| Back to Multiple platform build/check report for BioC 3.16: simplified long |
|
This page was generated on 2023-04-12 11:05:13 -0400 (Wed, 12 Apr 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 20.04.5 LTS) | x86_64 | 4.2.3 (2023-03-15) -- "Shortstop Beagle" | 4502 |
| palomino4 | Windows Server 2022 Datacenter | x64 | 4.2.3 (2023-03-15 ucrt) -- "Shortstop Beagle" | 4282 |
| lconway | macOS 12.5.1 Monterey | x86_64 | 4.2.3 (2023-03-15) -- "Shortstop Beagle" | 4310 |
| Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X | ||||
|
To the developers/maintainers of the OncoSimulR package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/OncoSimulR.git to reflect on this report. See How and When does the builder pull? When will my changes propagate? for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 1398/2183 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| OncoSimulR 4.0.2 (landing page) Ramon Diaz-Uriarte
| nebbiolo2 | Linux (Ubuntu 20.04.5 LTS) / x86_64 | OK | OK | OK |  | ||||||||
| palomino4 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| lconway | macOS 12.5.1 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| Package: OncoSimulR |
| Version: 4.0.2 |
| Command: /home/biocbuild/bbs-3.16-bioc/R/bin/R CMD check --install=check:OncoSimulR.install-out.txt --library=/home/biocbuild/bbs-3.16-bioc/R/site-library --timings OncoSimulR_4.0.2.tar.gz |
| StartedAt: 2023-04-10 22:29:22 -0400 (Mon, 10 Apr 2023) |
| EndedAt: 2023-04-10 22:54:15 -0400 (Mon, 10 Apr 2023) |
| EllapsedTime: 1493.1 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: OncoSimulR.Rcheck |
| Warnings: 0 |
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###
### Running command:
###
### /home/biocbuild/bbs-3.16-bioc/R/bin/R CMD check --install=check:OncoSimulR.install-out.txt --library=/home/biocbuild/bbs-3.16-bioc/R/site-library --timings OncoSimulR_4.0.2.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.16-bioc/meat/OncoSimulR.Rcheck’
* using R version 4.2.3 (2023-03-15)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* checking for file ‘OncoSimulR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘OncoSimulR’ version ‘4.0.2’
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘OncoSimulR’ can be installed ... OK
* checking installed package size ... NOTE
installed size is 65.4Mb
sub-directories of 1Mb or more:
libs 63.5Mb
* 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-3.16-bioc/meat/OncoSimulR.Rcheck/00check.log’
for details.
OncoSimulR.Rcheck/00install.out
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###
### Running command:
###
### /home/biocbuild/bbs-3.16-bioc/R/bin/R CMD INSTALL OncoSimulR
###
##############################################################################
##############################################################################
* installing to library ‘/home/biocbuild/bbs-3.16-bioc/R/site-library’
* installing *source* package ‘OncoSimulR’ ...
** using staged installation
** libs
gcc -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.16-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-3.16-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.16-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-3.16-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.16-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-3.16-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.16-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-3.16-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.16-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-3.16-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.16-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-3.16-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.16-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-3.16-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.16-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-3.16-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.16-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-3.16-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.16-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-3.16-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.16-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-3.16-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -Wall -c FitnessLandscape/LinearAlgebra.c -o FitnessLandscape/LinearAlgebra.o
FitnessLandscape/LinearAlgebra.c: In function ‘svdcmp’:
FitnessLandscape/LinearAlgebra.c:640:27: warning: ‘l’ may be used uninitialized in this function [-Wmaybe-uninitialized]
640 | v[j][i]=(u[i][j]/u[i][l])/g;
| ^
gcc -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.16-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-3.16-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.16-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-3.16-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.16-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-3.16-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.16-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-3.16-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.16-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-3.16-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.16-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++14 -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -Wall -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.16-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++14 -shared -L/home/biocbuild/bbs-3.16-bioc/R/lib -L/usr/local/lib -o OncoSimulR.so OncoSimulR_init.o RcppExports.o unity_osimul.o -L/home/biocbuild/bbs-3.16-bioc/R/lib -lR
installing via 'install.libs.R' to /home/biocbuild/bbs-3.16-bioc/R/site-library/00LOCK-OncoSimulR/00new/OncoSimulR
[1] ""
Installing fl_statistics fl_generate to /home/biocbuild/bbs-3.16-bioc/R/site-library/00LOCK-OncoSimulR/00new/OncoSimulR/exec
Installing library OncoSimulR.so to /home/biocbuild/bbs-3.16-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 4.2.3 (2023-03-15) -- "Shortstop Beagle"
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 Mon Apr 10 22:30:35 2023
exprtk parser error:
Error[00] Position: 00 Type: [ Syntax Error] Msg: ERR201 - Undefined symbol: 'n_2_3' Expression: n_2_3
exprtk parser error:
Error[00] Position: 00 Type: [ Syntax Error] Msg: ERR201 - Undefined symbol: 'f_2_3' Expression: f_2_3
Ending FDF-small-fitness-specs Mon Apr 10 22:30:36 2023
Took 0.4
Starting LOD_POM at Mon Apr 10 22:30:36 2023
Ending LOD_POM at Mon Apr 10 22:30:52 2023
Took 16.45
Starting test.Z-all-fitness at Mon Apr 10 22:30:52 2023
Ending test.Z-all-fitness at Mon Apr 10 22:30:52 2023
Took 0.1
Starting test.Z-driver-counts at Mon Apr 10 22:30:52 2023
Ending test.Z-driver-counts at Mon Apr 10 22:30:52 2023
Took 0.17
Starting test.Z-fixation at Mon Apr 10 22:30:52 2023
Ending test.Z-fixation at Mon Apr 10 22:30:53 2023
Took 0.63
Starting interventions tests Mon Apr 10 22:30:53 2023
[1] "Checking intervention: intOverBAffectsR"
[1] "Checking intervention: intOverTotPop"
Init Mutant with birth == 1.0
[1] "Checking intervention: intOverBAffectsR"
[1] "Checking intervention: intOverTotPop"
Init Mutant with birth == 1.0
Ending interventions tests Mon Apr 10 22:34:01 2023
Took 187.41
Starting test.Z-magellan at Mon Apr 10 22:34:01 2023
Ended test.Z-magellan at Mon Apr 10 22:34:03 2023
Starting test.Z-mutator at Mon Apr 10 22:34:03 2023
Ending test.Z-mutator at Mon Apr 10 22:34:04 2023
Took 0.71
Starting test.Z-mutatorFDF at Mon Apr 10 22:34:04 2023
Ending test.Z-mutatorFDF at Mon Apr 10 22:34:04 2023
Took 0.17
Starting test.Z-oncoSimulIndiv at Mon Apr 10 22:34:04 2023
Ending test.Z-oncoSimulIndiv at Mon Apr 10 22:34:07 2023
Took 2.32
Starting test.Z-oncoSimulIndivConstant at Mon Apr 10 22:34:07 2023
Ending test.Z-oncoSimulIndivConstant at Mon Apr 10 22:34:10 2023
Took 3.06
Starting test.Z-oncoSimulIndivDeath at Mon Apr 10 22:34:10 2023
Ending test.Z-oncoSimulIndivDeath at Mon Apr 10 22:34:11 2023
Took 1.18
Starting test.Z-oncoSimulIndivFDF at Mon Apr 10 22:34:11 2023
Hitted wall time. Exiting.
Hitting wall time is regarded as an error.
Ending test.Z-oncoSimulIndivFDF at Mon Apr 10 22:34:12 2023
Took 0.54
Starting test.Z-rfitness-landscape at Mon Apr 10 22:34:12 2023
Ending test.Z-rfitness-landscape at Mon Apr 10 22:34:12 2023
Took 0.17
Starting Z-sample-only-last tests Mon Apr 10 22:34:12 2023
Ending Z-sample-only-last tests Mon Apr 10 22:34:12 2023
Took 0
Starting Z-total-present-drivers tests Mon Apr 10 22:34:12 2023
Ending Z-total-present-drivers tests Mon Apr 10 22:34:13 2023
Took 1.23
Dummy empty test Mon Apr 10 22:34:13 2023
Starting accessible_genotypes at Mon Apr 10 22:34:13 2023
Ending accessible_genotypes at Mon Apr 10 22:34:19 2023
Took 5.64
Starting all fitness at Mon Apr 10 22:34:19 2023
Ending all-fitness at Mon Apr 10 22:34:23 2023
Took 4.09
Starting test.allFitnessEffectsFDF at Mon Apr 10 22:34:23 2023
Ending test.allFitnessEffectsFDF at Mon Apr 10 22:34:23 2023
Took 0.14
Starting test.allFitnessEffectsDeath at Mon Apr 10 22:34:23 2023
Ending test.allFitnessEffectsDeath at Mon Apr 10 22:34:23 2023
Took 0.62
Starting test.allFitnessEffectsFDF at Mon Apr 10 22:34:23 2023
Ending test.allFitnessEffectsFDF at Mon Apr 10 22:34:24 2023
Took 0.75
Starting driverCounts at Mon Apr 10 22:34:24 2023
Ending driverCounts at Mon Apr 10 22:34:45 2023
Took 20.99
Starting epist-order-modules at Mon Apr 10 22:34:45 2023
Ending epist-order-modules at Mon Apr 10 22:34:45 2023
Took 0.03
Starting test.evaluatingGenotypesDeath at Mon Apr 10 22:34:45 2023
Ending test.evaluatingGenotypesDeath at Mon Apr 10 22:34:45 2023
Took 0.17
Starting test.evaluatingGenotypesFDF at Mon Apr 10 22:34:45 2023
Ending test.evaluatingGenotypesFDF at Mon Apr 10 22:34:46 2023
Took 0.21
Starting exercise-plotting-code at Mon Apr 10 22:34:46 2023
Ending exercise-plotting-code at Mon Apr 10 22:34:56 2023
Took 10.05
Starting exercise-rfitness at Mon Apr 10 22:34:56 2023
Ending exercise-rfitness at Mon Apr 10 22:35:09 2023
Took 13.57
Starting to_Magella at Mon Apr 10 22:35:09 2023
Ending to_Magella at Mon Apr 10 22:35:09 2023
Took 0.02
Starting fitness preds at Mon Apr 10 22:35:09 2023
Observed vs expected, case III
done tries 1
Ending fitness preds long at Mon Apr 10 22:35:20 2023
Took 10.61
Starting fixation at Mon Apr 10 22:35:20 2023
Ending fixation at Mon Apr 10 22:36:12 2023
Took 52.15
Starting test.flfast-additional.R test at Mon Apr 10 22:36:12 2023
Ending test.flfast-additional.R test at Mon Apr 10 22:36:14 2023
Took 2.21
Starting test.flfast-mutator.R test at Mon Apr 10 22:36:14 2023
Finished test.flfast-mutator.R test at Mon Apr 10 22:36:17 2023
Took 2.7
Starting genotFitness at Mon Apr 10 22:36:17 2023
Ending genotFitness at Mon Apr 10 22:36:17 2023
Took 0.3
Starting genot_fitness_to_epistasis at Mon Apr 10 22:36:17 2023
Ending genot_fitness_to_epistasis at Mon Apr 10 22:36:17 2023
Took 0.09
Starting init-mutant tests Mon Apr 10 22:36:17 2023
exprtk parser error:
Error[00] Position: 18 Type: [ Syntax Error] Msg: ERR201 - Undefined symbol: 'f_2' Expression: 1.1 + 0.7*((f_1 + f_2) > 0.3)
Ending init-mutant tests Mon Apr 10 22:36:32 2023
Took 14.86
Starting interventions tests Mon Apr 10 22:36:32 2023
[1] "Checking intervention: intOverA"
[1] "Checking intervention: intOverA"
[1] "Checking intervention: intOverA"
[1] "Checking intervention: intOverA"
[1] "Checking intervention: intOverMultiplicatesA"
In intervention:intOverMultiplicatesA with WhatHappens: n_1 = n_1 * 2. You cannot intervene to generate more population.[1] "Checking intervention: intOverA"
Init Mutant with birth == 1.0
[1] "Checking intervention: intOverA"
Init Mutant with birth == 1.0
[1] "Checking intervention: intOverTotPop"
[1] "Checking intervention: intOverTotPop"
[1] "Checking intervention: intOverA"
[1] "Checking intervention: intOverB"
[1] "Checking intervention: intOverC"
[1] "Checking intervention: intOverD"
Init Mutant with birth == 1.0
[1] "Checking intervention: intOverA"
[1] "Checking intervention: intOverB"
[1] "Checking intervention: intOverC"
[1] "Checking intervention: intOverD"
Init Mutant with birth == 1.0
[1] "Checking intervention: Bothering R strain, by reducing C"
[1] "Checking user variable: user_var_1"
[1] "Checking rule: rule_1"
[1] "Checking rule: rule_2"
[1] "Checking rule: rule_3"
[1] "Checking intervention: intOverTotPop"
[1] "Checking intervention: intOverTotPop2"
[1] "Checking intervention: intOverTotPop3"
[1] "Checking user variable: user_var_1"
[1] "Checking rule: rule_1"
[1] "Checking rule: rule_2"
[1] "Checking rule: rule_3"
[1] "Checking intervention: intOverTotPop"
Ending interventions tests Mon Apr 10 22:46:08 2023
Took 575.92
Starting test.magellan at Mon Apr 10 22:46:08 2023
Ending test.magellan at Mon Apr 10 22:46:08 2023
Took 0.17
Starting test.modules-root-no-root at Mon Apr 10 22:46:08 2023
Ending test.modules-root-no-root at Mon Apr 10 22:46:08 2023
Took 0.06
Starting at mutPropGrowth Mon Apr 10 22:46:08 2023
Ended test.mutPropGrowth: Mon Apr 10 22:46:39 2023
Took 30.72
Starting test.mutator-oncoSimulSample.R test at Mon Apr 10 22:46:39 2023
Finished test.mutator-oncoSimulSample.R test at Mon Apr 10 22:46:53 2023
Took 13.4 seconds
Starting test.mutator.R test at Mon Apr 10 22:46:53 2023[1] 1.973296e-08
[1] 1.172863e-12
Finished test.mutator.R test at Mon Apr 10 22:47:32 2023
Took 39.4
Starting test.mutatorFDF.R test at Mon Apr 10 22:47:32 2023
Starting test.no-v1 at Mon Apr 10 22:47:33 2023
Ending test.no-v1 at Mon Apr 10 22:47:33 2023
Took 0.01
Starting oncoSimulIndiv-miscell tests Mon Apr 10 22:47:33 2023
Ending oncoSimulIndiv-miscell tests Mon Apr 10 22:48:12 2023
Took 39.31
Starting oncoSimulSample-failures tests Mon Apr 10 22:48:12 2023
Ending oncoSimulSample-failures tests Mon Apr 10 22:48:17 2023
Took 4.69
Starting oncoSimulSample-limits tests Mon Apr 10 22:48:17 2023
Ending oncoSimulSample-limits tests Mon Apr 10 22:48:17 2023
Took 0.17
Starting per-gene-mutation rates at Mon Apr 10 22:48:17 2023
Ending per-gene-mutation rates at Mon Apr 10 22:48:59 2023
Took 42.07
Starting plotFitnessLandscape at Mon Apr 10 22:48:59 2023
Ending plotFitnessLandscape at Mon Apr 10 22:49:02 2023
Took 2.87
Starting poset-transformations tests Mon Apr 10 22:49:02 2023
Ending poset-transformations tests Mon Apr 10 22:49:10 2023
Took 7.8
Starting sample-prob Mon Apr 10 22:49:10 2023
[1] 3.476432e-25
[1] 1.712381e-19
[1] 2.001199e-08
[1] 1.219971e-11
[1] 2.682396e-14
[1] 3.516311e-12
[1] 5.303404e-12
[1] 3.04692e-16
[1] 4.656784e-07
[1] 1.154491e-10
[1] 5.090341e-11
[1] 9.813075e-08
Ending sample-prob tests Mon Apr 10 22:49:25 2023
Took 15.13
Starting samplePop tests Mon Apr 10 22:49:25 2023
Ending samplePop tests Mon Apr 10 22:49:38 2023
Took 13.08
Starting simuls-runs-examples tests Mon Apr 10 22:49:38 2023
Ending simuls-runs-examples tests Mon Apr 10 22:50:06 2023
Took 28.18
Starting user variable tests Mon Apr 10 22:50:06 2023
[1] "Checking user variable: user_var_1"
[1] "Checking rule: rule_1"
Ending user variable tests Mon Apr 10 22:50:06 2023
Took 0.06
Starting warning-mutPropGrowth tests Mon Apr 10 22:50:06 2023
Ending warning-mutPropGrowth tests Mon Apr 10 22:50:07 2023
Took 0.82
Starting wide2long tests Mon Apr 10 22:50:07 2023
Ending wide2long tests Mon Apr 10 22:50:08 2023
Took 0.76
[ FAIL 0 | WARN 16 | SKIP 5 | PASS 12474 ]
══ Skipped tests ═══════════════════════════════════════════════════════════════
• empty test (5)
[ FAIL 0 | WARN 16 | SKIP 5 | PASS 12474 ]
>
> proc.time()
user system elapsed
951.540 65.611 1176.415
OncoSimulR.Rcheck/OncoSimulR-Ex.timings
| name | user | system | elapsed | |
| OncoSimulWide2Long | 0.588 | 0.056 | 0.647 | |
| POM | 0.513 | 0.144 | 0.390 | |
| allFitnessEffects | 1.549 | 0.016 | 1.567 | |
| benchmarks | 0.008 | 0.000 | 0.007 | |
| createInterventions | 0.289 | 0.000 | 0.289 | |
| createUserVars | 0.434 | 0.008 | 0.442 | |
| evalAllGenotypes | 0.190 | 0.000 | 0.191 | |
| example-missing-drivers | 0.222 | 0.020 | 0.241 | |
| examplePosets | 0.308 | 0.000 | 0.308 | |
| examplesFitnessEffects | 0.039 | 0.000 | 0.040 | |
| freq-dep-simul-examples | 0.009 | 0.000 | 0.010 | |
| mcfLs | 0 | 0 | 0 | |
| oncoSimulIndiv | 1.363 | 0.150 | 1.442 | |
| plot.fitnessEffects | 0.211 | 0.008 | 0.219 | |
| plot.oncosimul | 0.900 | 0.000 | 0.899 | |
| plotClonePhylog | 1.403 | 0.064 | 1.466 | |
| plotFitnessLandscape | 1.239 | 0.000 | 1.238 | |
| plotPoset | 0.119 | 0.000 | 0.119 | |
| poset | 0.141 | 0.004 | 0.144 | |
| rfitness | 0.649 | 0.034 | 0.683 | |
| samplePop | 0.139 | 0.098 | 0.182 | |
| simOGraph | 0.067 | 0.000 | 0.067 | |
| to_Magellan | 0.222 | 0.020 | 0.241 | |
| vignette_pre_computed | 0.009 | 0.000 | 0.009 | |