Back to Multiple platform build/check report for BioC 3.22: simplified long |
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This page was generated on 2025-08-30 12:06 -0400 (Sat, 30 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" | 4824 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4615 |
kjohnson3 | macOS 13.7.7 Ventura | arm64 | 4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" | 4562 |
taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4541 |
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 1482/2320 | 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 | OK | OK | ||||||||||
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: 2025-08-29 22:37:46 -0400 (Fri, 29 Aug 2025) |
EndedAt: 2025-08-29 22:45:22 -0400 (Fri, 29 Aug 2025) |
EllapsedTime: 455.8 seconds |
RetCode: 0 |
Status: OK |
CheckDir: OncoSimulR.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### 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 ### ############################################################################## ############################################################################## * 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
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL OncoSimulR ### ############################################################################## ############################################################################## * 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 29 22:39:28 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 29 22:39:28 2025 Took 0.49 Starting LOD_POM at Fri Aug 29 22:39:28 2025 Ending LOD_POM at Fri Aug 29 22:39:45 2025 Took 16.42 Starting test.Z-all-fitness at Fri Aug 29 22:39:45 2025 Ending test.Z-all-fitness at Fri Aug 29 22:39:45 2025 Took 0.14 Starting test.Z-driver-counts at Fri Aug 29 22:39:45 2025 Ending test.Z-driver-counts at Fri Aug 29 22:39:45 2025 Took 0.14 Starting test.Z-fixation at Fri Aug 29 22:39:45 2025 Ending test.Z-fixation at Fri Aug 29 22:39:45 2025 Took 0.31 Starting test.Z-magellan at Fri Aug 29 22:39:45 2025 Ended test.Z-magellan at Fri Aug 29 22:39:47 2025 Starting test.Z-mutator at Fri Aug 29 22:39:47 2025 Ending test.Z-mutator at Fri Aug 29 22:39:48 2025 Took 0.46 Starting test.Z-mutatorFDF at Fri Aug 29 22:39:48 2025 Ending test.Z-mutatorFDF at Fri Aug 29 22:39:48 2025 Took 0.15 Starting test.Z-oncoSimulIndiv at Fri Aug 29 22:39:48 2025 Ending test.Z-oncoSimulIndiv at Fri Aug 29 22:39:48 2025 Took 0.51 Starting test.Z-oncoSimulIndivConstant at Fri Aug 29 22:39:48 2025 Ending test.Z-oncoSimulIndivConstant at Fri Aug 29 22:39:51 2025 Took 2.91 Starting test.Z-oncoSimulIndivDeath at Fri Aug 29 22:39:51 2025 Ending test.Z-oncoSimulIndivDeath at Fri Aug 29 22:39:52 2025 Took 1.02 Starting test.Z-oncoSimulIndivFDF at Fri Aug 29 22:39:52 2025 Hitted wall time. Exiting. Hitting wall time is regarded as an error. Ending test.Z-oncoSimulIndivFDF at Fri Aug 29 22:39:53 2025 Took 0.32 Starting test.Z-rfitness-landscape at Fri Aug 29 22:39:53 2025 Ending test.Z-rfitness-landscape at Fri Aug 29 22:39:53 2025 Took 0.24 Starting Z-sample-only-last tests Fri Aug 29 22:39:53 2025 Ending Z-sample-only-last tests Fri Aug 29 22:39:53 2025 Took 0 Starting Z-total-present-drivers tests Fri Aug 29 22:39:53 2025 Ending Z-total-present-drivers tests Fri Aug 29 22:39:54 2025 Took 0.88 Dummy empty test Fri Aug 29 22:39:54 2025 Starting accessible_genotypes at Fri Aug 29 22:39:54 2025 Ending accessible_genotypes at Fri Aug 29 22:40:03 2025 Took 9.09 Starting all fitness at Fri Aug 29 22:40:03 2025 Ending all-fitness at Fri Aug 29 22:40:08 2025 Took 5.24 Starting test.allFitnessEffectsFDF at Fri Aug 29 22:40:08 2025 Ending test.allFitnessEffectsFDF at Fri Aug 29 22:40:08 2025 Took 0.15 Starting test.allFitnessEffectsDeath at Fri Aug 29 22:40:08 2025 Ending test.allFitnessEffectsDeath at Fri Aug 29 22:40:09 2025 Took 0.43 Starting test.allFitnessEffectsFDF at Fri Aug 29 22:40:09 2025 Ending test.allFitnessEffectsFDF at Fri Aug 29 22:40:09 2025 Took 0.42 Starting driverCounts at Fri Aug 29 22:40:09 2025 Ending driverCounts at Fri Aug 29 22:40:21 2025 Took 11.58 Starting epist-order-modules at Fri Aug 29 22:40:21 2025 Ending epist-order-modules at Fri Aug 29 22:40:21 2025 Took 0.07 Starting test.evaluatingGenotypesDeath at Fri Aug 29 22:40:21 2025 Ending test.evaluatingGenotypesDeath at Fri Aug 29 22:40:21 2025 Took 0.22 Starting test.evaluatingGenotypesFDF at Fri Aug 29 22:40:21 2025 Ending test.evaluatingGenotypesFDF at Fri Aug 29 22:40:21 2025 Took 0.22 Starting exercise-plotting-code at Fri Aug 29 22:40:21 2025 Ending exercise-plotting-code at Fri Aug 29 22:40:24 2025 Took 3.09 Starting exercise-rfitness at Fri Aug 29 22:40:24 2025 Ending exercise-rfitness at Fri Aug 29 22:40:37 2025 Took 12.72 Starting to_Magella at Fri Aug 29 22:40:37 2025 Ending to_Magella at Fri Aug 29 22:40:37 2025 Took 0.04 Starting fitness preds at Fri Aug 29 22:40:37 2025 Observed vs expected, case III done tries 1 Ending fitness preds long at Fri Aug 29 22:40:45 2025 Took 7.51 Starting fixation at Fri Aug 29 22:40:45 2025 Ending fixation at Fri Aug 29 22:41:02 2025 Took 17.9 Starting test.flfast-additional.R test at Fri Aug 29 22:41:02 2025 DEBUG2: Value of rnb = nan DEBUG2: Value of m = 1 DEBUG2: Value of pe = 0 DEBUG2: Value of pm = 0.999995 this is spP popSize = 1 birth = 1 death = 0 W = 1.00001 R = 1.00001 mutation = 6e-06 timeLastUpdate = 2.3857 absfitness = -inf numMutablePos = 6 Unrecoverable exception: Algo 2: retval not finite. Aborting. Ending test.flfast-additional.R test at Fri Aug 29 22:41:04 2025 Took 1.26 Starting test.flfast-mutator.R test at Fri Aug 29 22:41:04 2025 Finished test.flfast-mutator.R test at Fri Aug 29 22:41:05 2025 Took 1.31 Starting genotFitness at Fri Aug 29 22:41:05 2025 Ending genotFitness at Fri Aug 29 22:41:05 2025 Took 0.2 Starting genot_fitness_to_epistasis at Fri Aug 29 22:41:05 2025 Ending genot_fitness_to_epistasis at Fri Aug 29 22:41:05 2025 Took 0.04 Starting init-mutant tests Fri Aug 29 22:41:05 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 29 22:41:12 2025 Took 7.06 Starting interventions tests Fri Aug 29 22:41:12 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] 0.59 0.59 0.59 [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 29 22:41:17 2025 Took 4.59 Starting test.magellan at Fri Aug 29 22:41:17 2025 Ending test.magellan at Fri Aug 29 22:41:17 2025 Took 0.25 Starting test.modules-root-no-root at Fri Aug 29 22:41:17 2025 Ending test.modules-root-no-root at Fri Aug 29 22:41:17 2025 Took 0.09 Starting at mutPropGrowth Fri Aug 29 22:41:17 2025 Ended test.mutPropGrowth: Fri Aug 29 22:41:24 2025 Took 6.3 Starting test.mutator-oncoSimulSample.R test at Fri Aug 29 22:41:24 2025 Finished test.mutator-oncoSimulSample.R test at Fri Aug 29 22:41:33 2025 Took 9.18 seconds Starting test.mutator.R test at Fri Aug 29 22:41:33 2025[1] 1.683572e-11 [1] 4.662259e-13 Finished test.mutator.R test at Fri Aug 29 22:42:27 2025 Took 54.6 Starting test.mutatorFDF.R test at Fri Aug 29 22:42:27 2025 Starting oncoSimulIndiv-miscell tests Fri Aug 29 22:42:28 2025 Ending oncoSimulIndiv-miscell tests Fri Aug 29 22:42:43 2025 Took 14.9 Starting oncoSimulSample-failures tests Fri Aug 29 22:42:43 2025 Ending oncoSimulSample-failures tests Fri Aug 29 22:42:47 2025 Took 3.4 Starting oncoSimulSample-limits tests Fri Aug 29 22:42:47 2025 Ending oncoSimulSample-limits tests Fri Aug 29 22:42:47 2025 Took 0.11 Starting per-gene-mutation rates at Fri Aug 29 22:42:47 2025 Ending per-gene-mutation rates at Fri Aug 29 22:43:47 2025 Took 60.24 Starting plotFitnessLandscape at Fri Aug 29 22:43:47 2025 Ending plotFitnessLandscape at Fri Aug 29 22:43:51 2025 Took 3.92 Starting poset-transformations tests Fri Aug 29 22:43:51 2025 Ending poset-transformations tests Fri Aug 29 22:44:08 2025 Took 17.55 Starting sample-prob Fri Aug 29 22:44:08 2025 [1] 1.273173e-20 [1] 1.267878e-09 [1] 7.499038e-11 [1] 3.203804e-11 [1] 1.180004e-14 [1] 3.018671e-10 [1] 5.176493e-11 [1] 7.933929e-15 [1] 8.538608e-09 [1] 9.598269e-10 [1] 4.480702e-09 [1] 5.67255e-08 Ending sample-prob tests Fri Aug 29 22:44:21 2025 Took 12.78 Starting samplePop tests Fri Aug 29 22:44:21 2025 Ending samplePop tests Fri Aug 29 22:44:36 2025 Took 14.74 Starting simuls-runs-examples tests Fri Aug 29 22:44:36 2025 Ending simuls-runs-examples tests Fri Aug 29 22:44:48 2025 Took 11.97 Starting user variable tests Fri Aug 29 22:44:48 2025 [1] "Checking user variable: user_var_1" [1] "Checking rule: rule_1" Ending user variable tests Fri Aug 29 22:44:48 2025 Took 0.11 Starting warning-mutPropGrowth tests Fri Aug 29 22:44:48 2025 Ending warning-mutPropGrowth tests Fri Aug 29 22:44:49 2025 Took 0.58 Starting wide2long tests Fri Aug 29 22:44:49 2025 Ending wide2long tests Fri Aug 29 22:44:49 2025 Took 0.23 [ FAIL 0 | WARN 19 | SKIP 7 | PASS 8387 ] ══ 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 8387 ] > > proc.time() user system elapsed 255.65 107.73 327.85
OncoSimulR.Rcheck/OncoSimulR-Ex.timings
name | user | system | elapsed | |
OncoSimulWide2Long | 0.162 | 0.004 | 0.167 | |
POM | 0.980 | 0.097 | 0.706 | |
allFitnessEffects | 1.871 | 0.063 | 1.947 | |
benchmarks | 0.008 | 0.005 | 0.012 | |
createInterventions | 0.346 | 0.015 | 0.363 | |
createUserVars | 0.473 | 0.011 | 0.487 | |
evalAllGenotypes | 0.232 | 0.013 | 0.245 | |
example-missing-drivers | 0.227 | 0.017 | 0.245 | |
examplePosets | 0.279 | 0.007 | 0.288 | |
examplesFitnessEffects | 0.087 | 0.003 | 0.091 | |
freq-dep-simul-examples | 0.007 | 0.001 | 0.009 | |
mcfLs | 0 | 0 | 0 | |
oncoSimulIndiv | 1.129 | 0.179 | 1.270 | |
plot.fitnessEffects | 0.244 | 0.029 | 0.276 | |
plot.oncosimul | 0.387 | 0.021 | 0.411 | |
plotClonePhylog | 1.601 | 0.068 | 1.679 | |
plotFitnessLandscape | 1.231 | 0.045 | 1.283 | |
plotPoset | 0.107 | 0.007 | 0.116 | |
poset | 0.120 | 0.006 | 0.128 | |
rfitness | 0.641 | 0.014 | 0.700 | |
samplePop | 0.056 | 0.087 | 0.113 | |
simOGraph | 0.088 | 0.015 | 0.103 | |
to_Magellan | 0.221 | 0.073 | 0.410 | |
vignette_pre_computed | 0.008 | 0.003 | 0.012 | |