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This page was generated on 2022-06-24 11:05:37 -0400 (Fri, 24 Jun 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_644.2.0 Patched (2022-06-02 r82447) -- "Vigorous Calisthenics" 4331
palomino4Windows Server 2022 Datacenterx644.2.0 Patched (2022-06-02 r82447 ucrt) -- "Vigorous Calisthenics" 4136
lconwaymacOS 12.2.1 Montereyx86_644.2.0 Patched (2022-05-29 r82424) -- "Vigorous Calisthenics" 4147
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

CHECK results for OncoSimulR on nebbiolo2


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.

raw results

Package 1357/2118HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
OncoSimulR 3.5.0  (landing page)
Ramon Diaz-Uriarte
Snapshot Date: 2022-06-23 14:00:04 -0400 (Thu, 23 Jun 2022)
git_url: https://git.bioconductor.org/packages/OncoSimulR
git_branch: master
git_last_commit: 7af7ac6
git_last_commit_date: 2022-04-26 11:20:38 -0400 (Tue, 26 Apr 2022)
nebbiolo2Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino4Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.2.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: OncoSimulR
Version: 3.5.0
Command: /home/biocbuild/bbs-3.16-bioc/R/bin/R CMD check --install=check:OncoSimulR.install-out.txt --library=/home/biocbuild/bbs-3.16-bioc/R/library --no-vignettes --timings OncoSimulR_3.5.0.tar.gz
StartedAt: 2022-06-23 21:01:53 -0400 (Thu, 23 Jun 2022)
EndedAt: 2022-06-23 21:09:00 -0400 (Thu, 23 Jun 2022)
EllapsedTime: 427.6 seconds
RetCode: 0
Status:   OK  
CheckDir: OncoSimulR.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.16-bioc/R/bin/R CMD check --install=check:OncoSimulR.install-out.txt --library=/home/biocbuild/bbs-3.16-bioc/R/library --no-vignettes --timings OncoSimulR_3.5.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.16-bioc/meat/OncoSimulR.Rcheck’
* using R version 4.2.0 Patched (2022-06-02 r82447)
* using platform: x86_64-pc-linux-gnu (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 ‘3.5.0’
* 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 65.3Mb
  sub-directories of 1Mb or more:
    libs  63.7Mb
* 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: 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.16-bioc/meat/OncoSimulR.Rcheck/00check.log’
for details.



Installation output

OncoSimulR.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.16-bioc/R/bin/R CMD INSTALL OncoSimulR
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.16-bioc/R/library’
* installing *source* package ‘OncoSimulR’ ...
** using staged installation
** libs
gcc -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c FitnessLandscape/gamma.c -o FitnessLandscape/gamma.o
gcc -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c FitnessLandscape/landscape.c -o FitnessLandscape/landscape.o
gcc -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c FitnessLandscape/random.c -o FitnessLandscape/random.o
gcc -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c FitnessLandscape/sort.c -o FitnessLandscape/sort.o
gcc -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c FitnessLandscape/chain.c -o FitnessLandscape/chain.o
gcc -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c FitnessLandscape/input.c -o FitnessLandscape/input.o
gcc -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c FitnessLandscape/genotypes.c -o FitnessLandscape/genotypes.o
gcc -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c FitnessLandscape/ordered_pairs.c -o FitnessLandscape/ordered_pairs.o
gcc -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c FitnessLandscape/calculus.c -o FitnessLandscape/calculus.o
gcc -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c FitnessLandscape/vector.c -o FitnessLandscape/vector.o
gcc -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c FitnessLandscape/generalized_chain.c -o FitnessLandscape/generalized_chain.o
gcc -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c FitnessLandscape/LinearAlgebra.c -o FitnessLandscape/LinearAlgebra.o
FitnessLandscape/LinearAlgebra.c: In function ‘svdcmp’:
FitnessLandscape/LinearAlgebra.c:640:27: warning: ‘l’ may be used uninitialized in this function [-Wmaybe-uninitialized]
  640 |      v[j][i]=(u[i][j]/u[i][l])/g;
      |                           ^
gcc -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c FitnessLandscape/summary_statistics.c -o FitnessLandscape/summary_statistics.o
gcc -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c FitnessLandscape/epistasis_type.c -o FitnessLandscape/epistasis_type.o
gcc -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c FitnessLandscape/decomposition.c -o FitnessLandscape/decomposition.o
gcc -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c FitnessLandscape/models.c -o FitnessLandscape/models.o
gcc -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c FitnessLandscape/verbose.c -o FitnessLandscape/verbose.o
ar -r liblandscape.a FitnessLandscape/gamma.o FitnessLandscape/landscape.o FitnessLandscape/random.o FitnessLandscape/sort.o FitnessLandscape/chain.o FitnessLandscape/input.o FitnessLandscape/genotypes.o FitnessLandscape/ordered_pairs.o FitnessLandscape/calculus.o FitnessLandscape/vector.o FitnessLandscape/generalized_chain.o FitnessLandscape/LinearAlgebra.o FitnessLandscape/summary_statistics.o FitnessLandscape/epistasis_type.o FitnessLandscape/decomposition.o FitnessLandscape/models.o FitnessLandscape/verbose.o ;
ar: creating liblandscape.a
ranlib liblandscape.a;
gcc -O -Wall -o fl_statistics -I/FitnessLandscape/. -L. FitnessLandscape/main_fl_statistics.c -llandscape -lm;
gcc -O -Wall -o fl_generate -I/FitnessLandscape/. -L. FitnessLandscape/main_fl_generate.c -llandscape -lm;
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c BNB_nr.cpp -o BNB_nr.o
gcc -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c OncoSimulR_init.c -o OncoSimulR_init.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c accessible_genotypes.cpp -o accessible_genotypes.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c bnb_common.cpp -o bnb_common.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c new_restrict.cpp -o new_restrict.o
g++ -std=gnu++11 -shared -L/home/biocbuild/bbs-3.16-bioc/R/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 -L/home/biocbuild/bbs-3.16-bioc/R/lib -lR
installing via 'install.libs.R' to /home/biocbuild/bbs-3.16-bioc/R/library/00LOCK-OncoSimulR/00new/OncoSimulR
[1] ""
Installing fl_statistics fl_generate to /home/biocbuild/bbs-3.16-bioc/R/library/00LOCK-OncoSimulR/00new/OncoSimulR/exec
Installing library OncoSimulR.so to /home/biocbuild/bbs-3.16-bioc/R/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 4.2.0 Patched (2022-06-02 r82447) -- "Vigorous Calisthenics"
Copyright (C) 2022 The R Foundation for Statistical Computing
Platform: x86_64-pc-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 Thu Jun 23 21:03:01 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 Thu Jun 23 21:03:02 2022 
  Took  0.39 


 Starting LOD_POM at Thu Jun 23 21:03:02 2022 

 Ending LOD_POM at Thu Jun 23 21:03:18 2022 
  Took  16.82 


 Starting test.Z-all-fitness at Thu Jun 23 21:03:18 2022 

 Ending test.Z-all-fitness at Thu Jun 23 21:03:19 2022 
  Took  0.11 


 Starting test.Z-driver-counts at Thu Jun 23 21:03:19 2022 

 Ending test.Z-driver-counts at Thu Jun 23 21:03:19 2022 
  Took  0.18 


 Starting test.Z-fixation at Thu Jun 23 21:03:19 2022 

 Ending test.Z-fixation at Thu Jun 23 21:03:19 2022 
  Took  0.64 


 Starting test.Z-magellan at Thu Jun 23 21:03:19 2022 

 Ended test.Z-magellan at Thu Jun 23 21:03:21 2022 

 Starting test.Z-mutator at Thu Jun 23 21:03:21 2022 

 Ending test.Z-mutator at Thu Jun 23 21:03:21 2022 
  Took  0.38 


 Starting test.Z-mutatorFDF at Thu Jun 23 21:03:21 2022 

 Ending test.Z-mutatorFDF at Thu Jun 23 21:03:21 2022 
  Took  0.1 


 Starting test.Z-oncoSimulIndiv at Thu Jun 23 21:03:21 2022 

 Ending test.Z-oncoSimulIndiv at Thu Jun 23 21:03:23 2022 
  Took  1.72 


 Starting test.Z-oncoSimulIndivFDF at Thu Jun 23 21:03:23 2022 

 Ending test.Z-oncoSimulIndivFDF at Thu Jun 23 21:03:23 2022 
  Took  0.13 


 Starting test.Z-rfitness-landscape at Thu Jun 23 21:03:23 2022 

 Ending test.Z-rfitness-landscape at Thu Jun 23 21:03:23 2022 
  Took  0.14 


 Starting Z-sample-only-last tests Thu Jun 23 21:03:23 2022 

 Ending Z-sample-only-last tests Thu Jun 23 21:03:23 2022 
  Took  0 


 Starting Z-total-present-drivers tests Thu Jun 23 21:03:23 2022 

 Ending Z-total-present-drivers tests Thu Jun 23 21:03:25 2022 
  Took  1.19 


 Dummy empty test  Thu Jun 23 21:03:25 2022 

 Starting accessible_genotypes at Thu Jun 23 21:03:25 2022 

 Ending accessible_genotypes at Thu Jun 23 21:03:31 2022 
  Took  6.12 


 Starting all fitness at Thu Jun 23 21:03:31 2022
 Ending all-fitness at Thu Jun 23 21:03:35 2022 
  Took  4.35 


 Starting test.allFitnessEffectsFDF at Thu Jun 23 21:03:35 2022 

 Ending test.allFitnessEffectsFDF at Thu Jun 23 21:03:35 2022 
  Took  0.12 


 Starting test.allFitnessEffectsFDF at Thu Jun 23 21:03:35 2022 

 Ending test.allFitnessEffectsFDF at Thu Jun 23 21:03:36 2022 
  Took  0.33 


 Starting driverCounts at Thu Jun 23 21:03:36 2022
 Ending driverCounts at Thu Jun 23 21:03:45 2022 
  Took  9.29 


 Starting epist-order-modules at Thu Jun 23 21:03:45 2022
 Ending epist-order-modules at Thu Jun 23 21:03:45 2022 
  Took  0.08 


 Starting test.evaluatingGenotypesFDF at Thu Jun 23 21:03:45 2022 

 Ending test.evaluatingGenotypesFDF at Thu Jun 23 21:03:45 2022 
  Took  0.17 


 Starting exercise-plotting-code at Thu Jun 23 21:03:45 2022
 Ending exercise-plotting-code at Thu Jun 23 21:03:51 2022 
  Took  6.11 


 Starting exercise-rfitness at Thu Jun 23 21:03:51 2022 

 Ending exercise-rfitness at Thu Jun 23 21:03:59 2022 
  Took  7.77 


 Starting to_Magella at Thu Jun 23 21:03:59 2022 

 Ending to_Magella at Thu Jun 23 21:03:59 2022 
  Took  0.02 


 Starting fitness preds at Thu Jun 23 21:03:59 2022 

 Observed vs expected, case III

 done tries 1 

 Ending fitness preds long at Thu Jun 23 21:04:09 2022 
  Took  9.77 


 Starting fixation  at Thu Jun 23 21:04:09 2022 

 Ending fixation  at Thu Jun 23 21:04:42 2022 
  Took  32.65 


 Starting test.flfast-additional.R test at Thu Jun 23 21:04:42 2022
 Ending test.flfast-additional.R test at Thu Jun 23 21:04:43 2022 
  Took  1.76 


 Starting test.flfast-mutator.R test at Thu Jun 23 21:04:43 2022
 Finished test.flfast-mutator.R test at Thu Jun 23 21:04:45 2022 
  Took  1.79 


 Starting genotFitness at Thu Jun 23 21:04:45 2022 

 Ending genotFitness at Thu Jun 23 21:04:45 2022 
  Took  0.12 


 Starting genot_fitness_to_epistasis at Thu Jun 23 21:04:45 2022 

 Ending genot_fitness_to_epistasis at Thu Jun 23 21:04:45 2022 
  Took  0.03 


 Starting init-mutant tests Thu Jun 23 21:04:45 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 Thu Jun 23 21:04:54 2022 
  Took  8.67 


 Starting test.magellan at Thu Jun 23 21:04:54 2022 

 Ending test.magellan at Thu Jun 23 21:04:54 2022 
  Took  0.15 


 Starting test.modules-root-no-root at Thu Jun 23 21:04:54 2022 

 Ending test.modules-root-no-root at Thu Jun 23 21:04:54 2022 
  Took  0.05 


 Starting at mutPropGrowth  Thu Jun 23 21:04:54 2022 

 Ended test.mutPropGrowth:  Thu Jun 23 21:05:06 2022 
  Took  12.34 


 Starting test.mutator-oncoSimulSample.R test at Thu Jun 23 21:05:06 2022 

 Finished test.mutator-oncoSimulSample.R test at Thu Jun 23 21:05:17 2022 
  Took  10.55 seconds 


 Starting test.mutator.R test at Thu Jun 23 21:05:17 2022[1] 6.474981e-10
[1] 2.673791e-13

 Finished test.mutator.R test at Thu Jun 23 21:05:36 2022 
  Took  18.51 


 Starting test.mutatorFDF.R test at Thu Jun 23 21:05:36 2022
 Starting test.no-v1 at Thu Jun 23 21:05:36 2022 

 Ending test.no-v1 at Thu Jun 23 21:05:36 2022 
  Took  0.01 


 Starting oncoSimulIndiv-miscell tests Thu Jun 23 21:05:36 2022 

 Ending oncoSimulIndiv-miscell tests Thu Jun 23 21:05:57 2022 
  Took  20.42 


 Starting oncoSimulSample-failures tests Thu Jun 23 21:05:57 2022 

 Ending oncoSimulSample-failures tests Thu Jun 23 21:06:01 2022 
  Took  3.82 


 Starting oncoSimulSample-limits tests Thu Jun 23 21:06:01 2022 

 Ending oncoSimulSample-limits tests Thu Jun 23 21:06:01 2022 
  Took  0.06 


 Starting per-gene-mutation rates at Thu Jun 23 21:06:01 2022 

 Ending per-gene-mutation rates at Thu Jun 23 21:06:51 2022 
  Took  50.46 


 Starting plotFitnessLandscape at Thu Jun 23 21:06:51 2022
 Ending plotFitnessLandscape at Thu Jun 23 21:07:04 2022 
  Took  12.43 


 Starting poset-transformations tests Thu Jun 23 21:07:04 2022 

 Ending poset-transformations tests Thu Jun 23 21:07:21 2022 
  Took  17.82 


 Starting sample-prob Thu Jun 23 21:07:21 2022 
[1] 2.661756e-25
[1] 6.639622e-08
[1] 9.075418e-10
[1] 1.291964e-11
[1] 1.910909e-14
[1] 5.489345e-11
[1] 1.485312e-11
[1] 1.473044e-16
[1] 8.116277e-09
[1] 3.689791e-11
[1] 8.01661e-05
[1] 4.849111e-09

 Ending sample-prob tests Thu Jun 23 21:07:40 2022 
 Took  18.75 



 Starting samplePop tests Thu Jun 23 21:07:40 2022 

 Ending samplePop tests Thu Jun 23 21:08:09 2022 
  Took  28.64 


 Starting simuls-runs-examples tests Thu Jun 23 21:08:09 2022 

 Ending simuls-runs-examples tests Thu Jun 23 21:08:44 2022 
  Took  35.02 


 Starting warning-mutPropGrowth tests Thu Jun 23 21:08:44 2022 

 Ending warning-mutPropGrowth tests Thu Jun 23 21:08:46 2022 
  Took  2.4 


 Starting wide2long tests Thu Jun 23 21:08:46 2022 

 Ending wide2long tests Thu Jun 23 21:08:48 2022 
  Took  1.35 

[ FAIL 0 | WARN 1 | SKIP 5 | PASS 8176 ]

══ Skipped tests ═══════════════════════════════════════════════════════════════
• empty test (5)

[ FAIL 0 | WARN 1 | SKIP 5 | PASS 8176 ]
> 
> proc.time()
   user  system elapsed 
376.401  48.805 353.656 

Example timings

OncoSimulR.Rcheck/OncoSimulR-Ex.timings

nameusersystemelapsed
OncoSimulWide2Long0.4260.0440.472
POM0.7880.1030.692
allFitnessEffects1.3950.0201.420
benchmarks0.0080.0000.007
evalAllGenotypes0.1550.0000.155
example-missing-drivers0.2220.0120.234
examplePosets0.3270.0000.328
examplesFitnessEffects0.0460.0000.046
freq-dep-simul-examples0.010.000.01
mcfLs000
oncoSimulIndiv2.6530.3132.394
plot.fitnessEffects0.2180.0200.238
plot.oncosimul0.8620.0120.875
plotClonePhylog1.4300.0921.522
plotFitnessLandscape101
plotPoset0.0940.0040.098
poset0.1180.0000.118
rfitness0.5570.0170.575
samplePop0.6110.1040.447
simOGraph0.0530.0040.056
to_Magellan0.1910.0370.227