| Back to Multiple platform build/check report for BioC 3.20: simplified long |
|
This page was generated on 2025-02-03 12:05 -0500 (Mon, 03 Feb 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4746 |
| palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" | 4494 |
| merida1 | macOS 12.7.5 Monterey | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4517 |
| kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4469 |
| taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4400 |
| 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 1462/2289 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| OncoSimulR 4.8.0 (landing page) Ramon Diaz-Uriarte
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK |  | ||||||||
| palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| merida1 | macOS 12.7.5 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson1 | macOS 13.6.6 Ventura / arm64 | ... NOT SUPPORTED ... | ||||||||||||
| taishan | Linux (openEuler 24.03 LTS) / 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: 4.8.0 |
| Command: /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:OncoSimulR.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings OncoSimulR_4.8.0.tar.gz |
| StartedAt: 2025-01-31 00:42:20 -0500 (Fri, 31 Jan 2025) |
| EndedAt: 2025-01-31 00:48:26 -0500 (Fri, 31 Jan 2025) |
| EllapsedTime: 366.5 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: OncoSimulR.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:OncoSimulR.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings OncoSimulR_4.8.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/OncoSimulR.Rcheck’
* using R version 4.4.2 (2024-10-31)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0
GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0
* running under: Ubuntu 24.04.1 LTS
* using session charset: UTF-8
* checking for file ‘OncoSimulR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘OncoSimulR’ version ‘4.8.0’
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... NOTE
Found the following hidden files and directories:
.BBSoptions
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘OncoSimulR’ can be installed ... OK
* used C compiler: ‘gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’
* used C++ compiler: ‘g++ (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’
* checking installed package size ... NOTE
installed size is 45.5Mb
sub-directories of 1Mb or more:
libs 43.7Mb
* 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 loading without being on the library search path ... OK
* checking whether startup messages can be suppressed ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... 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 re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE
Status: 3 NOTEs
See
‘/home/biocbuild/bbs-3.20-bioc/meat/OncoSimulR.Rcheck/00check.log’
for details.
OncoSimulR.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD INSTALL OncoSimulR ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.20-bioc/R/site-library’ * installing *source* package ‘OncoSimulR’ ... ** using staged installation ** libs using C compiler: ‘gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’ using C++ compiler: ‘g++ (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’ gcc -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -Wall -c FitnessLandscape/gamma.c -o FitnessLandscape/gamma.o gcc -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -Wall -c FitnessLandscape/landscape.c -o FitnessLandscape/landscape.o gcc -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -Wall -c FitnessLandscape/random.c -o FitnessLandscape/random.o gcc -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -Wall -c FitnessLandscape/sort.c -o FitnessLandscape/sort.o gcc -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -Wall -c FitnessLandscape/chain.c -o FitnessLandscape/chain.o gcc -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -Wall -c FitnessLandscape/input.c -o FitnessLandscape/input.o gcc -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -Wall -c FitnessLandscape/genotypes.c -o FitnessLandscape/genotypes.o gcc -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -Wall -c FitnessLandscape/ordered_pairs.c -o FitnessLandscape/ordered_pairs.o gcc -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -Wall -c FitnessLandscape/calculus.c -o FitnessLandscape/calculus.o gcc -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -Wall -c FitnessLandscape/vector.c -o FitnessLandscape/vector.o gcc -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -Wall -c FitnessLandscape/generalized_chain.c -o FitnessLandscape/generalized_chain.o gcc -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -Wall -c FitnessLandscape/LinearAlgebra.c -o FitnessLandscape/LinearAlgebra.o gcc -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -Wall -c FitnessLandscape/summary_statistics.c -o FitnessLandscape/summary_statistics.o gcc -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -Wall -c FitnessLandscape/epistasis_type.c -o FitnessLandscape/epistasis_type.o gcc -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -Wall -c FitnessLandscape/decomposition.c -o FitnessLandscape/decomposition.o gcc -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -Wall -c FitnessLandscape/models.c -o FitnessLandscape/models.o gcc -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -Wall -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 liblandscape.a ranlib liblandscape.a; gcc -O -Wall -o fl_statistics -I/FitnessLandscape/. -L. FitnessLandscape/main_fl_statistics.c -llandscape -lm; gcc -O -Wall -o fl_generate -I/FitnessLandscape/. -L. FitnessLandscape/main_fl_generate.c -llandscape -lm; gcc -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -Wall -c OncoSimulR_init.c -o OncoSimulR_init.o g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -Wall -c RcppExports.cpp -o RcppExports.o g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -Wall -c unity_osimul.cpp -o unity_osimul.o g++ -std=gnu++17 -shared -L/home/biocbuild/bbs-3.20-bioc/R/lib -L/usr/local/lib -o OncoSimulR.so OncoSimulR_init.o RcppExports.o unity_osimul.o -L/home/biocbuild/bbs-3.20-bioc/R/lib -lR installing via 'install.libs.R' to /home/biocbuild/bbs-3.20-bioc/R/site-library/00LOCK-OncoSimulR/00new/OncoSimulR [1] "" Installing fl_statistics fl_generate to /home/biocbuild/bbs-3.20-bioc/R/site-library/00LOCK-OncoSimulR/00new/OncoSimulR/exec Installing library OncoSimulR.so to /home/biocbuild/bbs-3.20-bioc/R/site-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 4.4.2 (2024-10-31) -- "Pile of Leaves"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> library(testthat)
> library(OncoSimulR)
This is package OncoSimulR. If you are running it on an aarch64 (arm64) platform with a MacOS note that the package fails some tests in that platform + OS that I have no way of debugging. Please read file README_tests_kjohnson3_aarch64-apple-darwin20.txt in the tests directory. As of 2024-10-09, this platform is unsupported until we can properly debug it.
>
> test_check("OncoSimulR")
Starting FDF-letter-fitness-order Fri Jan 31 00:43:27 2025
exprtk parser error:
Error[00] Position: 00 Type: [ Syntax Error] Msg: ERR202 - Undefined symbol: 'n_2_3' Expression: n_2_3
exprtk parser error:
Error[00] Position: 00 Type: [ Syntax Error] Msg: ERR202 - Undefined symbol: 'f_2_3' Expression: f_2_3
Ending FDF-small-fitness-specs Fri Jan 31 00:43:27 2025
Took 0.43
Starting LOD_POM at Fri Jan 31 00:43:27 2025
Ending LOD_POM at Fri Jan 31 00:43:36 2025
Took 9.38
Starting test.Z-all-fitness at Fri Jan 31 00:43:36 2025
Ending test.Z-all-fitness at Fri Jan 31 00:43:37 2025
Took 0.09
Starting test.Z-driver-counts at Fri Jan 31 00:43:37 2025
Ending test.Z-driver-counts at Fri Jan 31 00:43:37 2025
Took 0.09
Starting test.Z-fixation at Fri Jan 31 00:43:37 2025
Ending test.Z-fixation at Fri Jan 31 00:43:37 2025
Took 0.2
Starting test.Z-magellan at Fri Jan 31 00:43:37 2025
Ended test.Z-magellan at Fri Jan 31 00:43:38 2025
Starting test.Z-mutator at Fri Jan 31 00:43:38 2025
Ending test.Z-mutator at Fri Jan 31 00:43:39 2025
Took 0.28
Starting test.Z-mutatorFDF at Fri Jan 31 00:43:39 2025
Ending test.Z-mutatorFDF at Fri Jan 31 00:43:39 2025
Took 0.09
Starting test.Z-oncoSimulIndiv at Fri Jan 31 00:43:39 2025
Ending test.Z-oncoSimulIndiv at Fri Jan 31 00:43:39 2025
Took 0.34
Starting test.Z-oncoSimulIndivConstant at Fri Jan 31 00:43:39 2025
Ending test.Z-oncoSimulIndivConstant at Fri Jan 31 00:43:41 2025
Took 2.17
Starting test.Z-oncoSimulIndivDeath at Fri Jan 31 00:43:41 2025
Ending test.Z-oncoSimulIndivDeath at Fri Jan 31 00:43:42 2025
Took 0.7
Starting test.Z-oncoSimulIndivFDF at Fri Jan 31 00:43:42 2025
Hitted wall time. Exiting.
Hitting wall time is regarded as an error.
Ending test.Z-oncoSimulIndivFDF at Fri Jan 31 00:43:43 2025
Took 0.54
Starting test.Z-rfitness-landscape at Fri Jan 31 00:43:43 2025
Ending test.Z-rfitness-landscape at Fri Jan 31 00:43:43 2025
Took 0.17
Starting Z-sample-only-last tests Fri Jan 31 00:43:43 2025
Ending Z-sample-only-last tests Fri Jan 31 00:43:43 2025
Took 0
Starting Z-total-present-drivers tests Fri Jan 31 00:43:43 2025
Ending Z-total-present-drivers tests Fri Jan 31 00:43:43 2025
Took 0.73
Dummy empty test Fri Jan 31 00:43:43 2025
Starting accessible_genotypes at Fri Jan 31 00:43:43 2025
Ending accessible_genotypes at Fri Jan 31 00:43:50 2025
Took 6.17
Starting all fitness at Fri Jan 31 00:43:50 2025
Ending all-fitness at Fri Jan 31 00:43:54 2025
Took 4.3
Starting test.allFitnessEffectsFDF at Fri Jan 31 00:43:54 2025
Ending test.allFitnessEffectsFDF at Fri Jan 31 00:43:54 2025
Took 0.11
Starting test.allFitnessEffectsDeath at Fri Jan 31 00:43:54 2025
Ending test.allFitnessEffectsDeath at Fri Jan 31 00:43:54 2025
Took 0.33
Starting test.allFitnessEffectsFDF at Fri Jan 31 00:43:54 2025
Ending test.allFitnessEffectsFDF at Fri Jan 31 00:43:55 2025
Took 0.34
Starting driverCounts at Fri Jan 31 00:43:55 2025
Ending driverCounts at Fri Jan 31 00:44:01 2025
Took 6.39
Starting epist-order-modules at Fri Jan 31 00:44:01 2025
Ending epist-order-modules at Fri Jan 31 00:44:01 2025
Took 0.04
Starting test.evaluatingGenotypesDeath at Fri Jan 31 00:44:01 2025
Ending test.evaluatingGenotypesDeath at Fri Jan 31 00:44:01 2025
Took 0.2
Starting test.evaluatingGenotypesFDF at Fri Jan 31 00:44:01 2025
Ending test.evaluatingGenotypesFDF at Fri Jan 31 00:44:02 2025
Took 0.16
Starting exercise-plotting-code at Fri Jan 31 00:44:02 2025
Ending exercise-plotting-code at Fri Jan 31 00:44:04 2025
Took 2.24
Starting exercise-rfitness at Fri Jan 31 00:44:04 2025
Ending exercise-rfitness at Fri Jan 31 00:44:12 2025
Took 7.94
Starting to_Magella at Fri Jan 31 00:44:12 2025
Ending to_Magella at Fri Jan 31 00:44:12 2025
Took 0.03
Starting fitness preds at Fri Jan 31 00:44:12 2025
Observed vs expected, case III
done tries 1
Ending fitness preds long at Fri Jan 31 00:44:17 2025
Took 5.18
Starting fixation at Fri Jan 31 00:44:17 2025
Ending fixation at Fri Jan 31 00:44:27 2025
Took 10.42
Starting test.flfast-additional.R test at Fri Jan 31 00:44:27 2025
Ending test.flfast-additional.R test at Fri Jan 31 00:44:29 2025
Took 1.11
Starting test.flfast-mutator.R test at Fri Jan 31 00:44:29 2025
Finished test.flfast-mutator.R test at Fri Jan 31 00:44:30 2025
Took 1.22
Starting genotFitness at Fri Jan 31 00:44:30 2025
Ending genotFitness at Fri Jan 31 00:44:30 2025
Took 0.17
Starting genot_fitness_to_epistasis at Fri Jan 31 00:44:30 2025
Ending genot_fitness_to_epistasis at Fri Jan 31 00:44:30 2025
Took 0.03
Starting init-mutant tests Fri Jan 31 00:44:30 2025
exprtk parser error:
Error[00] Position: 18 Type: [ Syntax Error] Msg: ERR202 - Undefined symbol: 'f_2' Expression: 1.1 + 0.7*((f_1 + f_2) > 0.3)
Ending init-mutant tests Fri Jan 31 00:44:35 2025
Took 4.77
Starting interventions tests Fri Jan 31 00:44:35 2025
[1] "Checking intervention: intOverA"
[1] "Checking intervention: intOverA"
[1] "Checking intervention: intOverA"
[1] "Checking intervention: intOverA"
[1] "Checking intervention: intOverMultiplicatesA"
In intervention:intOverMultiplicatesA with WhatHappens: n_1 = n_1 * 2. You cannot intervene to generate more population.[1] "Checking intervention: intOverA"
[1] "Checking intervention: intOverA"
[1] "Checking intervention: intOverTotPop"
[1] 0.73 0.73 0.73
[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 Fri Jan 31 00:44:38 2025
Took 3.72
Starting test.magellan at Fri Jan 31 00:44:38 2025
Ending test.magellan at Fri Jan 31 00:44:39 2025
Took 0.13
Starting test.modules-root-no-root at Fri Jan 31 00:44:39 2025
Ending test.modules-root-no-root at Fri Jan 31 00:44:39 2025
Took 0.09
Starting at mutPropGrowth Fri Jan 31 00:44:39 2025
Ended test.mutPropGrowth: Fri Jan 31 00:44:44 2025
Took 4.86
Starting test.mutator-oncoSimulSample.R test at Fri Jan 31 00:44:44 2025
Finished test.mutator-oncoSimulSample.R test at Fri Jan 31 00:44:50 2025
Took 6.75 seconds
Starting test.mutator.R test at Fri Jan 31 00:44:50 2025[1] 8.79732e-13
[1] 3.303325e-13
Finished test.mutator.R test at Fri Jan 31 00:45:01 2025
Took 10.61
Starting test.mutatorFDF.R test at Fri Jan 31 00:45:01 2025
Starting test.no-v1 at Fri Jan 31 00:45:01 2025
Ending test.no-v1 at Fri Jan 31 00:45:01 2025
Took 0.01
Starting oncoSimulIndiv-miscell tests Fri Jan 31 00:45:01 2025
Ending oncoSimulIndiv-miscell tests Fri Jan 31 00:45:08 2025
Took 6.37
Starting oncoSimulSample-failures tests Fri Jan 31 00:45:08 2025
Ending oncoSimulSample-failures tests Fri Jan 31 00:45:12 2025
Took 3.76
Starting oncoSimulSample-limits tests Fri Jan 31 00:45:12 2025
Ending oncoSimulSample-limits tests Fri Jan 31 00:45:12 2025
Took 0.06
Starting per-gene-mutation rates at Fri Jan 31 00:45:12 2025
Ending per-gene-mutation rates at Fri Jan 31 00:45:33 2025
Took 21.43
Starting plotFitnessLandscape at Fri Jan 31 00:45:33 2025
Ending plotFitnessLandscape at Fri Jan 31 00:45:36 2025
Took 3.14
Starting poset-transformations tests Fri Jan 31 00:45:36 2025
Ending poset-transformations tests Fri Jan 31 00:45:46 2025
Took 9.68
Starting sample-prob Fri Jan 31 00:45:46 2025
[1] 1.421457e-22
[1] 2.80405e-14
[1] 6.186258e-10
[1] 1.381719e-11
[1] 1.552566e-12
[1] 9.956079e-15
[1] 5.660741e-11
[1] 7.505988e-11
[1] 2.799718e-10
[1] 4.859663e-10
[1] 4.241266e-08
[1] 7.331816e-09
Ending sample-prob tests Fri Jan 31 00:45:51 2025
Took 5.53
Starting samplePop tests Fri Jan 31 00:45:51 2025
Ending samplePop tests Fri Jan 31 00:45:55 2025
Took 3.76
Starting simuls-runs-examples tests Fri Jan 31 00:45:55 2025
Ending simuls-runs-examples tests Fri Jan 31 00:46:01 2025
Took 5.8
Starting user variable tests Fri Jan 31 00:46:01 2025
[1] "Checking user variable: user_var_1"
[1] "Checking rule: rule_1"
Ending user variable tests Fri Jan 31 00:46:01 2025
Took 0.11
Starting warning-mutPropGrowth tests Fri Jan 31 00:46:01 2025
Ending warning-mutPropGrowth tests Fri Jan 31 00:46:01 2025
Took 0.34
Starting wide2long tests Fri Jan 31 00:46:01 2025
Ending wide2long tests Fri Jan 31 00:46:02 2025
Took 0.22
[ FAIL 0 | WARN 19 | SKIP 5 | PASS 8419 ]
══ Skipped tests (5) ═══════════════════════════════════════════════════════════
• empty test (5): 'test.FDF-letter-fitness-order.R:376:1',
'test.ZZ-dummy-skip-warn-test.R:8:1', 'test.ZZ-dummy-skip-warn-test.R:12:1',
'test.fixation.R:4:1', 'test.init-mutant.R:1099:1'
[ FAIL 0 | WARN 19 | SKIP 5 | PASS 8419 ]
>
> proc.time()
user system elapsed
174.784 29.630 159.523
OncoSimulR.Rcheck/OncoSimulR-Ex.timings
| name | user | system | elapsed | |
| OncoSimulWide2Long | 0.128 | 0.001 | 0.131 | |
| POM | 0.437 | 0.038 | 0.308 | |
| allFitnessEffects | 1.553 | 0.069 | 1.625 | |
| benchmarks | 0.008 | 0.001 | 0.007 | |
| createInterventions | 0.272 | 0.000 | 0.273 | |
| createUserVars | 0.425 | 0.000 | 0.425 | |
| evalAllGenotypes | 0.179 | 0.003 | 0.182 | |
| example-missing-drivers | 0.202 | 0.010 | 0.214 | |
| examplePosets | 0.221 | 0.001 | 0.223 | |
| examplesFitnessEffects | 0.071 | 0.000 | 0.071 | |
| freq-dep-simul-examples | 0.006 | 0.003 | 0.009 | |
| mcfLs | 0 | 0 | 0 | |
| oncoSimulIndiv | 0.915 | 0.089 | 0.957 | |
| plot.fitnessEffects | 0.229 | 0.018 | 0.247 | |
| plot.oncosimul | 0.406 | 0.004 | 0.411 | |
| plotClonePhylog | 1.177 | 0.256 | 1.433 | |
| plotFitnessLandscape | 0.964 | 0.008 | 0.972 | |
| plotPoset | 0.070 | 0.004 | 0.073 | |
| poset | 0.091 | 0.001 | 0.092 | |
| rfitness | 0.634 | 0.002 | 0.636 | |
| samplePop | 0.062 | 0.067 | 0.088 | |
| simOGraph | 0.055 | 0.005 | 0.059 | |
| to_Magellan | 0.172 | 0.025 | 0.198 | |
| vignette_pre_computed | 0.007 | 0.002 | 0.009 | |