -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c FitnessLandscape/input.c -o FitnessLandscape/input.o
gcc  -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include'   -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c FitnessLandscape/genotypes.c -o FitnessLandscape/genotypes.o
gcc  -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include'   -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c FitnessLandscape/ordered_pairs.c -o FitnessLandscape/ordered_pairs.o
gcc  -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include'   -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c FitnessLandscape/calculus.c -o FitnessLandscape/calculus.o
gcc  -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include'   -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c FitnessLandscape/vector.c -o FitnessLandscape/vector.o
gcc  -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include'   -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c FitnessLandscape/generalized_chain.c -o FitnessLandscape/generalized_chain.o
gcc  -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include'   -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c FitnessLandscape/LinearAlgebra.c -o FitnessLandscape/LinearAlgebra.o
gcc  -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include'   -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c FitnessLandscape/summary_statistics.c -o FitnessLandscape/summary_statistics.o
gcc  -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include'   -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c FitnessLandscape/epistasis_type.c -o FitnessLandscape/epistasis_type.o
gcc  -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include'   -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c FitnessLandscape/decomposition.c -o FitnessLandscape/decomposition.o
gcc  -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include'   -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c FitnessLandscape/models.c -o FitnessLandscape/models.o
gcc  -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include'   -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -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 ;
C:\rtools42\x86_64-w64-mingw32.static.posix\bin\ar.exe: creating liblandscape.a
ranlib liblandscape.a;
gcc  -O -Wall -o fl_statistics -I/FitnessLandscape/. -L. FitnessLandscape/main_fl_statistics.c -llandscape -lm;
gcc  -O -Wall -o fl_generate -I/FitnessLandscape/. -L. FitnessLandscape/main_fl_generate.c -llandscape -lm;
gcc  -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include'   -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c OncoSimulR_init.c -o OncoSimulR_init.o
g++ -std=gnu++14  -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include'   -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -Wa,-mbig-obj -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++14  -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include'   -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -Wa,-mbig-obj -c unity_osimul.cpp -o unity_osimul.o
In file included from unity_osimul.cpp:4:
UnityOncoSimul/BNB_nr.cpp: In function 'void nr_innerBNB(const fitnessEffectsAll&, const std::vector<double>&, const double&, TypeModel, const int&, const std::vector<double>&, const double&, const double&, const double&, const std::vector<std::vector<int> >&, const time_t&, const double&, const double&, const double&, const int&, const double&, const double&, const int&, double&, double&, double&, double&, double&, int&, int&, int&, std::vector<Genotype>&, std::vector<double>&, std::vector<int>&, std::vector<double>&, std::vector<Intervention>&, std::vector<double>&, std::vector<double>&, std::vector<int>&, std::vector<int>&, bool&, std::mt19937&, double&, bool&, const std::map<int, std::__cxx11::basic_string<char> >&, const fitness_as_genes&, PhylogName&, bool, const fitnessEffectsAll&, const std::vector<int>&, const double&, const double&, const double&, const bool&, const std::vector<std::vector<int> >&, const double&, const int&, const double&, int&, int&, std::map<std::__cxx11::basic_string<char>, std::__cxx11::basic_string<char> >&, POM&, Rcpp::List, Rcpp::List, Rcpp::List)':
UnityOncoSimul/BNB_nr.cpp:860:10: warning: 'minNextMutationTime' may be used uninitialized in this function [-Wmaybe-uninitialized]
  860 |   double minNextMutationTime;
      |          ^~~~~~~~~~~~~~~~~~~
g++ -std=gnu++14 -shared -s -static-libgcc -o OncoSimulR.dll tmp.def OncoSimulR_init.o RcppExports.o unity_osimul.o -LC:/rtools42/x86_64-w64-mingw32.static.posix/lib/x64 -LC:/rtools42/x86_64-w64-mingw32.static.posix/lib -LF:/biocbuild/bbs-3.16-bioc/R/bin/x64 -lR
installing via 'install.libs.R' to F:/biocbuild/bbs-3.16-bioc/R/library/00LOCK-OncoSimulR/00new/OncoSimulR
[1] "/x64"
Installing fl_statistics.exe fl_generate.exe to F:/biocbuild/bbs-3.16-bioc/R/library/00LOCK-OncoSimulR/00new/OncoSimulR/exec/x64
Installing library OncoSimulR.dll to F:/biocbuild/bbs-3.16-bioc/R/library/00LOCK-OncoSimulR/00new/OncoSimulR/libs/x64
** 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
** 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 4.2.3 (2023-03-15 ucrt) -- "Shortstop Beagle"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (64-bit)

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)
> 
> test_check("OncoSimulR")

 Starting FDF-letter-fitness-order Tue Apr 11 04:12:46 2023 

exprtk parser error: 

Error[00] Position: 00 Type: [  Syntax Error] Msg: ERR201 - Undefined symbol: 'n_2_3' Expression: n_2_3

exprtk parser error: 

Error[00] Position: 00 Type: [  Syntax Error] Msg: ERR201 - Undefined symbol: 'f_2_3' Expression: f_2_3

 Ending FDF-small-fitness-specs Tue Apr 11 04:12:47 2023 
  Took  0.54 


 Starting LOD_POM at Tue Apr 11 04:12:47 2023 

 Ending LOD_POM at Tue Apr 11 04:13:05 2023 
  Took  18.45 


 Starting test.Z-all-fitness at Tue Apr 11 04:13:05 2023 

 Ending test.Z-all-fitness at Tue Apr 11 04:13:05 2023 
  Took  0.12 


 Starting test.Z-driver-counts at Tue Apr 11 04:13:05 2023 

 Ending test.Z-driver-counts at Tue Apr 11 04:13:06 2023 
  Took  0.22 


 Starting test.Z-fixation at Tue Apr 11 04:13:06 2023 

 Ending test.Z-fixation at Tue Apr 11 04:13:06 2023 
  Took  0.74 


 Starting interventions tests Tue Apr 11 04:13:06 2023 
[1] "Checking intervention: intOverBAffectsR"
[1] "Checking intervention: intOverTotPop"
Init Mutant with birth == 1.0
[1] "Checking intervention: intOverBAffectsR"
[1] "Checking intervention: intOverTotPop"
Init Mutant with birth == 1.0

 Ending interventions tests Tue Apr 11 04:17:38 2023 
  Took  271.53 


 Starting test.Z-magellan at Tue Apr 11 04:17:38 2023 

 Ended test.Z-magellan at Tue Apr 11 04:17:40 2023 

 Starting test.Z-mutator at Tue Apr 11 04:17:40 2023 

 Ending test.Z-mutator at Tue Apr 11 04:17:41 2023 
  Took  0.58 


 Starting test.Z-mutatorFDF at Tue Apr 11 04:17:41 2023 

 Ending test.Z-mutatorFDF at Tue Apr 11 04:17:41 2023 
  Took  0.18 


 Starting test.Z-oncoSimulIndiv at Tue Apr 11 04:17:41 2023 

 Ending test.Z-oncoSimulIndiv at Tue Apr 11 04:17:42 2023 
  Took  1.56 


 Starting test.Z-oncoSimulIndivConstant at Tue Apr 11 04:17:42 2023 

 Ending test.Z-oncoSimulIndivConstant at Tue Apr 11 04:17:46 2023 
  Took  3.49 


 Starting test.Z-oncoSimulIndivDeath at Tue Apr 11 04:17:46 2023 


 Ending test.Z-oncoSimulIndivDeath at Tue Apr 11 04:17:47 2023 
  Took  1.33 


 Starting test.Z-oncoSimulIndivFDF at Tue Apr 11 04:17:47 2023 

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

 Ending test.Z-oncoSimulIndivFDF at Tue Apr 11 04:17:48 2023 
  Took  0.39 


 Starting test.Z-rfitness-landscape at Tue Apr 11 04:17:48 2023 

 Ending test.Z-rfitness-landscape at Tue Apr 11 04:17:48 2023 
  Took  0.16 


 Starting Z-sample-only-last tests Tue Apr 11 04:17:48 2023 

 Ending Z-sample-only-last tests Tue Apr 11 04:17:48 2023 
  Took  0 


 Starting Z-total-present-drivers tests Tue Apr 11 04:17:48 2023 

 Ending Z-total-present-drivers tests Tue Apr 11 04:17:49 2023 
  Took  1.02 


 Dummy empty test  Tue Apr 11 04:17:49 2023 

 Starting accessible_genotypes at Tue Apr 11 04:17:49 2023 

 Ending accessible_genotypes at Tue Apr 11 04:17:55 2023 
  Took  6.69 


 Starting all fitness at Tue Apr 11 04:17:55 2023
 Ending all-fitness at Tue Apr 11 04:18:00 2023 
  Took  4.17 


 Starting test.allFitnessEffectsFDF at Tue Apr 11 04:18:00 2023 

 Ending test.allFitnessEffectsFDF at Tue Apr 11 04:18:00 2023 
  Took  0.11 


 Starting test.allFitnessEffectsDeath at Tue Apr 11 04:18:00 2023 

 Ending test.allFitnessEffectsDeath at Tue Apr 11 04:18:00 2023 
  Took  0.35 


 Starting test.allFitnessEffectsFDF at Tue Apr 11 04:18:00 2023 

 Ending test.allFitnessEffectsFDF at Tue Apr 11 04:18:00 2023 
  Took  0.38 


 Starting driverCounts at Tue Apr 11 04:18:00 2023
 Ending driverCounts at Tue Apr 11 04:18:08 2023 
  Took  7.56 


 Starting epist-order-modules at Tue Apr 11 04:18:08 2023
 Ending epist-order-modules at Tue Apr 11 04:18:08 2023 
  Took  0.03 


 Starting test.evaluatingGenotypesDeath at Tue Apr 11 04:18:08 2023 

 Ending test.evaluatingGenotypesDeath at Tue Apr 11 04:18:08 2023 
  Took  0.16 


 Starting test.evaluatingGenotypesFDF at Tue Apr 11 04:18:08 2023 

 Ending test.evaluatingGenotypesFDF at Tue Apr 11 04:18:08 2023 
  Took  0.18 


 Starting exercise-plotting-code at Tue Apr 11 04:18:08 2023
 Ending exercise-plotting-code at Tue Apr 11 04:18:15 2023 
  Took  6.11 


 Starting exercise-rfitness at Tue Apr 11 04:18:15 2023 

 Ending exercise-rfitness at Tue Apr 11 04:18:28 2023 
  Took  13.09 


 Starting to_Magella at Tue Apr 11 04:18:28 2023 

 Ending to_Magella at Tue Apr 11 04:18:28 2023 
  Took  0.05 


 Starting fitness preds at Tue Apr 11 04:18:28 2023 

 Observed vs expected, case III

 done tries 1 

 Ending fitness preds long at Tue Apr 11 04:18:39 2023 
  Took  11.24 


 Starting fixation  at Tue Apr 11 04:18:39 2023 

 Ending fixation  at Tue Apr 11 04:19:26 2023 
  Took  47.52 


 Starting test.flfast-additional.R test at Tue Apr 11 04:19:26 2023
 Ending test.flfast-additional.R test at Tue Apr 11 04:19:28 2023 
  Took  1.78 


 Starting test.flfast-mutator.R test at Tue Apr 11 04:19:28 2023
 Finished test.flfast-mutator.R test at Tue Apr 11 04:19:31 2023 
  Took  2.45 


 Starting genotFitness at Tue Apr 11 04:19:31 2023 

 Ending genotFitness at Tue Apr 11 04:19:31 2023 
  Took  0.24 


 Starting genot_fitness_to_epistasis at Tue Apr 11 04:19:31 2023 

 Ending genot_fitness_to_epistasis at Tue Apr 11 04:19:31 2023 
  Took  0.05 


 Starting init-mutant tests Tue Apr 11 04:19:31 2023 

exprtk parser error: 

Error[00] Position: 18 Type: [  Syntax Error] Msg: ERR201 - Undefined symbol: 'f_2' Expression: 1.1 + 0.7*((f_1 + f_2) > 0.3)

 Ending init-mutant tests Tue Apr 11 04:19:44 2023 
  Took  13.28 


 Starting interventions tests Tue Apr 11 04:19:44 2023 
[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"
Init Mutant with birth == 1.0
[1] "Checking intervention: intOverA"
Init Mutant with birth == 1.0
[1] "Checking intervention: intOverTotPop"
[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
[1] "Checking intervention: intOverA"
[1] "Checking intervention: intOverB"
[1] "Checking intervention: intOverC"
[1] "Checking intervention: intOverD"
Init Mutant with birth == 1.0
[1] "Checking intervention: Bothering R strain, by reducing C"
[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 11 04:26:39 2023 
  Took  414.49 


 Starting test.magellan at Tue Apr 11 04:26:39 2023 

 Ending test.magellan at Tue Apr 11 04:26:40 2023 
  Took  0.78 


 Starting test.modules-root-no-root at Tue Apr 11 04:26:40 2023 

 Ending test.modules-root-no-root at Tue Apr 11 04:26:40 2023 
  Took  0.08 


 Starting at mutPropGrowth  Tue Apr 11 04:26:40 2023 

 Ended test.mutPropGrowth:  Tue Apr 11 04:26:51 2023 
  Took  11.48 


 Starting test.mutator-oncoSimulSample.R test at Tue Apr 11 04:26:51 2023 

 Finished test.mutator-oncoSimulSample.R test at Tue Apr 11 04:27:01 2023 
  Took  9.78 seconds 


 Starting test.mutator.R test at Tue Apr 11 04:27:01 2023[1] 4.026642e-07
[1] 5.091431e-11

 Finished test.mutator.R test at Tue Apr 11 04:27:21 2023 
  Took  20 


 Starting test.mutatorFDF.R test at Tue Apr 11 04:27:21 2023
 Starting test.no-v1 at Tue Apr 11 04:27:22 2023 

 Ending test.no-v1 at Tue Apr 11 04:27:22 2023 
  Took  0.01 


 Starting oncoSimulIndiv-miscell tests Tue Apr 11 04:27:22 2023 

 Ending oncoSimulIndiv-miscell tests Tue Apr 11 04:27:33 2023 
  Took  10.82 


 Starting oncoSimulSample-failures tests Tue Apr 11 04:27:33 2023 

 Ending oncoSimulSample-failures tests Tue Apr 11 04:27:37 2023 
  Took  3.85 


 Starting oncoSimulSample-limits tests Tue Apr 11 04:27:37 2023 

 Ending oncoSimulSample-limits tests Tue Apr 11 04:27:37 2023 
  Took  0.08 


 Starting per-gene-mutation rates at Tue Apr 11 04:27:37 2023 

 Ending per-gene-mutation rates at Tue Apr 11 04:28:17 2023 
  Took  40.39 


 Starting plotFitnessLandscape at Tue Apr 11 04:28:17 2023
 Ending plotFitnessLandscape at Tue Apr 11 04:28:20 2023 
  Took  2.56 


 Starting poset-transformations tests Tue Apr 11 04:28:20 2023 

 Ending poset-transformations tests Tue Apr 11 04:28:27 2023 
  Took  7.59 


 Starting sample-prob Tue Apr 11 04:28:27 2023 
[1] 1.551684e-19
[1] 2.471192e-16
[1] 1.084999e-09
[1] 1.168026e-11
[1] 1.910411e-13
[1] 3.789788e-13
[1] 2.750728e-10
[1] 5.133303e-12
[1] 8.169219e-08
[1] 1.335673e-10
[1] 4.396786e-09
[1] 2.595297e-09

 Ending sample-prob tests Tue Apr 11 04:28:39 2023 
 Took  11.78 



 Starting samplePop tests Tue Apr 11 04:28:39 2023 

 Ending samplePop tests Tue Apr 11 04:28:53 2023 
  Took  13.5 


 Starting simuls-runs-examples tests Tue Apr 11 04:28:53 2023 

 Ending simuls-runs-examples tests Tue Apr 11 04:29:05 2023 
  Took  12.84 


 Starting user variable tests Tue Apr 11 04:29:05 2023 
[1] "Checking user variable: user_var_1"
[1] "Checking rule: rule_1"

 Ending user variable tests Tue Apr 11 04:29:06 2023 
  Took  0.08 


 Starting warning-mutPropGrowth tests Tue Apr 11 04:29:06 2023 

 Ending warning-mutPropGrowth tests Tue Apr 11 04:29:06 2023 
  Took  0.74 


 Starting wide2long tests Tue Apr 11 04:29:06 2023 

 Ending wide2long tests Tue Apr 11 04:29:07 2023 
  Took  0.37 

[ FAIL 0 | WARN 16 | SKIP 6 | PASS 12471 ]

══ Skipped tests ═══════════════════════════════════════════════════════════════
• On Windows (1)
• empty test (5)

[ FAIL 0 | WARN 16 | SKIP 6 | PASS 12471 ]
> 
> proc.time()
   user  system elapsed 
 969.34    4.56  985.09