Ramon Diaz-Uriarte
| Snapshot Date: 2025-02-05 13:48 -0500 (Wed, 05 Feb 2025) |
| git_url: https://git.bioconductor.org/packages/OncoSimulR |
| git_branch: devel |
| git_last_commit: 3291e0a |
| git_last_commit_date: 2024-10-29 09:53:24 -0500 (Tue, 29 Oct 2024) |
| Back to Multiple platform build/check report for BioC 3.21: simplified long |
|
This page was generated on 2025-02-06 11:41 -0500 (Thu, 06 Feb 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | R Under development (unstable) (2025-01-20 r87609) -- "Unsuffered Consequences" | 4719 |
| palomino7 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2025-01-21 r87610 ucrt) -- "Unsuffered Consequences" | 4480 |
| lconway | macOS 12.7.1 Monterey | x86_64 | R Under development (unstable) (2025-01-22 r87618) -- "Unsuffered Consequences" | 4491 |
| kjohnson3 | macOS 13.7.1 Ventura | arm64 | R Under development (unstable) (2025-01-20 r87609) -- "Unsuffered Consequences" | 4444 |
| 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 1465/2295 | 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 ... | ||||||||||||
|
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: 4.9.0 |
| Command: E:\biocbuild\bbs-3.21-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:OncoSimulR.install-out.txt --library=E:\biocbuild\bbs-3.21-bioc\R\library --no-vignettes --timings OncoSimulR_4.9.0.tar.gz |
| StartedAt: 2025-02-06 04:15:53 -0500 (Thu, 06 Feb 2025) |
| EndedAt: 2025-02-06 04:24:20 -0500 (Thu, 06 Feb 2025) |
| EllapsedTime: 506.9 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: OncoSimulR.Rcheck |
| Warnings: 0 |
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###
### Running command:
###
### E:\biocbuild\bbs-3.21-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:OncoSimulR.install-out.txt --library=E:\biocbuild\bbs-3.21-bioc\R\library --no-vignettes --timings OncoSimulR_4.9.0.tar.gz
###
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* using log directory 'E:/biocbuild/bbs-3.21-bioc/meat/OncoSimulR.Rcheck'
* using R Under development (unstable) (2025-01-21 r87610 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
gcc.exe (GCC) 13.3.0
GNU Fortran (GCC) 13.3.0
* 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 '4.9.0'
* 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 whether package 'OncoSimulR' can be installed ... OK
* used C compiler: 'gcc.exe (GCC) 13.3.0'
* used C++ compiler: 'G__~1.EXE (GCC) 13.3.0'
* checking installed package size ... INFO
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 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 for x64 is not available
File 'E:/biocbuild/bbs-3.21-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
'E:/biocbuild/bbs-3.21-bioc/meat/OncoSimulR.Rcheck/00check.log'
for details.
OncoSimulR.Rcheck/00install.out
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###
### Running command:
###
### E:\biocbuild\bbs-3.21-bioc\R\bin\R.exe CMD INSTALL OncoSimulR
###
##############################################################################
##############################################################################
* installing to library 'E:/biocbuild/bbs-3.21-bioc/R/library'
* installing *source* package 'OncoSimulR' ...
** this is package 'OncoSimulR' version '4.9.0'
** using staged installation
** libs
using C compiler: 'gcc.exe (GCC) 13.3.0'
using C++ compiler: 'G__~1.EXE (GCC) 13.3.0'
gcc -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'E:/biocbuild/bbs-3.21-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"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'E:/biocbuild/bbs-3.21-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"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'E:/biocbuild/bbs-3.21-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"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'E:/biocbuild/bbs-3.21-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"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'E:/biocbuild/bbs-3.21-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"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'E:/biocbuild/bbs-3.21-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"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'E:/biocbuild/bbs-3.21-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"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'E:/biocbuild/bbs-3.21-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"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'E:/biocbuild/bbs-3.21-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"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'E:/biocbuild/bbs-3.21-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"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'E:/biocbuild/bbs-3.21-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"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'E:/biocbuild/bbs-3.21-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"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'E:/biocbuild/bbs-3.21-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"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'E:/biocbuild/bbs-3.21-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"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'E:/biocbuild/bbs-3.21-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"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'E:/biocbuild/bbs-3.21-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"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'E:/biocbuild/bbs-3.21-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"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'E:/biocbuild/bbs-3.21-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"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'E:/biocbuild/bbs-3.21-bioc/R/library/Rcpp/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -DR_NO_REMAP -Wa,-mbig-obj -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++17 -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'E:/biocbuild/bbs-3.21-bioc/R/library/Rcpp/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -DR_NO_REMAP -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 -LE:/biocbuild/bbs-3.21-bioc/R/bin/x64 -lR
installing via 'install.libs.R' to E:/biocbuild/bbs-3.21-bioc/R/library/00LOCK-OncoSimulR/00new/OncoSimulR
[1] "/x64"
Installing fl_statistics.exe fl_generate.exe to E:/biocbuild/bbs-3.21-bioc/R/library/00LOCK-OncoSimulR/00new/OncoSimulR/exec/x64
Installing library OncoSimulR.dll to E:/biocbuild/bbs-3.21-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 Under development (unstable) (2025-01-21 r87610 ucrt) -- "Unsuffered Consequences"
Copyright (C) 2025 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)
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 Thu Feb 6 04:19:12 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 Thu Feb 6 04:19:12 2025
Took 0.67
Starting LOD_POM at Thu Feb 6 04:19:12 2025
Ending LOD_POM at Thu Feb 6 04:19:25 2025
Took 12.5
Starting test.Z-all-fitness at Thu Feb 6 04:19:25 2025
Ending test.Z-all-fitness at Thu Feb 6 04:19:25 2025
Took 0.19
Starting test.Z-driver-counts at Thu Feb 6 04:19:25 2025
Ending test.Z-driver-counts at Thu Feb 6 04:19:25 2025
Took 0.14
Starting test.Z-fixation at Thu Feb 6 04:19:25 2025
Ending test.Z-fixation at Thu Feb 6 04:19:26 2025
Took 0.51
Starting test.Z-magellan at Thu Feb 6 04:19:26 2025
Ended test.Z-magellan at Thu Feb 6 04:19:27 2025
Starting test.Z-mutator at Thu Feb 6 04:19:27 2025
Ending test.Z-mutator at Thu Feb 6 04:19:28 2025
Took 0.5
Starting test.Z-mutatorFDF at Thu Feb 6 04:19:28 2025
Ending test.Z-mutatorFDF at Thu Feb 6 04:19:28 2025
Took 0.18
Starting test.Z-oncoSimulIndiv at Thu Feb 6 04:19:28 2025
Ending test.Z-oncoSimulIndiv at Thu Feb 6 04:19:29 2025
Took 0.7
Starting test.Z-oncoSimulIndivConstant at Thu Feb 6 04:19:29 2025
Ending test.Z-oncoSimulIndivConstant at Thu Feb 6 04:19:34 2025
Took 4.77
Starting test.Z-oncoSimulIndivDeath at Thu Feb 6 04:19:34 2025
Ending test.Z-oncoSimulIndivDeath at Thu Feb 6 04:19:35 2025
Took 1.34
Starting test.Z-oncoSimulIndivFDF at Thu Feb 6 04:19:35 2025
Hitted wall time. Exiting.
Hitting wall time is regarded as an error.
Ending test.Z-oncoSimulIndivFDF at Thu Feb 6 04:19:36 2025
Took 0.63
Starting test.Z-rfitness-landscape at Thu Feb 6 04:19:36 2025
Ending test.Z-rfitness-landscape at Thu Feb 6 04:19:36 2025
Took 0.34
Starting Z-sample-only-last tests Thu Feb 6 04:19:36 2025
Ending Z-sample-only-last tests Thu Feb 6 04:19:36 2025
Took 0
Starting Z-total-present-drivers tests Thu Feb 6 04:19:36 2025
Ending Z-total-present-drivers tests Thu Feb 6 04:19:37 2025
Took 1.16
Dummy empty test Thu Feb 6 04:19:37 2025
Starting accessible_genotypes at Thu Feb 6 04:19:37 2025
Ending accessible_genotypes at Thu Feb 6 04:19:47 2025
Took 9.71
Starting all fitness at Thu Feb 6 04:19:47 2025
Ending all-fitness at Thu Feb 6 04:19:54 2025
Took 6.91
Starting test.allFitnessEffectsFDF at Thu Feb 6 04:19:54 2025
Ending test.allFitnessEffectsFDF at Thu Feb 6 04:19:54 2025
Took 0.12
Starting test.allFitnessEffectsDeath at Thu Feb 6 04:19:54 2025
Ending test.allFitnessEffectsDeath at Thu Feb 6 04:19:54 2025
Took 0.5
Starting test.allFitnessEffectsFDF at Thu Feb 6 04:19:54 2025
Ending test.allFitnessEffectsFDF at Thu Feb 6 04:19:55 2025
Took 0.64
Starting driverCounts at Thu Feb 6 04:19:55 2025
Ending driverCounts at Thu Feb 6 04:20:04 2025
Took 8.94
Starting epist-order-modules at Thu Feb 6 04:20:04 2025
Ending epist-order-modules at Thu Feb 6 04:20:04 2025
Took 0.05
Starting test.evaluatingGenotypesDeath at Thu Feb 6 04:20:04 2025
Ending test.evaluatingGenotypesDeath at Thu Feb 6 04:20:04 2025
Took 0.16
Starting test.evaluatingGenotypesFDF at Thu Feb 6 04:20:04 2025
Ending test.evaluatingGenotypesFDF at Thu Feb 6 04:20:04 2025
Took 0.25
Starting exercise-plotting-code at Thu Feb 6 04:20:04 2025
Ending exercise-plotting-code at Thu Feb 6 04:20:09 2025
Took 4.19
Starting exercise-rfitness at Thu Feb 6 04:20:09 2025
Ending exercise-rfitness at Thu Feb 6 04:20:25 2025
Took 16.79
Starting to_Magella at Thu Feb 6 04:20:25 2025
Ending to_Magella at Thu Feb 6 04:20:26 2025
Took 0.1
Starting fitness preds at Thu Feb 6 04:20:26 2025
Observed vs expected, case III
done tries 1
Ending fitness preds long at Thu Feb 6 04:20:35 2025
Took 9.06
Starting fixation at Thu Feb 6 04:20:35 2025
Ending fixation at Thu Feb 6 04:21:04 2025
Took 29.39
Starting test.flfast-additional.R test at Thu Feb 6 04:21:04 2025
Ending test.flfast-additional.R test at Thu Feb 6 04:21:06 2025
Took 1.94
Starting test.flfast-mutator.R test at Thu Feb 6 04:21:06 2025
Finished test.flfast-mutator.R test at Thu Feb 6 04:21:07 2025
Took 1.47
Starting genotFitness at Thu Feb 6 04:21:07 2025
Ending genotFitness at Thu Feb 6 04:21:08 2025
Took 0.26
Starting genot_fitness_to_epistasis at Thu Feb 6 04:21:08 2025
Ending genot_fitness_to_epistasis at Thu Feb 6 04:21:08 2025
Took 0.06
Starting init-mutant tests Thu Feb 6 04:21:08 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 Thu Feb 6 04:21:17 2025
Took 9.64
Starting interventions tests Thu Feb 6 04:21:17 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] 0.41 0.41 0.41
[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 Thu Feb 6 04:21:25 2025
Took 7.65
Starting test.magellan at Thu Feb 6 04:21:25 2025
Ending test.magellan at Thu Feb 6 04:21:26 2025
Took 0.73
Starting test.modules-root-no-root at Thu Feb 6 04:21:26 2025
Ending test.modules-root-no-root at Thu Feb 6 04:21:26 2025
Took 0.09
Starting at mutPropGrowth Thu Feb 6 04:21:26 2025
Ended test.mutPropGrowth: Thu Feb 6 04:21:33 2025
Took 7.54
Starting test.mutator-oncoSimulSample.R test at Thu Feb 6 04:21:33 2025
Finished test.mutator-oncoSimulSample.R test at Thu Feb 6 04:21:44 2025
Took 10.09 seconds
Starting test.mutator.R test at Thu Feb 6 04:21:44 2025[1] 2.442784e-10
[1] 1.104431e-13
Finished test.mutator.R test at Thu Feb 6 04:22:06 2025
Took 22.28
Starting test.mutatorFDF.R test at Thu Feb 6 04:22:06 2025
Starting test.no-v1 at Thu Feb 6 04:22:07 2025
Ending test.no-v1 at Thu Feb 6 04:22:07 2025
Took 0.01
Starting oncoSimulIndiv-miscell tests Thu Feb 6 04:22:07 2025
Ending oncoSimulIndiv-miscell tests Thu Feb 6 04:22:18 2025
Took 11.39
Starting oncoSimulSample-failures tests Thu Feb 6 04:22:18 2025
Ending oncoSimulSample-failures tests Thu Feb 6 04:22:22 2025
Took 3.55
Starting oncoSimulSample-limits tests Thu Feb 6 04:22:22 2025
Ending oncoSimulSample-limits tests Thu Feb 6 04:22:22 2025
Took 0.06
Starting per-gene-mutation rates at Thu Feb 6 04:22:22 2025
Ending per-gene-mutation rates at Thu Feb 6 04:23:02 2025
Took 40.24
Starting plotFitnessLandscape at Thu Feb 6 04:23:02 2025
Ending plotFitnessLandscape at Thu Feb 6 04:23:08 2025
Took 5.82
Starting poset-transformations tests Thu Feb 6 04:23:08 2025
Ending poset-transformations tests Thu Feb 6 04:23:27 2025
Took 19.13
Starting sample-prob Thu Feb 6 04:23:27 2025
[1] 2.220018e-26
[1] 1.241257e-09
[1] 8.697161e-10
[1] 1.334462e-11
[1] 1.753547e-12
[1] 4.102111e-12
[1] 7.924521e-09
[1] 5.896422e-15
[1] 1.51632e-09
[1] 5.941586e-10
[1] 2.84472e-08
[1] 1.287614e-09
Ending sample-prob tests Thu Feb 6 04:23:38 2025
Took 10.72
Starting samplePop tests Thu Feb 6 04:23:38 2025
Ending samplePop tests Thu Feb 6 04:23:45 2025
Took 7.06
Starting simuls-runs-examples tests Thu Feb 6 04:23:45 2025
Ending simuls-runs-examples tests Thu Feb 6 04:23:54 2025
Took 8.52
Starting user variable tests Thu Feb 6 04:23:54 2025
[1] "Checking user variable: user_var_1"
[1] "Checking rule: rule_1"
Ending user variable tests Thu Feb 6 04:23:54 2025
Took 0.15
Starting warning-mutPropGrowth tests Thu Feb 6 04:23:54 2025
Ending warning-mutPropGrowth tests Thu Feb 6 04:23:54 2025
Took 0.44
Starting wide2long tests Thu Feb 6 04:23:54 2025
Ending wide2long tests Thu Feb 6 04:23:55 2025
Took 0.27
[ FAIL 0 | WARN 19 | SKIP 6 | PASS 8376 ]
══ 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:1099:1'
[ FAIL 0 | WARN 19 | SKIP 6 | PASS 8376 ]
>
> proc.time()
user system elapsed
264.62 8.48 288.31
OncoSimulR.Rcheck/OncoSimulR-Ex.timings
| name | user | system | elapsed | |
| OncoSimulWide2Long | 0.17 | 0.00 | 0.17 | |
| POM | 1.14 | 0.00 | 1.14 | |
| allFitnessEffects | 2.05 | 0.09 | 2.14 | |
| benchmarks | 0.02 | 0.00 | 0.01 | |
| createInterventions | 0.48 | 0.00 | 0.49 | |
| createUserVars | 0.89 | 0.00 | 0.89 | |
| evalAllGenotypes | 0.3 | 0.0 | 0.3 | |
| example-missing-drivers | 0.53 | 0.03 | 0.56 | |
| examplePosets | 0.39 | 0.00 | 0.39 | |
| examplesFitnessEffects | 0.14 | 0.02 | 0.16 | |
| freq-dep-simul-examples | 0.02 | 0.00 | 0.01 | |
| mcfLs | 0 | 0 | 0 | |
| oncoSimulIndiv | 1.51 | 0.03 | 1.55 | |
| plot.fitnessEffects | 0.21 | 0.02 | 0.22 | |
| plot.oncosimul | 0.41 | 0.01 | 0.42 | |
| plotClonePhylog | 1.34 | 0.10 | 1.44 | |
| plotFitnessLandscape | 1.44 | 0.07 | 1.52 | |
| plotPoset | 0.11 | 0.00 | 0.11 | |
| poset | 0.15 | 0.00 | 0.15 | |
| rfitness | 0.63 | 0.02 | 1.35 | |
| samplePop | 0.09 | 0.00 | 0.09 | |
| simOGraph | 0.10 | 0.02 | 0.11 | |
| to_Magellan | 0.14 | 0.03 | 1.23 | |
| vignette_pre_computed | 0.01 | 0.00 | 0.02 | |