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This page was generated on 2025-01-20 12:17 -0500 (Mon, 20 Jan 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.1 LTS)x86_644.4.2 (2024-10-31) -- "Pile of Leaves" 4746
palomino8Windows Server 2022 Datacenterx644.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" 4493
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 1462/2289HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
OncoSimulR 4.8.0  (landing page)
Ramon Diaz-Uriarte
Snapshot Date: 2025-01-19 12:27 -0500 (Sun, 19 Jan 2025)
git_url: https://git.bioconductor.org/packages/OncoSimulR
git_branch: RELEASE_3_20
git_last_commit: 52cb97a
git_last_commit_date: 2024-10-29 09:53:24 -0500 (Tue, 29 Oct 2024)
nebbiolo2Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino8Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published

CHECK results for OncoSimulR on palomino8

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: 4.8.0
Command: F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:OncoSimulR.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings OncoSimulR_4.8.0.tar.gz
StartedAt: 2025-01-20 02:55:13 -0500 (Mon, 20 Jan 2025)
EndedAt: 2025-01-20 03:04:33 -0500 (Mon, 20 Jan 2025)
EllapsedTime: 559.6 seconds
RetCode: 0
Status:   OK  
CheckDir: OncoSimulR.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:OncoSimulR.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings OncoSimulR_4.8.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'F:/biocbuild/bbs-3.20-bioc/meat/OncoSimulR.Rcheck'
* using R version 4.4.2 (2024-10-31 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 13.3.0
    GNU Fortran (GCC) 13.3.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'OncoSimulR/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'OncoSimulR' version '4.8.0'
* 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:
  .BBSoptions
These were most likely included in error. See section 'Package
structure' in the 'Writing R Extensions' manual.
* checking for portable file names ... OK
* checking whether package 'OncoSimulR' can be installed ... OK
* used C compiler: 'gcc.exe (GCC) 13.3.0'
* used C++ compiler: 'G__~1.EXE (GCC) 13.3.0'
* checking installed package size ... NOTE
  installed size is  8.3Mb
  sub-directories of 1Mb or more:
    libs   6.6Mb
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking 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 for x64 is not available
File 'F:/biocbuild/bbs-3.20-bioc/R/library/OncoSimulR/libs/x64/OncoSimulR.dll':
  Found '_exit', possibly from '_exit' (C)
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
  Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)

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

See 'Writing portable packages' in the 'Writing R Extensions' manual.
* checking files in 'vignettes' ... OK
* checking examples ... OK
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
  Running 'testthat.R'
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... 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
  'F:/biocbuild/bbs-3.20-bioc/meat/OncoSimulR.Rcheck/00check.log'
for details.

Installation output

OncoSimulR.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD INSTALL OncoSimulR
###
##############################################################################
##############################################################################


* installing to library 'F:/biocbuild/bbs-3.20-bioc/R/library'
* installing *source* package 'OncoSimulR' ...
** using staged installation
** libs
using C compiler: 'gcc.exe (GCC) 13.3.0'
using C++ compiler: 'G__~1.EXE (GCC) 13.3.0'
gcc  -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c FitnessLandscape/gamma.c -o FitnessLandscape/gamma.o
gcc  -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c FitnessLandscape/landscape.c -o FitnessLandscape/landscape.o
gcc  -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c FitnessLandscape/random.c -o FitnessLandscape/random.o
gcc  -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c FitnessLandscape/sort.c -o FitnessLandscape/sort.o
gcc  -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c FitnessLandscape/chain.c -o FitnessLandscape/chain.o
gcc  -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c FitnessLandscape/input.c -o FitnessLandscape/input.o
gcc  -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c FitnessLandscape/genotypes.c -o FitnessLandscape/genotypes.o
gcc  -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c FitnessLandscape/ordered_pairs.c -o FitnessLandscape/ordered_pairs.o
gcc  -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c FitnessLandscape/calculus.c -o FitnessLandscape/calculus.o
gcc  -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c FitnessLandscape/vector.c -o FitnessLandscape/vector.o
gcc  -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c FitnessLandscape/generalized_chain.c -o FitnessLandscape/generalized_chain.o
gcc  -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c FitnessLandscape/LinearAlgebra.c -o FitnessLandscape/LinearAlgebra.o
gcc  -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c FitnessLandscape/summary_statistics.c -o FitnessLandscape/summary_statistics.o
gcc  -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c FitnessLandscape/epistasis_type.c -o FitnessLandscape/epistasis_type.o
gcc  -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c FitnessLandscape/decomposition.c -o FitnessLandscape/decomposition.o
gcc  -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c FitnessLandscape/models.c -o FitnessLandscape/models.o
gcc  -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c FitnessLandscape/verbose.c -o FitnessLandscape/verbose.o
ar -r liblandscape.a FitnessLandscape/gamma.o FitnessLandscape/landscape.o FitnessLandscape/random.o FitnessLandscape/sort.o FitnessLandscape/chain.o FitnessLandscape/input.o FitnessLandscape/genotypes.o FitnessLandscape/ordered_pairs.o FitnessLandscape/calculus.o FitnessLandscape/vector.o FitnessLandscape/generalized_chain.o FitnessLandscape/LinearAlgebra.o FitnessLandscape/summary_statistics.o FitnessLandscape/epistasis_type.o FitnessLandscape/decomposition.o FitnessLandscape/models.o FitnessLandscape/verbose.o ;
C:\rtools44\x86_64-w64-mingw32.static.posix\bin\ar.exe: creating liblandscape.a
ranlib liblandscape.a;
gcc  -O -Wall -o fl_statistics -I/FitnessLandscape/. -L. FitnessLandscape/main_fl_statistics.c -llandscape -lm;
gcc  -O -Wall -o fl_generate -I/FitnessLandscape/. -L. FitnessLandscape/main_fl_generate.c -llandscape -lm;
gcc  -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c OncoSimulR_init.c -o OncoSimulR_init.o
g++ -std=gnu++17  -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -Wa,-mbig-obj -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++17  -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -Wa,-mbig-obj -c unity_osimul.cpp -o unity_osimul.o
In file included from unity_osimul.cpp:4:
UnityOncoSimul/BNB_nr.cpp: In function 'void nr_innerBNB(const fitnessEffectsAll&, const std::vector<double>&, const double&, TypeModel, const int&, const std::vector<double>&, const double&, const double&, const double&, const std::vector<std::vector<int> >&, const time_t&, const double&, const double&, const double&, const int&, const double&, const double&, const int&, double&, double&, double&, double&, double&, int&, int&, int&, std::vector<Genotype>&, std::vector<double>&, std::vector<int>&, std::vector<double>&, std::vector<Intervention>&, std::vector<double>&, std::vector<double>&, std::vector<int>&, std::vector<int>&, bool&, std::mt19937&, double&, bool&, const std::map<int, std::__cxx11::basic_string<char> >&, const fitness_as_genes&, PhylogName&, bool, const fitnessEffectsAll&, const std::vector<int>&, const double&, const double&, const double&, const bool&, const std::vector<std::vector<int> >&, const double&, const int&, const double&, int&, int&, std::map<std::__cxx11::basic_string<char>, std::__cxx11::basic_string<char> >&, POM&, Rcpp::List, Rcpp::List, Rcpp::List)':
UnityOncoSimul/BNB_nr.cpp:860:10: warning: 'minNextMutationTime' may be used uninitialized [-Wmaybe-uninitialized]
  860 |   double minNextMutationTime;
      |          ^~~~~~~~~~~~~~~~~~~
g++ -std=gnu++17 -shared -s -static-libgcc -o OncoSimulR.dll tmp.def OncoSimulR_init.o RcppExports.o unity_osimul.o -LC:/rtools44/x86_64-w64-mingw32.static.posix/lib/x64 -LC:/rtools44/x86_64-w64-mingw32.static.posix/lib -LF:/biocbuild/bbs-3.20-bioc/R/bin/x64 -lR
installing via 'install.libs.R' to F:/biocbuild/bbs-3.20-bioc/R/library/00LOCK-OncoSimulR/00new/OncoSimulR
[1] "/x64"
Installing fl_statistics.exe fl_generate.exe to F:/biocbuild/bbs-3.20-bioc/R/library/00LOCK-OncoSimulR/00new/OncoSimulR/exec/x64
Installing library OncoSimulR.dll to F:/biocbuild/bbs-3.20-bioc/R/library/00LOCK-OncoSimulR/00new/OncoSimulR/libs/x64
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (OncoSimulR)

Tests output

OncoSimulR.Rcheck/tests/testthat.Rout


R version 4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64

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 in that platform + OS that I have no way of debugging. Please read file README_tests_kjohnson3_aarch64-apple-darwin20.txt in the tests directory. As of 2024-10-09, this platform is unsupported until we can properly debug it.
> 
> test_check("OncoSimulR")

 Starting FDF-letter-fitness-order Mon Jan 20 02:59:10 2025 

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 Mon Jan 20 02:59:11 2025 
  Took  0.52 


 Starting LOD_POM at Mon Jan 20 02:59:11 2025 

 Ending LOD_POM at Mon Jan 20 02:59:29 2025 
  Took  18 


 Starting test.Z-all-fitness at Mon Jan 20 02:59:29 2025 

 Ending test.Z-all-fitness at Mon Jan 20 02:59:29 2025 
  Took  0.17 


 Starting test.Z-driver-counts at Mon Jan 20 02:59:29 2025 

 Ending test.Z-driver-counts at Mon Jan 20 02:59:29 2025 
  Took  0.13 


 Starting test.Z-fixation at Mon Jan 20 02:59:29 2025 

 Ending test.Z-fixation at Mon Jan 20 02:59:29 2025 
  Took  0.53 


 Starting test.Z-magellan at Mon Jan 20 02:59:29 2025 

 Ended test.Z-magellan at Mon Jan 20 02:59:31 2025 

 Starting test.Z-mutator at Mon Jan 20 02:59:31 2025 

 Ending test.Z-mutator at Mon Jan 20 02:59:32 2025 
  Took  0.35 


 Starting test.Z-mutatorFDF at Mon Jan 20 02:59:32 2025 

 Ending test.Z-mutatorFDF at Mon Jan 20 02:59:32 2025 
  Took  0.12 


 Starting test.Z-oncoSimulIndiv at Mon Jan 20 02:59:32 2025 

 Ending test.Z-oncoSimulIndiv at Mon Jan 20 02:59:32 2025 
  Took  0.49 


 Starting test.Z-oncoSimulIndivConstant at Mon Jan 20 02:59:32 2025 

 Ending test.Z-oncoSimulIndivConstant at Mon Jan 20 02:59:37 2025 
  Took  5.03 


 Starting test.Z-oncoSimulIndivDeath at Mon Jan 20 02:59:37 2025 


 Ending test.Z-oncoSimulIndivDeath at Mon Jan 20 02:59:39 2025 
  Took  1.62 


 Starting test.Z-oncoSimulIndivFDF at Mon Jan 20 02:59:39 2025 

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

 Ending test.Z-oncoSimulIndivFDF at Mon Jan 20 02:59:40 2025 
  Took  0.68 


 Starting test.Z-rfitness-landscape at Mon Jan 20 02:59:40 2025 

 Ending test.Z-rfitness-landscape at Mon Jan 20 02:59:40 2025 
  Took  0.2 


 Starting Z-sample-only-last tests Mon Jan 20 02:59:40 2025 

 Ending Z-sample-only-last tests Mon Jan 20 02:59:40 2025 
  Took  0 


 Starting Z-total-present-drivers tests Mon Jan 20 02:59:40 2025 

 Ending Z-total-present-drivers tests Mon Jan 20 02:59:41 2025 
  Took  0.85 


 Dummy empty test  Mon Jan 20 02:59:41 2025 

 Starting accessible_genotypes at Mon Jan 20 02:59:41 2025 

 Ending accessible_genotypes at Mon Jan 20 02:59:51 2025 
  Took  10.51 


 Starting all fitness at Mon Jan 20 02:59:51 2025
 Ending all-fitness at Mon Jan 20 02:59:58 2025 
  Took  7.35 


 Starting test.allFitnessEffectsFDF at Mon Jan 20 02:59:58 2025 

 Ending test.allFitnessEffectsFDF at Mon Jan 20 02:59:59 2025 
  Took  0.13 


 Starting test.allFitnessEffectsDeath at Mon Jan 20 02:59:59 2025 

 Ending test.allFitnessEffectsDeath at Mon Jan 20 02:59:59 2025 
  Took  0.53 


 Starting test.allFitnessEffectsFDF at Mon Jan 20 02:59:59 2025 

 Ending test.allFitnessEffectsFDF at Mon Jan 20 03:00:00 2025 
  Took  0.53 


 Starting driverCounts at Mon Jan 20 03:00:00 2025
 Ending driverCounts at Mon Jan 20 03:00:09 2025 
  Took  9.05 


 Starting epist-order-modules at Mon Jan 20 03:00:09 2025
 Ending epist-order-modules at Mon Jan 20 03:00:09 2025 
  Took  0.07 


 Starting test.evaluatingGenotypesDeath at Mon Jan 20 03:00:09 2025 

 Ending test.evaluatingGenotypesDeath at Mon Jan 20 03:00:09 2025 
  Took  0.26 


 Starting test.evaluatingGenotypesFDF at Mon Jan 20 03:00:09 2025 

 Ending test.evaluatingGenotypesFDF at Mon Jan 20 03:00:09 2025 
  Took  0.23 


 Starting exercise-plotting-code at Mon Jan 20 03:00:09 2025
 Ending exercise-plotting-code at Mon Jan 20 03:00:14 2025 
  Took  4.29 


 Starting exercise-rfitness at Mon Jan 20 03:00:14 2025 

 Ending exercise-rfitness at Mon Jan 20 03:00:31 2025 
  Took  16.9 


 Starting to_Magella at Mon Jan 20 03:00:31 2025 

 Ending to_Magella at Mon Jan 20 03:00:31 2025 
  Took  0.1 


 Starting fitness preds at Mon Jan 20 03:00:31 2025 

 Observed vs expected, case III

 done tries 1 

 Ending fitness preds long at Mon Jan 20 03:00:39 2025 
  Took  8.85 


 Starting fixation  at Mon Jan 20 03:00:40 2025 

 Ending fixation  at Mon Jan 20 03:01:08 2025 
  Took  28.22 


 Starting test.flfast-additional.R test at Mon Jan 20 03:01:08 2025
 Ending test.flfast-additional.R test at Mon Jan 20 03:01:09 2025 
  Took  1.3 


 Starting test.flfast-mutator.R test at Mon Jan 20 03:01:09 2025
 Finished test.flfast-mutator.R test at Mon Jan 20 03:01:10 2025 
  Took  1.45 


 Starting genotFitness at Mon Jan 20 03:01:11 2025 

 Ending genotFitness at Mon Jan 20 03:01:11 2025 
  Took  0.18 


 Starting genot_fitness_to_epistasis at Mon Jan 20 03:01:11 2025 

 Ending genot_fitness_to_epistasis at Mon Jan 20 03:01:11 2025 
  Took  0.04 


 Starting init-mutant tests Mon Jan 20 03:01:11 2025 

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 Mon Jan 20 03:01:19 2025 
  Took  8.57 


 Starting interventions tests Mon Jan 20 03:01:19 2025 
[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] 0.74 0.74 0.74
[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
Init Mutant with birth == 1.0
[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 Mon Jan 20 03:01:26 2025 
  Took  6.81 


 Starting test.magellan at Mon Jan 20 03:01:26 2025 

 Ending test.magellan at Mon Jan 20 03:01:27 2025 
  Took  0.78 


 Starting test.modules-root-no-root at Mon Jan 20 03:01:27 2025 

 Ending test.modules-root-no-root at Mon Jan 20 03:01:27 2025 
  Took  0.07 


 Starting at mutPropGrowth  Mon Jan 20 03:01:27 2025 

 Ended test.mutPropGrowth:  Mon Jan 20 03:01:35 2025 
  Took  7.9 


 Starting test.mutator-oncoSimulSample.R test at Mon Jan 20 03:01:35 2025 

 Finished test.mutator-oncoSimulSample.R test at Mon Jan 20 03:01:45 2025 
  Took  10.02 seconds 


 Starting test.mutator.R test at Mon Jan 20 03:01:45 2025[1] 6.856077e-09
[1] 9.111417e-12

 Finished test.mutator.R test at Mon Jan 20 03:02:06 2025 
  Took  20.66 


 Starting test.mutatorFDF.R test at Mon Jan 20 03:02:06 2025
 Starting test.no-v1 at Mon Jan 20 03:02:06 2025 

 Ending test.no-v1 at Mon Jan 20 03:02:06 2025 
  Took  0.02 


 Starting oncoSimulIndiv-miscell tests Mon Jan 20 03:02:06 2025 

 Ending oncoSimulIndiv-miscell tests Mon Jan 20 03:02:19 2025 
  Took  12.53 


 Starting oncoSimulSample-failures tests Mon Jan 20 03:02:19 2025 

 Ending oncoSimulSample-failures tests Mon Jan 20 03:02:23 2025 
  Took  3.55 


 Starting oncoSimulSample-limits tests Mon Jan 20 03:02:23 2025 

 Ending oncoSimulSample-limits tests Mon Jan 20 03:02:23 2025 
  Took  0.12 


 Starting per-gene-mutation rates at Mon Jan 20 03:02:23 2025 

 Ending per-gene-mutation rates at Mon Jan 20 03:03:12 2025 
  Took  49.58 


 Starting plotFitnessLandscape at Mon Jan 20 03:03:12 2025
 Ending plotFitnessLandscape at Mon Jan 20 03:03:17 2025 
  Took  5.19 


 Starting poset-transformations tests Mon Jan 20 03:03:17 2025 

 Ending poset-transformations tests Mon Jan 20 03:03:39 2025 
  Took  21.43 


 Starting sample-prob Mon Jan 20 03:03:39 2025 
[1] 5.793046e-24
[1] 4.857112e-12
[1] 6.170804e-11
[1] 1.22231e-11
[1] 1.842292e-14
[1] 1.177208e-13
[1] 6.455551e-10
[1] 1.633402e-12
[1] 2.174954e-08
[1] 2.438665e-12
[1] 7.961342e-10
[1] 9.965432e-09

 Ending sample-prob tests Mon Jan 20 03:03:51 2025 
 Took  12.53 



 Starting samplePop tests Mon Jan 20 03:03:51 2025 

 Ending samplePop tests Mon Jan 20 03:03:59 2025 
  Took  7.74 


 Starting simuls-runs-examples tests Mon Jan 20 03:03:59 2025 

 Ending simuls-runs-examples tests Mon Jan 20 03:04:09 2025 
  Took  9.42 


 Starting user variable tests Mon Jan 20 03:04:09 2025 
[1] "Checking user variable: user_var_1"
[1] "Checking rule: rule_1"

 Ending user variable tests Mon Jan 20 03:04:09 2025 
  Took  0.26 


 Starting warning-mutPropGrowth tests Mon Jan 20 03:04:09 2025 

 Ending warning-mutPropGrowth tests Mon Jan 20 03:04:09 2025 
  Took  0.47 


 Starting wide2long tests Mon Jan 20 03:04:09 2025 

 Ending wide2long tests Mon Jan 20 03:04:10 2025 
  Took  0.27 

[ FAIL 0 | WARN 19 | SKIP 6 | PASS 8397 ]

══ Skipped tests (6) ═══════════════════════════════════════════════════════════
• On Windows (1): 'test.Z-magellan.R:664:5'
• empty test (5): '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'

[ FAIL 0 | WARN 19 | SKIP 6 | PASS 8397 ]
> 
> proc.time()
   user  system elapsed 
 275.96    7.32  305.98

Example timings

OncoSimulR.Rcheck/OncoSimulR-Ex.timings

nameusersystemelapsed
OncoSimulWide2Long0.210.000.22
POM1.340.001.35
allFitnessEffects2.110.042.16
benchmarks0.010.000.01
createInterventions0.60.00.6
createUserVars0.70.00.7
evalAllGenotypes0.200.020.22
example-missing-drivers0.420.000.42
examplePosets0.400.000.39
examplesFitnessEffects0.120.010.14
freq-dep-simul-examples0.020.000.02
mcfLs000
oncoSimulIndiv1.570.021.59
plot.fitnessEffects0.270.010.28
plot.oncosimul0.550.000.55
plotClonePhylog1.320.071.39
plotFitnessLandscape1.250.081.33
plotPoset0.100.000.09
poset0.110.010.13
rfitness0.790.021.11
samplePop0.100.010.11
simOGraph0.080.000.07
to_Magellan0.120.050.80
vignette_pre_computed0.000.010.02