| Back to Build/check report for BioC 3.17: simplified long |
|
This page was generated on 2023-03-27 05:50:39 -0000 (Mon, 27 Mar 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| kunpeng1 | Linux (Ubuntu 22.04.1 LTS) | aarch64 | R Under development (unstable) (2023-03-12 r83975) -- "Unsuffered Consequences" | 6083 |
| 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 1412/2195 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| OncoSimulR 4.1.4 (landing page) Ramon Diaz-Uriarte
| kunpeng1 | Linux (Ubuntu 22.04.1 LTS) / aarch64 | OK | OK | ERROR | |||||||||
| 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: 2023-03-25 08:19:14 -0000 (Sat, 25 Mar 2023) |
| EndedAt: 2023-03-25 08:30:43 -0000 (Sat, 25 Mar 2023) |
| EllapsedTime: 689.1 seconds |
| RetCode: 1 |
| Status: ERROR |
| CheckDir: OncoSimulR.Rcheck |
| Warnings: NA |
##############################################################################
##############################################################################
###
### 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
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/OncoSimulR.Rcheck’
* using R Under development (unstable) (2023-03-12 r83975)
* using platform: aarch64-unknown-linux-gnu (64-bit)
* R was compiled by
gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
* running under: Ubuntu 22.04.2 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 11.3.0-1ubuntu1~22.04) 11.3.0’
* used C++ compiler: ‘g++ (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0’
* checking installed package size ... NOTE
installed size is 45.0Mb
sub-directories of 1Mb or more:
libs 43.3Mb
* 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 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’
ERROR
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
[ FAIL 1 | WARN 13 | SKIP 5 | PASS 8409 ]
══ Skipped tests ═══════════════════════════════════════════════════════════════
• empty test (5)
══ Failed tests ════════════════════════════════════════════════════════════════
── Failure ('test.Z-oncoSimulIndiv.R:138:9'): exercise no positions left for mutation, updating in null mut, new format ──
any(grepl("updating in null mutation", st)) is not TRUE
`actual`: FALSE
`expected`: TRUE
[ FAIL 1 | WARN 13 | SKIP 5 | PASS 8409 ]
Error: Test failures
Execution halted
* 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: 1 ERROR, 2 NOTEs
See
‘/home/biocbuild/bbs-3.17-bioc/meat/OncoSimulR.Rcheck/00check.log’
for details.
OncoSimulR.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL OncoSimulR ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/site-library’ * installing *source* package ‘OncoSimulR’ ... ** using staged installation ** libs using C compiler: ‘gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0’ using C++ compiler: ‘g++ (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0’ gcc -I"/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/library/Rcpp/include' -I/usr/local/include -fPIC -g -O2 -c FitnessLandscape/gamma.c -o FitnessLandscape/gamma.o gcc -I"/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/library/Rcpp/include' -I/usr/local/include -fPIC -g -O2 -c FitnessLandscape/landscape.c -o FitnessLandscape/landscape.o gcc -I"/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/library/Rcpp/include' -I/usr/local/include -fPIC -g -O2 -c FitnessLandscape/random.c -o FitnessLandscape/random.o gcc -I"/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/library/Rcpp/include' -I/usr/local/include -fPIC -g -O2 -c FitnessLandscape/sort.c -o FitnessLandscape/sort.o gcc -I"/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/library/Rcpp/include' -I/usr/local/include -fPIC -g -O2 -c FitnessLandscape/chain.c -o FitnessLandscape/chain.o gcc -I"/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/library/Rcpp/include' -I/usr/local/include -fPIC -g -O2 -c FitnessLandscape/input.c -o FitnessLandscape/input.o gcc -I"/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/library/Rcpp/include' -I/usr/local/include -fPIC -g -O2 -c FitnessLandscape/genotypes.c -o FitnessLandscape/genotypes.o gcc -I"/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/library/Rcpp/include' -I/usr/local/include -fPIC -g -O2 -c FitnessLandscape/ordered_pairs.c -o FitnessLandscape/ordered_pairs.o gcc -I"/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/library/Rcpp/include' -I/usr/local/include -fPIC -g -O2 -c FitnessLandscape/calculus.c -o FitnessLandscape/calculus.o gcc -I"/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/library/Rcpp/include' -I/usr/local/include -fPIC -g -O2 -c FitnessLandscape/vector.c -o FitnessLandscape/vector.o gcc -I"/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/library/Rcpp/include' -I/usr/local/include -fPIC -g -O2 -c FitnessLandscape/generalized_chain.c -o FitnessLandscape/generalized_chain.o gcc -I"/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/library/Rcpp/include' -I/usr/local/include -fPIC -g -O2 -c FitnessLandscape/LinearAlgebra.c -o FitnessLandscape/LinearAlgebra.o gcc -I"/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/library/Rcpp/include' -I/usr/local/include -fPIC -g -O2 -c FitnessLandscape/summary_statistics.c -o FitnessLandscape/summary_statistics.o gcc -I"/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/library/Rcpp/include' -I/usr/local/include -fPIC -g -O2 -c FitnessLandscape/epistasis_type.c -o FitnessLandscape/epistasis_type.o gcc -I"/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/library/Rcpp/include' -I/usr/local/include -fPIC -g -O2 -c FitnessLandscape/decomposition.c -o FitnessLandscape/decomposition.o gcc -I"/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/library/Rcpp/include' -I/usr/local/include -fPIC -g -O2 -c FitnessLandscape/models.c -o FitnessLandscape/models.o gcc -I"/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/library/Rcpp/include' -I/usr/local/include -fPIC -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 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-devel_2023-03-12_r83975-bin/lib/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/library/Rcpp/include' -I/usr/local/include -fPIC -g -O2 -c OncoSimulR_init.c -o OncoSimulR_init.o g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/library/Rcpp/include' -I/usr/local/include -fPIC -g -O2 -c RcppExports.cpp -o RcppExports.o g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/library/Rcpp/include' -I/usr/local/include -fPIC -g -O2 -c unity_osimul.cpp -o unity_osimul.o g++ -std=gnu++17 -shared -L/usr/local/lib -o OncoSimulR.so OncoSimulR_init.o RcppExports.o unity_osimul.o installing via 'install.libs.R' to /home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/site-library/00LOCK-OncoSimulR/00new/OncoSimulR [1] "" Installing fl_statistics fl_generate to /home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/site-library/00LOCK-OncoSimulR/00new/OncoSimulR/exec Installing library OncoSimulR.so to /home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/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.fail
R Under development (unstable) (2023-03-12 r83975) -- "Unsuffered Consequences"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: aarch64-unknown-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 Sat Mar 25 08:20:38 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 Sat Mar 25 08:20:38 2023
Took 0.51
Starting LOD_POM at Sat Mar 25 08:20:38 2023
Ending LOD_POM at Sat Mar 25 08:21:11 2023
Took 33.19
Starting test.Z-all-fitness at Sat Mar 25 08:21:12 2023
Ending test.Z-all-fitness at Sat Mar 25 08:21:12 2023
Took 0.13
Starting test.Z-driver-counts at Sat Mar 25 08:21:12 2023
Ending test.Z-driver-counts at Sat Mar 25 08:21:12 2023
Took 0.3
Starting test.Z-fixation at Sat Mar 25 08:21:12 2023
Ending test.Z-fixation at Sat Mar 25 08:21:13 2023
Took 1.06
Starting test.Z-magellan at Sat Mar 25 08:21:13 2023
Ended test.Z-magellan at Sat Mar 25 08:21:15 2023
Starting test.Z-mutator at Sat Mar 25 08:21:15 2023
Ending test.Z-mutator at Sat Mar 25 08:21:15 2023
Took 0.4
Starting test.Z-mutatorFDF at Sat Mar 25 08:21:15 2023
Ending test.Z-mutatorFDF at Sat Mar 25 08:21:15 2023
Took 0.14
Starting test.Z-oncoSimulIndiv at Sat Mar 25 08:21:15 2023
Ending test.Z-oncoSimulIndiv at Sat Mar 25 08:21:18 2023
Took 2.85
Starting test.Z-oncoSimulIndivConstant at Sat Mar 25 08:21:18 2023
Ending test.Z-oncoSimulIndivConstant at Sat Mar 25 08:21:21 2023
Took 3.22
Starting test.Z-oncoSimulIndivDeath at Sat Mar 25 08:21:21 2023
Ending test.Z-oncoSimulIndivDeath at Sat Mar 25 08:21:23 2023
Took 1.34
Starting test.Z-oncoSimulIndivFDF at Sat Mar 25 08:21:23 2023
Hitted wall time. Exiting.
Hitting wall time is regarded as an error.
Ending test.Z-oncoSimulIndivFDF at Sat Mar 25 08:21:24 2023
Took 0.73
Starting test.Z-rfitness-landscape at Sat Mar 25 08:21:24 2023
Ending test.Z-rfitness-landscape at Sat Mar 25 08:21:24 2023
Took 0.18
Starting Z-sample-only-last tests Sat Mar 25 08:21:24 2023
Ending Z-sample-only-last tests Sat Mar 25 08:21:24 2023
Took 0
Starting Z-total-present-drivers tests Sat Mar 25 08:21:24 2023
Ending Z-total-present-drivers tests Sat Mar 25 08:21:26 2023
Took 1.89
Dummy empty test Sat Mar 25 08:21:26 2023
Starting accessible_genotypes at Sat Mar 25 08:21:26 2023
Ending accessible_genotypes at Sat Mar 25 08:21:35 2023
Took 8.9
Starting all fitness at Sat Mar 25 08:21:35 2023
Ending all-fitness at Sat Mar 25 08:21:41 2023
Took 6.8
Starting test.allFitnessEffectsFDF at Sat Mar 25 08:21:41 2023
Ending test.allFitnessEffectsFDF at Sat Mar 25 08:21:42 2023
Took 0.15
Starting test.allFitnessEffectsDeath at Sat Mar 25 08:21:42 2023
Ending test.allFitnessEffectsDeath at Sat Mar 25 08:21:42 2023
Took 0.48
Starting test.allFitnessEffectsFDF at Sat Mar 25 08:21:42 2023
Ending test.allFitnessEffectsFDF at Sat Mar 25 08:21:42 2023
Took 0.48
Starting driverCounts at Sat Mar 25 08:21:42 2023
Ending driverCounts at Sat Mar 25 08:21:55 2023
Took 12.24
Starting epist-order-modules at Sat Mar 25 08:21:55 2023
Ending epist-order-modules at Sat Mar 25 08:21:55 2023
Took 0.04
Starting test.evaluatingGenotypesDeath at Sat Mar 25 08:21:55 2023
Ending test.evaluatingGenotypesDeath at Sat Mar 25 08:21:55 2023
Took 0.22
Starting test.evaluatingGenotypesFDF at Sat Mar 25 08:21:55 2023
Ending test.evaluatingGenotypesFDF at Sat Mar 25 08:21:55 2023
Took 0.22
Starting exercise-plotting-code at Sat Mar 25 08:21:55 2023
Ending exercise-plotting-code at Sat Mar 25 08:22:05 2023
Took 10.11
Starting exercise-rfitness at Sat Mar 25 08:22:05 2023
Ending exercise-rfitness at Sat Mar 25 08:22:17 2023
Took 11.33
Starting to_Magella at Sat Mar 25 08:22:17 2023
Ending to_Magella at Sat Mar 25 08:22:17 2023
Took 0.04
Starting fitness preds at Sat Mar 25 08:22:17 2023
Observed vs expected, case III
done tries 1
Ending fitness preds long at Sat Mar 25 08:22:31 2023
Took 14.24
Starting fixation at Sat Mar 25 08:22:31 2023
Ending fixation at Sat Mar 25 08:23:20 2023
Took 48.78
Starting test.flfast-additional.R test at Sat Mar 25 08:23:20 2023
Ending test.flfast-additional.R test at Sat Mar 25 08:23:21 2023
Took 1.48
Starting test.flfast-mutator.R test at Sat Mar 25 08:23:21 2023
Finished test.flfast-mutator.R test at Sat Mar 25 08:23:23 2023
Took 1.91
Starting genotFitness at Sat Mar 25 08:23:23 2023
Ending genotFitness at Sat Mar 25 08:23:23 2023
Took 0.18
Starting genot_fitness_to_epistasis at Sat Mar 25 08:23:23 2023
Ending genot_fitness_to_epistasis at Sat Mar 25 08:23:23 2023
Took 0.06
Starting init-mutant tests Sat Mar 25 08:23:23 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 Sat Mar 25 08:23:38 2023
Took 14.71
Starting interventions tests Sat Mar 25 08:23:38 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] 0.61 0.61 0.61
[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 Sat Mar 25 08:23:43 2023
Took 5.15
Starting test.magellan at Sat Mar 25 08:23:43 2023
Ending test.magellan at Sat Mar 25 08:23:43 2023
Took 0.14
Starting test.modules-root-no-root at Sat Mar 25 08:23:43 2023
Ending test.modules-root-no-root at Sat Mar 25 08:23:43 2023
Took 0.08
Starting at mutPropGrowth Sat Mar 25 08:23:43 2023
Ended test.mutPropGrowth: Sat Mar 25 08:24:03 2023
Took 19.31
Starting test.mutator-oncoSimulSample.R test at Sat Mar 25 08:24:03 2023
Finished test.mutator-oncoSimulSample.R test at Sat Mar 25 08:24:17 2023
Took 13.8 seconds
Starting test.mutator.R test at Sat Mar 25 08:24:17 2023[1] 6.061723e-09
[1] 4.875911e-13
Finished test.mutator.R test at Sat Mar 25 08:24:39 2023
Took 22.29
Starting test.mutatorFDF.R test at Sat Mar 25 08:24:39 2023
Starting test.no-v1 at Sat Mar 25 08:24:40 2023
Ending test.no-v1 at Sat Mar 25 08:24:40 2023
Took 0.01
Starting oncoSimulIndiv-miscell tests Sat Mar 25 08:24:40 2023
Ending oncoSimulIndiv-miscell tests Sat Mar 25 08:25:18 2023
Took 38.25
Starting oncoSimulSample-failures tests Sat Mar 25 08:25:18 2023
Ending oncoSimulSample-failures tests Sat Mar 25 08:25:22 2023
Took 3.66
Starting oncoSimulSample-limits tests Sat Mar 25 08:25:22 2023
Ending oncoSimulSample-limits tests Sat Mar 25 08:25:22 2023
Took 0.09
Starting per-gene-mutation rates at Sat Mar 25 08:25:22 2023
Ending per-gene-mutation rates at Sat Mar 25 08:26:12 2023
Took 49.88
Starting plotFitnessLandscape at Sat Mar 25 08:26:12 2023
Ending plotFitnessLandscape at Sat Mar 25 08:26:15 2023
Took 3.31
Starting poset-transformations tests Sat Mar 25 08:26:15 2023
Ending poset-transformations tests Sat Mar 25 08:26:24 2023
Took 9.43
Starting sample-prob Sat Mar 25 08:26:24 2023
[1] 2.106832e-21
[1] 1.650592e-10
[1] 6.919687e-10
[1] 1.346349e-11
[1] 1.495919e-12
[1] 2.83487e-14
[1] 3.090791e-11
[1] 8.488336e-15
[1] 6.741867e-10
[1] 2.82789e-09
[1] 5.239867e-08
[1] 9.819467e-10
Ending sample-prob tests Sat Mar 25 08:26:37 2023
Took 12.56
Starting samplePop tests Sat Mar 25 08:26:37 2023
Ending samplePop tests Sat Mar 25 08:26:54 2023
Took 17.48
Starting simuls-runs-examples tests Sat Mar 25 08:26:54 2023
Ending simuls-runs-examples tests Sat Mar 25 08:27:29 2023
Took 34.93
Starting user variable tests Sat Mar 25 08:27:29 2023
[1] "Checking user variable: user_var_1"
[1] "Checking rule: rule_1"
Ending user variable tests Sat Mar 25 08:27:29 2023
Took 0.11
Starting warning-mutPropGrowth tests Sat Mar 25 08:27:29 2023
Ending warning-mutPropGrowth tests Sat Mar 25 08:27:31 2023
Took 1.61
Starting wide2long tests Sat Mar 25 08:27:31 2023
Ending wide2long tests Sat Mar 25 08:27:32 2023
Took 0.87
[ FAIL 1 | WARN 13 | SKIP 5 | PASS 8409 ]
══ Skipped tests ═══════════════════════════════════════════════════════════════
• empty test (5)
══ Failed tests ════════════════════════════════════════════════════════════════
── Failure ('test.Z-oncoSimulIndiv.R:138:9'): exercise no positions left for mutation, updating in null mut, new format ──
any(grepl("updating in null mutation", st)) is not TRUE
`actual`: FALSE
`expected`: TRUE
[ FAIL 1 | WARN 13 | SKIP 5 | PASS 8409 ]
Error: Test failures
Execution halted
OncoSimulR.Rcheck/OncoSimulR-Ex.timings
| name | user | system | elapsed | |
| OncoSimulWide2Long | 1.005 | 0.040 | 1.051 | |
| POM | 0.807 | 0.095 | 0.556 | |
| allFitnessEffects | 2.095 | 0.040 | 2.143 | |
| benchmarks | 0.008 | 0.004 | 0.011 | |
| createInterventions | 0.377 | 0.000 | 0.377 | |
| createUserVars | 0.553 | 0.012 | 0.565 | |
| evalAllGenotypes | 0.259 | 0.028 | 0.286 | |
| example-missing-drivers | 0.287 | 0.016 | 0.303 | |
| examplePosets | 0.373 | 0.000 | 0.373 | |
| examplesFitnessEffects | 0.054 | 0.000 | 0.053 | |
| freq-dep-simul-examples | 0.012 | 0.000 | 0.012 | |
| mcfLs | 0 | 0 | 0 | |
| oncoSimulIndiv | 2.049 | 0.173 | 2.154 | |
| plot.fitnessEffects | 0.267 | 0.033 | 0.300 | |
| plot.oncosimul | 1.493 | 0.000 | 1.493 | |
| plotClonePhylog | 1.779 | 0.176 | 1.955 | |
| plotFitnessLandscape | 1.574 | 0.004 | 1.578 | |
| plotPoset | 0.127 | 0.000 | 0.127 | |
| poset | 0.142 | 0.000 | 0.142 | |
| rfitness | 0.816 | 0.006 | 0.825 | |
| samplePop | 0.084 | 0.067 | 0.097 | |
| simOGraph | 0.071 | 0.004 | 0.075 | |
| to_Magellan | 0.199 | 0.019 | 0.220 | |
| vignette_pre_computed | 0.009 | 0.000 | 0.009 | |