Ramon Diaz-Uriarte
| Snapshot Date: 2024-12-23 13:40 -0500 (Mon, 23 Dec 2024) |
| git_url: https://git.bioconductor.org/packages/OncoSimulR |
| git_branch: devel |
| git_last_commit: 3291e0a |
| git_last_commit_date: 2024-10-29 09:53:24 -0500 (Tue, 29 Oct 2024) |
| Back to Multiple platform build/check report for BioC 3.21: simplified long |
|
This page was generated on 2024-12-24 11:40 -0500 (Tue, 24 Dec 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | R Under development (unstable) (2024-10-21 r87258) -- "Unsuffered Consequences" | 4754 |
| palomino7 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2024-10-26 r87273 ucrt) -- "Unsuffered Consequences" | 4472 |
| lconway | macOS 12.7.1 Monterey | x86_64 | R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" | 4426 |
| kjohnson3 | macOS 13.7.1 Ventura | arm64 | R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" | 4381 |
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | R Under development (unstable) (2024-11-24 r87369) -- "Unsuffered Consequences" | 4373 |
| 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 1454/2274 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| OncoSimulR 4.9.0 (landing page) Ramon Diaz-Uriarte
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino7 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson3 | macOS 13.7.1 Ventura / arm64 | ... NOT SUPPORTED ... | ||||||||||||
| 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. |
| Package: OncoSimulR |
| Version: 4.9.0 |
| Command: /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:OncoSimulR.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings OncoSimulR_4.9.0.tar.gz |
| StartedAt: 2024-12-24 00:34:09 -0500 (Tue, 24 Dec 2024) |
| EndedAt: 2024-12-24 00:40:11 -0500 (Tue, 24 Dec 2024) |
| EllapsedTime: 361.6 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: OncoSimulR.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:OncoSimulR.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings OncoSimulR_4.9.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/OncoSimulR.Rcheck’
* using R Under development (unstable) (2024-10-21 r87258)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0
GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0
* running under: Ubuntu 24.04.1 LTS
* using session charset: UTF-8
* checking for file ‘OncoSimulR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘OncoSimulR’ version ‘4.9.0’
* 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 ... NOTE
Found the following hidden files and directories:
.BBSoptions
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* 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 13.3.0-6ubuntu2~24.04) 13.3.0’
* used C++ compiler: ‘g++ (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’
* checking installed package size ... INFO
installed size is 19.6Mb
sub-directories of 1Mb or more:
libs 18.2Mb
* 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 whether startup messages can be suppressed ... 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 ... NOTE
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
plot.oncosimul.Rd: brewer.pal
plotClonePhylog.Rd: get.adjacency
plotFitnessLandscape.Rd: ggrepel
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
* 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-3.21-bioc/meat/OncoSimulR.Rcheck/00check.log’
for details.
OncoSimulR.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD INSTALL OncoSimulR ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.21-bioc/R/site-library’ * installing *source* package ‘OncoSimulR’ ... ** using staged installation ** libs using C compiler: ‘gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’ using C++ compiler: ‘g++ (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’ gcc -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I/usr/local/include -DSTRICT_R_HEADERS=1 -fpic -g -O2 -Wall -c FitnessLandscape/gamma.c -o FitnessLandscape/gamma.o gcc -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I/usr/local/include -DSTRICT_R_HEADERS=1 -fpic -g -O2 -Wall -c FitnessLandscape/landscape.c -o FitnessLandscape/landscape.o gcc -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I/usr/local/include -DSTRICT_R_HEADERS=1 -fpic -g -O2 -Wall -c FitnessLandscape/random.c -o FitnessLandscape/random.o gcc -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I/usr/local/include -DSTRICT_R_HEADERS=1 -fpic -g -O2 -Wall -c FitnessLandscape/sort.c -o FitnessLandscape/sort.o gcc -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I/usr/local/include -DSTRICT_R_HEADERS=1 -fpic -g -O2 -Wall -c FitnessLandscape/chain.c -o FitnessLandscape/chain.o gcc -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I/usr/local/include -DSTRICT_R_HEADERS=1 -fpic -g -O2 -Wall -c FitnessLandscape/input.c -o FitnessLandscape/input.o gcc -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I/usr/local/include -DSTRICT_R_HEADERS=1 -fpic -g -O2 -Wall -c FitnessLandscape/genotypes.c -o FitnessLandscape/genotypes.o gcc -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I/usr/local/include -DSTRICT_R_HEADERS=1 -fpic -g -O2 -Wall -c FitnessLandscape/ordered_pairs.c -o FitnessLandscape/ordered_pairs.o gcc -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I/usr/local/include -DSTRICT_R_HEADERS=1 -fpic -g -O2 -Wall -c FitnessLandscape/calculus.c -o FitnessLandscape/calculus.o gcc -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I/usr/local/include -DSTRICT_R_HEADERS=1 -fpic -g -O2 -Wall -c FitnessLandscape/vector.c -o FitnessLandscape/vector.o gcc -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I/usr/local/include -DSTRICT_R_HEADERS=1 -fpic -g -O2 -Wall -c FitnessLandscape/generalized_chain.c -o FitnessLandscape/generalized_chain.o gcc -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I/usr/local/include -DSTRICT_R_HEADERS=1 -fpic -g -O2 -Wall -c FitnessLandscape/LinearAlgebra.c -o FitnessLandscape/LinearAlgebra.o gcc -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I/usr/local/include -DSTRICT_R_HEADERS=1 -fpic -g -O2 -Wall -c FitnessLandscape/summary_statistics.c -o FitnessLandscape/summary_statistics.o gcc -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I/usr/local/include -DSTRICT_R_HEADERS=1 -fpic -g -O2 -Wall -c FitnessLandscape/epistasis_type.c -o FitnessLandscape/epistasis_type.o gcc -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I/usr/local/include -DSTRICT_R_HEADERS=1 -fpic -g -O2 -Wall -c FitnessLandscape/decomposition.c -o FitnessLandscape/decomposition.o gcc -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I/usr/local/include -DSTRICT_R_HEADERS=1 -fpic -g -O2 -Wall -c FitnessLandscape/models.c -o FitnessLandscape/models.o gcc -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I/usr/local/include -DSTRICT_R_HEADERS=1 -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-3.21-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I/usr/local/include -DSTRICT_R_HEADERS=1 -fpic -g -O2 -Wall -c OncoSimulR_init.c -o OncoSimulR_init.o g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I/usr/local/include -DSTRICT_R_HEADERS=1 -fpic -g -O2 -Wall -DR_NO_REMAP -c RcppExports.cpp -o RcppExports.o g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I/usr/local/include -DSTRICT_R_HEADERS=1 -fpic -g -O2 -Wall -DR_NO_REMAP -c unity_osimul.cpp -o unity_osimul.o g++ -std=gnu++17 -shared -L/home/biocbuild/bbs-3.21-bioc/R/lib -L/usr/local/lib -o OncoSimulR.so OncoSimulR_init.o RcppExports.o unity_osimul.o -L/home/biocbuild/bbs-3.21-bioc/R/lib -lR installing via 'install.libs.R' to /home/biocbuild/bbs-3.21-bioc/R/site-library/00LOCK-OncoSimulR/00new/OncoSimulR [1] "" Installing fl_statistics fl_generate to /home/biocbuild/bbs-3.21-bioc/R/site-library/00LOCK-OncoSimulR/00new/OncoSimulR/exec Installing library OncoSimulR.so to /home/biocbuild/bbs-3.21-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) (2024-10-21 r87258) -- "Unsuffered Consequences"
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)
This is package OncoSimulR. If you are running it on an aarch64 (arm64) platform with a MacOS note that the package fails some tests in that platform + OS that I have no way of debugging. Please read file README_tests_kjohnson3_aarch64-apple-darwin20.txt in the tests directory. As of 2024-10-09, this platform is unsupported until we can properly debug it.
>
> test_check("OncoSimulR")
Starting FDF-letter-fitness-order Tue Dec 24 00:35:17 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 Tue Dec 24 00:35:17 2024
Took 0.45
Starting LOD_POM at Tue Dec 24 00:35:17 2024
Ending LOD_POM at Tue Dec 24 00:35:29 2024
Took 11.77
Starting test.Z-all-fitness at Tue Dec 24 00:35:29 2024
Ending test.Z-all-fitness at Tue Dec 24 00:35:29 2024
Took 0.09
Starting test.Z-driver-counts at Tue Dec 24 00:35:29 2024
Ending test.Z-driver-counts at Tue Dec 24 00:35:29 2024
Took 0.11
Starting test.Z-fixation at Tue Dec 24 00:35:29 2024
Ending test.Z-fixation at Tue Dec 24 00:35:30 2024
Took 0.21
Starting test.Z-magellan at Tue Dec 24 00:35:30 2024
Ended test.Z-magellan at Tue Dec 24 00:35:31 2024
Starting test.Z-mutator at Tue Dec 24 00:35:31 2024
Ending test.Z-mutator at Tue Dec 24 00:35:31 2024
Took 0.33
Starting test.Z-mutatorFDF at Tue Dec 24 00:35:31 2024
Ending test.Z-mutatorFDF at Tue Dec 24 00:35:31 2024
Took 0.09
Starting test.Z-oncoSimulIndiv at Tue Dec 24 00:35:32 2024
Ending test.Z-oncoSimulIndiv at Tue Dec 24 00:35:32 2024
Took 0.34
Starting test.Z-oncoSimulIndivConstant at Tue Dec 24 00:35:32 2024
Ending test.Z-oncoSimulIndivConstant at Tue Dec 24 00:35:34 2024
Took 2.2
Starting test.Z-oncoSimulIndivDeath at Tue Dec 24 00:35:34 2024
Ending test.Z-oncoSimulIndivDeath at Tue Dec 24 00:35:35 2024
Took 0.74
Starting test.Z-oncoSimulIndivFDF at Tue Dec 24 00:35:35 2024
Hitted wall time. Exiting.
Hitting wall time is regarded as an error.
Ending test.Z-oncoSimulIndivFDF at Tue Dec 24 00:35:36 2024
Took 0.72
Starting test.Z-rfitness-landscape at Tue Dec 24 00:35:36 2024
Ending test.Z-rfitness-landscape at Tue Dec 24 00:35:36 2024
Took 0.18
Starting Z-sample-only-last tests Tue Dec 24 00:35:36 2024
Ending Z-sample-only-last tests Tue Dec 24 00:35:36 2024
Took 0
Starting Z-total-present-drivers tests Tue Dec 24 00:35:36 2024
Ending Z-total-present-drivers tests Tue Dec 24 00:35:36 2024
Took 0.72
Dummy empty test Tue Dec 24 00:35:36 2024
Starting accessible_genotypes at Tue Dec 24 00:35:36 2024
Ending accessible_genotypes at Tue Dec 24 00:35:43 2024
Took 6.48
Starting all fitness at Tue Dec 24 00:35:43 2024
Ending all-fitness at Tue Dec 24 00:35:47 2024
Took 4.42
Starting test.allFitnessEffectsFDF at Tue Dec 24 00:35:47 2024
Ending test.allFitnessEffectsFDF at Tue Dec 24 00:35:47 2024
Took 0.11
Starting test.allFitnessEffectsDeath at Tue Dec 24 00:35:47 2024
Ending test.allFitnessEffectsDeath at Tue Dec 24 00:35:48 2024
Took 0.35
Starting test.allFitnessEffectsFDF at Tue Dec 24 00:35:48 2024
Ending test.allFitnessEffectsFDF at Tue Dec 24 00:35:48 2024
Took 0.36
Starting driverCounts at Tue Dec 24 00:35:48 2024
Ending driverCounts at Tue Dec 24 00:35:55 2024
Took 7.01
Starting epist-order-modules at Tue Dec 24 00:35:55 2024
Ending epist-order-modules at Tue Dec 24 00:35:55 2024
Took 0.07
Starting test.evaluatingGenotypesDeath at Tue Dec 24 00:35:55 2024
Ending test.evaluatingGenotypesDeath at Tue Dec 24 00:35:55 2024
Took 0.17
Starting test.evaluatingGenotypesFDF at Tue Dec 24 00:35:55 2024
Ending test.evaluatingGenotypesFDF at Tue Dec 24 00:35:56 2024
Took 0.18
Starting exercise-plotting-code at Tue Dec 24 00:35:56 2024
Ending exercise-plotting-code at Tue Dec 24 00:35:58 2024
Took 2.25
Starting exercise-rfitness at Tue Dec 24 00:35:58 2024
Ending exercise-rfitness at Tue Dec 24 00:36:07 2024
Took 8.67
Starting to_Magella at Tue Dec 24 00:36:07 2024
Ending to_Magella at Tue Dec 24 00:36:07 2024
Took 0.03
Starting fitness preds at Tue Dec 24 00:36:07 2024
Observed vs expected, case III
done tries 1
Ending fitness preds long at Tue Dec 24 00:36:11 2024
Took 4.65
Starting fixation at Tue Dec 24 00:36:11 2024
Ending fixation at Tue Dec 24 00:36:23 2024
Took 11.49
Starting test.flfast-additional.R test at Tue Dec 24 00:36:23 2024
Ending test.flfast-additional.R test at Tue Dec 24 00:36:24 2024
Took 1.06
Starting test.flfast-mutator.R test at Tue Dec 24 00:36:24 2024
Finished test.flfast-mutator.R test at Tue Dec 24 00:36:25 2024
Took 1.1
Starting genotFitness at Tue Dec 24 00:36:25 2024
Ending genotFitness at Tue Dec 24 00:36:25 2024
Took 0.19
Starting genot_fitness_to_epistasis at Tue Dec 24 00:36:25 2024
Ending genot_fitness_to_epistasis at Tue Dec 24 00:36:25 2024
Took 0.04
Starting init-mutant tests Tue Dec 24 00:36:25 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 Tue Dec 24 00:36:30 2024
Took 5.07
Starting interventions tests Tue Dec 24 00:36:30 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] 0.45 0.45 0.45
[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 Tue Dec 24 00:36:34 2024
Took 3.88
Starting test.magellan at Tue Dec 24 00:36:34 2024
Ending test.magellan at Tue Dec 24 00:36:34 2024
Took 0.13
Starting test.modules-root-no-root at Tue Dec 24 00:36:34 2024
Ending test.modules-root-no-root at Tue Dec 24 00:36:34 2024
Took 0.07
Starting at mutPropGrowth Tue Dec 24 00:36:34 2024
Ended test.mutPropGrowth: Tue Dec 24 00:36:39 2024
Took 4.99
Starting test.mutator-oncoSimulSample.R test at Tue Dec 24 00:36:39 2024
Finished test.mutator-oncoSimulSample.R test at Tue Dec 24 00:36:47 2024
Took 7.44 seconds
Starting test.mutator.R test at Tue Dec 24 00:36:47 2024[1] 2.224799e-08
[1] 2.397223e-12
Finished test.mutator.R test at Tue Dec 24 00:36:58 2024
Took 10.82
Starting test.mutatorFDF.R test at Tue Dec 24 00:36:58 2024
Starting test.no-v1 at Tue Dec 24 00:36:58 2024
Ending test.no-v1 at Tue Dec 24 00:36:58 2024
Took 0.01
Starting oncoSimulIndiv-miscell tests Tue Dec 24 00:36:58 2024
Ending oncoSimulIndiv-miscell tests Tue Dec 24 00:37:05 2024
Took 6.39
Starting oncoSimulSample-failures tests Tue Dec 24 00:37:05 2024
Ending oncoSimulSample-failures tests Tue Dec 24 00:37:09 2024
Took 4
Starting oncoSimulSample-limits tests Tue Dec 24 00:37:09 2024
Ending oncoSimulSample-limits tests Tue Dec 24 00:37:09 2024
Took 0.07
Starting per-gene-mutation rates at Tue Dec 24 00:37:09 2024
Ending per-gene-mutation rates at Tue Dec 24 00:37:30 2024
Took 21.39
Starting plotFitnessLandscape at Tue Dec 24 00:37:30 2024
Ending plotFitnessLandscape at Tue Dec 24 00:37:33 2024
Took 3.38
Starting poset-transformations tests Tue Dec 24 00:37:33 2024
Ending poset-transformations tests Tue Dec 24 00:37:43 2024
Took 9.87
Starting sample-prob Tue Dec 24 00:37:43 2024
[1] 3.446831e-30
[1] 4.624111e-15
[1] 6.729231e-09
[1] 1.269161e-11
[1] 2.179041e-15
[1] 1.197733e-14
[1] 5.299261e-09
[1] 5.504593e-13
[1] 6.081113e-10
[1] 1.166409e-09
[1] 2.525157e-09
[1] 3.509921e-08
Ending sample-prob tests Tue Dec 24 00:37:49 2024
Took 5.36
Starting samplePop tests Tue Dec 24 00:37:49 2024
Ending samplePop tests Tue Dec 24 00:37:52 2024
Took 3.84
Starting simuls-runs-examples tests Tue Dec 24 00:37:52 2024
Ending simuls-runs-examples tests Tue Dec 24 00:37:56 2024
Took 3.43
Starting user variable tests Tue Dec 24 00:37:56 2024
[1] "Checking user variable: user_var_1"
[1] "Checking rule: rule_1"
Ending user variable tests Tue Dec 24 00:37:56 2024
Took 0.1
Starting warning-mutPropGrowth tests Tue Dec 24 00:37:56 2024
Ending warning-mutPropGrowth tests Tue Dec 24 00:37:56 2024
Took 0.37
Starting wide2long tests Tue Dec 24 00:37:56 2024
Ending wide2long tests Tue Dec 24 00:37:57 2024
Took 0.19
[ FAIL 0 | WARN 19 | SKIP 5 | PASS 8417 ]
══ 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:1099:1'
[ FAIL 0 | WARN 19 | SKIP 5 | PASS 8417 ]
>
> proc.time()
user system elapsed
179.426 29.448 163.990
OncoSimulR.Rcheck/OncoSimulR-Ex.timings
| name | user | system | elapsed | |
| OncoSimulWide2Long | 0.127 | 0.002 | 0.134 | |
| POM | 0.419 | 0.043 | 0.295 | |
| allFitnessEffects | 1.672 | 0.045 | 1.723 | |
| benchmarks | 0.008 | 0.004 | 0.011 | |
| createInterventions | 0.275 | 0.001 | 0.277 | |
| createUserVars | 0.419 | 0.003 | 0.422 | |
| evalAllGenotypes | 0.183 | 0.015 | 0.198 | |
| example-missing-drivers | 0.207 | 0.005 | 0.213 | |
| examplePosets | 0.242 | 0.002 | 0.244 | |
| examplesFitnessEffects | 0.073 | 0.002 | 0.075 | |
| freq-dep-simul-examples | 0.006 | 0.003 | 0.010 | |
| mcfLs | 0 | 0 | 0 | |
| oncoSimulIndiv | 1.022 | 0.117 | 1.046 | |
| plot.fitnessEffects | 0.221 | 0.040 | 0.262 | |
| plot.oncosimul | 0.400 | 0.014 | 0.413 | |
| plotClonePhylog | 1.064 | 0.068 | 1.131 | |
| plotFitnessLandscape | 1.008 | 0.013 | 1.021 | |
| plotPoset | 0.078 | 0.001 | 0.079 | |
| poset | 0.097 | 0.004 | 0.101 | |
| rfitness | 0.528 | 0.001 | 0.531 | |
| samplePop | 0.030 | 0.046 | 0.065 | |
| simOGraph | 0.066 | 0.008 | 0.074 | |
| to_Magellan | 0.172 | 0.031 | 0.204 | |
| vignette_pre_computed | 0.006 | 0.002 | 0.008 | |