##############################################################################
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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_3.4.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.15-bioc/meat/OncoSimulR.Rcheck’
* using R version 4.2.1 (2022-06-23)
* using platform: x86_64-apple-darwin17.0 (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 ‘3.4.0’
* 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 ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘OncoSimulR’ can be installed ... OK
* checking installed package size ... NOTE
  installed size is  9.0Mb
  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 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 is not available
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                user system elapsed
oncoSimulIndiv 5.066  1.017   5.218
* 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
  ‘/Users/biocbuild/bbs-3.15-bioc/meat/OncoSimulR.Rcheck/00check.log’
for details.

##############################################################################
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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL OncoSimulR
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.2/Resources/library’
* installing *source* package ‘OncoSimulR’ ...
** using staged installation
** libs
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rcpp/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c FitnessLandscape/gamma.c -o FitnessLandscape/gamma.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rcpp/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c FitnessLandscape/landscape.c -o FitnessLandscape/landscape.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rcpp/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c FitnessLandscape/random.c -o FitnessLandscape/random.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rcpp/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c FitnessLandscape/sort.c -o FitnessLandscape/sort.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rcpp/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c FitnessLandscape/chain.c -o FitnessLandscape/chain.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rcpp/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c FitnessLandscape/input.c -o FitnessLandscape/input.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rcpp/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c FitnessLandscape/genotypes.c -o FitnessLandscape/genotypes.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rcpp/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c FitnessLandscape/ordered_pairs.c -o FitnessLandscape/ordered_pairs.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rcpp/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c FitnessLandscape/calculus.c -o FitnessLandscape/calculus.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rcpp/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c FitnessLandscape/vector.c -o FitnessLandscape/vector.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rcpp/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c FitnessLandscape/generalized_chain.c -o FitnessLandscape/generalized_chain.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rcpp/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c FitnessLandscape/LinearAlgebra.c -o FitnessLandscape/LinearAlgebra.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rcpp/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c FitnessLandscape/summary_statistics.c -o FitnessLandscape/summary_statistics.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rcpp/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c FitnessLandscape/epistasis_type.c -o FitnessLandscape/epistasis_type.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rcpp/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c FitnessLandscape/decomposition.c -o FitnessLandscape/decomposition.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rcpp/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c FitnessLandscape/models.c -o FitnessLandscape/models.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rcpp/include' -I/usr/local/include   -fPIC  -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 -mmacosx-version-min=10.13 -O -Wall -o fl_statistics -I/FitnessLandscape/. -L. FitnessLandscape/main_fl_statistics.c -llandscape -lm;
clang -mmacosx-version-min=10.13 -O -Wall -o fl_generate -I/FitnessLandscape/. -L. FitnessLandscape/main_fl_generate.c -llandscape -lm;
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rcpp/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c BNB_nr.cpp -o BNB_nr.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rcpp/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c OncoSimulR_init.c -o OncoSimulR_init.o
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rcpp/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c RcppExports.cpp -o RcppExports.o
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rcpp/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c accessible_genotypes.cpp -o accessible_genotypes.o
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rcpp/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c bnb_common.cpp -o bnb_common.o
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rcpp/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c new_restrict.cpp -o new_restrict.o
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -o OncoSimulR.so BNB_nr.o OncoSimulR_init.o RcppExports.o accessible_genotypes.o bnb_common.o new_restrict.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing via 'install.libs.R' to /Library/Frameworks/R.framework/Versions/4.2/Resources/library/00LOCK-OncoSimulR/00new/OncoSimulR
[1] ""
Installing fl_statistics fl_generate to /Library/Frameworks/R.framework/Versions/4.2/Resources/library/00LOCK-OncoSimulR/00new/OncoSimulR/exec
Installing library OncoSimulR.so to /Library/Frameworks/R.framework/Versions/4.2/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 4.2.1 (2022-06-23) -- "Funny-Looking Kid"
Copyright (C) 2022 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin17.0 (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 Wed Oct 19 05:45:11 2022 

exprtk parser error: 

Error[00] Position: 00 Type: [  Syntax Error] Msg: ERR197 - Undefined symbol: 'n_2_3' Expression: n_2_3

exprtk parser error: 

Error[00] Position: 00 Type: [  Syntax Error] Msg: ERR197 - Undefined symbol: 'f_2_3' Expression: f_2_3

 Ending FDF-small-fitness-specs Wed Oct 19 05:45:12 2022 
  Took  0.79 


 Starting LOD_POM at Wed Oct 19 05:45:12 2022 

 Ending LOD_POM at Wed Oct 19 05:45:51 2022 
  Took  38.92 


 Starting test.Z-all-fitness at Wed Oct 19 05:45:51 2022 

 Ending test.Z-all-fitness at Wed Oct 19 05:45:51 2022 
  Took  0.19 


 Starting test.Z-driver-counts at Wed Oct 19 05:45:51 2022 

 Ending test.Z-driver-counts at Wed Oct 19 05:45:52 2022 
  Took  0.33 


 Starting test.Z-fixation at Wed Oct 19 05:45:52 2022 

 Ending test.Z-fixation at Wed Oct 19 05:45:53 2022 
  Took  1.2 


 Starting test.Z-magellan at Wed Oct 19 05:45:53 2022 

 Ended test.Z-magellan at Wed Oct 19 05:45:56 2022 

 Starting test.Z-mutator at Wed Oct 19 05:45:56 2022 

 Ending test.Z-mutator at Wed Oct 19 05:45:57 2022 
  Took  0.58 


 Starting test.Z-mutatorFDF at Wed Oct 19 05:45:57 2022 

 Ending test.Z-mutatorFDF at Wed Oct 19 05:45:57 2022 
  Took  0.18 


 Starting test.Z-oncoSimulIndiv at Wed Oct 19 05:45:57 2022 

 Ending test.Z-oncoSimulIndiv at Wed Oct 19 05:46:00 2022 
  Took  3.06 


 Starting test.Z-oncoSimulIndivFDF at Wed Oct 19 05:46:00 2022 

 Ending test.Z-oncoSimulIndivFDF at Wed Oct 19 05:46:00 2022 
  Took  0.29 


 Starting test.Z-rfitness-landscape at Wed Oct 19 05:46:00 2022 

 Ending test.Z-rfitness-landscape at Wed Oct 19 05:46:00 2022 
  Took  0.23 


 Starting Z-sample-only-last tests Wed Oct 19 05:46:00 2022 

 Ending Z-sample-only-last tests Wed Oct 19 05:46:00 2022 
  Took  0 


 Starting Z-total-present-drivers tests Wed Oct 19 05:46:01 2022 

 Ending Z-total-present-drivers tests Wed Oct 19 05:46:03 2022 
  Took  2.82 


 Dummy empty test  Wed Oct 19 05:46:03 2022 

 Starting accessible_genotypes at Wed Oct 19 05:46:03 2022 

 Ending accessible_genotypes at Wed Oct 19 05:46:16 2022 
  Took  12.44 


 Starting all fitness at Wed Oct 19 05:46:16 2022
 Ending all-fitness at Wed Oct 19 05:46:26 2022 
  Took  9.85 


 Starting test.allFitnessEffectsFDF at Wed Oct 19 05:46:26 2022 

 Ending test.allFitnessEffectsFDF at Wed Oct 19 05:46:26 2022 
  Took  0.24 


 Starting test.allFitnessEffectsFDF at Wed Oct 19 05:46:26 2022 

 Ending test.allFitnessEffectsFDF at Wed Oct 19 05:46:27 2022 
  Took  0.73 


 Starting driverCounts at Wed Oct 19 05:46:27 2022
 Ending driverCounts at Wed Oct 19 05:46:45 2022 
  Took  17.99 


 Starting epist-order-modules at Wed Oct 19 05:46:45 2022
 Ending epist-order-modules at Wed Oct 19 05:46:45 2022 
  Took  0.07 


 Starting test.evaluatingGenotypesFDF at Wed Oct 19 05:46:45 2022 

 Ending test.evaluatingGenotypesFDF at Wed Oct 19 05:46:45 2022 
  Took  0.34 


 Starting exercise-plotting-code at Wed Oct 19 05:46:45 2022
 Ending exercise-plotting-code at Wed Oct 19 05:47:00 2022 
  Took  15.05 


 Starting exercise-rfitness at Wed Oct 19 05:47:00 2022 

 Ending exercise-rfitness at Wed Oct 19 05:47:17 2022 
  Took  16.63 


 Starting to_Magella at Wed Oct 19 05:47:17 2022 

 Ending to_Magella at Wed Oct 19 05:47:17 2022 
  Took  0.06 


 Starting fitness preds at Wed Oct 19 05:47:17 2022 

 Observed vs expected, case III

 T.not is 
[1] TRUE
 [1] 3.249133e-43 1.034464e-31 2.821747e-40 4.524906e-40 5.258647e-42
 [6] 4.279934e-37 0.000000e+00 0.000000e+00 6.329048e-34 1.924935e-37
[11] 8.432340e-33 3.983840e-34 7.016907e-31 1.815778e-46 2.190866e-25
[16] 2.349637e-23 9.921218e-37 5.848835e-16

 T.yest 
[1] FALSE
 [1] 0.0101517332 0.8568082366 0.5532992468 0.2845291186 0.7778857170
 [6] 0.5705558140 0.6807836076 0.0447778259 0.7426688885 0.3531965116
[11] 0.5588224759 0.6126900579 0.6881338473 0.9790966233 0.6274993277
[16] 0.2207164081 0.0152586165 0.9030132892 0.8299425938 0.0936187521
[21] 0.2414752347 0.6033665976 0.0627112981 0.3464941610 0.4663867412
[26] 0.1642738553 0.3299156796 0.0001599904 0.8987450565 0.7233130146

 larger values of T.yest 
[1] 28

 lm and plot

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

Residuals:
       Min         1Q     Median         3Q        Max 
-0.0168331 -0.0043226 -0.0009089  0.0027969  0.0291779 

Coefficients:
               Estimate Std. Error  t value Pr(>|t|)    
(Intercept)   -0.010594   0.006162   -1.719   0.0966 .  
log(Expected)  1.001162   0.000518 1932.852   <2e-16 ***
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1

Residual standard error: 0.009317 on 28 degrees of freedom
Multiple R-squared:      1,	Adjusted R-squared:      1 
F-statistic: 3.736e+06 on 1 and 28 DF,  p-value: < 2.2e-16

Linear hypothesis test

Hypothesis:
(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 0.0030837                               
2     28 0.0024304  2 0.00065329 3.7631 0.03569 *
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1

 done tries 2 

 Ending fitness preds long at Wed Oct 19 05:48:03 2022 
  Took  45.85 


 Starting fixation  at Wed Oct 19 05:48:03 2022 

 Ending fixation  at Wed Oct 19 05:49:09 2022 
  Took  66.52 


 Starting test.flfast-additional.R test at Wed Oct 19 05:49:09 2022
 DEBUG2: Value of rnb = nan

 DEBUG2: Value of m = 1

 DEBUG2: Value of pe = 0

 DEBUG2: Value of pm = 0.999998

 this is spP

 popSize = 1
 birth = 1
 death = 0
 W = 1.00001
 R = 1.00001
 mutation = 6e-06
 timeLastUpdate = 2.76384
 absfitness = -inf
 numMutablePos = 6

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

 Ending test.flfast-additional.R test at Wed Oct 19 05:49:13 2022 
  Took  3.85 


 Starting test.flfast-mutator.R test at Wed Oct 19 05:49:13 2022
 Finished test.flfast-mutator.R test at Wed Oct 19 05:49:18 2022 
  Took  5.09 


 Starting genotFitness at Wed Oct 19 05:49:18 2022 

 Ending genotFitness at Wed Oct 19 05:49:18 2022 
  Took  0.28 


 Starting genot_fitness_to_epistasis at Wed Oct 19 05:49:18 2022 

 Ending genot_fitness_to_epistasis at Wed Oct 19 05:49:19 2022 
  Took  0.06 


 Starting init-mutant tests Wed Oct 19 05:49:19 2022 

exprtk parser error: 

Error[00] Position: 18 Type: [  Syntax Error] Msg: ERR197 - Undefined symbol: 'f_2' Expression: 1.1 + 0.7*((f_1 + f_2) > 0.3)

 Ending init-mutant tests Wed Oct 19 05:49:38 2022 
  Took  19.84 


 Starting test.magellan at Wed Oct 19 05:49:38 2022 

 Ending test.magellan at Wed Oct 19 05:49:39 2022 
  Took  0.28 


 Starting test.modules-root-no-root at Wed Oct 19 05:49:39 2022 

 Ending test.modules-root-no-root at Wed Oct 19 05:49:39 2022 
  Took  0.12 


 Starting at mutPropGrowth  Wed Oct 19 05:49:39 2022 

 Ended test.mutPropGrowth:  Wed Oct 19 05:50:02 2022 
  Took  22.9 


 Starting test.mutator-oncoSimulSample.R test at Wed Oct 19 05:50:02 2022 

 Finished test.mutator-oncoSimulSample.R test at Wed Oct 19 05:50:21 2022 
  Took  19.38 seconds 


 Starting test.mutator.R test at Wed Oct 19 05:50:21 2022[1] 7.969195e-08
[1] 1.021428e-09

 Finished test.mutator.R test at Wed Oct 19 05:50:59 2022 
  Took  37.76 


 Starting test.mutatorFDF.R test at Wed Oct 19 05:50:59 2022
 Starting test.no-v1 at Wed Oct 19 05:51:00 2022 

 Ending test.no-v1 at Wed Oct 19 05:51:00 2022 
  Took  0.02 


 Starting oncoSimulIndiv-miscell tests Wed Oct 19 05:51:00 2022 

 Ending oncoSimulIndiv-miscell tests Wed Oct 19 05:51:49 2022 
  Took  48.59 


 Starting oncoSimulSample-failures tests Wed Oct 19 05:51:49 2022 

 Ending oncoSimulSample-failures tests Wed Oct 19 05:51:53 2022 
  Took  4.04 


 Starting oncoSimulSample-limits tests Wed Oct 19 05:51:53 2022 

 Ending oncoSimulSample-limits tests Wed Oct 19 05:51:53 2022 
  Took  0.14 


 Starting per-gene-mutation rates at Wed Oct 19 05:51:53 2022 

 Ending per-gene-mutation rates at Wed Oct 19 05:53:29 2022 
  Took  96.35 


 Starting plotFitnessLandscape at Wed Oct 19 05:53:29 2022
 Ending plotFitnessLandscape at Wed Oct 19 05:53:35 2022 
  Took  5.55 


 Starting poset-transformations tests Wed Oct 19 05:53:35 2022 

 Ending poset-transformations tests Wed Oct 19 05:53:51 2022 
  Took  16.23 


 Starting sample-prob Wed Oct 19 05:53:51 2022 
[1] 1.401176e-22
[1] 2.517264e-07
[1] 2.132955e-10
[1] 2.732096e-11
[1] 2.455078e-14
[1] 1.138048e-11
[1] 1.733134e-13
[1] 5.135412e-17
[1] 1.717626e-07
[1] 4.57603e-08
[1] 6.995443e-08
[1] 2.507795e-08

 Ending sample-prob tests Wed Oct 19 05:54:11 2022 
 Took  20.21 



 Starting samplePop tests Wed Oct 19 05:54:11 2022 

 Ending samplePop tests Wed Oct 19 05:54:37 2022 
  Took  25.45 


 Starting simuls-runs-examples tests Wed Oct 19 05:54:37 2022 

 Ending simuls-runs-examples tests Wed Oct 19 05:55:41 2022 
  Took  64.14 


 Starting warning-mutPropGrowth tests Wed Oct 19 05:55:41 2022 

 Ending warning-mutPropGrowth tests Wed Oct 19 05:55:45 2022 
  Took  3.87 


 Starting wide2long tests Wed Oct 19 05:55:45 2022 

 Ending wide2long tests Wed Oct 19 05:55:45 2022 
  Took  0.83 

[ FAIL 0 | WARN 1 | SKIP 7 | PASS 8174 ]

══ Skipped tests ═══════════════════════════════════════════════════════════════
• On Mac (2)
• empty test (5)

[ FAIL 0 | WARN 1 | SKIP 7 | PASS 8174 ]
> 
> proc.time()
   user  system elapsed 
690.222 126.125 642.913