| Back to Multiple platform build/check report for BioC 3.14 |
|
This page was generated on 2022-04-13 12:05:42 -0400 (Wed, 13 Apr 2022).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 20.04.4 LTS) | x86_64 | 4.1.3 (2022-03-10) -- "One Push-Up" | 4324 |
| tokay2 | Windows Server 2012 R2 Standard | x64 | 4.1.3 (2022-03-10) -- "One Push-Up" | 4077 |
| machv2 | macOS 10.14.6 Mojave | x86_64 | 4.1.3 (2022-03-10) -- "One Push-Up" | 4137 |
| 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 1334/2083 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| OncoSimulR 3.2.0 (landing page) Ramon Diaz-Uriarte
| nebbiolo2 | Linux (Ubuntu 20.04.4 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: 3.2.0 |
| Command: /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD check --install=check:OncoSimulR.install-out.txt --library=/home/biocbuild/bbs-3.14-bioc/R/library --no-vignettes --timings OncoSimulR_3.2.0.tar.gz |
| StartedAt: 2022-04-12 08:32:50 -0400 (Tue, 12 Apr 2022) |
| EndedAt: 2022-04-12 08:40:04 -0400 (Tue, 12 Apr 2022) |
| EllapsedTime: 433.9 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: OncoSimulR.Rcheck |
| Warnings: 0 |
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###
### Running command:
###
### /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD check --install=check:OncoSimulR.install-out.txt --library=/home/biocbuild/bbs-3.14-bioc/R/library --no-vignettes --timings OncoSimulR_3.2.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.14-bioc/meat/OncoSimulR.Rcheck’
* using R version 4.1.3 (2022-03-10)
* 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 ‘3.2.0’
* 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-3.14-bioc/meat/OncoSimulR.Rcheck/00check.log’
for details.
OncoSimulR.Rcheck/00install.out
##############################################################################
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###
### Running command:
###
### /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD INSTALL OncoSimulR
###
##############################################################################
##############################################################################
* installing to library ‘/home/biocbuild/bbs-3.14-bioc/R/library’
* installing *source* package ‘OncoSimulR’ ...
** using staged installation
** libs
gcc -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.14-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-3.14-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.14-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-3.14-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.14-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-3.14-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.14-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-3.14-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.14-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-3.14-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.14-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-3.14-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.14-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-3.14-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.14-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-3.14-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.14-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-3.14-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.14-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-3.14-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.14-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-3.14-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.14-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-3.14-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.14-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-3.14-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.14-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-3.14-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.14-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-3.14-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.14-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-3.14-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.14-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-3.14-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.14-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-3.14-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.14-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-3.14-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.14-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-3.14-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.14-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-3.14-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.14-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-3.14-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.14-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-3.14-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-3.14-bioc/R/lib -lR
installing via 'install.libs.R' to /home/biocbuild/bbs-3.14-bioc/R/library/00LOCK-OncoSimulR/00new/OncoSimulR
[1] ""
Installing fl_statistics fl_generate to /home/biocbuild/bbs-3.14-bioc/R/library/00LOCK-OncoSimulR/00new/OncoSimulR/exec
Installing library OncoSimulR.so to /home/biocbuild/bbs-3.14-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 4.1.3 (2022-03-10) -- "One Push-Up"
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 Tue Apr 12 08:34:03 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 Tue Apr 12 08:34:03 2022
Took 0.39
Starting LOD_POM at Tue Apr 12 08:34:03 2022
Ending LOD_POM at Tue Apr 12 08:34:18 2022
Took 14.58
Starting test.Z-all-fitness at Tue Apr 12 08:34:18 2022
Ending test.Z-all-fitness at Tue Apr 12 08:34:18 2022
Took 0.09
Starting test.Z-driver-counts at Tue Apr 12 08:34:18 2022
Ending test.Z-driver-counts at Tue Apr 12 08:34:18 2022
Took 0.18
Starting test.Z-fixation at Tue Apr 12 08:34:18 2022
Ending test.Z-fixation at Tue Apr 12 08:34:19 2022
Took 0.63
Starting test.Z-magellan at Tue Apr 12 08:34:19 2022
Ended test.Z-magellan at Tue Apr 12 08:34:20 2022
Starting test.Z-mutator at Tue Apr 12 08:34:20 2022
Ending test.Z-mutator at Tue Apr 12 08:34:21 2022
Took 0.33
Starting test.Z-mutatorFDF at Tue Apr 12 08:34:21 2022
Ending test.Z-mutatorFDF at Tue Apr 12 08:34:21 2022
Took 0.09
Starting test.Z-oncoSimulIndiv at Tue Apr 12 08:34:21 2022
Ending test.Z-oncoSimulIndiv at Tue Apr 12 08:34:22 2022
Took 1.55
Starting test.Z-oncoSimulIndivFDF at Tue Apr 12 08:34:22 2022
Ending test.Z-oncoSimulIndivFDF at Tue Apr 12 08:34:23 2022
Took 0.12
Starting test.Z-rfitness-landscape at Tue Apr 12 08:34:23 2022
Ending test.Z-rfitness-landscape at Tue Apr 12 08:34:23 2022
Took 0.12
Starting Z-sample-only-last tests Tue Apr 12 08:34:23 2022
Ending Z-sample-only-last tests Tue Apr 12 08:34:23 2022
Took 0
Starting Z-total-present-drivers tests Tue Apr 12 08:34:23 2022
Ending Z-total-present-drivers tests Tue Apr 12 08:34:24 2022
Took 1.14
Dummy empty test Tue Apr 12 08:34:24 2022
Starting accessible_genotypes at Tue Apr 12 08:34:24 2022
Ending accessible_genotypes at Tue Apr 12 08:34:29 2022
Took 5.49
Starting all fitness at Tue Apr 12 08:34:29 2022
Ending all-fitness at Tue Apr 12 08:34:34 2022
Took 5
Starting test.allFitnessEffectsFDF at Tue Apr 12 08:34:34 2022
Ending test.allFitnessEffectsFDF at Tue Apr 12 08:34:35 2022
Took 0.11
Starting test.allFitnessEffectsFDF at Tue Apr 12 08:34:35 2022
Ending test.allFitnessEffectsFDF at Tue Apr 12 08:34:35 2022
Took 0.35
Starting driverCounts at Tue Apr 12 08:34:35 2022
Ending driverCounts at Tue Apr 12 08:34:44 2022
Took 8.65
Starting epist-order-modules at Tue Apr 12 08:34:44 2022
Ending epist-order-modules at Tue Apr 12 08:34:44 2022
Took 0.04
Starting test.evaluatingGenotypesFDF at Tue Apr 12 08:34:44 2022
Ending test.evaluatingGenotypesFDF at Tue Apr 12 08:34:44 2022
Took 0.15
Starting exercise-plotting-code at Tue Apr 12 08:34:44 2022
Ending exercise-plotting-code at Tue Apr 12 08:34:50 2022
Took 5.93
Starting exercise-rfitness at Tue Apr 12 08:34:50 2022
Ending exercise-rfitness at Tue Apr 12 08:34:57 2022
Took 7.01
Starting to_Magella at Tue Apr 12 08:34:57 2022
Ending to_Magella at Tue Apr 12 08:34:57 2022
Took 0.02
Starting fitness preds at Tue Apr 12 08:34:57 2022
Observed vs expected, case III
done tries 1
Ending fitness preds long at Tue Apr 12 08:35:07 2022
Took 10.39
Starting fixation at Tue Apr 12 08:35:07 2022
Ending fixation at Tue Apr 12 08:35:36 2022
Took 28.5
Starting test.flfast-additional.R test at Tue Apr 12 08:35:36 2022
Ending test.flfast-additional.R test at Tue Apr 12 08:35:37 2022
Took 1.36
Starting test.flfast-mutator.R test at Tue Apr 12 08:35:37 2022
Finished test.flfast-mutator.R test at Tue Apr 12 08:35:39 2022
Took 2.1
Starting genotFitness at Tue Apr 12 08:35:39 2022
Ending genotFitness at Tue Apr 12 08:35:39 2022
Took 0.13
Starting genot_fitness_to_epistasis at Tue Apr 12 08:35:39 2022
Ending genot_fitness_to_epistasis at Tue Apr 12 08:35:39 2022
Took 0.03
Starting init-mutant tests Tue Apr 12 08:35:39 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 Tue Apr 12 08:35:48 2022
Took 9.01
Starting test.magellan at Tue Apr 12 08:35:48 2022
Ending test.magellan at Tue Apr 12 08:35:48 2022
Took 0.18
Starting test.modules-root-no-root at Tue Apr 12 08:35:48 2022
Ending test.modules-root-no-root at Tue Apr 12 08:35:48 2022
Took 0.05
Starting at mutPropGrowth Tue Apr 12 08:35:48 2022
Ended test.mutPropGrowth: Tue Apr 12 08:36:01 2022
Took 12.55
Starting test.mutator-oncoSimulSample.R test at Tue Apr 12 08:36:01 2022
Finished test.mutator-oncoSimulSample.R test at Tue Apr 12 08:36:11 2022
Took 9.88 seconds
Starting test.mutator.R test at Tue Apr 12 08:36:11 2022[1] 2.471187e-07
[1] 2.877663e-12
Finished test.mutator.R test at Tue Apr 12 08:36:28 2022
Took 17.41
Starting test.mutatorFDF.R test at Tue Apr 12 08:36:28 2022
Starting test.no-v1 at Tue Apr 12 08:36:29 2022
Ending test.no-v1 at Tue Apr 12 08:36:29 2022
Took 0.01
Starting oncoSimulIndiv-miscell tests Tue Apr 12 08:36:29 2022
Ending oncoSimulIndiv-miscell tests Tue Apr 12 08:36:49 2022
Took 20.19
Starting oncoSimulSample-failures tests Tue Apr 12 08:36:49 2022
Ending oncoSimulSample-failures tests Tue Apr 12 08:36:53 2022
Took 3.47
Starting oncoSimulSample-limits tests Tue Apr 12 08:36:53 2022
Ending oncoSimulSample-limits tests Tue Apr 12 08:36:53 2022
Took 0.06
Starting per-gene-mutation rates at Tue Apr 12 08:36:53 2022
Ending per-gene-mutation rates at Tue Apr 12 08:37:38 2022
Took 45.72
Starting plotFitnessLandscape at Tue Apr 12 08:37:38 2022
Ending plotFitnessLandscape at Tue Apr 12 08:37:42 2022
Took 3.9
Starting poset-transformations tests Tue Apr 12 08:37:42 2022
Ending poset-transformations tests Tue Apr 12 08:37:55 2022
Took 12.93
Starting sample-prob Tue Apr 12 08:37:55 2022
[1] 6.198478e-30
[1] 1.804889e-12
[1] 8.718171e-09
[1] 1.09188e-10
[1] 8.393062e-13
[1] 4.862427e-12
[1] 1.695022e-07
[1] 2.93905e-19
[1] 2.189069e-11
[1] 2.378799e-11
[1] 1.941469e-10
[1] 8.833727e-10
Ending sample-prob tests Tue Apr 12 08:38:13 2022
Took 17.57
Starting samplePop tests Tue Apr 12 08:38:13 2022
Ending samplePop tests Tue Apr 12 08:38:43 2022
Took 30.64
Starting simuls-runs-examples tests Tue Apr 12 08:38:43 2022
Ending simuls-runs-examples tests Tue Apr 12 08:39:34 2022
Took 50.29
Starting warning-mutPropGrowth tests Tue Apr 12 08:39:34 2022
Ending warning-mutPropGrowth tests Tue Apr 12 08:39:36 2022
Took 2.63
Starting wide2long tests Tue Apr 12 08:39:36 2022
Ending wide2long tests Tue Apr 12 08:39:37 2022
Took 0.82
[ FAIL 0 | WARN 1 | SKIP 5 | PASS 8196 ]
══ Skipped tests ═══════════════════════════════════════════════════════════════
• empty test (5)
[ FAIL 0 | WARN 1 | SKIP 5 | PASS 8196 ]
>
> proc.time()
user system elapsed
377.316 48.637 341.700
OncoSimulR.Rcheck/OncoSimulR-Ex.timings
| name | user | system | elapsed | |
| OncoSimulWide2Long | 0.421 | 0.045 | 0.467 | |
| POM | 0.818 | 0.104 | 0.704 | |
| allFitnessEffects | 1.253 | 0.032 | 1.289 | |
| benchmarks | 0.008 | 0.000 | 0.008 | |
| evalAllGenotypes | 0.163 | 0.000 | 0.163 | |
| example-missing-drivers | 0.228 | 0.016 | 0.244 | |
| examplePosets | 0.284 | 0.000 | 0.284 | |
| examplesFitnessEffects | 0.049 | 0.000 | 0.049 | |
| freq-dep-simul-examples | 0.009 | 0.000 | 0.009 | |
| mcfLs | 0.000 | 0.000 | 0.001 | |
| oncoSimulIndiv | 2.859 | 0.431 | 2.785 | |
| plot.fitnessEffects | 0.221 | 0.068 | 0.289 | |
| plot.oncosimul | 1.172 | 0.056 | 1.228 | |
| plotClonePhylog | 1.268 | 0.120 | 1.388 | |
| plotFitnessLandscape | 0.896 | 0.036 | 0.931 | |
| plotPoset | 0.100 | 0.000 | 0.099 | |
| poset | 0.119 | 0.000 | 0.119 | |
| rfitness | 3.171 | 0.052 | 3.223 | |
| samplePop | 0.736 | 0.209 | 0.572 | |
| simOGraph | 0.054 | 0.008 | 0.063 | |
| to_Magellan | 0.185 | 0.025 | 0.210 | |