Back to Multiple platform build/check report for BioC 3.21: simplified long |
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This page was generated on 2024-12-23 11:47 -0500 (Mon, 23 Dec 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | R Under development (unstable) (2024-10-21 r87258) -- "Unsuffered Consequences" | 4754 |
palomino7 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2024-10-26 r87273 ucrt) -- "Unsuffered Consequences" | 4472 |
lconway | macOS 12.7.1 Monterey | x86_64 | R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" | 4426 |
kjohnson3 | macOS 13.7.1 Ventura | arm64 | R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" | 4381 |
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | R Under development (unstable) (2024-11-24 r87369) -- "Unsuffered Consequences" | 4372 |
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 1454/2274 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
OncoSimulR 4.9.0 (landing page) Ramon Diaz-Uriarte
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | |||||||||
palomino7 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | |||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | |||||||||
kjohnson3 | macOS 13.7.1 Ventura / arm64 | ... NOT SUPPORTED ... | ||||||||||||
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / 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: 4.9.0 |
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_4.9.0.tar.gz |
StartedAt: 2024-12-23 10:23:12 -0000 (Mon, 23 Dec 2024) |
EndedAt: 2024-12-23 10:28:56 -0000 (Mon, 23 Dec 2024) |
EllapsedTime: 343.4 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_4.9.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/OncoSimulR.Rcheck’ * using R Under development (unstable) (2024-11-24 r87369) * 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 ‘4.9.0’ * checking package namespace information ... OK * checking package dependencies ... OK * checking if this is a source package ... OK * checking if there is a namespace ... OK * checking for hidden files and directories ... NOTE Found the following hidden files and directories: .BBSoptions These were most likely included in error. See section ‘Package structure’ in the ‘Writing R Extensions’ manual. * checking for portable file names ... OK * checking for sufficient/correct file permissions ... OK * checking whether package ‘OncoSimulR’ can be installed ... OK * used C compiler: ‘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 ... NOTE Found the following Rd file(s) with Rd \link{} targets missing package anchors: plot.oncosimul.Rd: brewer.pal plotClonePhylog.Rd: get.adjacency plotFitnessLandscape.Rd: ggrepel Please provide package anchors for all Rd \link{} targets not in the package itself and the base packages. * 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: 3 NOTEs See ‘/home/biocbuild/bbs-3.21-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-devel_2024-11-24/site-library’ * installing *source* package ‘OncoSimulR’ ... ** 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 -I"/home/biocbuild/R/R/include" -DNDEBUG -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/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 -I"/home/biocbuild/R/R/include" -DNDEBUG -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/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 -I"/home/biocbuild/R/R/include" -DNDEBUG -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/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 -I"/home/biocbuild/R/R/include" -DNDEBUG -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/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 -I"/home/biocbuild/R/R/include" -DNDEBUG -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/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 -I"/home/biocbuild/R/R/include" -DNDEBUG -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/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 -I"/home/biocbuild/R/R/include" -DNDEBUG -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/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 -I"/home/biocbuild/R/R/include" -DNDEBUG -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/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 -I"/home/biocbuild/R/R/include" -DNDEBUG -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/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 -I"/home/biocbuild/R/R/include" -DNDEBUG -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/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 -I"/home/biocbuild/R/R/include" -DNDEBUG -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/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 -I"/home/biocbuild/R/R/include" -DNDEBUG -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/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 -I"/home/biocbuild/R/R/include" -DNDEBUG -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/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 -I"/home/biocbuild/R/R/include" -DNDEBUG -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/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 -I"/home/biocbuild/R/R/include" -DNDEBUG -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/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 -I"/home/biocbuild/R/R/include" -DNDEBUG -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/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 -I"/home/biocbuild/R/R/include" -DNDEBUG -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/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 -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 -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 -I"/home/biocbuild/R/R/include" -DNDEBUG -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/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/include" -DNDEBUG -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/Rcpp/include' -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -DR_NO_REMAP -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/include" -DNDEBUG -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/Rcpp/include' -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -DR_NO_REMAP -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/lib -L/usr/local/lib -o OncoSimulR.so OncoSimulR_init.o RcppExports.o unity_osimul.o -L/home/biocbuild/R/R/lib -lR installing via 'install.libs.R' to /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/00LOCK-OncoSimulR/00new/OncoSimulR [1] "" Installing fl_statistics fl_generate to /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/00LOCK-OncoSimulR/00new/OncoSimulR/exec Installing library OncoSimulR.so to /home/biocbuild/R/R-4.5.0-devel_2024-11-24/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 Under development (unstable) (2024-11-24 r87369) -- "Unsuffered Consequences" Copyright (C) 2024 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 Mon Dec 23 10:24:43 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 Dec 23 10:24:44 2024 Took 0.55 Starting LOD_POM at Mon Dec 23 10:24:44 2024 Ending LOD_POM at Mon Dec 23 10:24:59 2024 Took 15.58 Starting test.Z-all-fitness at Mon Dec 23 10:24:59 2024 Ending test.Z-all-fitness at Mon Dec 23 10:24:59 2024 Took 0.14 Starting test.Z-driver-counts at Mon Dec 23 10:24:59 2024 Ending test.Z-driver-counts at Mon Dec 23 10:24:59 2024 Took 0.18 Starting test.Z-fixation at Mon Dec 23 10:24:59 2024 Ending test.Z-fixation at Mon Dec 23 10:25:00 2024 Took 0.36 Starting test.Z-magellan at Mon Dec 23 10:25:00 2024 Ended test.Z-magellan at Mon Dec 23 10:25:02 2024 Starting test.Z-mutator at Mon Dec 23 10:25:02 2024 Ending test.Z-mutator at Mon Dec 23 10:25:02 2024 Took 0.45 Starting test.Z-mutatorFDF at Mon Dec 23 10:25:02 2024 Ending test.Z-mutatorFDF at Mon Dec 23 10:25:02 2024 Took 0.15 Starting test.Z-oncoSimulIndiv at Mon Dec 23 10:25:02 2024 Ending test.Z-oncoSimulIndiv at Mon Dec 23 10:25:03 2024 Took 0.72 Starting test.Z-oncoSimulIndivConstant at Mon Dec 23 10:25:03 2024 Ending test.Z-oncoSimulIndivConstant at Mon Dec 23 10:25:06 2024 Took 2.63 Starting test.Z-oncoSimulIndivDeath at Mon Dec 23 10:25:06 2024 Ending test.Z-oncoSimulIndivDeath at Mon Dec 23 10:25:07 2024 Took 1 Starting test.Z-oncoSimulIndivFDF at Mon Dec 23 10:25:07 2024 Hitted wall time. Exiting. Hitting wall time is regarded as an error. Ending test.Z-oncoSimulIndivFDF at Mon Dec 23 10:25:08 2024 Took 0.92 Starting test.Z-rfitness-landscape at Mon Dec 23 10:25:08 2024 Ending test.Z-rfitness-landscape at Mon Dec 23 10:25:08 2024 Took 0.28 Starting Z-sample-only-last tests Mon Dec 23 10:25:08 2024 Ending Z-sample-only-last tests Mon Dec 23 10:25:08 2024 Took 0 Starting Z-total-present-drivers tests Mon Dec 23 10:25:08 2024 Ending Z-total-present-drivers tests Mon Dec 23 10:25:09 2024 Took 0.96 Dummy empty test Mon Dec 23 10:25:09 2024 Starting accessible_genotypes at Mon Dec 23 10:25:09 2024 Ending accessible_genotypes at Mon Dec 23 10:25:19 2024 Took 10.05 Starting all fitness at Mon Dec 23 10:25:19 2024 Ending all-fitness at Mon Dec 23 10:25:25 2024 Took 6.41 Starting test.allFitnessEffectsFDF at Mon Dec 23 10:25:25 2024 Ending test.allFitnessEffectsFDF at Mon Dec 23 10:25:25 2024 Took 0.16 Starting test.allFitnessEffectsDeath at Mon Dec 23 10:25:25 2024 Ending test.allFitnessEffectsDeath at Mon Dec 23 10:25:26 2024 Took 0.5 Starting test.allFitnessEffectsFDF at Mon Dec 23 10:25:26 2024 Ending test.allFitnessEffectsFDF at Mon Dec 23 10:25:26 2024 Took 0.5 Starting driverCounts at Mon Dec 23 10:25:26 2024 Ending driverCounts at Mon Dec 23 10:25:36 2024 Took 9.2 Starting epist-order-modules at Mon Dec 23 10:25:36 2024 Ending epist-order-modules at Mon Dec 23 10:25:36 2024 Took 0.08 Starting test.evaluatingGenotypesDeath at Mon Dec 23 10:25:36 2024 Ending test.evaluatingGenotypesDeath at Mon Dec 23 10:25:36 2024 Took 0.25 Starting test.evaluatingGenotypesFDF at Mon Dec 23 10:25:36 2024 Ending test.evaluatingGenotypesFDF at Mon Dec 23 10:25:36 2024 Took 0.27 Starting exercise-plotting-code at Mon Dec 23 10:25:36 2024 Ending exercise-plotting-code at Mon Dec 23 10:25:40 2024 Took 4.11 Starting exercise-rfitness at Mon Dec 23 10:25:40 2024 Ending exercise-rfitness at Mon Dec 23 10:25:54 2024 Took 13.48 Starting to_Magella at Mon Dec 23 10:25:54 2024 Ending to_Magella at Mon Dec 23 10:25:54 2024 Took 0.05 Starting fitness preds at Mon Dec 23 10:25:54 2024 Observed vs expected, case III done tries 1 Ending fitness preds long at Mon Dec 23 10:26:00 2024 Took 6.33 Starting fixation at Mon Dec 23 10:26:00 2024 Ending fixation at Mon Dec 23 10:26:19 2024 Took 18.7 Starting test.flfast-additional.R test at Mon Dec 23 10:26:19 2024 DEBUG2: Value of rnb = nan DEBUG2: Value of m = 1 DEBUG2: Value of pe = 0 DEBUG2: Value of pm = 0.999993 this is spP popSize = 1 birth = 1 death = 0 W = 1.00001 R = 1.00001 mutation = 6e-06 timeLastUpdate = 1.23999 absfitness = -inf numMutablePos = 6 Unrecoverable exception: Algo 2: retval not finite. Aborting. Ending test.flfast-additional.R test at Mon Dec 23 10:26:21 2024 Took 1.73 Starting test.flfast-mutator.R test at Mon Dec 23 10:26:21 2024 Finished test.flfast-mutator.R test at Mon Dec 23 10:26:22 2024 Took 1.72 Starting genotFitness at Mon Dec 23 10:26:22 2024 Ending genotFitness at Mon Dec 23 10:26:23 2024 Took 0.24 Starting genot_fitness_to_epistasis at Mon Dec 23 10:26:23 2024 Ending genot_fitness_to_epistasis at Mon Dec 23 10:26:23 2024 Took 0.05 Starting init-mutant tests Mon Dec 23 10:26:23 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 Dec 23 10:26:30 2024 Took 7.39 Starting interventions tests Mon Dec 23 10:26:30 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] 0.58 0.58 0.58 [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 Dec 23 10:26:35 2024 Took 4.94 Starting test.magellan at Mon Dec 23 10:26:35 2024 Ending test.magellan at Mon Dec 23 10:26:35 2024 Took 0.15 Starting test.modules-root-no-root at Mon Dec 23 10:26:35 2024 Ending test.modules-root-no-root at Mon Dec 23 10:26:35 2024 Took 0.16 Starting at mutPropGrowth Mon Dec 23 10:26:35 2024 Ended test.mutPropGrowth: Mon Dec 23 10:26:44 2024 Took 8.83 Starting test.mutator-oncoSimulSample.R test at Mon Dec 23 10:26:44 2024 Finished test.mutator-oncoSimulSample.R test at Mon Dec 23 10:26:59 2024 Took 14.95 seconds Starting test.mutator.R test at Mon Dec 23 10:26:59 2024[1] 1.346351e-06 [1] 1.724003e-12 Finished test.mutator.R test at Mon Dec 23 10:27:14 2024 Took 14.4 Starting test.mutatorFDF.R test at Mon Dec 23 10:27:14 2024 Starting test.no-v1 at Mon Dec 23 10:27:14 2024 Ending test.no-v1 at Mon Dec 23 10:27:14 2024 Took 0.02 Starting oncoSimulIndiv-miscell tests Mon Dec 23 10:27:14 2024 Ending oncoSimulIndiv-miscell tests Mon Dec 23 10:27:27 2024 Took 13.08 Starting oncoSimulSample-failures tests Mon Dec 23 10:27:27 2024 Ending oncoSimulSample-failures tests Mon Dec 23 10:27:32 2024 Took 4.06 Starting oncoSimulSample-limits tests Mon Dec 23 10:27:32 2024 Ending oncoSimulSample-limits tests Mon Dec 23 10:27:32 2024 Took 0.12 Starting per-gene-mutation rates at Mon Dec 23 10:27:32 2024 Ending per-gene-mutation rates at Mon Dec 23 10:28:03 2024 Took 31.51 Starting plotFitnessLandscape at Mon Dec 23 10:28:03 2024 Ending plotFitnessLandscape at Mon Dec 23 10:28:08 2024 Took 4.47 Starting poset-transformations tests Mon Dec 23 10:28:08 2024 Ending poset-transformations tests Mon Dec 23 10:28:22 2024 Took 14.22 Starting sample-prob Mon Dec 23 10:28:22 2024 [1] 3.924535e-29 [1] 1.849802e-13 [1] 7.911978e-10 [1] 1.331927e-11 [1] 4.502068e-12 [1] 1.1257e-13 [1] 1.047958e-08 [1] 1.076565e-17 [1] 1.995116e-12 [1] 1.840841e-11 [1] 4.18324e-10 [1] 2.604111e-09 Ending sample-prob tests Mon Dec 23 10:28:29 2024 Took 7.36 Starting samplePop tests Mon Dec 23 10:28:29 2024 Ending samplePop tests Mon Dec 23 10:28:35 2024 Took 6.13 Starting simuls-runs-examples tests Mon Dec 23 10:28:35 2024 Ending simuls-runs-examples tests Mon Dec 23 10:28:44 2024 Took 8.31 Starting user variable tests Mon Dec 23 10:28:44 2024 [1] "Checking user variable: user_var_1" [1] "Checking rule: rule_1" Ending user variable tests Mon Dec 23 10:28:44 2024 Took 0.12 Starting warning-mutPropGrowth tests Mon Dec 23 10:28:44 2024 Ending warning-mutPropGrowth tests Mon Dec 23 10:28:44 2024 Took 0.57 Starting wide2long tests Mon Dec 23 10:28:44 2024 Ending wide2long tests Mon Dec 23 10:28:45 2024 Took 0.31 [ FAIL 0 | WARN 19 | SKIP 5 | PASS 8388 ] ══ 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 8388 ] > > proc.time() user system elapsed 275.415 34.938 247.280
OncoSimulR.Rcheck/OncoSimulR-Ex.timings
name | user | system | elapsed | |
OncoSimulWide2Long | 0.265 | 0.001 | 0.270 | |
POM | 0.742 | 0.028 | 0.488 | |
allFitnessEffects | 2.337 | 0.060 | 2.414 | |
benchmarks | 0.013 | 0.000 | 0.013 | |
createInterventions | 0.337 | 0.004 | 0.342 | |
createUserVars | 0.510 | 0.000 | 0.511 | |
evalAllGenotypes | 0.270 | 0.012 | 0.286 | |
example-missing-drivers | 0.303 | 0.012 | 0.316 | |
examplePosets | 0.343 | 0.024 | 0.370 | |
examplesFitnessEffects | 0.103 | 0.004 | 0.107 | |
freq-dep-simul-examples | 0.011 | 0.000 | 0.011 | |
mcfLs | 0 | 0 | 0 | |
oncoSimulIndiv | 1.257 | 0.120 | 1.321 | |
plot.fitnessEffects | 0.254 | 0.075 | 0.331 | |
plot.oncosimul | 0.590 | 0.012 | 0.603 | |
plotClonePhylog | 1.521 | 0.092 | 1.617 | |
plotFitnessLandscape | 1.529 | 0.008 | 1.541 | |
plotPoset | 0.113 | 0.000 | 0.118 | |
poset | 0.146 | 0.008 | 0.154 | |
rfitness | 0.894 | 0.027 | 0.927 | |
samplePop | 0.063 | 0.046 | 0.075 | |
simOGraph | 0.066 | 0.020 | 0.086 | |
to_Magellan | 0.223 | 0.021 | 0.246 | |
vignette_pre_computed | 0.009 | 0.000 | 0.009 | |