Ramon Diaz-Uriarte
| Snapshot Date: 2024-05-30 18:57:37 -0400 (Thu, 30 May 2024) |
| git_url: https://git.bioconductor.org/packages/OncoSimulR |
| git_branch: devel |
| git_last_commit: c3dd5c6 |
| git_last_commit_date: 2024-04-30 10:37:33 -0400 (Tue, 30 Apr 2024) |
| Back to Multiple platform build/check report for BioC 3.20: simplified long |
|
This page was generated on 2024-05-31 19:31:36 -0400 (Fri, 31 May 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.0 RC (2024-04-16 r86468) -- "Puppy Cup" | 4669 |
| palomino4 | Windows Server 2022 Datacenter | x64 | 4.4.0 RC (2024-04-16 r86468 ucrt) -- "Puppy Cup" | 4404 |
| merida1 | macOS 12.7.4 Monterey | x86_64 | 4.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup" | 4431 |
| kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup" | 4384 |
| 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 1427/2233 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| OncoSimulR 4.7.0 (landing page) Ramon Diaz-Uriarte
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino4 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| merida1 | macOS 12.7.4 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson1 | macOS 13.6.6 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: 4.7.0 |
| Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:OncoSimulR.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings OncoSimulR_4.7.0.tar.gz |
| StartedAt: 2024-05-31 12:33:47 -0400 (Fri, 31 May 2024) |
| EndedAt: 2024-05-31 12:44:39 -0400 (Fri, 31 May 2024) |
| EllapsedTime: 651.3 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: OncoSimulR.Rcheck |
| Warnings: 0 |
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###
### Running command:
###
### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:OncoSimulR.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings OncoSimulR_4.7.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/OncoSimulR.Rcheck’
* using R version 4.4.0 Patched (2024-04-24 r86482)
* using platform: x86_64-apple-darwin20
* R was compiled by
Apple clang version 14.0.0 (clang-1400.0.29.202)
GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.7.4
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘OncoSimulR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘OncoSimulR’ version ‘4.7.0’
* 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: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
* used C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
* used SDK: ‘MacOSX11.3.sdk’
* checking installed package size ... NOTE
installed size is 9.3Mb
sub-directories of 1Mb or more:
libs 7.9Mb
* 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 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 running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: 3 NOTEs
See
‘/Users/biocbuild/bbs-3.20-bioc/meat/OncoSimulR.Rcheck/00check.log’
for details.
OncoSimulR.Rcheck/00install.out
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###
### Running command:
###
### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL OncoSimulR
###
##############################################################################
##############################################################################
* installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library’
* installing *source* package ‘OncoSimulR’ ...
** using staged installation
** libs
using C compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
using C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
using SDK: ‘MacOSX11.3.sdk’
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c FitnessLandscape/gamma.c -o FitnessLandscape/gamma.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c FitnessLandscape/landscape.c -o FitnessLandscape/landscape.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c FitnessLandscape/random.c -o FitnessLandscape/random.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c FitnessLandscape/sort.c -o FitnessLandscape/sort.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c FitnessLandscape/chain.c -o FitnessLandscape/chain.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c FitnessLandscape/input.c -o FitnessLandscape/input.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c FitnessLandscape/genotypes.c -o FitnessLandscape/genotypes.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c FitnessLandscape/ordered_pairs.c -o FitnessLandscape/ordered_pairs.o
FitnessLandscape/ordered_pairs.c:138:6: warning: variable 'tot_pairs' set but not used [-Wunused-but-set-variable]
int tot_pairs=0;
^
1 warning generated.
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c FitnessLandscape/calculus.c -o FitnessLandscape/calculus.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c FitnessLandscape/vector.c -o FitnessLandscape/vector.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c FitnessLandscape/generalized_chain.c -o FitnessLandscape/generalized_chain.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c FitnessLandscape/LinearAlgebra.c -o FitnessLandscape/LinearAlgebra.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c FitnessLandscape/summary_statistics.c -o FitnessLandscape/summary_statistics.o
FitnessLandscape/summary_statistics.c:515:9: warning: variable 'meanVarianceNumberOfStepsFL' set but not used [-Wunused-but-set-variable]
double meanVarianceNumberOfStepsFL = 0;
^
1 warning generated.
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c FitnessLandscape/epistasis_type.c -o FitnessLandscape/epistasis_type.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c FitnessLandscape/decomposition.c -o FitnessLandscape/decomposition.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c FitnessLandscape/models.c -o FitnessLandscape/models.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -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 archive liblandscape.a
ranlib liblandscape.a;
clang -arch x86_64 -O -Wall -o fl_statistics -I/FitnessLandscape/. -L. FitnessLandscape/main_fl_statistics.c -llandscape -lm;
clang -arch x86_64 -O -Wall -o fl_generate -I/FitnessLandscape/. -L. FitnessLandscape/main_fl_generate.c -llandscape -lm;
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c OncoSimulR_init.c -o OncoSimulR_init.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c RcppExports.cpp -o RcppExports.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c unity_osimul.cpp -o unity_osimul.o
In file included from unity_osimul.cpp:10:
./UnityOncoSimul/intervention_private_2.cpp:17:10: warning: variable 'totalPop' set but not used [-Wunused-but-set-variable]
double totalPop = 0.0;
^
1 warning generated.
clang++ -arch x86_64 -std=gnu++17 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/x86_64/lib -o OncoSimulR.so OncoSimulR_init.o RcppExports.o unity_osimul.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing via 'install.libs.R' to /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/00LOCK-OncoSimulR/00new/OncoSimulR
[1] ""
Installing fl_statistics fl_generate to /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/00LOCK-OncoSimulR/00new/OncoSimulR/exec
Installing library OncoSimulR.so to /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/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 Patched (2024-04-24 r86482) -- "Puppy Cup"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20
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 12:36:40 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 12:36:41 2024
Took 1.21
Starting LOD_POM at Fri May 31 12:36:41 2024
Ending LOD_POM at Fri May 31 12:37:06 2024
Took 25.23
Starting test.Z-all-fitness at Fri May 31 12:37:06 2024
Ending test.Z-all-fitness at Fri May 31 12:37:06 2024
Took 0.27
Starting test.Z-driver-counts at Fri May 31 12:37:06 2024
Ending test.Z-driver-counts at Fri May 31 12:37:07 2024
Took 0.3
Starting test.Z-fixation at Fri May 31 12:37:07 2024
Ending test.Z-fixation at Fri May 31 12:37:07 2024
Took 0.65
Starting test.Z-magellan at Fri May 31 12:37:07 2024
Ended test.Z-magellan at Fri May 31 12:37:11 2024
Starting test.Z-mutator at Fri May 31 12:37:11 2024
Ending test.Z-mutator at Fri May 31 12:37:12 2024
Took 0.77
Starting test.Z-mutatorFDF at Fri May 31 12:37:12 2024
Ending test.Z-mutatorFDF at Fri May 31 12:37:12 2024
Took 0.24
Starting test.Z-oncoSimulIndiv at Fri May 31 12:37:12 2024
Ending test.Z-oncoSimulIndiv at Fri May 31 12:37:13 2024
Took 1.15
Starting test.Z-oncoSimulIndivConstant at Fri May 31 12:37:13 2024
Ending test.Z-oncoSimulIndivConstant at Fri May 31 12:37:18 2024
Took 4.94
Starting test.Z-oncoSimulIndivDeath at Fri May 31 12:37:18 2024
Ending test.Z-oncoSimulIndivDeath at Fri May 31 12:37:20 2024
Took 1.81
Starting test.Z-oncoSimulIndivFDF at Fri May 31 12:37:20 2024
Hitted wall time. Exiting.
Hitting wall time is regarded as an error.
Ending test.Z-oncoSimulIndivFDF at Fri May 31 12:37:21 2024
Took 0.7
Starting test.Z-rfitness-landscape at Fri May 31 12:37:21 2024
Ending test.Z-rfitness-landscape at Fri May 31 12:37:21 2024
Took 0.49
Starting Z-sample-only-last tests Fri May 31 12:37:21 2024
Ending Z-sample-only-last tests Fri May 31 12:37:21 2024
Took 0
Starting Z-total-present-drivers tests Fri May 31 12:37:21 2024
Ending Z-total-present-drivers tests Fri May 31 12:37:23 2024
Took 1.76
Dummy empty test Fri May 31 12:37:23 2024
Starting accessible_genotypes at Fri May 31 12:37:23 2024
Ending accessible_genotypes at Fri May 31 12:37:42 2024
Took 19.39
Starting all fitness at Fri May 31 12:37:42 2024
Ending all-fitness at Fri May 31 12:37:56 2024
Took 13.36
Starting test.allFitnessEffectsFDF at Fri May 31 12:37:56 2024
Ending test.allFitnessEffectsFDF at Fri May 31 12:37:56 2024
Took 0.33
Starting test.allFitnessEffectsDeath at Fri May 31 12:37:56 2024
Ending test.allFitnessEffectsDeath at Fri May 31 12:37:57 2024
Took 1
Starting test.allFitnessEffectsFDF at Fri May 31 12:37:57 2024
Ending test.allFitnessEffectsFDF at Fri May 31 12:37:58 2024
Took 0.99
Starting driverCounts at Fri May 31 12:37:58 2024
Ending driverCounts at Fri May 31 12:38:17 2024
Took 19.05
Starting epist-order-modules at Fri May 31 12:38:17 2024
Ending epist-order-modules at Fri May 31 12:38:17 2024
Took 0.12
Starting test.evaluatingGenotypesDeath at Fri May 31 12:38:17 2024
Ending test.evaluatingGenotypesDeath at Fri May 31 12:38:18 2024
Took 0.47
Starting test.evaluatingGenotypesFDF at Fri May 31 12:38:18 2024
Ending test.evaluatingGenotypesFDF at Fri May 31 12:38:18 2024
Took 0.5
Starting exercise-plotting-code at Fri May 31 12:38:18 2024
Ending exercise-plotting-code at Fri May 31 12:38:25 2024
Took 6.73
Starting exercise-rfitness at Fri May 31 12:38:25 2024
Ending exercise-rfitness at Fri May 31 12:38:50 2024
Took 24.95
Starting to_Magella at Fri May 31 12:38:50 2024
Ending to_Magella at Fri May 31 12:38:50 2024
Took 0.13
Starting fitness preds at Fri May 31 12:38:50 2024
Observed vs expected, case III
done tries 1
Ending fitness preds long at Fri May 31 12:39:04 2024
Took 14.15
Starting fixation at Fri May 31 12:39:04 2024
Ending fixation at Fri May 31 12:39:43 2024
Took 39.27
Starting test.flfast-additional.R test at Fri May 31 12:39:44 2024
Ending test.flfast-additional.R test at Fri May 31 12:39:47 2024
Took 3.14
Starting test.flfast-mutator.R test at Fri May 31 12:39:47 2024
Finished test.flfast-mutator.R test at Fri May 31 12:39:50 2024
Took 2.93
Starting genotFitness at Fri May 31 12:39:50 2024
Ending genotFitness at Fri May 31 12:39:50 2024
Took 0.43
Starting genot_fitness_to_epistasis at Fri May 31 12:39:50 2024
Ending genot_fitness_to_epistasis at Fri May 31 12:39:50 2024
Took 0.1
Starting init-mutant tests Fri May 31 12:39:50 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 12:40:05 2024
Took 14.77
Starting interventions tests Fri May 31 12:40:05 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] 0.6 0.6 0.6
[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 12:40:14 2024
Took 8.96
Starting test.magellan at Fri May 31 12:40:14 2024
Ending test.magellan at Fri May 31 12:40:14 2024
Took 0.34
Starting test.modules-root-no-root at Fri May 31 12:40:14 2024
Ending test.modules-root-no-root at Fri May 31 12:40:14 2024
Took 0.2
Starting at mutPropGrowth Fri May 31 12:40:14 2024
Ended test.mutPropGrowth: Fri May 31 12:40:30 2024
Took 15.02
Starting test.mutator-oncoSimulSample.R test at Fri May 31 12:40:30 2024
Finished test.mutator-oncoSimulSample.R test at Fri May 31 12:40:48 2024
Took 18.63 seconds
Starting test.mutator.R test at Fri May 31 12:40:48 2024[1] 4.735375e-09
[1] 9.998832e-13
Finished test.mutator.R test at Fri May 31 12:41:24 2024
Took 35.51
Starting test.mutatorFDF.R test at Fri May 31 12:41:24 2024
Starting test.no-v1 at Fri May 31 12:41:25 2024
Ending test.no-v1 at Fri May 31 12:41:25 2024
Took 0.05
Starting oncoSimulIndiv-miscell tests Fri May 31 12:41:25 2024
Ending oncoSimulIndiv-miscell tests Fri May 31 12:41:37 2024
Took 12.24
Starting oncoSimulSample-failures tests Fri May 31 12:41:37 2024
Ending oncoSimulSample-failures tests Fri May 31 12:41:42 2024
Took 4.29
Starting oncoSimulSample-limits tests Fri May 31 12:41:42 2024
Ending oncoSimulSample-limits tests Fri May 31 12:41:42 2024
Took 0.16
Starting per-gene-mutation rates at Fri May 31 12:41:42 2024
Ending per-gene-mutation rates at Fri May 31 12:42:49 2024
Took 67.03
Starting plotFitnessLandscape at Fri May 31 12:42:49 2024
Ending plotFitnessLandscape at Fri May 31 12:42:57 2024
Took 8.05
Starting poset-transformations tests Fri May 31 12:42:57 2024
Ending poset-transformations tests Fri May 31 12:43:24 2024
Took 27.41
Starting sample-prob Fri May 31 12:43:24 2024
[1] 1.818731e-22
[1] 3.797989e-14
[1] 7.985532e-09
[1] 1.248316e-11
[1] 6.196274e-13
[1] 3.884753e-15
[1] 1.066129e-11
[1] 3.768374e-14
[1] 3.795525e-09
[1] 6.486006e-10
[1] 5.043443e-11
[1] 6.255507e-10
Ending sample-prob tests Fri May 31 12:43:40 2024
Took 15.86
Starting samplePop tests Fri May 31 12:43:40 2024
Ending samplePop tests Fri May 31 12:43:52 2024
Took 11.48
Starting simuls-runs-examples tests Fri May 31 12:43:52 2024
Ending simuls-runs-examples tests Fri May 31 12:44:05 2024
Took 13.42
Starting user variable tests Fri May 31 12:44:05 2024
[1] "Checking user variable: user_var_1"
[1] "Checking rule: rule_1"
Ending user variable tests Fri May 31 12:44:05 2024
Took 0.25
Starting warning-mutPropGrowth tests Fri May 31 12:44:05 2024
Ending warning-mutPropGrowth tests Fri May 31 12:44:06 2024
Took 0.99
Starting wide2long tests Fri May 31 12:44:06 2024
Ending wide2long tests Fri May 31 12:44:07 2024
Took 0.38
[ FAIL 0 | WARN 20 | SKIP 7 | PASS 8420 ]
══ Skipped tests (7) ═══════════════════════════════════════════════════════════
• On Mac (2): 'test.Z-magellan.R:664:5', 'test.Z-oncoSimulIndivFDF.R:125:3'
• 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 20 | SKIP 7 | PASS 8420 ]
>
> proc.time()
user system elapsed
486.071 74.721 459.623
OncoSimulR.Rcheck/OncoSimulR-Ex.timings
| name | user | system | elapsed | |
| OncoSimulWide2Long | 0.431 | 0.010 | 0.487 | |
| POM | 1.829 | 0.101 | 1.163 | |
| allFitnessEffects | 4.198 | 0.195 | 4.968 | |
| benchmarks | 0.022 | 0.017 | 0.057 | |
| createInterventions | 0.533 | 0.018 | 0.659 | |
| createUserVars | 0.807 | 0.030 | 0.946 | |
| evalAllGenotypes | 0.495 | 0.050 | 0.634 | |
| example-missing-drivers | 0.518 | 0.041 | 0.672 | |
| examplePosets | 0.585 | 0.016 | 0.707 | |
| examplesFitnessEffects | 0.084 | 0.008 | 0.104 | |
| freq-dep-simul-examples | 0.018 | 0.004 | 0.023 | |
| mcfLs | 0.000 | 0.001 | 0.001 | |
| oncoSimulIndiv | 2.418 | 0.345 | 3.185 | |
| plot.fitnessEffects | 0.509 | 0.071 | 0.719 | |
| plot.oncosimul | 0.774 | 0.059 | 1.115 | |
| plotClonePhylog | 3.225 | 0.159 | 3.910 | |
| plotFitnessLandscape | 2.738 | 0.101 | 3.287 | |
| plotPoset | 0.195 | 0.014 | 0.251 | |
| poset | 0.239 | 0.017 | 0.326 | |
| rfitness | 1.513 | 0.029 | 1.831 | |
| samplePop | 0.181 | 0.101 | 0.265 | |
| simOGraph | 0.120 | 0.027 | 0.166 | |
| to_Magellan | 0.397 | 0.118 | 0.659 | |
| vignette_pre_computed | 0.013 | 0.007 | 0.051 | |