Ramon Diaz-Uriarte
| Snapshot Date: 2024-08-06 14:00 -0400 (Tue, 06 Aug 2024) |
| git_url: https://git.bioconductor.org/packages/OncoSimulR |
| git_branch: devel |
| git_last_commit: abef61d |
| git_last_commit_date: 2024-07-30 05:28:04 -0400 (Tue, 30 Jul 2024) |
| Back to Multiple platform build/check report for BioC 3.20: simplified long |
|
This page was generated on 2024-08-07 11:45 -0400 (Wed, 07 Aug 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" | 4701 |
| palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" | 4400 |
| lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4469 |
| kjohnson3 | macOS 13.6.5 Ventura | arm64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4418 |
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4411 |
| 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 1441/2254 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| OncoSimulR 4.7.4 (landing page) Ramon Diaz-Uriarte
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino8 | 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 | OK | ERROR | OK | |||||||||
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | OK | ||||||||||
|
To the developers/maintainers of the OncoSimulR package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/OncoSimulR.git to reflect on this report. See Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. |
| Package: OncoSimulR |
| Version: 4.7.4 |
| 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_4.7.4.tar.gz |
| StartedAt: 2024-08-06 23:32:55 -0400 (Tue, 06 Aug 2024) |
| EndedAt: 2024-08-06 23:34:33 -0400 (Tue, 06 Aug 2024) |
| EllapsedTime: 98.1 seconds |
| RetCode: 1 |
| Status: ERROR |
| CheckDir: OncoSimulR.Rcheck |
| Warnings: NA |
##############################################################################
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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_4.7.4.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/OncoSimulR.Rcheck’
* using R version 4.4.1 (2024-06-14)
* using platform: aarch64-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 Ventura 13.6.7
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘OncoSimulR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘OncoSimulR’ version ‘4.7.4’
* 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 15.0.0 (clang-1500.1.0.2.5)’
* used C++ compiler: ‘Apple clang version 15.0.0 (clang-1500.1.0.2.5)’
* used SDK: ‘MacOSX11.3.sdk’
* checking installed package size ... NOTE
installed size is 9.8Mb
sub-directories of 1Mb or more:
libs 8.4Mb
* 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 ... OK
* 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 $(LAPACK_LIBS) ... OK
* checking use of PKG_*FLAGS in Makefiles ... OK
* checking include directives in Makefiles ... OK
* checking compiled code ... NOTE
Note: information on .o files is not available
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’
ERROR
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
}`: argument is of length zero
Backtrace:
▆
1. ├─base::colSums(OncoSimulR:::geneCounts(bb)) at test.per-gene-mutation-rates.R:397:9
2. │ └─base::is.data.frame(x)
3. └─OncoSimulR:::geneCounts(bb)
4. ├─base::do.call(rbind, lapply(x, function(z) get.gene.counts(z)$counts))
5. └─base::lapply(x, function(z) get.gene.counts(z)$counts)
6. └─OncoSimulR (local) FUN(X[[i]], ...)
7. └─OncoSimulR:::get.gene.counts(z)
8. └─OncoSimulR:::get.the.time.for.sample(x, timeSample, NULL)
[ FAIL 10 | WARN 34 | SKIP 7 | PASS 8403 ]
Error: Test failures
Execution halted
* 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: 1 ERROR, 2 NOTEs
See
‘/Users/biocbuild/bbs-3.20-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
###
##############################################################################
##############################################################################
* installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library’
* installing *source* package ‘OncoSimulR’ ...
** using staged installation
** libs
using C compiler: ‘Apple clang version 15.0.0 (clang-1500.1.0.2.5)’
using C++ compiler: ‘Apple clang version 15.0.0 (clang-1500.1.0.2.5)’
using SDK: ‘MacOSX11.3.sdk’
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c FitnessLandscape/gamma.c -o FitnessLandscape/gamma.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c FitnessLandscape/landscape.c -o FitnessLandscape/landscape.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c FitnessLandscape/random.c -o FitnessLandscape/random.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c FitnessLandscape/sort.c -o FitnessLandscape/sort.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c FitnessLandscape/chain.c -o FitnessLandscape/chain.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c FitnessLandscape/input.c -o FitnessLandscape/input.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c FitnessLandscape/genotypes.c -o FitnessLandscape/genotypes.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/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 arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c FitnessLandscape/calculus.c -o FitnessLandscape/calculus.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c FitnessLandscape/vector.c -o FitnessLandscape/vector.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c FitnessLandscape/generalized_chain.c -o FitnessLandscape/generalized_chain.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c FitnessLandscape/LinearAlgebra.c -o FitnessLandscape/LinearAlgebra.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/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;
^
FitnessLandscape/summary_statistics.c:673:6: warning: variable 'nbBl' set but not used [-Wunused-but-set-variable]
int nbBl=1;
^
2 warnings generated.
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c FitnessLandscape/epistasis_type.c -o FitnessLandscape/epistasis_type.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c FitnessLandscape/decomposition.c -o FitnessLandscape/decomposition.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c FitnessLandscape/models.c -o FitnessLandscape/models.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/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 arm64 -O -Wall -o fl_statistics -I/FitnessLandscape/. -L. FitnessLandscape/main_fl_statistics.c -llandscape -lm;
clang -arch arm64 -O -Wall -o fl_generate -I/FitnessLandscape/. -L. FitnessLandscape/main_fl_generate.c -llandscape -lm;
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c OncoSimulR_init.c -o OncoSimulR_init.o
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c RcppExports.cpp -o RcppExports.o
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/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 arm64 -std=gnu++17 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/arm64/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-arm64/Resources/library/00LOCK-OncoSimulR/00new/OncoSimulR
[1] ""
Installing fl_statistics fl_generate to /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/00LOCK-OncoSimulR/00new/OncoSimulR/exec
Installing library OncoSimulR.so to /Library/Frameworks/R.framework/Versions/4.4-arm64/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.fail
R version 4.4.1 (2024-06-14) -- "Race for Your Life"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: aarch64-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 Tue Aug 6 23:33:22 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 Aug 6 23:33:22 2024
Took 0.14
Starting LOD_POM at Tue Aug 6 23:33:22 2024
Ending LOD_POM at Tue Aug 6 23:33:26 2024
Took 3.42
Starting test.Z-all-fitness at Tue Aug 6 23:33:26 2024
Ending test.Z-all-fitness at Tue Aug 6 23:33:26 2024
Took 0.03
Starting test.Z-driver-counts at Tue Aug 6 23:33:26 2024
Ending test.Z-driver-counts at Tue Aug 6 23:33:26 2024
Took 0.04
Starting test.Z-fixation at Tue Aug 6 23:33:26 2024
Ending test.Z-fixation at Tue Aug 6 23:33:26 2024
Took 0.1
Starting test.Z-magellan at Tue Aug 6 23:33:26 2024
Ended test.Z-magellan at Tue Aug 6 23:33:27 2024
Starting test.Z-mutator at Tue Aug 6 23:33:27 2024
Ending test.Z-mutator at Tue Aug 6 23:33:27 2024
Took 0.1
Starting test.Z-mutatorFDF at Tue Aug 6 23:33:27 2024
Ending test.Z-mutatorFDF at Tue Aug 6 23:33:27 2024
Took 0.03
Starting test.Z-oncoSimulIndiv at Tue Aug 6 23:33:27 2024
Ending test.Z-oncoSimulIndiv at Tue Aug 6 23:33:27 2024
Took 0.16
Starting test.Z-oncoSimulIndivConstant at Tue Aug 6 23:33:27 2024
Ending test.Z-oncoSimulIndivConstant at Tue Aug 6 23:33:28 2024
Took 0.65
Starting test.Z-oncoSimulIndivDeath at Tue Aug 6 23:33:28 2024
Ending test.Z-oncoSimulIndivDeath at Tue Aug 6 23:33:28 2024
Took 0.29
Starting test.Z-oncoSimulIndivFDF at Tue Aug 6 23:33:28 2024
Hitted wall time. Exiting.
Hitting wall time is regarded as an error.
Ending test.Z-oncoSimulIndivFDF at Tue Aug 6 23:33:29 2024
Took 0.32
Starting test.Z-rfitness-landscape at Tue Aug 6 23:33:29 2024
Ending test.Z-rfitness-landscape at Tue Aug 6 23:33:29 2024
Took 0.07
Starting Z-sample-only-last tests Tue Aug 6 23:33:29 2024
Ending Z-sample-only-last tests Tue Aug 6 23:33:29 2024
Took 0
Starting Z-total-present-drivers tests Tue Aug 6 23:33:29 2024
Ending Z-total-present-drivers tests Tue Aug 6 23:33:29 2024
Took 0.23
Dummy empty test Tue Aug 6 23:33:29 2024
Starting accessible_genotypes at Tue Aug 6 23:33:29 2024
Ending accessible_genotypes at Tue Aug 6 23:33:31 2024
Took 2.09
Starting all fitness at Tue Aug 6 23:33:31 2024
Ending all-fitness at Tue Aug 6 23:33:32 2024
Took 1.51
Starting test.allFitnessEffectsFDF at Tue Aug 6 23:33:32 2024
Ending test.allFitnessEffectsFDF at Tue Aug 6 23:33:32 2024
Took 0.03
Starting test.allFitnessEffectsDeath at Tue Aug 6 23:33:32 2024
Ending test.allFitnessEffectsDeath at Tue Aug 6 23:33:33 2024
Took 0.11
Starting test.allFitnessEffectsFDF at Tue Aug 6 23:33:33 2024
Ending test.allFitnessEffectsFDF at Tue Aug 6 23:33:33 2024
Took 0.11
Starting driverCounts at Tue Aug 6 23:33:33 2024
Ending driverCounts at Tue Aug 6 23:33:36 2024
Took 2.98
Starting epist-order-modules at Tue Aug 6 23:33:36 2024
Ending epist-order-modules at Tue Aug 6 23:33:36 2024
Took 0.02
Starting test.evaluatingGenotypesDeath at Tue Aug 6 23:33:36 2024
Ending test.evaluatingGenotypesDeath at Tue Aug 6 23:33:36 2024
Took 0.06
Starting test.evaluatingGenotypesFDF at Tue Aug 6 23:33:36 2024
Ending test.evaluatingGenotypesFDF at Tue Aug 6 23:33:36 2024
Took 0.05
Starting exercise-plotting-code at Tue Aug 6 23:33:36 2024
Ending exercise-plotting-code at Tue Aug 6 23:33:37 2024
Took 1.03
Starting exercise-rfitness at Tue Aug 6 23:33:37 2024
Ending exercise-rfitness at Tue Aug 6 23:33:39 2024
Took 2.62
Starting to_Magella at Tue Aug 6 23:33:39 2024
Ending to_Magella at Tue Aug 6 23:33:39 2024
Took 0.01
Starting fitness preds at Tue Aug 6 23:33:39 2024
Observed vs expected, case III
ERROR: Algo 2: (1.0 - pe/pm) > 1.0
Unrecoverable exception: Algo 2: 1 - pe/pm > 1. Aborting.
ERROR: Algo 2: (1.0 - pe/pm) > 1.0
Unrecoverable exception: Algo 2: 1 - pe/pm > 1. Aborting.
ERROR: Algo 2: (1.0 - pe/pm) > 1.0
Unrecoverable exception: Algo 2: 1 - pe/pm > 1. Aborting.
ERROR: Algo 2: (1.0 - pe/pm) > 1.0
Unrecoverable exception: Algo 2: 1 - pe/pm > 1. Aborting.
ERROR: Algo 2: (1.0 - pe/pm) > 1.0
Unrecoverable exception: Algo 2: 1 - pe/pm > 1. Aborting.
ERROR: Algo 2: (1.0 - pe/pm) > 1.0
Unrecoverable exception: Algo 2: 1 - pe/pm > 1. Aborting.
ERROR: Algo 2: (1.0 - pe/pm) > 1.0
Unrecoverable exception: Algo 2: 1 - pe/pm > 1. Aborting.
ERROR: Algo 2: (1.0 - pe/pm) > 1.0
Unrecoverable exception: Algo 2: 1 - pe/pm > 1. Aborting.
ERROR: Algo 2: (1.0 - pe/pm) > 1.0
Unrecoverable exception: Algo 2: 1 - pe/pm > 1. Aborting.
ERROR: Algo 2: (1.0 - pe/pm) > 1.0
Unrecoverable exception: Algo 2: 1 - pe/pm > 1. Aborting.
ERROR: Algo 2: (1.0 - pe/pm) > 1.0
Unrecoverable exception: Algo 2: 1 - pe/pm > 1. Aborting.
ERROR: Algo 2: (1.0 - pe/pm) > 1.0
Unrecoverable exception: Algo 2: 1 - pe/pm > 1. Aborting.
ERROR: Algo 2: (1.0 - pe/pm) > 1.0
Unrecoverable exception: Algo 2: 1 - pe/pm > 1. Aborting.
ERROR: Algo 2: (1.0 - pe/pm) > 1.0
Unrecoverable exception: Algo 2: 1 - pe/pm > 1. Aborting.
ERROR: Algo 2: (1.0 - pe/pm) > 1.0
Unrecoverable exception: Algo 2: 1 - pe/pm > 1. Aborting.
ERROR: Algo 2: (1.0 - pe/pm) > 1.0
Unrecoverable exception: Algo 2: 1 - pe/pm > 1. Aborting.
ERROR: Algo 2: (1.0 - pe/pm) > 1.0
Unrecoverable exception: Algo 2: 1 - pe/pm > 1. Aborting.
ERROR: Algo 2: (1.0 - pe/pm) > 1.0
Unrecoverable exception: Algo 2: 1 - pe/pm > 1. Aborting.
ERROR: Algo 2: (1.0 - pe/pm) > 1.0
Unrecoverable exception: Algo 2: 1 - pe/pm > 1. Aborting.
ERROR: Algo 2: (1.0 - pe/pm) > 1.0
Unrecoverable exception: Algo 2: 1 - pe/pm > 1. Aborting.
ERROR: Algo 2: (1.0 - pe/pm) > 1.0
Unrecoverable exception: Algo 2: 1 - pe/pm > 1. Aborting.
ERROR: Algo 2: (1.0 - pe/pm) > 1.0
Unrecoverable exception: Algo 2: 1 - pe/pm > 1. Aborting.
ERROR: Algo 2: (1.0 - pe/pm) > 1.0
Unrecoverable exception: Algo 2: 1 - pe/pm > 1. Aborting.
ERROR: Algo 2: (1.0 - pe/pm) > 1.0
Unrecoverable exception: Algo 2: 1 - pe/pm > 1. Aborting.
ERROR: Algo 2: (1.0 - pe/pm) > 1.0
Unrecoverable exception: Algo 2: 1 - pe/pm > 1. Aborting.
ERROR: Algo 2: (1.0 - pe/pm) > 1.0
Unrecoverable exception: Algo 2: 1 - pe/pm > 1. Aborting.
ERROR: Algo 2: (1.0 - pe/pm) > 1.0
Unrecoverable exception: Algo 2: 1 - pe/pm > 1. Aborting.
ERROR: Algo 2: (1.0 - pe/pm) > 1.0
Unrecoverable exception: Algo 2: 1 - pe/pm > 1. Aborting.
ERROR: Algo 2: (1.0 - pe/pm) > 1.0
Unrecoverable exception: Algo 2: 1 - pe/pm > 1. Aborting.
ERROR: Algo 2: (1.0 - pe/pm) > 1.0
Unrecoverable exception: Algo 2: 1 - pe/pm > 1. Aborting.
ERROR: Algo 2: (1.0 - pe/pm) > 1.0
Unrecoverable exception: Algo 2: 1 - pe/pm > 1. Aborting.
ERROR: Algo 2: (1.0 - pe/pm) > 1.0
Unrecoverable exception: Algo 2: 1 - pe/pm > 1. Aborting.
ERROR: Algo 2: (1.0 - pe/pm) > 1.0
Unrecoverable exception: Algo 2: 1 - pe/pm > 1. Aborting.
ERROR: Algo 2: (1.0 - pe/pm) > 1.0
Unrecoverable exception: Algo 2: 1 - pe/pm > 1. Aborting.
ERROR: Algo 2: (1.0 - pe/pm) > 1.0
Unrecoverable exception: Algo 2: 1 - pe/pm > 1. Aborting.
ERROR: Algo 2: (1.0 - pe/pm) > 1.0
Unrecoverable exception: Algo 2: 1 - pe/pm > 1. Aborting.
ERROR: Algo 2: (1.0 - pe/pm) > 1.0
Unrecoverable exception: Algo 2: 1 - pe/pm > 1. Aborting.
ERROR: Algo 2: (1.0 - pe/pm) > 1.0
Unrecoverable exception: Algo 2: 1 - pe/pm > 1. Aborting.
ERROR: Algo 2: (1.0 - pe/pm) > 1.0
Unrecoverable exception: Algo 2: 1 - pe/pm > 1. Aborting.
ERROR: Algo 2: (1.0 - pe/pm) > 1.0
Unrecoverable exception: Algo 2: 1 - pe/pm > 1. Aborting.
ERROR: Algo 2: (1.0 - pe/pm) > 1.0
Unrecoverable exception: Algo 2: 1 - pe/pm > 1. Aborting.
ERROR: Algo 2: (1.0 - pe/pm) > 1.0
Unrecoverable exception: Algo 2: 1 - pe/pm > 1. Aborting.
ERROR: Algo 2: (1.0 - pe/pm) > 1.0
Unrecoverable exception: Algo 2: 1 - pe/pm > 1. Aborting.
ERROR: Algo 2: (1.0 - pe/pm) > 1.0
Unrecoverable exception: Algo 2: 1 - pe/pm > 1. Aborting.
ERROR: Algo 2: (1.0 - pe/pm) > 1.0
Unrecoverable exception: Algo 2: 1 - pe/pm > 1. Aborting.
ERROR: Algo 2: (1.0 - pe/pm) > 1.0
Unrecoverable exception: Algo 2: 1 - pe/pm > 1. Aborting.
ERROR: Algo 2: (1.0 - pe/pm) > 1.0
Unrecoverable exception: Algo 2: 1 - pe/pm > 1. Aborting.
ERROR: Algo 2: (1.0 - pe/pm) > 1.0
Unrecoverable exception: Algo 2: 1 - pe/pm > 1. Aborting.
ERROR: Algo 2: (1.0 - pe/pm) > 1.0
Unrecoverable exception: Algo 2: 1 - pe/pm > 1. Aborting.
ERROR: Algo 2: (1.0 - pe/pm) > 1.0
Unrecoverable exception: Algo 2: 1 - pe/pm > 1. Aborting.
ERROR: Algo 2: (1.0 - pe/pm) > 1.0
Unrecoverable exception: Algo 2: 1 - pe/pm > 1. Aborting.
ERROR: Algo 2: (1.0 - pe/pm) > 1.0
Unrecoverable exception: Algo 2: 1 - pe/pm > 1. Aborting.
ERROR: Algo 2: (1.0 - pe/pm) > 1.0
Unrecoverable exception: Algo 2: 1 - pe/pm > 1. Aborting.
ERROR: Algo 2: (1.0 - pe/pm) > 1.0
Unrecoverable exception: Algo 2: 1 - pe/pm > 1. Aborting.
ERROR: Algo 2: (1.0 - pe/pm) > 1.0
Unrecoverable exception: Algo 2: 1 - pe/pm > 1. Aborting.
ERROR: Algo 2: (1.0 - pe/pm) > 1.0
Unrecoverable exception: Algo 2: 1 - pe/pm > 1. Aborting.
ERROR: Algo 2: (1.0 - pe/pm) > 1.0
Unrecoverable exception: Algo 2: 1 - pe/pm > 1. Aborting.
ERROR: Algo 2: (1.0 - pe/pm) > 1.0
Unrecoverable exception: Algo 2: 1 - pe/pm > 1. Aborting.
ERROR: Algo 2: (1.0 - pe/pm) > 1.0
Unrecoverable exception: Algo 2: 1 - pe/pm > 1. Aborting.
ERROR: Algo 2: (1.0 - pe/pm) > 1.0
Unrecoverable exception: Algo 2: 1 - pe/pm > 1. Aborting.
ERROR: Algo 2: (1.0 - pe/pm) > 1.0
Unrecoverable exception: Algo 2: 1 - pe/pm > 1. Aborting.
ERROR: Algo 2: (1.0 - pe/pm) > 1.0
Unrecoverable exception: Algo 2: 1 - pe/pm > 1. Aborting.
ERROR: Algo 2: (1.0 - pe/pm) > 1.0
Unrecoverable exception: Algo 2: 1 - pe/pm > 1. Aborting.
ERROR: Algo 2: (1.0 - pe/pm) > 1.0
Unrecoverable exception: Algo 2: 1 - pe/pm > 1. Aborting.
ERROR: Algo 2: (1.0 - pe/pm) > 1.0
Unrecoverable exception: Algo 2: 1 - pe/pm > 1. Aborting.
ERROR: Algo 2: (1.0 - pe/pm) > 1.0
Unrecoverable exception: Algo 2: 1 - pe/pm > 1. Aborting.
ERROR: Algo 2: (1.0 - pe/pm) > 1.0
Unrecoverable exception: Algo 2: 1 - pe/pm > 1. Aborting.
ERROR: Algo 2: (1.0 - pe/pm) > 1.0
Unrecoverable exception: Algo 2: 1 - pe/pm > 1. Aborting.
ERROR: Algo 2: (1.0 - pe/pm) > 1.0
Unrecoverable exception: Algo 2: 1 - pe/pm > 1. Aborting.
ERROR: Algo 2: (1.0 - pe/pm) > 1.0
Unrecoverable exception: Algo 2: 1 - pe/pm > 1. Aborting.
ERROR: Algo 2: (1.0 - pe/pm) > 1.0
Unrecoverable exception: Algo 2: 1 - pe/pm > 1. Aborting.
ERROR: Algo 2: (1.0 - pe/pm) > 1.0
Unrecoverable exception: Algo 2: 1 - pe/pm > 1. Aborting.
ERROR: Algo 2: (1.0 - pe/pm) > 1.0
Unrecoverable exception: Algo 2: 1 - pe/pm > 1. Aborting.
ERROR: Algo 2: (1.0 - pe/pm) > 1.0
Unrecoverable exception: Algo 2: 1 - pe/pm > 1. Aborting.
ERROR: Algo 2: (1.0 - pe/pm) > 1.0
Unrecoverable exception: Algo 2: 1 - pe/pm > 1. Aborting.
ERROR: Algo 2: (1.0 - pe/pm) > 1.0
Unrecoverable exception: Algo 2: 1 - pe/pm > 1. Aborting.
ERROR: Algo 2: (1.0 - pe/pm) > 1.0
Unrecoverable exception: Algo 2: 1 - pe/pm > 1. Aborting.
ERROR: Algo 2: (1.0 - pe/pm) > 1.0
Unrecoverable exception: Algo 2: 1 - pe/pm > 1. Aborting.
ERROR: Algo 2: (1.0 - pe/pm) > 1.0
Unrecoverable exception: Algo 2: 1 - pe/pm > 1. Aborting.
ERROR: Algo 2: (1.0 - pe/pm) > 1.0
Unrecoverable exception: Algo 2: 1 - pe/pm > 1. Aborting.
ERROR: Algo 2: (1.0 - pe/pm) > 1.0
Unrecoverable exception: Algo 2: 1 - pe/pm > 1. Aborting.
ERROR: Algo 2: (1.0 - pe/pm) > 1.0
Unrecoverable exception: Algo 2: 1 - pe/pm > 1. Aborting.
ERROR: Algo 2: (1.0 - pe/pm) > 1.0
Unrecoverable exception: Algo 2: 1 - pe/pm > 1. Aborting.
ERROR: Algo 2: (1.0 - pe/pm) > 1.0
Unrecoverable exception: Algo 2: 1 - pe/pm > 1. Aborting.
ERROR: Algo 2: (1.0 - pe/pm) > 1.0
Unrecoverable exception: Algo 2: 1 - pe/pm > 1. Aborting.
ERROR: Algo 2: (1.0 - pe/pm) > 1.0
Unrecoverable exception: Algo 2: 1 - pe/pm > 1. Aborting.
ERROR: Algo 2: (1.0 - pe/pm) > 1.0
Unrecoverable exception: Algo 2: 1 - pe/pm > 1. Aborting.
ERROR: Algo 2: (1.0 - pe/pm) > 1.0
Unrecoverable exception: Algo 2: 1 - pe/pm > 1. Aborting.
ERROR: Algo 2: (1.0 - pe/pm) > 1.0
Unrecoverable exception: Algo 2: 1 - pe/pm > 1. Aborting.
ERROR: Algo 2: (1.0 - pe/pm) > 1.0
Unrecoverable exception: Algo 2: 1 - pe/pm > 1. Aborting.
ERROR: Algo 2: (1.0 - pe/pm) > 1.0
Unrecoverable exception: Algo 2: 1 - pe/pm > 1. Aborting.
ERROR: Algo 2: (1.0 - pe/pm) > 1.0
Unrecoverable exception: Algo 2: 1 - pe/pm > 1. Aborting.
ERROR: Algo 2: (1.0 - pe/pm) > 1.0
Unrecoverable exception: Algo 2: 1 - pe/pm > 1. Aborting.
ERROR: Algo 2: (1.0 - pe/pm) > 1.0
Unrecoverable exception: Algo 2: 1 - pe/pm > 1. Aborting.
ERROR: Algo 2: (1.0 - pe/pm) > 1.0
Unrecoverable exception: Algo 2: 1 - pe/pm > 1. Aborting.
ERROR: Algo 2: (1.0 - pe/pm) > 1.0
Unrecoverable exception: Algo 2: 1 - pe/pm > 1. Aborting.
ERROR: Algo 2: (1.0 - pe/pm) > 1.0
Unrecoverable exception: Algo 2: 1 - pe/pm > 1. Aborting.
ERROR: Algo 2: (1.0 - pe/pm) > 1.0
Unrecoverable exception: Algo 2: 1 - pe/pm > 1. Aborting.
ERROR: Algo 2: (1.0 - pe/pm) > 1.0
Unrecoverable exception: Algo 2: 1 - pe/pm > 1. Aborting.
ERROR: Algo 2: (1.0 - pe/pm) > 1.0
Unrecoverable exception: Algo 2: 1 - pe/pm > 1. Aborting.
ERROR: Algo 2: (1.0 - pe/pm) > 1.0
Unrecoverable exception: Algo 2: 1 - pe/pm > 1. Aborting.
ERROR: Algo 2: (1.0 - pe/pm) > 1.0
Unrecoverable exception: Algo 2: 1 - pe/pm > 1. Aborting.
ERROR: Algo 2: (1.0 - pe/pm) > 1.0
Unrecoverable exception: Algo 2: 1 - pe/pm > 1. Aborting.
ERROR: Algo 2: (1.0 - pe/pm) > 1.0
Unrecoverable exception: Algo 2: 1 - pe/pm > 1. Aborting.
ERROR: Algo 2: (1.0 - pe/pm) > 1.0
Unrecoverable exception: Algo 2: 1 - pe/pm > 1. Aborting.
ERROR: Algo 2: (1.0 - pe/pm) > 1.0
Unrecoverable exception: Algo 2: 1 - pe/pm > 1. Aborting.
ERROR: Algo 2: (1.0 - pe/pm) > 1.0
Unrecoverable exception: Algo 2: 1 - pe/pm > 1. Aborting.
ERROR: Algo 2: (1.0 - pe/pm) > 1.0
Unrecoverable exception: Algo 2: 1 - pe/pm > 1. Aborting.
ERROR: Algo 2: (1.0 - pe/pm) > 1.0
Unrecoverable exception: Algo 2: 1 - pe/pm > 1. Aborting.
ERROR: Algo 2: (1.0 - pe/pm) > 1.0
Unrecoverable exception: Algo 2: 1 - pe/pm > 1. Aborting.
ERROR: Algo 2: (1.0 - pe/pm) > 1.0
Unrecoverable exception: Algo 2: 1 - pe/pm > 1. Aborting.
ERROR: Algo 2: (1.0 - pe/pm) > 1.0
Unrecoverable exception: Algo 2: 1 - pe/pm > 1. Aborting.
ERROR: Algo 2: (1.0 - pe/pm) > 1.0
Unrecoverable exception: Algo 2: 1 - pe/pm > 1. Aborting.
ERROR: Algo 2: (1.0 - pe/pm) > 1.0
Unrecoverable exception: Algo 2: 1 - pe/pm > 1. Aborting.
ERROR: Algo 2: (1.0 - pe/pm) > 1.0
Unrecoverable exception: Algo 2: 1 - pe/pm > 1. Aborting.
ERROR: Algo 2: (1.0 - pe/pm) > 1.0
Unrecoverable exception: Algo 2: 1 - pe/pm > 1. Aborting.
ERROR: Algo 2: (1.0 - pe/pm) > 1.0
Unrecoverable exception: Algo 2: 1 - pe/pm > 1. Aborting.
ERROR: Algo 2: (1.0 - pe/pm) > 1.0
Unrecoverable exception: Algo 2: 1 - pe/pm > 1. Aborting.
ERROR: Algo 2: (1.0 - pe/pm) > 1.0
Unrecoverable exception: Algo 2: 1 - pe/pm > 1. Aborting.
ERROR: Algo 2: (1.0 - pe/pm) > 1.0
Unrecoverable exception: Algo 2: 1 - pe/pm > 1. Aborting.
ERROR: Algo 2: (1.0 - pe/pm) > 1.0
Unrecoverable exception: Algo 2: 1 - pe/pm > 1. Aborting.
ERROR: Algo 2: (1.0 - pe/pm) > 1.0
Unrecoverable exception: Algo 2: 1 - pe/pm > 1. Aborting.
ERROR: Algo 2: (1.0 - pe/pm) > 1.0
ERROR: Algo 2: (1.0 - pe/pm) > 1.0
Unrecoverable exception: Algo 2: 1 - pe/pm > 1. Aborting.
Unrecoverable exception: Algo 2: 1 - pe/pm > 1. Aborting.
ERROR: Algo 2: (1.0 - pe/pm) > 1.0
Unrecoverable exception: Algo 2: 1 - pe/pm > 1. Aborting.
ERROR: Algo 2: (1.0 - pe/pm) > 1.0
Unrecoverable exception: Algo 2: 1 - pe/pm > 1. Aborting.
ERROR: Algo 2: (1.0 - pe/pm) > 1.0
Unrecoverable exception: Algo 2: 1 - pe/pm > 1. Aborting.
ERROR: Algo 2: (1.0 - pe/pm) > 1.0
Unrecoverable exception: Algo 2: 1 - pe/pm > 1. Aborting.
ERROR: Algo 2: (1.0 - pe/pm) > 1.0
Unrecoverable exception: Algo 2: 1 - pe/pm > 1. Aborting.
ERROR: Algo 2: (1.0 - pe/pm) > 1.0
Unrecoverable exception: Algo 2: 1 - pe/pm > 1. Aborting.
ERROR: Algo 2: (1.0 - pe/pm) > 1.0
Unrecoverable exception: Algo 2: 1 - pe/pm > 1. Aborting.
ERROR: Algo 2: (1.0 - pe/pm) > 1.0
Unrecoverable exception: Algo 2: 1 - pe/pm > 1. Aborting.
ERROR: Algo 2: (1.0 - pe/pm) > 1.0
Unrecoverable exception: Algo 2: 1 - pe/pm > 1. Aborting.
ERROR: Algo 2: (1.0 - pe/pm) > 1.0
Unrecoverable exception: Algo 2: 1 - pe/pm > 1. Aborting.
ERROR: Algo 2: (1.0 - pe/pm) > 1.0
Unrecoverable exception: Algo 2: 1 - pe/pm > 1. Aborting.
ERROR: Algo 2: (1.0 - pe/pm) > 1.0
Unrecoverable exception: Algo 2: 1 - pe/pm > 1. Aborting.
ERROR: Algo 2: (1.0 - pe/pm) > 1.0
Unrecoverable exception: Algo 2: 1 - pe/pm > 1. Aborting.
ERROR: Algo 2: (1.0 - pe/pm) > 1.0
Unrecoverable exception: Algo 2: 1 - pe/pm > 1. Aborting.
ERROR: Algo 2: (1.0 - pe/pm) > 1.0
Unrecoverable exception: Algo 2: 1 - pe/pm > 1. Aborting.
Ending fitness preds long at Tue Aug 6 23:33:42 2024
Took 2.38
Starting fixation at Tue Aug 6 23:33:42 2024
Ending fixation at Tue Aug 6 23:33:48 2024
Took 5.65
Starting test.flfast-additional.R test at Tue Aug 6 23:33:48 2024
Ending test.flfast-additional.R test at Tue Aug 6 23:33:48 2024
Took 0.36
Starting test.flfast-mutator.R test at Tue Aug 6 23:33:48 2024
Finished test.flfast-mutator.R test at Tue Aug 6 23:33:48 2024
Took 0.36
Starting genotFitness at Tue Aug 6 23:33:48 2024
Ending genotFitness at Tue Aug 6 23:33:48 2024
Took 0.06
Starting genot_fitness_to_epistasis at Tue Aug 6 23:33:48 2024
Ending genot_fitness_to_epistasis at Tue Aug 6 23:33:48 2024
Took 0.01
Starting init-mutant tests Tue Aug 6 23:33:48 2024
ERROR: Algo 2: (1.0 - pe/pm) > 1.0
Unrecoverable exception: Algo 2: 1 - pe/pm > 1. Aborting.
ERROR: Algo 2: (1.0 - pe/pm) > 1.0
Unrecoverable exception: Algo 2: 1 - pe/pm > 1. Aborting.
ERROR: Algo 2: (1.0 - pe/pm) > 1.0
Unrecoverable exception: Algo 2: 1 - pe/pm > 1. Aborting.
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 Aug 6 23:33:50 2024
Took 1.94
Starting interventions tests Tue Aug 6 23:33:50 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] 0.54 0.54 0.54
[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
ERROR: Algo 2: (1.0 - pe/pm) > 1.0
Unrecoverable exception: Algo 2: 1 - pe/pm > 1. Aborting.
Init Mutant with birth == 1.0
ERROR: Algo 2: (1.0 - pe/pm) > 1.0
Unrecoverable exception: Algo 2: 1 - pe/pm > 1. Aborting.
[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 Aug 6 23:33:51 2024
Took 1.09
Starting test.magellan at Tue Aug 6 23:33:51 2024
Ending test.magellan at Tue Aug 6 23:33:51 2024
Took 0.07
Starting test.modules-root-no-root at Tue Aug 6 23:33:51 2024
Ending test.modules-root-no-root at Tue Aug 6 23:33:51 2024
Took 0.02
Starting at mutPropGrowth Tue Aug 6 23:33:51 2024
ERROR: Algo 2: (1.0 - pe/pm) > 1.0
Unrecoverable exception: Algo 2: 1 - pe/pm > 1. Aborting.
ERROR: Algo 2: (1.0 - pe/pm) > 1.0
Unrecoverable exception: Algo 2: 1 - pe/pm > 1. Aborting.
Ended test.mutPropGrowth: Tue Aug 6 23:33:53 2024
Took 1.76
Starting test.mutator-oncoSimulSample.R test at Tue Aug 6 23:33:53 2024
Finished test.mutator-oncoSimulSample.R test at Tue Aug 6 23:33:55 2024
Took 2.17 seconds
Starting test.mutator.R test at Tue Aug 6 23:33:55 2024[1] 1.685204e-10
[1] 1.608444e-13
Finished test.mutator.R test at Tue Aug 6 23:34:00 2024
Took 5.04
Starting test.mutatorFDF.R test at Tue Aug 6 23:34:00 2024
Starting test.no-v1 at Tue Aug 6 23:34:01 2024
Ending test.no-v1 at Tue Aug 6 23:34:01 2024
Took 0
Starting oncoSimulIndiv-miscell tests Tue Aug 6 23:34:01 2024
Ending oncoSimulIndiv-miscell tests Tue Aug 6 23:34:03 2024
Took 2.52
Starting oncoSimulSample-failures tests Tue Aug 6 23:34:03 2024
Ending oncoSimulSample-failures tests Tue Aug 6 23:34:07 2024
Took 3.43
Starting oncoSimulSample-limits tests Tue Aug 6 23:34:07 2024
Ending oncoSimulSample-limits tests Tue Aug 6 23:34:07 2024
Took 0.02
Starting per-gene-mutation rates at Tue Aug 6 23:34:07 2024
ERROR: Algo 2: (1.0 - pe/pm) > 1.0
Unrecoverable exception: Algo 2: 1 - pe/pm > 1. Aborting.
ERROR: Algo 2: (1.0 - pe/pm) > 1.0
Unrecoverable exception: Algo 2: 1 - pe/pm > 1. Aborting.
ERROR: Algo 2: (1.0 - pe/pm) > 1.0
Unrecoverable exception: Algo 2: 1 - pe/pm > 1. Aborting.
ERROR: Algo 2: (1.0 - pe/pm) > 1.0
Unrecoverable exception: Algo 2: 1 - pe/pm > 1. Aborting.
ERROR: Algo 2: (1.0 - pe/pm) > 1.0
Unrecoverable exception: Algo 2: 1 - pe/pm > 1. Aborting.
ERROR: Algo 2: (1.0 - pe/pm) > 1.0
Unrecoverable exception: Algo 2: 1 - pe/pm > 1. Aborting.
ERROR: Algo 2: (1.0 - pe/pm) > 1.0
Unrecoverable exception: Algo 2: 1 - pe/pm > 1. Aborting.
ERROR: Algo 2: (1.0 - pe/pm) > 1.0
Unrecoverable exception: Algo 2: 1 - pe/pm > 1. Aborting.
ERROR: Algo 2: (1.0 - pe/pm) > 1.0
Unrecoverable exception: Algo 2: 1 - pe/pm > 1. Aborting.
ERROR: Algo 2: (1.0 - pe/pm) > 1.0
Unrecoverable exception: Algo 2: 1 - pe/pm > 1. Aborting.
ERROR: Algo 2: (1.0 - pe/pm) > 1.0
Unrecoverable exception: Algo 2: 1 - pe/pm > 1. Aborting.
ERROR: Algo 2: (1.0 - pe/pm) > 1.0
Unrecoverable exception: Algo 2: 1 - pe/pm > 1. Aborting.
ERROR: Algo 2: (1.0 - pe/pm) > 1.0
Unrecoverable exception: Algo 2: 1 - pe/pm > 1. Aborting.
ERROR: Algo 2: (1.0 - pe/pm) > 1.0
Unrecoverable exception: Algo 2: 1 - pe/pm > 1. Aborting.
ERROR: Algo 2: (1.0 - pe/pm) > 1.0
Unrecoverable exception: Algo 2: 1 - pe/pm > 1. Aborting.
ERROR: Algo 2: (1.0 - pe/pm) > 1.0
Unrecoverable exception: Algo 2: 1 - pe/pm > 1. Aborting.
ERROR: Algo 2: (1.0 - pe/pm) > 1.0
Unrecoverable exception: Algo 2: 1 - pe/pm > 1. Aborting.
ERROR: Algo 2: (1.0 - pe/pm) > 1.0
Unrecoverable exception: Algo 2: 1 - pe/pm > 1. Aborting.
ERROR: Algo 2: (1.0 - pe/pm) > 1.0
Unrecoverable exception: Algo 2: 1 - pe/pm > 1. Aborting.
ERROR: Algo 2: (1.0 - pe/pm) > 1.0
Unrecoverable exception: Algo 2: 1 - pe/pm > 1. Aborting.
ERROR: Algo 2: (1.0 - pe/pm) > 1.0
Unrecoverable exception: Algo 2: 1 - pe/pm > 1. Aborting.
ERROR: Algo 2: (1.0 - pe/pm) > 1.0
Unrecoverable exception: Algo 2: 1 - pe/pm > 1. Aborting.
ERROR: Algo 2: (1.0 - pe/pm) > 1.0
Unrecoverable exception: Algo 2: 1 - pe/pm > 1. Aborting.
ERROR: Algo 2: (1.0 - pe/pm) > 1.0
Unrecoverable exception: Algo 2: 1 - pe/pm > 1. Aborting.
ERROR: Algo 2: (1.0 - pe/pm) > 1.0
Unrecoverable exception: Algo 2: 1 - pe/pm > 1. Aborting.
ERROR: Algo 2: (1.0 - pe/pm) > 1.0
Unrecoverable exception: Algo 2: 1 - pe/pm > 1. Aborting.
ERROR: Algo 2: (1.0 - pe/pm) > 1.0
Unrecoverable exception: Algo 2: 1 - pe/pm > 1. Aborting.
ERROR: Algo 2: (1.0 - pe/pm) > 1.0
Unrecoverable exception: Algo 2: 1 - pe/pm > 1. Aborting.
ERROR: Algo 2: (1.0 - pe/pm) > 1.0
Unrecoverable exception: Algo 2: 1 - pe/pm > 1. Aborting.
ERROR: Algo 2: (1.0 - pe/pm) > 1.0
Unrecoverable exception: Algo 2: 1 - pe/pm > 1. Aborting.
ERROR: Algo 2: (1.0 - pe/pm) > 1.0
Unrecoverable exception: Algo 2: 1 - pe/pm > 1. Aborting.
ERROR: Algo 2: (1.0 - pe/pm) > 1.0
Unrecoverable exception: Algo 2: 1 - pe/pm > 1. Aborting.
ERROR: Algo 2: (1.0 - pe/pm) > 1.0
Unrecoverable exception: Algo 2: 1 - pe/pm > 1. Aborting.
ERROR: Algo 2: (1.0 - pe/pm) > 1.0
Unrecoverable exception: Algo 2: 1 - pe/pm > 1. Aborting.
ERROR: Algo 2: (1.0 - pe/pm) > 1.0
Unrecoverable exception: Algo 2: 1 - pe/pm > 1. Aborting.
ERROR: Algo 2: (1.0 - pe/pm) > 1.0
Unrecoverable exception: Algo 2: 1 - pe/pm > 1. Aborting.
ERROR: Algo 2: (1.0 - pe/pm) > 1.0
Unrecoverable exception: Algo 2: 1 - pe/pm > 1. Aborting.
ERROR: Algo 2: (1.0 - pe/pm) > 1.0
Unrecoverable exception: Algo 2: 1 - pe/pm > 1. Aborting.
ERROR: Algo 2: (1.0 - pe/pm) > 1.0
Unrecoverable exception: Algo 2: 1 - pe/pm > 1. Aborting.
ERROR: Algo 2: (1.0 - pe/pm) > 1.0
Unrecoverable exception: Algo 2: 1 - pe/pm > 1. Aborting.
ERROR: Algo 2: (1.0 - pe/pm) > 1.0
Unrecoverable exception: Algo 2: 1 - pe/pm > 1. Aborting.
ERROR: Algo 2: (1.0 - pe/pm) > 1.0
Unrecoverable exception: Algo 2: 1 - pe/pm > 1. Aborting.
ERROR: Algo 2: (1.0 - pe/pm) > 1.0
Unrecoverable exception: Algo 2: 1 - pe/pm > 1. Aborting.
ERROR: Algo 2: (1.0 - pe/pm) > 1.0
Unrecoverable exception: Algo 2: 1 - pe/pm > 1. Aborting.
ERROR: Algo 2: (1.0 - pe/pm) > 1.0
Unrecoverable exception: Algo 2: 1 - pe/pm > 1. Aborting.
ERROR: Algo 2: (1.0 - pe/pm) > 1.0
Unrecoverable exception: Algo 2: 1 - pe/pm > 1. Aborting.
ERROR: Algo 2: (1.0 - pe/pm) > 1.0
Unrecoverable exception: Algo 2: 1 - pe/pm > 1. Aborting.
ERROR: Algo 2: (1.0 - pe/pm) > 1.0
Unrecoverable exception: Algo 2: 1 - pe/pm > 1. Aborting.
ERROR: Algo 2: (1.0 - pe/pm) > 1.0
Unrecoverable exception: Algo 2: 1 - pe/pm > 1. Aborting.
Ending per-gene-mutation rates at Tue Aug 6 23:34:15 2024
Took 8.57
Starting plotFitnessLandscape at Tue Aug 6 23:34:15 2024
Ending plotFitnessLandscape at Tue Aug 6 23:34:16 2024
Took 0.9
Starting poset-transformations tests Tue Aug 6 23:34:16 2024
Ending poset-transformations tests Tue Aug 6 23:34:19 2024
Took 3.11
Starting sample-prob Tue Aug 6 23:34:19 2024
[1] 7.340198e-28
[1] 1.003712e-09
[1] 3.936754e-10
[1] 1.163541e-11
[1] 3.133017e-12
[1] 4.767719e-11
[1] 2.273463e-12
[1] 1.584586e-14
[1] 1.201939e-09
[1] 8.85178e-10
[1] 2.967347e-10
[1] 1.700446e-09
Ending sample-prob tests Tue Aug 6 23:34:22 2024
Took 2.6
Starting samplePop tests Tue Aug 6 23:34:22 2024
ti set to DBL_MIN: spP.popSize = 1.00001e+08
Recoverable exception ti set to DBL_MIN. Rerunning.
Ending samplePop tests Tue Aug 6 23:34:23 2024
Took 1.74
Starting simuls-runs-examples tests Tue Aug 6 23:34:23 2024
Ending simuls-runs-examples tests Tue Aug 6 23:34:26 2024
Took 2.71
Starting user variable tests Tue Aug 6 23:34:26 2024
[1] "Checking user variable: user_var_1"
[1] "Checking rule: rule_1"
Ending user variable tests Tue Aug 6 23:34:26 2024
Took 0.03
Starting warning-mutPropGrowth tests Tue Aug 6 23:34:26 2024
Ending warning-mutPropGrowth tests Tue Aug 6 23:34:26 2024
Took 0.17
Starting wide2long tests Tue Aug 6 23:34:26 2024
Ending wide2long tests Tue Aug 6 23:34:26 2024
Took 0.07
[ FAIL 10 | WARN 34 | SKIP 7 | PASS 8403 ]
══ 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'
══ Failed tests ════════════════════════════════════════════════════════════════
── Failure ('test.Z-oncoSimulIndivDeath.R:404:3'): testing performance ─────────
osi7$NumClones not identical to 3.
target is NULL, current is numeric
── Failure ('test.Z-oncoSimulIndivDeath.R:406:3'): testing performance ─────────
osi7$TotalPopSize > 1e+08 is not TRUE
`actual`:
`expected`: TRUE
── Failure ('test.Z-oncoSimulIndivDeath.R:411:3'): testing performance ─────────
osi7$FinalTime > 1 is not TRUE
`actual`:
`expected`: TRUE
── Error ('test.fitness-preds.R:235:23'): Observed vs expected, case III ───────
Error in `t.test.default(log(x[2:(reps + 1)] + 1), mu = log(x[1] + 1))`: data are essentially constant
Backtrace:
▆
1. └─base::apply(...) at test.fitness-preds.R:234:9
2. └─OncoSimulR (local) FUN(newX[, i], ...)
3. ├─stats::t.test(log(x[2:(reps + 1)] + 1), mu = log(x[1] + 1)) at test.fitness-preds.R:235:23
4. └─stats:::t.test.default(...)
── Failure ('test.intervention.R:543:5'): 12. Intervening over 4 genotypes both over specific genotype and total population (McFL) | Trigger depends on N ──
sfd3_with_ints$pops.by.time[indexes, 2] not equal to floor(0.2 * sfd3_without_ints$pops.by.time[indexes, 2]).
target is NULL, current is numeric
── Failure ('test.intervention.R:545:5'): 12. Intervening over 4 genotypes both over specific genotype and total population (McFL) | Trigger depends on N ──
sfd3_with_ints$pops.by.time[indexes, 3] not equal to floor(0.42 * sfd3_without_ints$pops.by.time[indexes, 3]).
target is NULL, current is numeric
── Failure ('test.intervention.R:547:5'): 12. Intervening over 4 genotypes both over specific genotype and total population (McFL) | Trigger depends on N ──
sfd3_with_ints$pops.by.time[indexes, 4] not equal to floor(0.35 * sfd3_without_ints$pops.by.time[indexes, 4]).
target is NULL, current is numeric
── Failure ('test.intervention.R:549:5'): 12. Intervening over 4 genotypes both over specific genotype and total population (McFL) | Trigger depends on N ──
sfd3_with_ints$pops.by.time[indexes, 5] not equal to floor(0.125 * sfd3_without_ints$pops.by.time[indexes, 5]).
target is NULL, current is numeric
── Error ('test.mutPropGrowth.R:424:9'): mutPropGrowth diffs with s> 0, oncoSimulSample, McFL, stop on time ──
Error in `nca$popSummary[1:5, c(1:3, 8:9)]`: incorrect number of dimensions
── Error ('test.per-gene-mutation-rates.R:397:9'): McFL: Different freqs as they should be ordered when s and t > 1 ──
Error in `if (tmp$TotalPopSize == 0) {
warning(paste("Final population size is 0.", "Thus, there is nothing to sample with",
"sampling last. You will get NAs"))
the.time <- -99
} else {
the.time <- nrow(tmp$pops.by.time)
}`: argument is of length zero
Backtrace:
▆
1. ├─base::colSums(OncoSimulR:::geneCounts(bb)) at test.per-gene-mutation-rates.R:397:9
2. │ └─base::is.data.frame(x)
3. └─OncoSimulR:::geneCounts(bb)
4. ├─base::do.call(rbind, lapply(x, function(z) get.gene.counts(z)$counts))
5. └─base::lapply(x, function(z) get.gene.counts(z)$counts)
6. └─OncoSimulR (local) FUN(X[[i]], ...)
7. └─OncoSimulR:::get.gene.counts(z)
8. └─OncoSimulR:::get.the.time.for.sample(x, timeSample, NULL)
[ FAIL 10 | WARN 34 | SKIP 7 | PASS 8403 ]
Error: Test failures
Execution halted
OncoSimulR.Rcheck/OncoSimulR-Ex.timings
| name | user | system | elapsed | |
| OncoSimulWide2Long | 0.085 | 0.001 | 0.085 | |
| POM | 0.232 | 0.024 | 0.157 | |
| allFitnessEffects | 0.509 | 0.017 | 0.528 | |
| benchmarks | 0.003 | 0.001 | 0.004 | |
| createInterventions | 0.078 | 0.007 | 0.085 | |
| createUserVars | 0.117 | 0.015 | 0.131 | |
| evalAllGenotypes | 0.064 | 0.003 | 0.067 | |
| example-missing-drivers | 0.076 | 0.004 | 0.081 | |
| examplePosets | 0.068 | 0.001 | 0.070 | |
| examplesFitnessEffects | 0.012 | 0.002 | 0.013 | |
| freq-dep-simul-examples | 0.003 | 0.000 | 0.004 | |
| mcfLs | 0.000 | 0.000 | 0.001 | |
| oncoSimulIndiv | 0.329 | 0.067 | 0.383 | |
| plot.fitnessEffects | 0.070 | 0.013 | 0.083 | |
| plot.oncosimul | 0.164 | 0.006 | 0.170 | |
| plotClonePhylog | 0.587 | 0.020 | 0.607 | |
| plotFitnessLandscape | 0.309 | 0.006 | 0.316 | |
| plotPoset | 0.024 | 0.003 | 0.027 | |
| poset | 0.026 | 0.001 | 0.027 | |
| rfitness | 0.183 | 0.005 | 0.212 | |
| samplePop | 0.013 | 0.023 | 0.029 | |
| simOGraph | 0.016 | 0.007 | 0.023 | |
| to_Magellan | 0.060 | 0.025 | 0.111 | |
| vignette_pre_computed | 0.002 | 0.001 | 0.004 | |