Back to Multiple platform build/check report for BioC 3.22: simplified long |
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This page was generated on 2025-09-26 12:07 -0400 (Fri, 26 Sep 2025).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" | 4831 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4619 |
kjohnson3 | macOS 13.7.7 Ventura | arm64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4563 |
taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4563 |
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 1492/2334 | 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. - See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host. |
Package: OncoSimulR |
Version: 4.11.1 |
Command: /home/biocbuild/R/R/bin/R CMD check --install=check:OncoSimulR.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings OncoSimulR_4.11.1.tar.gz |
StartedAt: 2025-09-26 10:22:28 -0000 (Fri, 26 Sep 2025) |
EndedAt: 2025-09-26 10:28:35 -0000 (Fri, 26 Sep 2025) |
EllapsedTime: 367.5 seconds |
RetCode: 0 |
Status: OK |
CheckDir: OncoSimulR.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R/bin/R CMD check --install=check:OncoSimulR.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings OncoSimulR_4.11.1.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/OncoSimulR.Rcheck’ * using R version 4.5.0 (2025-04-11) * using platform: aarch64-unknown-linux-gnu * R was compiled by aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0 GNU Fortran (GCC) 14.2.0 * running under: openEuler 24.03 (LTS) * 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: ‘aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0’ * used C++ compiler: ‘aarch64-unknown-linux-gnu-g++ (GCC) 14.2.0’ * checking installed package size ... INFO installed size is 46.6Mb sub-directories of 1Mb or more: libs 44.9Mb * 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 loading without being on the library search path ... 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 ‘/home/biocbuild/bbs-3.22-bioc/meat/OncoSimulR.Rcheck/00check.log’ for details.
OncoSimulR.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R/bin/R CMD INSTALL OncoSimulR ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/R/R-4.5.0/site-library’ * installing *source* package ‘OncoSimulR’ ... ** this is package ‘OncoSimulR’ version ‘4.11.1’ ** using staged installation ** libs using C compiler: ‘aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0’ using C++ compiler: ‘aarch64-unknown-linux-gnu-g++ (GCC) 14.2.0’ /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -I"/home/biocbuild/R/R-4.5.0/include" -DNDEBUG -I'/home/biocbuild/R/R-4.5.0/site-library/Rcpp/include' -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -c FitnessLandscape/gamma.c -o FitnessLandscape/gamma.o /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -I"/home/biocbuild/R/R-4.5.0/include" -DNDEBUG -I'/home/biocbuild/R/R-4.5.0/site-library/Rcpp/include' -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -c FitnessLandscape/landscape.c -o FitnessLandscape/landscape.o /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -I"/home/biocbuild/R/R-4.5.0/include" -DNDEBUG -I'/home/biocbuild/R/R-4.5.0/site-library/Rcpp/include' -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -c FitnessLandscape/random.c -o FitnessLandscape/random.o /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -I"/home/biocbuild/R/R-4.5.0/include" -DNDEBUG -I'/home/biocbuild/R/R-4.5.0/site-library/Rcpp/include' -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -c FitnessLandscape/sort.c -o FitnessLandscape/sort.o /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -I"/home/biocbuild/R/R-4.5.0/include" -DNDEBUG -I'/home/biocbuild/R/R-4.5.0/site-library/Rcpp/include' -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -c FitnessLandscape/chain.c -o FitnessLandscape/chain.o /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -I"/home/biocbuild/R/R-4.5.0/include" -DNDEBUG -I'/home/biocbuild/R/R-4.5.0/site-library/Rcpp/include' -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -c FitnessLandscape/input.c -o FitnessLandscape/input.o /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -I"/home/biocbuild/R/R-4.5.0/include" -DNDEBUG -I'/home/biocbuild/R/R-4.5.0/site-library/Rcpp/include' -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -c FitnessLandscape/genotypes.c -o FitnessLandscape/genotypes.o /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -I"/home/biocbuild/R/R-4.5.0/include" -DNDEBUG -I'/home/biocbuild/R/R-4.5.0/site-library/Rcpp/include' -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -c FitnessLandscape/ordered_pairs.c -o FitnessLandscape/ordered_pairs.o /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -I"/home/biocbuild/R/R-4.5.0/include" -DNDEBUG -I'/home/biocbuild/R/R-4.5.0/site-library/Rcpp/include' -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -c FitnessLandscape/calculus.c -o FitnessLandscape/calculus.o /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -I"/home/biocbuild/R/R-4.5.0/include" -DNDEBUG -I'/home/biocbuild/R/R-4.5.0/site-library/Rcpp/include' -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -c FitnessLandscape/vector.c -o FitnessLandscape/vector.o /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -I"/home/biocbuild/R/R-4.5.0/include" -DNDEBUG -I'/home/biocbuild/R/R-4.5.0/site-library/Rcpp/include' -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -c FitnessLandscape/generalized_chain.c -o FitnessLandscape/generalized_chain.o /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -I"/home/biocbuild/R/R-4.5.0/include" -DNDEBUG -I'/home/biocbuild/R/R-4.5.0/site-library/Rcpp/include' -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -c FitnessLandscape/LinearAlgebra.c -o FitnessLandscape/LinearAlgebra.o /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -I"/home/biocbuild/R/R-4.5.0/include" -DNDEBUG -I'/home/biocbuild/R/R-4.5.0/site-library/Rcpp/include' -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -c FitnessLandscape/summary_statistics.c -o FitnessLandscape/summary_statistics.o /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -I"/home/biocbuild/R/R-4.5.0/include" -DNDEBUG -I'/home/biocbuild/R/R-4.5.0/site-library/Rcpp/include' -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -c FitnessLandscape/epistasis_type.c -o FitnessLandscape/epistasis_type.o /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -I"/home/biocbuild/R/R-4.5.0/include" -DNDEBUG -I'/home/biocbuild/R/R-4.5.0/site-library/Rcpp/include' -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -c FitnessLandscape/decomposition.c -o FitnessLandscape/decomposition.o /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -I"/home/biocbuild/R/R-4.5.0/include" -DNDEBUG -I'/home/biocbuild/R/R-4.5.0/site-library/Rcpp/include' -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -c FitnessLandscape/models.c -o FitnessLandscape/models.o /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -I"/home/biocbuild/R/R-4.5.0/include" -DNDEBUG -I'/home/biocbuild/R/R-4.5.0/site-library/Rcpp/include' -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -c FitnessLandscape/verbose.c -o FitnessLandscape/verbose.o ar -r liblandscape.a FitnessLandscape/gamma.o FitnessLandscape/landscape.o FitnessLandscape/random.o FitnessLandscape/sort.o FitnessLandscape/chain.o FitnessLandscape/input.o FitnessLandscape/genotypes.o FitnessLandscape/ordered_pairs.o FitnessLandscape/calculus.o FitnessLandscape/vector.o FitnessLandscape/generalized_chain.o FitnessLandscape/LinearAlgebra.o FitnessLandscape/summary_statistics.o FitnessLandscape/epistasis_type.o FitnessLandscape/decomposition.o FitnessLandscape/models.o FitnessLandscape/verbose.o ; ar: creating liblandscape.a ranlib liblandscape.a; /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -O -Wall -o fl_statistics -I/FitnessLandscape/. -L. FitnessLandscape/main_fl_statistics.c -llandscape -lm; /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -O -Wall -o fl_generate -I/FitnessLandscape/. -L. FitnessLandscape/main_fl_generate.c -llandscape -lm; /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -I"/home/biocbuild/R/R-4.5.0/include" -DNDEBUG -I'/home/biocbuild/R/R-4.5.0/site-library/Rcpp/include' -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -c OncoSimulR_init.c -o OncoSimulR_init.o /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.5.0/include" -DNDEBUG -I'/home/biocbuild/R/R-4.5.0/site-library/Rcpp/include' -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -c RcppExports.cpp -o RcppExports.o /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.5.0/include" -DNDEBUG -I'/home/biocbuild/R/R-4.5.0/site-library/Rcpp/include' -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -c unity_osimul.cpp -o unity_osimul.o /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++17 -shared -L/home/biocbuild/R/R-4.5.0/lib -L/usr/local/lib -o OncoSimulR.so OncoSimulR_init.o RcppExports.o unity_osimul.o -L/home/biocbuild/R/R-4.5.0/lib -lR installing via 'install.libs.R' to /home/biocbuild/R/R-4.5.0/site-library/00LOCK-OncoSimulR/00new/OncoSimulR [1] "" Installing fl_statistics fl_generate to /home/biocbuild/R/R-4.5.0/site-library/00LOCK-OncoSimulR/00new/OncoSimulR/exec Installing library OncoSimulR.so to /home/biocbuild/R/R-4.5.0/site-library/00LOCK-OncoSimulR/00new/OncoSimulR/libs ** R ** data ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (OncoSimulR)
OncoSimulR.Rcheck/tests/testthat.Rout
R version 4.5.0 (2025-04-11) -- "How About a Twenty-Six" Copyright (C) 2025 The R Foundation for Statistical Computing Platform: aarch64-unknown-linux-gnu R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. Type 'license()' or 'licence()' for distribution details. R is a collaborative project with many contributors. Type 'contributors()' for more information and 'citation()' on how to cite R or R packages in publications. Type 'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for an HTML browser interface to help. Type 'q()' to quit R. > library(testthat) > library(OncoSimulR) 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 Sep 26 10:24:10 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 Sep 26 10:24:11 2025 Took 0.59 Starting LOD_POM at Fri Sep 26 10:24:11 2025 Ending LOD_POM at Fri Sep 26 10:24:27 2025 Took 16.08 Starting test.Z-all-fitness at Fri Sep 26 10:24:27 2025 Ending test.Z-all-fitness at Fri Sep 26 10:24:27 2025 Took 0.14 Starting test.Z-driver-counts at Fri Sep 26 10:24:27 2025 Ending test.Z-driver-counts at Fri Sep 26 10:24:27 2025 Took 0.17 Starting test.Z-fixation at Fri Sep 26 10:24:27 2025 Ending test.Z-fixation at Fri Sep 26 10:24:28 2025 Took 0.37 Starting test.Z-magellan at Fri Sep 26 10:24:28 2025 Ended test.Z-magellan at Fri Sep 26 10:24:29 2025 Starting test.Z-mutator at Fri Sep 26 10:24:29 2025 Ending test.Z-mutator at Fri Sep 26 10:24:30 2025 Took 0.44 Starting test.Z-mutatorFDF at Fri Sep 26 10:24:30 2025 Ending test.Z-mutatorFDF at Fri Sep 26 10:24:30 2025 Took 0.14 Starting test.Z-oncoSimulIndiv at Fri Sep 26 10:24:30 2025 Ending test.Z-oncoSimulIndiv at Fri Sep 26 10:24:31 2025 Took 0.74 Starting test.Z-oncoSimulIndivConstant at Fri Sep 26 10:24:31 2025 Ending test.Z-oncoSimulIndivConstant at Fri Sep 26 10:24:33 2025 Took 2.63 Starting test.Z-oncoSimulIndivDeath at Fri Sep 26 10:24:33 2025 Ending test.Z-oncoSimulIndivDeath at Fri Sep 26 10:24:34 2025 Took 1.01 Starting test.Z-oncoSimulIndivFDF at Fri Sep 26 10:24:34 2025 Hitted wall time. Exiting. Hitting wall time is regarded as an error. Ending test.Z-oncoSimulIndivFDF at Fri Sep 26 10:24:36 2025 Took 1.18 Starting test.Z-rfitness-landscape at Fri Sep 26 10:24:36 2025 Ending test.Z-rfitness-landscape at Fri Sep 26 10:24:36 2025 Took 0.42 Starting Z-sample-only-last tests Fri Sep 26 10:24:36 2025 Ending Z-sample-only-last tests Fri Sep 26 10:24:36 2025 Took 0 Starting Z-total-present-drivers tests Fri Sep 26 10:24:36 2025 Ending Z-total-present-drivers tests Fri Sep 26 10:24:37 2025 Took 1.01 Dummy empty test Fri Sep 26 10:24:37 2025 Starting accessible_genotypes at Fri Sep 26 10:24:37 2025 Ending accessible_genotypes at Fri Sep 26 10:24:47 2025 Took 10.04 Starting all fitness at Fri Sep 26 10:24:47 2025 Ending all-fitness at Fri Sep 26 10:24:53 2025 Took 6.14 Starting test.allFitnessEffectsFDF at Fri Sep 26 10:24:53 2025 Ending test.allFitnessEffectsFDF at Fri Sep 26 10:24:53 2025 Took 0.17 Starting test.allFitnessEffectsDeath at Fri Sep 26 10:24:53 2025 Ending test.allFitnessEffectsDeath at Fri Sep 26 10:24:54 2025 Took 0.47 Starting test.allFitnessEffectsFDF at Fri Sep 26 10:24:54 2025 Ending test.allFitnessEffectsFDF at Fri Sep 26 10:24:54 2025 Took 0.49 Starting driverCounts at Fri Sep 26 10:24:54 2025 Ending driverCounts at Fri Sep 26 10:25:04 2025 Took 9.97 Starting epist-order-modules at Fri Sep 26 10:25:04 2025 Ending epist-order-modules at Fri Sep 26 10:25:04 2025 Took 0.08 Starting test.evaluatingGenotypesDeath at Fri Sep 26 10:25:04 2025 Ending test.evaluatingGenotypesDeath at Fri Sep 26 10:25:05 2025 Took 0.26 Starting test.evaluatingGenotypesFDF at Fri Sep 26 10:25:05 2025 Ending test.evaluatingGenotypesFDF at Fri Sep 26 10:25:05 2025 Took 0.26 Starting exercise-plotting-code at Fri Sep 26 10:25:05 2025 Ending exercise-plotting-code at Fri Sep 26 10:25:09 2025 Took 4.21 Starting exercise-rfitness at Fri Sep 26 10:25:09 2025 Ending exercise-rfitness at Fri Sep 26 10:25:22 2025 Took 13.21 Starting to_Magella at Fri Sep 26 10:25:22 2025 Ending to_Magella at Fri Sep 26 10:25:22 2025 Took 0.05 Starting fitness preds at Fri Sep 26 10:25:22 2025 Observed vs expected, case III done tries 1 Ending fitness preds long at Fri Sep 26 10:25:29 2025 Took 7.05 Starting fixation at Fri Sep 26 10:25:29 2025 Ending fixation at Fri Sep 26 10:25:48 2025 Took 18.86 Starting test.flfast-additional.R test at Fri Sep 26 10:25:48 2025 Ending test.flfast-additional.R test at Fri Sep 26 10:25:50 2025 Took 1.75 Starting test.flfast-mutator.R test at Fri Sep 26 10:25:50 2025 Finished test.flfast-mutator.R test at Fri Sep 26 10:25:52 2025 Took 1.58 Starting genotFitness at Fri Sep 26 10:25:52 2025 Ending genotFitness at Fri Sep 26 10:25:52 2025 Took 0.27 Starting genot_fitness_to_epistasis at Fri Sep 26 10:25:52 2025 Ending genot_fitness_to_epistasis at Fri Sep 26 10:25:52 2025 Took 0.05 Starting init-mutant tests Fri Sep 26 10:25:52 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 Sep 26 10:26:00 2025 Took 8.32 Starting interventions tests Fri Sep 26 10:26:00 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] 0.73 0.73 0.73 [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 Sep 26 10:26:06 2025 Took 5.58 Starting test.magellan at Fri Sep 26 10:26:06 2025 Ending test.magellan at Fri Sep 26 10:26:06 2025 Took 0.18 Starting test.modules-root-no-root at Fri Sep 26 10:26:06 2025 Ending test.modules-root-no-root at Fri Sep 26 10:26:06 2025 Took 0.11 Starting at mutPropGrowth Fri Sep 26 10:26:06 2025 Ended test.mutPropGrowth: Fri Sep 26 10:26:16 2025 Took 9.3 Starting test.mutator-oncoSimulSample.R test at Fri Sep 26 10:26:16 2025 Finished test.mutator-oncoSimulSample.R test at Fri Sep 26 10:26:27 2025 Took 11.41 seconds Starting test.mutator.R test at Fri Sep 26 10:26:27 2025[1] 2.932684e-10 [1] 6.948719e-14 Finished test.mutator.R test at Fri Sep 26 10:26:42 2025 Took 15.33 Starting test.mutatorFDF.R test at Fri Sep 26 10:26:42 2025 Starting oncoSimulIndiv-miscell tests Fri Sep 26 10:26:43 2025 Ending oncoSimulIndiv-miscell tests Fri Sep 26 10:27:01 2025 Took 18.2 Starting oncoSimulSample-failures tests Fri Sep 26 10:27:01 2025 Ending oncoSimulSample-failures tests Fri Sep 26 10:27:06 2025 Took 4.25 Starting oncoSimulSample-limits tests Fri Sep 26 10:27:06 2025 Ending oncoSimulSample-limits tests Fri Sep 26 10:27:06 2025 Took 0.1 Starting per-gene-mutation rates at Fri Sep 26 10:27:06 2025 Ending per-gene-mutation rates at Fri Sep 26 10:27:38 2025 Took 32.82 Starting plotFitnessLandscape at Fri Sep 26 10:27:39 2025 Ending plotFitnessLandscape at Fri Sep 26 10:27:44 2025 Took 5.31 Starting poset-transformations tests Fri Sep 26 10:27:44 2025 Ending poset-transformations tests Fri Sep 26 10:27:58 2025 Took 13.69 Starting sample-prob Fri Sep 26 10:27:58 2025 [1] 2.122834e-24 [1] 4.546395e-12 [1] 2.950645e-09 [1] 1.294429e-11 [1] 1.856207e-10 [1] 1.626088e-12 [1] 1.648566e-11 [1] 1.183207e-11 [1] 4.537442e-09 [1] 1.702593e-10 [1] 2.024793e-08 [1] 5.925182e-08 Ending sample-prob tests Fri Sep 26 10:28:05 2025 Took 7.94 Starting samplePop tests Fri Sep 26 10:28:05 2025 Ending samplePop tests Fri Sep 26 10:28:12 2025 Took 6.95 Starting simuls-runs-examples tests Fri Sep 26 10:28:12 2025 Ending simuls-runs-examples tests Fri Sep 26 10:28:23 2025 Took 11.01 Starting user variable tests Fri Sep 26 10:28:23 2025 [1] "Checking user variable: user_var_1" [1] "Checking rule: rule_1" Ending user variable tests Fri Sep 26 10:28:24 2025 Took 0.14 Starting warning-mutPropGrowth tests Fri Sep 26 10:28:24 2025 Ending warning-mutPropGrowth tests Fri Sep 26 10:28:24 2025 Took 0.54 Starting wide2long tests Fri Sep 26 10:28:24 2025 Ending wide2long tests Fri Sep 26 10:28:24 2025 Took 0.3 [ FAIL 0 | WARN 19 | SKIP 5 | PASS 8387 ] ══ Skipped tests (5) ═══════════════════════════════════════════════════════════ • empty test (5): 'test.FDF-letter-fitness-order.R:376:1', 'test.ZZ-dummy-skip-warn-test.R:8:1', 'test.ZZ-dummy-skip-warn-test.R:12:1', 'test.fixation.R:4:1', 'test.init-mutant.R:1099:1' [ FAIL 0 | WARN 19 | SKIP 5 | PASS 8387 ] > > proc.time() user system elapsed 288.143 37.654 260.430
OncoSimulR.Rcheck/OncoSimulR-Ex.timings
name | user | system | elapsed | |
OncoSimulWide2Long | 0.257 | 0.004 | 0.268 | |
POM | 0.844 | 0.056 | 0.626 | |
allFitnessEffects | 3.078 | 0.200 | 3.297 | |
benchmarks | 0.011 | 0.000 | 0.011 | |
createInterventions | 0.345 | 0.012 | 0.357 | |
createUserVars | 0.513 | 0.004 | 0.519 | |
evalAllGenotypes | 0.269 | 0.028 | 0.298 | |
example-missing-drivers | 0.300 | 0.008 | 0.308 | |
examplePosets | 0.342 | 0.004 | 0.346 | |
examplesFitnessEffects | 0.102 | 0.004 | 0.107 | |
freq-dep-simul-examples | 0.011 | 0.000 | 0.011 | |
mcfLs | 0 | 0 | 0 | |
oncoSimulIndiv | 1.322 | 0.194 | 1.471 | |
plot.fitnessEffects | 0.272 | 0.044 | 0.317 | |
plot.oncosimul | 0.606 | 0.012 | 0.618 | |
plotClonePhylog | 1.476 | 0.136 | 1.616 | |
plotFitnessLandscape | 2.069 | 0.104 | 2.179 | |
plotPoset | 0.118 | 0.012 | 0.129 | |
poset | 0.143 | 0.004 | 0.148 | |
rfitness | 1.166 | 0.118 | 1.292 | |
samplePop | 0.097 | 0.078 | 0.117 | |
simOGraph | 0.083 | 0.012 | 0.096 | |
to_Magellan | 0.212 | 0.030 | 0.245 | |
vignette_pre_computed | 0.005 | 0.004 | 0.010 | |