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This page was generated on 2022-06-24 11:06:54 -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 palomino4


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: F:\biocbuild\bbs-3.16-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:OncoSimulR.install-out.txt --library=F:\biocbuild\bbs-3.16-bioc\R\library --no-vignettes --timings OncoSimulR_3.5.0.tar.gz
StartedAt: 2022-06-24 04:07:04 -0400 (Fri, 24 Jun 2022)
EndedAt: 2022-06-24 04:15:40 -0400 (Fri, 24 Jun 2022)
EllapsedTime: 515.4 seconds
RetCode: 0
Status:   OK  
CheckDir: OncoSimulR.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.16-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:OncoSimulR.install-out.txt --library=F:\biocbuild\bbs-3.16-bioc\R\library --no-vignettes --timings OncoSimulR_3.5.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'F:/biocbuild/bbs-3.16-bioc/meat/OncoSimulR.Rcheck'
* using R version 4.2.0 Patched (2022-06-02 r82447 ucrt)
* using platform: x86_64-w64-mingw32 (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 whether package 'OncoSimulR' can be installed ... OK
* checking installed package size ... NOTE
  installed size is  8.3Mb
  sub-directories of 1Mb or more:
    libs   6.9Mb
* 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 for x64 is not available
File 'F:/biocbuild/bbs-3.16-bioc/R/library/OncoSimulR/libs/x64/OncoSimulR.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
  Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs. The detected symbols are linked into the code but
might come from libraries and not actually be called.

See 'Writing portable packages' in the 'Writing R Extensions' manual.
* 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
  'F:/biocbuild/bbs-3.16-bioc/meat/OncoSimulR.Rcheck/00check.log'
for details.



Installation output

OncoSimulR.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.16/bioc/src/contrib/OncoSimulR_3.5.0.tar.gz && rm -rf OncoSimulR.buildbin-libdir && mkdir OncoSimulR.buildbin-libdir && F:\biocbuild\bbs-3.16-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=OncoSimulR.buildbin-libdir OncoSimulR_3.5.0.tar.gz && F:\biocbuild\bbs-3.16-bioc\R\bin\R.exe CMD INSTALL OncoSimulR_3.5.0.zip && rm OncoSimulR_3.5.0.tar.gz OncoSimulR_3.5.0.zip
###
##############################################################################
##############################################################################


  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100 1267k  100 1267k    0     0  8333k      0 --:--:-- --:--:-- --:--:-- 8393k
only one architecture so ignoring '--merge-multiarch'
* installing *source* package 'OncoSimulR' ...
** using staged installation
** libs
gcc  -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include'   -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c FitnessLandscape/gamma.c -o FitnessLandscape/gamma.o
gcc  -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include'   -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c FitnessLandscape/landscape.c -o FitnessLandscape/landscape.o
gcc  -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include'   -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c FitnessLandscape/random.c -o FitnessLandscape/random.o
gcc  -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include'   -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c FitnessLandscape/sort.c -o FitnessLandscape/sort.o
gcc  -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include'   -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c FitnessLandscape/chain.c -o FitnessLandscape/chain.o
gcc  -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include'   -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c FitnessLandscape/input.c -o FitnessLandscape/input.o
gcc  -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include'   -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c FitnessLandscape/genotypes.c -o FitnessLandscape/genotypes.o
gcc  -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include'   -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c FitnessLandscape/ordered_pairs.c -o FitnessLandscape/ordered_pairs.o
gcc  -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include'   -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c FitnessLandscape/calculus.c -o FitnessLandscape/calculus.o
gcc  -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include'   -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c FitnessLandscape/vector.c -o FitnessLandscape/vector.o
gcc  -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include'   -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c FitnessLandscape/generalized_chain.c -o FitnessLandscape/generalized_chain.o
gcc  -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include'   -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c FitnessLandscape/LinearAlgebra.c -o FitnessLandscape/LinearAlgebra.o
gcc  -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include'   -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c FitnessLandscape/summary_statistics.c -o FitnessLandscape/summary_statistics.o
gcc  -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include'   -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c FitnessLandscape/epistasis_type.c -o FitnessLandscape/epistasis_type.o
gcc  -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include'   -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c FitnessLandscape/decomposition.c -o FitnessLandscape/decomposition.o
gcc  -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include'   -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c FitnessLandscape/models.c -o FitnessLandscape/models.o
gcc  -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include'   -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -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 ;
C:\rtools42\x86_64-w64-mingw32.static.posix\bin\ar.exe: 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"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include'   -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -Wa,-mbig-obj -O3 -c BNB_nr.cpp -o BNB_nr.o
gcc  -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include'   -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c OncoSimulR_init.c -o OncoSimulR_init.o
g++  -std=gnu++11 -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include'   -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -Wa,-mbig-obj -O3 -c RcppExports.cpp -o RcppExports.o
g++  -std=gnu++11 -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include'   -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -Wa,-mbig-obj -O3 -c accessible_genotypes.cpp -o accessible_genotypes.o
g++  -std=gnu++11 -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include'   -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -Wa,-mbig-obj -O3 -c bnb_common.cpp -o bnb_common.o
g++  -std=gnu++11 -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include'   -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -Wa,-mbig-obj -O3 -c new_restrict.cpp -o new_restrict.o
g++ -shared -s -static-libgcc -o OncoSimulR.dll tmp.def BNB_nr.o OncoSimulR_init.o RcppExports.o accessible_genotypes.o bnb_common.o new_restrict.o -Wa,-mbig-obj -O3 -LC:/rtools42/x86_64-w64-mingw32.static.posix/lib/x64 -LC:/rtools42/x86_64-w64-mingw32.static.posix/lib -LF:/biocbuild/bbs-3.16-bioc/R/bin/x64 -lR
installing via 'install.libs.R' to F:/biocbuild/bbs-3.16-bioc/meat/OncoSimulR.buildbin-libdir/00LOCK-OncoSimulR/00new/OncoSimulR
[1] "/x64"
Installing fl_statistics.exe fl_generate.exe to F:/biocbuild/bbs-3.16-bioc/meat/OncoSimulR.buildbin-libdir/00LOCK-OncoSimulR/00new/OncoSimulR/exec/x64
Installing library OncoSimulR.dll to F:/biocbuild/bbs-3.16-bioc/meat/OncoSimulR.buildbin-libdir/00LOCK-OncoSimulR/00new/OncoSimulR/libs/x64
** 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
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* MD5 sums
packaged installation of 'OncoSimulR' as OncoSimulR_3.5.0.zip
* DONE (OncoSimulR)
* installing to library 'F:/biocbuild/bbs-3.16-bioc/R/library'
package 'OncoSimulR' successfully unpacked and MD5 sums checked

Tests output

OncoSimulR.Rcheck/tests/testthat.Rout


R version 4.2.0 Patched (2022-06-02 r82447 ucrt) -- "Vigorous Calisthenics"
Copyright (C) 2022 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (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 Fri Jun 24 04:10:16 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 Fri Jun 24 04:10:16 2022 
  Took  0.53 


 Starting LOD_POM at Fri Jun 24 04:10:16 2022 

 Ending LOD_POM at Fri Jun 24 04:10:32 2022 
  Took  15.81 


 Starting test.Z-all-fitness at Fri Jun 24 04:10:32 2022 

 Ending test.Z-all-fitness at Fri Jun 24 04:10:32 2022 
  Took  0.1 


 Starting test.Z-driver-counts at Fri Jun 24 04:10:32 2022 

 Ending test.Z-driver-counts at Fri Jun 24 04:10:32 2022 
  Took  0.15 


 Starting test.Z-fixation at Fri Jun 24 04:10:32 2022 

 Ending test.Z-fixation at Fri Jun 24 04:10:33 2022 
  Took  0.66 


 Starting test.Z-magellan at Fri Jun 24 04:10:33 2022 

 Ended test.Z-magellan at Fri Jun 24 04:10:35 2022 

 Starting test.Z-mutator at Fri Jun 24 04:10:35 2022 

 Ending test.Z-mutator at Fri Jun 24 04:10:35 2022 
  Took  0.39 


 Starting test.Z-mutatorFDF at Fri Jun 24 04:10:35 2022 

 Ending test.Z-mutatorFDF at Fri Jun 24 04:10:35 2022 
  Took  0.15 


 Starting test.Z-oncoSimulIndiv at Fri Jun 24 04:10:35 2022 

 Ending test.Z-oncoSimulIndiv at Fri Jun 24 04:10:37 2022 
  Took  1.53 


 Starting test.Z-oncoSimulIndivFDF at Fri Jun 24 04:10:37 2022 

 Ending test.Z-oncoSimulIndivFDF at Fri Jun 24 04:10:37 2022 
  Took  0.15 


 Starting test.Z-rfitness-landscape at Fri Jun 24 04:10:37 2022 

 Ending test.Z-rfitness-landscape at Fri Jun 24 04:10:37 2022 
  Took  0.13 


 Starting Z-sample-only-last tests Fri Jun 24 04:10:37 2022 

 Ending Z-sample-only-last tests Fri Jun 24 04:10:37 2022 
  Took  0 


 Starting Z-total-present-drivers tests Fri Jun 24 04:10:37 2022 

 Ending Z-total-present-drivers tests Fri Jun 24 04:10:38 2022 
  Took  1.36 


 Dummy empty test  Fri Jun 24 04:10:38 2022 

 Starting accessible_genotypes at Fri Jun 24 04:10:38 2022 

 Ending accessible_genotypes at Fri Jun 24 04:10:46 2022 
  Took  7.7 


 Starting all fitness at Fri Jun 24 04:10:46 2022
 Ending all-fitness at Fri Jun 24 04:10:52 2022 
  Took  6.01 


 Starting test.allFitnessEffectsFDF at Fri Jun 24 04:10:52 2022 

 Ending test.allFitnessEffectsFDF at Fri Jun 24 04:10:52 2022 
  Took  0.11 


 Starting test.allFitnessEffectsFDF at Fri Jun 24 04:10:52 2022 

 Ending test.allFitnessEffectsFDF at Fri Jun 24 04:10:53 2022 
  Took  0.35 


 Starting driverCounts at Fri Jun 24 04:10:53 2022
 Ending driverCounts at Fri Jun 24 04:11:00 2022 
  Took  7.37 


 Starting epist-order-modules at Fri Jun 24 04:11:00 2022
 Ending epist-order-modules at Fri Jun 24 04:11:00 2022 
  Took  0.02 


 Starting test.evaluatingGenotypesFDF at Fri Jun 24 04:11:00 2022 

 Ending test.evaluatingGenotypesFDF at Fri Jun 24 04:11:00 2022 
  Took  0.17 


 Starting exercise-plotting-code at Fri Jun 24 04:11:00 2022
 Ending exercise-plotting-code at Fri Jun 24 04:11:07 2022 
  Took  7.19 


 Starting exercise-rfitness at Fri Jun 24 04:11:07 2022 

 Ending exercise-rfitness at Fri Jun 24 04:11:20 2022 
  Took  12.93 


 Starting to_Magella at Fri Jun 24 04:11:20 2022 

 Ending to_Magella at Fri Jun 24 04:11:20 2022 
  Took  0.05 


 Starting fitness preds at Fri Jun 24 04:11:20 2022 

 Observed vs expected, case III

 done tries 1 

 Ending fitness preds long at Fri Jun 24 04:11:32 2022 
  Took  11.36 


 Starting fixation  at Fri Jun 24 04:11:32 2022 

 Ending fixation  at Fri Jun 24 04:12:17 2022 
  Took  45.43 


 Starting test.flfast-additional.R test at Fri Jun 24 04:12:17 2022
 Ending test.flfast-additional.R test at Fri Jun 24 04:12:19 2022 
  Took  1.5 


 Starting test.flfast-mutator.R test at Fri Jun 24 04:12:19 2022
 Finished test.flfast-mutator.R test at Fri Jun 24 04:12:22 2022 
  Took  3.65 


 Starting genotFitness at Fri Jun 24 04:12:22 2022 

 Ending genotFitness at Fri Jun 24 04:12:22 2022 
  Took  0.13 


 Starting genot_fitness_to_epistasis at Fri Jun 24 04:12:22 2022 

 Ending genot_fitness_to_epistasis at Fri Jun 24 04:12:23 2022 
  Took  0.03 


 Starting init-mutant tests Fri Jun 24 04:12:23 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 Fri Jun 24 04:12:32 2022 
  Took  9.53 


 Starting test.magellan at Fri Jun 24 04:12:32 2022 

 Ending test.magellan at Fri Jun 24 04:12:33 2022 
  Took  0.66 


 Starting test.modules-root-no-root at Fri Jun 24 04:12:33 2022 

 Ending test.modules-root-no-root at Fri Jun 24 04:12:33 2022 
  Took  0.05 


 Starting at mutPropGrowth  Fri Jun 24 04:12:33 2022 

 Ended test.mutPropGrowth:  Fri Jun 24 04:12:43 2022 
  Took  10.39 


 Starting test.mutator-oncoSimulSample.R test at Fri Jun 24 04:12:43 2022 

 Finished test.mutator-oncoSimulSample.R test at Fri Jun 24 04:12:53 2022 
  Took  9.38 seconds 


 Starting test.mutator.R test at Fri Jun 24 04:12:53 2022[1] 5.186419e-08
[1] 1.104775e-09

 Finished test.mutator.R test at Fri Jun 24 04:13:13 2022 
  Took  20.8 


 Starting test.mutatorFDF.R test at Fri Jun 24 04:13:13 2022
 Starting test.no-v1 at Fri Jun 24 04:13:14 2022 

 Ending test.no-v1 at Fri Jun 24 04:13:14 2022 
  Took  0.01 


 Starting oncoSimulIndiv-miscell tests Fri Jun 24 04:13:14 2022 

 Ending oncoSimulIndiv-miscell tests Fri Jun 24 04:13:25 2022 
  Took  10.49 


 Starting oncoSimulSample-failures tests Fri Jun 24 04:13:25 2022 

 Ending oncoSimulSample-failures tests Fri Jun 24 04:13:29 2022 
  Took  3.96 


 Starting oncoSimulSample-limits tests Fri Jun 24 04:13:29 2022 

 Ending oncoSimulSample-limits tests Fri Jun 24 04:13:29 2022 
  Took  0.11 


 Starting per-gene-mutation rates at Fri Jun 24 04:13:29 2022 

 Ending per-gene-mutation rates at Fri Jun 24 04:14:26 2022 
  Took  57.18 


 Starting plotFitnessLandscape at Fri Jun 24 04:14:26 2022
 Ending plotFitnessLandscape at Fri Jun 24 04:14:30 2022 
  Took  3.67 


 Starting poset-transformations tests Fri Jun 24 04:14:30 2022 

 Ending poset-transformations tests Fri Jun 24 04:14:38 2022 
  Took  8.4 


 Starting sample-prob Fri Jun 24 04:14:38 2022 
[1] 2.438511e-27
[1] 4.783832e-20
[1] 1.246344e-09
[1] 1.321832e-11
[1] 9.187336e-13
[1] 7.165173e-12
[1] 2.589671e-11
[1] 9.884936e-16
[1] 1.425069e-10
[1] 5.566423e-09
[1] 2.283937e-05
[1] 1.12978e-09

 Ending sample-prob tests Fri Jun 24 04:14:56 2022 
 Took  18.47 



 Starting samplePop tests Fri Jun 24 04:14:56 2022 

 Ending samplePop tests Fri Jun 24 04:15:09 2022 
  Took  12.63 


 Starting simuls-runs-examples tests Fri Jun 24 04:15:09 2022 

 Ending simuls-runs-examples tests Fri Jun 24 04:15:20 2022 
  Took  10.96 


 Starting warning-mutPropGrowth tests Fri Jun 24 04:15:20 2022 

 Ending warning-mutPropGrowth tests Fri Jun 24 04:15:27 2022 
  Took  6.98 


 Starting wide2long tests Fri Jun 24 04:15:27 2022 

 Ending wide2long tests Fri Jun 24 04:15:27 2022 
  Took  0.33 

[ FAIL 0 | WARN 1 | SKIP 6 | PASS 8187 ]

══ Skipped tests ═══════════════════════════════════════════════════════════════
• On Windows (1)
• empty test (5)

[ FAIL 0 | WARN 1 | SKIP 6 | PASS 8187 ]
> 
> proc.time()
   user  system elapsed 
 299.50    5.48  315.57 

Example timings

OncoSimulR.Rcheck/OncoSimulR-Ex.timings

nameusersystemelapsed
OncoSimulWide2Long0.500.220.72
POM1.470.141.61
allFitnessEffects1.610.081.68
benchmarks0.010.000.02
evalAllGenotypes0.210.020.22
example-missing-drivers0.320.010.34
examplePosets0.360.000.36
examplesFitnessEffects0.030.020.05
freq-dep-simul-examples0.020.000.01
mcfLs000
oncoSimulIndiv3.370.043.43
plot.fitnessEffects0.220.000.29
plot.oncosimul0.840.000.84
plotClonePhylog1.330.081.41
plotFitnessLandscape1.090.001.09
plotPoset0.110.020.12
poset0.280.000.28
rfitness0.630.010.93
samplePop0.480.000.48
simOGraph0.050.020.06
to_Magellan0.040.030.78