Ramon Diaz-Uriarte
| Snapshot Date: 2025-08-15 13:45 -0400 (Fri, 15 Aug 2025) |
| git_url: https://git.bioconductor.org/packages/OncoSimulR |
| git_branch: devel |
| git_last_commit: 833d3cc |
| git_last_commit_date: 2025-06-09 15:18:07 -0400 (Mon, 09 Jun 2025) |
| Back to Multiple platform build/check report for BioC 3.22: simplified long |
|
This page was generated on 2025-08-16 12:05 -0400 (Sat, 16 Aug 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4818 |
| lconway | macOS 12.7.1 Monterey | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4596 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | 4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" | 4538 |
| taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4535 |
| 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 1479/2317 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| OncoSimulR 4.11.1 (landing page) Ramon Diaz-Uriarte
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson3 | macOS 13.7.7 Ventura / arm64 | ... NOT SUPPORTED ... | ||||||||||||
| taishan | Linux (openEuler 24.03 LTS) / aarch64 | OK | TIMEOUT | skipped | ||||||||||
|
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: 4.11.1 |
| 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_4.11.1.tar.gz |
| StartedAt: 2025-08-15 22:34:22 -0400 (Fri, 15 Aug 2025) |
| EndedAt: 2025-08-15 22:41:55 -0400 (Fri, 15 Aug 2025) |
| EllapsedTime: 453.2 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_4.11.1.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.22-bioc/meat/OncoSimulR.Rcheck’
* using R version 4.5.1 (2025-06-13)
* 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 Monterey 12.7.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘OncoSimulR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘OncoSimulR’ version ‘4.11.1’
* 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 14.0.0 (clang-1400.0.29.202)’
* used C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
* used SDK: ‘MacOSX11.3.sdk’
* checking installed package size ... INFO
installed size is 9.4Mb
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 ... NOTE
Note: information on .o files is not available
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’
OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: 2 NOTEs
See
‘/Users/biocbuild/bbs-3.22-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/4.5-x86_64/Resources/library’
* installing *source* package ‘OncoSimulR’ ...
** this is package ‘OncoSimulR’ version ‘4.11.1’
** using staged installation
** libs
using C compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
using C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
using SDK: ‘MacOSX11.3.sdk’
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-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/4.5-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/4.5-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/4.5-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/4.5-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/4.5-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/4.5-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/4.5-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/4.5-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/4.5-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/4.5-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/4.5-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/4.5-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;
^
1 warning generated.
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-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/4.5-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/4.5-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/4.5-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/4.5-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/4.5-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/4.5-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/4.5-x86_64/Resources/library/00LOCK-OncoSimulR/00new/OncoSimulR
[1] ""
Installing fl_statistics fl_generate to /Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/00LOCK-OncoSimulR/00new/OncoSimulR/exec
Installing library OncoSimulR.so to /Library/Frameworks/R.framework/Versions/4.5-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 version 4.5.1 (2025-06-13) -- "Great Square Root"
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 Fri Aug 15 22:35:57 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 Fri Aug 15 22:35:58 2025
Took 0.48
Starting LOD_POM at Fri Aug 15 22:35:58 2025
Ending LOD_POM at Fri Aug 15 22:36:10 2025
Took 12.39
Starting test.Z-all-fitness at Fri Aug 15 22:36:10 2025
Ending test.Z-all-fitness at Fri Aug 15 22:36:11 2025
Took 0.14
Starting test.Z-driver-counts at Fri Aug 15 22:36:11 2025
Ending test.Z-driver-counts at Fri Aug 15 22:36:11 2025
Took 0.11
Starting test.Z-fixation at Fri Aug 15 22:36:11 2025
Ending test.Z-fixation at Fri Aug 15 22:36:11 2025
Took 0.31
Starting test.Z-magellan at Fri Aug 15 22:36:11 2025
Ended test.Z-magellan at Fri Aug 15 22:36:13 2025
Starting test.Z-mutator at Fri Aug 15 22:36:13 2025
Ending test.Z-mutator at Fri Aug 15 22:36:13 2025
Took 0.44
Starting test.Z-mutatorFDF at Fri Aug 15 22:36:13 2025
Ending test.Z-mutatorFDF at Fri Aug 15 22:36:13 2025
Took 0.15
Starting test.Z-oncoSimulIndiv at Fri Aug 15 22:36:13 2025
Ending test.Z-oncoSimulIndiv at Fri Aug 15 22:36:14 2025
Took 0.5
Starting test.Z-oncoSimulIndivConstant at Fri Aug 15 22:36:14 2025
Ending test.Z-oncoSimulIndivConstant at Fri Aug 15 22:36:17 2025
Took 2.75
Starting test.Z-oncoSimulIndivDeath at Fri Aug 15 22:36:17 2025
Ending test.Z-oncoSimulIndivDeath at Fri Aug 15 22:36:18 2025
Took 0.94
Starting test.Z-oncoSimulIndivFDF at Fri Aug 15 22:36:18 2025
Hitted wall time. Exiting.
Hitting wall time is regarded as an error.
Ending test.Z-oncoSimulIndivFDF at Fri Aug 15 22:36:19 2025
Took 0.86
Starting test.Z-rfitness-landscape at Fri Aug 15 22:36:19 2025
Ending test.Z-rfitness-landscape at Fri Aug 15 22:36:19 2025
Took 0.26
Starting Z-sample-only-last tests Fri Aug 15 22:36:19 2025
Ending Z-sample-only-last tests Fri Aug 15 22:36:19 2025
Took 0
Starting Z-total-present-drivers tests Fri Aug 15 22:36:19 2025
Ending Z-total-present-drivers tests Fri Aug 15 22:36:20 2025
Took 0.82
Dummy empty test Fri Aug 15 22:36:20 2025
Starting accessible_genotypes at Fri Aug 15 22:36:20 2025
Ending accessible_genotypes at Fri Aug 15 22:36:29 2025
Took 8.87
Starting all fitness at Fri Aug 15 22:36:29 2025
Ending all-fitness at Fri Aug 15 22:36:34 2025
Took 5.36
Starting test.allFitnessEffectsFDF at Fri Aug 15 22:36:34 2025
Ending test.allFitnessEffectsFDF at Fri Aug 15 22:36:34 2025
Took 0.15
Starting test.allFitnessEffectsDeath at Fri Aug 15 22:36:34 2025
Ending test.allFitnessEffectsDeath at Fri Aug 15 22:36:35 2025
Took 0.44
Starting test.allFitnessEffectsFDF at Fri Aug 15 22:36:35 2025
Ending test.allFitnessEffectsFDF at Fri Aug 15 22:36:35 2025
Took 0.45
Starting driverCounts at Fri Aug 15 22:36:35 2025
Ending driverCounts at Fri Aug 15 22:36:46 2025
Took 11.47
Starting epist-order-modules at Fri Aug 15 22:36:46 2025
Ending epist-order-modules at Fri Aug 15 22:36:47 2025
Took 0.07
Starting test.evaluatingGenotypesDeath at Fri Aug 15 22:36:47 2025
Ending test.evaluatingGenotypesDeath at Fri Aug 15 22:36:47 2025
Took 0.22
Starting test.evaluatingGenotypesFDF at Fri Aug 15 22:36:47 2025
Ending test.evaluatingGenotypesFDF at Fri Aug 15 22:36:47 2025
Took 0.21
Starting exercise-plotting-code at Fri Aug 15 22:36:47 2025
Ending exercise-plotting-code at Fri Aug 15 22:36:50 2025
Took 3.18
Starting exercise-rfitness at Fri Aug 15 22:36:50 2025
Ending exercise-rfitness at Fri Aug 15 22:37:03 2025
Took 12.9
Starting to_Magella at Fri Aug 15 22:37:03 2025
Ending to_Magella at Fri Aug 15 22:37:03 2025
Took 0.04
Starting fitness preds at Fri Aug 15 22:37:03 2025
Observed vs expected, case III
done tries 1
Ending fitness preds long at Fri Aug 15 22:37:11 2025
Took 8.1
Starting fixation at Fri Aug 15 22:37:11 2025
Ending fixation at Fri Aug 15 22:37:30 2025
Took 18.71
Starting test.flfast-additional.R test at Fri Aug 15 22:37:30 2025
Ending test.flfast-additional.R test at Fri Aug 15 22:37:31 2025
Took 1.38
Starting test.flfast-mutator.R test at Fri Aug 15 22:37:31 2025
Finished test.flfast-mutator.R test at Fri Aug 15 22:37:33 2025
Took 1.18
Starting genotFitness at Fri Aug 15 22:37:33 2025
Ending genotFitness at Fri Aug 15 22:37:33 2025
Took 0.19
Starting genot_fitness_to_epistasis at Fri Aug 15 22:37:33 2025
Ending genot_fitness_to_epistasis at Fri Aug 15 22:37:33 2025
Took 0.04
Starting init-mutant tests Fri Aug 15 22:37:33 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 Fri Aug 15 22:37:40 2025
Took 7.04
Starting interventions tests Fri Aug 15 22:37:40 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] 0.64 0.64 0.64
[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 Fri Aug 15 22:37:45 2025
Took 4.93
Starting test.magellan at Fri Aug 15 22:37:45 2025
Ending test.magellan at Fri Aug 15 22:37:45 2025
Took 0.25
Starting test.modules-root-no-root at Fri Aug 15 22:37:45 2025
Ending test.modules-root-no-root at Fri Aug 15 22:37:45 2025
Took 0.08
Starting at mutPropGrowth Fri Aug 15 22:37:45 2025
Ended test.mutPropGrowth: Fri Aug 15 22:37:52 2025
Took 6.44
Starting test.mutator-oncoSimulSample.R test at Fri Aug 15 22:37:52 2025
Finished test.mutator-oncoSimulSample.R test at Fri Aug 15 22:38:01 2025
Took 9.02 seconds
Starting test.mutator.R test at Fri Aug 15 22:38:01 2025[1] 1.4399e-08
[1] 8.281807e-12
Finished test.mutator.R test at Fri Aug 15 22:38:41 2025
Took 40.8
Starting test.mutatorFDF.R test at Fri Aug 15 22:38:41 2025
Starting oncoSimulIndiv-miscell tests Fri Aug 15 22:38:44 2025
Ending oncoSimulIndiv-miscell tests Fri Aug 15 22:39:11 2025
Took 26.84
Starting oncoSimulSample-failures tests Fri Aug 15 22:39:11 2025
Ending oncoSimulSample-failures tests Fri Aug 15 22:39:15 2025
Took 4.06
Starting oncoSimulSample-limits tests Fri Aug 15 22:39:15 2025
Ending oncoSimulSample-limits tests Fri Aug 15 22:39:15 2025
Took 0.18
Starting per-gene-mutation rates at Fri Aug 15 22:39:15 2025
Ending per-gene-mutation rates at Fri Aug 15 22:40:24 2025
Took 69.62
Starting plotFitnessLandscape at Fri Aug 15 22:40:24 2025
Ending plotFitnessLandscape at Fri Aug 15 22:40:30 2025
Took 5.17
Starting poset-transformations tests Fri Aug 15 22:40:30 2025
Ending poset-transformations tests Fri Aug 15 22:40:41 2025
Took 11.67
Starting sample-prob Fri Aug 15 22:40:41 2025
[1] 1.436889e-26
[1] 1.699287e-11
[1] 2.984236e-09
[1] 2.67563e-11
[1] 3.228893e-10
[1] 2.317106e-12
[1] 5.029973e-11
[1] 1.246432e-16
[1] 1.038409e-07
[1] 1.110324e-11
[1] 7.212203e-09
[1] 2.023799e-08
Ending sample-prob tests Fri Aug 15 22:40:57 2025
Took 15.19
Starting samplePop tests Fri Aug 15 22:40:57 2025
Ending samplePop tests Fri Aug 15 22:41:07 2025
Took 10.54
Starting simuls-runs-examples tests Fri Aug 15 22:41:07 2025
Ending simuls-runs-examples tests Fri Aug 15 22:41:19 2025
Took 11.57
Starting user variable tests Fri Aug 15 22:41:19 2025
[1] "Checking user variable: user_var_1"
[1] "Checking rule: rule_1"
Ending user variable tests Fri Aug 15 22:41:19 2025
Took 0.16
Starting warning-mutPropGrowth tests Fri Aug 15 22:41:19 2025
Ending warning-mutPropGrowth tests Fri Aug 15 22:41:20 2025
Took 0.72
Starting wide2long tests Fri Aug 15 22:41:20 2025
Ending wide2long tests Fri Aug 15 22:41:20 2025
Took 0.41
[ FAIL 0 | WARN 19 | SKIP 7 | PASS 8392 ]
══ Skipped tests (7) ═══════════════════════════════════════════════════════════
• On Mac (2): 'test.Z-magellan.R:664:5', 'test.Z-oncoSimulIndivFDF.R:125:3'
• 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 7 | PASS 8392 ]
>
> proc.time()
user system elapsed
258.191 103.452 329.512
OncoSimulR.Rcheck/OncoSimulR-Ex.timings
| name | user | system | elapsed | |
| OncoSimulWide2Long | 0.161 | 0.004 | 0.165 | |
| POM | 1.000 | 0.106 | 0.729 | |
| allFitnessEffects | 1.877 | 0.062 | 1.948 | |
| benchmarks | 0.009 | 0.006 | 0.015 | |
| createInterventions | 0.353 | 0.013 | 0.369 | |
| createUserVars | 0.474 | 0.017 | 0.496 | |
| evalAllGenotypes | 0.231 | 0.012 | 0.245 | |
| example-missing-drivers | 0.241 | 0.017 | 0.261 | |
| examplePosets | 0.318 | 0.008 | 0.328 | |
| examplesFitnessEffects | 0.118 | 0.006 | 0.127 | |
| freq-dep-simul-examples | 0.010 | 0.002 | 0.013 | |
| mcfLs | 0.000 | 0.000 | 0.001 | |
| oncoSimulIndiv | 1.242 | 0.225 | 1.432 | |
| plot.fitnessEffects | 0.302 | 0.034 | 0.339 | |
| plot.oncosimul | 0.406 | 0.021 | 0.430 | |
| plotClonePhylog | 1.621 | 0.067 | 1.696 | |
| plotFitnessLandscape | 1.270 | 0.047 | 1.324 | |
| plotPoset | 0.104 | 0.006 | 0.113 | |
| poset | 0.115 | 0.007 | 0.123 | |
| rfitness | 0.725 | 0.015 | 0.787 | |
| samplePop | 0.104 | 0.076 | 0.149 | |
| simOGraph | 0.104 | 0.021 | 0.127 | |
| to_Magellan | 0.224 | 0.069 | 0.391 | |
| vignette_pre_computed | 0.008 | 0.003 | 0.011 | |