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This page was generated on 2024-11-05 12:08 -0500 (Tue, 05 Nov 2024).

HostnameOSArch (*)R versionInstalled pkgs
teran2Linux (Ubuntu 24.04.1 LTS)x86_644.4.1 (2024-06-14) -- "Race for Your Life" 4503
nebbiolo2Linux (Ubuntu 24.04.1 LTS)x86_644.4.1 (2024-06-14) -- "Race for Your Life" 4763
palomino8Windows Server 2022 Datacenterx644.4.1 (2024-06-14 ucrt) -- "Race for Your Life" 4506
lconwaymacOS 12.7.1 Montereyx86_644.4.1 (2024-06-14) -- "Race for Your Life" 4539
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch644.4.1 (2024-06-14) -- "Race for Your Life" 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: 2024-11-04 13:40 -0500 (Mon, 04 Nov 2024)
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)
teran2Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
nebbiolo2Linux (Ubuntu 24.04.1 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
kunpeng2Linux (openEuler 22.03 LTS-SP1) / aarch64  OK    OK    OK  

CHECK results for OncoSimulR on kunpeng2

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.
- See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host.

raw results


Summary

Package: OncoSimulR
Version: 4.8.0
Command: /home/biocbuild/R/R/bin/R CMD check --install=check:OncoSimulR.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings OncoSimulR_4.8.0.tar.gz
StartedAt: 2024-11-05 10:41:44 -0000 (Tue, 05 Nov 2024)
EndedAt: 2024-11-05 10:47:22 -0000 (Tue, 05 Nov 2024)
EllapsedTime: 338.6 seconds
RetCode: 0
Status:   OK  
CheckDir: OncoSimulR.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD check --install=check:OncoSimulR.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings OncoSimulR_4.8.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/OncoSimulR.Rcheck’
* using R version 4.4.1 (2024-06-14)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
    gcc (GCC) 12.2.1 20220819 (openEuler 12.2.1-14)
    GNU Fortran (GCC) 10.3.1
* running under: openEuler 22.03 (LTS-SP1)
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘OncoSimulR’ can be installed ... OK
* used C compiler: ‘gcc (conda-forge gcc 14.2.0-1) 14.2.0’
* used C++ compiler: ‘g++ (conda-forge gcc 14.2.0-1) 14.2.0’
* checking installed package size ... NOTE
  installed size is 46.7Mb
  sub-directories of 1Mb or more:
    libs  44.8Mb
* 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 loading without being on the library search path ... 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: 3 NOTEs
See
  ‘/home/biocbuild/bbs-3.20-bioc/meat/OncoSimulR.Rcheck/00check.log’
for details.

Installation output

OncoSimulR.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD INSTALL OncoSimulR
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/R/R-4.4.1/site-library’
* installing *source* package ‘OncoSimulR’ ...
** using staged installation
** libs
using C compiler: ‘gcc (conda-forge gcc 14.2.0-1) 14.2.0’
using C++ compiler: ‘g++ (conda-forge gcc 14.2.0-1) 14.2.0’
gcc -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.4.1/site-library/Rcpp/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -c FitnessLandscape/gamma.c -o FitnessLandscape/gamma.o
gcc -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.4.1/site-library/Rcpp/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -c FitnessLandscape/landscape.c -o FitnessLandscape/landscape.o
gcc -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.4.1/site-library/Rcpp/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -c FitnessLandscape/random.c -o FitnessLandscape/random.o
gcc -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.4.1/site-library/Rcpp/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -c FitnessLandscape/sort.c -o FitnessLandscape/sort.o
gcc -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.4.1/site-library/Rcpp/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -c FitnessLandscape/chain.c -o FitnessLandscape/chain.o
gcc -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.4.1/site-library/Rcpp/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -c FitnessLandscape/input.c -o FitnessLandscape/input.o
gcc -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.4.1/site-library/Rcpp/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -c FitnessLandscape/genotypes.c -o FitnessLandscape/genotypes.o
gcc -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.4.1/site-library/Rcpp/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -c FitnessLandscape/ordered_pairs.c -o FitnessLandscape/ordered_pairs.o
gcc -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.4.1/site-library/Rcpp/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -c FitnessLandscape/calculus.c -o FitnessLandscape/calculus.o
gcc -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.4.1/site-library/Rcpp/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -c FitnessLandscape/vector.c -o FitnessLandscape/vector.o
gcc -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.4.1/site-library/Rcpp/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -c FitnessLandscape/generalized_chain.c -o FitnessLandscape/generalized_chain.o
gcc -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.4.1/site-library/Rcpp/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -c FitnessLandscape/LinearAlgebra.c -o FitnessLandscape/LinearAlgebra.o
gcc -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.4.1/site-library/Rcpp/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -c FitnessLandscape/summary_statistics.c -o FitnessLandscape/summary_statistics.o
gcc -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.4.1/site-library/Rcpp/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -c FitnessLandscape/epistasis_type.c -o FitnessLandscape/epistasis_type.o
gcc -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.4.1/site-library/Rcpp/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -c FitnessLandscape/decomposition.c -o FitnessLandscape/decomposition.o
gcc -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.4.1/site-library/Rcpp/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -c FitnessLandscape/models.c -o FitnessLandscape/models.o
gcc -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.4.1/site-library/Rcpp/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -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 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"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.4.1/site-library/Rcpp/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -c OncoSimulR_init.c -o OncoSimulR_init.o
g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.4.1/site-library/Rcpp/include' -I/usr/local/include    -fPIC  -g -O2  -Wall  -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.4.1/site-library/Rcpp/include' -I/usr/local/include    -fPIC  -g -O2  -Wall  -c unity_osimul.cpp -o unity_osimul.o
g++ -std=gnu++17 -shared -L/home/biocbuild/R/R-4.4.1/lib -L/usr/local/lib -o OncoSimulR.so OncoSimulR_init.o RcppExports.o unity_osimul.o -L/home/biocbuild/R/R-4.4.1/lib -lR
installing via 'install.libs.R' to /home/biocbuild/R/R-4.4.1/site-library/00LOCK-OncoSimulR/00new/OncoSimulR
[1] ""
Installing fl_statistics fl_generate to /home/biocbuild/R/R-4.4.1/site-library/00LOCK-OncoSimulR/00new/OncoSimulR/exec
Installing library OncoSimulR.so to /home/biocbuild/R/R-4.4.1/site-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-unknown-linux-gnu

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 Tue Nov  5 10:43:13 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 Tue Nov  5 10:43:13 2024 
  Took  0.63 


 Starting LOD_POM at Tue Nov  5 10:43:14 2024 

 Ending LOD_POM at Tue Nov  5 10:43:27 2024 
  Took  13.5 


 Starting test.Z-all-fitness at Tue Nov  5 10:43:27 2024 

 Ending test.Z-all-fitness at Tue Nov  5 10:43:27 2024 
  Took  0.12 


 Starting test.Z-driver-counts at Tue Nov  5 10:43:27 2024 

 Ending test.Z-driver-counts at Tue Nov  5 10:43:27 2024 
  Took  0.17 


 Starting test.Z-fixation at Tue Nov  5 10:43:27 2024 

 Ending test.Z-fixation at Tue Nov  5 10:43:28 2024 
  Took  0.37 


 Starting test.Z-magellan at Tue Nov  5 10:43:28 2024 

 Ended test.Z-magellan at Tue Nov  5 10:43:29 2024 

 Starting test.Z-mutator at Tue Nov  5 10:43:29 2024 

 Ending test.Z-mutator at Tue Nov  5 10:43:30 2024 
  Took  0.44 


 Starting test.Z-mutatorFDF at Tue Nov  5 10:43:30 2024 

 Ending test.Z-mutatorFDF at Tue Nov  5 10:43:30 2024 
  Took  0.14 


 Starting test.Z-oncoSimulIndiv at Tue Nov  5 10:43:30 2024 

 Ending test.Z-oncoSimulIndiv at Tue Nov  5 10:43:31 2024 
  Took  0.77 


 Starting test.Z-oncoSimulIndivConstant at Tue Nov  5 10:43:31 2024 

 Ending test.Z-oncoSimulIndivConstant at Tue Nov  5 10:43:34 2024 
  Took  2.91 


 Starting test.Z-oncoSimulIndivDeath at Tue Nov  5 10:43:34 2024 


 Ending test.Z-oncoSimulIndivDeath at Tue Nov  5 10:43:35 2024 
  Took  1.04 


 Starting test.Z-oncoSimulIndivFDF at Tue Nov  5 10:43:35 2024 

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

 Ending test.Z-oncoSimulIndivFDF at Tue Nov  5 10:43:36 2024 
  Took  0.69 


 Starting test.Z-rfitness-landscape at Tue Nov  5 10:43:36 2024 

 Ending test.Z-rfitness-landscape at Tue Nov  5 10:43:36 2024 
  Took  0.25 


 Starting Z-sample-only-last tests Tue Nov  5 10:43:36 2024 

 Ending Z-sample-only-last tests Tue Nov  5 10:43:36 2024 
  Took  0 


 Starting Z-total-present-drivers tests Tue Nov  5 10:43:36 2024 

 Ending Z-total-present-drivers tests Tue Nov  5 10:43:37 2024 
  Took  1 


 Dummy empty test  Tue Nov  5 10:43:37 2024 

 Starting accessible_genotypes at Tue Nov  5 10:43:37 2024 

 Ending accessible_genotypes at Tue Nov  5 10:43:46 2024 
  Took  9.64 


 Starting all fitness at Tue Nov  5 10:43:46 2024
 Ending all-fitness at Tue Nov  5 10:43:53 2024 
  Took  6.76 


 Starting test.allFitnessEffectsFDF at Tue Nov  5 10:43:53 2024 

 Ending test.allFitnessEffectsFDF at Tue Nov  5 10:43:53 2024 
  Took  0.17 


 Starting test.allFitnessEffectsDeath at Tue Nov  5 10:43:53 2024 

 Ending test.allFitnessEffectsDeath at Tue Nov  5 10:43:54 2024 
  Took  0.51 


 Starting test.allFitnessEffectsFDF at Tue Nov  5 10:43:54 2024 

 Ending test.allFitnessEffectsFDF at Tue Nov  5 10:43:54 2024 
  Took  0.54 


 Starting driverCounts at Tue Nov  5 10:43:54 2024
 Ending driverCounts at Tue Nov  5 10:44:03 2024 
  Took  8.26 


 Starting epist-order-modules at Tue Nov  5 10:44:03 2024
 Ending epist-order-modules at Tue Nov  5 10:44:03 2024 
  Took  0.07 


 Starting test.evaluatingGenotypesDeath at Tue Nov  5 10:44:03 2024 

 Ending test.evaluatingGenotypesDeath at Tue Nov  5 10:44:03 2024 
  Took  0.25 


 Starting test.evaluatingGenotypesFDF at Tue Nov  5 10:44:03 2024 

 Ending test.evaluatingGenotypesFDF at Tue Nov  5 10:44:03 2024 
  Took  0.26 


 Starting exercise-plotting-code at Tue Nov  5 10:44:03 2024
 Ending exercise-plotting-code at Tue Nov  5 10:44:07 2024 
  Took  3.94 


 Starting exercise-rfitness at Tue Nov  5 10:44:07 2024 

 Ending exercise-rfitness at Tue Nov  5 10:44:20 2024 
  Took  12.36 


 Starting to_Magella at Tue Nov  5 10:44:20 2024 

 Ending to_Magella at Tue Nov  5 10:44:20 2024 
  Took  0.04 


 Starting fitness preds at Tue Nov  5 10:44:20 2024 

 Observed vs expected, case III

 done tries 1 

 Ending fitness preds long at Tue Nov  5 10:44:27 2024 
  Took  7.14 


 Starting fixation  at Tue Nov  5 10:44:27 2024 

 Ending fixation  at Tue Nov  5 10:44:45 2024 
  Took  18.62 


 Starting test.flfast-additional.R test at Tue Nov  5 10:44:45 2024
 Ending test.flfast-additional.R test at Tue Nov  5 10:44:47 2024 
  Took  1.72 


 Starting test.flfast-mutator.R test at Tue Nov  5 10:44:47 2024
 Finished test.flfast-mutator.R test at Tue Nov  5 10:44:48 2024 
  Took  1.3 


 Starting genotFitness at Tue Nov  5 10:44:48 2024 

 Ending genotFitness at Tue Nov  5 10:44:49 2024 
  Took  0.26 


 Starting genot_fitness_to_epistasis at Tue Nov  5 10:44:49 2024 

 Ending genot_fitness_to_epistasis at Tue Nov  5 10:44:49 2024 
  Took  0.05 


 Starting init-mutant tests Tue Nov  5 10:44:49 2024 

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 Tue Nov  5 10:44:56 2024 
  Took  7.62 


 Starting interventions tests Tue Nov  5 10:44:56 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] 0.51 0.51 0.51
[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 Tue Nov  5 10:45:02 2024 
  Took  5.22 


 Starting test.magellan at Tue Nov  5 10:45:02 2024 

 Ending test.magellan at Tue Nov  5 10:45:02 2024 
  Took  0.15 


 Starting test.modules-root-no-root at Tue Nov  5 10:45:02 2024 

 Ending test.modules-root-no-root at Tue Nov  5 10:45:02 2024 
  Took  0.11 


 Starting at mutPropGrowth  Tue Nov  5 10:45:02 2024 

 Ended test.mutPropGrowth:  Tue Nov  5 10:45:11 2024 
  Took  9.06 


 Starting test.mutator-oncoSimulSample.R test at Tue Nov  5 10:45:11 2024 

 Finished test.mutator-oncoSimulSample.R test at Tue Nov  5 10:45:25 2024 
  Took  13.79 seconds 


 Starting test.mutator.R test at Tue Nov  5 10:45:25 2024[1] 2.063684e-09
[1] 4.149905e-13

 Finished test.mutator.R test at Tue Nov  5 10:45:39 2024 
  Took  13.85 


 Starting test.mutatorFDF.R test at Tue Nov  5 10:45:39 2024
 Starting test.no-v1 at Tue Nov  5 10:45:39 2024 

 Ending test.no-v1 at Tue Nov  5 10:45:39 2024 
  Took  0.02 


 Starting oncoSimulIndiv-miscell tests Tue Nov  5 10:45:39 2024 

 Ending oncoSimulIndiv-miscell tests Tue Nov  5 10:45:53 2024 
  Took  13.16 


 Starting oncoSimulSample-failures tests Tue Nov  5 10:45:53 2024 

 Ending oncoSimulSample-failures tests Tue Nov  5 10:45:57 2024 
  Took  3.92 


 Starting oncoSimulSample-limits tests Tue Nov  5 10:45:57 2024 

 Ending oncoSimulSample-limits tests Tue Nov  5 10:45:57 2024 
  Took  0.09 


 Starting per-gene-mutation rates at Tue Nov  5 10:45:57 2024 

 Ending per-gene-mutation rates at Tue Nov  5 10:46:29 2024 
  Took  32.06 


 Starting plotFitnessLandscape at Tue Nov  5 10:46:29 2024
 Ending plotFitnessLandscape at Tue Nov  5 10:46:33 2024 
  Took  4.63 


 Starting poset-transformations tests Tue Nov  5 10:46:33 2024 

 Ending poset-transformations tests Tue Nov  5 10:46:47 2024 
  Took  13.53 


 Starting sample-prob Tue Nov  5 10:46:47 2024 
[1] 6.707541e-30
[1] 3.526726e-12
[1] 3.650612e-09
[1] 1.333616e-11
[1] 2.054533e-14
[1] 2.670067e-13
[1] 3.080573e-15
[1] 2.4946e-14
[1] 8.55216e-11
[1] 6.909534e-11
[1] 3.784508e-07
[1] 1.029734e-09

 Ending sample-prob tests Tue Nov  5 10:46:54 2024 
 Took  7.48 



 Starting samplePop tests Tue Nov  5 10:46:54 2024 

 Ending samplePop tests Tue Nov  5 10:47:01 2024 
  Took  7.09 


 Starting simuls-runs-examples tests Tue Nov  5 10:47:01 2024 

 Ending simuls-runs-examples tests Tue Nov  5 10:47:12 2024 
  Took  10.24 


 Starting user variable tests Tue Nov  5 10:47:12 2024 
[1] "Checking user variable: user_var_1"
[1] "Checking rule: rule_1"

 Ending user variable tests Tue Nov  5 10:47:12 2024 
  Took  0.15 


 Starting warning-mutPropGrowth tests Tue Nov  5 10:47:12 2024 

 Ending warning-mutPropGrowth tests Tue Nov  5 10:47:12 2024 
  Took  0.54 


 Starting wide2long tests Tue Nov  5 10:47:12 2024 

 Ending wide2long tests Tue Nov  5 10:47:13 2024 
  Took  0.3 

[ FAIL 0 | WARN 18 | SKIP 5 | PASS 8402 ]

══ Skipped tests (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 18 | SKIP 5 | PASS 8402 ]
> 
> proc.time()
   user  system elapsed 
278.649  32.988 245.740

Example timings

OncoSimulR.Rcheck/OncoSimulR-Ex.timings

nameusersystemelapsed
OncoSimulWide2Long0.2800.0000.288
POM0.9190.0320.658
allFitnessEffects2.2120.0442.270
benchmarks0.0070.0040.011
createInterventions0.3550.0040.360
createUserVars0.5300.0000.531
evalAllGenotypes0.2710.0080.279
example-missing-drivers0.2890.0280.318
examplePosets0.3310.0120.344
examplesFitnessEffects0.0490.0000.049
freq-dep-simul-examples0.0120.0000.011
mcfLs0.0000.0000.001
oncoSimulIndiv1.2630.1401.353
plot.fitnessEffects0.2650.0440.310
plot.oncosimul0.6360.0220.658
plotClonePhylog1.6240.0561.684
plotFitnessLandscape1.5390.0471.591
plotPoset0.1110.0050.116
poset0.1620.0030.167
rfitness0.8080.0230.836
samplePop0.0660.0600.075
simOGraph0.0710.0120.083
to_Magellan0.1890.0410.233
vignette_pre_computed0.0050.0040.009