Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-06-11 15:42 -0400 (Tue, 11 Jun 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.0 RC (2024-04-16 r86468) -- "Puppy Cup" | 4679 |
palomino4 | Windows Server 2022 Datacenter | x64 | 4.4.0 RC (2024-04-16 r86468 ucrt) -- "Puppy Cup" | 4414 |
merida1 | macOS 12.7.4 Monterey | x86_64 | 4.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup" | 4441 |
kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup" | 4394 |
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 1432/2239 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
OncoSimulR 4.7.0 (landing page) Ramon Diaz-Uriarte
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | |||||||||
palomino4 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | |||||||||
merida1 | macOS 12.7.4 Monterey / x86_64 | OK | OK | OK | OK | |||||||||
kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | ERROR | skipped | 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: 4.7.0 |
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_4.7.0.tar.gz |
StartedAt: 2024-06-10 07:27:15 -0400 (Mon, 10 Jun 2024) |
EndedAt: 2024-06-10 07:39:00 -0400 (Mon, 10 Jun 2024) |
EllapsedTime: 705.3 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_4.7.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/OncoSimulR.Rcheck’ * using R version 4.4.0 Patched (2024-04-24 r86482) * using platform: x86_64-apple-darwin20 * R was compiled by Apple clang version 14.0.0 (clang-1400.0.29.202) GNU Fortran (GCC) 12.2.0 * running under: macOS Monterey 12.7.4 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘OncoSimulR/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘OncoSimulR’ version ‘4.7.0’ * 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: ‘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 ... NOTE 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 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 Examples with CPU (user + system) or elapsed time > 5s user system elapsed allFitnessEffects 4.113 0.182 5.025 * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘testthat.R’ OK * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... OK * checking running R code from vignettes ... SKIPPED * checking re-building of vignette outputs ... SKIPPED * checking PDF version of manual ... OK * DONE Status: 3 NOTEs See ‘/Users/biocbuild/bbs-3.20-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/4.4-x86_64/Resources/library’ * installing *source* package ‘OncoSimulR’ ... ** 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/4.4-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/4.4-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/4.4-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/4.4-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/4.4-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/4.4-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/4.4-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/4.4-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/4.4-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/4.4-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/4.4-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/4.4-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/4.4-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/4.4-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/4.4-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/4.4-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/4.4-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/4.4-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/4.4-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/4.4-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 -Wl,-framework -Wl,CoreFoundation installing via 'install.libs.R' to /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/00LOCK-OncoSimulR/00new/OncoSimulR [1] "" Installing fl_statistics fl_generate to /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/00LOCK-OncoSimulR/00new/OncoSimulR/exec Installing library OncoSimulR.so to /Library/Frameworks/R.framework/Versions/4.4-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 4.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup" Copyright (C) 2024 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) > > test_check("OncoSimulR") Starting FDF-letter-fitness-order Mon Jun 10 07:30:19 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 10 07:30:21 2024 Took 1.29 Starting LOD_POM at Mon Jun 10 07:30:21 2024 Ending LOD_POM at Mon Jun 10 07:30:47 2024 Took 26.83 Starting test.Z-all-fitness at Mon Jun 10 07:30:48 2024 Ending test.Z-all-fitness at Mon Jun 10 07:30:48 2024 Took 0.3 Starting test.Z-driver-counts at Mon Jun 10 07:30:48 2024 Ending test.Z-driver-counts at Mon Jun 10 07:30:48 2024 Took 0.34 Starting test.Z-fixation at Mon Jun 10 07:30:48 2024 Ending test.Z-fixation at Mon Jun 10 07:30:49 2024 Took 0.68 Starting test.Z-magellan at Mon Jun 10 07:30:49 2024 Ended test.Z-magellan at Mon Jun 10 07:30:53 2024 Starting test.Z-mutator at Mon Jun 10 07:30:53 2024 Ending test.Z-mutator at Mon Jun 10 07:30:54 2024 Took 0.87 Starting test.Z-mutatorFDF at Mon Jun 10 07:30:54 2024 Ending test.Z-mutatorFDF at Mon Jun 10 07:30:54 2024 Took 0.3 Starting test.Z-oncoSimulIndiv at Mon Jun 10 07:30:54 2024 Ending test.Z-oncoSimulIndiv at Mon Jun 10 07:30:55 2024 Took 1.27 Starting test.Z-oncoSimulIndivConstant at Mon Jun 10 07:30:55 2024 Ending test.Z-oncoSimulIndivConstant at Mon Jun 10 07:31:01 2024 Took 5.4 Starting test.Z-oncoSimulIndivDeath at Mon Jun 10 07:31:01 2024 Ending test.Z-oncoSimulIndivDeath at Mon Jun 10 07:31:03 2024 Took 2 Starting test.Z-oncoSimulIndivFDF at Mon Jun 10 07:31:03 2024 Hitted wall time. Exiting. Hitting wall time is regarded as an error. Ending test.Z-oncoSimulIndivFDF at Mon Jun 10 07:31:04 2024 Took 0.97 Starting test.Z-rfitness-landscape at Mon Jun 10 07:31:04 2024 Ending test.Z-rfitness-landscape at Mon Jun 10 07:31:04 2024 Took 0.5 Starting Z-sample-only-last tests Mon Jun 10 07:31:04 2024 Ending Z-sample-only-last tests Mon Jun 10 07:31:04 2024 Took 0 Starting Z-total-present-drivers tests Mon Jun 10 07:31:04 2024 Ending Z-total-present-drivers tests Mon Jun 10 07:31:06 2024 Took 1.76 Dummy empty test Mon Jun 10 07:31:06 2024 Starting accessible_genotypes at Mon Jun 10 07:31:06 2024 Ending accessible_genotypes at Mon Jun 10 07:31:26 2024 Took 20.24 Starting all fitness at Mon Jun 10 07:31:26 2024 Ending all-fitness at Mon Jun 10 07:31:42 2024 Took 16.24 Starting test.allFitnessEffectsFDF at Mon Jun 10 07:31:42 2024 Ending test.allFitnessEffectsFDF at Mon Jun 10 07:31:43 2024 Took 0.32 Starting test.allFitnessEffectsDeath at Mon Jun 10 07:31:43 2024 Ending test.allFitnessEffectsDeath at Mon Jun 10 07:31:44 2024 Took 1.18 Starting test.allFitnessEffectsFDF at Mon Jun 10 07:31:44 2024 Ending test.allFitnessEffectsFDF at Mon Jun 10 07:31:45 2024 Took 1.04 Starting driverCounts at Mon Jun 10 07:31:45 2024 Ending driverCounts at Mon Jun 10 07:32:12 2024 Took 27.2 Starting epist-order-modules at Mon Jun 10 07:32:12 2024 Ending epist-order-modules at Mon Jun 10 07:32:12 2024 Took 0.13 Starting test.evaluatingGenotypesDeath at Mon Jun 10 07:32:12 2024 Ending test.evaluatingGenotypesDeath at Mon Jun 10 07:32:13 2024 Took 0.51 Starting test.evaluatingGenotypesFDF at Mon Jun 10 07:32:13 2024 Ending test.evaluatingGenotypesFDF at Mon Jun 10 07:32:13 2024 Took 0.49 Starting exercise-plotting-code at Mon Jun 10 07:32:13 2024 Ending exercise-plotting-code at Mon Jun 10 07:32:20 2024 Took 6.85 Starting exercise-rfitness at Mon Jun 10 07:32:20 2024 Ending exercise-rfitness at Mon Jun 10 07:32:45 2024 Took 24.97 Starting to_Magella at Mon Jun 10 07:32:45 2024 Ending to_Magella at Mon Jun 10 07:32:45 2024 Took 0.1 Starting fitness preds at Mon Jun 10 07:32:45 2024 Observed vs expected, case III done tries 1 Ending fitness preds long at Mon Jun 10 07:33:01 2024 Took 15.49 Starting fixation at Mon Jun 10 07:33:01 2024 Ending fixation at Mon Jun 10 07:33:43 2024 Took 42.46 Starting test.flfast-additional.R test at Mon Jun 10 07:33:43 2024 Ending test.flfast-additional.R test at Mon Jun 10 07:33:46 2024 Took 3.14 Starting test.flfast-mutator.R test at Mon Jun 10 07:33:46 2024 Finished test.flfast-mutator.R test at Mon Jun 10 07:33:51 2024 Took 4.35 Starting genotFitness at Mon Jun 10 07:33:51 2024 Ending genotFitness at Mon Jun 10 07:33:51 2024 Took 0.45 Starting genot_fitness_to_epistasis at Mon Jun 10 07:33:51 2024 Ending genot_fitness_to_epistasis at Mon Jun 10 07:33:51 2024 Took 0.11 Starting init-mutant tests Mon Jun 10 07:33:51 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 10 07:34:07 2024 Took 15.28 Starting interventions tests Mon Jun 10 07:34:07 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] 0.45 0.45 0.45 [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 10 07:34:16 2024 Took 9.46 Starting test.magellan at Mon Jun 10 07:34:16 2024 Ending test.magellan at Mon Jun 10 07:34:17 2024 Took 0.39 Starting test.modules-root-no-root at Mon Jun 10 07:34:17 2024 Ending test.modules-root-no-root at Mon Jun 10 07:34:17 2024 Took 0.21 Starting at mutPropGrowth Mon Jun 10 07:34:17 2024 Ended test.mutPropGrowth: Mon Jun 10 07:34:33 2024 Took 16.61 Starting test.mutator-oncoSimulSample.R test at Mon Jun 10 07:34:33 2024 Finished test.mutator-oncoSimulSample.R test at Mon Jun 10 07:34:56 2024 Took 22.76 seconds Starting test.mutator.R test at Mon Jun 10 07:34:56 2024[1] 2.130959e-06 [1] 2.375869e-11 Finished test.mutator.R test at Mon Jun 10 07:35:33 2024 Took 36.58 Starting test.mutatorFDF.R test at Mon Jun 10 07:35:33 2024 Starting test.no-v1 at Mon Jun 10 07:35:34 2024 Ending test.no-v1 at Mon Jun 10 07:35:34 2024 Took 0.03 Starting oncoSimulIndiv-miscell tests Mon Jun 10 07:35:34 2024 Ending oncoSimulIndiv-miscell tests Mon Jun 10 07:35:47 2024 Took 12.27 Starting oncoSimulSample-failures tests Mon Jun 10 07:35:47 2024 Ending oncoSimulSample-failures tests Mon Jun 10 07:35:51 2024 Took 4 Starting oncoSimulSample-limits tests Mon Jun 10 07:35:51 2024 Ending oncoSimulSample-limits tests Mon Jun 10 07:35:51 2024 Took 0.2 Starting per-gene-mutation rates at Mon Jun 10 07:35:51 2024 Ending per-gene-mutation rates at Mon Jun 10 07:37:05 2024 Took 74.62 Starting plotFitnessLandscape at Mon Jun 10 07:37:05 2024 Ending plotFitnessLandscape at Mon Jun 10 07:37:14 2024 Took 8.65 Starting poset-transformations tests Mon Jun 10 07:37:14 2024 Ending poset-transformations tests Mon Jun 10 07:37:41 2024 Took 27.12 Starting sample-prob Mon Jun 10 07:37:41 2024 [1] 2.772552e-21 [1] 1.865921e-11 [1] 1.722243e-08 [1] 1.093183e-11 [1] 5.805533e-15 [1] 5.786209e-14 [1] 8.133444e-08 [1] 5.995338e-12 [1] 6.117467e-09 [1] 2.737777e-12 [1] 5.026674e-07 [1] 2.093683e-09 Ending sample-prob tests Mon Jun 10 07:37:57 2024 Took 15.48 Starting samplePop tests Mon Jun 10 07:37:57 2024 Ending samplePop tests Mon Jun 10 07:38:11 2024 Took 14.41 Starting simuls-runs-examples tests Mon Jun 10 07:38:11 2024 Ending simuls-runs-examples tests Mon Jun 10 07:38:25 2024 Took 13.83 Starting user variable tests Mon Jun 10 07:38:25 2024 [1] "Checking user variable: user_var_1" [1] "Checking rule: rule_1" Ending user variable tests Mon Jun 10 07:38:25 2024 Took 0.23 Starting warning-mutPropGrowth tests Mon Jun 10 07:38:25 2024 Ending warning-mutPropGrowth tests Mon Jun 10 07:38:26 2024 Took 0.95 Starting wide2long tests Mon Jun 10 07:38:26 2024 Ending wide2long tests Mon Jun 10 07:38:27 2024 Took 0.45 [ FAIL 0 | WARN 18 | SKIP 7 | PASS 8421 ] ══ 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:1097:1' [ FAIL 0 | WARN 18 | SKIP 7 | PASS 8421 ] > > proc.time() user system elapsed 491.749 76.465 500.119
OncoSimulR.Rcheck/OncoSimulR-Ex.timings
name | user | system | elapsed | |
OncoSimulWide2Long | 0.410 | 0.014 | 0.502 | |
POM | 1.821 | 0.107 | 1.218 | |
allFitnessEffects | 4.113 | 0.182 | 5.025 | |
benchmarks | 0.022 | 0.014 | 0.040 | |
createInterventions | 0.537 | 0.019 | 0.610 | |
createUserVars | 0.799 | 0.026 | 0.898 | |
evalAllGenotypes | 0.490 | 0.032 | 0.568 | |
example-missing-drivers | 0.520 | 0.034 | 0.657 | |
examplePosets | 0.589 | 0.010 | 0.650 | |
examplesFitnessEffects | 0.087 | 0.006 | 0.142 | |
freq-dep-simul-examples | 0.018 | 0.004 | 0.023 | |
mcfLs | 0.000 | 0.001 | 0.000 | |
oncoSimulIndiv | 2.272 | 0.279 | 2.750 | |
plot.fitnessEffects | 0.510 | 0.068 | 0.790 | |
plot.oncosimul | 0.808 | 0.065 | 1.148 | |
plotClonePhylog | 3.214 | 0.160 | 3.987 | |
plotFitnessLandscape | 2.765 | 0.115 | 3.632 | |
plotPoset | 0.196 | 0.021 | 0.376 | |
poset | 0.233 | 0.023 | 0.380 | |
rfitness | 1.399 | 0.045 | 1.867 | |
samplePop | 0.123 | 0.095 | 0.305 | |
simOGraph | 0.123 | 0.030 | 0.218 | |
to_Magellan | 0.402 | 0.129 | 0.870 | |
vignette_pre_computed | 0.013 | 0.008 | 0.022 | |