Back to Multiple platform build/check report for BioC 3.13
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This page was generated on 2021-06-18 14:06:53 -0400 (Fri, 18 Jun 2021).

CHECK results for OncoSimulR on machv2

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? here for more information.
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raw results

Package 1308/2041HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
OncoSimulR 3.0.0  (landing page)
Ramon Diaz-Uriarte
Snapshot Date: 2021-06-17 06:50:12 -0400 (Thu, 17 Jun 2021)
URL: https://git.bioconductor.org/packages/OncoSimulR
Branch: RELEASE_3_13
Last Commit: 3add541
Last Changed Date: 2021-05-19 12:06:18 -0400 (Wed, 19 May 2021)
nebbiolo1Linux (Ubuntu 20.04.2 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: OncoSimulR
Version: 3.0.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:OncoSimulR.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings OncoSimulR_3.0.0.tar.gz
StartedAt: 2021-06-17 21:41:17 -0400 (Thu, 17 Jun 2021)
EndedAt: 2021-06-17 21:51:24 -0400 (Thu, 17 Jun 2021)
EllapsedTime: 607.1 seconds
RetCode: 0
Status:   OK  
CheckDir: OncoSimulR.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:OncoSimulR.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings OncoSimulR_3.0.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.13-bioc/meat/OncoSimulR.Rcheck’
* using R version 4.1.0 (2021-05-18)
* 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 ‘3.0.0’
* 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:
  .git_fetch_output.txt
  .git_merge_output.txt
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
* checking installed package size ... NOTE
  installed size is  8.9Mb
  sub-directories of 1Mb or more:
    libs   7.8Mb
* 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’
 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: 3 NOTEs
See
  ‘/Users/biocbuild/bbs-3.13-bioc/meat/OncoSimulR.Rcheck/00check.log’
for details.



Installation output

OncoSimulR.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/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
In file included from BNB_nr.cpp:20:
In file included from ./debug_common.h:4:
In file included from /Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include/Rcpp.h:57:
/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include/Rcpp/DataFrame.h:136:18: warning: unused variable 'data' [-Wunused-variable]
            SEXP data = Parent::get__();
                 ^
1 warning generated.
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
In file included from RcppExports.cpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include/Rcpp.h:57:
/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include/Rcpp/DataFrame.h:136:18: warning: unused variable 'data' [-Wunused-variable]
            SEXP data = Parent::get__();
                 ^
1 warning generated.
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
In file included from accessible_genotypes.cpp:16:
In file included from /Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include/Rcpp.h:57:
/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include/Rcpp/DataFrame.h:136:18: warning: unused variable 'data' [-Wunused-variable]
            SEXP data = Parent::get__();
                 ^
1 warning generated.
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
In file included from bnb_common.cpp:17:
In file included from ./bnb_common.h:21:
In file included from /Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include/Rcpp.h:57:
/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include/Rcpp/DataFrame.h:136:18: warning: unused variable 'data' [-Wunused-variable]
            SEXP data = Parent::get__();
                 ^
1 warning generated.
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
In file included from new_restrict.cpp:18:
In file included from ./debug_common.h:4:
In file included from /Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include/Rcpp.h:57:
/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include/Rcpp/DataFrame.h:136:18: warning: unused variable 'data' [-Wunused-variable]
            SEXP data = Parent::get__();
                 ^
1 warning generated.
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)

Tests output

OncoSimulR.Rcheck/tests/testthat.Rout


R version 4.1.0 (2021-05-18) -- "Camp Pontanezen"
Copyright (C) 2021 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 Thu Jun 17 21:43:09 2021 

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 Thu Jun 17 21:43:09 2021 
  Took  0.61 


 Starting LOD_POM at Thu Jun 17 21:43:09 2021 

 Ending LOD_POM at Thu Jun 17 21:43:45 2021 
  Took  35.6 


 Starting test.Z-all-fitness at Thu Jun 17 21:43:45 2021 

 Ending test.Z-all-fitness at Thu Jun 17 21:43:45 2021 
  Took  0.08 


 Starting test.Z-driver-counts at Thu Jun 17 21:43:45 2021 

 Ending test.Z-driver-counts at Thu Jun 17 21:43:45 2021 
  Took  0.27 


 Starting test.Z-fixation at Thu Jun 17 21:43:45 2021 

 Ending test.Z-fixation at Thu Jun 17 21:43:46 2021 
  Took  0.93 


 Starting test.Z-magellan at Thu Jun 17 21:43:46 2021 

 Ended test.Z-magellan at Thu Jun 17 21:43:49 2021 

 Starting test.Z-mutator at Thu Jun 17 21:43:49 2021 

 Ending test.Z-mutator at Thu Jun 17 21:43:49 2021 
  Took  0.38 


 Starting test.Z-mutatorFDF at Thu Jun 17 21:43:49 2021 

 Ending test.Z-mutatorFDF at Thu Jun 17 21:43:50 2021 
  Took  0.13 


 Starting test.Z-oncoSimulIndiv at Thu Jun 17 21:43:50 2021 

 Ending test.Z-oncoSimulIndiv at Thu Jun 17 21:43:52 2021 
  Took  2.37 


 Starting test.Z-oncoSimulIndivFDF at Thu Jun 17 21:43:52 2021 

 Ending test.Z-oncoSimulIndivFDF at Thu Jun 17 21:43:52 2021 
  Took  0.18 


 Starting test.Z-rfitness-landscape at Thu Jun 17 21:43:52 2021 

 Ending test.Z-rfitness-landscape at Thu Jun 17 21:43:52 2021 
  Took  0.18 


 Starting Z-sample-only-last tests Thu Jun 17 21:43:52 2021 

 Ending Z-sample-only-last tests Thu Jun 17 21:43:52 2021 
  Took  0 


 Starting Z-total-present-drivers tests Thu Jun 17 21:43:52 2021 

 Ending Z-total-present-drivers tests Thu Jun 17 21:43:55 2021 
  Took  2.35 


 Dummy empty test  Thu Jun 17 21:43:55 2021 

 Starting accessible_genotypes at Thu Jun 17 21:43:55 2021 

 Ending accessible_genotypes at Thu Jun 17 21:44:02 2021 
  Took  7.43 


 Starting all fitness at Thu Jun 17 21:44:02 2021
 Ending all-fitness at Thu Jun 17 21:44:10 2021 
  Took  7.6 


 Starting test.allFitnessEffectsFDF at Thu Jun 17 21:44:10 2021 

 Ending test.allFitnessEffectsFDF at Thu Jun 17 21:44:10 2021 
  Took  0.23 


 Starting test.allFitnessEffectsFDF at Thu Jun 17 21:44:10 2021 

 Ending test.allFitnessEffectsFDF at Thu Jun 17 21:44:11 2021 
  Took  0.5 


 Starting driverCounts at Thu Jun 17 21:44:11 2021
 Ending driverCounts at Thu Jun 17 21:44:26 2021 
  Took  15.05 


 Starting epist-order-modules at Thu Jun 17 21:44:26 2021
 Ending epist-order-modules at Thu Jun 17 21:44:26 2021 
  Took  0.06 


 Starting test.evaluatingGenotypesFDF at Thu Jun 17 21:44:26 2021 

 Ending test.evaluatingGenotypesFDF at Thu Jun 17 21:44:26 2021 
  Took  0.24 


 Starting exercise-plotting-code at Thu Jun 17 21:44:26 2021
 Ending exercise-plotting-code at Thu Jun 17 21:44:38 2021 
  Took  12.19 


 Starting exercise-rfitness at Thu Jun 17 21:44:38 2021 

 Ending exercise-rfitness at Thu Jun 17 21:44:46 2021 
  Took  8.29 


 Starting to_Magella at Thu Jun 17 21:44:46 2021 

 Ending to_Magella at Thu Jun 17 21:44:46 2021 
  Took  0.05 


 Starting fitness preds at Thu Jun 17 21:44:46 2021 

 Observed vs expected, case III

 done tries 1 

 Ending fitness preds long at Thu Jun 17 21:45:06 2021 
  Took  19.19 


 Starting fixation  at Thu Jun 17 21:45:06 2021 

 Ending fixation  at Thu Jun 17 21:45:52 2021 
  Took  46.63 


 Starting test.flfast-additional.R test at Thu Jun 17 21:45:52 2021
 Ending test.flfast-additional.R test at Thu Jun 17 21:45:55 2021 
  Took  2.95 


 Starting test.flfast-mutator.R test at Thu Jun 17 21:45:55 2021
 Finished test.flfast-mutator.R test at Thu Jun 17 21:46:01 2021 
  Took  5.71 


 Starting genotFitness at Thu Jun 17 21:46:01 2021 

 Ending genotFitness at Thu Jun 17 21:46:01 2021 
  Took  0.14 


 Starting genot_fitness_to_epistasis at Thu Jun 17 21:46:01 2021 

 Ending genot_fitness_to_epistasis at Thu Jun 17 21:46:01 2021 
  Took  0.04 


 Starting init-mutant tests Thu Jun 17 21:46:01 2021 

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 Thu Jun 17 21:46:17 2021 
  Took  15.66 


 Starting test.magellan at Thu Jun 17 21:46:17 2021 

 Ending test.magellan at Thu Jun 17 21:46:17 2021 
  Took  0.27 


 Starting test.modules-root-no-root at Thu Jun 17 21:46:17 2021 

 Ending test.modules-root-no-root at Thu Jun 17 21:46:17 2021 
  Took  0.09 


 Starting at mutPropGrowth  Thu Jun 17 21:46:17 2021 

 Ended test.mutPropGrowth:  Thu Jun 17 21:46:35 2021 
  Took  18.04 


 Starting test.mutator-oncoSimulSample.R test at Thu Jun 17 21:46:35 2021 

 Finished test.mutator-oncoSimulSample.R test at Thu Jun 17 21:46:50 2021 
  Took  14.88 seconds 


 Starting test.mutator.R test at Thu Jun 17 21:46:50 2021[1] 1.420208e-07
[1] 1.136884e-13

 Finished test.mutator.R test at Thu Jun 17 21:47:21 2021 
  Took  30.52 


 Starting test.mutatorFDF.R test at Thu Jun 17 21:47:21 2021
 Starting test.no-v1 at Thu Jun 17 21:47:22 2021 

 Ending test.no-v1 at Thu Jun 17 21:47:22 2021 
  Took  0.01 


 Starting oncoSimulIndiv-miscell tests Thu Jun 17 21:47:22 2021 

 Ending oncoSimulIndiv-miscell tests Thu Jun 17 21:48:01 2021 
  Took  39.84 


 Starting oncoSimulSample-failures tests Thu Jun 17 21:48:01 2021 

 Ending oncoSimulSample-failures tests Thu Jun 17 21:48:06 2021 
  Took  4.14 


 Starting oncoSimulSample-limits tests Thu Jun 17 21:48:06 2021 

 Ending oncoSimulSample-limits tests Thu Jun 17 21:48:06 2021 
  Took  0.1 


 Starting per-gene-mutation rates at Thu Jun 17 21:48:06 2021 

 Ending per-gene-mutation rates at Thu Jun 17 21:49:23 2021 
  Took  77.39 


 Starting plotFitnessLandscape at Thu Jun 17 21:49:23 2021
 Ending plotFitnessLandscape at Thu Jun 17 21:49:27 2021 
  Took  3.94 


 Starting poset-transformations tests Thu Jun 17 21:49:27 2021 

 Ending poset-transformations tests Thu Jun 17 21:49:37 2021 
  Took  9.52 


 Starting sample-prob Thu Jun 17 21:49:37 2021 
[1] 1.633385e-27
[1] 2.148063e-12
[1] 5.634095e-11
[1] 1.186124e-11
[1] 2.05851e-12
[1] 2.522333e-16
[1] 3.049121e-13
[1] 4.17103e-18
[1] 2.182759e-09
[1] 8.717749e-10
[1] 6.645738e-07
[1] 3.392883e-09

 Ending sample-prob tests Thu Jun 17 21:49:56 2021 
 Took  19.45 



 Starting samplePop tests Thu Jun 17 21:49:56 2021 

 Ending samplePop tests Thu Jun 17 21:50:28 2021 
  Took  32.09 


 Starting simuls-runs-examples tests Thu Jun 17 21:50:28 2021 

 Ending simuls-runs-examples tests Thu Jun 17 21:51:05 2021 
  Took  36.78 


 Starting warning-mutPropGrowth tests Thu Jun 17 21:51:05 2021 

 Ending warning-mutPropGrowth tests Thu Jun 17 21:51:08 2021 
  Took  3.39 


 Starting wide2long tests Thu Jun 17 21:51:08 2021 

 Ending wide2long tests Thu Jun 17 21:51:09 2021 
  Took  0.8 

══ Skipped tests ═══════════════════════════════════════════════════════════════
• On Mac (2)
• empty test (1)

[ FAIL 0 | WARN 1 | SKIP 3 | PASS 8199 ]
> 
> proc.time()
   user  system elapsed 
542.156 103.198 488.794 

Example timings

OncoSimulR.Rcheck/OncoSimulR-Ex.timings

nameusersystemelapsed
OncoSimulWide2Long0.7230.1540.879
POM1.8520.2681.351
allFitnessEffects2.1330.0772.215
benchmarks0.0120.0070.019
evalAllGenotypes0.2660.0220.288
example-missing-drivers0.3930.0200.412
examplePosets0.3820.0060.388
examplesFitnessEffects0.0740.0030.078
freq-dep-simul-examples0.0130.0030.016
mcfLs0.0000.0010.000
oncoSimulIndiv3.4680.8393.702
plot.fitnessEffects0.3420.0310.376
plot.oncosimul0.8850.1131.000
plotClonePhylog3.3920.3583.753
plotFitnessLandscape1.4170.0321.450
plotPoset0.1640.0050.169
poset0.2120.0060.260
rfitness0.8880.0180.912
samplePop0.7770.3870.707
simOGraph0.1050.0180.124
to_Magellan0.2690.0580.371