| Back to Multiple platform build/check report for BioC 3.13 |
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This page was generated on 2021-10-15 15:05:47 -0400 (Fri, 15 Oct 2021).
|
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 1308/2041 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| OncoSimulR 3.0.0 (landing page) Ramon Diaz-Uriarte
| nebbiolo1 | Linux (Ubuntu 20.04.2 LTS) / x86_64 | OK | OK | OK |  | ||||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | | ||||||||
| machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | | ||||||||
| Package: OncoSimulR |
| Version: 3.0.0 |
| Command: /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD check --install=check:OncoSimulR.install-out.txt --library=/home/biocbuild/bbs-3.13-bioc/R/library --no-vignettes --timings OncoSimulR_3.0.0.tar.gz |
| StartedAt: 2021-10-14 10:52:08 -0400 (Thu, 14 Oct 2021) |
| EndedAt: 2021-10-14 10:59:16 -0400 (Thu, 14 Oct 2021) |
| EllapsedTime: 428.3 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: OncoSimulR.Rcheck |
| Warnings: 0 |
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###
### Running command:
###
### /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD check --install=check:OncoSimulR.install-out.txt --library=/home/biocbuild/bbs-3.13-bioc/R/library --no-vignettes --timings OncoSimulR_3.0.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.13-bioc/meat/OncoSimulR.Rcheck’
* using R version 4.1.1 (2021-08-10)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘OncoSimulR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘OncoSimulR’ version ‘3.0.0’
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘OncoSimulR’ can be installed ... OK
* checking installed package size ... NOTE
installed size is 24.3Mb
sub-directories of 1Mb or more:
libs 23.1Mb
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking use of PKG_*FLAGS in Makefiles ... OK
* checking include directives in Makefiles ... OK
* checking compiled code ... NOTE
Note: information on .o files is not available
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’
OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: 2 NOTEs
See
‘/home/biocbuild/bbs-3.13-bioc/meat/OncoSimulR.Rcheck/00check.log’
for details.
OncoSimulR.Rcheck/00install.out
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###
### Running command:
###
### /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD INSTALL OncoSimulR
###
##############################################################################
##############################################################################
* installing to library ‘/home/biocbuild/bbs-3.13-bioc/R/library’
* installing *source* package ‘OncoSimulR’ ...
** using staged installation
** libs
gcc -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -Wall -c FitnessLandscape/gamma.c -o FitnessLandscape/gamma.o
gcc -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -Wall -c FitnessLandscape/landscape.c -o FitnessLandscape/landscape.o
gcc -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -Wall -c FitnessLandscape/random.c -o FitnessLandscape/random.o
gcc -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -Wall -c FitnessLandscape/sort.c -o FitnessLandscape/sort.o
gcc -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -Wall -c FitnessLandscape/chain.c -o FitnessLandscape/chain.o
gcc -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -Wall -c FitnessLandscape/input.c -o FitnessLandscape/input.o
gcc -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -Wall -c FitnessLandscape/genotypes.c -o FitnessLandscape/genotypes.o
gcc -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -Wall -c FitnessLandscape/ordered_pairs.c -o FitnessLandscape/ordered_pairs.o
gcc -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -Wall -c FitnessLandscape/calculus.c -o FitnessLandscape/calculus.o
gcc -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -Wall -c FitnessLandscape/vector.c -o FitnessLandscape/vector.o
gcc -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -Wall -c FitnessLandscape/generalized_chain.c -o FitnessLandscape/generalized_chain.o
gcc -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -Wall -c FitnessLandscape/LinearAlgebra.c -o FitnessLandscape/LinearAlgebra.o
FitnessLandscape/LinearAlgebra.c: In function ‘svdcmp’:
FitnessLandscape/LinearAlgebra.c:640:27: warning: ‘l’ may be used uninitialized in this function [-Wmaybe-uninitialized]
640 | v[j][i]=(u[i][j]/u[i][l])/g;
| ^
gcc -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -Wall -c FitnessLandscape/summary_statistics.c -o FitnessLandscape/summary_statistics.o
gcc -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -Wall -c FitnessLandscape/epistasis_type.c -o FitnessLandscape/epistasis_type.o
gcc -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -Wall -c FitnessLandscape/decomposition.c -o FitnessLandscape/decomposition.o
gcc -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -Wall -c FitnessLandscape/models.c -o FitnessLandscape/models.o
gcc -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -Wall -c FitnessLandscape/verbose.c -o FitnessLandscape/verbose.o
ar -r liblandscape.a FitnessLandscape/gamma.o FitnessLandscape/landscape.o FitnessLandscape/random.o FitnessLandscape/sort.o FitnessLandscape/chain.o FitnessLandscape/input.o FitnessLandscape/genotypes.o FitnessLandscape/ordered_pairs.o FitnessLandscape/calculus.o FitnessLandscape/vector.o FitnessLandscape/generalized_chain.o FitnessLandscape/LinearAlgebra.o FitnessLandscape/summary_statistics.o FitnessLandscape/epistasis_type.o FitnessLandscape/decomposition.o FitnessLandscape/models.o FitnessLandscape/verbose.o ;
ar: creating liblandscape.a
ranlib liblandscape.a;
gcc -O -Wall -o fl_statistics -I/FitnessLandscape/. -L. FitnessLandscape/main_fl_statistics.c -llandscape -lm;
gcc -O -Wall -o fl_generate -I/FitnessLandscape/. -L. FitnessLandscape/main_fl_generate.c -llandscape -lm;
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -Wall -c BNB_nr.cpp -o BNB_nr.o
gcc -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -Wall -c OncoSimulR_init.c -o OncoSimulR_init.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -Wall -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -Wall -c accessible_genotypes.cpp -o accessible_genotypes.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -Wall -c bnb_common.cpp -o bnb_common.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -Wall -c new_restrict.cpp -o new_restrict.o
g++ -std=gnu++11 -shared -L/home/biocbuild/bbs-3.13-bioc/R/lib -L/usr/local/lib -o OncoSimulR.so BNB_nr.o OncoSimulR_init.o RcppExports.o accessible_genotypes.o bnb_common.o new_restrict.o -L/home/biocbuild/bbs-3.13-bioc/R/lib -lR
installing via 'install.libs.R' to /home/biocbuild/bbs-3.13-bioc/R/library/00LOCK-OncoSimulR/00new/OncoSimulR
[1] ""
Installing fl_statistics fl_generate to /home/biocbuild/bbs-3.13-bioc/R/library/00LOCK-OncoSimulR/00new/OncoSimulR/exec
Installing library OncoSimulR.so to /home/biocbuild/bbs-3.13-bioc/R/library/00LOCK-OncoSimulR/00new/OncoSimulR/libs
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (OncoSimulR)
OncoSimulR.Rcheck/tests/testthat.Rout
R version 4.1.1 (2021-08-10) -- "Kick Things"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> library(testthat)
> library(OncoSimulR)
>
> test_check("OncoSimulR")
Starting FDF-letter-fitness-order Thu Oct 14 10:53:18 2021
exprtk parser error:
Error[00] Position: 00 Type: [ Syntax Error] Msg: ERR197 - Undefined symbol: 'n_2_3' Expression: n_2_3
exprtk parser error:
Error[00] Position: 00 Type: [ Syntax Error] Msg: ERR197 - Undefined symbol: 'f_2_3' Expression: f_2_3
Ending FDF-small-fitness-specs Thu Oct 14 10:53:18 2021
Took 0.39
Starting LOD_POM at Thu Oct 14 10:53:18 2021
Ending LOD_POM at Thu Oct 14 10:53:36 2021
Took 17.98
Starting test.Z-all-fitness at Thu Oct 14 10:53:36 2021
Ending test.Z-all-fitness at Thu Oct 14 10:53:36 2021
Took 0.06
Starting test.Z-driver-counts at Thu Oct 14 10:53:36 2021
Ending test.Z-driver-counts at Thu Oct 14 10:53:37 2021
Took 0.16
Starting test.Z-fixation at Thu Oct 14 10:53:37 2021
Ending test.Z-fixation at Thu Oct 14 10:53:37 2021
Took 0.64
Starting test.Z-magellan at Thu Oct 14 10:53:37 2021
Ended test.Z-magellan at Thu Oct 14 10:53:39 2021
Starting test.Z-mutator at Thu Oct 14 10:53:39 2021
Ending test.Z-mutator at Thu Oct 14 10:53:39 2021
Took 0.24
Starting test.Z-mutatorFDF at Thu Oct 14 10:53:39 2021
Ending test.Z-mutatorFDF at Thu Oct 14 10:53:39 2021
Took 0.07
Starting test.Z-oncoSimulIndiv at Thu Oct 14 10:53:39 2021
Ending test.Z-oncoSimulIndiv at Thu Oct 14 10:53:41 2021
Took 1.45
Starting test.Z-oncoSimulIndivFDF at Thu Oct 14 10:53:41 2021
Ending test.Z-oncoSimulIndivFDF at Thu Oct 14 10:53:41 2021
Took 0.12
Starting test.Z-rfitness-landscape at Thu Oct 14 10:53:41 2021
Ending test.Z-rfitness-landscape at Thu Oct 14 10:53:41 2021
Took 0.11
Starting Z-sample-only-last tests Thu Oct 14 10:53:41 2021
Ending Z-sample-only-last tests Thu Oct 14 10:53:41 2021
Took 0
Starting Z-total-present-drivers tests Thu Oct 14 10:53:41 2021
Ending Z-total-present-drivers tests Thu Oct 14 10:53:42 2021
Took 1.13
Dummy empty test Thu Oct 14 10:53:42 2021
Starting accessible_genotypes at Thu Oct 14 10:53:42 2021
Ending accessible_genotypes at Thu Oct 14 10:53:47 2021
Took 4.62
Starting all fitness at Thu Oct 14 10:53:47 2021
Ending all-fitness at Thu Oct 14 10:53:50 2021
Took 3.67
Starting test.allFitnessEffectsFDF at Thu Oct 14 10:53:50 2021
Ending test.allFitnessEffectsFDF at Thu Oct 14 10:53:50 2021
Took 0.1
Starting test.allFitnessEffectsFDF at Thu Oct 14 10:53:50 2021
Ending test.allFitnessEffectsFDF at Thu Oct 14 10:53:51 2021
Took 0.28
Starting driverCounts at Thu Oct 14 10:53:51 2021
Ending driverCounts at Thu Oct 14 10:54:00 2021
Took 9.02
Starting epist-order-modules at Thu Oct 14 10:54:00 2021
Ending epist-order-modules at Thu Oct 14 10:54:00 2021
Took 0.03
Starting test.evaluatingGenotypesFDF at Thu Oct 14 10:54:00 2021
Ending test.evaluatingGenotypesFDF at Thu Oct 14 10:54:00 2021
Took 0.16
Starting exercise-plotting-code at Thu Oct 14 10:54:00 2021
Ending exercise-plotting-code at Thu Oct 14 10:54:05 2021
Took 5.53
Starting exercise-rfitness at Thu Oct 14 10:54:05 2021
Ending exercise-rfitness at Thu Oct 14 10:54:11 2021
Took 5.23
Starting to_Magella at Thu Oct 14 10:54:11 2021
Ending to_Magella at Thu Oct 14 10:54:11 2021
Took 0.02
Starting fitness preds at Thu Oct 14 10:54:11 2021
Observed vs expected, case III
done tries 1
Ending fitness preds long at Thu Oct 14 10:54:20 2021
Took 8.85
Starting fixation at Thu Oct 14 10:54:20 2021
Ending fixation at Thu Oct 14 10:54:47 2021
Took 27.54
Starting test.flfast-additional.R test at Thu Oct 14 10:54:47 2021
DEBUG2: Value of rnb = nan
DEBUG2: Value of m = 1
DEBUG2: Value of pe = 0
DEBUG2: Value of pm = 0.999994
this is spP
popSize = 1
birth = 1
death = 0
W = 1.00001
R = 1.00001
mutation = 6e-06
timeLastUpdate = 6.32253
absfitness = -inf
numMutablePos = 6
Unrecoverable exception: Algo 2: retval not finite. Aborting.
Ending test.flfast-additional.R test at Thu Oct 14 10:54:49 2021
Took 1.86
Starting test.flfast-mutator.R test at Thu Oct 14 10:54:49 2021
Finished test.flfast-mutator.R test at Thu Oct 14 10:54:51 2021
Took 1.8
Starting genotFitness at Thu Oct 14 10:54:51 2021
Ending genotFitness at Thu Oct 14 10:54:51 2021
Took 0.1
Starting genot_fitness_to_epistasis at Thu Oct 14 10:54:51 2021
Ending genot_fitness_to_epistasis at Thu Oct 14 10:54:51 2021
Took 0.02
Starting init-mutant tests Thu Oct 14 10:54:51 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 Thu Oct 14 10:54:59 2021
Took 8.33
Starting test.magellan at Thu Oct 14 10:54:59 2021
Ending test.magellan at Thu Oct 14 10:54:59 2021
Took 0.15
Starting test.modules-root-no-root at Thu Oct 14 10:54:59 2021
Ending test.modules-root-no-root at Thu Oct 14 10:54:59 2021
Took 0.05
Starting at mutPropGrowth Thu Oct 14 10:54:59 2021
Ended test.mutPropGrowth: Thu Oct 14 10:55:11 2021
Took 11.93
Starting test.mutator-oncoSimulSample.R test at Thu Oct 14 10:55:11 2021
Finished test.mutator-oncoSimulSample.R test at Thu Oct 14 10:55:21 2021
Took 9.7 seconds
Starting test.mutator.R test at Thu Oct 14 10:55:21 2021[1] 2.621894e-11
[1] 1.048067e-12
Finished test.mutator.R test at Thu Oct 14 10:55:35 2021
Took 14.13
Starting test.mutatorFDF.R test at Thu Oct 14 10:55:35 2021
Starting test.no-v1 at Thu Oct 14 10:55:36 2021
Ending test.no-v1 at Thu Oct 14 10:55:36 2021
Took 0.01
Starting oncoSimulIndiv-miscell tests Thu Oct 14 10:55:36 2021
Ending oncoSimulIndiv-miscell tests Thu Oct 14 10:55:56 2021
Took 20.6
Starting oncoSimulSample-failures tests Thu Oct 14 10:55:56 2021
Ending oncoSimulSample-failures tests Thu Oct 14 10:56:01 2021
Took 4.2
Starting oncoSimulSample-limits tests Thu Oct 14 10:56:01 2021
Ending oncoSimulSample-limits tests Thu Oct 14 10:56:01 2021
Took 0.06
Starting per-gene-mutation rates at Thu Oct 14 10:56:01 2021
Ending per-gene-mutation rates at Thu Oct 14 10:56:37 2021
Took 36.16
Starting plotFitnessLandscape at Thu Oct 14 10:56:37 2021
Ending plotFitnessLandscape at Thu Oct 14 10:56:39 2021
Took 2.17
Starting poset-transformations tests Thu Oct 14 10:56:39 2021
Ending poset-transformations tests Thu Oct 14 10:56:46 2021
Took 7.53
Starting sample-prob Thu Oct 14 10:56:47 2021
[1] 9.12429e-24
[1] 8.984245e-11
[1] 7.940822e-10
[1] 2.917294e-11
[1] 3.472205e-13
[1] 3.347425e-13
[1] 2.3546e-11
[1] 3.973851e-15
[1] 2.09563e-08
[1] 1.000294e-10
[1] 4.358809e-11
[1] 2.599701e-09
Ending sample-prob tests Thu Oct 14 10:57:04 2021
Took 17.94
Starting samplePop tests Thu Oct 14 10:57:04 2021
Ending samplePop tests Thu Oct 14 10:57:50 2021
Took 45.26
Starting simuls-runs-examples tests Thu Oct 14 10:57:50 2021
Ending simuls-runs-examples tests Thu Oct 14 10:58:53 2021
Took 63.46
Starting warning-mutPropGrowth tests Thu Oct 14 10:58:53 2021
Ending warning-mutPropGrowth tests Thu Oct 14 10:58:57 2021
Took 3.5
Starting wide2long tests Thu Oct 14 10:58:57 2021
Ending wide2long tests Thu Oct 14 10:58:58 2021
Took 1.07
══ Skipped tests ═══════════════════════════════════════════════════════════════
• empty test (5)
[ FAIL 0 | WARN 1 | SKIP 5 | PASS 8201 ]
>
> proc.time()
user system elapsed
356.725 50.593 348.309
OncoSimulR.Rcheck/OncoSimulR-Ex.timings
| name | user | system | elapsed | |
| OncoSimulWide2Long | 0.399 | 0.032 | 0.435 | |
| POM | 0.757 | 0.084 | 0.650 | |
| allFitnessEffects | 1.238 | 0.036 | 1.277 | |
| benchmarks | 0.004 | 0.008 | 0.012 | |
| evalAllGenotypes | 0.158 | 0.008 | 0.167 | |
| example-missing-drivers | 0.221 | 0.012 | 0.233 | |
| examplePosets | 0.293 | 0.000 | 0.293 | |
| examplesFitnessEffects | 0.046 | 0.000 | 0.046 | |
| freq-dep-simul-examples | 0.009 | 0.000 | 0.009 | |
| mcfLs | 0 | 0 | 0 | |
| oncoSimulIndiv | 2.700 | 0.351 | 2.564 | |
| plot.fitnessEffects | 0.20 | 0.02 | 0.22 | |
| plot.oncosimul | 0.839 | 0.000 | 0.838 | |
| plotClonePhylog | 1.434 | 0.016 | 1.449 | |
| plotFitnessLandscape | 0.871 | 0.080 | 0.951 | |
| plotPoset | 0.106 | 0.000 | 0.106 | |
| poset | 0.127 | 0.000 | 0.127 | |
| rfitness | 0.476 | 0.020 | 0.497 | |
| samplePop | 0.467 | 0.169 | 0.367 | |
| simOGraph | 0.067 | 0.008 | 0.075 | |
| to_Magellan | 0.185 | 0.035 | 0.221 | |