Back to Multiple platform build/check report for BioC 3.19: simplified long |
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This page was generated on 2024-05-17 11:37:12 -0400 (Fri, 17 May 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4751 |
palomino3 | Windows Server 2022 Datacenter | x64 | 4.4.0 (2024-04-24 ucrt) -- "Puppy Cup" | 4485 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4515 |
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 1472/2300 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
OncoSimulR 4.6.0 (landing page) Ramon Diaz-Uriarte
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | |||||||||
palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | |||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | |||||||||
kjohnson3 | macOS 13.6.5 Ventura / arm64 | see weekly results here | ||||||||||||
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: 4.6.0 |
Command: F:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:OncoSimulR.install-out.txt --library=F:\biocbuild\bbs-3.19-bioc\R\library --no-vignettes --timings OncoSimulR_4.6.0.tar.gz |
StartedAt: 2024-05-17 04:44:02 -0400 (Fri, 17 May 2024) |
EndedAt: 2024-05-17 04:52:22 -0400 (Fri, 17 May 2024) |
EllapsedTime: 499.4 seconds |
RetCode: 0 |
Status: OK |
CheckDir: OncoSimulR.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:OncoSimulR.install-out.txt --library=F:\biocbuild\bbs-3.19-bioc\R\library --no-vignettes --timings OncoSimulR_4.6.0.tar.gz ### ############################################################################## ############################################################################## * using log directory 'F:/biocbuild/bbs-3.19-bioc/meat/OncoSimulR.Rcheck' * using R version 4.4.0 (2024-04-24 ucrt) * using platform: x86_64-w64-mingw32 * R was compiled by gcc.exe (GCC) 13.2.0 GNU Fortran (GCC) 13.2.0 * running under: Windows Server 2022 x64 (build 20348) * using session charset: UTF-8 * using option '--no-vignettes' * checking for file 'OncoSimulR/DESCRIPTION' ... OK * checking extension type ... Package * this is package 'OncoSimulR' version '4.6.0' * 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 whether package 'OncoSimulR' can be installed ... OK * used C compiler: 'gcc.exe (GCC) 13.2.0' * used C++ compiler: 'G__~1.EXE (GCC) 13.2.0' * checking installed package size ... NOTE installed size is 8.3Mb sub-directories of 1Mb or more: libs 6.6Mb * 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 for x64 is not available File 'F:/biocbuild/bbs-3.19-bioc/R/library/OncoSimulR/libs/x64/OncoSimulR.dll': Found '_exit', possibly from '_exit' (C) Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran) Found 'exit', possibly from 'exit' (C), 'stop' (Fortran) Compiled code should not call entry points which might terminate R nor write to stdout/stderr instead of to the console, nor use Fortran I/O nor system RNGs nor [v]sprintf. The detected symbols are linked into the code but might come from libraries and not actually be called. See 'Writing portable packages' in the 'Writing R Extensions' manual. * 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 'F:/biocbuild/bbs-3.19-bioc/meat/OncoSimulR.Rcheck/00check.log' for details.
OncoSimulR.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD INSTALL OncoSimulR ### ############################################################################## ############################################################################## * installing to library 'F:/biocbuild/bbs-3.19-bioc/R/library' * installing *source* package 'OncoSimulR' ... ** using staged installation ** libs using C compiler: 'gcc.exe (GCC) 13.2.0' using C++ compiler: 'G__~1.EXE (GCC) 13.2.0' gcc -I"F:/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.19-bioc/R/library/Rcpp/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c FitnessLandscape/gamma.c -o FitnessLandscape/gamma.o gcc -I"F:/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.19-bioc/R/library/Rcpp/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c FitnessLandscape/landscape.c -o FitnessLandscape/landscape.o gcc -I"F:/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.19-bioc/R/library/Rcpp/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c FitnessLandscape/random.c -o FitnessLandscape/random.o gcc -I"F:/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.19-bioc/R/library/Rcpp/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c FitnessLandscape/sort.c -o FitnessLandscape/sort.o gcc -I"F:/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.19-bioc/R/library/Rcpp/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c FitnessLandscape/chain.c -o FitnessLandscape/chain.o gcc -I"F:/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.19-bioc/R/library/Rcpp/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c FitnessLandscape/input.c -o FitnessLandscape/input.o gcc -I"F:/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.19-bioc/R/library/Rcpp/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c FitnessLandscape/genotypes.c -o FitnessLandscape/genotypes.o gcc -I"F:/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.19-bioc/R/library/Rcpp/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c FitnessLandscape/ordered_pairs.c -o FitnessLandscape/ordered_pairs.o gcc -I"F:/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.19-bioc/R/library/Rcpp/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c FitnessLandscape/calculus.c -o FitnessLandscape/calculus.o gcc -I"F:/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.19-bioc/R/library/Rcpp/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c FitnessLandscape/vector.c -o FitnessLandscape/vector.o gcc -I"F:/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.19-bioc/R/library/Rcpp/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c FitnessLandscape/generalized_chain.c -o FitnessLandscape/generalized_chain.o gcc -I"F:/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.19-bioc/R/library/Rcpp/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c FitnessLandscape/LinearAlgebra.c -o FitnessLandscape/LinearAlgebra.o gcc -I"F:/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.19-bioc/R/library/Rcpp/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c FitnessLandscape/summary_statistics.c -o FitnessLandscape/summary_statistics.o gcc -I"F:/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.19-bioc/R/library/Rcpp/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c FitnessLandscape/epistasis_type.c -o FitnessLandscape/epistasis_type.o gcc -I"F:/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.19-bioc/R/library/Rcpp/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c FitnessLandscape/decomposition.c -o FitnessLandscape/decomposition.o gcc -I"F:/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.19-bioc/R/library/Rcpp/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c FitnessLandscape/models.c -o FitnessLandscape/models.o gcc -I"F:/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.19-bioc/R/library/Rcpp/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -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 ; C:\rtools44\x86_64-w64-mingw32.static.posix\bin\ar.exe: creating liblandscape.a ranlib liblandscape.a; gcc -O -Wall -o fl_statistics -I/FitnessLandscape/. -L. FitnessLandscape/main_fl_statistics.c -llandscape -lm; gcc -O -Wall -o fl_generate -I/FitnessLandscape/. -L. FitnessLandscape/main_fl_generate.c -llandscape -lm; gcc -I"F:/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.19-bioc/R/library/Rcpp/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c OncoSimulR_init.c -o OncoSimulR_init.o g++ -std=gnu++17 -I"F:/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.19-bioc/R/library/Rcpp/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -Wa,-mbig-obj -c RcppExports.cpp -o RcppExports.o g++ -std=gnu++17 -I"F:/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.19-bioc/R/library/Rcpp/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -Wa,-mbig-obj -c unity_osimul.cpp -o unity_osimul.o In file included from unity_osimul.cpp:4: UnityOncoSimul/BNB_nr.cpp: In function 'void nr_innerBNB(const fitnessEffectsAll&, const std::vector<double>&, const double&, TypeModel, const int&, const std::vector<double>&, const double&, const double&, const double&, const std::vector<std::vector<int> >&, const time_t&, const double&, const double&, const double&, const int&, const double&, const double&, const int&, double&, double&, double&, double&, double&, int&, int&, int&, std::vector<Genotype>&, std::vector<double>&, std::vector<int>&, std::vector<double>&, std::vector<Intervention>&, std::vector<double>&, std::vector<double>&, std::vector<int>&, std::vector<int>&, bool&, std::mt19937&, double&, bool&, const std::map<int, std::__cxx11::basic_string<char> >&, const fitness_as_genes&, PhylogName&, bool, const fitnessEffectsAll&, const std::vector<int>&, const double&, const double&, const double&, const bool&, const std::vector<std::vector<int> >&, const double&, const int&, const double&, int&, int&, std::map<std::__cxx11::basic_string<char>, std::__cxx11::basic_string<char> >&, POM&, Rcpp::List, Rcpp::List, Rcpp::List)': UnityOncoSimul/BNB_nr.cpp:860:10: warning: 'minNextMutationTime' may be used uninitialized [-Wmaybe-uninitialized] 860 | double minNextMutationTime; | ^~~~~~~~~~~~~~~~~~~ g++ -std=gnu++17 -shared -s -static-libgcc -o OncoSimulR.dll tmp.def OncoSimulR_init.o RcppExports.o unity_osimul.o -LC:/rtools44/x86_64-w64-mingw32.static.posix/lib/x64 -LC:/rtools44/x86_64-w64-mingw32.static.posix/lib -LF:/biocbuild/bbs-3.19-bioc/R/bin/x64 -lR installing via 'install.libs.R' to F:/biocbuild/bbs-3.19-bioc/R/library/00LOCK-OncoSimulR/00new/OncoSimulR [1] "/x64" Installing fl_statistics.exe fl_generate.exe to F:/biocbuild/bbs-3.19-bioc/R/library/00LOCK-OncoSimulR/00new/OncoSimulR/exec/x64 Installing library OncoSimulR.dll to F:/biocbuild/bbs-3.19-bioc/R/library/00LOCK-OncoSimulR/00new/OncoSimulR/libs/x64 ** 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 ** 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 (2024-04-24 ucrt) -- "Puppy Cup" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: x86_64-w64-mingw32/x64 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 Fri May 17 04:47:50 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 Fri May 17 04:47:51 2024 Took 0.59 Starting LOD_POM at Fri May 17 04:47:51 2024 Ending LOD_POM at Fri May 17 04:48:08 2024 Took 16.65 Starting test.Z-all-fitness at Fri May 17 04:48:08 2024 Ending test.Z-all-fitness at Fri May 17 04:48:08 2024 Took 0.13 Starting test.Z-driver-counts at Fri May 17 04:48:08 2024 Ending test.Z-driver-counts at Fri May 17 04:48:08 2024 Took 0.13 Starting test.Z-fixation at Fri May 17 04:48:08 2024 Ending test.Z-fixation at Fri May 17 04:48:08 2024 Took 0.33 Starting test.Z-magellan at Fri May 17 04:48:08 2024 Ended test.Z-magellan at Fri May 17 04:48:10 2024 Starting test.Z-mutator at Fri May 17 04:48:10 2024 Ending test.Z-mutator at Fri May 17 04:48:10 2024 Took 0.5 Starting test.Z-mutatorFDF at Fri May 17 04:48:10 2024 Ending test.Z-mutatorFDF at Fri May 17 04:48:10 2024 Took 0.14 Starting test.Z-oncoSimulIndiv at Fri May 17 04:48:10 2024 Ending test.Z-oncoSimulIndiv at Fri May 17 04:48:11 2024 Took 0.54 Starting test.Z-oncoSimulIndivConstant at Fri May 17 04:48:11 2024 Ending test.Z-oncoSimulIndivConstant at Fri May 17 04:48:15 2024 Took 4.23 Starting test.Z-oncoSimulIndivDeath at Fri May 17 04:48:15 2024 Ending test.Z-oncoSimulIndivDeath at Fri May 17 04:48:17 2024 Took 1.3 Starting test.Z-oncoSimulIndivFDF at Fri May 17 04:48:17 2024 Hitted wall time. Exiting. Hitting wall time is regarded as an error. Ending test.Z-oncoSimulIndivFDF at Fri May 17 04:48:18 2024 Took 0.93 Starting test.Z-rfitness-landscape at Fri May 17 04:48:18 2024 Ending test.Z-rfitness-landscape at Fri May 17 04:48:18 2024 Took 0.19 Starting Z-sample-only-last tests Fri May 17 04:48:18 2024 Ending Z-sample-only-last tests Fri May 17 04:48:18 2024 Took 0 Starting Z-total-present-drivers tests Fri May 17 04:48:18 2024 Ending Z-total-present-drivers tests Fri May 17 04:48:19 2024 Took 0.94 Dummy empty test Fri May 17 04:48:19 2024 Starting accessible_genotypes at Fri May 17 04:48:19 2024 Ending accessible_genotypes at Fri May 17 04:48:27 2024 Took 8.45 Starting all fitness at Fri May 17 04:48:27 2024 Ending all-fitness at Fri May 17 04:48:33 2024 Took 5.55 Starting test.allFitnessEffectsFDF at Fri May 17 04:48:33 2024 Ending test.allFitnessEffectsFDF at Fri May 17 04:48:33 2024 Took 0.12 Starting test.allFitnessEffectsDeath at Fri May 17 04:48:33 2024 Ending test.allFitnessEffectsDeath at Fri May 17 04:48:33 2024 Took 0.44 Starting test.allFitnessEffectsFDF at Fri May 17 04:48:33 2024 Ending test.allFitnessEffectsFDF at Fri May 17 04:48:34 2024 Took 0.44 Starting driverCounts at Fri May 17 04:48:34 2024 Ending driverCounts at Fri May 17 04:48:41 2024 Took 7.73 Starting epist-order-modules at Fri May 17 04:48:41 2024 Ending epist-order-modules at Fri May 17 04:48:42 2024 Took 0.05 Starting test.evaluatingGenotypesDeath at Fri May 17 04:48:42 2024 Ending test.evaluatingGenotypesDeath at Fri May 17 04:48:42 2024 Took 0.18 Starting test.evaluatingGenotypesFDF at Fri May 17 04:48:42 2024 Ending test.evaluatingGenotypesFDF at Fri May 17 04:48:42 2024 Took 0.24 Starting exercise-plotting-code at Fri May 17 04:48:42 2024 Ending exercise-plotting-code at Fri May 17 04:48:45 2024 Took 3.39 Starting exercise-rfitness at Fri May 17 04:48:45 2024 Ending exercise-rfitness at Fri May 17 04:49:01 2024 Took 15.82 Starting to_Magella at Fri May 17 04:49:01 2024 Ending to_Magella at Fri May 17 04:49:01 2024 Took 0.1 Starting fitness preds at Fri May 17 04:49:01 2024 Observed vs expected, case III done tries 1 Ending fitness preds long at Fri May 17 04:49:09 2024 Took 7.25 Starting fixation at Fri May 17 04:49:09 2024 Ending fixation at Fri May 17 04:49:33 2024 Took 24.13 Starting test.flfast-additional.R test at Fri May 17 04:49:33 2024 Ending test.flfast-additional.R test at Fri May 17 04:49:34 2024 Took 1.07 Starting test.flfast-mutator.R test at Fri May 17 04:49:34 2024 Finished test.flfast-mutator.R test at Fri May 17 04:49:35 2024 Took 1.66 Starting genotFitness at Fri May 17 04:49:35 2024 Ending genotFitness at Fri May 17 04:49:36 2024 Took 0.2 Starting genot_fitness_to_epistasis at Fri May 17 04:49:36 2024 Ending genot_fitness_to_epistasis at Fri May 17 04:49:36 2024 Took 0.07 Starting init-mutant tests Fri May 17 04:49:36 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 Fri May 17 04:49:46 2024 Took 10.39 Starting interventions tests Fri May 17 04:49:46 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] 0.55 0.55 0.55 [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 May 17 04:49:53 2024 Took 7.04 Starting test.magellan at Fri May 17 04:49:53 2024 Ending test.magellan at Fri May 17 04:49:55 2024 Took 2.09 Starting test.modules-root-no-root at Fri May 17 04:49:55 2024 Ending test.modules-root-no-root at Fri May 17 04:49:55 2024 Took 0.08 Starting at mutPropGrowth Fri May 17 04:49:55 2024 Ended test.mutPropGrowth: Fri May 17 04:50:02 2024 Took 6.7 Starting test.mutator-oncoSimulSample.R test at Fri May 17 04:50:02 2024 Finished test.mutator-oncoSimulSample.R test at Fri May 17 04:50:11 2024 Took 8.81 seconds Starting test.mutator.R test at Fri May 17 04:50:11 2024[1] 1.854315e-06 [1] 2.046815e-08 Finished test.mutator.R test at Fri May 17 04:50:29 2024 Took 17.57 Starting test.mutatorFDF.R test at Fri May 17 04:50:29 2024 Starting test.no-v1 at Fri May 17 04:50:30 2024 Ending test.no-v1 at Fri May 17 04:50:30 2024 Took 0.02 Starting oncoSimulIndiv-miscell tests Fri May 17 04:50:30 2024 Ending oncoSimulIndiv-miscell tests Fri May 17 04:50:36 2024 Took 6.39 Starting oncoSimulSample-failures tests Fri May 17 04:50:36 2024 Ending oncoSimulSample-failures tests Fri May 17 04:50:40 2024 Took 3.58 Starting oncoSimulSample-limits tests Fri May 17 04:50:40 2024 Ending oncoSimulSample-limits tests Fri May 17 04:50:40 2024 Took 0.08 Starting per-gene-mutation rates at Fri May 17 04:50:40 2024 Ending per-gene-mutation rates at Fri May 17 04:51:10 2024 Took 30.42 Starting plotFitnessLandscape at Fri May 17 04:51:10 2024 Ending plotFitnessLandscape at Fri May 17 04:51:14 2024 Took 3.75 Starting poset-transformations tests Fri May 17 04:51:14 2024 Ending poset-transformations tests Fri May 17 04:51:27 2024 Took 12.81 Starting sample-prob Fri May 17 04:51:27 2024 [1] 1.682735e-29 [1] 4.639688e-10 [1] 2.385787e-11 [1] 1.290323e-11 [1] 6.744545e-15 [1] 4.889385e-14 [1] 1.827265e-12 [1] 5.664162e-14 [1] 3.233853e-08 [1] 5.320711e-09 [1] 3.454841e-08 [1] 9.001921e-10 Ending sample-prob tests Fri May 17 04:51:35 2024 Took 8.24 Starting samplePop tests Fri May 17 04:51:35 2024 Ending samplePop tests Fri May 17 04:51:42 2024 Took 7.5 Starting simuls-runs-examples tests Fri May 17 04:51:43 2024 Ending simuls-runs-examples tests Fri May 17 04:51:50 2024 Took 7.72 Starting user variable tests Fri May 17 04:51:50 2024 [1] "Checking user variable: user_var_1" [1] "Checking rule: rule_1" Ending user variable tests Fri May 17 04:51:51 2024 Took 0.76 Starting warning-mutPropGrowth tests Fri May 17 04:51:52 2024 Ending warning-mutPropGrowth tests Fri May 17 04:51:52 2024 Took 0.61 Starting wide2long tests Fri May 17 04:51:52 2024 Ending wide2long tests Fri May 17 04:51:53 2024 Took 0.58 [ FAIL 0 | WARN 18 | SKIP 6 | PASS 8371 ] ══ Skipped tests (6) ═══════════════════════════════════════════════════════════ • On Windows (1): 'test.Z-magellan.R:664:5' • 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:1097:1' [ FAIL 0 | WARN 18 | SKIP 6 | PASS 8371 ] > > proc.time() user system elapsed 226.81 8.64 248.75
OncoSimulR.Rcheck/OncoSimulR-Ex.timings
name | user | system | elapsed | |
OncoSimulWide2Long | 0.17 | 0.00 | 0.31 | |
POM | 1.14 | 0.02 | 1.17 | |
allFitnessEffects | 2.00 | 0.02 | 2.41 | |
benchmarks | 0.03 | 0.00 | 0.03 | |
createInterventions | 0.50 | 0.00 | 0.53 | |
createUserVars | 0.67 | 0.00 | 0.67 | |
evalAllGenotypes | 0.17 | 0.00 | 0.19 | |
example-missing-drivers | 0.30 | 0.01 | 0.33 | |
examplePosets | 0.20 | 0.05 | 0.25 | |
examplesFitnessEffects | 0.05 | 0.00 | 0.04 | |
freq-dep-simul-examples | 0 | 0 | 0 | |
mcfLs | 0 | 0 | 0 | |
oncoSimulIndiv | 1.69 | 0.01 | 1.72 | |
plot.fitnessEffects | 0.22 | 0.00 | 0.22 | |
plot.oncosimul | 0.47 | 0.02 | 0.48 | |
plotClonePhylog | 1.17 | 0.05 | 1.22 | |
plotFitnessLandscape | 1.12 | 0.03 | 1.18 | |
plotPoset | 0.11 | 0.00 | 0.11 | |
poset | 0.11 | 0.02 | 0.12 | |
rfitness | 0.61 | 0.00 | 1.41 | |
samplePop | 0.06 | 0.00 | 0.06 | |
simOGraph | 0.07 | 0.00 | 0.06 | |
to_Magellan | 0.09 | 0.05 | 1.45 | |
vignette_pre_computed | 0.02 | 0.00 | 0.02 | |