Back to Multiple platform build/check report for BioC 3.20:   simplified   long
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This page was generated on 2024-10-10 11:48 -0400 (Thu, 10 Oct 2024).

HostnameOSArch (*)R versionInstalled pkgs
teran2Linux (Ubuntu 24.04.1 LTS)x86_644.4.1 (2024-06-14) -- "Race for Your Life" 4468
nebbiolo2Linux (Ubuntu 22.04.3 LTS)x86_644.4.1 (2024-06-14) -- "Race for Your Life" 4715
palomino8Windows Server 2022 Datacenterx644.4.1 (2024-06-14 ucrt) -- "Race for Your Life" 4473
lconwaymacOS 12.7.1 Montereyx86_644.4.1 (2024-06-14) -- "Race for Your Life" 4504
kjohnson3macOS 13.6.5 Venturaarm644.4.1 (2024-06-14) -- "Race for Your Life" 4452
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch644.4.1 (2024-06-14) -- "Race for Your Life" 4452
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

Package 1450/2270HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
OncoSimulR 4.7.7  (landing page)
Ramon Diaz-Uriarte
Snapshot Date: 2024-10-09 13:40 -0400 (Wed, 09 Oct 2024)
git_url: https://git.bioconductor.org/packages/OncoSimulR
git_branch: devel
git_last_commit: 67b7fa8
git_last_commit_date: 2024-09-18 16:48:52 -0400 (Wed, 18 Sep 2024)
teran2Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
nebbiolo2Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    OK  
palomino8Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson3macOS 13.6.5 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published
kunpeng2Linux (openEuler 22.03 LTS-SP1) / aarch64  OK    OK    OK  

CHECK results for OncoSimulR on kjohnson3

To the developers/maintainers of the OncoSimulR package:
- 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 Troubleshooting Build Report for more information.
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results


Summary

Package: OncoSimulR
Version: 4.7.7
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_4.7.7.tar.gz
StartedAt: 2024-10-09 23:11:58 -0400 (Wed, 09 Oct 2024)
EndedAt: 2024-10-09 23:13:32 -0400 (Wed, 09 Oct 2024)
EllapsedTime: 94.1 seconds
RetCode: 0
Status:   OK  
CheckDir: OncoSimulR.Rcheck
Warnings: 0

Command output

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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_4.7.7.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/OncoSimulR.Rcheck’
* using R version 4.4.1 (2024-06-14)
* using platform: aarch64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Ventura 13.6.7
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘OncoSimulR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘OncoSimulR’ version ‘4.7.7’
* 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
* used C compiler: ‘Apple clang version 15.0.0 (clang-1500.1.0.2.5)’
* used C++ compiler: ‘Apple clang version 15.0.0 (clang-1500.1.0.2.5)’
* used SDK: ‘MacOSX11.3.sdk’
* checking installed package size ... NOTE
  installed size is  9.8Mb
  sub-directories of 1Mb or more:
    libs   8.4Mb
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking whether startup messages can be suppressed ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking use of PKG_*FLAGS in Makefiles ... OK
* checking include directives in Makefiles ... OK
* checking compiled code ... NOTE
Note: information on .o files is not available
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.20-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/4.4-arm64/Resources/library’
* installing *source* package ‘OncoSimulR’ ...
** using staged installation
** libs
using C compiler: ‘Apple clang version 15.0.0 (clang-1500.1.0.2.5)’
using C++ compiler: ‘Apple clang version 15.0.0 (clang-1500.1.0.2.5)’
using SDK: ‘MacOSX11.3.sdk’
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c FitnessLandscape/gamma.c -o FitnessLandscape/gamma.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c FitnessLandscape/landscape.c -o FitnessLandscape/landscape.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c FitnessLandscape/random.c -o FitnessLandscape/random.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c FitnessLandscape/sort.c -o FitnessLandscape/sort.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c FitnessLandscape/chain.c -o FitnessLandscape/chain.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c FitnessLandscape/input.c -o FitnessLandscape/input.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c FitnessLandscape/genotypes.c -o FitnessLandscape/genotypes.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -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 -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c FitnessLandscape/calculus.c -o FitnessLandscape/calculus.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c FitnessLandscape/vector.c -o FitnessLandscape/vector.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c FitnessLandscape/generalized_chain.c -o FitnessLandscape/generalized_chain.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c FitnessLandscape/LinearAlgebra.c -o FitnessLandscape/LinearAlgebra.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -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;
               ^
FitnessLandscape/summary_statistics.c:673:6: warning: variable 'nbBl' set but not used [-Wunused-but-set-variable]
        int nbBl=1;
            ^
2 warnings generated.
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c FitnessLandscape/epistasis_type.c -o FitnessLandscape/epistasis_type.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c FitnessLandscape/decomposition.c -o FitnessLandscape/decomposition.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c FitnessLandscape/models.c -o FitnessLandscape/models.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -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 -arch arm64 -O -Wall -o fl_statistics -I/FitnessLandscape/. -L. FitnessLandscape/main_fl_statistics.c -llandscape -lm;
clang -arch arm64 -O -Wall -o fl_generate -I/FitnessLandscape/. -L. FitnessLandscape/main_fl_generate.c -llandscape -lm;
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c OncoSimulR_init.c -o OncoSimulR_init.o
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c RcppExports.cpp -o RcppExports.o
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c unity_osimul.cpp -o unity_osimul.o
In file included from unity_osimul.cpp:10:
./UnityOncoSimul/intervention_private_2.cpp:17:10: warning: variable 'totalPop' set but not used [-Wunused-but-set-variable]
  double totalPop = 0.0;
         ^
1 warning generated.
clang++ -arch arm64 -std=gnu++17 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/arm64/lib -o OncoSimulR.so OncoSimulR_init.o RcppExports.o unity_osimul.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing via 'install.libs.R' to /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/00LOCK-OncoSimulR/00new/OncoSimulR
[1] ""
Installing fl_statistics fl_generate to /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/00LOCK-OncoSimulR/00new/OncoSimulR/exec
Installing library OncoSimulR.so to /Library/Frameworks/R.framework/Versions/4.4-arm64/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 4.4.1 (2024-06-14) -- "Race for Your Life"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin20

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(testthat)
> library(OncoSimulR)
This is package OncoSimulR.If you are running it on an aarch64 (arm64) platform with a MacOS note that the package fails some tests that I have no way of debugging. Please read file README_tests_kjohnson3_aarch64-apple-darwin20.txt in the tests directory.
> 
> test_check("OncoSimulR")

 Starting FDF-letter-fitness-order Wed Oct  9 23:12:26 2024 

exprtk parser error: 

Error[00] Position: 00 Type: [  Syntax Error] Msg: ERR202 - Undefined symbol: 'n_2_3' Expression: n_2_3

exprtk parser error: 

Error[00] Position: 00 Type: [  Syntax Error] Msg: ERR202 - Undefined symbol: 'f_2_3' Expression: f_2_3

 Ending FDF-small-fitness-specs Wed Oct  9 23:12:26 2024 
  Took  0.14 


 Starting LOD_POM at Wed Oct  9 23:12:26 2024 

 Ending LOD_POM at Wed Oct  9 23:12:29 2024 
  Took  3.25 


 Starting test.Z-all-fitness at Wed Oct  9 23:12:29 2024 

 Ending test.Z-all-fitness at Wed Oct  9 23:12:29 2024 
  Took  0.03 


 Starting test.Z-driver-counts at Wed Oct  9 23:12:30 2024 

 Ending test.Z-driver-counts at Wed Oct  9 23:12:30 2024 
  Took  0.04 


 Starting test.Z-fixation at Wed Oct  9 23:12:30 2024 

 Ending test.Z-fixation at Wed Oct  9 23:12:30 2024 
  Took  0.09 


 Starting test.Z-magellan at Wed Oct  9 23:12:30 2024 

 Ended test.Z-magellan at Wed Oct  9 23:12:31 2024 

 Starting test.Z-mutator at Wed Oct  9 23:12:31 2024 

 Ending test.Z-mutator at Wed Oct  9 23:12:31 2024 
  Took  0.1 


 Starting test.Z-mutatorFDF at Wed Oct  9 23:12:31 2024 

 Ending test.Z-mutatorFDF at Wed Oct  9 23:12:31 2024 
  Took  0.03 


 Starting test.Z-oncoSimulIndiv at Wed Oct  9 23:12:31 2024 

 Ending test.Z-oncoSimulIndiv at Wed Oct  9 23:12:31 2024 
  Took  0.16 


 Starting test.Z-oncoSimulIndivConstant at Wed Oct  9 23:12:31 2024 

 Ending test.Z-oncoSimulIndivConstant at Wed Oct  9 23:12:32 2024 
  Took  0.71 


 Starting test.Z-oncoSimulIndivDeath at Wed Oct  9 23:12:32 2024 


 Ending test.Z-oncoSimulIndivDeath at Wed Oct  9 23:12:32 2024 
  Took  0.22 


 Starting test.Z-oncoSimulIndivFDF at Wed Oct  9 23:12:32 2024 

 Ending test.Z-oncoSimulIndivFDF at Wed Oct  9 23:12:32 2024 
  Took  0.05 


 Starting test.Z-rfitness-landscape at Wed Oct  9 23:12:32 2024 

 Ending test.Z-rfitness-landscape at Wed Oct  9 23:12:32 2024 
  Took  0.06 


 Starting Z-sample-only-last tests Wed Oct  9 23:12:32 2024 

 Ending Z-sample-only-last tests Wed Oct  9 23:12:32 2024 
  Took  0 


 Starting Z-total-present-drivers tests Wed Oct  9 23:12:32 2024 

 Ending Z-total-present-drivers tests Wed Oct  9 23:12:32 2024 
  Took  0.23 


 Dummy empty test  Wed Oct  9 23:12:32 2024 

 Starting accessible_genotypes at Wed Oct  9 23:12:32 2024 

 Ending accessible_genotypes at Wed Oct  9 23:12:34 2024 
  Took  2.11 


 Starting all fitness at Wed Oct  9 23:12:34 2024
 Ending all-fitness at Wed Oct  9 23:12:36 2024 
  Took  1.48 


 Starting test.allFitnessEffectsFDF at Wed Oct  9 23:12:36 2024 

 Ending test.allFitnessEffectsFDF at Wed Oct  9 23:12:36 2024 
  Took  0.04 


 Starting test.allFitnessEffectsDeath at Wed Oct  9 23:12:36 2024 

 Ending test.allFitnessEffectsDeath at Wed Oct  9 23:12:36 2024 
  Took  0.11 


 Starting test.allFitnessEffectsFDF at Wed Oct  9 23:12:36 2024 

 Ending test.allFitnessEffectsFDF at Wed Oct  9 23:12:36 2024 
  Took  0.11 


 Starting driverCounts at Wed Oct  9 23:12:36 2024
 Ending driverCounts at Wed Oct  9 23:12:39 2024 
  Took  3.29 


 Starting epist-order-modules at Wed Oct  9 23:12:39 2024
 Ending epist-order-modules at Wed Oct  9 23:12:39 2024 
  Took  0.02 


 Starting test.evaluatingGenotypesDeath at Wed Oct  9 23:12:39 2024 

 Ending test.evaluatingGenotypesDeath at Wed Oct  9 23:12:39 2024 
  Took  0.05 


 Starting test.evaluatingGenotypesFDF at Wed Oct  9 23:12:39 2024 

 Ending test.evaluatingGenotypesFDF at Wed Oct  9 23:12:39 2024 
  Took  0.05 


 Starting exercise-plotting-code at Wed Oct  9 23:12:39 2024
 Ending exercise-plotting-code at Wed Oct  9 23:12:40 2024 
  Took  1.01 


 Starting exercise-rfitness at Wed Oct  9 23:12:40 2024 

 Ending exercise-rfitness at Wed Oct  9 23:12:43 2024 
  Took  2.73 


 Starting to_Magella at Wed Oct  9 23:12:43 2024 

 Ending to_Magella at Wed Oct  9 23:12:43 2024 
  Took  0.01 


 Starting fitness preds at Wed Oct  9 23:12:43 2024 

 Ending fitness preds long at Wed Oct  9 23:12:43 2024 
  Took  0 


 Starting fixation  at Wed Oct  9 23:12:43 2024 

 Ending fixation  at Wed Oct  9 23:12:49 2024 
  Took  5.36 


 Starting test.flfast-additional.R test at Wed Oct  9 23:12:49 2024
 Ending test.flfast-additional.R test at Wed Oct  9 23:12:49 2024 
  Took  0.34 


 Starting test.flfast-mutator.R test at Wed Oct  9 23:12:49 2024
 Finished test.flfast-mutator.R test at Wed Oct  9 23:12:49 2024 
  Took  0.35 


 Starting genotFitness at Wed Oct  9 23:12:49 2024 

 Ending genotFitness at Wed Oct  9 23:12:49 2024 
  Took  0.05 


 Starting genot_fitness_to_epistasis at Wed Oct  9 23:12:49 2024 

 Ending genot_fitness_to_epistasis at Wed Oct  9 23:12:49 2024 
  Took  0.01 


 Starting init-mutant tests Wed Oct  9 23:12:49 2024 

 ERROR: Algo 2: (1.0 - pe/pm) > 1.0

 Unrecoverable exception: Algo 2:  1 - pe/pm > 1. Aborting. 

 ERROR: Algo 2: (1.0 - pe/pm) > 1.0

 Unrecoverable exception: Algo 2:  1 - pe/pm > 1. Aborting. 

 ERROR: Algo 2: (1.0 - pe/pm) > 1.0

 Unrecoverable exception: Algo 2:  1 - pe/pm > 1. Aborting. 

exprtk parser error: 

Error[00] Position: 18 Type: [  Syntax Error] Msg: ERR202 - Undefined symbol: 'f_2' Expression: 1.1 + 0.7*((f_1 + f_2) > 0.3)

 Ending init-mutant tests Wed Oct  9 23:12:51 2024 
  Took  2.02 


 Starting interventions tests Wed Oct  9 23:12:51 2024 
[1] "Checking intervention: intOverA"
[1] "Checking intervention: intOverA"
[1] "Checking intervention: intOverA"
[1] "Checking intervention: intOverA"
[1] "Checking intervention: intOverMultiplicatesA"
In intervention:intOverMultiplicatesA with WhatHappens: n_1 = n_1 * 2. You cannot intervene to generate more population.[1] "Checking intervention: intOverA"
[1] "Checking intervention: intOverA"
[1] "Checking intervention: intOverTotPop"
[1] 0.46 0.46 0.46
[1] "Checking intervention: intOverTotPop"
[1] "Checking intervention: intOverA"
[1] "Checking intervention: intOverB"
[1] "Checking intervention: intOverC"
[1] "Checking intervention: intOverD"
Init Mutant with birth == 1.0
Init Mutant with birth == 1.0
[1] "Checking intervention: intOverA"
[1] "Checking intervention: intOverB"
[1] "Checking intervention: intOverC"
[1] "Checking intervention: intOverD"
Init Mutant with birth == 1.0

 ERROR: Algo 2: (1.0 - pe/pm) > 1.0

 Unrecoverable exception: Algo 2:  1 - pe/pm > 1. Aborting. 
Init Mutant with birth == 1.0

 ERROR: Algo 2: (1.0 - pe/pm) > 1.0

 Unrecoverable exception: Algo 2:  1 - pe/pm > 1. Aborting. 
[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 Wed Oct  9 23:12:52 2024 
  Took  1.09 


 Starting test.magellan at Wed Oct  9 23:12:52 2024 

 Ending test.magellan at Wed Oct  9 23:12:53 2024 
  Took  0.07 


 Starting test.modules-root-no-root at Wed Oct  9 23:12:53 2024 

 Ending test.modules-root-no-root at Wed Oct  9 23:12:53 2024 
  Took  0.02 


 Starting at mutPropGrowth  Wed Oct  9 23:12:53 2024 

 Ended test.mutPropGrowth:  Wed Oct  9 23:12:54 2024 
  Took  1.76 


 Starting test.mutator-oncoSimulSample.R test at Wed Oct  9 23:12:54 2024 

 Finished test.mutator-oncoSimulSample.R test at Wed Oct  9 23:12:57 2024 
  Took  2.21 seconds 


 Starting test.mutator.R test at Wed Oct  9 23:12:57 2024[1] 2.338896e-07
[1] 2.890816e-12

 Finished test.mutator.R test at Wed Oct  9 23:13:02 2024 
  Took  5.11 


 Starting test.mutatorFDF.R test at Wed Oct  9 23:13:02 2024
 Starting test.no-v1 at Wed Oct  9 23:13:02 2024 

 Ending test.no-v1 at Wed Oct  9 23:13:02 2024 
  Took  0 


 Starting oncoSimulIndiv-miscell tests Wed Oct  9 23:13:02 2024 

 Ending oncoSimulIndiv-miscell tests Wed Oct  9 23:13:04 2024 
  Took  2.49 


 Starting oncoSimulSample-failures tests Wed Oct  9 23:13:04 2024 

 Ending oncoSimulSample-failures tests Wed Oct  9 23:13:08 2024 
  Took  3.2 


 Starting oncoSimulSample-limits tests Wed Oct  9 23:13:08 2024 

 Ending oncoSimulSample-limits tests Wed Oct  9 23:13:08 2024 
  Took  0.02 


 Starting per-gene-mutation rates at Wed Oct  9 23:13:08 2024 

 ERROR: Algo 2: (1.0 - pe/pm) > 1.0

 Unrecoverable exception: Algo 2:  1 - pe/pm > 1. Aborting. 

 ERROR: Algo 2: (1.0 - pe/pm) > 1.0

 Unrecoverable exception: Algo 2:  1 - pe/pm > 1. Aborting. 

 ERROR: Algo 2: (1.0 - pe/pm) > 1.0

 ERROR: Algo 2: (1.0 - pe/pm) > 1.0

 Unrecoverable exception: Algo 2:  1 - pe/pm > 1. Aborting. 

 Unrecoverable exception: Algo 2:  1 - pe/pm > 1. Aborting. 

 ERROR: Algo 2: (1.0 - pe/pm) > 1.0

 Unrecoverable exception: Algo 2:  1 - pe/pm > 1. Aborting. 

 ERROR: Algo 2: (1.0 - pe/pm) > 1.0

 Unrecoverable exception: Algo 2:  1 - pe/pm > 1. Aborting. 

 ERROR: Algo 2: (1.0 - pe/pm) > 1.0

 Unrecoverable exception: Algo 2:  1 - pe/pm > 1. Aborting. 

 ERROR: Algo 2: (1.0 - pe/pm) > 1.0

 Unrecoverable exception: Algo 2:  1 - pe/pm > 1. Aborting. 

 ERROR: Algo 2: (1.0 - pe/pm) > 1.0

 Unrecoverable exception: Algo 2:  1 - pe/pm > 1. Aborting. 

 ERROR: Algo 2: (1.0 - pe/pm) > 1.0

 Unrecoverable exception: Algo 2:  1 - pe/pm > 1. Aborting. 

 ERROR: Algo 2: (1.0 - pe/pm) > 1.0

 Unrecoverable exception: Algo 2:  1 - pe/pm > 1. Aborting. 

 ERROR: Algo 2: (1.0 - pe/pm) > 1.0

 Unrecoverable exception: Algo 2:  1 - pe/pm > 1. Aborting. 

 ERROR: Algo 2: (1.0 - pe/pm) > 1.0

 Unrecoverable exception: Algo 2:  1 - pe/pm > 1. Aborting. 

 ERROR: Algo 2: (1.0 - pe/pm) > 1.0

 Unrecoverable exception: Algo 2:  1 - pe/pm > 1. Aborting. 

 ERROR: Algo 2: (1.0 - pe/pm) > 1.0

 Unrecoverable exception: Algo 2:  1 - pe/pm > 1. Aborting. 

 ERROR: Algo 2: (1.0 - pe/pm) > 1.0

 Unrecoverable exception: Algo 2:  1 - pe/pm > 1. Aborting. 

 Ending per-gene-mutation rates at Wed Oct  9 23:13:16 2024 
  Took  8.65 


 Starting plotFitnessLandscape at Wed Oct  9 23:13:16 2024
 Ending plotFitnessLandscape at Wed Oct  9 23:13:17 2024 
  Took  0.88 


 Starting poset-transformations tests Wed Oct  9 23:13:17 2024 

 Ending poset-transformations tests Wed Oct  9 23:13:20 2024 
  Took  3.07 


 Starting sample-prob Wed Oct  9 23:13:20 2024 
[1] 3.05713e-23
[1] 1.511172e-13
[1] 7.35658e-09
[1] 1.22231e-11
[1] 8.199957e-12
[1] 4.00752e-15
[1] 3.920075e-10
[1] 2.337794e-17
[1] 5.699924e-09
[1] 7.572637e-10
[1] 5.250671e-08
[1] 4.264941e-09

 Ending sample-prob tests Wed Oct  9 23:13:22 2024 
 Took  1.93 



 Starting samplePop tests Wed Oct  9 23:13:22 2024 

 Ending samplePop tests Wed Oct  9 23:13:24 2024 
  Took  1.86 


 Starting simuls-runs-examples tests Wed Oct  9 23:13:24 2024 

 Ending simuls-runs-examples tests Wed Oct  9 23:13:26 2024 
  Took  2.42 


 Starting user variable tests Wed Oct  9 23:13:26 2024 
[1] "Checking user variable: user_var_1"
[1] "Checking rule: rule_1"

 Ending user variable tests Wed Oct  9 23:13:26 2024 
  Took  0.03 


 Starting warning-mutPropGrowth tests Wed Oct  9 23:13:26 2024 

 Ending warning-mutPropGrowth tests Wed Oct  9 23:13:27 2024 
  Took  0.11 


 Starting wide2long tests Wed Oct  9 23:13:27 2024 

 Ending wide2long tests Wed Oct  9 23:13:27 2024 
  Took  0.07 

[ FAIL 0 | WARN 34 | SKIP 8 | PASS 8374 ]

══ Skipped tests (8) ═══════════════════════════════════════════════════════════
• On Mac (2): 'test.Z-magellan.R:664:5', 'test.Z-oncoSimulIndivFDF.R:125:3'
• empty test (6): 'test.FDF-letter-fitness-order.R:376:1',
  'test.ZZ-dummy-skip-warn-test.R:8:1', 'test.ZZ-dummy-skip-warn-test.R:12:1',
  'test.fixation.R:4:1', 'test.init-mutant.R:1099:1',
  'test.intervention.R:466:1'

[ FAIL 0 | WARN 34 | SKIP 8 | PASS 8374 ]
> 
> proc.time()
   user  system elapsed 
 66.370  12.415  61.928

Example timings

OncoSimulR.Rcheck/OncoSimulR-Ex.timings

nameusersystemelapsed
OncoSimulWide2Long0.0580.0020.059
POM0.2320.0170.150
allFitnessEffects0.4970.0190.527
benchmarks0.0020.0020.005
createInterventions0.0790.0040.086
createUserVars0.1160.0010.117
evalAllGenotypes0.0700.0050.074
example-missing-drivers0.0800.0060.086
examplePosets0.0700.0020.072
examplesFitnessEffects0.0120.0010.012
freq-dep-simul-examples0.0030.0010.004
mcfLs0.0000.0000.001
oncoSimulIndiv0.2940.0620.337
plot.fitnessEffects0.0710.0100.082
plot.oncosimul0.1650.0070.172
plotClonePhylog0.5880.0200.608
plotFitnessLandscape0.3080.0050.314
plotPoset0.0220.0010.023
poset0.0250.0020.026
rfitness0.1720.0040.201
samplePop0.0150.0200.028
simOGraph0.0160.0060.022
to_Magellan0.0590.0250.113
vignette_pre_computed0.0020.0010.003