Back to Multiple platform build/check report for BioC 3.19:   simplified   long
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This page was generated on 2024-06-25 17:39 -0400 (Tue, 25 Jun 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_644.4.0 (2024-04-24) -- "Puppy Cup" 4760
palomino3Windows Server 2022 Datacenterx644.4.0 (2024-04-24 ucrt) -- "Puppy Cup" 4494
merida1macOS 12.7.4 Montereyx86_644.4.0 (2024-04-24) -- "Puppy Cup" 4508
kjohnson1macOS 13.6.6 Venturaarm644.4.0 (2024-04-24) -- "Puppy Cup" 4466
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 1472/2300HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
OncoSimulR 4.6.0  (landing page)
Ramon Diaz-Uriarte
Snapshot Date: 2024-06-23 14:00 -0400 (Sun, 23 Jun 2024)
git_url: https://git.bioconductor.org/packages/OncoSimulR
git_branch: RELEASE_3_19
git_last_commit: 4fd9846
git_last_commit_date: 2024-04-30 10:37:33 -0400 (Tue, 30 Apr 2024)
nebbiolo1Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino3Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 12.7.4 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.6.6 Ventura / arm64  OK    ERROR  skippedskipped

CHECK results for OncoSimulR on nebbiolo1

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: 4.6.0
Command: /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:OncoSimulR.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings OncoSimulR_4.6.0.tar.gz
StartedAt: 2024-06-24 02:00:02 -0400 (Mon, 24 Jun 2024)
EndedAt: 2024-06-24 02:08:15 -0400 (Mon, 24 Jun 2024)
EllapsedTime: 492.5 seconds
RetCode: 0
Status:   OK  
CheckDir: OncoSimulR.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:OncoSimulR.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings OncoSimulR_4.6.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/OncoSimulR.Rcheck’
* using R version 4.4.0 (2024-04-24)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
    GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
* running under: Ubuntu 22.04.4 LTS
* using session charset: UTF-8
* checking for file ‘OncoSimulR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘OncoSimulR’ version ‘4.6.0’
* 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
* used C compiler: ‘gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’
* used C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’
* checking installed package size ... NOTE
  installed size is 19.6Mb
  sub-directories of 1Mb or more:
    libs  18.1Mb
* 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 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 ... NOTE
checkRd: (-1) oncoSimulIndiv.Rd:255-259: Lost braces in \itemize; meant \describe ?
checkRd: (-1) oncoSimulIndiv.Rd:261-263: Lost braces in \itemize; meant \describe ?
checkRd: (-1) oncoSimulIndiv.Rd:265-266: Lost braces in \itemize; meant \describe ?
checkRd: (-1) oncoSimulIndiv.Rd:268-270: Lost braces in \itemize; meant \describe ?
checkRd: (-1) oncoSimulIndiv.Rd:272-274: Lost braces in \itemize; meant \describe ?
* 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 re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 3 NOTEs
See
  ‘/home/biocbuild/bbs-3.19-bioc/meat/OncoSimulR.Rcheck/00check.log’
for details.

Installation output

OncoSimulR.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD INSTALL OncoSimulR
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.19-bioc/R/site-library’
* installing *source* package ‘OncoSimulR’ ...
** using staged installation
** libs
using C compiler: ‘gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’
using C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’
gcc -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/Rcpp/include' -I/usr/local/include    -fpic  -g -O2  -Wall -c FitnessLandscape/gamma.c -o FitnessLandscape/gamma.o
gcc -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/Rcpp/include' -I/usr/local/include    -fpic  -g -O2  -Wall -c FitnessLandscape/landscape.c -o FitnessLandscape/landscape.o
gcc -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/Rcpp/include' -I/usr/local/include    -fpic  -g -O2  -Wall -c FitnessLandscape/random.c -o FitnessLandscape/random.o
gcc -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/Rcpp/include' -I/usr/local/include    -fpic  -g -O2  -Wall -c FitnessLandscape/sort.c -o FitnessLandscape/sort.o
gcc -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/Rcpp/include' -I/usr/local/include    -fpic  -g -O2  -Wall -c FitnessLandscape/chain.c -o FitnessLandscape/chain.o
gcc -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/Rcpp/include' -I/usr/local/include    -fpic  -g -O2  -Wall -c FitnessLandscape/input.c -o FitnessLandscape/input.o
gcc -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/Rcpp/include' -I/usr/local/include    -fpic  -g -O2  -Wall -c FitnessLandscape/genotypes.c -o FitnessLandscape/genotypes.o
gcc -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.19-bioc/R/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/bbs-3.19-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/Rcpp/include' -I/usr/local/include    -fpic  -g -O2  -Wall -c FitnessLandscape/calculus.c -o FitnessLandscape/calculus.o
gcc -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/Rcpp/include' -I/usr/local/include    -fpic  -g -O2  -Wall -c FitnessLandscape/vector.c -o FitnessLandscape/vector.o
gcc -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.19-bioc/R/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/bbs-3.19-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/Rcpp/include' -I/usr/local/include    -fpic  -g -O2  -Wall -c FitnessLandscape/LinearAlgebra.c -o FitnessLandscape/LinearAlgebra.o
gcc -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.19-bioc/R/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/bbs-3.19-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.19-bioc/R/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/bbs-3.19-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/Rcpp/include' -I/usr/local/include    -fpic  -g -O2  -Wall -c FitnessLandscape/decomposition.c -o FitnessLandscape/decomposition.o
gcc -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/Rcpp/include' -I/usr/local/include    -fpic  -g -O2  -Wall -c FitnessLandscape/models.c -o FitnessLandscape/models.o
gcc -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.19-bioc/R/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/bbs-3.19-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.19-bioc/R/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/bbs-3.19-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.19-bioc/R/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/bbs-3.19-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.19-bioc/R/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/bbs-3.19-bioc/R/lib -L/usr/local/lib -o OncoSimulR.so OncoSimulR_init.o RcppExports.o unity_osimul.o -L/home/biocbuild/bbs-3.19-bioc/R/lib -lR
installing via 'install.libs.R' to /home/biocbuild/bbs-3.19-bioc/R/site-library/00LOCK-OncoSimulR/00new/OncoSimulR
[1] ""
Installing fl_statistics fl_generate to /home/biocbuild/bbs-3.19-bioc/R/site-library/00LOCK-OncoSimulR/00new/OncoSimulR/exec
Installing library OncoSimulR.so to /home/biocbuild/bbs-3.19-bioc/R/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 4.4.0 (2024-04-24) -- "Puppy Cup"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-pc-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)
> 
> test_check("OncoSimulR")

 Starting FDF-letter-fitness-order Mon Jun 24 02:01:40 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 Mon Jun 24 02:01:40 2024 
  Took  0.43 


 Starting LOD_POM at Mon Jun 24 02:01:40 2024 

 Ending LOD_POM at Mon Jun 24 02:01:49 2024 
  Took  8.97 


 Starting test.Z-all-fitness at Mon Jun 24 02:01:49 2024 

 Ending test.Z-all-fitness at Mon Jun 24 02:01:49 2024 
  Took  0.17 


 Starting test.Z-driver-counts at Mon Jun 24 02:01:49 2024 

 Ending test.Z-driver-counts at Mon Jun 24 02:01:50 2024 
  Took  0.18 


 Starting test.Z-fixation at Mon Jun 24 02:01:50 2024 

 Ending test.Z-fixation at Mon Jun 24 02:01:50 2024 
  Took  0.34 


 Starting test.Z-magellan at Mon Jun 24 02:01:50 2024 

 Ended test.Z-magellan at Mon Jun 24 02:01:52 2024 

 Starting test.Z-mutator at Mon Jun 24 02:01:52 2024 

 Ending test.Z-mutator at Mon Jun 24 02:01:53 2024 
  Took  0.6 


 Starting test.Z-mutatorFDF at Mon Jun 24 02:01:53 2024 

 Ending test.Z-mutatorFDF at Mon Jun 24 02:01:53 2024 
  Took  0.16 


 Starting test.Z-oncoSimulIndiv at Mon Jun 24 02:01:53 2024 

 Ending test.Z-oncoSimulIndiv at Mon Jun 24 02:01:54 2024 
  Took  0.6 


 Starting test.Z-oncoSimulIndivConstant at Mon Jun 24 02:01:54 2024 

 Ending test.Z-oncoSimulIndivConstant at Mon Jun 24 02:01:57 2024 
  Took  3.3 


 Starting test.Z-oncoSimulIndivDeath at Mon Jun 24 02:01:57 2024 


 Ending test.Z-oncoSimulIndivDeath at Mon Jun 24 02:01:58 2024 
  Took  1.27 


 Starting test.Z-oncoSimulIndivFDF at Mon Jun 24 02:01:58 2024 

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

 Ending test.Z-oncoSimulIndivFDF at Mon Jun 24 02:01:59 2024 
  Took  0.34 


 Starting test.Z-rfitness-landscape at Mon Jun 24 02:01:59 2024 

 Ending test.Z-rfitness-landscape at Mon Jun 24 02:01:59 2024 
  Took  0.37 


 Starting Z-sample-only-last tests Mon Jun 24 02:01:59 2024 

 Ending Z-sample-only-last tests Mon Jun 24 02:01:59 2024 
  Took  0 


 Starting Z-total-present-drivers tests Mon Jun 24 02:01:59 2024 

 Ending Z-total-present-drivers tests Mon Jun 24 02:02:00 2024 
  Took  1.2 


 Dummy empty test  Mon Jun 24 02:02:00 2024 

 Starting accessible_genotypes at Mon Jun 24 02:02:00 2024 

 Ending accessible_genotypes at Mon Jun 24 02:02:08 2024 
  Took  7.52 


 Starting all fitness at Mon Jun 24 02:02:08 2024
 Ending all-fitness at Mon Jun 24 02:02:12 2024 
  Took  4.17 


 Starting test.allFitnessEffectsFDF at Mon Jun 24 02:02:12 2024 

 Ending test.allFitnessEffectsFDF at Mon Jun 24 02:02:12 2024 
  Took  0.11 


 Starting test.allFitnessEffectsDeath at Mon Jun 24 02:02:12 2024 

 Ending test.allFitnessEffectsDeath at Mon Jun 24 02:02:12 2024 
  Took  0.3 


 Starting test.allFitnessEffectsFDF at Mon Jun 24 02:02:12 2024 

 Ending test.allFitnessEffectsFDF at Mon Jun 24 02:02:13 2024 
  Took  0.36 


 Starting driverCounts at Mon Jun 24 02:02:13 2024
 Ending driverCounts at Mon Jun 24 02:02:29 2024 
  Took  16.4 


 Starting epist-order-modules at Mon Jun 24 02:02:29 2024
 Ending epist-order-modules at Mon Jun 24 02:02:29 2024 
  Took  0.12 


 Starting test.evaluatingGenotypesDeath at Mon Jun 24 02:02:29 2024 

 Ending test.evaluatingGenotypesDeath at Mon Jun 24 02:02:30 2024 
  Took  0.36 


 Starting test.evaluatingGenotypesFDF at Mon Jun 24 02:02:30 2024 

 Ending test.evaluatingGenotypesFDF at Mon Jun 24 02:02:30 2024 
  Took  0.41 


 Starting exercise-plotting-code at Mon Jun 24 02:02:30 2024
 Ending exercise-plotting-code at Mon Jun 24 02:02:34 2024 
  Took  3.79 


 Starting exercise-rfitness at Mon Jun 24 02:02:34 2024 

 Ending exercise-rfitness at Mon Jun 24 02:02:41 2024 
  Took  7.72 


 Starting to_Magella at Mon Jun 24 02:02:41 2024 

 Ending to_Magella at Mon Jun 24 02:02:42 2024 
  Took  0.03 


 Starting fitness preds at Mon Jun 24 02:02:42 2024 

 Observed vs expected, case III

 done tries 1 

 Ending fitness preds long at Mon Jun 24 02:02:46 2024 
  Took  4.34 


 Starting fixation  at Mon Jun 24 02:02:46 2024 

 Ending fixation  at Mon Jun 24 02:02:57 2024 
  Took  10.85 


 Starting test.flfast-additional.R test at Mon Jun 24 02:02:57 2024
 Ending test.flfast-additional.R test at Mon Jun 24 02:02:58 2024 
  Took  1.19 


 Starting test.flfast-mutator.R test at Mon Jun 24 02:02:58 2024
 Finished test.flfast-mutator.R test at Mon Jun 24 02:02:59 2024 
  Took  1.18 


 Starting genotFitness at Mon Jun 24 02:02:59 2024 

 Ending genotFitness at Mon Jun 24 02:02:59 2024 
  Took  0.25 


 Starting genot_fitness_to_epistasis at Mon Jun 24 02:02:59 2024 

 Ending genot_fitness_to_epistasis at Mon Jun 24 02:02:59 2024 
  Took  0.06 


 Starting init-mutant tests Mon Jun 24 02:02:59 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 Mon Jun 24 02:03:08 2024 
  Took  8.46 


 Starting interventions tests Mon Jun 24 02:03:08 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] 0.72 0.72 0.72
[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 Jun 24 02:03:13 2024 
  Took  4.62 


 Starting test.magellan at Mon Jun 24 02:03:13 2024 

 Ending test.magellan at Mon Jun 24 02:03:13 2024 
  Took  0.19 


 Starting test.modules-root-no-root at Mon Jun 24 02:03:13 2024 

 Ending test.modules-root-no-root at Mon Jun 24 02:03:13 2024 
  Took  0.14 


 Starting at mutPropGrowth  Mon Jun 24 02:03:13 2024 

 Ended test.mutPropGrowth:  Mon Jun 24 02:03:19 2024 
  Took  5.83 


 Starting test.mutator-oncoSimulSample.R test at Mon Jun 24 02:03:19 2024 

 Finished test.mutator-oncoSimulSample.R test at Mon Jun 24 02:03:25 2024 
  Took  6.72 seconds 


 Starting test.mutator.R test at Mon Jun 24 02:03:25 2024[1] 0.0002119082
[1] 1.276082e-07

 Finished test.mutator.R test at Mon Jun 24 02:03:46 2024 
  Took  20.55 


 Starting test.mutatorFDF.R test at Mon Jun 24 02:03:46 2024
 Starting test.no-v1 at Mon Jun 24 02:03:47 2024 

 Ending test.no-v1 at Mon Jun 24 02:03:47 2024 
  Took  0.01 


 Starting oncoSimulIndiv-miscell tests Mon Jun 24 02:03:47 2024 

 Ending oncoSimulIndiv-miscell tests Mon Jun 24 02:03:54 2024 
  Took  6.68 


 Starting oncoSimulSample-failures tests Mon Jun 24 02:03:54 2024 

 Ending oncoSimulSample-failures tests Mon Jun 24 02:03:58 2024 
  Took  3.95 


 Starting oncoSimulSample-limits tests Mon Jun 24 02:03:58 2024 

 Ending oncoSimulSample-limits tests Mon Jun 24 02:03:58 2024 
  Took  0.07 


 Starting per-gene-mutation rates at Mon Jun 24 02:03:58 2024 

 Ending per-gene-mutation rates at Mon Jun 24 02:04:25 2024 
  Took  27.35 


 Starting plotFitnessLandscape at Mon Jun 24 02:04:25 2024
 Ending plotFitnessLandscape at Mon Jun 24 02:04:30 2024 
  Took  4.73 


 Starting poset-transformations tests Mon Jun 24 02:04:30 2024 

 Ending poset-transformations tests Mon Jun 24 02:04:48 2024 
  Took  18.18 


 Starting sample-prob Mon Jun 24 02:04:48 2024 
[1] 1.617173e-18
[1] 2.186113e-14
[1] 5.202482e-10
[1] 1.337848e-11
[1] 3.652875e-15
[1] 2.521365e-13
[1] 1.224848e-09
[1] 3.117975e-12
[1] 1.416488e-07
[1] 1.213928e-11
[1] 1.716916e-06
[1] 1.566444e-08

 Ending sample-prob tests Mon Jun 24 02:04:53 2024 
 Took  5.23 



 Starting samplePop tests Mon Jun 24 02:04:53 2024 

 Ending samplePop tests Mon Jun 24 02:04:57 2024 
  Took  3.46 


 Starting simuls-runs-examples tests Mon Jun 24 02:04:57 2024 

 Ending simuls-runs-examples tests Mon Jun 24 02:05:00 2024 
  Took  3.15 


 Starting user variable tests Mon Jun 24 02:05:00 2024 
[1] "Checking user variable: user_var_1"
[1] "Checking rule: rule_1"

 Ending user variable tests Mon Jun 24 02:05:00 2024 
  Took  0.12 


 Starting warning-mutPropGrowth tests Mon Jun 24 02:05:00 2024 

 Ending warning-mutPropGrowth tests Mon Jun 24 02:05:00 2024 
  Took  0.28 


 Starting wide2long tests Mon Jun 24 02:05:00 2024 

 Ending wide2long tests Mon Jun 24 02:05:00 2024 
  Took  0.14 

[ FAIL 0 | WARN 18 | SKIP 5 | PASS 8419 ]

══ 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:1097:1'

[ FAIL 0 | WARN 18 | SKIP 5 | PASS 8419 ]
> 
> proc.time()
   user  system elapsed 
217.542  36.421 204.805

Example timings

OncoSimulR.Rcheck/OncoSimulR-Ex.timings

nameusersystemelapsed
OncoSimulWide2Long0.2410.0000.278
POM1.1000.0920.916
allFitnessEffects3.2200.1953.699
benchmarks0.0160.0040.020
createInterventions0.4530.0000.453
createUserVars0.6880.0000.690
evalAllGenotypes0.3580.0170.419
example-missing-drivers0.4300.0160.446
examplePosets0.6320.0750.710
examplesFitnessEffects0.0810.0040.084
freq-dep-simul-examples0.0220.0000.021
mcfLs0.0010.0000.000
oncoSimulIndiv1.5340.2071.696
plot.fitnessEffects0.4080.0510.465
plot.oncosimul0.7080.0240.741
plotClonePhylog2.9200.1673.092
plotFitnessLandscape2.0250.1432.171
plotPoset0.1140.0000.114
poset0.1310.0040.135
rfitness0.5000.0070.507
samplePop0.0430.0370.051
simOGraph0.0370.0120.050
to_Magellan0.1610.0260.187
vignette_pre_computed0.0070.0000.007