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) |
| Back to Multiple platform build/check report for BioC 3.16 |
|
This page was generated on 2022-06-24 11:05:37 -0400 (Fri, 24 Jun 2022).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 20.04.4 LTS) | x86_64 | 4.2.0 Patched (2022-06-02 r82447) -- "Vigorous Calisthenics" | 4331 |
| palomino4 | Windows Server 2022 Datacenter | x64 | 4.2.0 Patched (2022-06-02 r82447 ucrt) -- "Vigorous Calisthenics" | 4136 |
| lconway | macOS 12.2.1 Monterey | x86_64 | 4.2.0 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 | ||||
|
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. |
| Package 1357/2118 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| OncoSimulR 3.5.0 (landing page) Ramon Diaz-Uriarte
| nebbiolo2 | Linux (Ubuntu 20.04.4 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino4 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| lconway | macOS 12.2.1 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| Package: OncoSimulR |
| Version: 3.5.0 |
| Command: /home/biocbuild/bbs-3.16-bioc/R/bin/R CMD check --install=check:OncoSimulR.install-out.txt --library=/home/biocbuild/bbs-3.16-bioc/R/library --no-vignettes --timings OncoSimulR_3.5.0.tar.gz |
| StartedAt: 2022-06-23 21:01:53 -0400 (Thu, 23 Jun 2022) |
| EndedAt: 2022-06-23 21:09:00 -0400 (Thu, 23 Jun 2022) |
| EllapsedTime: 427.6 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: OncoSimulR.Rcheck |
| Warnings: 0 |
##############################################################################
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###
### Running command:
###
### /home/biocbuild/bbs-3.16-bioc/R/bin/R CMD check --install=check:OncoSimulR.install-out.txt --library=/home/biocbuild/bbs-3.16-bioc/R/library --no-vignettes --timings OncoSimulR_3.5.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.16-bioc/meat/OncoSimulR.Rcheck’
* using R version 4.2.0 Patched (2022-06-02 r82447)
* 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 ‘3.5.0’
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘OncoSimulR’ can be installed ... OK
* checking installed package size ... NOTE
installed size is 65.3Mb
sub-directories of 1Mb or more:
libs 63.7Mb
* 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 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-3.16-bioc/meat/OncoSimulR.Rcheck/00check.log’
for details.
OncoSimulR.Rcheck/00install.out
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/bbs-3.16-bioc/R/bin/R CMD INSTALL OncoSimulR
###
##############################################################################
##############################################################################
* installing to library ‘/home/biocbuild/bbs-3.16-bioc/R/library’
* installing *source* package ‘OncoSimulR’ ...
** using staged installation
** libs
gcc -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.16-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-3.16-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.16-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-3.16-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.16-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-3.16-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.16-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-3.16-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.16-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-3.16-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.16-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-3.16-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.16-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-3.16-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.16-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-3.16-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.16-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-3.16-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.16-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-3.16-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.16-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-3.16-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.16-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-3.16-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.16-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-3.16-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.16-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-3.16-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.16-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-3.16-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.16-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-3.16-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.16-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-3.16-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.16-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-3.16-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.16-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-3.16-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.16-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-3.16-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.16-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-3.16-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.16-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-3.16-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.16-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-3.16-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-3.16-bioc/R/lib -lR
installing via 'install.libs.R' to /home/biocbuild/bbs-3.16-bioc/R/library/00LOCK-OncoSimulR/00new/OncoSimulR
[1] ""
Installing fl_statistics fl_generate to /home/biocbuild/bbs-3.16-bioc/R/library/00LOCK-OncoSimulR/00new/OncoSimulR/exec
Installing library OncoSimulR.so to /home/biocbuild/bbs-3.16-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 4.2.0 Patched (2022-06-02 r82447) -- "Vigorous Calisthenics"
Copyright (C) 2022 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> library(testthat)
> library(OncoSimulR)
>
> test_check("OncoSimulR")
Starting FDF-letter-fitness-order Thu Jun 23 21:03:01 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 Jun 23 21:03:02 2022
Took 0.39
Starting LOD_POM at Thu Jun 23 21:03:02 2022
Ending LOD_POM at Thu Jun 23 21:03:18 2022
Took 16.82
Starting test.Z-all-fitness at Thu Jun 23 21:03:18 2022
Ending test.Z-all-fitness at Thu Jun 23 21:03:19 2022
Took 0.11
Starting test.Z-driver-counts at Thu Jun 23 21:03:19 2022
Ending test.Z-driver-counts at Thu Jun 23 21:03:19 2022
Took 0.18
Starting test.Z-fixation at Thu Jun 23 21:03:19 2022
Ending test.Z-fixation at Thu Jun 23 21:03:19 2022
Took 0.64
Starting test.Z-magellan at Thu Jun 23 21:03:19 2022
Ended test.Z-magellan at Thu Jun 23 21:03:21 2022
Starting test.Z-mutator at Thu Jun 23 21:03:21 2022
Ending test.Z-mutator at Thu Jun 23 21:03:21 2022
Took 0.38
Starting test.Z-mutatorFDF at Thu Jun 23 21:03:21 2022
Ending test.Z-mutatorFDF at Thu Jun 23 21:03:21 2022
Took 0.1
Starting test.Z-oncoSimulIndiv at Thu Jun 23 21:03:21 2022
Ending test.Z-oncoSimulIndiv at Thu Jun 23 21:03:23 2022
Took 1.72
Starting test.Z-oncoSimulIndivFDF at Thu Jun 23 21:03:23 2022
Ending test.Z-oncoSimulIndivFDF at Thu Jun 23 21:03:23 2022
Took 0.13
Starting test.Z-rfitness-landscape at Thu Jun 23 21:03:23 2022
Ending test.Z-rfitness-landscape at Thu Jun 23 21:03:23 2022
Took 0.14
Starting Z-sample-only-last tests Thu Jun 23 21:03:23 2022
Ending Z-sample-only-last tests Thu Jun 23 21:03:23 2022
Took 0
Starting Z-total-present-drivers tests Thu Jun 23 21:03:23 2022
Ending Z-total-present-drivers tests Thu Jun 23 21:03:25 2022
Took 1.19
Dummy empty test Thu Jun 23 21:03:25 2022
Starting accessible_genotypes at Thu Jun 23 21:03:25 2022
Ending accessible_genotypes at Thu Jun 23 21:03:31 2022
Took 6.12
Starting all fitness at Thu Jun 23 21:03:31 2022
Ending all-fitness at Thu Jun 23 21:03:35 2022
Took 4.35
Starting test.allFitnessEffectsFDF at Thu Jun 23 21:03:35 2022
Ending test.allFitnessEffectsFDF at Thu Jun 23 21:03:35 2022
Took 0.12
Starting test.allFitnessEffectsFDF at Thu Jun 23 21:03:35 2022
Ending test.allFitnessEffectsFDF at Thu Jun 23 21:03:36 2022
Took 0.33
Starting driverCounts at Thu Jun 23 21:03:36 2022
Ending driverCounts at Thu Jun 23 21:03:45 2022
Took 9.29
Starting epist-order-modules at Thu Jun 23 21:03:45 2022
Ending epist-order-modules at Thu Jun 23 21:03:45 2022
Took 0.08
Starting test.evaluatingGenotypesFDF at Thu Jun 23 21:03:45 2022
Ending test.evaluatingGenotypesFDF at Thu Jun 23 21:03:45 2022
Took 0.17
Starting exercise-plotting-code at Thu Jun 23 21:03:45 2022
Ending exercise-plotting-code at Thu Jun 23 21:03:51 2022
Took 6.11
Starting exercise-rfitness at Thu Jun 23 21:03:51 2022
Ending exercise-rfitness at Thu Jun 23 21:03:59 2022
Took 7.77
Starting to_Magella at Thu Jun 23 21:03:59 2022
Ending to_Magella at Thu Jun 23 21:03:59 2022
Took 0.02
Starting fitness preds at Thu Jun 23 21:03:59 2022
Observed vs expected, case III
done tries 1
Ending fitness preds long at Thu Jun 23 21:04:09 2022
Took 9.77
Starting fixation at Thu Jun 23 21:04:09 2022
Ending fixation at Thu Jun 23 21:04:42 2022
Took 32.65
Starting test.flfast-additional.R test at Thu Jun 23 21:04:42 2022
Ending test.flfast-additional.R test at Thu Jun 23 21:04:43 2022
Took 1.76
Starting test.flfast-mutator.R test at Thu Jun 23 21:04:43 2022
Finished test.flfast-mutator.R test at Thu Jun 23 21:04:45 2022
Took 1.79
Starting genotFitness at Thu Jun 23 21:04:45 2022
Ending genotFitness at Thu Jun 23 21:04:45 2022
Took 0.12
Starting genot_fitness_to_epistasis at Thu Jun 23 21:04:45 2022
Ending genot_fitness_to_epistasis at Thu Jun 23 21:04:45 2022
Took 0.03
Starting init-mutant tests Thu Jun 23 21:04:45 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 Jun 23 21:04:54 2022
Took 8.67
Starting test.magellan at Thu Jun 23 21:04:54 2022
Ending test.magellan at Thu Jun 23 21:04:54 2022
Took 0.15
Starting test.modules-root-no-root at Thu Jun 23 21:04:54 2022
Ending test.modules-root-no-root at Thu Jun 23 21:04:54 2022
Took 0.05
Starting at mutPropGrowth Thu Jun 23 21:04:54 2022
Ended test.mutPropGrowth: Thu Jun 23 21:05:06 2022
Took 12.34
Starting test.mutator-oncoSimulSample.R test at Thu Jun 23 21:05:06 2022
Finished test.mutator-oncoSimulSample.R test at Thu Jun 23 21:05:17 2022
Took 10.55 seconds
Starting test.mutator.R test at Thu Jun 23 21:05:17 2022[1] 6.474981e-10
[1] 2.673791e-13
Finished test.mutator.R test at Thu Jun 23 21:05:36 2022
Took 18.51
Starting test.mutatorFDF.R test at Thu Jun 23 21:05:36 2022
Starting test.no-v1 at Thu Jun 23 21:05:36 2022
Ending test.no-v1 at Thu Jun 23 21:05:36 2022
Took 0.01
Starting oncoSimulIndiv-miscell tests Thu Jun 23 21:05:36 2022
Ending oncoSimulIndiv-miscell tests Thu Jun 23 21:05:57 2022
Took 20.42
Starting oncoSimulSample-failures tests Thu Jun 23 21:05:57 2022
Ending oncoSimulSample-failures tests Thu Jun 23 21:06:01 2022
Took 3.82
Starting oncoSimulSample-limits tests Thu Jun 23 21:06:01 2022
Ending oncoSimulSample-limits tests Thu Jun 23 21:06:01 2022
Took 0.06
Starting per-gene-mutation rates at Thu Jun 23 21:06:01 2022
Ending per-gene-mutation rates at Thu Jun 23 21:06:51 2022
Took 50.46
Starting plotFitnessLandscape at Thu Jun 23 21:06:51 2022
Ending plotFitnessLandscape at Thu Jun 23 21:07:04 2022
Took 12.43
Starting poset-transformations tests Thu Jun 23 21:07:04 2022
Ending poset-transformations tests Thu Jun 23 21:07:21 2022
Took 17.82
Starting sample-prob Thu Jun 23 21:07:21 2022
[1] 2.661756e-25
[1] 6.639622e-08
[1] 9.075418e-10
[1] 1.291964e-11
[1] 1.910909e-14
[1] 5.489345e-11
[1] 1.485312e-11
[1] 1.473044e-16
[1] 8.116277e-09
[1] 3.689791e-11
[1] 8.01661e-05
[1] 4.849111e-09
Ending sample-prob tests Thu Jun 23 21:07:40 2022
Took 18.75
Starting samplePop tests Thu Jun 23 21:07:40 2022
Ending samplePop tests Thu Jun 23 21:08:09 2022
Took 28.64
Starting simuls-runs-examples tests Thu Jun 23 21:08:09 2022
Ending simuls-runs-examples tests Thu Jun 23 21:08:44 2022
Took 35.02
Starting warning-mutPropGrowth tests Thu Jun 23 21:08:44 2022
Ending warning-mutPropGrowth tests Thu Jun 23 21:08:46 2022
Took 2.4
Starting wide2long tests Thu Jun 23 21:08:46 2022
Ending wide2long tests Thu Jun 23 21:08:48 2022
Took 1.35
[ FAIL 0 | WARN 1 | SKIP 5 | PASS 8176 ]
══ Skipped tests ═══════════════════════════════════════════════════════════════
• empty test (5)
[ FAIL 0 | WARN 1 | SKIP 5 | PASS 8176 ]
>
> proc.time()
user system elapsed
376.401 48.805 353.656
OncoSimulR.Rcheck/OncoSimulR-Ex.timings
| name | user | system | elapsed | |
| OncoSimulWide2Long | 0.426 | 0.044 | 0.472 | |
| POM | 0.788 | 0.103 | 0.692 | |
| allFitnessEffects | 1.395 | 0.020 | 1.420 | |
| benchmarks | 0.008 | 0.000 | 0.007 | |
| evalAllGenotypes | 0.155 | 0.000 | 0.155 | |
| example-missing-drivers | 0.222 | 0.012 | 0.234 | |
| examplePosets | 0.327 | 0.000 | 0.328 | |
| examplesFitnessEffects | 0.046 | 0.000 | 0.046 | |
| freq-dep-simul-examples | 0.01 | 0.00 | 0.01 | |
| mcfLs | 0 | 0 | 0 | |
| oncoSimulIndiv | 2.653 | 0.313 | 2.394 | |
| plot.fitnessEffects | 0.218 | 0.020 | 0.238 | |
| plot.oncosimul | 0.862 | 0.012 | 0.875 | |
| plotClonePhylog | 1.430 | 0.092 | 1.522 | |
| plotFitnessLandscape | 1 | 0 | 1 | |
| plotPoset | 0.094 | 0.004 | 0.098 | |
| poset | 0.118 | 0.000 | 0.118 | |
| rfitness | 0.557 | 0.017 | 0.575 | |
| samplePop | 0.611 | 0.104 | 0.447 | |
| simOGraph | 0.053 | 0.004 | 0.056 | |
| to_Magellan | 0.191 | 0.037 | 0.227 | |