| Back to Multiple platform build/check report for BioC 3.16: simplified long |
|
This page was generated on 2023-04-12 11:06:18 -0400 (Wed, 12 Apr 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 20.04.5 LTS) | x86_64 | 4.2.3 (2023-03-15) -- "Shortstop Beagle" | 4502 |
| palomino4 | Windows Server 2022 Datacenter | x64 | 4.2.3 (2023-03-15 ucrt) -- "Shortstop Beagle" | 4282 |
| lconway | macOS 12.5.1 Monterey | x86_64 | 4.2.3 (2023-03-15) -- "Shortstop Beagle" | 4310 |
| 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 | ||||
|
To the developers/maintainers of the OncoSimulR package: - Please 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 How and When does the builder pull? When will my changes propagate? for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 1398/2183 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| OncoSimulR 4.0.2 (landing page) Ramon Diaz-Uriarte
| nebbiolo2 | Linux (Ubuntu 20.04.5 LTS) / x86_64 | OK | OK | OK |  | ||||||||
| palomino4 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| lconway | macOS 12.5.1 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| Package: OncoSimulR |
| Version: 4.0.2 |
| 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_4.0.2.tar.gz |
| StartedAt: 2023-04-10 21:38:01 -0400 (Mon, 10 Apr 2023) |
| EndedAt: 2023-04-10 21:54:05 -0400 (Mon, 10 Apr 2023) |
| EllapsedTime: 963.8 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_4.0.2.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.16-bioc/meat/OncoSimulR.Rcheck’
* using R version 4.2.3 (2023-03-15)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘OncoSimulR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘OncoSimulR’ version ‘4.0.2’
* 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
* checking installed package size ... NOTE
installed size is 9.4Mb
sub-directories of 1Mb or more:
libs 8.0Mb
* 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 R 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’
OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: 2 NOTEs
See
‘/Users/biocbuild/bbs-3.16-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/4.2/Resources/library’
* installing *source* package ‘OncoSimulR’ ...
** using staged installation
** libs
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rcpp/include' -I/usr/local/include -fPIC -Wall -g -O2 -c FitnessLandscape/gamma.c -o FitnessLandscape/gamma.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rcpp/include' -I/usr/local/include -fPIC -Wall -g -O2 -c FitnessLandscape/landscape.c -o FitnessLandscape/landscape.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rcpp/include' -I/usr/local/include -fPIC -Wall -g -O2 -c FitnessLandscape/random.c -o FitnessLandscape/random.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rcpp/include' -I/usr/local/include -fPIC -Wall -g -O2 -c FitnessLandscape/sort.c -o FitnessLandscape/sort.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rcpp/include' -I/usr/local/include -fPIC -Wall -g -O2 -c FitnessLandscape/chain.c -o FitnessLandscape/chain.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rcpp/include' -I/usr/local/include -fPIC -Wall -g -O2 -c FitnessLandscape/input.c -o FitnessLandscape/input.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rcpp/include' -I/usr/local/include -fPIC -Wall -g -O2 -c FitnessLandscape/genotypes.c -o FitnessLandscape/genotypes.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rcpp/include' -I/usr/local/include -fPIC -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 -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rcpp/include' -I/usr/local/include -fPIC -Wall -g -O2 -c FitnessLandscape/calculus.c -o FitnessLandscape/calculus.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rcpp/include' -I/usr/local/include -fPIC -Wall -g -O2 -c FitnessLandscape/vector.c -o FitnessLandscape/vector.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rcpp/include' -I/usr/local/include -fPIC -Wall -g -O2 -c FitnessLandscape/generalized_chain.c -o FitnessLandscape/generalized_chain.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rcpp/include' -I/usr/local/include -fPIC -Wall -g -O2 -c FitnessLandscape/LinearAlgebra.c -o FitnessLandscape/LinearAlgebra.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rcpp/include' -I/usr/local/include -fPIC -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 -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rcpp/include' -I/usr/local/include -fPIC -Wall -g -O2 -c FitnessLandscape/epistasis_type.c -o FitnessLandscape/epistasis_type.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rcpp/include' -I/usr/local/include -fPIC -Wall -g -O2 -c FitnessLandscape/decomposition.c -o FitnessLandscape/decomposition.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rcpp/include' -I/usr/local/include -fPIC -Wall -g -O2 -c FitnessLandscape/models.c -o FitnessLandscape/models.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rcpp/include' -I/usr/local/include -fPIC -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 -mmacosx-version-min=10.13 -O -Wall -o fl_statistics -I/FitnessLandscape/. -L. FitnessLandscape/main_fl_statistics.c -llandscape -lm;
clang -mmacosx-version-min=10.13 -O -Wall -o fl_generate -I/FitnessLandscape/. -L. FitnessLandscape/main_fl_generate.c -llandscape -lm;
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rcpp/include' -I/usr/local/include -fPIC -Wall -g -O2 -c OncoSimulR_init.c -o OncoSimulR_init.o
clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rcpp/include' -I/usr/local/include -fPIC -Wall -g -O2 -c RcppExports.cpp -o RcppExports.o
clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rcpp/include' -I/usr/local/include -fPIC -Wall -g -O2 -c unity_osimul.cpp -o unity_osimul.o
In file included from unity_osimul.cpp:10:
./UnityOncoSimul/intervention_private_2.cpp:17:12: warning: variable 'totalPop' set but not used [-Wunused-but-set-variable]
double totalPop = 0.0;
^
1 warning generated.
clang++ -mmacosx-version-min=10.13 -std=gnu++14 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/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/4.2/Resources/library/00LOCK-OncoSimulR/00new/OncoSimulR
[1] ""
Installing fl_statistics fl_generate to /Library/Frameworks/R.framework/Versions/4.2/Resources/library/00LOCK-OncoSimulR/00new/OncoSimulR/exec
Installing library OncoSimulR.so to /Library/Frameworks/R.framework/Versions/4.2/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 4.2.3 (2023-03-15) -- "Shortstop Beagle"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin17.0 (64-bit)
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 Mon Apr 10 21:39:18 2023
exprtk parser error:
Error[00] Position: 00 Type: [ Syntax Error] Msg: ERR201 - Undefined symbol: 'n_2_3' Expression: n_2_3
exprtk parser error:
Error[00] Position: 00 Type: [ Syntax Error] Msg: ERR201 - Undefined symbol: 'f_2_3' Expression: f_2_3
Ending FDF-small-fitness-specs Mon Apr 10 21:39:19 2023
Took 0.38
Starting LOD_POM at Mon Apr 10 21:39:19 2023
Ending LOD_POM at Mon Apr 10 21:39:35 2023
Took 15.78
Starting test.Z-all-fitness at Mon Apr 10 21:39:35 2023
Ending test.Z-all-fitness at Mon Apr 10 21:39:35 2023
Took 0.1
Starting test.Z-driver-counts at Mon Apr 10 21:39:35 2023
Ending test.Z-driver-counts at Mon Apr 10 21:39:35 2023
Took 0.16
Starting test.Z-fixation at Mon Apr 10 21:39:35 2023
Ending test.Z-fixation at Mon Apr 10 21:39:35 2023
Took 0.6
Starting interventions tests Mon Apr 10 21:39:35 2023
[1] "Checking intervention: intOverBAffectsR"
[1] "Checking intervention: intOverTotPop"
Init Mutant with birth == 1.0
[1] "Checking intervention: intOverBAffectsR"
[1] "Checking intervention: intOverTotPop"
Init Mutant with birth == 1.0
Ending interventions tests Mon Apr 10 21:43:44 2023
Took 248.27
Starting test.Z-magellan at Mon Apr 10 21:43:44 2023
Ended test.Z-magellan at Mon Apr 10 21:43:47 2023
Starting test.Z-mutator at Mon Apr 10 21:43:47 2023
Ending test.Z-mutator at Mon Apr 10 21:43:47 2023
Took 0.58
Starting test.Z-mutatorFDF at Mon Apr 10 21:43:47 2023
Ending test.Z-mutatorFDF at Mon Apr 10 21:43:48 2023
Took 0.22
Starting test.Z-oncoSimulIndiv at Mon Apr 10 21:43:48 2023
Ending test.Z-oncoSimulIndiv at Mon Apr 10 21:43:51 2023
Took 3.36
Starting test.Z-oncoSimulIndivConstant at Mon Apr 10 21:43:51 2023
Ending test.Z-oncoSimulIndivConstant at Mon Apr 10 21:43:56 2023
Took 5.17
Starting test.Z-oncoSimulIndivDeath at Mon Apr 10 21:43:56 2023
Ending test.Z-oncoSimulIndivDeath at Mon Apr 10 21:43:59 2023
Took 3.06
Starting test.Z-oncoSimulIndivFDF at Mon Apr 10 21:43:59 2023
Hitted wall time. Exiting.
Hitting wall time is regarded as an error.
Ending test.Z-oncoSimulIndivFDF at Mon Apr 10 21:44:01 2023
Took 1.38
Starting test.Z-rfitness-landscape at Mon Apr 10 21:44:01 2023
Ending test.Z-rfitness-landscape at Mon Apr 10 21:44:01 2023
Took 0.23
Starting Z-sample-only-last tests Mon Apr 10 21:44:01 2023
Ending Z-sample-only-last tests Mon Apr 10 21:44:01 2023
Took 0.01
Starting Z-total-present-drivers tests Mon Apr 10 21:44:01 2023
Ending Z-total-present-drivers tests Mon Apr 10 21:44:03 2023
Took 1.94
Dummy empty test Mon Apr 10 21:44:03 2023
Starting accessible_genotypes at Mon Apr 10 21:44:03 2023
Ending accessible_genotypes at Mon Apr 10 21:44:09 2023
Took 6.13
Starting all fitness at Mon Apr 10 21:44:09 2023
Ending all-fitness at Mon Apr 10 21:44:14 2023
Took 4.82
Starting test.allFitnessEffectsFDF at Mon Apr 10 21:44:14 2023
Ending test.allFitnessEffectsFDF at Mon Apr 10 21:44:14 2023
Took 0.25
Starting test.allFitnessEffectsDeath at Mon Apr 10 21:44:14 2023
Ending test.allFitnessEffectsDeath at Mon Apr 10 21:44:15 2023
Took 0.7
Starting test.allFitnessEffectsFDF at Mon Apr 10 21:44:15 2023
Ending test.allFitnessEffectsFDF at Mon Apr 10 21:44:15 2023
Took 0.5
Starting driverCounts at Mon Apr 10 21:44:15 2023
Ending driverCounts at Mon Apr 10 21:44:36 2023
Took 20.58
Starting epist-order-modules at Mon Apr 10 21:44:36 2023
Ending epist-order-modules at Mon Apr 10 21:44:36 2023
Took 0.12
Starting test.evaluatingGenotypesDeath at Mon Apr 10 21:44:36 2023
Ending test.evaluatingGenotypesDeath at Mon Apr 10 21:44:36 2023
Took 0.35
Starting test.evaluatingGenotypesFDF at Mon Apr 10 21:44:36 2023
Ending test.evaluatingGenotypesFDF at Mon Apr 10 21:44:37 2023
Took 0.36
Starting exercise-plotting-code at Mon Apr 10 21:44:37 2023
Ending exercise-plotting-code at Mon Apr 10 21:44:50 2023
Took 13.42
Starting exercise-rfitness at Mon Apr 10 21:44:50 2023
Ending exercise-rfitness at Mon Apr 10 21:44:58 2023
Took 7.87
Starting to_Magella at Mon Apr 10 21:44:58 2023
Ending to_Magella at Mon Apr 10 21:44:58 2023
Took 0.03
Starting fitness preds at Mon Apr 10 21:44:58 2023
Observed vs expected, case III
done tries 1
Ending fitness preds long at Mon Apr 10 21:45:20 2023
Took 21.67
Starting fixation at Mon Apr 10 21:45:20 2023
Ending fixation at Mon Apr 10 21:45:50 2023
Took 30.24
Starting test.flfast-additional.R test at Mon Apr 10 21:45:50 2023
Ending test.flfast-additional.R test at Mon Apr 10 21:45:51 2023
Took 1.34
Starting test.flfast-mutator.R test at Mon Apr 10 21:45:51 2023
Finished test.flfast-mutator.R test at Mon Apr 10 21:45:56 2023
Took 4.53
Starting genotFitness at Mon Apr 10 21:45:56 2023
Ending genotFitness at Mon Apr 10 21:45:56 2023
Took 0.33
Starting genot_fitness_to_epistasis at Mon Apr 10 21:45:56 2023
Ending genot_fitness_to_epistasis at Mon Apr 10 21:45:56 2023
Took 0.06
Starting init-mutant tests Mon Apr 10 21:45:56 2023
exprtk parser error:
Error[00] Position: 18 Type: [ Syntax Error] Msg: ERR201 - Undefined symbol: 'f_2' Expression: 1.1 + 0.7*((f_1 + f_2) > 0.3)
Ending init-mutant tests Mon Apr 10 21:46:10 2023
Took 13.22
Starting interventions tests Mon Apr 10 21:46:10 2023
[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"
Init Mutant with birth == 1.0
[1] "Checking intervention: intOverA"
Init Mutant with birth == 1.0
[1] "Checking intervention: intOverTotPop"
[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
[1] "Checking intervention: intOverA"
[1] "Checking intervention: intOverB"
[1] "Checking intervention: intOverC"
[1] "Checking intervention: intOverD"
Init Mutant with birth == 1.0
[1] "Checking intervention: Bothering R strain, by reducing C"
[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 Mon Apr 10 21:51:20 2023
Took 310.55
Starting test.magellan at Mon Apr 10 21:51:20 2023
Ending test.magellan at Mon Apr 10 21:51:20 2023
Took 0.22
Starting test.modules-root-no-root at Mon Apr 10 21:51:20 2023
Ending test.modules-root-no-root at Mon Apr 10 21:51:20 2023
Took 0.06
Starting at mutPropGrowth Mon Apr 10 21:51:20 2023
Ended test.mutPropGrowth: Mon Apr 10 21:51:33 2023
Took 12.53
Starting test.mutator-oncoSimulSample.R test at Mon Apr 10 21:51:33 2023
Finished test.mutator-oncoSimulSample.R test at Mon Apr 10 21:51:45 2023
Took 12.01 seconds
Starting test.mutator.R test at Mon Apr 10 21:51:45 2023[1] 6.441038e-08
[1] 7.164288e-12
Finished test.mutator.R test at Mon Apr 10 21:52:04 2023
Took 18.52
Starting test.mutatorFDF.R test at Mon Apr 10 21:52:04 2023
Starting test.no-v1 at Mon Apr 10 21:52:04 2023
Ending test.no-v1 at Mon Apr 10 21:52:04 2023
Took 0.01
Starting oncoSimulIndiv-miscell tests Mon Apr 10 21:52:04 2023
Ending oncoSimulIndiv-miscell tests Mon Apr 10 21:52:16 2023
Took 11.92
Starting oncoSimulSample-failures tests Mon Apr 10 21:52:16 2023
Ending oncoSimulSample-failures tests Mon Apr 10 21:52:20 2023
Took 3.57
Starting oncoSimulSample-limits tests Mon Apr 10 21:52:20 2023
Ending oncoSimulSample-limits tests Mon Apr 10 21:52:20 2023
Took 0.05
Starting per-gene-mutation rates at Mon Apr 10 21:52:20 2023
Ending per-gene-mutation rates at Mon Apr 10 21:52:56 2023
Took 35.99
Starting plotFitnessLandscape at Mon Apr 10 21:52:56 2023
Ending plotFitnessLandscape at Mon Apr 10 21:52:58 2023
Took 2.37
Starting poset-transformations tests Mon Apr 10 21:52:58 2023
Ending poset-transformations tests Mon Apr 10 21:53:05 2023
Took 6.62
Starting sample-prob Mon Apr 10 21:53:05 2023
[1] 2.264915e-18
[1] 1.697811e-14
[1] 2.039985e-10
[1] 1.30848e-11
[1] 1.122885e-12
[1] 1.580282e-12
[1] 2.159284e-08
[1] 2.615321e-12
[1] 5.393202e-10
[1] 1.874727e-12
[1] 4.594593e-11
[1] 9.33857e-10
Ending sample-prob tests Mon Apr 10 21:53:15 2023
Took 10.57
Starting samplePop tests Mon Apr 10 21:53:15 2023
Ending samplePop tests Mon Apr 10 21:53:30 2023
Took 14.68
Starting simuls-runs-examples tests Mon Apr 10 21:53:30 2023
Ending simuls-runs-examples tests Mon Apr 10 21:53:49 2023
Took 18.82
Starting user variable tests Mon Apr 10 21:53:49 2023
[1] "Checking user variable: user_var_1"
[1] "Checking rule: rule_1"
Ending user variable tests Mon Apr 10 21:53:49 2023
Took 0.09
Starting warning-mutPropGrowth tests Mon Apr 10 21:53:49 2023
Ending warning-mutPropGrowth tests Mon Apr 10 21:53:50 2023
Took 0.8
Starting wide2long tests Mon Apr 10 21:53:50 2023
Ending wide2long tests Mon Apr 10 21:53:50 2023
Took 0.41
[ FAIL 0 | WARN 16 | SKIP 7 | PASS 12455 ]
══ Skipped tests ═══════════════════════════════════════════════════════════════
• On Mac (2)
• empty test (5)
[ FAIL 0 | WARN 16 | SKIP 7 | PASS 12455 ]
>
> proc.time()
user system elapsed
729.417 174.327 875.865
OncoSimulR.Rcheck/OncoSimulR-Ex.timings
| name | user | system | elapsed | |
| OncoSimulWide2Long | 0.389 | 0.118 | 0.509 | |
| POM | 0.861 | 0.219 | 0.591 | |
| allFitnessEffects | 1.398 | 0.049 | 1.454 | |
| benchmarks | 0.009 | 0.005 | 0.014 | |
| createInterventions | 0.261 | 0.006 | 0.267 | |
| createUserVars | 0.373 | 0.010 | 0.384 | |
| evalAllGenotypes | 0.176 | 0.011 | 0.187 | |
| example-missing-drivers | 0.204 | 0.016 | 0.222 | |
| examplePosets | 0.274 | 0.006 | 0.281 | |
| examplesFitnessEffects | 0.038 | 0.003 | 0.042 | |
| freq-dep-simul-examples | 0.008 | 0.002 | 0.011 | |
| mcfLs | 0 | 0 | 0 | |
| oncoSimulIndiv | 1.352 | 0.316 | 1.639 | |
| plot.fitnessEffects | 0.201 | 0.023 | 0.227 | |
| plot.oncosimul | 0.698 | 0.108 | 0.810 | |
| plotClonePhylog | 2.286 | 0.272 | 2.566 | |
| plotFitnessLandscape | 1.040 | 0.011 | 1.054 | |
| plotPoset | 0.165 | 0.006 | 0.172 | |
| poset | 0.119 | 0.005 | 0.126 | |
| rfitness | 0.552 | 0.012 | 0.923 | |
| samplePop | 0.066 | 0.099 | 0.130 | |
| simOGraph | 0.064 | 0.012 | 0.076 | |
| to_Magellan | 0.179 | 0.059 | 0.748 | |
| vignette_pre_computed | 0.006 | 0.004 | 0.011 | |