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This page was generated on 2021-06-19 12:06:00 -0400 (Sat, 19 Jun 2021).

CHECK results for OncoSimulR on riesling1

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.

raw results

Package 1277/1993HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
OncoSimulR 3.1.0  (landing page)
Ramon Diaz-Uriarte
Snapshot Date: 2021-06-18 14:50:08 -0400 (Fri, 18 Jun 2021)
URL: https://git.bioconductor.org/packages/OncoSimulR
Branch: master
Last Commit: d7183c4
Last Changed Date: 2021-05-19 12:06:18 -0400 (Wed, 19 May 2021)
nebbiolo2Linux (Ubuntu 20.04.2 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
riesling1Windows Server 2019 Standard / x64  OK    OK    OK    OK  NO, package depends on 'Rgraphviz' which is not available
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: OncoSimulR
Version: 3.1.0
Command: D:\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:OncoSimulR.install-out.txt --library=D:\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings OncoSimulR_3.1.0.tar.gz
StartedAt: 2021-06-19 01:21:47 -0400 (Sat, 19 Jun 2021)
EndedAt: 2021-06-19 01:34:18 -0400 (Sat, 19 Jun 2021)
EllapsedTime: 750.3 seconds
RetCode: 0
Status:   OK  
CheckDir: OncoSimulR.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   D:\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:OncoSimulR.install-out.txt --library=D:\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings OncoSimulR_3.1.0.tar.gz
###
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* using log directory 'D:/biocbuild/bbs-3.14-bioc/meat/OncoSimulR.Rcheck'
* using R version 4.1.0 (2021-05-18)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'OncoSimulR/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'OncoSimulR' version '3.1.0'
* 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 17.4Mb
  sub-directories of 1Mb or more:
    exec   2.2Mb
    libs  14.1Mb
* 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 i386 is not available
Note: information on .o files for x64 is not available
File 'D:/biocbuild/bbs-3.14-bioc/R/library/OncoSimulR/libs/i386/OncoSimulR.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
  Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
  Found 'printf', possibly from 'printf' (C)
File 'D:/biocbuild/bbs-3.14-bioc/R/library/OncoSimulR/libs/x64/OncoSimulR.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
  Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
  Found 'printf', possibly from 'printf' (C)

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 ...
** running examples for arch 'i386' ... OK
** running examples for arch 'x64' ... OK
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'testthat.R'
 OK
** running tests for arch 'x64' ...
  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
  'D:/biocbuild/bbs-3.14-bioc/meat/OncoSimulR.Rcheck/00check.log'
for details.



Installation output

OncoSimulR.Rcheck/00install.out

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.14/bioc/src/contrib/OncoSimulR_3.1.0.tar.gz && rm -rf OncoSimulR.buildbin-libdir && mkdir OncoSimulR.buildbin-libdir && D:\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=OncoSimulR.buildbin-libdir OncoSimulR_3.1.0.tar.gz && D:\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL OncoSimulR_3.1.0.zip && rm OncoSimulR_3.1.0.tar.gz OncoSimulR_3.1.0.zip
###
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  % 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  4430k      0 --:--:-- --:--:-- --:--:-- 4430k

install for i386

* installing *source* package 'OncoSimulR' ...
** using staged installation
** libs
"C:/rtools40/mingw32/bin/"gcc  -I"D:/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG  -I'D:/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c FitnessLandscape/gamma.c -o FitnessLandscape/gamma.o
"C:/rtools40/mingw32/bin/"gcc  -I"D:/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG  -I'D:/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c FitnessLandscape/landscape.c -o FitnessLandscape/landscape.o
"C:/rtools40/mingw32/bin/"gcc  -I"D:/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG  -I'D:/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c FitnessLandscape/random.c -o FitnessLandscape/random.o
"C:/rtools40/mingw32/bin/"gcc  -I"D:/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG  -I'D:/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c FitnessLandscape/sort.c -o FitnessLandscape/sort.o
"C:/rtools40/mingw32/bin/"gcc  -I"D:/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG  -I'D:/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c FitnessLandscape/chain.c -o FitnessLandscape/chain.o
"C:/rtools40/mingw32/bin/"gcc  -I"D:/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG  -I'D:/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c FitnessLandscape/input.c -o FitnessLandscape/input.o
"C:/rtools40/mingw32/bin/"gcc  -I"D:/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG  -I'D:/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c FitnessLandscape/genotypes.c -o FitnessLandscape/genotypes.o
"C:/rtools40/mingw32/bin/"gcc  -I"D:/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG  -I'D:/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c FitnessLandscape/ordered_pairs.c -o FitnessLandscape/ordered_pairs.o
"C:/rtools40/mingw32/bin/"gcc  -I"D:/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG  -I'D:/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c FitnessLandscape/calculus.c -o FitnessLandscape/calculus.o
"C:/rtools40/mingw32/bin/"gcc  -I"D:/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG  -I'D:/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c FitnessLandscape/vector.c -o FitnessLandscape/vector.o
"C:/rtools40/mingw32/bin/"gcc  -I"D:/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG  -I'D:/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c FitnessLandscape/generalized_chain.c -o FitnessLandscape/generalized_chain.o
"C:/rtools40/mingw32/bin/"gcc  -I"D:/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG  -I'D:/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -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]
      v[j][i]=(u[i][j]/u[i][l])/g;
                           ^
"C:/rtools40/mingw32/bin/"gcc  -I"D:/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG  -I'D:/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c FitnessLandscape/summary_statistics.c -o FitnessLandscape/summary_statistics.o
"C:/rtools40/mingw32/bin/"gcc  -I"D:/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG  -I'D:/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c FitnessLandscape/epistasis_type.c -o FitnessLandscape/epistasis_type.o
"C:/rtools40/mingw32/bin/"gcc  -I"D:/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG  -I'D:/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c FitnessLandscape/decomposition.c -o FitnessLandscape/decomposition.o
"C:/rtools40/mingw32/bin/"gcc  -I"D:/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG  -I'D:/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c FitnessLandscape/models.c -o FitnessLandscape/models.o
"C:/rtools40/mingw32/bin/"gcc  -I"D:/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG  -I'D:/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c FitnessLandscape/verbose.c -o FitnessLandscape/verbose.o
"C:/rtools40/mingw32/bin/"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:\rtools40\mingw32\bin\ar.exe: creating liblandscape.a
"C:/rtools40/mingw32/bin/"ranlib liblandscape.a;
"C:/rtools40/mingw32/bin/"gcc  -O -Wall -o fl_statistics -I/FitnessLandscape/. -L. FitnessLandscape/main_fl_statistics.c -llandscape -lm;
"C:/rtools40/mingw32/bin/"gcc  -O -Wall -o fl_generate -I/FitnessLandscape/. -L. FitnessLandscape/main_fl_generate.c -llandscape -lm;
"C:/rtools40/mingw32/bin/"g++  -std=gnu++11 -I"D:/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG  -I'D:/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -Wa,-mbig-obj -O3 -c BNB_nr.cpp -o BNB_nr.o
"C:/rtools40/mingw32/bin/"gcc  -I"D:/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG  -I'D:/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c OncoSimulR_init.c -o OncoSimulR_init.o
"C:/rtools40/mingw32/bin/"g++  -std=gnu++11 -I"D:/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG  -I'D:/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -Wa,-mbig-obj -O3 -c RcppExports.cpp -o RcppExports.o
"C:/rtools40/mingw32/bin/"g++  -std=gnu++11 -I"D:/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG  -I'D:/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -Wa,-mbig-obj -O3 -c accessible_genotypes.cpp -o accessible_genotypes.o
"C:/rtools40/mingw32/bin/"g++  -std=gnu++11 -I"D:/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG  -I'D:/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -Wa,-mbig-obj -O3 -c bnb_common.cpp -o bnb_common.o
"C:/rtools40/mingw32/bin/"g++  -std=gnu++11 -I"D:/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG  -I'D:/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -Wa,-mbig-obj -O3 -c new_restrict.cpp -o new_restrict.o
C:/rtools40/mingw32/bin/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:/extsoft/lib/i386 -LC:/extsoft/lib -LD:/biocbuild/bbs-3.14-bioc/R/bin/i386 -lR
installing via 'install.libs.R' to D:/biocbuild/bbs-3.14-bioc/meat/OncoSimulR.buildbin-libdir/00LOCK-OncoSimulR/00new/OncoSimulR
[1] "/i386"
Installing fl_statistics.exe fl_generate.exe to D:/biocbuild/bbs-3.14-bioc/meat/OncoSimulR.buildbin-libdir/00LOCK-OncoSimulR/00new/OncoSimulR/exec/i386
Installing library OncoSimulR.dll to D:/biocbuild/bbs-3.14-bioc/meat/OncoSimulR.buildbin-libdir/00LOCK-OncoSimulR/00new/OncoSimulR/libs/i386
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'OncoSimulR'
    finding HTML links ... done
    OncoSimulWide2Long                      html  
    POM                                     html  
    allFitnessEffects                       html  
    benchmarks                              html  
    evalAllGenotypes                        html  
    example-missing-drivers                 html  
    examplePosets                           html  
    examplesFitnessEffects                  html  
    freq-dep-simul-examples                 html  
    mcfLs                                   html  
    oncoSimulIndiv                          html  
    plot.fitnessEffects                     html  
    plot.oncosimul                          html  
    finding level-2 HTML links ... done

    plotClonePhylog                         html  
    plotFitnessLandscape                    html  
    plotPoset                               html  
    poset                                   html  
    rfitness                                html  
    samplePop                               html  
    simOGraph                               html  
    to_Magellan                             html  
** 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

install for x64

* installing *source* package 'OncoSimulR' ...
** libs
"C:/rtools40/mingw64/bin/"gcc  -I"D:/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG  -I'D:/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c FitnessLandscape/gamma.c -o FitnessLandscape/gamma.o
"C:/rtools40/mingw64/bin/"gcc  -I"D:/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG  -I'D:/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c FitnessLandscape/landscape.c -o FitnessLandscape/landscape.o
"C:/rtools40/mingw64/bin/"gcc  -I"D:/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG  -I'D:/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c FitnessLandscape/random.c -o FitnessLandscape/random.o
"C:/rtools40/mingw64/bin/"gcc  -I"D:/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG  -I'D:/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c FitnessLandscape/sort.c -o FitnessLandscape/sort.o
"C:/rtools40/mingw64/bin/"gcc  -I"D:/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG  -I'D:/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c FitnessLandscape/chain.c -o FitnessLandscape/chain.o
"C:/rtools40/mingw64/bin/"gcc  -I"D:/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG  -I'D:/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c FitnessLandscape/input.c -o FitnessLandscape/input.o
"C:/rtools40/mingw64/bin/"gcc  -I"D:/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG  -I'D:/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c FitnessLandscape/genotypes.c -o FitnessLandscape/genotypes.o
"C:/rtools40/mingw64/bin/"gcc  -I"D:/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG  -I'D:/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c FitnessLandscape/ordered_pairs.c -o FitnessLandscape/ordered_pairs.o
"C:/rtools40/mingw64/bin/"gcc  -I"D:/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG  -I'D:/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c FitnessLandscape/calculus.c -o FitnessLandscape/calculus.o
"C:/rtools40/mingw64/bin/"gcc  -I"D:/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG  -I'D:/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c FitnessLandscape/vector.c -o FitnessLandscape/vector.o
"C:/rtools40/mingw64/bin/"gcc  -I"D:/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG  -I'D:/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c FitnessLandscape/generalized_chain.c -o FitnessLandscape/generalized_chain.o
"C:/rtools40/mingw64/bin/"gcc  -I"D:/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG  -I'D:/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -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]
      v[j][i]=(u[i][j]/u[i][l])/g;
                           ^
"C:/rtools40/mingw64/bin/"gcc  -I"D:/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG  -I'D:/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c FitnessLandscape/summary_statistics.c -o FitnessLandscape/summary_statistics.o
"C:/rtools40/mingw64/bin/"gcc  -I"D:/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG  -I'D:/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c FitnessLandscape/epistasis_type.c -o FitnessLandscape/epistasis_type.o
"C:/rtools40/mingw64/bin/"gcc  -I"D:/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG  -I'D:/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c FitnessLandscape/decomposition.c -o FitnessLandscape/decomposition.o
"C:/rtools40/mingw64/bin/"gcc  -I"D:/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG  -I'D:/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c FitnessLandscape/models.c -o FitnessLandscape/models.o
"C:/rtools40/mingw64/bin/"gcc  -I"D:/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG  -I'D:/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c FitnessLandscape/verbose.c -o FitnessLandscape/verbose.o
"C:/rtools40/mingw64/bin/"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:\rtools40\mingw64\bin\ar.exe: creating liblandscape.a
"C:/rtools40/mingw64/bin/"ranlib liblandscape.a;
"C:/rtools40/mingw64/bin/"gcc  -O -Wall -o fl_statistics -I/FitnessLandscape/. -L. FitnessLandscape/main_fl_statistics.c -llandscape -lm;
"C:/rtools40/mingw64/bin/"gcc  -O -Wall -o fl_generate -I/FitnessLandscape/. -L. FitnessLandscape/main_fl_generate.c -llandscape -lm;
"C:/rtools40/mingw64/bin/"g++  -std=gnu++11 -I"D:/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG  -I'D:/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -Wa,-mbig-obj -O3 -c BNB_nr.cpp -o BNB_nr.o
"C:/rtools40/mingw64/bin/"gcc  -I"D:/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG  -I'D:/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c OncoSimulR_init.c -o OncoSimulR_init.o
"C:/rtools40/mingw64/bin/"g++  -std=gnu++11 -I"D:/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG  -I'D:/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -Wa,-mbig-obj -O3 -c RcppExports.cpp -o RcppExports.o
"C:/rtools40/mingw64/bin/"g++  -std=gnu++11 -I"D:/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG  -I'D:/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -Wa,-mbig-obj -O3 -c accessible_genotypes.cpp -o accessible_genotypes.o
"C:/rtools40/mingw64/bin/"g++  -std=gnu++11 -I"D:/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG  -I'D:/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -Wa,-mbig-obj -O3 -c bnb_common.cpp -o bnb_common.o
"C:/rtools40/mingw64/bin/"g++  -std=gnu++11 -I"D:/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG  -I'D:/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -Wa,-mbig-obj -O3 -c new_restrict.cpp -o new_restrict.o
C:/rtools40/mingw64/bin/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:/extsoft/lib/x64 -LC:/extsoft/lib -LD:/biocbuild/bbs-3.14-bioc/R/bin/x64 -lR
installing via 'install.libs.R' to D:/biocbuild/bbs-3.14-bioc/meat/OncoSimulR.buildbin-libdir/OncoSimulR
[1] "/x64"
Installing fl_statistics.exe fl_generate.exe to D:/biocbuild/bbs-3.14-bioc/meat/OncoSimulR.buildbin-libdir/OncoSimulR/exec/x64
Installing library OncoSimulR.dll to D:/biocbuild/bbs-3.14-bioc/meat/OncoSimulR.buildbin-libdir/OncoSimulR/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'OncoSimulR' as OncoSimulR_3.1.0.zip
* DONE (OncoSimulR)
* installing to library 'D:/biocbuild/bbs-3.14-bioc/R/library'
package 'OncoSimulR' successfully unpacked and MD5 sums checked

Tests output

OncoSimulR.Rcheck/tests_i386/testthat.Rout


R version 4.1.0 (2021-05-18) -- "Camp Pontanezen"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-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 Sat Jun 19 01:24:21 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 Sat Jun 19 01:24:21 2021 
  Took  0.28 


 Starting LOD_POM at Sat Jun 19 01:24:21 2021 

 Ending LOD_POM at Sat Jun 19 01:24:33 2021 
  Took  12.37 


 Starting test.Z-all-fitness at Sat Jun 19 01:24:33 2021 

 Ending test.Z-all-fitness at Sat Jun 19 01:24:33 2021 
  Took  0.03 


 Starting test.Z-driver-counts at Sat Jun 19 01:24:33 2021 

 Ending test.Z-driver-counts at Sat Jun 19 01:24:33 2021 
  Took  0.12 


 Starting test.Z-fixation at Sat Jun 19 01:24:33 2021 

 Ending test.Z-fixation at Sat Jun 19 01:24:34 2021 
  Took  0.45 


 Starting test.Z-magellan at Sat Jun 19 01:24:34 2021 

 Ended test.Z-magellan at Sat Jun 19 01:24:35 2021 

 Starting test.Z-mutator at Sat Jun 19 01:24:35 2021 

 Ending test.Z-mutator at Sat Jun 19 01:24:35 2021 
  Took  0.14 


 Starting test.Z-mutatorFDF at Sat Jun 19 01:24:35 2021 

 Ending test.Z-mutatorFDF at Sat Jun 19 01:24:35 2021 
  Took  0.05 


 Starting test.Z-oncoSimulIndiv at Sat Jun 19 01:24:35 2021 

 Ending test.Z-oncoSimulIndiv at Sat Jun 19 01:24:36 2021 
  Took  0.97 


 Starting test.Z-oncoSimulIndivFDF at Sat Jun 19 01:24:36 2021 

 Ending test.Z-oncoSimulIndivFDF at Sat Jun 19 01:24:36 2021 
  Took  0.11 


 Starting test.Z-rfitness-landscape at Sat Jun 19 01:24:36 2021 

 Ending test.Z-rfitness-landscape at Sat Jun 19 01:24:36 2021 
  Took  0.06 


 Starting Z-sample-only-last tests Sat Jun 19 01:24:36 2021 

 Ending Z-sample-only-last tests Sat Jun 19 01:24:36 2021 
  Took  0 


 Starting Z-total-present-drivers tests Sat Jun 19 01:24:36 2021 

 Ending Z-total-present-drivers tests Sat Jun 19 01:24:37 2021 
  Took  0.94 


 Dummy empty test  Sat Jun 19 01:24:37 2021 

 Starting accessible_genotypes at Sat Jun 19 01:24:37 2021 

 Ending accessible_genotypes at Sat Jun 19 01:24:41 2021 
  Took  3.3 


 Starting all fitness at Sat Jun 19 01:24:41 2021
 Ending all-fitness at Sat Jun 19 01:24:43 2021 
  Took  2.52 


 Starting test.allFitnessEffectsFDF at Sat Jun 19 01:24:43 2021 

 Ending test.allFitnessEffectsFDF at Sat Jun 19 01:24:43 2021 
  Took  0.08 


 Starting test.allFitnessEffectsFDF at Sat Jun 19 01:24:43 2021 

 Ending test.allFitnessEffectsFDF at Sat Jun 19 01:24:43 2021 
  Took  0.22 


 Starting driverCounts at Sat Jun 19 01:24:43 2021
 Ending driverCounts at Sat Jun 19 01:24:47 2021 
  Took  3.91 


 Starting epist-order-modules at Sat Jun 19 01:24:47 2021
 Ending epist-order-modules at Sat Jun 19 01:24:47 2021 
  Took  0.02 


 Starting test.evaluatingGenotypesFDF at Sat Jun 19 01:24:47 2021 

 Ending test.evaluatingGenotypesFDF at Sat Jun 19 01:24:47 2021 
  Took  0.08 


 Starting exercise-plotting-code at Sat Jun 19 01:24:47 2021
 Ending exercise-plotting-code at Sat Jun 19 01:24:54 2021 
  Took  6.33 


 Starting exercise-rfitness at Sat Jun 19 01:24:54 2021 

 Ending exercise-rfitness at Sat Jun 19 01:25:00 2021 
  Took  6.39 


 Starting to_Magella at Sat Jun 19 01:25:00 2021 

 Ending to_Magella at Sat Jun 19 01:25:00 2021 
  Took  0.02 


 Starting fitness preds at Sat Jun 19 01:25:00 2021 

 Observed vs expected, case III

 done tries 1 

 Ending fitness preds long at Sat Jun 19 01:25:09 2021 
  Took  8.7 


 Starting fixation  at Sat Jun 19 01:25:09 2021 

 Ending fixation  at Sat Jun 19 01:25:49 2021 
  Took  40.12 


 Starting test.flfast-additional.R test at Sat Jun 19 01:25:49 2021
 Ending test.flfast-additional.R test at Sat Jun 19 01:25:50 2021 
  Took  1.17 


 Starting test.flfast-mutator.R test at Sat Jun 19 01:25:50 2021
 Finished test.flfast-mutator.R test at Sat Jun 19 01:25:51 2021 
  Took  1.11 


 Starting genotFitness at Sat Jun 19 01:25:51 2021 

 Ending genotFitness at Sat Jun 19 01:25:51 2021 
  Took  0.08 


 Starting genot_fitness_to_epistasis at Sat Jun 19 01:25:51 2021 

 Ending genot_fitness_to_epistasis at Sat Jun 19 01:25:51 2021 
  Took  0.02 


 Starting init-mutant tests Sat Jun 19 01:25:51 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 Sat Jun 19 01:25:59 2021 
  Took  7.59 


 Starting test.magellan at Sat Jun 19 01:25:59 2021 

 Ending test.magellan at Sat Jun 19 01:26:00 2021 
  Took  0.58 


 Starting test.modules-root-no-root at Sat Jun 19 01:26:00 2021 

 Ending test.modules-root-no-root at Sat Jun 19 01:26:00 2021 
  Took  0.03 


 Starting at mutPropGrowth  Sat Jun 19 01:26:00 2021 

 Ended test.mutPropGrowth:  Sat Jun 19 01:26:08 2021 
  Took  8.51 


 Starting test.mutator-oncoSimulSample.R test at Sat Jun 19 01:26:08 2021 

 Finished test.mutator-oncoSimulSample.R test at Sat Jun 19 01:26:17 2021 
  Took  8.89 seconds 


 Starting test.mutator.R test at Sat Jun 19 01:26:17 2021[1] 4.38607e-09
[1] 1.0582e-13

 Finished test.mutator.R test at Sat Jun 19 01:26:38 2021 
  Took  20.95 


 Starting test.mutatorFDF.R test at Sat Jun 19 01:26:38 2021
 Starting test.no-v1 at Sat Jun 19 01:26:39 2021 

 Ending test.no-v1 at Sat Jun 19 01:26:39 2021 
  Took  0.02 


 Starting oncoSimulIndiv-miscell tests Sat Jun 19 01:26:39 2021 

 Ending oncoSimulIndiv-miscell tests Sat Jun 19 01:26:58 2021 
  Took  19.73 


 Starting oncoSimulSample-failures tests Sat Jun 19 01:26:58 2021 

 Ending oncoSimulSample-failures tests Sat Jun 19 01:27:03 2021 
  Took  4.23 


 Starting oncoSimulSample-limits tests Sat Jun 19 01:27:03 2021 

 Ending oncoSimulSample-limits tests Sat Jun 19 01:27:03 2021 
  Took  0.14 


 Starting per-gene-mutation rates at Sat Jun 19 01:27:03 2021 

 Ending per-gene-mutation rates at Sat Jun 19 01:27:42 2021 
  Took  39.13 


 Starting plotFitnessLandscape at Sat Jun 19 01:27:42 2021
 Ending plotFitnessLandscape at Sat Jun 19 01:27:44 2021 
  Took  1.59 


 Starting poset-transformations tests Sat Jun 19 01:27:44 2021 

 Ending poset-transformations tests Sat Jun 19 01:27:48 2021 
  Took  4 


 Starting sample-prob Sat Jun 19 01:27:48 2021 
[1] 5.092107e-12
[1] 6.52601e-09
[1] 2.354969e-11
[1] 2.566202e-12
[1] 3.701311e-08
[1] 1.192942e-12
[1] 1.00168e-07
[1] 3.693046e-19
[1] 1.539426e-08
[1] 2.068281e-15
[1] 2.939717e-16
[1] 1.779405e-10

 Ending sample-prob tests Sat Jun 19 01:27:54 2021 
 Took  6.81 



 Starting samplePop tests Sat Jun 19 01:27:54 2021 

 Ending samplePop tests Sat Jun 19 01:28:07 2021 
  Took  12.79 


 Starting simuls-runs-examples tests Sat Jun 19 01:28:07 2021 

 Ending simuls-runs-examples tests Sat Jun 19 01:28:29 2021 
  Took  21.68 


 Starting warning-mutPropGrowth tests Sat Jun 19 01:28:29 2021 

 Ending warning-mutPropGrowth tests Sat Jun 19 01:28:34 2021 
  Took  4.86 


 Starting wide2long tests Sat Jun 19 01:28:34 2021 

 Ending wide2long tests Sat Jun 19 01:28:35 2021 
  Took  0.77 

== Skipped tests ===============================================================
* On Windows (1)
* empty test (1)

[ FAIL 0 | WARN 1 | SKIP 2 | PASS 8188 ]
> 
> proc.time()
   user  system elapsed 
 245.32    1.40  258.95 

OncoSimulR.Rcheck/tests_x64/testthat.Rout


R version 4.1.0 (2021-05-18) -- "Camp Pontanezen"
Copyright (C) 2021 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 Sat Jun 19 01:28:40 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 Sat Jun 19 01:28:41 2021 
  Took  0.5 


 Starting LOD_POM at Sat Jun 19 01:28:41 2021 

 Ending LOD_POM at Sat Jun 19 01:29:02 2021 
  Took  21.5 


 Starting test.Z-all-fitness at Sat Jun 19 01:29:02 2021 

 Ending test.Z-all-fitness at Sat Jun 19 01:29:03 2021 
  Took  0.41 


 Starting test.Z-driver-counts at Sat Jun 19 01:29:03 2021 

 Ending test.Z-driver-counts at Sat Jun 19 01:29:03 2021 
  Took  0.36 


 Starting test.Z-fixation at Sat Jun 19 01:29:03 2021 

 Ending test.Z-fixation at Sat Jun 19 01:29:04 2021 
  Took  0.78 


 Starting test.Z-magellan at Sat Jun 19 01:29:04 2021 

 Ended test.Z-magellan at Sat Jun 19 01:29:06 2021 

 Starting test.Z-mutator at Sat Jun 19 01:29:06 2021 

 Ending test.Z-mutator at Sat Jun 19 01:29:07 2021 
  Took  0.61 


 Starting test.Z-mutatorFDF at Sat Jun 19 01:29:07 2021 

 Ending test.Z-mutatorFDF at Sat Jun 19 01:29:07 2021 
  Took  0.17 


 Starting test.Z-oncoSimulIndiv at Sat Jun 19 01:29:07 2021 

 Ending test.Z-oncoSimulIndiv at Sat Jun 19 01:29:08 2021 
  Took  1.5 


 Starting test.Z-oncoSimulIndivFDF at Sat Jun 19 01:29:08 2021 

 Ending test.Z-oncoSimulIndivFDF at Sat Jun 19 01:29:09 2021 
  Took  0.11 


 Starting test.Z-rfitness-landscape at Sat Jun 19 01:29:09 2021 

 Ending test.Z-rfitness-landscape at Sat Jun 19 01:29:09 2021 
  Took  0.08 


 Starting Z-sample-only-last tests Sat Jun 19 01:29:09 2021 

 Ending Z-sample-only-last tests Sat Jun 19 01:29:09 2021 
  Took  0 


 Starting Z-total-present-drivers tests Sat Jun 19 01:29:09 2021 

 Ending Z-total-present-drivers tests Sat Jun 19 01:29:10 2021 
  Took  0.91 


 Dummy empty test  Sat Jun 19 01:29:10 2021 

 Starting accessible_genotypes at Sat Jun 19 01:29:10 2021 

 Ending accessible_genotypes at Sat Jun 19 01:29:15 2021 
  Took  5.37 


 Starting all fitness at Sat Jun 19 01:29:15 2021
 Ending all-fitness at Sat Jun 19 01:29:18 2021 
  Took  2.66 


 Starting test.allFitnessEffectsFDF at Sat Jun 19 01:29:18 2021 

 Ending test.allFitnessEffectsFDF at Sat Jun 19 01:29:18 2021 
  Took  0.08 


 Starting test.allFitnessEffectsFDF at Sat Jun 19 01:29:18 2021 

 Ending test.allFitnessEffectsFDF at Sat Jun 19 01:29:18 2021 
  Took  0.22 


 Starting driverCounts at Sat Jun 19 01:29:18 2021
 Ending driverCounts at Sat Jun 19 01:29:22 2021 
  Took  4.3 


 Starting epist-order-modules at Sat Jun 19 01:29:22 2021
 Ending epist-order-modules at Sat Jun 19 01:29:22 2021 
  Took  0.02 


 Starting test.evaluatingGenotypesFDF at Sat Jun 19 01:29:22 2021 

 Ending test.evaluatingGenotypesFDF at Sat Jun 19 01:29:22 2021 
  Took  0.08 


 Starting exercise-plotting-code at Sat Jun 19 01:29:22 2021
 Ending exercise-plotting-code at Sat Jun 19 01:29:29 2021 
  Took  6.81 


 Starting exercise-rfitness at Sat Jun 19 01:29:29 2021 

 Ending exercise-rfitness at Sat Jun 19 01:29:36 2021 
  Took  6.41 


 Starting to_Magella at Sat Jun 19 01:29:36 2021 

 Ending to_Magella at Sat Jun 19 01:29:36 2021 
  Took  0.02 


 Starting fitness preds at Sat Jun 19 01:29:36 2021 

 Observed vs expected, case III

 done tries 1 

 Ending fitness preds long at Sat Jun 19 01:29:44 2021 
  Took  8.75 


 Starting fixation  at Sat Jun 19 01:29:44 2021 

 Ending fixation  at Sat Jun 19 01:30:23 2021 
  Took  38.9 


 Starting test.flfast-additional.R test at Sat Jun 19 01:30:23 2021
 DEBUG2: Value of rnb = nan

 DEBUG2: Value of m = 1

 DEBUG2: Value of pe = 0

 DEBUG2: Value of pm = 0.999999

 this is spP

 popSize = 1
 birth = 1
 death = 0
 W = 1.00001
 R = 1.00001
 mutation = 6e-06
 timeLastUpdate = 2.89189
 absfitness = -inf
 numMutablePos = 6

 Unrecoverable exception: Algo 2: retval not finite. Aborting. 

 Ending test.flfast-additional.R test at Sat Jun 19 01:30:24 2021 
  Took  1.22 


 Starting test.flfast-mutator.R test at Sat Jun 19 01:30:24 2021
 Finished test.flfast-mutator.R test at Sat Jun 19 01:30:25 2021 
  Took  0.69 


 Starting genotFitness at Sat Jun 19 01:30:25 2021 

 Ending genotFitness at Sat Jun 19 01:30:25 2021 
  Took  0.08 


 Starting genot_fitness_to_epistasis at Sat Jun 19 01:30:25 2021 

 Ending genot_fitness_to_epistasis at Sat Jun 19 01:30:25 2021 
  Took  0.02 


 Starting init-mutant tests Sat Jun 19 01:30:25 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 Sat Jun 19 01:30:33 2021 
  Took  7.55 


 Starting test.magellan at Sat Jun 19 01:30:33 2021 

 Ending test.magellan at Sat Jun 19 01:30:33 2021 
  Took  0.56 


 Starting test.modules-root-no-root at Sat Jun 19 01:30:33 2021 

 Ending test.modules-root-no-root at Sat Jun 19 01:30:33 2021 
  Took  0.03 


 Starting at mutPropGrowth  Sat Jun 19 01:30:33 2021 

 Ended test.mutPropGrowth:  Sat Jun 19 01:30:42 2021 
  Took  8.87 


 Starting test.mutator-oncoSimulSample.R test at Sat Jun 19 01:30:42 2021 

 Finished test.mutator-oncoSimulSample.R test at Sat Jun 19 01:30:49 2021 
  Took  6.72 seconds 


 Starting test.mutator.R test at Sat Jun 19 01:30:49 2021[1] 5.695333e-07
[1] 2.687497e-12

 Finished test.mutator.R test at Sat Jun 19 01:31:15 2021 
  Took  25.75 


 Starting test.mutatorFDF.R test at Sat Jun 19 01:31:15 2021
 Starting test.no-v1 at Sat Jun 19 01:31:15 2021 

 Ending test.no-v1 at Sat Jun 19 01:31:15 2021 
  Took  0 


 Starting oncoSimulIndiv-miscell tests Sat Jun 19 01:31:15 2021 

 Ending oncoSimulIndiv-miscell tests Sat Jun 19 01:31:23 2021 
  Took  8.22 


 Starting oncoSimulSample-failures tests Sat Jun 19 01:31:23 2021 

 Ending oncoSimulSample-failures tests Sat Jun 19 01:31:28 2021 
  Took  4.17 


 Starting oncoSimulSample-limits tests Sat Jun 19 01:31:28 2021 

 Ending oncoSimulSample-limits tests Sat Jun 19 01:31:28 2021 
  Took  0.03 


 Starting per-gene-mutation rates at Sat Jun 19 01:31:28 2021 

 Ending per-gene-mutation rates at Sat Jun 19 01:32:01 2021 
  Took  33.07 


 Starting plotFitnessLandscape at Sat Jun 19 01:32:01 2021
 Ending plotFitnessLandscape at Sat Jun 19 01:32:02 2021 
  Took  1.56 


 Starting poset-transformations tests Sat Jun 19 01:32:02 2021 

 Ending poset-transformations tests Sat Jun 19 01:32:06 2021 
  Took  4.25 


 Starting sample-prob Sat Jun 19 01:32:06 2021 
[1] 2.523603e-15
[1] 6.365597e-10
[1] 1.139886e-11
[1] 1.098648e-12
[1] 6.364002e-13
[1] 5.721917e-13
[1] 3.80888e-10
[1] 1.053117e-10
[1] 5.683977e-07
[1] 5.891415e-09
[1] 1.202575e-07
[1] 2.135003e-10

 Ending sample-prob tests Sat Jun 19 01:32:13 2021 
 Took  6.78 



 Starting samplePop tests Sat Jun 19 01:32:13 2021 

 Ending samplePop tests Sat Jun 19 01:32:23 2021 
  Took  9.53 


 Starting simuls-runs-examples tests Sat Jun 19 01:32:23 2021 

 Ending simuls-runs-examples tests Sat Jun 19 01:32:34 2021 
  Took  11.28 


 Starting warning-mutPropGrowth tests Sat Jun 19 01:32:34 2021 

 Ending warning-mutPropGrowth tests Sat Jun 19 01:32:37 2021 
  Took  2.61 


 Starting wide2long tests Sat Jun 19 01:32:37 2021 

 Ending wide2long tests Sat Jun 19 01:32:37 2021 
  Took  0.31 

== Skipped tests ===============================================================
* On Windows (1)
* empty test (1)

[ FAIL 0 | WARN 1 | SKIP 2 | PASS 8198 ]
> 
> proc.time()
   user  system elapsed 
 223.48    1.73  239.71 

Example timings

OncoSimulR.Rcheck/examples_i386/OncoSimulR-Ex.timings

nameusersystemelapsed
OncoSimulWide2Long0.300.020.31
POM1.290.001.28
allFitnessEffects0.820.010.84
benchmarks0.000.020.02
evalAllGenotypes0.100.010.11
example-missing-drivers0.310.000.31
examplePosets0.20.00.2
examplesFitnessEffects0.030.000.03
freq-dep-simul-examples000
mcfLs000
oncoSimulIndiv1.840.021.86
plot.fitnessEffects0.140.000.14
plot.oncosimul0.720.000.72
plotClonePhylog0.820.020.83
plotFitnessLandscape0.570.000.57
plotPoset0.080.000.08
poset0.080.010.10
rfitness0.310.000.56
samplePop0.320.020.33
simOGraph0.040.000.04
to_Magellan0.030.000.64

OncoSimulR.Rcheck/examples_x64/OncoSimulR-Ex.timings

nameusersystemelapsed
OncoSimulWide2Long0.310.020.32
POM1.000.031.04
allFitnessEffects0.910.010.92
benchmarks0.000.020.01
evalAllGenotypes0.110.000.13
example-missing-drivers0.220.020.23
examplePosets0.220.010.24
examplesFitnessEffects0.040.000.04
freq-dep-simul-examples000
mcfLs000
oncoSimulIndiv1.780.001.78
plot.fitnessEffects0.140.000.15
plot.oncosimul0.610.000.61
plotClonePhylog0.840.030.88
plotFitnessLandscape0.640.000.64
plotPoset0.080.000.07
poset0.10.00.1
rfitness0.320.000.58
samplePop0.380.000.37
simOGraph0.030.020.05
to_Magellan0.060.000.62