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This page was generated on 2022-06-24 11:08:19 -0400 (Fri, 24 Jun 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_644.2.0 Patched (2022-06-02 r82447) -- "Vigorous Calisthenics" 4331
palomino4Windows Server 2022 Datacenterx644.2.0 Patched (2022-06-02 r82447 ucrt) -- "Vigorous Calisthenics" 4136
lconwaymacOS 12.2.1 Montereyx86_644.2.0 Patched (2022-05-29 r82424) -- "Vigorous Calisthenics" 4147
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

CHECK results for OncoSimulR on lconway


To the developers/maintainers of the OncoSimulR package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/OncoSimulR.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 1357/2118HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
OncoSimulR 3.5.0  (landing page)
Ramon Diaz-Uriarte
Snapshot Date: 2022-06-23 14:00:04 -0400 (Thu, 23 Jun 2022)
git_url: https://git.bioconductor.org/packages/OncoSimulR
git_branch: master
git_last_commit: 7af7ac6
git_last_commit_date: 2022-04-26 11:20:38 -0400 (Tue, 26 Apr 2022)
nebbiolo2Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino4Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.2.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: OncoSimulR
Version: 3.5.0
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_3.5.0.tar.gz
StartedAt: 2022-06-23 21:38:20 -0400 (Thu, 23 Jun 2022)
EndedAt: 2022-06-23 21:47:33 -0400 (Thu, 23 Jun 2022)
EllapsedTime: 552.4 seconds
RetCode: 0
Status:   OK  
CheckDir: OncoSimulR.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### 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_3.5.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.16-bioc/meat/OncoSimulR.Rcheck’
* using R version 4.2.0 Patched (2022-05-29 r82424)
* 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 ‘3.5.0’
* 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
* 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-3.16-bioc/meat/OncoSimulR.Rcheck/00check.log’
for details.



Installation output

OncoSimulR.Rcheck/00install.out

##############################################################################
##############################################################################
###
### 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
FitnessLandscape/ordered_pairs.c:138:6: warning: variable 'tot_pairs' set but not used [-Wunused-but-set-variable]
        int tot_pairs=0;
            ^
1 warning generated.
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
FitnessLandscape/summary_statistics.c:515:9: warning: variable 'meanVarianceNumberOfStepsFL' set but not used [-Wunused-but-set-variable]
        double meanVarianceNumberOfStepsFL = 0;
               ^
1 warning generated.
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)

Tests output

OncoSimulR.Rcheck/tests/testthat.Rout


R version 4.2.0 Patched (2022-05-29 r82424) -- "Vigorous Calisthenics"
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 Thu Jun 23 21:39:40 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 Thu Jun 23 21:39:41 2022 
  Took  0.42 


 Starting LOD_POM at Thu Jun 23 21:39:41 2022 

 Ending LOD_POM at Thu Jun 23 21:40:00 2022 
  Took  19.31 


 Starting test.Z-all-fitness at Thu Jun 23 21:40:00 2022 

 Ending test.Z-all-fitness at Thu Jun 23 21:40:00 2022 
  Took  0.1 


 Starting test.Z-driver-counts at Thu Jun 23 21:40:00 2022 

 Ending test.Z-driver-counts at Thu Jun 23 21:40:00 2022 
  Took  0.17 


 Starting test.Z-fixation at Thu Jun 23 21:40:00 2022 

 Ending test.Z-fixation at Thu Jun 23 21:40:01 2022 
  Took  0.84 


 Starting test.Z-magellan at Thu Jun 23 21:40:01 2022 

 Ended test.Z-magellan at Thu Jun 23 21:40:03 2022 

 Starting test.Z-mutator at Thu Jun 23 21:40:03 2022 

 Ending test.Z-mutator at Thu Jun 23 21:40:03 2022 
  Took  0.32 


 Starting test.Z-mutatorFDF at Thu Jun 23 21:40:03 2022 

 Ending test.Z-mutatorFDF at Thu Jun 23 21:40:03 2022 
  Took  0.08 


 Starting test.Z-oncoSimulIndiv at Thu Jun 23 21:40:03 2022 

 Ending test.Z-oncoSimulIndiv at Thu Jun 23 21:40:05 2022 
  Took  1.57 


 Starting test.Z-oncoSimulIndivFDF at Thu Jun 23 21:40:05 2022 

 Ending test.Z-oncoSimulIndivFDF at Thu Jun 23 21:40:05 2022 
  Took  0.13 


 Starting test.Z-rfitness-landscape at Thu Jun 23 21:40:05 2022 

 Ending test.Z-rfitness-landscape at Thu Jun 23 21:40:05 2022 
  Took  0.12 


 Starting Z-sample-only-last tests Thu Jun 23 21:40:05 2022 

 Ending Z-sample-only-last tests Thu Jun 23 21:40:05 2022 
  Took  0 


 Starting Z-total-present-drivers tests Thu Jun 23 21:40:05 2022 

 Ending Z-total-present-drivers tests Thu Jun 23 21:40:07 2022 
  Took  1.24 


 Dummy empty test  Thu Jun 23 21:40:07 2022 

 Starting accessible_genotypes at Thu Jun 23 21:40:07 2022 

 Ending accessible_genotypes at Thu Jun 23 21:40:12 2022 
  Took  5.66 


 Starting all fitness at Thu Jun 23 21:40:12 2022
 Ending all-fitness at Thu Jun 23 21:40:17 2022 
  Took  4.73 


 Starting test.allFitnessEffectsFDF at Thu Jun 23 21:40:17 2022 

 Ending test.allFitnessEffectsFDF at Thu Jun 23 21:40:17 2022 
  Took  0.26 


 Starting test.allFitnessEffectsFDF at Thu Jun 23 21:40:17 2022 

 Ending test.allFitnessEffectsFDF at Thu Jun 23 21:40:18 2022 
  Took  0.27 


 Starting driverCounts at Thu Jun 23 21:40:18 2022
 Ending driverCounts at Thu Jun 23 21:40:30 2022 
  Took  11.97 


 Starting epist-order-modules at Thu Jun 23 21:40:30 2022
 Ending epist-order-modules at Thu Jun 23 21:40:30 2022 
  Took  0.03 


 Starting test.evaluatingGenotypesFDF at Thu Jun 23 21:40:30 2022 

 Ending test.evaluatingGenotypesFDF at Thu Jun 23 21:40:30 2022 
  Took  0.17 


 Starting exercise-plotting-code at Thu Jun 23 21:40:30 2022
 Ending exercise-plotting-code at Thu Jun 23 21:40:39 2022 
  Took  8.83 


 Starting exercise-rfitness at Thu Jun 23 21:40:39 2022 

 Ending exercise-rfitness at Thu Jun 23 21:40:47 2022 
  Took  8.23 


 Starting to_Magella at Thu Jun 23 21:40:47 2022 

 Ending to_Magella at Thu Jun 23 21:40:47 2022 
  Took  0.03 


 Starting fitness preds at Thu Jun 23 21:40:47 2022 

 Observed vs expected, case III

 done tries 1 

 Ending fitness preds long at Thu Jun 23 21:41:02 2022 
  Took  15.45 


 Starting fixation  at Thu Jun 23 21:41:02 2022 

 Ending fixation  at Thu Jun 23 21:41:36 2022 
  Took  33.71 


 Starting test.flfast-additional.R test at Thu Jun 23 21:41:36 2022
 Ending test.flfast-additional.R test at Thu Jun 23 21:41:38 2022 
  Took  1.79 


 Starting test.flfast-mutator.R test at Thu Jun 23 21:41:38 2022
 Finished test.flfast-mutator.R test at Thu Jun 23 21:41:41 2022 
  Took  2.82 


 Starting genotFitness at Thu Jun 23 21:41:41 2022 

 Ending genotFitness at Thu Jun 23 21:41:41 2022 
  Took  0.14 


 Starting genot_fitness_to_epistasis at Thu Jun 23 21:41:41 2022 

 Ending genot_fitness_to_epistasis at Thu Jun 23 21:41:41 2022 
  Took  0.03 


 Starting init-mutant tests Thu Jun 23 21:41:41 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 Thu Jun 23 21:41:51 2022 
  Took  10.16 


 Starting test.magellan at Thu Jun 23 21:41:51 2022 

 Ending test.magellan at Thu Jun 23 21:41:51 2022 
  Took  0.22 


 Starting test.modules-root-no-root at Thu Jun 23 21:41:51 2022 

 Ending test.modules-root-no-root at Thu Jun 23 21:41:51 2022 
  Took  0.06 


 Starting at mutPropGrowth  Thu Jun 23 21:41:51 2022 

 Ended test.mutPropGrowth:  Thu Jun 23 21:42:11 2022 
  Took  20.19 


 Starting test.mutator-oncoSimulSample.R test at Thu Jun 23 21:42:11 2022 

 Finished test.mutator-oncoSimulSample.R test at Thu Jun 23 21:42:23 2022 
  Took  11.62 seconds 


 Starting test.mutator.R test at Thu Jun 23 21:42:23 2022[1] 2.138322e-10
[1] 6.398358e-13

 Finished test.mutator.R test at Thu Jun 23 21:43:56 2022 
  Took  92.93 


 Starting test.mutatorFDF.R test at Thu Jun 23 21:43:56 2022
 Starting test.no-v1 at Thu Jun 23 21:43:58 2022 

 Ending test.no-v1 at Thu Jun 23 21:43:58 2022 
  Took  0.02 


 Starting oncoSimulIndiv-miscell tests Thu Jun 23 21:43:58 2022 

 Ending oncoSimulIndiv-miscell tests Thu Jun 23 21:45:06 2022 
  Took  68.42 


 Starting oncoSimulSample-failures tests Thu Jun 23 21:45:06 2022 

 Ending oncoSimulSample-failures tests Thu Jun 23 21:45:11 2022 
  Took  4.13 


 Starting oncoSimulSample-limits tests Thu Jun 23 21:45:11 2022 

 Ending oncoSimulSample-limits tests Thu Jun 23 21:45:11 2022 
  Took  0.14 


 Starting per-gene-mutation rates at Thu Jun 23 21:45:11 2022 

 Ending per-gene-mutation rates at Thu Jun 23 21:46:00 2022 
  Took  49.09 


 Starting plotFitnessLandscape at Thu Jun 23 21:46:00 2022
 Ending plotFitnessLandscape at Thu Jun 23 21:46:03 2022 
  Took  2.73 


 Starting poset-transformations tests Thu Jun 23 21:46:03 2022 

 Ending poset-transformations tests Thu Jun 23 21:46:10 2022 
  Took  7.41 


 Starting sample-prob Thu Jun 23 21:46:10 2022 
[1] 6.560428e-27
[1] 3.425714e-16
[1] 2.474418e-08
[1] 1.273206e-11
[1] 1.42582e-13
[1] 2.486467e-12
[1] 1.464325e-11
[1] 3.41021e-15
[1] 8.947644e-09
[1] 2.297256e-09
[1] 8.716311e-12
[1] 7.014664e-10

 Ending sample-prob tests Thu Jun 23 21:46:22 2022 
 Took  11.8 



 Starting samplePop tests Thu Jun 23 21:46:22 2022 

 Ending samplePop tests Thu Jun 23 21:46:40 2022 
  Took  17.7 


 Starting simuls-runs-examples tests Thu Jun 23 21:46:40 2022 

 Ending simuls-runs-examples tests Thu Jun 23 21:47:19 2022 
  Took  39.59 


 Starting warning-mutPropGrowth tests Thu Jun 23 21:47:19 2022 

 Ending warning-mutPropGrowth tests Thu Jun 23 21:47:20 2022 
  Took  1.26 


 Starting wide2long tests Thu Jun 23 21:47:20 2022 

 Ending wide2long tests Thu Jun 23 21:47:21 2022 
  Took  0.24 

[ 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 
365.885 129.132 464.568 

Example timings

OncoSimulR.Rcheck/OncoSimulR-Ex.timings

nameusersystemelapsed
OncoSimulWide2Long0.4410.1230.567
POM1.0380.1540.776
allFitnessEffects1.3940.0531.451
benchmarks0.0070.0040.012
evalAllGenotypes0.1740.0100.185
example-missing-drivers0.1980.0140.213
examplePosets0.3110.0110.322
examplesFitnessEffects0.0440.0020.046
freq-dep-simul-examples0.0070.0010.009
mcfLs0.0000.0000.001
oncoSimulIndiv2.7070.7642.910
plot.fitnessEffects0.2570.0230.283
plot.oncosimul0.6940.1000.798
plotClonePhylog2.4190.2702.697
plotFitnessLandscape1.0780.0111.095
plotPoset0.1070.0060.115
poset0.1370.0060.146
rfitness0.6710.0131.054
samplePop1.1810.6791.027
simOGraph0.0710.0130.085
to_Magellan0.1900.0620.852