##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:OncoSimulR.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings OncoSimulR_3.0.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.13-bioc/meat/OncoSimulR.Rcheck’
* using R version 4.1.1 (2021-08-10)
* 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 ‘3.0.0’
* 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:
  .git_fetch_output.txt
  .git_merge_output.txt
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
* checking installed package size ... NOTE
  installed size is  8.9Mb
  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 4.827  1.063   5.139
* 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: 3 NOTEs
See
  ‘/Users/biocbuild/bbs-3.13-bioc/meat/OncoSimulR.Rcheck/00check.log’
for details.

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


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.1/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/4.1/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/4.1/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/4.1/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/4.1/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/4.1/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/4.1/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/4.1/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/4.1/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/4.1/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/4.1/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/4.1/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/4.1/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/4.1/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/4.1/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/4.1/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/4.1/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/4.1/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/4.1/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/4.1/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/4.1/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/4.1/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/4.1/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/4.1/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/4.1/Resources/library/00LOCK-OncoSimulR/00new/OncoSimulR
[1] ""
Installing fl_statistics fl_generate to /Library/Frameworks/R.framework/Versions/4.1/Resources/library/00LOCK-OncoSimulR/00new/OncoSimulR/exec
Installing library OncoSimulR.so to /Library/Frameworks/R.framework/Versions/4.1/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 4.1.1 (2021-08-10) -- "Kick Things"
Copyright (C) 2021 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 Thu Oct 14 21:57:15 2021 

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 Thu Oct 14 21:57:16 2021 
  Took  0.55 


 Starting LOD_POM at Thu Oct 14 21:57:16 2021 

 Ending LOD_POM at Thu Oct 14 21:57:44 2021 
  Took  27.81 


 Starting test.Z-all-fitness at Thu Oct 14 21:57:44 2021 

 Ending test.Z-all-fitness at Thu Oct 14 21:57:44 2021 
  Took  0.08 


 Starting test.Z-driver-counts at Thu Oct 14 21:57:44 2021 

 Ending test.Z-driver-counts at Thu Oct 14 21:57:44 2021 
  Took  0.29 


 Starting test.Z-fixation at Thu Oct 14 21:57:44 2021 

 Ending test.Z-fixation at Thu Oct 14 21:57:45 2021 
  Took  1.09 


 Starting test.Z-magellan at Thu Oct 14 21:57:45 2021 

 Ended test.Z-magellan at Thu Oct 14 21:57:48 2021 

 Starting test.Z-mutator at Thu Oct 14 21:57:48 2021 

 Ending test.Z-mutator at Thu Oct 14 21:57:49 2021 
  Took  0.41 


 Starting test.Z-mutatorFDF at Thu Oct 14 21:57:49 2021 

 Ending test.Z-mutatorFDF at Thu Oct 14 21:57:49 2021 
  Took  0.11 


 Starting test.Z-oncoSimulIndiv at Thu Oct 14 21:57:49 2021 

 Ending test.Z-oncoSimulIndiv at Thu Oct 14 21:57:51 2021 
  Took  2.5 


 Starting test.Z-oncoSimulIndivFDF at Thu Oct 14 21:57:51 2021 

 Ending test.Z-oncoSimulIndivFDF at Thu Oct 14 21:57:51 2021 
  Took  0.2 


 Starting test.Z-rfitness-landscape at Thu Oct 14 21:57:51 2021 

 Ending test.Z-rfitness-landscape at Thu Oct 14 21:57:52 2021 
  Took  0.18 


 Starting Z-sample-only-last tests Thu Oct 14 21:57:52 2021 

 Ending Z-sample-only-last tests Thu Oct 14 21:57:52 2021 
  Took  0 


 Starting Z-total-present-drivers tests Thu Oct 14 21:57:52 2021 

 Ending Z-total-present-drivers tests Thu Oct 14 21:57:54 2021 
  Took  2.05 


 Dummy empty test  Thu Oct 14 21:57:54 2021 

 Starting accessible_genotypes at Thu Oct 14 21:57:54 2021 

 Ending accessible_genotypes at Thu Oct 14 21:58:02 2021 
  Took  8.15 


 Starting all fitness at Thu Oct 14 21:58:02 2021
 Ending all-fitness at Thu Oct 14 21:58:09 2021 
  Took  7.17 


 Starting test.allFitnessEffectsFDF at Thu Oct 14 21:58:09 2021 

 Ending test.allFitnessEffectsFDF at Thu Oct 14 21:58:09 2021 
  Took  0.23 


 Starting test.allFitnessEffectsFDF at Thu Oct 14 21:58:09 2021 

 Ending test.allFitnessEffectsFDF at Thu Oct 14 21:58:10 2021 
  Took  0.39 


 Starting driverCounts at Thu Oct 14 21:58:10 2021
 Ending driverCounts at Thu Oct 14 21:58:26 2021 
  Took  16.43 


 Starting epist-order-modules at Thu Oct 14 21:58:26 2021
 Ending epist-order-modules at Thu Oct 14 21:58:26 2021 
  Took  0.06 


 Starting test.evaluatingGenotypesFDF at Thu Oct 14 21:58:26 2021 

 Ending test.evaluatingGenotypesFDF at Thu Oct 14 21:58:26 2021 
  Took  0.29 


 Starting exercise-plotting-code at Thu Oct 14 21:58:26 2021
 Ending exercise-plotting-code at Thu Oct 14 21:58:39 2021 
  Took  12.74 


 Starting exercise-rfitness at Thu Oct 14 21:58:39 2021 

 Ending exercise-rfitness at Thu Oct 14 21:58:48 2021 
  Took  8.72 


 Starting to_Magella at Thu Oct 14 21:58:48 2021 

 Ending to_Magella at Thu Oct 14 21:58:48 2021 
  Took  0.04 


 Starting fitness preds at Thu Oct 14 21:58:48 2021 

 Observed vs expected, case III

 T.not is 
[1] TRUE
 [1] 1.835661e-39 2.693315e-36 5.663780e-34 4.928713e-43 6.708014e-43
 [6] 1.617460e-39 0.000000e+00 0.000000e+00 2.175343e-34 2.648771e-41
[11] 4.408199e-30 8.084578e-37 2.932197e-26 1.120341e-46 6.906675e-22
[16] 4.741977e-22 2.327970e-35 5.410383e-13

 T.yest 
[1] TRUE
 [1] 0.32298943 0.42218401 0.07794397 0.04819953 0.04483940 0.13931112
 [7] 0.42704956 0.69967992 0.57120496 0.17507166 0.98143787 0.24779024
[13] 0.38077099 0.54987485 0.62883548 0.30465096 0.90947487 0.95114558
[19] 0.87438458 0.79996957 0.86636992 0.60766819 0.88955902 0.13936043
[25] 0.93432397 0.64797203 0.89805986 0.98018118 0.14073754 0.85367729

 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 
-0.0122930 -0.0031394 -0.0003269  0.0035092  0.0162593 

Coefficients:
                Estimate Std. Error  t value Pr(>|t|)    
(Intercept)   -0.0101656  0.0045301   -2.244   0.0329 *  
log(Expected)  1.0010767  0.0003808 2628.786   <2e-16 ***
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1

Residual standard error: 0.00685 on 28 degrees of freedom
Multiple R-squared:      1,	Adjusted R-squared:      1 
F-statistic: 6.911e+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 0.0018267                               
2     28 0.0013137  2 0.00051299 5.4668 0.0099 **
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1

 done tries 2 

 Ending fitness preds long at Thu Oct 14 21:59:28 2021 
  Took  40.19 


 Starting fixation  at Thu Oct 14 21:59:28 2021 

 Ending fixation  at Thu Oct 14 22:00:13 2021 
  Took  44.54 


 Starting test.flfast-additional.R test at Thu Oct 14 22:00:13 2021
 Ending test.flfast-additional.R test at Thu Oct 14 22:00:15 2021 
  Took  2.65 


 Starting test.flfast-mutator.R test at Thu Oct 14 22:00:15 2021
 Finished test.flfast-mutator.R test at Thu Oct 14 22:00:19 2021 
  Took  3.4 


 Starting genotFitness at Thu Oct 14 22:00:19 2021 

 Ending genotFitness at Thu Oct 14 22:00:19 2021 
  Took  0.18 


 Starting genot_fitness_to_epistasis at Thu Oct 14 22:00:19 2021 

 Ending genot_fitness_to_epistasis at Thu Oct 14 22:00:19 2021 
  Took  0.03 


 Starting init-mutant tests Thu Oct 14 22:00:19 2021 

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 Thu Oct 14 22:00:35 2021 
  Took  16.06 


 Starting test.magellan at Thu Oct 14 22:00:35 2021 

 Ending test.magellan at Thu Oct 14 22:00:35 2021 
  Took  0.3 


 Starting test.modules-root-no-root at Thu Oct 14 22:00:35 2021 

 Ending test.modules-root-no-root at Thu Oct 14 22:00:35 2021 
  Took  0.11 


 Starting at mutPropGrowth  Thu Oct 14 22:00:36 2021 

 Ended test.mutPropGrowth:  Thu Oct 14 22:00:55 2021 
  Took  19.49 


 Starting test.mutator-oncoSimulSample.R test at Thu Oct 14 22:00:55 2021 

 Finished test.mutator-oncoSimulSample.R test at Thu Oct 14 22:01:11 2021 
  Took  16.09 seconds 


 Starting test.mutator.R test at Thu Oct 14 22:01:11 2021[1] 5.832951e-12
[1] 6.787391e-12

 Finished test.mutator.R test at Thu Oct 14 22:01:45 2021 
  Took  33.81 


 Starting test.mutatorFDF.R test at Thu Oct 14 22:01:45 2021
 Starting test.no-v1 at Thu Oct 14 22:01:46 2021 

 Ending test.no-v1 at Thu Oct 14 22:01:46 2021 
  Took  0.01 


 Starting oncoSimulIndiv-miscell tests Thu Oct 14 22:01:46 2021 

 Ending oncoSimulIndiv-miscell tests Thu Oct 14 22:02:31 2021 
  Took  45.36 


 Starting oncoSimulSample-failures tests Thu Oct 14 22:02:31 2021 

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

 Ending oncoSimulSample-failures tests Thu Oct 14 22:02:36 2021 
  Took  4.2 


 Starting oncoSimulSample-limits tests Thu Oct 14 22:02:36 2021 

 Ending oncoSimulSample-limits tests Thu Oct 14 22:02:36 2021 
  Took  0.11 


 Starting per-gene-mutation rates at Thu Oct 14 22:02:36 2021 

 Ending per-gene-mutation rates at Thu Oct 14 22:03:39 2021 
  Took  63.37 


 Starting plotFitnessLandscape at Thu Oct 14 22:03:39 2021
 Ending plotFitnessLandscape at Thu Oct 14 22:03:43 2021 
  Took  3.99 


 Starting poset-transformations tests Thu Oct 14 22:03:43 2021 

 Ending poset-transformations tests Thu Oct 14 22:04:04 2021 
  Took  20.59 


 Starting sample-prob Thu Oct 14 22:04:04 2021 
[1] 1.49272e-26
[1] 2.817881e-13
[1] 9.459999e-10
[1] 1.326871e-11
[1] 2.164592e-14
[1] 5.1149e-14
[1] 2.076649e-14
[1] 1.145209e-13
[1] 3.640082e-11
[1] 1.089427e-12
[1] 2.119227e-08
[1] 4.089262e-09

 Ending sample-prob tests Thu Oct 14 22:04:24 2021 
 Took  20.65 



 Starting samplePop tests Thu Oct 14 22:04:24 2021 

 Ending samplePop tests Thu Oct 14 22:04:51 2021 
  Took  26.32 


 Starting simuls-runs-examples tests Thu Oct 14 22:04:51 2021 

 Ending simuls-runs-examples tests Thu Oct 14 22:05:33 2021 
  Took  42.47 


 Starting warning-mutPropGrowth tests Thu Oct 14 22:05:33 2021 

 Ending warning-mutPropGrowth tests Thu Oct 14 22:05:35 2021 
  Took  1.97 


 Starting wide2long tests Thu Oct 14 22:05:35 2021 

 Ending wide2long tests Thu Oct 14 22:05:36 2021 
  Took  0.74 

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

[ FAIL 0 | WARN 1 | SKIP 7 | PASS 8167 ]
> 
> proc.time()
   user  system elapsed 
558.212 113.695 507.475