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CHECK results for OncoSimulR on nebbiolo1

This page was generated on 2021-06-11 14:05:46 -0400 (Fri, 11 Jun 2021).

Package 1308/2041HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
OncoSimulR 3.0.0  (landing page)
Ramon Diaz-Uriarte
Snapshot Date: 2021-06-10 06:50:12 -0400 (Thu, 10 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
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.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

Summary

Package: OncoSimulR
Version: 3.0.0
Command: /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD check --install=check:OncoSimulR.install-out.txt --library=/home/biocbuild/bbs-3.13-bioc/R/library --no-vignettes --timings OncoSimulR_3.0.0.tar.gz
StartedAt: 2021-06-10 13:02:31 -0400 (Thu, 10 Jun 2021)
EndedAt: 2021-06-10 13:09:18 -0400 (Thu, 10 Jun 2021)
EllapsedTime: 406.7 seconds
RetCode: 0
Status:   OK  
CheckDir: OncoSimulR.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD check --install=check:OncoSimulR.install-out.txt --library=/home/biocbuild/bbs-3.13-bioc/R/library --no-vignettes --timings OncoSimulR_3.0.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.13-bioc/meat/OncoSimulR.Rcheck’
* using R version 4.1.0 (2021-05-18)
* 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 ‘3.0.0’
* 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 ... 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 24.3Mb
  sub-directories of 1Mb or more:
    libs  23.1Mb
* 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-3.13-bioc/meat/OncoSimulR.Rcheck/00check.log’
for details.



Installation output

OncoSimulR.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD INSTALL OncoSimulR
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.13-bioc/R/library’
* installing *source* package ‘OncoSimulR’ ...
** using staged installation
** libs
gcc -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.13-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-3.13-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.13-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-3.13-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.13-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-3.13-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.13-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-3.13-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.13-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-3.13-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.13-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-3.13-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.13-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-3.13-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.13-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-3.13-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.13-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-3.13-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.13-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-3.13-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.13-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-3.13-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.13-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-3.13-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.13-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-3.13-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.13-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-3.13-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.13-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-3.13-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.13-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-3.13-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.13-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-3.13-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.13-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-3.13-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.13-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-3.13-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.13-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-3.13-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.13-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-3.13-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.13-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-3.13-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.13-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-3.13-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-3.13-bioc/R/lib -lR
installing via 'install.libs.R' to /home/biocbuild/bbs-3.13-bioc/R/library/00LOCK-OncoSimulR/00new/OncoSimulR
[1] ""
Installing fl_statistics fl_generate to /home/biocbuild/bbs-3.13-bioc/R/library/00LOCK-OncoSimulR/00new/OncoSimulR/exec
Installing library OncoSimulR.so to /home/biocbuild/bbs-3.13-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 4.1.0 (2021-05-18) -- "Camp Pontanezen"
Copyright (C) 2021 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 10 13:03:42 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 10 13:03:42 2021 
  Took  0.37 


 Starting LOD_POM at Thu Jun 10 13:03:42 2021 

 Ending LOD_POM at Thu Jun 10 13:03:58 2021 
  Took  16.06 


 Starting test.Z-all-fitness at Thu Jun 10 13:03:58 2021 

 Ending test.Z-all-fitness at Thu Jun 10 13:03:58 2021 
  Took  0.06 


 Starting test.Z-driver-counts at Thu Jun 10 13:03:58 2021 

 Ending test.Z-driver-counts at Thu Jun 10 13:03:58 2021 
  Took  0.17 


 Starting test.Z-fixation at Thu Jun 10 13:03:58 2021 

 Ending test.Z-fixation at Thu Jun 10 13:03:59 2021 
  Took  0.59 


 Starting test.Z-magellan at Thu Jun 10 13:03:59 2021 

 Ended test.Z-magellan at Thu Jun 10 13:04:01 2021 

 Starting test.Z-mutator at Thu Jun 10 13:04:01 2021 

 Ending test.Z-mutator at Thu Jun 10 13:04:01 2021 
  Took  0.21 


 Starting test.Z-mutatorFDF at Thu Jun 10 13:04:01 2021 

 Ending test.Z-mutatorFDF at Thu Jun 10 13:04:01 2021 
  Took  0.07 


 Starting test.Z-oncoSimulIndiv at Thu Jun 10 13:04:01 2021 

 Ending test.Z-oncoSimulIndiv at Thu Jun 10 13:04:02 2021 
  Took  1.36 


 Starting test.Z-oncoSimulIndivFDF at Thu Jun 10 13:04:02 2021 

 Ending test.Z-oncoSimulIndivFDF at Thu Jun 10 13:04:02 2021 
  Took  0.11 


 Starting test.Z-rfitness-landscape at Thu Jun 10 13:04:02 2021 

 Ending test.Z-rfitness-landscape at Thu Jun 10 13:04:02 2021 
  Took  0.12 


 Starting Z-sample-only-last tests Thu Jun 10 13:04:02 2021 

 Ending Z-sample-only-last tests Thu Jun 10 13:04:02 2021 
  Took  0 


 Starting Z-total-present-drivers tests Thu Jun 10 13:04:02 2021 

 Ending Z-total-present-drivers tests Thu Jun 10 13:04:04 2021 
  Took  1.11 


 Dummy empty test  Thu Jun 10 13:04:04 2021 

 Starting accessible_genotypes at Thu Jun 10 13:04:04 2021 

 Ending accessible_genotypes at Thu Jun 10 13:04:08 2021 
  Took  4.32 


 Starting all fitness at Thu Jun 10 13:04:08 2021
 Ending all-fitness at Thu Jun 10 13:04:12 2021 
  Took  3.74 


 Starting test.allFitnessEffectsFDF at Thu Jun 10 13:04:12 2021 

 Ending test.allFitnessEffectsFDF at Thu Jun 10 13:04:12 2021 
  Took  0.1 


 Starting test.allFitnessEffectsFDF at Thu Jun 10 13:04:12 2021 

 Ending test.allFitnessEffectsFDF at Thu Jun 10 13:04:12 2021 
  Took  0.27 


 Starting driverCounts at Thu Jun 10 13:04:12 2021
 Ending driverCounts at Thu Jun 10 13:04:21 2021 
  Took  8.61 


 Starting epist-order-modules at Thu Jun 10 13:04:21 2021
 Ending epist-order-modules at Thu Jun 10 13:04:21 2021 
  Took  0.04 


 Starting test.evaluatingGenotypesFDF at Thu Jun 10 13:04:21 2021 

 Ending test.evaluatingGenotypesFDF at Thu Jun 10 13:04:21 2021 
  Took  0.12 


 Starting exercise-plotting-code at Thu Jun 10 13:04:21 2021
 Ending exercise-plotting-code at Thu Jun 10 13:04:27 2021 
  Took  6.45 


 Starting exercise-rfitness at Thu Jun 10 13:04:27 2021 

 Ending exercise-rfitness at Thu Jun 10 13:04:32 2021 
  Took  4.77 


 Starting to_Magella at Thu Jun 10 13:04:32 2021 

 Ending to_Magella at Thu Jun 10 13:04:32 2021 
  Took  0.02 


 Starting fitness preds at Thu Jun 10 13:04:32 2021 

 Observed vs expected, case III

 T.not is 
[1] TRUE
 [1] 1.471679e-41 4.690269e-35 2.833790e-37 3.416010e-39 3.674399e-40
 [6] 8.078018e-38 0.000000e+00 0.000000e+00 2.315013e-34 9.289264e-40
[11] 1.778048e-33 2.948770e-37 5.181051e-27 2.436085e-48 4.336302e-24
[16] 9.380875e-22 4.227085e-37 1.132600e-16

 T.yest 
[1] TRUE
 [1] 0.23603037 0.60925848 0.39617491 0.11671311 0.71550936 0.70962820
 [7] 0.52144059 0.91725173 0.51954687 0.53337010 0.79843560 0.74856312
[13] 0.22909023 0.73630123 0.94629815 0.84096589 0.66327210 0.67547808
[19] 0.50812041 0.17436594 0.25013859 0.42937605 0.59612004 0.02585723
[25] 0.20844756 0.96631060 0.64425673 0.96637196 0.19936430 0.87109234

 larger values of T.yest 
integer(0)

 lm and plot

Call:
lm(formula = log(Observed) ~ log(Expected), data = d1)

Residuals:
       Min         1Q     Median         3Q        Max 
-0.0215125 -0.0020747  0.0005903  0.0021386  0.0111104 

Coefficients:
               Estimate Std. Error t value Pr(>|t|)    
(Intercept)   0.0115064  0.0040380    2.85  0.00812 ** 
log(Expected) 0.9987906  0.0003394 2942.39  < 2e-16 ***
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1

Residual standard error: 0.006106 on 28 degrees of freedom
Multiple R-squared:      1,	Adjusted R-squared:      1 
F-statistic: 8.658e+06 on 1 and 28 DF,  p-value: < 2.2e-16

Linear hypothesis test

Hypothesis:
(Intercept) = 0
log(Expected) = 1

Model 1: restricted model
Model 2: log(Observed) ~ log(Expected)

  Res.Df       RSS Df  Sum of Sq      F   Pr(>F)   
1     30 0.0016788                                 
2     28 0.0010438  2 0.00063496 8.5163 0.001291 **
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1

 done tries 2 

 Ending fitness preds long at Thu Jun 10 13:04:52 2021 
  Took  20.07 


 Starting fixation  at Thu Jun 10 13:04:52 2021 

 Ending fixation  at Thu Jun 10 13:05:19 2021 
  Took  27.04 


 Starting test.flfast-additional.R test at Thu Jun 10 13:05:19 2021
 Ending test.flfast-additional.R test at Thu Jun 10 13:05:20 2021 
  Took  1.3 


 Starting test.flfast-mutator.R test at Thu Jun 10 13:05:20 2021
 Finished test.flfast-mutator.R test at Thu Jun 10 13:05:24 2021 
  Took  3.11 


 Starting genotFitness at Thu Jun 10 13:05:24 2021 

 Ending genotFitness at Thu Jun 10 13:05:24 2021 
  Took  0.1 


 Starting genot_fitness_to_epistasis at Thu Jun 10 13:05:24 2021 

 Ending genot_fitness_to_epistasis at Thu Jun 10 13:05:24 2021 
  Took  0.02 


 Starting init-mutant tests Thu Jun 10 13:05:24 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 10 13:05:32 2021 
  Took  8.09 


 Starting test.magellan at Thu Jun 10 13:05:32 2021 

 Ending test.magellan at Thu Jun 10 13:05:32 2021 
  Took  0.13 


 Starting test.modules-root-no-root at Thu Jun 10 13:05:32 2021 

 Ending test.modules-root-no-root at Thu Jun 10 13:05:32 2021 
  Took  0.04 


 Starting at mutPropGrowth  Thu Jun 10 13:05:32 2021 

 Ended test.mutPropGrowth:  Thu Jun 10 13:05:43 2021 
  Took  11.16 


 Starting test.mutator-oncoSimulSample.R test at Thu Jun 10 13:05:43 2021 

 Finished test.mutator-oncoSimulSample.R test at Thu Jun 10 13:05:53 2021 
  Took  9.91 seconds 


 Starting test.mutator.R test at Thu Jun 10 13:05:53 2021[1] 2.694162e-08
[1] 2.060562e-13

 Finished test.mutator.R test at Thu Jun 10 13:06:09 2021 
  Took  15.53 


 Starting test.mutatorFDF.R test at Thu Jun 10 13:06:09 2021
 Starting test.no-v1 at Thu Jun 10 13:06:09 2021 

 Ending test.no-v1 at Thu Jun 10 13:06:09 2021 
  Took  0.01 


 Starting oncoSimulIndiv-miscell tests Thu Jun 10 13:06:09 2021 

 Ending oncoSimulIndiv-miscell tests Thu Jun 10 13:06:29 2021 
  Took  20.28 


 Starting oncoSimulSample-failures tests Thu Jun 10 13:06:29 2021 

 Ending oncoSimulSample-failures tests Thu Jun 10 13:06:34 2021 
  Took  4.16 


 Starting oncoSimulSample-limits tests Thu Jun 10 13:06:34 2021 

 Ending oncoSimulSample-limits tests Thu Jun 10 13:06:34 2021 
  Took  0.07 


 Starting per-gene-mutation rates at Thu Jun 10 13:06:34 2021 

 Ending per-gene-mutation rates at Thu Jun 10 13:07:15 2021 
  Took  41.25 


 Starting plotFitnessLandscape at Thu Jun 10 13:07:15 2021
 Ending plotFitnessLandscape at Thu Jun 10 13:07:18 2021 
  Took  3.14 


 Starting poset-transformations tests Thu Jun 10 13:07:18 2021 

 Ending poset-transformations tests Thu Jun 10 13:07:26 2021 
  Took  7.81 


 Starting sample-prob Thu Jun 10 13:07:26 2021 
[1] 7.374592e-21
[1] 8.256851e-15
[1] 4.945823e-10
[1] 1.248316e-11
[1] 4.850757e-16
[1] 5.204665e-15
[1] 8.017922e-12
[1] 2.113739e-16
[1] 5.145247e-10
[1] 1.652866e-10
[1] 5.31732e-10
[1] 1.487772e-08

 Ending sample-prob tests Thu Jun 10 13:07:42 2021 
 Took  16.38 



 Starting samplePop tests Thu Jun 10 13:07:42 2021 

 Ending samplePop tests Thu Jun 10 13:08:16 2021 
  Took  33.56 


 Starting simuls-runs-examples tests Thu Jun 10 13:08:16 2021 

 Ending simuls-runs-examples tests Thu Jun 10 13:09:07 2021 
  Took  51.46 


 Starting warning-mutPropGrowth tests Thu Jun 10 13:09:07 2021 

 Ending warning-mutPropGrowth tests Thu Jun 10 13:09:10 2021 
  Took  2.39 


 Starting wide2long tests Thu Jun 10 13:09:10 2021 

 Ending wide2long tests Thu Jun 10 13:09:10 2021 
  Took  0.76 

══ Skipped tests ═══════════════════════════════════════════════════════════════
• empty test (1)

[ FAIL 0 | WARN 1 | SKIP 1 | PASS 8204 ]
> 
> proc.time()
   user  system elapsed 
361.813  51.239 333.590 

Example timings

OncoSimulR.Rcheck/OncoSimulR-Ex.timings

nameusersystemelapsed
OncoSimulWide2Long0.4120.0360.452
POM0.7660.0800.647
allFitnessEffects1.2250.0401.267
benchmarks0.0090.0040.012
evalAllGenotypes0.1600.0120.171
example-missing-drivers0.2680.0120.279
examplePosets0.2990.0000.300
examplesFitnessEffects0.0390.0080.046
freq-dep-simul-examples0.0090.0000.009
mcfLs000
oncoSimulIndiv2.3570.3812.340
plot.fitnessEffects0.2000.0120.213
plot.oncosimul0.8740.0080.881
plotClonePhylog1.2520.0161.268
plotFitnessLandscape0.9090.0360.945
plotPoset0.0940.0000.093
poset0.1140.0000.113
rfitness0.5180.0060.525
samplePop0.4900.1370.387
simOGraph0.0680.0060.073
to_Magellan0.2070.0250.232