| Back to Multiple platform build/check report for BioC 3.19: simplified long |
|
This page was generated on 2024-05-31 17:03:07 -0400 (Fri, 31 May 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4753 |
| kjohnson3 | macOS 13.6.5 Ventura | arm64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 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 1472/2300 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| OncoSimulR 4.6.0 (landing page) Ramon Diaz-Uriarte
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK |  | ||||||||
| kjohnson3 | macOS 13.6.5 Ventura / arm64 | OK | ERROR | skipped | skipped | |||||||||
|
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: 4.6.0 |
| Command: /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:OncoSimulR.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings OncoSimulR_4.6.0.tar.gz |
| StartedAt: 2024-05-31 06:18:56 -0400 (Fri, 31 May 2024) |
| EndedAt: 2024-05-31 06:28:05 -0400 (Fri, 31 May 2024) |
| EllapsedTime: 548.3 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: OncoSimulR.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:OncoSimulR.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings OncoSimulR_4.6.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/OncoSimulR.Rcheck’
* using R version 4.4.0 (2024-04-24)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
* running under: Ubuntu 22.04.4 LTS
* using session charset: UTF-8
* checking for file ‘OncoSimulR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘OncoSimulR’ version ‘4.6.0’
* 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 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 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 ... NOTE
checkRd: (-1) oncoSimulIndiv.Rd:255-259: Lost braces in \itemize; meant \describe ?
checkRd: (-1) oncoSimulIndiv.Rd:261-263: Lost braces in \itemize; meant \describe ?
checkRd: (-1) oncoSimulIndiv.Rd:265-266: Lost braces in \itemize; meant \describe ?
checkRd: (-1) oncoSimulIndiv.Rd:268-270: Lost braces in \itemize; meant \describe ?
checkRd: (-1) oncoSimulIndiv.Rd:272-274: Lost braces in \itemize; meant \describe ?
* 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-3.19-bioc/meat/OncoSimulR.Rcheck/00check.log’
for details.
OncoSimulR.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD INSTALL OncoSimulR ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.19-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-3.19-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.19-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-3.19-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.19-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-3.19-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.19-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-3.19-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.19-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-3.19-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.19-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-3.19-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.19-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-3.19-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.19-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-3.19-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.19-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-3.19-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.19-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-3.19-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.19-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-3.19-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.19-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-3.19-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.19-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-3.19-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.19-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-3.19-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.19-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-3.19-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.19-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-3.19-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.19-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-3.19-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.19-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-3.19-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.19-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-3.19-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.19-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-3.19-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.19-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-3.19-bioc/R/lib -L/usr/local/lib -o OncoSimulR.so OncoSimulR_init.o RcppExports.o unity_osimul.o -L/home/biocbuild/bbs-3.19-bioc/R/lib -lR installing via 'install.libs.R' to /home/biocbuild/bbs-3.19-bioc/R/site-library/00LOCK-OncoSimulR/00new/OncoSimulR [1] "" Installing fl_statistics fl_generate to /home/biocbuild/bbs-3.19-bioc/R/site-library/00LOCK-OncoSimulR/00new/OncoSimulR/exec Installing library OncoSimulR.so to /home/biocbuild/bbs-3.19-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 4.4.0 (2024-04-24) -- "Puppy Cup"
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)
>
> test_check("OncoSimulR")
Starting FDF-letter-fitness-order Fri May 31 06:20:50 2024
exprtk parser error:
Error[00] Position: 00 Type: [ Syntax Error] Msg: ERR202 - Undefined symbol: 'n_2_3' Expression: n_2_3
exprtk parser error:
Error[00] Position: 00 Type: [ Syntax Error] Msg: ERR202 - Undefined symbol: 'f_2_3' Expression: f_2_3
Ending FDF-small-fitness-specs Fri May 31 06:20:50 2024
Took 0.52
Starting LOD_POM at Fri May 31 06:20:50 2024
Ending LOD_POM at Fri May 31 06:20:58 2024
Took 8.22
Starting test.Z-all-fitness at Fri May 31 06:20:58 2024
Ending test.Z-all-fitness at Fri May 31 06:20:58 2024
Took 0.11
Starting test.Z-driver-counts at Fri May 31 06:20:58 2024
Ending test.Z-driver-counts at Fri May 31 06:20:59 2024
Took 0.1
Starting test.Z-fixation at Fri May 31 06:20:59 2024
Ending test.Z-fixation at Fri May 31 06:20:59 2024
Took 0.2
Starting test.Z-magellan at Fri May 31 06:20:59 2024
Ended test.Z-magellan at Fri May 31 06:21:00 2024
Starting test.Z-mutator at Fri May 31 06:21:00 2024
Ending test.Z-mutator at Fri May 31 06:21:01 2024
Took 0.29
Starting test.Z-mutatorFDF at Fri May 31 06:21:01 2024
Ending test.Z-mutatorFDF at Fri May 31 06:21:01 2024
Took 0.09
Starting test.Z-oncoSimulIndiv at Fri May 31 06:21:01 2024
Ending test.Z-oncoSimulIndiv at Fri May 31 06:21:01 2024
Took 0.34
Starting test.Z-oncoSimulIndivConstant at Fri May 31 06:21:01 2024
Ending test.Z-oncoSimulIndivConstant at Fri May 31 06:21:04 2024
Took 2.47
Starting test.Z-oncoSimulIndivDeath at Fri May 31 06:21:04 2024
Ending test.Z-oncoSimulIndivDeath at Fri May 31 06:21:05 2024
Took 1.37
Starting test.Z-oncoSimulIndivFDF at Fri May 31 06:21:05 2024
Hitted wall time. Exiting.
Hitting wall time is regarded as an error.
Ending test.Z-oncoSimulIndivFDF at Fri May 31 06:21:06 2024
Took 0.63
Starting test.Z-rfitness-landscape at Fri May 31 06:21:06 2024
Ending test.Z-rfitness-landscape at Fri May 31 06:21:06 2024
Took 0.4
Starting Z-sample-only-last tests Fri May 31 06:21:06 2024
Ending Z-sample-only-last tests Fri May 31 06:21:06 2024
Took 0
Starting Z-total-present-drivers tests Fri May 31 06:21:06 2024
Ending Z-total-present-drivers tests Fri May 31 06:21:07 2024
Took 1.21
Dummy empty test Fri May 31 06:21:07 2024
Starting accessible_genotypes at Fri May 31 06:21:07 2024
Ending accessible_genotypes at Fri May 31 06:21:24 2024
Took 16.73
Starting all fitness at Fri May 31 06:21:24 2024
Ending all-fitness at Fri May 31 06:21:29 2024
Took 4.69
Starting test.allFitnessEffectsFDF at Fri May 31 06:21:29 2024
Ending test.allFitnessEffectsFDF at Fri May 31 06:21:29 2024
Took 0.11
Starting test.allFitnessEffectsDeath at Fri May 31 06:21:29 2024
Ending test.allFitnessEffectsDeath at Fri May 31 06:21:29 2024
Took 0.37
Starting test.allFitnessEffectsFDF at Fri May 31 06:21:29 2024
Ending test.allFitnessEffectsFDF at Fri May 31 06:21:30 2024
Took 0.54
Starting driverCounts at Fri May 31 06:21:30 2024
Ending driverCounts at Fri May 31 06:21:35 2024
Took 5.43
Starting epist-order-modules at Fri May 31 06:21:35 2024
Ending epist-order-modules at Fri May 31 06:21:35 2024
Took 0.05
Starting test.evaluatingGenotypesDeath at Fri May 31 06:21:35 2024
Ending test.evaluatingGenotypesDeath at Fri May 31 06:21:35 2024
Took 0.15
Starting test.evaluatingGenotypesFDF at Fri May 31 06:21:35 2024
Ending test.evaluatingGenotypesFDF at Fri May 31 06:21:36 2024
Took 0.16
Starting exercise-plotting-code at Fri May 31 06:21:36 2024
Ending exercise-plotting-code at Fri May 31 06:21:38 2024
Took 2.14
Starting exercise-rfitness at Fri May 31 06:21:38 2024
Ending exercise-rfitness at Fri May 31 06:21:47 2024
Took 9.04
Starting to_Magella at Fri May 31 06:21:47 2024
Ending to_Magella at Fri May 31 06:21:47 2024
Took 0.06
Starting fitness preds at Fri May 31 06:21:47 2024
Observed vs expected, case III
done tries 1
Ending fitness preds long at Fri May 31 06:21:58 2024
Took 11.71
Starting fixation at Fri May 31 06:21:58 2024
Ending fixation at Fri May 31 06:22:11 2024
Took 12.97
Starting test.flfast-additional.R test at Fri May 31 06:22:11 2024
DEBUG2: Value of rnb = nan
DEBUG2: Value of m = 1
DEBUG2: Value of pe = 0
DEBUG2: Value of pm = 0.999993
this is spP
popSize = 1
birth = 1
death = 0
W = 1.00001
R = 1.00001
mutation = 6e-06
timeLastUpdate = 1.23999
absfitness = -inf
numMutablePos = 6
Unrecoverable exception: Algo 2: retval not finite. Aborting.
Ending test.flfast-additional.R test at Fri May 31 06:22:13 2024
Took 1.16
Starting test.flfast-mutator.R test at Fri May 31 06:22:13 2024
Finished test.flfast-mutator.R test at Fri May 31 06:22:14 2024
Took 0.97
Starting genotFitness at Fri May 31 06:22:14 2024
Ending genotFitness at Fri May 31 06:22:14 2024
Took 0.19
Starting genot_fitness_to_epistasis at Fri May 31 06:22:14 2024
Ending genot_fitness_to_epistasis at Fri May 31 06:22:14 2024
Took 0.03
Starting init-mutant tests Fri May 31 06:22:14 2024
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 May 31 06:22:22 2024
Took 7.82
Starting interventions tests Fri May 31 06:22:22 2024
[1] "Checking intervention: intOverA"
[1] "Checking intervention: intOverA"
[1] "Checking intervention: intOverA"
[1] "Checking intervention: intOverA"
[1] "Checking intervention: intOverMultiplicatesA"
In intervention:intOverMultiplicatesA with WhatHappens: n_1 = n_1 * 2. You cannot intervene to generate more population.[1] "Checking intervention: intOverA"
[1] "Checking intervention: intOverA"
[1] "Checking intervention: intOverTotPop"
[1] 0.77 0.77 0.77
[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 May 31 06:22:28 2024
Took 6.12
Starting test.magellan at Fri May 31 06:22:28 2024
Ending test.magellan at Fri May 31 06:22:28 2024
Took 0.24
Starting test.modules-root-no-root at Fri May 31 06:22:28 2024
Ending test.modules-root-no-root at Fri May 31 06:22:28 2024
Took 0.16
Starting at mutPropGrowth Fri May 31 06:22:28 2024
Ended test.mutPropGrowth: Fri May 31 06:22:38 2024
Took 10.07
Starting test.mutator-oncoSimulSample.R test at Fri May 31 06:22:38 2024
Finished test.mutator-oncoSimulSample.R test at Fri May 31 06:22:47 2024
Took 8.98 seconds
Starting test.mutator.R test at Fri May 31 06:22:47 2024[1] 7.991143e-06
[1] 8.798268e-11
Finished test.mutator.R test at Fri May 31 06:23:05 2024
Took 17.96
Starting test.mutatorFDF.R test at Fri May 31 06:23:05 2024
Starting test.no-v1 at Fri May 31 06:23:06 2024
Ending test.no-v1 at Fri May 31 06:23:06 2024
Took 0.01
Starting oncoSimulIndiv-miscell tests Fri May 31 06:23:06 2024
Ending oncoSimulIndiv-miscell tests Fri May 31 06:23:12 2024
Took 6.26
Starting oncoSimulSample-failures tests Fri May 31 06:23:12 2024
Ending oncoSimulSample-failures tests Fri May 31 06:23:17 2024
Took 4.46
Starting oncoSimulSample-limits tests Fri May 31 06:23:17 2024
Ending oncoSimulSample-limits tests Fri May 31 06:23:17 2024
Took 0.11
Starting per-gene-mutation rates at Fri May 31 06:23:17 2024
Ending per-gene-mutation rates at Fri May 31 06:23:48 2024
Took 31.5
Starting plotFitnessLandscape at Fri May 31 06:23:48 2024
Ending plotFitnessLandscape at Fri May 31 06:23:52 2024
Took 3.58
Starting poset-transformations tests Fri May 31 06:23:52 2024
Ending poset-transformations tests Fri May 31 06:24:10 2024
Took 18.09
Starting sample-prob Fri May 31 06:24:10 2024
[1] 2.107548e-20
[1] 3.015301e-11
[1] 2.371825e-10
[1] 2.669947e-11
[1] 5.181752e-13
[1] 1.543105e-12
[1] 1.055257e-15
[1] 2.209903e-16
[1] 8.520567e-09
[1] 2.186318e-10
[1] 5.377819e-08
[1] 5.14023e-08
Ending sample-prob tests Fri May 31 06:24:14 2024
Took 4.58
Starting samplePop tests Fri May 31 06:24:14 2024
Ending samplePop tests Fri May 31 06:24:18 2024
Took 3.42
Starting simuls-runs-examples tests Fri May 31 06:24:18 2024
Ending simuls-runs-examples tests Fri May 31 06:24:23 2024
Took 4.93
Starting user variable tests Fri May 31 06:24:23 2024
[1] "Checking user variable: user_var_1"
[1] "Checking rule: rule_1"
Ending user variable tests Fri May 31 06:24:23 2024
Took 0.18
Starting warning-mutPropGrowth tests Fri May 31 06:24:23 2024
Ending warning-mutPropGrowth tests Fri May 31 06:24:24 2024
Took 0.53
Starting wide2long tests Fri May 31 06:24:24 2024
Ending wide2long tests Fri May 31 06:24:24 2024
Took 0.28
[ FAIL 0 | WARN 18 | SKIP 5 | PASS 8428 ]
══ 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 18 | SKIP 5 | PASS 8428 ]
>
> proc.time()
user system elapsed
234.215 38.719 221.786
OncoSimulR.Rcheck/OncoSimulR-Ex.timings
| name | user | system | elapsed | |
| OncoSimulWide2Long | 0.144 | 0.009 | 0.155 | |
| POM | 0.626 | 0.056 | 0.514 | |
| allFitnessEffects | 1.895 | 0.068 | 1.965 | |
| benchmarks | 0.001 | 0.011 | 0.013 | |
| createInterventions | 0.288 | 0.000 | 0.287 | |
| createUserVars | 0.434 | 0.000 | 0.435 | |
| evalAllGenotypes | 0.214 | 0.012 | 0.225 | |
| example-missing-drivers | 0.274 | 0.004 | 0.279 | |
| examplePosets | 0.276 | 0.000 | 0.275 | |
| examplesFitnessEffects | 0.031 | 0.020 | 0.052 | |
| freq-dep-simul-examples | 0.013 | 0.000 | 0.013 | |
| mcfLs | 0 | 0 | 0 | |
| oncoSimulIndiv | 0.965 | 0.140 | 1.028 | |
| plot.fitnessEffects | 0.229 | 0.008 | 0.238 | |
| plot.oncosimul | 0.465 | 0.008 | 0.473 | |
| plotClonePhylog | 2.158 | 0.120 | 2.278 | |
| plotFitnessLandscape | 2.146 | 0.124 | 2.787 | |
| plotPoset | 0.164 | 0.016 | 0.259 | |
| poset | 0.205 | 0.000 | 0.352 | |
| rfitness | 1.276 | 0.024 | 1.338 | |
| samplePop | 0.071 | 0.101 | 0.201 | |
| simOGraph | 0.139 | 0.051 | 0.130 | |
| to_Magellan | 0.302 | 0.038 | 0.482 | |
| vignette_pre_computed | 0.012 | 0.004 | 0.016 | |