Ramon Diaz-Uriarte
| Snapshot Date: 2025-11-23 13:40 -0500 (Sun, 23 Nov 2025) |
| git_url: https://git.bioconductor.org/packages/OncoSimulR |
| git_branch: devel |
| git_last_commit: d241471 |
| git_last_commit_date: 2025-10-29 10:20:29 -0500 (Wed, 29 Oct 2025) |
| Back to Multiple platform build/check report for BioC 3.23: simplified long |
|
This page was generated on 2025-11-24 11:39 -0500 (Mon, 24 Nov 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | R Under development (unstable) (2025-10-20 r88955) -- "Unsuffered Consequences" | 4829 |
| lconway | macOS 12.7.6 Monterey | x86_64 | R Under development (unstable) (2025-10-21 r88958) -- "Unsuffered Consequences" | 4605 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | R Under development (unstable) (2025-11-04 r88984) -- "Unsuffered Consequences" | 4568 |
| 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 1493/2327 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| OncoSimulR 4.13.0 (landing page) Ramon Diaz-Uriarte
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
| lconway | macOS 12.7.6 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson3 | macOS 13.7.7 Ventura / arm64 | ... NOT SUPPORTED ... | ||||||||||||
|
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. |
| Package: OncoSimulR |
| Version: 4.13.0 |
| Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:OncoSimulR.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings OncoSimulR_4.13.0.tar.gz |
| StartedAt: 2025-11-23 23:00:58 -0500 (Sun, 23 Nov 2025) |
| EndedAt: 2025-11-23 23:09:05 -0500 (Sun, 23 Nov 2025) |
| EllapsedTime: 487.1 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: OncoSimulR.Rcheck |
| Warnings: 0 |
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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_4.13.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.23-bioc/meat/OncoSimulR.Rcheck’
* using R Under development (unstable) (2025-10-21 r88958)
* using platform: x86_64-apple-darwin20
* R was compiled by
Apple clang version 14.0.0 (clang-1400.0.29.202)
GNU Fortran (GCC) 14.2.0
* running under: macOS Ventura 13.7.8
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘OncoSimulR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘OncoSimulR’ version ‘4.13.0’
* 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: ‘Apple clang version 14.0.3 (clang-1403.0.22.14.1)’
* used C++ compiler: ‘Apple clang version 14.0.3 (clang-1403.0.22.14.1)’
* used SDK: ‘MacOSX11.3.1.sdk’
* checking installed package size ... INFO
installed size is 9.3Mb
sub-directories of 1Mb or more:
libs 7.9Mb
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking 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 ... INFO
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: 1 NOTE
See
‘/Users/biocbuild/bbs-3.23-bioc/meat/OncoSimulR.Rcheck/00check.log’
for details.
OncoSimulR.Rcheck/00install.out
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###
### Running command:
###
### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL OncoSimulR
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.6-x86_64/Resources/library’
* installing *source* package ‘OncoSimulR’ ...
** this is package ‘OncoSimulR’ version ‘4.13.0’
** using staged installation
** libs
using C compiler: ‘Apple clang version 14.0.3 (clang-1403.0.22.14.1)’
using C++ compiler: ‘Apple clang version 14.0.3 (clang-1403.0.22.14.1)’
using SDK: ‘MacOSX11.3.1.sdk’
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.6-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c FitnessLandscape/gamma.c -o FitnessLandscape/gamma.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.6-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c FitnessLandscape/landscape.c -o FitnessLandscape/landscape.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.6-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c FitnessLandscape/random.c -o FitnessLandscape/random.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.6-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c FitnessLandscape/sort.c -o FitnessLandscape/sort.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.6-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c FitnessLandscape/chain.c -o FitnessLandscape/chain.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.6-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c FitnessLandscape/input.c -o FitnessLandscape/input.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.6-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c FitnessLandscape/genotypes.c -o FitnessLandscape/genotypes.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.6-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/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 x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.6-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c FitnessLandscape/calculus.c -o FitnessLandscape/calculus.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.6-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c FitnessLandscape/vector.c -o FitnessLandscape/vector.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.6-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c FitnessLandscape/generalized_chain.c -o FitnessLandscape/generalized_chain.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.6-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c FitnessLandscape/LinearAlgebra.c -o FitnessLandscape/LinearAlgebra.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.6-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/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 x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.6-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c FitnessLandscape/epistasis_type.c -o FitnessLandscape/epistasis_type.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.6-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c FitnessLandscape/decomposition.c -o FitnessLandscape/decomposition.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.6-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c FitnessLandscape/models.c -o FitnessLandscape/models.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.6-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/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 x86_64 -O -Wall -o fl_statistics -I/FitnessLandscape/. -L. FitnessLandscape/main_fl_statistics.c -llandscape -lm;
clang -arch x86_64 -O -Wall -o fl_generate -I/FitnessLandscape/. -L. FitnessLandscape/main_fl_generate.c -llandscape -lm;
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.6-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c OncoSimulR_init.c -o OncoSimulR_init.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.6-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c RcppExports.cpp -o RcppExports.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.6-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/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 x86_64 -std=gnu++17 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/x86_64/lib -o OncoSimulR.so OncoSimulR_init.o RcppExports.o unity_osimul.o -F/Library/Frameworks/R.framework/.. -framework R
installing via 'install.libs.R' to /Library/Frameworks/R.framework/Versions/4.6-x86_64/Resources/library/00LOCK-OncoSimulR/00new/OncoSimulR
[1] ""
Installing fl_statistics fl_generate to /Library/Frameworks/R.framework/Versions/4.6-x86_64/Resources/library/00LOCK-OncoSimulR/00new/OncoSimulR/exec
Installing library OncoSimulR.so to /Library/Frameworks/R.framework/Versions/4.6-x86_64/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)
OncoSimulR.Rcheck/tests/testthat.Rout
R Under development (unstable) (2025-10-21 r88958) -- "Unsuffered Consequences"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-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 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 Sun Nov 23 23:02:50 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 Sun Nov 23 23:02:50 2025
Took 0.52
Starting LOD_POM at Sun Nov 23 23:02:50 2025
Ending LOD_POM at Sun Nov 23 23:03:02 2025
Took 11.46
Starting test.Z-all-fitness at Sun Nov 23 23:03:02 2025
Ending test.Z-all-fitness at Sun Nov 23 23:03:02 2025
Took 0.14
Starting test.Z-driver-counts at Sun Nov 23 23:03:02 2025
Ending test.Z-driver-counts at Sun Nov 23 23:03:02 2025
Took 0.12
Starting test.Z-fixation at Sun Nov 23 23:03:02 2025
Ending test.Z-fixation at Sun Nov 23 23:03:02 2025
Took 0.27
Starting test.Z-magellan at Sun Nov 23 23:03:02 2025
Ended test.Z-magellan at Sun Nov 23 23:03:04 2025
Starting test.Z-mutator at Sun Nov 23 23:03:04 2025
Ending test.Z-mutator at Sun Nov 23 23:03:04 2025
Took 0.41
Starting test.Z-mutatorFDF at Sun Nov 23 23:03:04 2025
Ending test.Z-mutatorFDF at Sun Nov 23 23:03:05 2025
Took 0.13
Starting test.Z-oncoSimulIndiv at Sun Nov 23 23:03:05 2025
Ending test.Z-oncoSimulIndiv at Sun Nov 23 23:03:05 2025
Took 0.45
Starting test.Z-oncoSimulIndivConstant at Sun Nov 23 23:03:05 2025
Ending test.Z-oncoSimulIndivConstant at Sun Nov 23 23:03:08 2025
Took 2.52
Starting test.Z-oncoSimulIndivDeath at Sun Nov 23 23:03:08 2025
Ending test.Z-oncoSimulIndivDeath at Sun Nov 23 23:03:09 2025
Took 0.97
Starting test.Z-oncoSimulIndivFDF at Sun Nov 23 23:03:09 2025
Hitted wall time. Exiting.
Hitting wall time is regarded as an error.
Ending test.Z-oncoSimulIndivFDF at Sun Nov 23 23:03:10 2025
Took 0.94
Starting test.Z-rfitness-landscape at Sun Nov 23 23:03:10 2025
Ending test.Z-rfitness-landscape at Sun Nov 23 23:03:10 2025
Took 0.34
Starting Z-sample-only-last tests Sun Nov 23 23:03:10 2025
Ending Z-sample-only-last tests Sun Nov 23 23:03:10 2025
Took 0
Starting Z-total-present-drivers tests Sun Nov 23 23:03:10 2025
Ending Z-total-present-drivers tests Sun Nov 23 23:03:11 2025
Took 0.73
Dummy empty test Sun Nov 23 23:03:11 2025
Starting accessible_genotypes at Sun Nov 23 23:03:11 2025
Ending accessible_genotypes at Sun Nov 23 23:03:20 2025
Took 9.17
Starting all fitness at Sun Nov 23 23:03:20 2025
Ending all-fitness at Sun Nov 23 23:03:25 2025
Took 5.31
Starting test.allFitnessEffectsFDF at Sun Nov 23 23:03:25 2025
Ending test.allFitnessEffectsFDF at Sun Nov 23 23:03:25 2025
Took 0.16
Starting test.allFitnessEffectsDeath at Sun Nov 23 23:03:25 2025
Ending test.allFitnessEffectsDeath at Sun Nov 23 23:03:26 2025
Took 0.48
Starting test.allFitnessEffectsFDF at Sun Nov 23 23:03:26 2025
Ending test.allFitnessEffectsFDF at Sun Nov 23 23:03:26 2025
Took 0.46
Starting driverCounts at Sun Nov 23 23:03:26 2025
Ending driverCounts at Sun Nov 23 23:03:37 2025
Took 10.94
Starting epist-order-modules at Sun Nov 23 23:03:37 2025
Ending epist-order-modules at Sun Nov 23 23:03:37 2025
Took 0.09
Starting test.evaluatingGenotypesDeath at Sun Nov 23 23:03:37 2025
Ending test.evaluatingGenotypesDeath at Sun Nov 23 23:03:38 2025
Took 0.22
Starting test.evaluatingGenotypesFDF at Sun Nov 23 23:03:38 2025
Ending test.evaluatingGenotypesFDF at Sun Nov 23 23:03:38 2025
Took 0.25
Starting exercise-plotting-code at Sun Nov 23 23:03:38 2025
Ending exercise-plotting-code at Sun Nov 23 23:03:41 2025
Took 3.02
Starting exercise-rfitness at Sun Nov 23 23:03:41 2025
Ending exercise-rfitness at Sun Nov 23 23:03:53 2025
Took 12.35
Starting to_Magella at Sun Nov 23 23:03:53 2025
Ending to_Magella at Sun Nov 23 23:03:53 2025
Took 0.04
Starting fitness preds at Sun Nov 23 23:03:53 2025
Observed vs expected, case III
done tries 1
Ending fitness preds long at Sun Nov 23 23:04:02 2025
Took 8.82
Starting fixation at Sun Nov 23 23:04:02 2025
Ending fixation at Sun Nov 23 23:04:20 2025
Took 17.94
Starting test.flfast-additional.R test at Sun Nov 23 23:04:20 2025
Ending test.flfast-additional.R test at Sun Nov 23 23:04:21 2025
Took 1.29
Starting test.flfast-mutator.R test at Sun Nov 23 23:04:21 2025
Finished test.flfast-mutator.R test at Sun Nov 23 23:04:23 2025
Took 1.23
Starting genotFitness at Sun Nov 23 23:04:23 2025
Ending genotFitness at Sun Nov 23 23:04:23 2025
Took 0.22
Starting genot_fitness_to_epistasis at Sun Nov 23 23:04:23 2025
Ending genot_fitness_to_epistasis at Sun Nov 23 23:04:23 2025
Took 0.04
Starting init-mutant tests Sun Nov 23 23:04:23 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 Sun Nov 23 23:04:38 2025
Took 15.36
Starting interventions tests Sun Nov 23 23:04:38 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] 0.78 0.78 0.78
[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 Sun Nov 23 23:05:19 2025
Took 40.82
Starting test.magellan at Sun Nov 23 23:05:19 2025
Ending test.magellan at Sun Nov 23 23:05:23 2025
Took 3.76
Starting test.modules-root-no-root at Sun Nov 23 23:05:23 2025
Ending test.modules-root-no-root at Sun Nov 23 23:05:23 2025
Took 0.09
Starting at mutPropGrowth Sun Nov 23 23:05:23 2025
Ended test.mutPropGrowth: Sun Nov 23 23:05:53 2025
Took 30.1
Starting test.mutator-oncoSimulSample.R test at Sun Nov 23 23:05:53 2025
Finished test.mutator-oncoSimulSample.R test at Sun Nov 23 23:06:06 2025
Took 12.77 seconds
Starting test.mutator.R test at Sun Nov 23 23:06:06 2025[1] 5.851952e-07
[1] 1.688647e-09
Finished test.mutator.R test at Sun Nov 23 23:06:30 2025
Took 24.38
Starting test.mutatorFDF.R test at Sun Nov 23 23:06:30 2025
Starting oncoSimulIndiv-miscell tests Sun Nov 23 23:06:31 2025
Ending oncoSimulIndiv-miscell tests Sun Nov 23 23:06:40 2025
Took 8.79
Starting oncoSimulSample-failures tests Sun Nov 23 23:06:40 2025
Ending oncoSimulSample-failures tests Sun Nov 23 23:06:44 2025
Took 3.89
Starting oncoSimulSample-limits tests Sun Nov 23 23:06:44 2025
Ending oncoSimulSample-limits tests Sun Nov 23 23:06:44 2025
Took 0.07
Starting per-gene-mutation rates at Sun Nov 23 23:06:44 2025
Ending per-gene-mutation rates at Sun Nov 23 23:07:45 2025
Took 61.26
Starting plotFitnessLandscape at Sun Nov 23 23:07:45 2025
Ending plotFitnessLandscape at Sun Nov 23 23:07:55 2025
Took 10.37
Starting poset-transformations tests Sun Nov 23 23:07:55 2025
Ending poset-transformations tests Sun Nov 23 23:08:14 2025
Took 19.07
Starting sample-prob Sun Nov 23 23:08:14 2025
[1] 2.238428e-17
[1] 1.026908e-13
[1] 6.609713e-12
[1] -1.554312e-15
[1] 8.391116e-13
[1] 3.47881e-15
[1] 7.17651e-12
[1] 8.394543e-13
[1] 7.099876e-13
[1] 3.58602e-14
[1] 7.133438e-11
[1] 1.075806e-12
Ending sample-prob tests Sun Nov 23 23:08:26 2025
Took 11.93
Starting samplePop tests Sun Nov 23 23:08:26 2025
Ending samplePop tests Sun Nov 23 23:08:34 2025
Took 7.38
Starting simuls-runs-examples tests Sun Nov 23 23:08:34 2025
Ending simuls-runs-examples tests Sun Nov 23 23:08:47 2025
Took 13.05
Starting user variable tests Sun Nov 23 23:08:47 2025
[1] "Checking user variable: user_var_1"
[1] "Checking rule: rule_1"
Ending user variable tests Sun Nov 23 23:08:47 2025
Took 0.15
Starting warning-mutPropGrowth tests Sun Nov 23 23:08:47 2025
Ending warning-mutPropGrowth tests Sun Nov 23 23:08:47 2025
Took 0.29
Starting wide2long tests Sun Nov 23 23:08:47 2025
Ending wide2long tests Sun Nov 23 23:08:47 2025
Took 0.19
[ FAIL 0 | WARN 19 | SKIP 8 | PASS 8397 ]
══ 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'
[ FAIL 0 | WARN 19 | SKIP 8 | PASS 8397 ]
>
> proc.time()
user system elapsed
267.454 100.851 363.493
OncoSimulR.Rcheck/OncoSimulR-Ex.timings
| name | user | system | elapsed | |
| OncoSimulWide2Long | 0.154 | 0.004 | 0.157 | |
| POM | 0.999 | 0.083 | 0.711 | |
| allFitnessEffects | 2.539 | 0.090 | 2.650 | |
| benchmarks | 0.008 | 0.004 | 0.013 | |
| createInterventions | 0.310 | 0.014 | 0.325 | |
| createUserVars | 0.450 | 0.016 | 0.470 | |
| evalAllGenotypes | 0.226 | 0.013 | 0.241 | |
| example-missing-drivers | 0.247 | 0.018 | 0.267 | |
| examplePosets | 0.306 | 0.010 | 0.321 | |
| examplesFitnessEffects | 0.083 | 0.005 | 0.089 | |
| freq-dep-simul-examples | 0.007 | 0.003 | 0.011 | |
| mcfLs | 0 | 0 | 0 | |
| oncoSimulIndiv | 1.137 | 0.179 | 1.282 | |
| plot.fitnessEffects | 0.282 | 0.030 | 0.314 | |
| plot.oncosimul | 0.404 | 0.022 | 0.429 | |
| plotClonePhylog | 1.748 | 0.075 | 1.834 | |
| plotFitnessLandscape | 1.665 | 0.076 | 1.757 | |
| plotPoset | 0.091 | 0.007 | 0.101 | |
| poset | 0.120 | 0.007 | 0.130 | |
| rfitness | 0.914 | 0.019 | 0.978 | |
| samplePop | 0.056 | 0.066 | 0.096 | |
| simOGraph | 0.088 | 0.015 | 0.105 | |
| to_Magellan | 0.217 | 0.086 | 0.419 | |
| vignette_pre_computed | 0.008 | 0.004 | 0.012 | |