| Back to Multiple platform build/check report for BioC 3.18: simplified long |
|
This page was generated on 2023-11-02 11:41:02 -0400 (Thu, 02 Nov 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 22.04.2 LTS) | x86_64 | 4.3.1 (2023-06-16) -- "Beagle Scouts" | 4729 |
| palomino4 | Windows Server 2022 Datacenter | x64 | 4.3.1 (2023-06-16 ucrt) -- "Beagle Scouts" | 4463 |
| lconway | macOS 12.6.5 Monterey | x86_64 | 4.3.1 Patched (2023-06-17 r84564) -- "Beagle Scouts" | 4478 |
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | 4.3.1 (2023-06-16) -- "Beagle Scouts" | 4464 |
| 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 1457/2266 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| OncoSimulR 4.4.0 (landing page) Ramon Diaz-Uriarte
| nebbiolo2 | Linux (Ubuntu 22.04.2 LTS) / x86_64 | OK | OK | OK |  | ||||||||
| palomino4 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| lconway | macOS 12.6.5 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson1 | macOS 13.6.1 Ventura / arm64 | see weekly results here | ||||||||||||
| 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. - See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host. |
| Package: OncoSimulR |
| Version: 4.4.0 |
| Command: /home/biocbuild/R/R-4.3.1/bin/R CMD check --install=check:OncoSimulR.install-out.txt --library=/home/biocbuild/R/R-4.3.1/site-library --no-vignettes --timings OncoSimulR_4.4.0.tar.gz |
| StartedAt: 2023-11-02 12:48:56 -0000 (Thu, 02 Nov 2023) |
| EndedAt: 2023-11-02 12:59:01 -0000 (Thu, 02 Nov 2023) |
| EllapsedTime: 604.7 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: OncoSimulR.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/R/R-4.3.1/bin/R CMD check --install=check:OncoSimulR.install-out.txt --library=/home/biocbuild/R/R-4.3.1/site-library --no-vignettes --timings OncoSimulR_4.4.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.18-bioc/meat/OncoSimulR.Rcheck’
* using R version 4.3.1 (2023-06-16)
* using platform: aarch64-unknown-linux-gnu (64-bit)
* R was compiled by
gcc (GCC) 10.3.1
GNU Fortran (GCC) 10.3.1
* running under: openEuler 22.03 (LTS-SP1)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘OncoSimulR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘OncoSimulR’ version ‘4.4.0’
* 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 (GCC) 10.3.1’
* used C++ compiler: ‘g++ (GCC) 10.3.1’
* checking installed package size ... NOTE
installed size is 54.0Mb
sub-directories of 1Mb or more:
libs 52.1Mb
* 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 ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: 2 NOTEs
See
‘/home/biocbuild/bbs-3.18-bioc/meat/OncoSimulR.Rcheck/00check.log’
for details.
OncoSimulR.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R-4.3.1/bin/R CMD INSTALL OncoSimulR ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/R/R-4.3.1/site-library’ * installing *source* package ‘OncoSimulR’ ... ** using staged installation ** libs using C compiler: ‘gcc (GCC) 10.3.1’ using C++ compiler: ‘g++ (GCC) 10.3.1’ gcc -I"/home/biocbuild/R/R-4.3.1/include" -DNDEBUG -I'/home/biocbuild/R/R-4.3.1/site-library/Rcpp/include' -I/usr/local/include -fPIC -g -O2 -Wall -c FitnessLandscape/gamma.c -o FitnessLandscape/gamma.o gcc -I"/home/biocbuild/R/R-4.3.1/include" -DNDEBUG -I'/home/biocbuild/R/R-4.3.1/site-library/Rcpp/include' -I/usr/local/include -fPIC -g -O2 -Wall -c FitnessLandscape/landscape.c -o FitnessLandscape/landscape.o gcc -I"/home/biocbuild/R/R-4.3.1/include" -DNDEBUG -I'/home/biocbuild/R/R-4.3.1/site-library/Rcpp/include' -I/usr/local/include -fPIC -g -O2 -Wall -c FitnessLandscape/random.c -o FitnessLandscape/random.o gcc -I"/home/biocbuild/R/R-4.3.1/include" -DNDEBUG -I'/home/biocbuild/R/R-4.3.1/site-library/Rcpp/include' -I/usr/local/include -fPIC -g -O2 -Wall -c FitnessLandscape/sort.c -o FitnessLandscape/sort.o gcc -I"/home/biocbuild/R/R-4.3.1/include" -DNDEBUG -I'/home/biocbuild/R/R-4.3.1/site-library/Rcpp/include' -I/usr/local/include -fPIC -g -O2 -Wall -c FitnessLandscape/chain.c -o FitnessLandscape/chain.o gcc -I"/home/biocbuild/R/R-4.3.1/include" -DNDEBUG -I'/home/biocbuild/R/R-4.3.1/site-library/Rcpp/include' -I/usr/local/include -fPIC -g -O2 -Wall -c FitnessLandscape/input.c -o FitnessLandscape/input.o gcc -I"/home/biocbuild/R/R-4.3.1/include" -DNDEBUG -I'/home/biocbuild/R/R-4.3.1/site-library/Rcpp/include' -I/usr/local/include -fPIC -g -O2 -Wall -c FitnessLandscape/genotypes.c -o FitnessLandscape/genotypes.o gcc -I"/home/biocbuild/R/R-4.3.1/include" -DNDEBUG -I'/home/biocbuild/R/R-4.3.1/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/R/R-4.3.1/include" -DNDEBUG -I'/home/biocbuild/R/R-4.3.1/site-library/Rcpp/include' -I/usr/local/include -fPIC -g -O2 -Wall -c FitnessLandscape/calculus.c -o FitnessLandscape/calculus.o gcc -I"/home/biocbuild/R/R-4.3.1/include" -DNDEBUG -I'/home/biocbuild/R/R-4.3.1/site-library/Rcpp/include' -I/usr/local/include -fPIC -g -O2 -Wall -c FitnessLandscape/vector.c -o FitnessLandscape/vector.o gcc -I"/home/biocbuild/R/R-4.3.1/include" -DNDEBUG -I'/home/biocbuild/R/R-4.3.1/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/R/R-4.3.1/include" -DNDEBUG -I'/home/biocbuild/R/R-4.3.1/site-library/Rcpp/include' -I/usr/local/include -fPIC -g -O2 -Wall -c FitnessLandscape/LinearAlgebra.c -o FitnessLandscape/LinearAlgebra.o gcc -I"/home/biocbuild/R/R-4.3.1/include" -DNDEBUG -I'/home/biocbuild/R/R-4.3.1/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/R/R-4.3.1/include" -DNDEBUG -I'/home/biocbuild/R/R-4.3.1/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/R/R-4.3.1/include" -DNDEBUG -I'/home/biocbuild/R/R-4.3.1/site-library/Rcpp/include' -I/usr/local/include -fPIC -g -O2 -Wall -c FitnessLandscape/decomposition.c -o FitnessLandscape/decomposition.o gcc -I"/home/biocbuild/R/R-4.3.1/include" -DNDEBUG -I'/home/biocbuild/R/R-4.3.1/site-library/Rcpp/include' -I/usr/local/include -fPIC -g -O2 -Wall -c FitnessLandscape/models.c -o FitnessLandscape/models.o gcc -I"/home/biocbuild/R/R-4.3.1/include" -DNDEBUG -I'/home/biocbuild/R/R-4.3.1/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/R/R-4.3.1/include" -DNDEBUG -I'/home/biocbuild/R/R-4.3.1/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/R/R-4.3.1/include" -DNDEBUG -I'/home/biocbuild/R/R-4.3.1/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/R/R-4.3.1/include" -DNDEBUG -I'/home/biocbuild/R/R-4.3.1/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/R/R-4.3.1/lib -L/usr/local/lib -o OncoSimulR.so OncoSimulR_init.o RcppExports.o unity_osimul.o -L/home/biocbuild/R/R-4.3.1/lib -lR installing via 'install.libs.R' to /home/biocbuild/R/R-4.3.1/site-library/00LOCK-OncoSimulR/00new/OncoSimulR [1] "" Installing fl_statistics fl_generate to /home/biocbuild/R/R-4.3.1/site-library/00LOCK-OncoSimulR/00new/OncoSimulR/exec Installing library OncoSimulR.so to /home/biocbuild/R/R-4.3.1/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: aarch64-unknown-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 Thu Nov 2 12:50:27 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 Thu Nov 2 12:50:27 2023
Took 0.59
Starting LOD_POM at Thu Nov 2 12:50:27 2023
Ending LOD_POM at Thu Nov 2 12:50:59 2023
Took 31.26
Starting test.Z-all-fitness at Thu Nov 2 12:50:59 2023
Ending test.Z-all-fitness at Thu Nov 2 12:50:59 2023
Took 0.17
Starting test.Z-driver-counts at Thu Nov 2 12:50:59 2023
Ending test.Z-driver-counts at Thu Nov 2 12:50:59 2023
Took 0.32
Starting test.Z-fixation at Thu Nov 2 12:50:59 2023
Ending test.Z-fixation at Thu Nov 2 12:51:00 2023
Took 1.11
Starting test.Z-magellan at Thu Nov 2 12:51:00 2023
Ended test.Z-magellan at Thu Nov 2 12:51:02 2023
Starting test.Z-mutator at Thu Nov 2 12:51:02 2023
Ending test.Z-mutator at Thu Nov 2 12:51:02 2023
Took 0.5
Starting test.Z-mutatorFDF at Thu Nov 2 12:51:03 2023
Ending test.Z-mutatorFDF at Thu Nov 2 12:51:03 2023
Took 0.16
Starting test.Z-oncoSimulIndiv at Thu Nov 2 12:51:03 2023
Ending test.Z-oncoSimulIndiv at Thu Nov 2 12:51:05 2023
Took 2.65
Starting test.Z-oncoSimulIndivConstant at Thu Nov 2 12:51:05 2023
Ending test.Z-oncoSimulIndivConstant at Thu Nov 2 12:51:08 2023
Took 3.07
Starting test.Z-oncoSimulIndivDeath at Thu Nov 2 12:51:08 2023
Ending test.Z-oncoSimulIndivDeath at Thu Nov 2 12:51:10 2023
Took 1.37
Starting test.Z-oncoSimulIndivFDF at Thu Nov 2 12:51:10 2023
Hitted wall time. Exiting.
Hitting wall time is regarded as an error.
Ending test.Z-oncoSimulIndivFDF at Thu Nov 2 12:51:11 2023
Took 0.75
Starting test.Z-rfitness-landscape at Thu Nov 2 12:51:11 2023
Ending test.Z-rfitness-landscape at Thu Nov 2 12:51:11 2023
Took 0.24
Starting Z-sample-only-last tests Thu Nov 2 12:51:11 2023
Ending Z-sample-only-last tests Thu Nov 2 12:51:11 2023
Took 0
Starting Z-total-present-drivers tests Thu Nov 2 12:51:11 2023
Ending Z-total-present-drivers tests Thu Nov 2 12:51:13 2023
Took 1.8
Dummy empty test Thu Nov 2 12:51:13 2023
Starting accessible_genotypes at Thu Nov 2 12:51:13 2023
Ending accessible_genotypes at Thu Nov 2 12:51:24 2023
Took 11.01
Starting all fitness at Thu Nov 2 12:51:24 2023
Ending all-fitness at Thu Nov 2 12:51:30 2023
Took 6.84
Starting test.allFitnessEffectsFDF at Thu Nov 2 12:51:30 2023
Ending test.allFitnessEffectsFDF at Thu Nov 2 12:51:31 2023
Took 0.18
Starting test.allFitnessEffectsDeath at Thu Nov 2 12:51:31 2023
Ending test.allFitnessEffectsDeath at Thu Nov 2 12:51:31 2023
Took 0.59
Starting test.allFitnessEffectsFDF at Thu Nov 2 12:51:31 2023
Ending test.allFitnessEffectsFDF at Thu Nov 2 12:51:32 2023
Took 0.56
Starting driverCounts at Thu Nov 2 12:51:32 2023
Ending driverCounts at Thu Nov 2 12:51:43 2023
Took 11.22
Starting epist-order-modules at Thu Nov 2 12:51:43 2023
Ending epist-order-modules at Thu Nov 2 12:51:43 2023
Took 0.08
Starting test.evaluatingGenotypesDeath at Thu Nov 2 12:51:43 2023
Ending test.evaluatingGenotypesDeath at Thu Nov 2 12:51:43 2023
Took 0.26
Starting test.evaluatingGenotypesFDF at Thu Nov 2 12:51:43 2023
Ending test.evaluatingGenotypesFDF at Thu Nov 2 12:51:44 2023
Took 0.38
Starting exercise-plotting-code at Thu Nov 2 12:51:44 2023
Ending exercise-plotting-code at Thu Nov 2 12:51:54 2023
Took 10.46
Starting exercise-rfitness at Thu Nov 2 12:51:54 2023
Ending exercise-rfitness at Thu Nov 2 12:52:09 2023
Took 14.26
Starting to_Magella at Thu Nov 2 12:52:09 2023
Ending to_Magella at Thu Nov 2 12:52:09 2023
Took 0.04
Starting fitness preds at Thu Nov 2 12:52:09 2023
Observed vs expected, case III
done tries 1
Ending fitness preds long at Thu Nov 2 12:52:37 2023
Took 28.01
Starting fixation at Thu Nov 2 12:52:37 2023
Ending fixation at Thu Nov 2 12:53:24 2023
Took 47.37
Starting test.flfast-additional.R test at Thu Nov 2 12:53:24 2023
Ending test.flfast-additional.R test at Thu Nov 2 12:53:26 2023
Took 1.66
Starting test.flfast-mutator.R test at Thu Nov 2 12:53:26 2023
Finished test.flfast-mutator.R test at Thu Nov 2 12:53:28 2023
Took 2.83
Starting genotFitness at Thu Nov 2 12:53:29 2023
Ending genotFitness at Thu Nov 2 12:53:29 2023
Took 0.25
Starting genot_fitness_to_epistasis at Thu Nov 2 12:53:29 2023
Ending genot_fitness_to_epistasis at Thu Nov 2 12:53:29 2023
Took 0.05
Starting init-mutant tests Thu Nov 2 12:53:29 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 Thu Nov 2 12:53:43 2023
Took 13.88
Starting interventions tests Thu Nov 2 12:53:43 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] 0.71 0.71 0.71
[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 Thu Nov 2 12:53:48 2023
Took 5.23
Starting test.magellan at Thu Nov 2 12:53:48 2023
Ending test.magellan at Thu Nov 2 12:53:48 2023
Took 0.22
Starting test.modules-root-no-root at Thu Nov 2 12:53:48 2023
Ending test.modules-root-no-root at Thu Nov 2 12:53:48 2023
Took 0.11
Starting at mutPropGrowth Thu Nov 2 12:53:48 2023
Ended test.mutPropGrowth: Thu Nov 2 12:54:09 2023
Took 20.34
Starting test.mutator-oncoSimulSample.R test at Thu Nov 2 12:54:09 2023
Finished test.mutator-oncoSimulSample.R test at Thu Nov 2 12:54:30 2023
Took 21.11 seconds
Starting test.mutator.R test at Thu Nov 2 12:54:30 2023[1] 9.846283e-12
[1] 8.088418e-16
Finished test.mutator.R test at Thu Nov 2 12:54:55 2023
Took 25.64
Starting test.mutatorFDF.R test at Thu Nov 2 12:54:55 2023
Starting test.no-v1 at Thu Nov 2 12:54:56 2023
Ending test.no-v1 at Thu Nov 2 12:54:56 2023
Took 0.02
Starting oncoSimulIndiv-miscell tests Thu Nov 2 12:54:56 2023
Ending oncoSimulIndiv-miscell tests Thu Nov 2 12:55:35 2023
Took 38.52
Starting oncoSimulSample-failures tests Thu Nov 2 12:55:35 2023
Ending oncoSimulSample-failures tests Thu Nov 2 12:55:40 2023
Took 4.8
Starting oncoSimulSample-limits tests Thu Nov 2 12:55:40 2023
Ending oncoSimulSample-limits tests Thu Nov 2 12:55:40 2023
Took 0.1
Starting per-gene-mutation rates at Thu Nov 2 12:55:40 2023
Ending per-gene-mutation rates at Thu Nov 2 12:57:10 2023
Took 90.79
Starting plotFitnessLandscape at Thu Nov 2 12:57:10 2023
Ending plotFitnessLandscape at Thu Nov 2 12:57:17 2023
Took 6.82
Starting poset-transformations tests Thu Nov 2 12:57:17 2023
Ending poset-transformations tests Thu Nov 2 12:57:35 2023
Took 17.83
Starting sample-prob Thu Nov 2 12:57:35 2023
[1] 8.084183e-26
[1] 9.997779e-11
[1] 2.928879e-08
[1] 4.329539e-11
[1] 1.525314e-13
[1] 4.312118e-14
[1] 3.470965e-12
[1] 9.490867e-14
[1] 1.551561e-09
[1] 8.883457e-10
[1] 4.733473e-10
[1] 4.263111e-08
Ending sample-prob tests Thu Nov 2 12:57:49 2023
Took 13.7
Starting samplePop tests Thu Nov 2 12:57:49 2023
Ending samplePop tests Thu Nov 2 12:58:15 2023
Took 26.21
Starting simuls-runs-examples tests Thu Nov 2 12:58:15 2023
Ending simuls-runs-examples tests Thu Nov 2 12:58:49 2023
Took 33.97
Starting user variable tests Thu Nov 2 12:58:49 2023
[1] "Checking user variable: user_var_1"
[1] "Checking rule: rule_1"
Ending user variable tests Thu Nov 2 12:58:49 2023
Took 0.12
Starting warning-mutPropGrowth tests Thu Nov 2 12:58:49 2023
Ending warning-mutPropGrowth tests Thu Nov 2 12:58:52 2023
Took 3.17
Starting wide2long tests Thu Nov 2 12:58:52 2023
Ending wide2long tests Thu Nov 2 12:58:53 2023
Took 0.86
[ FAIL 0 | WARN 13 | SKIP 5 | PASS 8391 ]
══ 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 8391 ]
>
> proc.time()
user system elapsed
557.769 85.675 512.148
OncoSimulR.Rcheck/OncoSimulR-Ex.timings
| name | user | system | elapsed | |
| OncoSimulWide2Long | 0.948 | 0.032 | 0.987 | |
| POM | 0.841 | 0.096 | 0.577 | |
| allFitnessEffects | 2.270 | 0.056 | 2.341 | |
| benchmarks | 0.003 | 0.008 | 0.011 | |
| createInterventions | 0.383 | 0.008 | 0.392 | |
| createUserVars | 0.553 | 0.012 | 0.567 | |
| evalAllGenotypes | 0.261 | 0.016 | 0.279 | |
| example-missing-drivers | 0.296 | 0.012 | 0.308 | |
| examplePosets | 0.372 | 0.004 | 0.376 | |
| examplesFitnessEffects | 0.052 | 0.000 | 0.052 | |
| freq-dep-simul-examples | 0.012 | 0.000 | 0.012 | |
| mcfLs | 0 | 0 | 0 | |
| oncoSimulIndiv | 1.886 | 0.236 | 2.021 | |
| plot.fitnessEffects | 0.272 | 0.012 | 0.289 | |
| plot.oncosimul | 1.475 | 0.012 | 1.489 | |
| plotClonePhylog | 1.850 | 0.107 | 1.960 | |
| plotFitnessLandscape | 1.796 | 0.004 | 1.803 | |
| plotPoset | 0.136 | 0.000 | 0.136 | |
| poset | 0.153 | 0.004 | 0.157 | |
| rfitness | 0.958 | 0.000 | 0.962 | |
| samplePop | 0.183 | 0.132 | 0.229 | |
| simOGraph | 0.070 | 0.016 | 0.087 | |
| to_Magellan | 0.212 | 0.038 | 0.253 | |
| vignette_pre_computed | 0.005 | 0.004 | 0.009 | |