Ramon Diaz-Uriarte
| Snapshot Date: 2024-07-15 14:00 -0400 (Mon, 15 Jul 2024) |
| git_url: https://git.bioconductor.org/packages/OncoSimulR |
| git_branch: devel |
| git_last_commit: c3dd5c6 |
| git_last_commit_date: 2024-04-30 10:37:33 -0400 (Tue, 30 Apr 2024) |
| Back to Multiple platform build/check report for BioC 3.20: simplified long |
|
This page was generated on 2024-07-16 11:40 -0400 (Tue, 16 Jul 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4677 |
| palomino6 | Windows Server 2022 Datacenter | x64 | 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" | 4416 |
| lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4444 |
| kjohnson3 | macOS 13.6.5 Ventura | arm64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4393 |
| palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" | 4373 |
| 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 1434/2243 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| OncoSimulR 4.7.0 (landing page) Ramon Diaz-Uriarte
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino6 | 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 | OK | ERROR | skipped | skipped | |||||||||
| palomino8 | Windows Server 2022 Datacenter / x64 | OK | 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. |
| Package: OncoSimulR |
| Version: 4.7.0 |
| Command: C:\Users\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:OncoSimulR.install-out.txt --library=C:\Users\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings OncoSimulR_4.7.0.tar.gz |
| StartedAt: 2024-07-16 02:26:04 -0400 (Tue, 16 Jul 2024) |
| EndedAt: 2024-07-16 02:32:04 -0400 (Tue, 16 Jul 2024) |
| EllapsedTime: 359.8 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: OncoSimulR.Rcheck |
| Warnings: 0 |
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###
### Running command:
###
### C:\Users\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:OncoSimulR.install-out.txt --library=C:\Users\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings OncoSimulR_4.7.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.20-bioc/meat/OncoSimulR.Rcheck'
* using R version 4.4.1 (2024-06-14 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 '4.7.0'
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking 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 'C:/Users/biocbuild/bbs-3.20-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
'C:/Users/biocbuild/bbs-3.20-bioc/meat/OncoSimulR.Rcheck/00check.log'
for details.
OncoSimulR.Rcheck/00install.out
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###
### Running command:
###
### C:\Users\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD INSTALL OncoSimulR
###
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* installing to library 'C:/Users/biocbuild/bbs-3.20-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"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.20-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"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.20-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"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.20-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"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.20-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"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.20-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"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.20-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"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.20-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"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.20-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"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.20-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"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.20-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"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.20-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"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.20-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"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.20-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"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.20-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"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.20-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"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.20-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"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.20-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"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.20-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"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.20-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"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.20-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 -LC:/Users/biocbuild/bbs-3.20-bioc/R/bin/x64 -lR
installing via 'install.libs.R' to C:/Users/biocbuild/bbs-3.20-bioc/R/library/00LOCK-OncoSimulR/00new/OncoSimulR
[1] "/x64"
Installing fl_statistics.exe fl_generate.exe to C:/Users/biocbuild/bbs-3.20-bioc/R/library/00LOCK-OncoSimulR/00new/OncoSimulR/exec/x64
Installing library OncoSimulR.dll to C:/Users/biocbuild/bbs-3.20-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 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life"
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 Tue Jul 16 02:28:35 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 Tue Jul 16 02:28:35 2024
Took 0.39
Starting LOD_POM at Tue Jul 16 02:28:35 2024
Ending LOD_POM at Tue Jul 16 02:28:47 2024
Took 11.96
Starting test.Z-all-fitness at Tue Jul 16 02:28:47 2024
Ending test.Z-all-fitness at Tue Jul 16 02:28:47 2024
Took 0.13
Starting test.Z-driver-counts at Tue Jul 16 02:28:47 2024
Ending test.Z-driver-counts at Tue Jul 16 02:28:47 2024
Took 0.12
Starting test.Z-fixation at Tue Jul 16 02:28:47 2024
Ending test.Z-fixation at Tue Jul 16 02:28:48 2024
Took 0.28
Starting test.Z-magellan at Tue Jul 16 02:28:48 2024
Ended test.Z-magellan at Tue Jul 16 02:28:49 2024
Starting test.Z-mutator at Tue Jul 16 02:28:49 2024
Ending test.Z-mutator at Tue Jul 16 02:28:49 2024
Took 0.31
Starting test.Z-mutatorFDF at Tue Jul 16 02:28:49 2024
Ending test.Z-mutatorFDF at Tue Jul 16 02:28:49 2024
Took 0.11
Starting test.Z-oncoSimulIndiv at Tue Jul 16 02:28:49 2024
Ending test.Z-oncoSimulIndiv at Tue Jul 16 02:28:50 2024
Took 0.48
Starting test.Z-oncoSimulIndivConstant at Tue Jul 16 02:28:50 2024
Ending test.Z-oncoSimulIndivConstant at Tue Jul 16 02:28:52 2024
Took 2.31
Starting test.Z-oncoSimulIndivDeath at Tue Jul 16 02:28:52 2024
Ending test.Z-oncoSimulIndivDeath at Tue Jul 16 02:28:53 2024
Took 1.4
Starting test.Z-oncoSimulIndivFDF at Tue Jul 16 02:28:53 2024
Hitted wall time. Exiting.
Hitting wall time is regarded as an error.
Ending test.Z-oncoSimulIndivFDF at Tue Jul 16 02:28:55 2024
Took 1.05
Starting test.Z-rfitness-landscape at Tue Jul 16 02:28:55 2024
Ending test.Z-rfitness-landscape at Tue Jul 16 02:28:55 2024
Took 0.16
Starting Z-sample-only-last tests Tue Jul 16 02:28:55 2024
Ending Z-sample-only-last tests Tue Jul 16 02:28:55 2024
Took 0
Starting Z-total-present-drivers tests Tue Jul 16 02:28:55 2024
Ending Z-total-present-drivers tests Tue Jul 16 02:28:55 2024
Took 0.68
Dummy empty test Tue Jul 16 02:28:55 2024
Starting accessible_genotypes at Tue Jul 16 02:28:55 2024
Ending accessible_genotypes at Tue Jul 16 02:29:03 2024
Took 7.84
Starting all fitness at Tue Jul 16 02:29:03 2024
Ending all-fitness at Tue Jul 16 02:29:09 2024
Took 5.52
Starting test.allFitnessEffectsFDF at Tue Jul 16 02:29:09 2024
Ending test.allFitnessEffectsFDF at Tue Jul 16 02:29:09 2024
Took 0.11
Starting test.allFitnessEffectsDeath at Tue Jul 16 02:29:09 2024
Ending test.allFitnessEffectsDeath at Tue Jul 16 02:29:09 2024
Took 0.36
Starting test.allFitnessEffectsFDF at Tue Jul 16 02:29:09 2024
Ending test.allFitnessEffectsFDF at Tue Jul 16 02:29:10 2024
Took 0.36
Starting driverCounts at Tue Jul 16 02:29:10 2024
Ending driverCounts at Tue Jul 16 02:29:16 2024
Took 6.64
Starting epist-order-modules at Tue Jul 16 02:29:16 2024
Ending epist-order-modules at Tue Jul 16 02:29:16 2024
Took 0.05
Starting test.evaluatingGenotypesDeath at Tue Jul 16 02:29:16 2024
Ending test.evaluatingGenotypesDeath at Tue Jul 16 02:29:16 2024
Took 0.15
Starting test.evaluatingGenotypesFDF at Tue Jul 16 02:29:17 2024
Ending test.evaluatingGenotypesFDF at Tue Jul 16 02:29:17 2024
Took 0.19
Starting exercise-plotting-code at Tue Jul 16 02:29:17 2024
Ending exercise-plotting-code at Tue Jul 16 02:29:19 2024
Took 2.64
Starting exercise-rfitness at Tue Jul 16 02:29:19 2024
Ending exercise-rfitness at Tue Jul 16 02:29:33 2024
Took 13.95
Starting to_Magella at Tue Jul 16 02:29:33 2024
Ending to_Magella at Tue Jul 16 02:29:33 2024
Took 0.07
Starting fitness preds at Tue Jul 16 02:29:33 2024
Observed vs expected, case III
done tries 1
Ending fitness preds long at Tue Jul 16 02:29:39 2024
Took 5.85
Starting fixation at Tue Jul 16 02:29:39 2024
Ending fixation at Tue Jul 16 02:29:59 2024
Took 19.74
Starting test.flfast-additional.R test at Tue Jul 16 02:29:59 2024
Ending test.flfast-additional.R test at Tue Jul 16 02:30:00 2024
Took 1.24
Starting test.flfast-mutator.R test at Tue Jul 16 02:30:00 2024
Finished test.flfast-mutator.R test at Tue Jul 16 02:30:01 2024
Took 1.02
Starting genotFitness at Tue Jul 16 02:30:01 2024
Ending genotFitness at Tue Jul 16 02:30:01 2024
Took 0.16
Starting genot_fitness_to_epistasis at Tue Jul 16 02:30:01 2024
Ending genot_fitness_to_epistasis at Tue Jul 16 02:30:01 2024
Took 0.04
Starting init-mutant tests Tue Jul 16 02:30:01 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 Tue Jul 16 02:30:08 2024
Took 6.33
Starting interventions tests Tue Jul 16 02:30:08 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] 0.41 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 Tue Jul 16 02:30:13 2024
Took 5.51
Starting test.magellan at Tue Jul 16 02:30:13 2024
Ending test.magellan at Tue Jul 16 02:30:14 2024
Took 0.66
Starting test.modules-root-no-root at Tue Jul 16 02:30:14 2024
Ending test.modules-root-no-root at Tue Jul 16 02:30:14 2024
Took 0.07
Starting at mutPropGrowth Tue Jul 16 02:30:14 2024
Ended test.mutPropGrowth: Tue Jul 16 02:30:20 2024
Took 5.64
Starting test.mutator-oncoSimulSample.R test at Tue Jul 16 02:30:20 2024
Finished test.mutator-oncoSimulSample.R test at Tue Jul 16 02:30:27 2024
Took 7.55 seconds
Starting test.mutator.R test at Tue Jul 16 02:30:27 2024[1] 1.800565e-07
[1] 2.793022e-11
Finished test.mutator.R test at Tue Jul 16 02:30:42 2024
Took 15.2
Starting test.mutatorFDF.R test at Tue Jul 16 02:30:42 2024
Starting test.no-v1 at Tue Jul 16 02:30:43 2024
Ending test.no-v1 at Tue Jul 16 02:30:43 2024
Took 0.01
Starting oncoSimulIndiv-miscell tests Tue Jul 16 02:30:43 2024
Ending oncoSimulIndiv-miscell tests Tue Jul 16 02:30:50 2024
Took 6.69
Starting oncoSimulSample-failures tests Tue Jul 16 02:30:50 2024
Ending oncoSimulSample-failures tests Tue Jul 16 02:30:54 2024
Took 3.81
Starting oncoSimulSample-limits tests Tue Jul 16 02:30:54 2024
Ending oncoSimulSample-limits tests Tue Jul 16 02:30:54 2024
Took 0.28
Starting per-gene-mutation rates at Tue Jul 16 02:30:54 2024
Ending per-gene-mutation rates at Tue Jul 16 02:31:19 2024
Took 24.68
Starting plotFitnessLandscape at Tue Jul 16 02:31:19 2024
Ending plotFitnessLandscape at Tue Jul 16 02:31:22 2024
Took 2.99
Starting poset-transformations tests Tue Jul 16 02:31:22 2024
Ending poset-transformations tests Tue Jul 16 02:31:32 2024
Took 10.76
Starting sample-prob Tue Jul 16 02:31:32 2024
[1] 3.490344e-23
[1] 3.595397e-13
[1] 3.12901e-11
[1] 1.264323e-11
[1] 5.954296e-12
[1] 1.354341e-12
[1] 7.403528e-09
[1] 5.350257e-13
[1] 1.742281e-09
[1] 5.463286e-09
[1] 4.55028e-09
[1] 6.041475e-10
Ending sample-prob tests Tue Jul 16 02:31:39 2024
Took 6.33
Starting samplePop tests Tue Jul 16 02:31:39 2024
Ending samplePop tests Tue Jul 16 02:31:44 2024
Took 5.2
Starting simuls-runs-examples tests Tue Jul 16 02:31:44 2024
Ending simuls-runs-examples tests Tue Jul 16 02:31:49 2024
Took 5.11
Starting user variable tests Tue Jul 16 02:31:49 2024
[1] "Checking user variable: user_var_1"
[1] "Checking rule: rule_1"
Ending user variable tests Tue Jul 16 02:31:49 2024
Took 0.09
Starting warning-mutPropGrowth tests Tue Jul 16 02:31:49 2024
Ending warning-mutPropGrowth tests Tue Jul 16 02:31:49 2024
Took 0.35
Starting wide2long tests Tue Jul 16 02:31:49 2024
Ending wide2long tests Tue Jul 16 02:31:50 2024
Took 0.18
[ FAIL 0 | WARN 18 | SKIP 6 | PASS 8404 ]
══ 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 8404 ]
>
> proc.time()
user system elapsed
181.62 9.32 200.62
OncoSimulR.Rcheck/OncoSimulR-Ex.timings
| name | user | system | elapsed | |
| OncoSimulWide2Long | 0.15 | 0.00 | 0.15 | |
| POM | 1.05 | 0.00 | 1.05 | |
| allFitnessEffects | 1.86 | 0.13 | 1.87 | |
| benchmarks | 0.00 | 0.01 | 0.02 | |
| createInterventions | 0.28 | 0.00 | 0.28 | |
| createUserVars | 0.43 | 0.00 | 0.44 | |
| evalAllGenotypes | 0.16 | 0.00 | 0.15 | |
| example-missing-drivers | 0.34 | 0.05 | 0.40 | |
| examplePosets | 0.22 | 0.05 | 0.26 | |
| examplesFitnessEffects | 0.03 | 0.00 | 0.03 | |
| freq-dep-simul-examples | 0.02 | 0.00 | 0.02 | |
| mcfLs | 0 | 0 | 0 | |
| oncoSimulIndiv | 0.92 | 0.03 | 0.95 | |
| plot.fitnessEffects | 0.17 | 0.01 | 0.19 | |
| plot.oncosimul | 0.41 | 0.00 | 0.40 | |
| plotClonePhylog | 0.95 | 0.07 | 1.05 | |
| plotFitnessLandscape | 0.88 | 0.06 | 0.95 | |
| plotPoset | 0.08 | 0.00 | 0.08 | |
| poset | 0.09 | 0.64 | 0.74 | |
| rfitness | 0.44 | 0.00 | 0.70 | |
| samplePop | 0.03 | 0.02 | 0.05 | |
| simOGraph | 0.05 | 0.00 | 0.04 | |
| to_Magellan | 0.04 | 0.06 | 0.77 | |
| vignette_pre_computed | 0.02 | 0.00 | 0.02 | |