Ramon Diaz-Uriarte
| Snapshot Date: 2022-03-17 13:55:23 -0400 (Thu, 17 Mar 2022) |
| git_url: https://git.bioconductor.org/packages/OncoSimulR |
| git_branch: master |
| git_last_commit: 154875d |
| git_last_commit_date: 2021-10-26 12:14:49 -0400 (Tue, 26 Oct 2021) |
| Back to Multiple platform build/check report for BioC 3.15 |
|
This page was generated on 2022-03-18 11:08:13 -0400 (Fri, 18 Mar 2022).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 20.04.4 LTS) | x86_64 | R Under development (unstable) (2022-02-17 r81757) -- "Unsuffered Consequences" | 4334 |
| riesling1 | Windows Server 2019 Standard | x64 | R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences" | 4097 |
| palomino3 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2022-02-17 r81757 ucrt) -- "Unsuffered Consequences" | 4083 |
| merida1 | macOS 10.14.6 Mojave | x86_64 | R Under development (unstable) (2022-03-02 r81842) -- "Unsuffered Consequences" | 4134 |
| 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 | ||||
|
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. |
| Package 1342/2090 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| OncoSimulR 3.3.0 (landing page) Ramon Diaz-Uriarte
| nebbiolo1 | Linux (Ubuntu 20.04.4 LTS) / x86_64 | OK | OK | OK | | ||||||||
| riesling1 | Windows Server 2019 Standard / x64 | OK | OK | OK | OK | |||||||||
| palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| merida1 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | | ||||||||
| Package: OncoSimulR |
| Version: 3.3.0 |
| Command: D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:OncoSimulR.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings OncoSimulR_3.3.0.tar.gz |
| StartedAt: 2022-03-17 19:46:27 -0400 (Thu, 17 Mar 2022) |
| EndedAt: 2022-03-17 19:53:39 -0400 (Thu, 17 Mar 2022) |
| EllapsedTime: 431.7 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: OncoSimulR.Rcheck |
| Warnings: 0 |
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###
### Running command:
###
### D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:OncoSimulR.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings OncoSimulR_3.3.0.tar.gz
###
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* using log directory 'D:/biocbuild/bbs-3.15-bioc/meat/OncoSimulR.Rcheck'
* using R Under development (unstable) (2021-11-21 r81221)
* 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 '3.3.0'
* 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 8.9Mb
sub-directories of 1Mb or more:
exec 1.1Mb
libs 6.7Mb
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of 'data' directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking use of PKG_*FLAGS in Makefiles ... OK
* checking include directives in Makefiles ... OK
* checking compiled code ... NOTE
Note: information on .o files for x64 is not available
File 'D:/biocbuild/bbs-3.15-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 ... 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
'D:/biocbuild/bbs-3.15-bioc/meat/OncoSimulR.Rcheck/00check.log'
for details.
OncoSimulR.Rcheck/00install.out
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###
### Running command:
###
### D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL OncoSimulR
###
##############################################################################
##############################################################################
* installing to library 'D:/biocbuild/bbs-3.15-bioc/R/library'
* installing *source* package 'OncoSimulR' ...
** using staged installation
** libs
"C:/rtools40/mingw64/bin/"gcc -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c FitnessLandscape/gamma.c -o FitnessLandscape/gamma.o
"C:/rtools40/mingw64/bin/"gcc -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c FitnessLandscape/landscape.c -o FitnessLandscape/landscape.o
"C:/rtools40/mingw64/bin/"gcc -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c FitnessLandscape/random.c -o FitnessLandscape/random.o
"C:/rtools40/mingw64/bin/"gcc -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c FitnessLandscape/sort.c -o FitnessLandscape/sort.o
"C:/rtools40/mingw64/bin/"gcc -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c FitnessLandscape/chain.c -o FitnessLandscape/chain.o
"C:/rtools40/mingw64/bin/"gcc -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c FitnessLandscape/input.c -o FitnessLandscape/input.o
"C:/rtools40/mingw64/bin/"gcc -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c FitnessLandscape/genotypes.c -o FitnessLandscape/genotypes.o
"C:/rtools40/mingw64/bin/"gcc -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c FitnessLandscape/ordered_pairs.c -o FitnessLandscape/ordered_pairs.o
"C:/rtools40/mingw64/bin/"gcc -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c FitnessLandscape/calculus.c -o FitnessLandscape/calculus.o
"C:/rtools40/mingw64/bin/"gcc -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c FitnessLandscape/vector.c -o FitnessLandscape/vector.o
"C:/rtools40/mingw64/bin/"gcc -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c FitnessLandscape/generalized_chain.c -o FitnessLandscape/generalized_chain.o
"C:/rtools40/mingw64/bin/"gcc -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -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-3.15-bioc/R/include" -DNDEBUG -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c FitnessLandscape/summary_statistics.c -o FitnessLandscape/summary_statistics.o
"C:/rtools40/mingw64/bin/"gcc -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c FitnessLandscape/epistasis_type.c -o FitnessLandscape/epistasis_type.o
"C:/rtools40/mingw64/bin/"gcc -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c FitnessLandscape/decomposition.c -o FitnessLandscape/decomposition.o
"C:/rtools40/mingw64/bin/"gcc -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c FitnessLandscape/models.c -o FitnessLandscape/models.o
"C:/rtools40/mingw64/bin/"gcc -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -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-3.15-bioc/R/include" -DNDEBUG -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -Wa,-mbig-obj -O3 -c BNB_nr.cpp -o BNB_nr.o
"C:/rtools40/mingw64/bin/"gcc -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c OncoSimulR_init.c -o OncoSimulR_init.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -Wa,-mbig-obj -O3 -c RcppExports.cpp -o RcppExports.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -Wa,-mbig-obj -O3 -c accessible_genotypes.cpp -o accessible_genotypes.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -Wa,-mbig-obj -O3 -c bnb_common.cpp -o bnb_common.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -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-3.15-bioc/R/bin/x64 -lR
installing via 'install.libs.R' to D:/biocbuild/bbs-3.15-bioc/R/library/00LOCK-OncoSimulR/00new/OncoSimulR
[1] "/x64"
Installing fl_statistics.exe fl_generate.exe to D:/biocbuild/bbs-3.15-bioc/R/library/00LOCK-OncoSimulR/00new/OncoSimulR/exec/x64
Installing library OncoSimulR.dll to D:/biocbuild/bbs-3.15-bioc/R/library/00LOCK-OncoSimulR/00new/OncoSimulR/libs/x64
** 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
* DONE (OncoSimulR)
Making 'packages.html' ...Warning in packageDescription(i, lib.loc = lib, fields = "Title", encoding = "UTF-8") :
DESCRIPTION file of package 'EBSEA' is missing or broken
done
OncoSimulR.Rcheck/tests/testthat.Rout
R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences"
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 Thu Mar 17 19:48:29 2022
exprtk parser error:
Error[00] Position: 00 Type: [ Syntax Error] Msg: ERR197 - Undefined symbol: 'n_2_3' Expression: n_2_3
exprtk parser error:
Error[00] Position: 00 Type: [ Syntax Error] Msg: ERR197 - Undefined symbol: 'f_2_3' Expression: f_2_3
Ending FDF-small-fitness-specs Thu Mar 17 19:48:29 2022
Took 0.31
Starting LOD_POM at Thu Mar 17 19:48:30 2022
Ending LOD_POM at Thu Mar 17 19:48:46 2022
Took 16.04
Starting test.Z-all-fitness at Thu Mar 17 19:48:46 2022
Ending test.Z-all-fitness at Thu Mar 17 19:48:46 2022
Took 0.08
Starting test.Z-driver-counts at Thu Mar 17 19:48:46 2022
Ending test.Z-driver-counts at Thu Mar 17 19:48:46 2022
Took 0.12
Starting test.Z-fixation at Thu Mar 17 19:48:46 2022
Ending test.Z-fixation at Thu Mar 17 19:48:46 2022
Took 0.47
Starting test.Z-magellan at Thu Mar 17 19:48:46 2022
Ended test.Z-magellan at Thu Mar 17 19:48:48 2022
Starting test.Z-mutator at Thu Mar 17 19:48:48 2022
Ending test.Z-mutator at Thu Mar 17 19:48:48 2022
Took 0.25
Starting test.Z-mutatorFDF at Thu Mar 17 19:48:48 2022
Ending test.Z-mutatorFDF at Thu Mar 17 19:48:48 2022
Took 0.08
Starting test.Z-oncoSimulIndiv at Thu Mar 17 19:48:48 2022
Ending test.Z-oncoSimulIndiv at Thu Mar 17 19:48:49 2022
Took 0.98
Starting test.Z-oncoSimulIndivFDF at Thu Mar 17 19:48:49 2022
Ending test.Z-oncoSimulIndivFDF at Thu Mar 17 19:48:49 2022
Took 0.16
Starting test.Z-rfitness-landscape at Thu Mar 17 19:48:49 2022
Ending test.Z-rfitness-landscape at Thu Mar 17 19:48:49 2022
Took 0.09
Starting Z-sample-only-last tests Thu Mar 17 19:48:49 2022
Ending Z-sample-only-last tests Thu Mar 17 19:48:49 2022
Took 0
Starting Z-total-present-drivers tests Thu Mar 17 19:48:49 2022
Ending Z-total-present-drivers tests Thu Mar 17 19:48:50 2022
Took 0.95
Dummy empty test Thu Mar 17 19:48:50 2022
Starting accessible_genotypes at Thu Mar 17 19:48:50 2022
Ending accessible_genotypes at Thu Mar 17 19:48:55 2022
Took 4.33
Starting all fitness at Thu Mar 17 19:48:55 2022
Ending all-fitness at Thu Mar 17 19:48:58 2022
Took 3.69
Starting test.allFitnessEffectsFDF at Thu Mar 17 19:48:58 2022
Ending test.allFitnessEffectsFDF at Thu Mar 17 19:48:59 2022
Took 0.08
Starting test.allFitnessEffectsFDF at Thu Mar 17 19:48:59 2022
Ending test.allFitnessEffectsFDF at Thu Mar 17 19:48:59 2022
Took 0.3
Starting driverCounts at Thu Mar 17 19:48:59 2022
Ending driverCounts at Thu Mar 17 19:49:04 2022
Took 5.41
Starting epist-order-modules at Thu Mar 17 19:49:04 2022
Ending epist-order-modules at Thu Mar 17 19:49:04 2022
Took 0.02
Starting test.evaluatingGenotypesFDF at Thu Mar 17 19:49:04 2022
Ending test.evaluatingGenotypesFDF at Thu Mar 17 19:49:04 2022
Took 0.11
Starting exercise-plotting-code at Thu Mar 17 19:49:04 2022
Ending exercise-plotting-code at Thu Mar 17 19:49:11 2022
Took 6.26
Starting exercise-rfitness at Thu Mar 17 19:49:11 2022
Ending exercise-rfitness at Thu Mar 17 19:49:20 2022
Took 9.17
Starting to_Magella at Thu Mar 17 19:49:20 2022
Ending to_Magella at Thu Mar 17 19:49:20 2022
Took 0.03
Starting fitness preds at Thu Mar 17 19:49:20 2022
Observed vs expected, case III
done tries 1
Ending fitness preds long at Thu Mar 17 19:49:29 2022
Took 8.84
Starting fixation at Thu Mar 17 19:49:29 2022
Ending fixation at Thu Mar 17 19:50:22 2022
Took 53.57
Starting test.flfast-additional.R test at Thu Mar 17 19:50:22 2022
Ending test.flfast-additional.R test at Thu Mar 17 19:50:24 2022
Took 1.31
Starting test.flfast-mutator.R test at Thu Mar 17 19:50:24 2022
Finished test.flfast-mutator.R test at Thu Mar 17 19:50:25 2022
Took 1.84
Starting genotFitness at Thu Mar 17 19:50:25 2022
Ending genotFitness at Thu Mar 17 19:50:26 2022
Took 0.12
Starting genot_fitness_to_epistasis at Thu Mar 17 19:50:26 2022
Ending genot_fitness_to_epistasis at Thu Mar 17 19:50:26 2022
Took 0.02
Starting init-mutant tests Thu Mar 17 19:50:26 2022
exprtk parser error:
Error[00] Position: 18 Type: [ Syntax Error] Msg: ERR197 - Undefined symbol: 'f_2' Expression: 1.1 + 0.7*((f_1 + f_2) > 0.3)
Ending init-mutant tests Thu Mar 17 19:50:36 2022
Took 10.15
Starting test.magellan at Thu Mar 17 19:50:36 2022
Ending test.magellan at Thu Mar 17 19:50:37 2022
Took 0.73
Starting test.modules-root-no-root at Thu Mar 17 19:50:37 2022
Ending test.modules-root-no-root at Thu Mar 17 19:50:37 2022
Took 0.06
Starting at mutPropGrowth Thu Mar 17 19:50:37 2022
Ended test.mutPropGrowth: Thu Mar 17 19:50:48 2022
Took 11.72
Starting test.mutator-oncoSimulSample.R test at Thu Mar 17 19:50:48 2022
Finished test.mutator-oncoSimulSample.R test at Thu Mar 17 19:51:02 2022
Took 13.75 seconds
Starting test.mutator.R test at Thu Mar 17 19:51:02 2022[1] 8.118493e-11
[1] 7.181935e-14
Finished test.mutator.R test at Thu Mar 17 19:51:33 2022
Took 31.07
Starting test.mutatorFDF.R test at Thu Mar 17 19:51:33 2022
Starting test.no-v1 at Thu Mar 17 19:51:34 2022
Ending test.no-v1 at Thu Mar 17 19:51:34 2022
Took 0
Starting oncoSimulIndiv-miscell tests Thu Mar 17 19:51:34 2022
Ending oncoSimulIndiv-miscell tests Thu Mar 17 19:51:41 2022
Took 7.03
Starting oncoSimulSample-failures tests Thu Mar 17 19:51:41 2022
Ending oncoSimulSample-failures tests Thu Mar 17 19:51:45 2022
Took 3.64
Starting oncoSimulSample-limits tests Thu Mar 17 19:51:45 2022
Ending oncoSimulSample-limits tests Thu Mar 17 19:51:45 2022
Took 0.05
Starting per-gene-mutation rates at Thu Mar 17 19:51:45 2022
Ending per-gene-mutation rates at Thu Mar 17 19:52:30 2022
Took 45.51
Starting plotFitnessLandscape at Thu Mar 17 19:52:30 2022
Ending plotFitnessLandscape at Thu Mar 17 19:52:34 2022
Took 4.34
Starting poset-transformations tests Thu Mar 17 19:52:34 2022
Ending poset-transformations tests Thu Mar 17 19:52:41 2022
Took 6.25
Starting sample-prob Thu Mar 17 19:52:41 2022
[1] 5.700764e-17
[1] 8.215606e-10
[1] 1.521286e-11
[1] 1.359895e-12
[1] 3.006889e-13
[1] 1.839881e-13
[1] 6.858653e-08
[1] 3.655656e-12
[1] 1.141422e-07
[1] 8.311435e-14
[1] 1.392951e-07
[1] 2.139363e-10
Ending sample-prob tests Thu Mar 17 19:52:52 2022
Took 11.53
Starting samplePop tests Thu Mar 17 19:52:52 2022
Ending samplePop tests Thu Mar 17 19:53:08 2022
Took 15.89
Starting simuls-runs-examples tests Thu Mar 17 19:53:08 2022
Ending simuls-runs-examples tests Thu Mar 17 19:53:23 2022
Took 14.64
Starting warning-mutPropGrowth tests Thu Mar 17 19:53:23 2022
Ending warning-mutPropGrowth tests Thu Mar 17 19:53:26 2022
Took 3.61
Starting wide2long tests Thu Mar 17 19:53:26 2022
Ending wide2long tests Thu Mar 17 19:53:27 2022
Took 0.45
[ FAIL 0 | WARN 1 | SKIP 6 | PASS 8200 ]
== Skipped tests ===============================================================
* On Windows (1)
* empty test (5)
[ FAIL 0 | WARN 1 | SKIP 6 | PASS 8200 ]
>
> proc.time()
user system elapsed
272.98 3.23 301.37
OncoSimulR.Rcheck/OncoSimulR-Ex.timings
| name | user | system | elapsed | |
| OncoSimulWide2Long | 0.36 | 0.20 | 0.57 | |
| POM | 1.23 | 0.16 | 1.39 | |
| allFitnessEffects | 1.16 | 0.05 | 1.20 | |
| benchmarks | 0.01 | 0.00 | 0.02 | |
| evalAllGenotypes | 0.11 | 0.03 | 0.14 | |
| example-missing-drivers | 0.27 | 0.00 | 0.26 | |
| examplePosets | 0.29 | 0.01 | 0.31 | |
| examplesFitnessEffects | 0.05 | 0.00 | 0.05 | |
| freq-dep-simul-examples | 0.02 | 0.00 | 0.02 | |
| mcfLs | 0 | 0 | 0 | |
| oncoSimulIndiv | 1.70 | 0.03 | 1.73 | |
| plot.fitnessEffects | 0.17 | 0.02 | 0.19 | |
| plot.oncosimul | 0.74 | 0.02 | 0.75 | |
| plotClonePhylog | 0.87 | 0.04 | 0.92 | |
| plotFitnessLandscape | 0.92 | 0.00 | 0.92 | |
| plotPoset | 0.1 | 0.0 | 0.1 | |
| poset | 0.11 | 0.00 | 0.11 | |
| rfitness | 0.43 | 0.02 | 0.71 | |
| samplePop | 0.38 | 0.00 | 0.38 | |
| simOGraph | 0.04 | 0.00 | 0.05 | |
| to_Magellan | 0.10 | 0.00 | 0.68 | |