| Back to Multiple platform build/check report for BioC 3.17 |
|
This page was generated on 2023-04-12 10:55:39 -0400 (Wed, 12 Apr 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 22.04.1 LTS) | x86_64 | 4.3.0 alpha (2023-04-03 r84154) | 4547 |
| nebbiolo2 | Linux (Ubuntu 20.04.5 LTS) | x86_64 | R Under development (unstable) (2023-02-14 r83833) -- "Unsuffered Consequences" | 4333 |
| 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: - 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. Note: If "R CMD check" recently failed on the Linux builder over a missing dependency, add the missing dependency to "Suggests" in your DESCRIPTION file. See the Renviron.bioc for details. |
| Package 1418/2207 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| OncoSimulR 4.1.4 (landing page) Ramon Diaz-Uriarte
| nebbiolo1 | Linux (Ubuntu 22.04.1 LTS) / x86_64 | OK | OK | OK | |||||||||
| nebbiolo2 | Linux (Ubuntu 20.04.5 LTS) / x86_64 | OK | OK | OK | ||||||||||
| Package: OncoSimulR |
| Version: 4.1.4 |
| 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_4.1.4.tar.gz |
| StartedAt: 2023-04-12 08:01:11 -0400 (Wed, 12 Apr 2023) |
| EndedAt: 2023-04-12 08:16:22 -0400 (Wed, 12 Apr 2023) |
| EllapsedTime: 910.9 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: OncoSimulR.Rcheck |
| Warnings: 0 |
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### 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_4.1.4.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/OncoSimulR.Rcheck’
* using R Under development (unstable) (2023-02-14 r83833)
* using platform: x86_64-pc-linux-gnu (64-bit)
* R was compiled by
gcc (Ubuntu 9.4.0-1ubuntu1~20.04.1) 9.4.0
GNU Fortran (Ubuntu 9.4.0-1ubuntu1~20.04.1) 9.4.0
* running under: Ubuntu 20.04.6 LTS
* using session charset: UTF-8
* checking for file ‘OncoSimulR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘OncoSimulR’ version ‘4.1.4’
* 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 9.4.0-1ubuntu1~20.04.1) 9.4.0’
* used C++ compiler: ‘g++ (Ubuntu 9.4.0-1ubuntu1~20.04.1) 9.4.0’
* checking installed package size ... NOTE
installed size is 66.3Mb
sub-directories of 1Mb or more:
libs 64.4Mb
* 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
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###
### Running command:
###
### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL OncoSimulR
###
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* 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 9.4.0-1ubuntu1~20.04.1) 9.4.0’
using C++ compiler: ‘g++ (Ubuntu 9.4.0-1ubuntu1~20.04.1) 9.4.0’
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
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-3.17-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 Under development (unstable) (2023-02-14 r83833) -- "Unsuffered Consequences"
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 Wed Apr 12 08:02:33 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 Wed Apr 12 08:02:34 2023
Took 0.45
Starting LOD_POM at Wed Apr 12 08:02:34 2023
Ending LOD_POM at Wed Apr 12 08:02:50 2023
Took 16.46
Starting test.Z-all-fitness at Wed Apr 12 08:02:50 2023
Ending test.Z-all-fitness at Wed Apr 12 08:02:51 2023
Took 0.1
Starting test.Z-driver-counts at Wed Apr 12 08:02:51 2023
Ending test.Z-driver-counts at Wed Apr 12 08:02:51 2023
Took 0.18
Starting test.Z-fixation at Wed Apr 12 08:02:51 2023
Ending test.Z-fixation at Wed Apr 12 08:02:51 2023
Took 0.57
Starting test.Z-magellan at Wed Apr 12 08:02:51 2023
Ended test.Z-magellan at Wed Apr 12 08:02:53 2023
Starting test.Z-mutator at Wed Apr 12 08:02:53 2023
Ending test.Z-mutator at Wed Apr 12 08:02:53 2023
Took 0.31
Starting test.Z-mutatorFDF at Wed Apr 12 08:02:53 2023
Ending test.Z-mutatorFDF at Wed Apr 12 08:02:53 2023
Took 0.11
Starting test.Z-oncoSimulIndiv at Wed Apr 12 08:02:53 2023
Ending test.Z-oncoSimulIndiv at Wed Apr 12 08:02:55 2023
Took 1.56
Starting test.Z-oncoSimulIndivConstant at Wed Apr 12 08:02:55 2023
Ending test.Z-oncoSimulIndivConstant at Wed Apr 12 08:02:58 2023
Took 2.54
Starting test.Z-oncoSimulIndivDeath at Wed Apr 12 08:02:58 2023
Ending test.Z-oncoSimulIndivDeath at Wed Apr 12 08:02:59 2023
Took 0.95
Starting test.Z-oncoSimulIndivFDF at Wed Apr 12 08:02:59 2023
Hitted wall time. Exiting.
Hitting wall time is regarded as an error.
Ending test.Z-oncoSimulIndivFDF at Wed Apr 12 08:03:00 2023
Took 0.96
Starting test.Z-rfitness-landscape at Wed Apr 12 08:03:00 2023
Ending test.Z-rfitness-landscape at Wed Apr 12 08:03:00 2023
Took 0.17
Starting Z-sample-only-last tests Wed Apr 12 08:03:00 2023
Ending Z-sample-only-last tests Wed Apr 12 08:03:00 2023
Took 0
Starting Z-total-present-drivers tests Wed Apr 12 08:03:00 2023
Ending Z-total-present-drivers tests Wed Apr 12 08:03:01 2023
Took 1.19
Dummy empty test Wed Apr 12 08:03:01 2023
Starting accessible_genotypes at Wed Apr 12 08:03:01 2023
Ending accessible_genotypes at Wed Apr 12 08:03:07 2023
Took 5.98
Starting all fitness at Wed Apr 12 08:03:07 2023
Ending all-fitness at Wed Apr 12 08:03:11 2023
Took 4.1
Starting test.allFitnessEffectsFDF at Wed Apr 12 08:03:11 2023
Ending test.allFitnessEffectsFDF at Wed Apr 12 08:03:11 2023
Took 0.12
Starting test.allFitnessEffectsDeath at Wed Apr 12 08:03:11 2023
Ending test.allFitnessEffectsDeath at Wed Apr 12 08:03:11 2023
Took 0.35
Starting test.allFitnessEffectsFDF at Wed Apr 12 08:03:11 2023
Ending test.allFitnessEffectsFDF at Wed Apr 12 08:03:12 2023
Took 0.37
Starting driverCounts at Wed Apr 12 08:03:12 2023
Ending driverCounts at Wed Apr 12 08:03:22 2023
Took 10.55
Starting epist-order-modules at Wed Apr 12 08:03:22 2023
Ending epist-order-modules at Wed Apr 12 08:03:22 2023
Took 0.05
Starting test.evaluatingGenotypesDeath at Wed Apr 12 08:03:22 2023
Ending test.evaluatingGenotypesDeath at Wed Apr 12 08:03:23 2023
Took 0.28
Starting test.evaluatingGenotypesFDF at Wed Apr 12 08:03:23 2023
Ending test.evaluatingGenotypesFDF at Wed Apr 12 08:03:23 2023
Took 0.23
Starting exercise-plotting-code at Wed Apr 12 08:03:23 2023
Ending exercise-plotting-code at Wed Apr 12 08:03:30 2023
Took 6.79
Starting exercise-rfitness at Wed Apr 12 08:03:30 2023
Ending exercise-rfitness at Wed Apr 12 08:03:38 2023
Took 8.14
Starting to_Magella at Wed Apr 12 08:03:38 2023
Ending to_Magella at Wed Apr 12 08:03:38 2023
Took 0.03
Starting fitness preds at Wed Apr 12 08:03:38 2023
Observed vs expected, case III
done tries 1
Ending fitness preds long at Wed Apr 12 08:03:49 2023
Took 11.39
Starting fixation at Wed Apr 12 08:03:49 2023
Ending fixation at Wed Apr 12 08:04:26 2023
Took 36.59
Starting test.flfast-additional.R test at Wed Apr 12 08:04:26 2023
Ending test.flfast-additional.R test at Wed Apr 12 08:04:27 2023
Took 1.47
Starting test.flfast-mutator.R test at Wed Apr 12 08:04:27 2023
Finished test.flfast-mutator.R test at Wed Apr 12 08:04:29 2023
Took 2.04
Starting genotFitness at Wed Apr 12 08:04:29 2023
Ending genotFitness at Wed Apr 12 08:04:30 2023
Took 0.14
Starting genot_fitness_to_epistasis at Wed Apr 12 08:04:30 2023
Ending genot_fitness_to_epistasis at Wed Apr 12 08:04:30 2023
Took 0.04
Starting init-mutant tests Wed Apr 12 08:04:30 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 Wed Apr 12 08:04:39 2023
Took 9.23
Starting interventions tests Wed Apr 12 08:04:39 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] 0.78 0.78 0.78
[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 Wed Apr 12 08:04:43 2023
Took 4.31
Starting test.magellan at Wed Apr 12 08:04:43 2023
Ending test.magellan at Wed Apr 12 08:04:43 2023
Took 0.14
Starting test.modules-root-no-root at Wed Apr 12 08:04:43 2023
Ending test.modules-root-no-root at Wed Apr 12 08:04:43 2023
Took 0.06
Starting at mutPropGrowth Wed Apr 12 08:04:43 2023
Ended test.mutPropGrowth: Wed Apr 12 08:04:58 2023
Took 14.07
Starting test.mutator-oncoSimulSample.R test at Wed Apr 12 08:04:58 2023
Finished test.mutator-oncoSimulSample.R test at Wed Apr 12 08:05:09 2023
Took 11.42 seconds
Starting test.mutator.R test at Wed Apr 12 08:05:09 2023[1] 1.280391e-06
[1] 5.517368e-11
Finished test.mutator.R test at Wed Apr 12 08:05:28 2023
Took 18.98
Starting test.mutatorFDF.R test at Wed Apr 12 08:05:28 2023
Starting test.no-v1 at Wed Apr 12 08:05:29 2023
Ending test.no-v1 at Wed Apr 12 08:05:29 2023
Took 0.01
Starting oncoSimulIndiv-miscell tests Wed Apr 12 08:05:29 2023
Ending oncoSimulIndiv-miscell tests Wed Apr 12 08:05:53 2023
Took 24.68
Starting oncoSimulSample-failures tests Wed Apr 12 08:05:53 2023
Ending oncoSimulSample-failures tests Wed Apr 12 08:05:58 2023
Took 4.12
Starting oncoSimulSample-limits tests Wed Apr 12 08:05:58 2023
Ending oncoSimulSample-limits tests Wed Apr 12 08:05:58 2023
Took 0.11
Starting per-gene-mutation rates at Wed Apr 12 08:05:58 2023
Ending per-gene-mutation rates at Wed Apr 12 08:06:38 2023
Took 40.13
Starting plotFitnessLandscape at Wed Apr 12 08:06:38 2023
Ending plotFitnessLandscape at Wed Apr 12 08:06:40 2023
Took 2.54
Starting poset-transformations tests Wed Apr 12 08:06:40 2023
Ending poset-transformations tests Wed Apr 12 08:06:47 2023
Took 7.02
Starting sample-prob Wed Apr 12 08:06:47 2023
[1] 2.332661e-26
[1] 4.128293e-11
[1] 2.142457e-10
[1] 1.153137e-11
[1] 1.134596e-14
[1] 3.652891e-16
[1] 4.63941e-13
[1] 1.42346e-10
[1] 4.597894e-10
[1] 8.734982e-10
[1] 2.480517e-09
[1] 5.690531e-10
Ending sample-prob tests Wed Apr 12 08:07:01 2023
Took 13.35
Starting samplePop tests Wed Apr 12 08:07:01 2023
Ending samplePop tests Wed Apr 12 08:07:22 2023
Took 21.67
Starting simuls-runs-examples tests Wed Apr 12 08:07:22 2023
Ending simuls-runs-examples tests Wed Apr 12 08:08:25 2023
Took 62.56
Starting user variable tests Wed Apr 12 08:08:25 2023
[1] "Checking user variable: user_var_1"
[1] "Checking rule: rule_1"
Ending user variable tests Wed Apr 12 08:08:25 2023
Took 0.13
Starting warning-mutPropGrowth tests Wed Apr 12 08:08:25 2023
Ending warning-mutPropGrowth tests Wed Apr 12 08:08:28 2023
Took 3.02
Starting wide2long tests Wed Apr 12 08:08:28 2023
Ending wide2long tests Wed Apr 12 08:08:29 2023
Took 1.3
[ FAIL 0 | WARN 13 | SKIP 5 | PASS 8420 ]
══ Skipped tests ═══════════════════════════════════════════════════════════════
• empty test (5)
[ FAIL 0 | WARN 13 | SKIP 5 | PASS 8420 ]
>
> proc.time()
user system elapsed
384.964 56.683 364.267
OncoSimulR.Rcheck/OncoSimulR-Ex.timings
| name | user | system | elapsed | |
| OncoSimulWide2Long | 0.627 | 0.060 | 0.691 | |
| POM | 0.515 | 0.120 | 0.347 | |
| allFitnessEffects | 1.845 | 0.044 | 1.891 | |
| benchmarks | 0.019 | 0.000 | 0.019 | |
| createInterventions | 0.302 | 0.000 | 0.302 | |
| createUserVars | 0.462 | 0.020 | 0.482 | |
| evalAllGenotypes | 0.223 | 0.036 | 0.259 | |
| example-missing-drivers | 0.236 | 0.024 | 0.260 | |
| examplePosets | 0.339 | 0.004 | 0.344 | |
| examplesFitnessEffects | 0.037 | 0.004 | 0.041 | |
| freq-dep-simul-examples | 0.011 | 0.000 | 0.011 | |
| mcfLs | 0.000 | 0.001 | 0.001 | |
| oncoSimulIndiv | 1.668 | 0.363 | 1.905 | |
| plot.fitnessEffects | 0.209 | 0.016 | 0.224 | |
| plot.oncosimul | 1.161 | 0.072 | 1.233 | |
| plotClonePhylog | 1.686 | 0.115 | 1.801 | |
| plotFitnessLandscape | 1.519 | 0.000 | 1.519 | |
| plotPoset | 0.113 | 0.000 | 0.113 | |
| poset | 0.131 | 0.008 | 0.138 | |
| rfitness | 0.747 | 0.002 | 0.749 | |
| samplePop | 0.185 | 0.169 | 0.237 | |
| simOGraph | 0.112 | 0.000 | 0.112 | |
| to_Magellan | 0.238 | 0.072 | 0.309 | |
| vignette_pre_computed | 0.013 | 0.000 | 0.013 | |