| Back to Multiple platform build/check report for BioC 3.17: simplified long |
|
This page was generated on 2023-10-16 11:35:35 -0400 (Mon, 16 Oct 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 22.04.2 LTS) | x86_64 | 4.3.1 (2023-06-16) -- "Beagle Scouts" | 4626 |
| palomino3 | Windows Server 2022 Datacenter | x64 | 4.3.1 (2023-06-16 ucrt) -- "Beagle Scouts" | 4379 |
| merida1 | macOS 12.6.4 Monterey | x86_64 | 4.3.1 (2023-06-16) -- "Beagle Scouts" | 4395 |
| 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 1430/2230 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| OncoSimulR 4.2.0 (landing page) Ramon Diaz-Uriarte
| nebbiolo1 | Linux (Ubuntu 22.04.2 LTS) / x86_64 | OK | OK | OK |  | ||||||||
| palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| merida1 | macOS 12.6.4 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson2 | macOS 12.6.1 Monterey / arm64 | see weekly results here | ||||||||||||
|
To the developers/maintainers of the OncoSimulR package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/OncoSimulR.git to reflect on this report. See Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. |
| Package: OncoSimulR |
| Version: 4.2.0 |
| Command: /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:OncoSimulR.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/site-library --timings OncoSimulR_4.2.0.tar.gz |
| StartedAt: 2023-10-15 23:27:01 -0400 (Sun, 15 Oct 2023) |
| EndedAt: 2023-10-15 23:40:52 -0400 (Sun, 15 Oct 2023) |
| EllapsedTime: 831.7 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: OncoSimulR.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:OncoSimulR.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/site-library --timings OncoSimulR_4.2.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/OncoSimulR.Rcheck’
* using R version 4.3.1 (2023-06-16)
* using platform: x86_64-pc-linux-gnu (64-bit)
* R was compiled by
gcc (Ubuntu 11.3.0-1ubuntu1~22.04.1) 11.3.0
GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04.1) 11.3.0
* running under: Ubuntu 22.04.3 LTS
* using session charset: UTF-8
* checking for file ‘OncoSimulR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘OncoSimulR’ version ‘4.2.0’
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘OncoSimulR’ can be installed ... OK
* used C compiler: ‘gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’
* used C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’
* checking installed package size ... NOTE
installed size is 19.6Mb
sub-directories of 1Mb or more:
libs 18.1Mb
* 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 loading without being on the library search path ... 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 ...
‘OncoSimulR.Rmd’ using ‘UTF-8’... OK
NONE
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE
Status: 2 NOTEs
See
‘/home/biocbuild/bbs-3.17-bioc/meat/OncoSimulR.Rcheck/00check.log’
for details.
OncoSimulR.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL OncoSimulR ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.17-bioc/R/site-library’ * installing *source* package ‘OncoSimulR’ ... ** using staged installation ** libs using C compiler: ‘gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ using C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.17-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-3.17-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.17-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-3.17-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.17-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-3.17-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.17-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-3.17-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.17-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-3.17-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.17-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-3.17-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.17-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-3.17-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.17-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-3.17-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.17-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-3.17-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.17-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-3.17-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.17-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-3.17-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.17-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-3.17-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.17-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-3.17-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.17-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-3.17-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.17-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-3.17-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.17-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-3.17-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.17-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-3.17-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.17-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-3.17-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.17-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-3.17-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.17-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-3.17-bioc/R/lib -L/usr/local/lib -o OncoSimulR.so OncoSimulR_init.o RcppExports.o unity_osimul.o -L/home/biocbuild/bbs-3.17-bioc/R/lib -lR installing via 'install.libs.R' to /home/biocbuild/bbs-3.17-bioc/R/site-library/00LOCK-OncoSimulR/00new/OncoSimulR [1] "" Installing fl_statistics fl_generate to /home/biocbuild/bbs-3.17-bioc/R/site-library/00LOCK-OncoSimulR/00new/OncoSimulR/exec Installing library OncoSimulR.so to /home/biocbuild/bbs-3.17-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 4.3.1 (2023-06-16) -- "Beagle Scouts"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (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 Sun Oct 15 23:28:10 2023
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 Sun Oct 15 23:28:10 2023
Took 0.46
Starting LOD_POM at Sun Oct 15 23:28:10 2023
Ending LOD_POM at Sun Oct 15 23:28:30 2023
Took 19.66
Starting test.Z-all-fitness at Sun Oct 15 23:28:30 2023
Ending test.Z-all-fitness at Sun Oct 15 23:28:30 2023
Took 0.11
Starting test.Z-driver-counts at Sun Oct 15 23:28:30 2023
Ending test.Z-driver-counts at Sun Oct 15 23:28:30 2023
Took 0.19
Starting test.Z-fixation at Sun Oct 15 23:28:30 2023
Ending test.Z-fixation at Sun Oct 15 23:28:31 2023
Took 0.63
Starting test.Z-magellan at Sun Oct 15 23:28:31 2023
Ended test.Z-magellan at Sun Oct 15 23:28:32 2023
Starting test.Z-mutator at Sun Oct 15 23:28:32 2023
Ending test.Z-mutator at Sun Oct 15 23:28:33 2023
Took 0.32
Starting test.Z-mutatorFDF at Sun Oct 15 23:28:33 2023
Ending test.Z-mutatorFDF at Sun Oct 15 23:28:33 2023
Took 0.1
Starting test.Z-oncoSimulIndiv at Sun Oct 15 23:28:33 2023
Ending test.Z-oncoSimulIndiv at Sun Oct 15 23:28:34 2023
Took 1.51
Starting test.Z-oncoSimulIndivConstant at Sun Oct 15 23:28:34 2023
Ending test.Z-oncoSimulIndivConstant at Sun Oct 15 23:28:37 2023
Took 2.35
Starting test.Z-oncoSimulIndivDeath at Sun Oct 15 23:28:37 2023
Ending test.Z-oncoSimulIndivDeath at Sun Oct 15 23:28:38 2023
Took 0.93
Starting test.Z-oncoSimulIndivFDF at Sun Oct 15 23:28:38 2023
Hitted wall time. Exiting.
Hitting wall time is regarded as an error.
Ending test.Z-oncoSimulIndivFDF at Sun Oct 15 23:28:39 2023
Took 0.99
Starting test.Z-rfitness-landscape at Sun Oct 15 23:28:39 2023
Ending test.Z-rfitness-landscape at Sun Oct 15 23:28:39 2023
Took 0.19
Starting Z-sample-only-last tests Sun Oct 15 23:28:39 2023
Ending Z-sample-only-last tests Sun Oct 15 23:28:39 2023
Took 0
Starting Z-total-present-drivers tests Sun Oct 15 23:28:39 2023
Ending Z-total-present-drivers tests Sun Oct 15 23:28:40 2023
Took 1.26
Dummy empty test Sun Oct 15 23:28:40 2023
Starting accessible_genotypes at Sun Oct 15 23:28:40 2023
Ending accessible_genotypes at Sun Oct 15 23:28:47 2023
Took 6.79
Starting all fitness at Sun Oct 15 23:28:47 2023
Ending all-fitness at Sun Oct 15 23:28:51 2023
Took 4.24
Starting test.allFitnessEffectsFDF at Sun Oct 15 23:28:51 2023
Ending test.allFitnessEffectsFDF at Sun Oct 15 23:28:51 2023
Took 0.11
Starting test.allFitnessEffectsDeath at Sun Oct 15 23:28:51 2023
Ending test.allFitnessEffectsDeath at Sun Oct 15 23:28:52 2023
Took 0.37
Starting test.allFitnessEffectsFDF at Sun Oct 15 23:28:52 2023
Ending test.allFitnessEffectsFDF at Sun Oct 15 23:28:52 2023
Took 0.37
Starting driverCounts at Sun Oct 15 23:28:52 2023
Ending driverCounts at Sun Oct 15 23:29:00 2023
Took 8.09
Starting epist-order-modules at Sun Oct 15 23:29:00 2023
Ending epist-order-modules at Sun Oct 15 23:29:00 2023
Took 0.06
Starting test.evaluatingGenotypesDeath at Sun Oct 15 23:29:00 2023
Ending test.evaluatingGenotypesDeath at Sun Oct 15 23:29:00 2023
Took 0.17
Starting test.evaluatingGenotypesFDF at Sun Oct 15 23:29:00 2023
Ending test.evaluatingGenotypesFDF at Sun Oct 15 23:29:00 2023
Took 0.18
Starting exercise-plotting-code at Sun Oct 15 23:29:00 2023
Ending exercise-plotting-code at Sun Oct 15 23:29:07 2023
Took 6.36
Starting exercise-rfitness at Sun Oct 15 23:29:07 2023
Ending exercise-rfitness at Sun Oct 15 23:29:16 2023
Took 8.96
Starting to_Magella at Sun Oct 15 23:29:16 2023
Ending to_Magella at Sun Oct 15 23:29:16 2023
Took 0.03
Starting fitness preds at Sun Oct 15 23:29:16 2023
Observed vs expected, case III
done tries 1
Ending fitness preds long at Sun Oct 15 23:29:30 2023
Took 13.85
Starting fixation at Sun Oct 15 23:29:30 2023
Ending fixation at Sun Oct 15 23:30:34 2023
Took 64.67
Starting test.flfast-additional.R test at Sun Oct 15 23:30:34 2023
Ending test.flfast-additional.R test at Sun Oct 15 23:30:36 2023
Took 1.87
Starting test.flfast-mutator.R test at Sun Oct 15 23:30:36 2023
Finished test.flfast-mutator.R test at Sun Oct 15 23:30:38 2023
Took 1.5
Starting genotFitness at Sun Oct 15 23:30:38 2023
Ending genotFitness at Sun Oct 15 23:30:38 2023
Took 0.19
Starting genot_fitness_to_epistasis at Sun Oct 15 23:30:38 2023
Ending genot_fitness_to_epistasis at Sun Oct 15 23:30:38 2023
Took 0.04
Starting init-mutant tests Sun Oct 15 23:30:38 2023
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 Sun Oct 15 23:30:55 2023
Took 16.8
Starting interventions tests Sun Oct 15 23:30:55 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"
[1] "Checking intervention: intOverA"
[1] "Checking intervention: intOverTotPop"
[1] 0.68 0.68 0.68
[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 Sun Oct 15 23:30:59 2023
Took 4.11
Starting test.magellan at Sun Oct 15 23:30:59 2023
Ending test.magellan at Sun Oct 15 23:30:59 2023
Took 0.13
Starting test.modules-root-no-root at Sun Oct 15 23:30:59 2023
Ending test.modules-root-no-root at Sun Oct 15 23:30:59 2023
Took 0.07
Starting at mutPropGrowth Sun Oct 15 23:30:59 2023
Ended test.mutPropGrowth: Sun Oct 15 23:31:22 2023
Took 22.51
Starting test.mutator-oncoSimulSample.R test at Sun Oct 15 23:31:22 2023
Finished test.mutator-oncoSimulSample.R test at Sun Oct 15 23:31:33 2023
Took 11.4 seconds
Starting test.mutator.R test at Sun Oct 15 23:31:33 2023[1] 4.746379e-10
[1] 5.573308e-13
Finished test.mutator.R test at Sun Oct 15 23:31:48 2023
Took 15.39
Starting test.mutatorFDF.R test at Sun Oct 15 23:31:48 2023
Starting test.no-v1 at Sun Oct 15 23:31:49 2023
Ending test.no-v1 at Sun Oct 15 23:31:49 2023
Took 0.05
Starting oncoSimulIndiv-miscell tests Sun Oct 15 23:31:50 2023
Ending oncoSimulIndiv-miscell tests Sun Oct 15 23:32:24 2023
Took 34.53
Starting oncoSimulSample-failures tests Sun Oct 15 23:32:24 2023
Ending oncoSimulSample-failures tests Sun Oct 15 23:32:29 2023
Took 4.55
Starting oncoSimulSample-limits tests Sun Oct 15 23:32:29 2023
Ending oncoSimulSample-limits tests Sun Oct 15 23:32:29 2023
Took 0.14
Starting per-gene-mutation rates at Sun Oct 15 23:32:29 2023
Ending per-gene-mutation rates at Sun Oct 15 23:33:19 2023
Took 50.38
Starting plotFitnessLandscape at Sun Oct 15 23:33:19 2023
Ending plotFitnessLandscape at Sun Oct 15 23:33:26 2023
Took 6.95
Starting poset-transformations tests Sun Oct 15 23:33:26 2023
Ending poset-transformations tests Sun Oct 15 23:33:40 2023
Took 13.62
Starting sample-prob Sun Oct 15 23:33:40 2023
[1] 1.182262e-32
[1] 7.907337e-12
[1] 4.759615e-11
[1] 1.288684e-11
[1] 1.51052e-12
[1] 2.12912e-15
[1] 1.067767e-09
[1] 7.382921e-15
[1] 2.679992e-10
[1] 2.46332e-08
[1] 3.836758e-08
[1] 1.949397e-09
Ending sample-prob tests Sun Oct 15 23:33:53 2023
Took 13.27
Starting samplePop tests Sun Oct 15 23:33:53 2023
Ending samplePop tests Sun Oct 15 23:34:10 2023
Took 16.87
Starting simuls-runs-examples tests Sun Oct 15 23:34:10 2023
Ending simuls-runs-examples tests Sun Oct 15 23:34:45 2023
Took 35.01
Starting user variable tests Sun Oct 15 23:34:45 2023
[1] "Checking user variable: user_var_1"
[1] "Checking rule: rule_1"
Ending user variable tests Sun Oct 15 23:34:45 2023
Took 0.15
Starting warning-mutPropGrowth tests Sun Oct 15 23:34:45 2023
Ending warning-mutPropGrowth tests Sun Oct 15 23:34:48 2023
Took 2.7
Starting wide2long tests Sun Oct 15 23:34:48 2023
Ending wide2long tests Sun Oct 15 23:34:49 2023
Took 0.96
[ FAIL 0 | WARN 13 | SKIP 5 | PASS 8387 ]
══ 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:1097:1'
[ FAIL 0 | WARN 13 | SKIP 5 | PASS 8387 ]
>
> proc.time()
user system elapsed
463.560 55.484 404.998
OncoSimulR.Rcheck/OncoSimulR-Ex.timings
| name | user | system | elapsed | |
| OncoSimulWide2Long | 0.575 | 0.032 | 0.609 | |
| POM | 0.478 | 0.079 | 0.349 | |
| allFitnessEffects | 1.666 | 0.036 | 1.704 | |
| benchmarks | 0.012 | 0.000 | 0.012 | |
| createInterventions | 0.282 | 0.008 | 0.290 | |
| createUserVars | 0.450 | 0.004 | 0.454 | |
| evalAllGenotypes | 0.178 | 0.020 | 0.198 | |
| example-missing-drivers | 0.236 | 0.016 | 0.252 | |
| examplePosets | 0.285 | 0.004 | 0.290 | |
| examplesFitnessEffects | 0.042 | 0.000 | 0.042 | |
| freq-dep-simul-examples | 0.01 | 0.00 | 0.01 | |
| mcfLs | 0 | 0 | 0 | |
| oncoSimulIndiv | 1.374 | 0.293 | 1.608 | |
| plot.fitnessEffects | 0.192 | 0.016 | 0.207 | |
| plot.oncosimul | 0.970 | 0.012 | 0.983 | |
| plotClonePhylog | 1.320 | 0.156 | 1.477 | |
| plotFitnessLandscape | 1.189 | 0.000 | 1.188 | |
| plotPoset | 0.099 | 0.000 | 0.099 | |
| poset | 0.103 | 0.004 | 0.107 | |
| rfitness | 0.610 | 0.012 | 0.622 | |
| samplePop | 0.053 | 0.063 | 0.077 | |
| simOGraph | 0.100 | 0.004 | 0.104 | |
| to_Magellan | 0.181 | 0.030 | 0.212 | |
| vignette_pre_computed | 0.008 | 0.000 | 0.009 | |