| Back to Multiple platform build/check report for BioC 3.19: simplified long |
|
This page was generated on 2024-05-30 11:35:46 -0400 (Thu, 30 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" | 4753 |
| lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4518 |
| 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 |  | ||||||||
| 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: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:OncoSimulR.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings OncoSimulR_4.6.0.tar.gz |
| StartedAt: 2024-05-29 22:35:34 -0400 (Wed, 29 May 2024) |
| EndedAt: 2024-05-29 22:43:09 -0400 (Wed, 29 May 2024) |
| EllapsedTime: 454.6 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: OncoSimulR.Rcheck |
| Warnings: 0 |
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### Running command:
###
### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:OncoSimulR.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings OncoSimulR_4.6.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.19-bioc/meat/OncoSimulR.Rcheck’
* using R version 4.4.0 (2024-04-24)
* using platform: x86_64-apple-darwin20
* R was compiled by
Apple clang version 14.0.0 (clang-1400.0.29.202)
GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.7.1
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘OncoSimulR’ can be installed ... OK
* used C compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
* used C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
* used SDK: ‘MacOSX11.3.sdk’
* checking installed package size ... NOTE
installed size is 9.3Mb
sub-directories of 1Mb or more:
libs 7.9Mb
* 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 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 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
‘/Users/biocbuild/bbs-3.19-bioc/meat/OncoSimulR.Rcheck/00check.log’
for details.
OncoSimulR.Rcheck/00install.out
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###
### Running command:
###
### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL OncoSimulR
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library’
* installing *source* package ‘OncoSimulR’ ...
** using staged installation
** libs
using C compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
using C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
using SDK: ‘MacOSX11.3.sdk’
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c FitnessLandscape/gamma.c -o FitnessLandscape/gamma.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c FitnessLandscape/landscape.c -o FitnessLandscape/landscape.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c FitnessLandscape/random.c -o FitnessLandscape/random.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c FitnessLandscape/sort.c -o FitnessLandscape/sort.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c FitnessLandscape/chain.c -o FitnessLandscape/chain.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c FitnessLandscape/input.c -o FitnessLandscape/input.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c FitnessLandscape/genotypes.c -o FitnessLandscape/genotypes.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c FitnessLandscape/ordered_pairs.c -o FitnessLandscape/ordered_pairs.o
FitnessLandscape/ordered_pairs.c:138:6: warning: variable 'tot_pairs' set but not used [-Wunused-but-set-variable]
int tot_pairs=0;
^
1 warning generated.
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c FitnessLandscape/calculus.c -o FitnessLandscape/calculus.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c FitnessLandscape/vector.c -o FitnessLandscape/vector.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c FitnessLandscape/generalized_chain.c -o FitnessLandscape/generalized_chain.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c FitnessLandscape/LinearAlgebra.c -o FitnessLandscape/LinearAlgebra.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c FitnessLandscape/summary_statistics.c -o FitnessLandscape/summary_statistics.o
FitnessLandscape/summary_statistics.c:515:9: warning: variable 'meanVarianceNumberOfStepsFL' set but not used [-Wunused-but-set-variable]
double meanVarianceNumberOfStepsFL = 0;
^
1 warning generated.
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c FitnessLandscape/epistasis_type.c -o FitnessLandscape/epistasis_type.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c FitnessLandscape/decomposition.c -o FitnessLandscape/decomposition.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c FitnessLandscape/models.c -o FitnessLandscape/models.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -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 archive liblandscape.a
ranlib liblandscape.a;
clang -arch x86_64 -O -Wall -o fl_statistics -I/FitnessLandscape/. -L. FitnessLandscape/main_fl_statistics.c -llandscape -lm;
clang -arch x86_64 -O -Wall -o fl_generate -I/FitnessLandscape/. -L. FitnessLandscape/main_fl_generate.c -llandscape -lm;
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c OncoSimulR_init.c -o OncoSimulR_init.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c RcppExports.cpp -o RcppExports.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c unity_osimul.cpp -o unity_osimul.o
In file included from unity_osimul.cpp:10:
./UnityOncoSimul/intervention_private_2.cpp:17:10: warning: variable 'totalPop' set but not used [-Wunused-but-set-variable]
double totalPop = 0.0;
^
1 warning generated.
clang++ -arch x86_64 -std=gnu++17 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/x86_64/lib -o OncoSimulR.so OncoSimulR_init.o RcppExports.o unity_osimul.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing via 'install.libs.R' to /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/00LOCK-OncoSimulR/00new/OncoSimulR
[1] ""
Installing fl_statistics fl_generate to /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/00LOCK-OncoSimulR/00new/OncoSimulR/exec
Installing library OncoSimulR.so to /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/00LOCK-OncoSimulR/00new/OncoSimulR/libs
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (OncoSimulR)
OncoSimulR.Rcheck/tests/testthat.Rout
R version 4.4.0 (2024-04-24) -- "Puppy Cup"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20
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 Wed May 29 22:37:16 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 Wed May 29 22:37:17 2024
Took 0.51
Starting LOD_POM at Wed May 29 22:37:17 2024
Ending LOD_POM at Wed May 29 22:37:26 2024
Took 9.34
Starting test.Z-all-fitness at Wed May 29 22:37:26 2024
Ending test.Z-all-fitness at Wed May 29 22:37:26 2024
Took 0.15
Starting test.Z-driver-counts at Wed May 29 22:37:26 2024
Ending test.Z-driver-counts at Wed May 29 22:37:27 2024
Took 0.13
Starting test.Z-fixation at Wed May 29 22:37:27 2024
Ending test.Z-fixation at Wed May 29 22:37:27 2024
Took 0.32
Starting test.Z-magellan at Wed May 29 22:37:27 2024
Ended test.Z-magellan at Wed May 29 22:37:29 2024
Starting test.Z-mutator at Wed May 29 22:37:29 2024
Ending test.Z-mutator at Wed May 29 22:37:29 2024
Took 0.47
Starting test.Z-mutatorFDF at Wed May 29 22:37:29 2024
Ending test.Z-mutatorFDF at Wed May 29 22:37:29 2024
Took 0.13
Starting test.Z-oncoSimulIndiv at Wed May 29 22:37:29 2024
Ending test.Z-oncoSimulIndiv at Wed May 29 22:37:30 2024
Took 0.55
Starting test.Z-oncoSimulIndivConstant at Wed May 29 22:37:30 2024
Ending test.Z-oncoSimulIndivConstant at Wed May 29 22:37:33 2024
Took 2.99
Starting test.Z-oncoSimulIndivDeath at Wed May 29 22:37:33 2024
Ending test.Z-oncoSimulIndivDeath at Wed May 29 22:37:34 2024
Took 1.01
Starting test.Z-oncoSimulIndivFDF at Wed May 29 22:37:34 2024
Hitted wall time. Exiting.
Hitting wall time is regarded as an error.
Ending test.Z-oncoSimulIndivFDF at Wed May 29 22:37:35 2024
Took 0.49
Starting test.Z-rfitness-landscape at Wed May 29 22:37:35 2024
Ending test.Z-rfitness-landscape at Wed May 29 22:37:35 2024
Took 0.27
Starting Z-sample-only-last tests Wed May 29 22:37:35 2024
Ending Z-sample-only-last tests Wed May 29 22:37:35 2024
Took 0
Starting Z-total-present-drivers tests Wed May 29 22:37:35 2024
Ending Z-total-present-drivers tests Wed May 29 22:37:36 2024
Took 0.97
Dummy empty test Wed May 29 22:37:36 2024
Starting accessible_genotypes at Wed May 29 22:37:36 2024
Ending accessible_genotypes at Wed May 29 22:37:46 2024
Took 9.95
Starting all fitness at Wed May 29 22:37:46 2024
Ending all-fitness at Wed May 29 22:37:51 2024
Took 5.62
Starting test.allFitnessEffectsFDF at Wed May 29 22:37:51 2024
Ending test.allFitnessEffectsFDF at Wed May 29 22:37:52 2024
Took 0.14
Starting test.allFitnessEffectsDeath at Wed May 29 22:37:52 2024
Ending test.allFitnessEffectsDeath at Wed May 29 22:37:52 2024
Took 0.52
Starting test.allFitnessEffectsFDF at Wed May 29 22:37:52 2024
Ending test.allFitnessEffectsFDF at Wed May 29 22:37:53 2024
Took 0.46
Starting driverCounts at Wed May 29 22:37:53 2024
Ending driverCounts at Wed May 29 22:38:05 2024
Took 12.06
Starting epist-order-modules at Wed May 29 22:38:05 2024
Ending epist-order-modules at Wed May 29 22:38:05 2024
Took 0.07
Starting test.evaluatingGenotypesDeath at Wed May 29 22:38:05 2024
Ending test.evaluatingGenotypesDeath at Wed May 29 22:38:05 2024
Took 0.22
Starting test.evaluatingGenotypesFDF at Wed May 29 22:38:05 2024
Ending test.evaluatingGenotypesFDF at Wed May 29 22:38:05 2024
Took 0.25
Starting exercise-plotting-code at Wed May 29 22:38:05 2024
Ending exercise-plotting-code at Wed May 29 22:38:08 2024
Took 3.18
Starting exercise-rfitness at Wed May 29 22:38:08 2024
Ending exercise-rfitness at Wed May 29 22:38:22 2024
Took 13.28
Starting to_Magella at Wed May 29 22:38:22 2024
Ending to_Magella at Wed May 29 22:38:22 2024
Took 0.06
Starting fitness preds at Wed May 29 22:38:22 2024
Observed vs expected, case III
done tries 1
Ending fitness preds long at Wed May 29 22:38:30 2024
Took 8.66
Starting fixation at Wed May 29 22:38:30 2024
Ending fixation at Wed May 29 22:38:49 2024
Took 18.89
Starting test.flfast-additional.R test at Wed May 29 22:38:49 2024
Ending test.flfast-additional.R test at Wed May 29 22:38:51 2024
Took 1.51
Starting test.flfast-mutator.R test at Wed May 29 22:38:51 2024
Finished test.flfast-mutator.R test at Wed May 29 22:38:52 2024
Took 1.58
Starting genotFitness at Wed May 29 22:38:52 2024
Ending genotFitness at Wed May 29 22:38:53 2024
Took 0.22
Starting genot_fitness_to_epistasis at Wed May 29 22:38:53 2024
Ending genot_fitness_to_epistasis at Wed May 29 22:38:53 2024
Took 0.05
Starting init-mutant tests Wed May 29 22:38:53 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 Wed May 29 22:39:00 2024
Took 7.76
Starting interventions tests Wed May 29 22:39:00 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] 0.6 0.6 0.6
[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 Wed May 29 22:39:06 2024
Took 5.16
Starting test.magellan at Wed May 29 22:39:06 2024
Ending test.magellan at Wed May 29 22:39:06 2024
Took 0.29
Starting test.modules-root-no-root at Wed May 29 22:39:06 2024
Ending test.modules-root-no-root at Wed May 29 22:39:06 2024
Took 0.1
Starting at mutPropGrowth Wed May 29 22:39:06 2024
Ended test.mutPropGrowth: Wed May 29 22:39:14 2024
Took 7.66
Starting test.mutator-oncoSimulSample.R test at Wed May 29 22:39:14 2024
Finished test.mutator-oncoSimulSample.R test at Wed May 29 22:39:23 2024
Took 9.58 seconds
Starting test.mutator.R test at Wed May 29 22:39:23 2024[1] 5.849901e-06
[1] 5.120697e-12
Finished test.mutator.R test at Wed May 29 22:39:41 2024
Took 17.55
Starting test.mutatorFDF.R test at Wed May 29 22:39:41 2024
Starting test.no-v1 at Wed May 29 22:39:41 2024
Ending test.no-v1 at Wed May 29 22:39:41 2024
Took 0.02
Starting oncoSimulIndiv-miscell tests Wed May 29 22:39:41 2024
Ending oncoSimulIndiv-miscell tests Wed May 29 22:39:47 2024
Took 5.19
Starting oncoSimulSample-failures tests Wed May 29 22:39:47 2024
Ending oncoSimulSample-failures tests Wed May 29 22:39:51 2024
Took 3.86
Starting oncoSimulSample-limits tests Wed May 29 22:39:51 2024
Ending oncoSimulSample-limits tests Wed May 29 22:39:51 2024
Took 0.07
Starting per-gene-mutation rates at Wed May 29 22:39:51 2024
Ending per-gene-mutation rates at Wed May 29 22:40:29 2024
Took 38.54
Starting plotFitnessLandscape at Wed May 29 22:40:29 2024
Ending plotFitnessLandscape at Wed May 29 22:40:34 2024
Took 4.41
Starting poset-transformations tests Wed May 29 22:40:34 2024
Ending poset-transformations tests Wed May 29 22:40:48 2024
Took 14.63
Starting sample-prob Wed May 29 22:40:48 2024
[1] 3.413374e-23
[1] 4.753268e-19
[1] 8.285756e-11
[1] 1.30682e-11
[1] 1.071539e-13
[1] 1.197579e-15
[1] 6.471615e-11
[1] 9.363603e-15
[1] 4.694274e-10
[1] 2.083513e-07
[1] 1.515741e-07
[1] 6.634063e-09
Ending sample-prob tests Wed May 29 22:41:51 2024
Took 62.97
Starting samplePop tests Wed May 29 22:41:51 2024
Ending samplePop tests Wed May 29 22:42:00 2024
Took 8.28
Starting simuls-runs-examples tests Wed May 29 22:42:00 2024
Ending simuls-runs-examples tests Wed May 29 22:42:08 2024
Took 8.28
Starting user variable tests Wed May 29 22:42:08 2024
[1] "Checking user variable: user_var_1"
[1] "Checking rule: rule_1"
Ending user variable tests Wed May 29 22:42:08 2024
Took 0.21
Starting warning-mutPropGrowth tests Wed May 29 22:42:08 2024
Ending warning-mutPropGrowth tests Wed May 29 22:42:08 2024
Took 0.37
Starting wide2long tests Wed May 29 22:42:08 2024
Ending wide2long tests Wed May 29 22:42:09 2024
Took 0.28
[ FAIL 0 | WARN 18 | SKIP 7 | PASS 8397 ]
══ Skipped tests (7) ═══════════════════════════════════════════════════════════
• On Mac (2): 'test.Z-magellan.R:664:5', 'test.Z-oncoSimulIndivFDF.R:125:3'
• 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 7 | PASS 8397 ]
>
> proc.time()
user system elapsed
252.691 102.478 297.885
OncoSimulR.Rcheck/OncoSimulR-Ex.timings
| name | user | system | elapsed | |
| OncoSimulWide2Long | 0.225 | 0.006 | 0.233 | |
| POM | 0.862 | 0.088 | 0.554 | |
| allFitnessEffects | 1.908 | 0.081 | 2.006 | |
| benchmarks | 0.008 | 0.005 | 0.013 | |
| createInterventions | 0.332 | 0.013 | 0.349 | |
| createUserVars | 0.487 | 0.019 | 0.509 | |
| evalAllGenotypes | 0.239 | 0.015 | 0.255 | |
| example-missing-drivers | 0.262 | 0.022 | 0.288 | |
| examplePosets | 0.283 | 0.008 | 0.294 | |
| examplesFitnessEffects | 0.040 | 0.003 | 0.044 | |
| freq-dep-simul-examples | 0.010 | 0.002 | 0.012 | |
| mcfLs | 0.000 | 0.000 | 0.001 | |
| oncoSimulIndiv | 1.241 | 0.223 | 1.423 | |
| plot.fitnessEffects | 0.275 | 0.028 | 0.309 | |
| plot.oncosimul | 0.415 | 0.025 | 0.446 | |
| plotClonePhylog | 1.775 | 0.089 | 1.880 | |
| plotFitnessLandscape | 1.310 | 0.035 | 1.357 | |
| plotPoset | 0.100 | 0.008 | 0.110 | |
| poset | 0.105 | 0.008 | 0.115 | |
| rfitness | 0.691 | 0.017 | 0.753 | |
| samplePop | 0.059 | 0.083 | 0.112 | |
| simOGraph | 0.072 | 0.014 | 0.090 | |
| to_Magellan | 0.222 | 0.073 | 0.415 | |
| vignette_pre_computed | 0.008 | 0.003 | 0.012 | |