| Back to Multiple platform build/check report for BioC 3.14 |
|
This page was generated on 2022-04-13 12:08:28 -0400 (Wed, 13 Apr 2022).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 20.04.4 LTS) | x86_64 | 4.1.3 (2022-03-10) -- "One Push-Up" | 4324 |
| tokay2 | Windows Server 2012 R2 Standard | x64 | 4.1.3 (2022-03-10) -- "One Push-Up" | 4077 |
| machv2 | macOS 10.14.6 Mojave | x86_64 | 4.1.3 (2022-03-10) -- "One Push-Up" | 4137 |
| 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 1334/2083 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| OncoSimulR 3.2.0 (landing page) Ramon Diaz-Uriarte
| nebbiolo2 | Linux (Ubuntu 20.04.4 LTS) / x86_64 | OK | OK | OK |  | ||||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | | ||||||||
| machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | | ||||||||
| Package: OncoSimulR |
| Version: 3.2.0 |
| 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_3.2.0.tar.gz |
| StartedAt: 2022-04-12 16:19:51 -0400 (Tue, 12 Apr 2022) |
| EndedAt: 2022-04-12 16:31:46 -0400 (Tue, 12 Apr 2022) |
| EllapsedTime: 715.3 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: OncoSimulR.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### 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_3.2.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.14-bioc/meat/OncoSimulR.Rcheck’
* using R version 4.1.3 (2022-03-10)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘OncoSimulR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘OncoSimulR’ version ‘3.2.0’
* 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
* checking installed package size ... NOTE
installed size is 9.0Mb
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 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
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
oncoSimulIndiv 4.164 0.908 4.356
* 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 ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: 2 NOTEs
See
‘/Users/biocbuild/bbs-3.14-bioc/meat/OncoSimulR.Rcheck/00check.log’
for details.
OncoSimulR.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL OncoSimulR ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.1/Resources/library’ * installing *source* package ‘OncoSimulR’ ... ** using staged installation ** libs clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I/usr/local/include -fPIC -Wall -g -O2 -c FitnessLandscape/gamma.c -o FitnessLandscape/gamma.o clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I/usr/local/include -fPIC -Wall -g -O2 -c FitnessLandscape/landscape.c -o FitnessLandscape/landscape.o clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I/usr/local/include -fPIC -Wall -g -O2 -c FitnessLandscape/random.c -o FitnessLandscape/random.o clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I/usr/local/include -fPIC -Wall -g -O2 -c FitnessLandscape/sort.c -o FitnessLandscape/sort.o clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I/usr/local/include -fPIC -Wall -g -O2 -c FitnessLandscape/chain.c -o FitnessLandscape/chain.o clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I/usr/local/include -fPIC -Wall -g -O2 -c FitnessLandscape/input.c -o FitnessLandscape/input.o clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I/usr/local/include -fPIC -Wall -g -O2 -c FitnessLandscape/genotypes.c -o FitnessLandscape/genotypes.o clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I/usr/local/include -fPIC -Wall -g -O2 -c FitnessLandscape/ordered_pairs.c -o FitnessLandscape/ordered_pairs.o clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I/usr/local/include -fPIC -Wall -g -O2 -c FitnessLandscape/calculus.c -o FitnessLandscape/calculus.o clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I/usr/local/include -fPIC -Wall -g -O2 -c FitnessLandscape/vector.c -o FitnessLandscape/vector.o clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I/usr/local/include -fPIC -Wall -g -O2 -c FitnessLandscape/generalized_chain.c -o FitnessLandscape/generalized_chain.o clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I/usr/local/include -fPIC -Wall -g -O2 -c FitnessLandscape/LinearAlgebra.c -o FitnessLandscape/LinearAlgebra.o clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I/usr/local/include -fPIC -Wall -g -O2 -c FitnessLandscape/summary_statistics.c -o FitnessLandscape/summary_statistics.o clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I/usr/local/include -fPIC -Wall -g -O2 -c FitnessLandscape/epistasis_type.c -o FitnessLandscape/epistasis_type.o clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I/usr/local/include -fPIC -Wall -g -O2 -c FitnessLandscape/decomposition.c -o FitnessLandscape/decomposition.o clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I/usr/local/include -fPIC -Wall -g -O2 -c FitnessLandscape/models.c -o FitnessLandscape/models.o clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I/usr/local/include -fPIC -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 -mmacosx-version-min=10.13 -O -Wall -o fl_statistics -I/FitnessLandscape/. -L. FitnessLandscape/main_fl_statistics.c -llandscape -lm; clang -mmacosx-version-min=10.13 -O -Wall -o fl_generate -I/FitnessLandscape/. -L. FitnessLandscape/main_fl_generate.c -llandscape -lm; clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I/usr/local/include -fPIC -Wall -g -O2 -c BNB_nr.cpp -o BNB_nr.o clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I/usr/local/include -fPIC -Wall -g -O2 -c OncoSimulR_init.c -o OncoSimulR_init.o clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I/usr/local/include -fPIC -Wall -g -O2 -c RcppExports.cpp -o RcppExports.o clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I/usr/local/include -fPIC -Wall -g -O2 -c accessible_genotypes.cpp -o accessible_genotypes.o clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I/usr/local/include -fPIC -Wall -g -O2 -c bnb_common.cpp -o bnb_common.o clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I/usr/local/include -fPIC -Wall -g -O2 -c new_restrict.cpp -o new_restrict.o clang++ -mmacosx-version-min=10.13 -std=gnu++11 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -o OncoSimulR.so BNB_nr.o OncoSimulR_init.o RcppExports.o accessible_genotypes.o bnb_common.o new_restrict.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation installing via 'install.libs.R' to /Library/Frameworks/R.framework/Versions/4.1/Resources/library/00LOCK-OncoSimulR/00new/OncoSimulR [1] "" Installing fl_statistics fl_generate to /Library/Frameworks/R.framework/Versions/4.1/Resources/library/00LOCK-OncoSimulR/00new/OncoSimulR/exec Installing library OncoSimulR.so to /Library/Frameworks/R.framework/Versions/4.1/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 4.1.3 (2022-03-10) -- "One Push-Up"
Copyright (C) 2022 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin17.0 (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 Tue Apr 12 16:21:53 2022
exprtk parser error:
Error[00] Position: 00 Type: [ Syntax Error] Msg: ERR197 - Undefined symbol: 'n_2_3' Expression: n_2_3
exprtk parser error:
Error[00] Position: 00 Type: [ Syntax Error] Msg: ERR197 - Undefined symbol: 'f_2_3' Expression: f_2_3
Ending FDF-small-fitness-specs Tue Apr 12 16:21:54 2022
Took 0.76
Starting LOD_POM at Tue Apr 12 16:21:54 2022
Ending LOD_POM at Tue Apr 12 16:22:27 2022
Took 33.24
Starting test.Z-all-fitness at Tue Apr 12 16:22:27 2022
Ending test.Z-all-fitness at Tue Apr 12 16:22:28 2022
Took 0.18
Starting test.Z-driver-counts at Tue Apr 12 16:22:28 2022
Ending test.Z-driver-counts at Tue Apr 12 16:22:28 2022
Took 0.3
Starting test.Z-fixation at Tue Apr 12 16:22:28 2022
Ending test.Z-fixation at Tue Apr 12 16:22:29 2022
Took 1.15
Starting test.Z-magellan at Tue Apr 12 16:22:29 2022
Ended test.Z-magellan at Tue Apr 12 16:22:32 2022
Starting test.Z-mutator at Tue Apr 12 16:22:32 2022
Ending test.Z-mutator at Tue Apr 12 16:22:33 2022
Took 0.58
Starting test.Z-mutatorFDF at Tue Apr 12 16:22:33 2022
Ending test.Z-mutatorFDF at Tue Apr 12 16:22:33 2022
Took 0.17
Starting test.Z-oncoSimulIndiv at Tue Apr 12 16:22:33 2022
Ending test.Z-oncoSimulIndiv at Tue Apr 12 16:22:36 2022
Took 2.97
Starting test.Z-oncoSimulIndivFDF at Tue Apr 12 16:22:36 2022
Ending test.Z-oncoSimulIndivFDF at Tue Apr 12 16:22:36 2022
Took 0.24
Starting test.Z-rfitness-landscape at Tue Apr 12 16:22:36 2022
Ending test.Z-rfitness-landscape at Tue Apr 12 16:22:36 2022
Took 0.27
Starting Z-sample-only-last tests Tue Apr 12 16:22:36 2022
Ending Z-sample-only-last tests Tue Apr 12 16:22:36 2022
Took 0
Starting Z-total-present-drivers tests Tue Apr 12 16:22:36 2022
Ending Z-total-present-drivers tests Tue Apr 12 16:22:39 2022
Took 2.5
Dummy empty test Tue Apr 12 16:22:39 2022
Starting accessible_genotypes at Tue Apr 12 16:22:39 2022
Ending accessible_genotypes at Tue Apr 12 16:22:50 2022
Took 11.01
Starting all fitness at Tue Apr 12 16:22:50 2022
Ending all-fitness at Tue Apr 12 16:22:59 2022
Took 9.12
Starting test.allFitnessEffectsFDF at Tue Apr 12 16:22:59 2022
Ending test.allFitnessEffectsFDF at Tue Apr 12 16:22:59 2022
Took 0.22
Starting test.allFitnessEffectsFDF at Tue Apr 12 16:22:59 2022
Ending test.allFitnessEffectsFDF at Tue Apr 12 16:23:00 2022
Took 0.68
Starting driverCounts at Tue Apr 12 16:23:00 2022
Ending driverCounts at Tue Apr 12 16:23:18 2022
Took 17.81
Starting epist-order-modules at Tue Apr 12 16:23:18 2022
Ending epist-order-modules at Tue Apr 12 16:23:18 2022
Took 0.07
Starting test.evaluatingGenotypesFDF at Tue Apr 12 16:23:18 2022
Ending test.evaluatingGenotypesFDF at Tue Apr 12 16:23:18 2022
Took 0.25
Starting exercise-plotting-code at Tue Apr 12 16:23:18 2022
Ending exercise-plotting-code at Tue Apr 12 16:23:32 2022
Took 14.23
Starting exercise-rfitness at Tue Apr 12 16:23:32 2022
Ending exercise-rfitness at Tue Apr 12 16:23:47 2022
Took 14.87
Starting to_Magella at Tue Apr 12 16:23:47 2022
Ending to_Magella at Tue Apr 12 16:23:47 2022
Took 0.06
Starting fitness preds at Tue Apr 12 16:23:47 2022
Observed vs expected, case III
done tries 1
Ending fitness preds long at Tue Apr 12 16:24:09 2022
Took 21.66
Starting fixation at Tue Apr 12 16:24:09 2022
Ending fixation at Tue Apr 12 16:25:06 2022
Took 57.26
Starting test.flfast-additional.R test at Tue Apr 12 16:25:06 2022
Ending test.flfast-additional.R test at Tue Apr 12 16:25:10 2022
Took 3.97
Starting test.flfast-mutator.R test at Tue Apr 12 16:25:10 2022
Finished test.flfast-mutator.R test at Tue Apr 12 16:25:14 2022
Took 3.75
Starting genotFitness at Tue Apr 12 16:25:14 2022
Ending genotFitness at Tue Apr 12 16:25:14 2022
Took 0.25
Starting genot_fitness_to_epistasis at Tue Apr 12 16:25:14 2022
Ending genot_fitness_to_epistasis at Tue Apr 12 16:25:14 2022
Took 0.06
Starting init-mutant tests Tue Apr 12 16:25:14 2022
exprtk parser error:
Error[00] Position: 18 Type: [ Syntax Error] Msg: ERR197 - Undefined symbol: 'f_2' Expression: 1.1 + 0.7*((f_1 + f_2) > 0.3)
Ending init-mutant tests Tue Apr 12 16:25:32 2022
Took 17.91
Starting test.magellan at Tue Apr 12 16:25:32 2022
Ending test.magellan at Tue Apr 12 16:25:33 2022
Took 0.29
Starting test.modules-root-no-root at Tue Apr 12 16:25:33 2022
Ending test.modules-root-no-root at Tue Apr 12 16:25:33 2022
Took 0.11
Starting at mutPropGrowth Tue Apr 12 16:25:33 2022
Ended test.mutPropGrowth: Tue Apr 12 16:25:56 2022
Took 23.2
Starting test.mutator-oncoSimulSample.R test at Tue Apr 12 16:25:56 2022
Finished test.mutator-oncoSimulSample.R test at Tue Apr 12 16:26:19 2022
Took 23.01 seconds
Starting test.mutator.R test at Tue Apr 12 16:26:19 2022[1] 8.829082e-10
[1] 1.910335e-12
Finished test.mutator.R test at Tue Apr 12 16:26:52 2022
Took 33.14
Starting test.mutatorFDF.R test at Tue Apr 12 16:26:52 2022
Starting test.no-v1 at Tue Apr 12 16:26:53 2022
Ending test.no-v1 at Tue Apr 12 16:26:53 2022
Took 0.01
Starting oncoSimulIndiv-miscell tests Tue Apr 12 16:26:53 2022
Ending oncoSimulIndiv-miscell tests Tue Apr 12 16:27:43 2022
Took 49.68
Starting oncoSimulSample-failures tests Tue Apr 12 16:27:43 2022
Ending oncoSimulSample-failures tests Tue Apr 12 16:27:47 2022
Took 3.7
Starting oncoSimulSample-limits tests Tue Apr 12 16:27:47 2022
Ending oncoSimulSample-limits tests Tue Apr 12 16:27:47 2022
Took 0.14
Starting per-gene-mutation rates at Tue Apr 12 16:27:47 2022
Ending per-gene-mutation rates at Tue Apr 12 16:29:05 2022
Took 78.52
Starting plotFitnessLandscape at Tue Apr 12 16:29:05 2022
Ending plotFitnessLandscape at Tue Apr 12 16:29:15 2022
Took 9.75
Starting poset-transformations tests Tue Apr 12 16:29:15 2022
Ending poset-transformations tests Tue Apr 12 16:29:37 2022
Took 22.29
Starting sample-prob Tue Apr 12 16:29:37 2022
[1] 3.663638e-20
[1] 7.090106e-10
[1] 2.427235e-11
[1] 1.37128e-11
[1] 7.954654e-15
[1] 3.069739e-14
[1] 4.8156e-11
[1] 2.266536e-14
[1] 1.8e-09
[1] 6.084478e-07
[1] 1.925804e-07
[1] 4.961813e-09
Ending sample-prob tests Tue Apr 12 16:29:57 2022
Took 19.46
Starting samplePop tests Tue Apr 12 16:29:57 2022
Ending samplePop tests Tue Apr 12 16:30:25 2022
Took 28.67
Starting simuls-runs-examples tests Tue Apr 12 16:30:25 2022
Ending simuls-runs-examples tests Tue Apr 12 16:31:10 2022
Took 44.38
Starting warning-mutPropGrowth tests Tue Apr 12 16:31:10 2022
Ending warning-mutPropGrowth tests Tue Apr 12 16:31:17 2022
Took 6.83
Starting wide2long tests Tue Apr 12 16:31:17 2022
Ending wide2long tests Tue Apr 12 16:31:18 2022
Took 1.43
[ FAIL 0 | WARN 1 | SKIP 7 | PASS 8170 ]
══ Skipped tests ═══════════════════════════════════════════════════════════════
• On Mac (2)
• empty test (5)
[ FAIL 0 | WARN 1 | SKIP 7 | PASS 8170 ]
>
> proc.time()
user system elapsed
623.601 112.616 577.688
OncoSimulR.Rcheck/OncoSimulR-Ex.timings
| name | user | system | elapsed | |
| OncoSimulWide2Long | 0.666 | 0.163 | 0.830 | |
| POM | 1.998 | 0.224 | 1.471 | |
| allFitnessEffects | 2.409 | 0.079 | 2.493 | |
| benchmarks | 0.012 | 0.009 | 0.021 | |
| evalAllGenotypes | 0.319 | 0.016 | 0.335 | |
| example-missing-drivers | 0.452 | 0.027 | 0.478 | |
| examplePosets | 0.527 | 0.007 | 0.535 | |
| examplesFitnessEffects | 0.099 | 0.004 | 0.104 | |
| freq-dep-simul-examples | 0.014 | 0.003 | 0.017 | |
| mcfLs | 0.000 | 0.001 | 0.000 | |
| oncoSimulIndiv | 4.164 | 0.908 | 4.356 | |
| plot.fitnessEffects | 0.355 | 0.029 | 0.387 | |
| plot.oncosimul | 1.028 | 0.126 | 1.197 | |
| plotClonePhylog | 4.327 | 0.383 | 4.718 | |
| plotFitnessLandscape | 1.783 | 0.023 | 1.813 | |
| plotPoset | 0.178 | 0.006 | 0.184 | |
| poset | 0.224 | 0.006 | 0.229 | |
| rfitness | 0.869 | 0.009 | 0.882 | |
| samplePop | 0.884 | 0.383 | 0.759 | |
| simOGraph | 0.123 | 0.018 | 0.142 | |
| to_Magellan | 0.317 | 0.067 | 0.455 | |