Ramon Diaz-Uriarte
| Snapshot Date: 2024-07-22 14:00 -0400 (Mon, 22 Jul 2024) |
| git_url: https://git.bioconductor.org/packages/OncoSimulR |
| git_branch: devel |
| git_last_commit: c3dd5c6 |
| git_last_commit_date: 2024-04-30 10:37:33 -0400 (Tue, 30 Apr 2024) |
| Back to Multiple platform build/check report for BioC 3.20: simplified long |
|
This page was generated on 2024-07-23 11:38 -0400 (Tue, 23 Jul 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4688 |
| palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" | 4280 |
| lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4455 |
| kjohnson3 | macOS 13.6.5 Ventura | arm64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4404 |
| 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 | ||||
| Package 1437/2248 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| OncoSimulR 4.7.0 (landing page) Ramon Diaz-Uriarte
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson3 | macOS 13.6.5 Ventura / arm64 | OK | ERROR | skipped | skipped | |||||||||
|
To the developers/maintainers of the OncoSimulR package: - 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 Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. |
| Package: OncoSimulR |
| Version: 4.7.0 |
| Command: /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:OncoSimulR.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings OncoSimulR_4.7.0.tar.gz |
| StartedAt: 2024-07-23 02:27:40 -0400 (Tue, 23 Jul 2024) |
| EndedAt: 2024-07-23 02:36:23 -0400 (Tue, 23 Jul 2024) |
| EllapsedTime: 523.5 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: OncoSimulR.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:OncoSimulR.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings OncoSimulR_4.7.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/OncoSimulR.Rcheck’
* using R version 4.4.1 (2024-06-14)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
* running under: Ubuntu 22.04.4 LTS
* using session charset: UTF-8
* checking for file ‘OncoSimulR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘OncoSimulR’ version ‘4.7.0’
* 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
* used C compiler: ‘gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’
* used C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’
* checking installed package size ... NOTE
installed size is 45.7Mb
sub-directories of 1Mb or more:
libs 44.0Mb
* 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 code 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 loading without being on the library search path ... 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 ... NOTE
checkRd: (-1) oncoSimulIndiv.Rd:255-259: Lost braces in \itemize; meant \describe ?
checkRd: (-1) oncoSimulIndiv.Rd:261-263: Lost braces in \itemize; meant \describe ?
checkRd: (-1) oncoSimulIndiv.Rd:265-266: Lost braces in \itemize; meant \describe ?
checkRd: (-1) oncoSimulIndiv.Rd:268-270: Lost braces in \itemize; meant \describe ?
checkRd: (-1) oncoSimulIndiv.Rd:272-274: Lost braces in \itemize; meant \describe ?
* 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 ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE
Status: 3 NOTEs
See
‘/home/biocbuild/bbs-3.20-bioc/meat/OncoSimulR.Rcheck/00check.log’
for details.
OncoSimulR.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD INSTALL OncoSimulR ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.20-bioc/R/site-library’ * installing *source* package ‘OncoSimulR’ ... ** using staged installation ** libs using C compiler: ‘gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ using C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ gcc -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -Wall -c FitnessLandscape/gamma.c -o FitnessLandscape/gamma.o gcc -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -Wall -c FitnessLandscape/landscape.c -o FitnessLandscape/landscape.o gcc -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -Wall -c FitnessLandscape/random.c -o FitnessLandscape/random.o gcc -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -Wall -c FitnessLandscape/sort.c -o FitnessLandscape/sort.o gcc -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -Wall -c FitnessLandscape/chain.c -o FitnessLandscape/chain.o gcc -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -Wall -c FitnessLandscape/input.c -o FitnessLandscape/input.o gcc -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -Wall -c FitnessLandscape/genotypes.c -o FitnessLandscape/genotypes.o gcc -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.20-bioc/R/site-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-3.20-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -Wall -c FitnessLandscape/calculus.c -o FitnessLandscape/calculus.o gcc -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -Wall -c FitnessLandscape/vector.c -o FitnessLandscape/vector.o gcc -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.20-bioc/R/site-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-3.20-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -Wall -c FitnessLandscape/LinearAlgebra.c -o FitnessLandscape/LinearAlgebra.o gcc -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.20-bioc/R/site-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-3.20-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.20-bioc/R/site-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-3.20-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -Wall -c FitnessLandscape/decomposition.c -o FitnessLandscape/decomposition.o gcc -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -Wall -c FitnessLandscape/models.c -o FitnessLandscape/models.o gcc -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.20-bioc/R/site-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; gcc -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -Wall -c OncoSimulR_init.c -o OncoSimulR_init.o g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -Wall -c RcppExports.cpp -o RcppExports.o g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -Wall -c unity_osimul.cpp -o unity_osimul.o g++ -std=gnu++17 -shared -L/home/biocbuild/bbs-3.20-bioc/R/lib -L/usr/local/lib -o OncoSimulR.so OncoSimulR_init.o RcppExports.o unity_osimul.o -L/home/biocbuild/bbs-3.20-bioc/R/lib -lR installing via 'install.libs.R' to /home/biocbuild/bbs-3.20-bioc/R/site-library/00LOCK-OncoSimulR/00new/OncoSimulR [1] "" Installing fl_statistics fl_generate to /home/biocbuild/bbs-3.20-bioc/R/site-library/00LOCK-OncoSimulR/00new/OncoSimulR/exec Installing library OncoSimulR.so to /home/biocbuild/bbs-3.20-bioc/R/site-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 4.4.1 (2024-06-14) -- "Race for Your Life"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu
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 Jul 23 02:29:10 2024
exprtk parser error:
Error[00] Position: 00 Type: [ Syntax Error] Msg: ERR202 - Undefined symbol: 'n_2_3' Expression: n_2_3
exprtk parser error:
Error[00] Position: 00 Type: [ Syntax Error] Msg: ERR202 - Undefined symbol: 'f_2_3' Expression: f_2_3
Ending FDF-small-fitness-specs Tue Jul 23 02:29:10 2024
Took 0.46
Starting LOD_POM at Tue Jul 23 02:29:10 2024
Ending LOD_POM at Tue Jul 23 02:29:26 2024
Took 15.3
Starting test.Z-all-fitness at Tue Jul 23 02:29:26 2024
Ending test.Z-all-fitness at Tue Jul 23 02:29:26 2024
Took 0.23
Starting test.Z-driver-counts at Tue Jul 23 02:29:26 2024
Ending test.Z-driver-counts at Tue Jul 23 02:29:26 2024
Took 0.21
Starting test.Z-fixation at Tue Jul 23 02:29:26 2024
Ending test.Z-fixation at Tue Jul 23 02:29:26 2024
Took 0.42
Starting test.Z-magellan at Tue Jul 23 02:29:27 2024
Ended test.Z-magellan at Tue Jul 23 02:29:29 2024
Starting test.Z-mutator at Tue Jul 23 02:29:29 2024
Ending test.Z-mutator at Tue Jul 23 02:29:30 2024
Took 0.64
Starting test.Z-mutatorFDF at Tue Jul 23 02:29:30 2024
Ending test.Z-mutatorFDF at Tue Jul 23 02:29:30 2024
Took 0.12
Starting test.Z-oncoSimulIndiv at Tue Jul 23 02:29:30 2024
Ending test.Z-oncoSimulIndiv at Tue Jul 23 02:29:31 2024
Took 0.37
Starting test.Z-oncoSimulIndivConstant at Tue Jul 23 02:29:31 2024
Ending test.Z-oncoSimulIndivConstant at Tue Jul 23 02:29:33 2024
Took 2.19
Starting test.Z-oncoSimulIndivDeath at Tue Jul 23 02:29:33 2024
Ending test.Z-oncoSimulIndivDeath at Tue Jul 23 02:29:34 2024
Took 0.82
Starting test.Z-oncoSimulIndivFDF at Tue Jul 23 02:29:34 2024
Hitted wall time. Exiting.
Hitting wall time is regarded as an error.
Ending test.Z-oncoSimulIndivFDF at Tue Jul 23 02:29:35 2024
Took 0.9
Starting test.Z-rfitness-landscape at Tue Jul 23 02:29:35 2024
Ending test.Z-rfitness-landscape at Tue Jul 23 02:29:35 2024
Took 0.21
Starting Z-sample-only-last tests Tue Jul 23 02:29:35 2024
Ending Z-sample-only-last tests Tue Jul 23 02:29:35 2024
Took 0
Starting Z-total-present-drivers tests Tue Jul 23 02:29:35 2024
Ending Z-total-present-drivers tests Tue Jul 23 02:29:35 2024
Took 0.71
Dummy empty test Tue Jul 23 02:29:35 2024
Starting accessible_genotypes at Tue Jul 23 02:29:35 2024
Ending accessible_genotypes at Tue Jul 23 02:29:45 2024
Took 9.71
Starting all fitness at Tue Jul 23 02:29:45 2024
Ending all-fitness at Tue Jul 23 02:29:54 2024
Took 8.64
Starting test.allFitnessEffectsFDF at Tue Jul 23 02:29:54 2024
Ending test.allFitnessEffectsFDF at Tue Jul 23 02:29:54 2024
Took 0.15
Starting test.allFitnessEffectsDeath at Tue Jul 23 02:29:54 2024
Ending test.allFitnessEffectsDeath at Tue Jul 23 02:29:55 2024
Took 0.49
Starting test.allFitnessEffectsFDF at Tue Jul 23 02:29:55 2024
Ending test.allFitnessEffectsFDF at Tue Jul 23 02:29:55 2024
Took 0.4
Starting driverCounts at Tue Jul 23 02:29:55 2024
Ending driverCounts at Tue Jul 23 02:30:02 2024
Took 7.53
Starting epist-order-modules at Tue Jul 23 02:30:02 2024
Ending epist-order-modules at Tue Jul 23 02:30:02 2024
Took 0.05
Starting test.evaluatingGenotypesDeath at Tue Jul 23 02:30:03 2024
Ending test.evaluatingGenotypesDeath at Tue Jul 23 02:30:03 2024
Took 0.17
Starting test.evaluatingGenotypesFDF at Tue Jul 23 02:30:03 2024
Ending test.evaluatingGenotypesFDF at Tue Jul 23 02:30:03 2024
Took 0.18
Starting exercise-plotting-code at Tue Jul 23 02:30:03 2024
Ending exercise-plotting-code at Tue Jul 23 02:30:05 2024
Took 2.29
Starting exercise-rfitness at Tue Jul 23 02:30:05 2024
Ending exercise-rfitness at Tue Jul 23 02:30:21 2024
Took 16.08
Starting to_Magella at Tue Jul 23 02:30:21 2024
Ending to_Magella at Tue Jul 23 02:30:21 2024
Took 0.08
Starting fitness preds at Tue Jul 23 02:30:21 2024
Observed vs expected, case III
T.not is
[1] TRUE
[1] 1.223431e-40 8.074464e-32 1.372574e-38 5.394503e-41 4.618925e-40
[6] 7.507792e-36 0.000000e+00 0.000000e+00 1.196615e-34 1.454366e-41
[11] 2.442989e-31 2.571359e-34 3.269069e-26 2.244875e-45 3.629670e-25
[16] 3.381034e-22 8.407398e-35 5.231203e-14
T.yest
[1] TRUE
[1] 0.08880792 0.56878898 0.35358379 0.68846787 0.03316459 0.48870099
[7] 0.75637748 0.97799688 0.48719964 0.21387234 0.45609706 0.64478379
[13] 0.19762972 0.44341283 0.44659256 0.09027266 0.09475884 0.71829964
[19] 0.49779167 0.59789482 0.31863551 0.86226934 0.46750078 0.38503793
[25] 0.54407652 0.77094247 0.12900384 0.17145483 0.39379503 0.98706042
larger values of T.yest
integer(0)
lm and plot
Call:
lm(formula = log(Observed) ~ log(Expected), data = d1)
Residuals:
Min 1Q Median 3Q Max
-0.015243 -0.005600 -0.001139 0.005247 0.016754
Coefficients:
Estimate Std. Error t value Pr(>|t|)
(Intercept) -0.0078792 0.0049543 -1.59 0.123
log(Expected) 1.0010013 0.0004165 2403.50 <2e-16 ***
---
Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
Residual standard error: 0.007491 on 28 degrees of freedom
Multiple R-squared: 1, Adjusted R-squared: 1
F-statistic: 5.777e+06 on 1 and 28 DF, p-value: < 2.2e-16
Linear hypothesis test
Hypothesis:
(Intercept) = 0
log(Expected) = 1
Model 1: restricted model
Model 2: log(Observed) ~ log(Expected)
Res.Df RSS Df Sum of Sq F Pr(>F)
1 30 0.0022779
2 28 0.0015713 2 0.00070659 6.2956 0.005523 **
---
Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
done tries 2
Ending fitness preds long at Tue Jul 23 02:30:34 2024
Took 13.04
Starting fixation at Tue Jul 23 02:30:34 2024
Ending fixation at Tue Jul 23 02:30:45 2024
Took 11.07
Starting test.flfast-additional.R test at Tue Jul 23 02:30:45 2024
Ending test.flfast-additional.R test at Tue Jul 23 02:30:47 2024
Took 1.29
Starting test.flfast-mutator.R test at Tue Jul 23 02:30:47 2024
Finished test.flfast-mutator.R test at Tue Jul 23 02:30:48 2024
Took 1.01
Starting genotFitness at Tue Jul 23 02:30:48 2024
Ending genotFitness at Tue Jul 23 02:30:48 2024
Took 0.15
Starting genot_fitness_to_epistasis at Tue Jul 23 02:30:48 2024
Ending genot_fitness_to_epistasis at Tue Jul 23 02:30:48 2024
Took 0.04
Starting init-mutant tests Tue Jul 23 02:30:48 2024
exprtk parser error:
Error[00] Position: 18 Type: [ Syntax Error] Msg: ERR202 - Undefined symbol: 'f_2' Expression: 1.1 + 0.7*((f_1 + f_2) > 0.3)
Ending init-mutant tests Tue Jul 23 02:30:55 2024
Took 6.78
Starting interventions tests Tue Jul 23 02:30:55 2024
[1] "Checking intervention: intOverA"
[1] "Checking intervention: intOverA"
[1] "Checking intervention: intOverA"
[1] "Checking intervention: intOverA"
[1] "Checking intervention: intOverMultiplicatesA"
In intervention:intOverMultiplicatesA with WhatHappens: n_1 = n_1 * 2. You cannot intervene to generate more population.[1] "Checking intervention: intOverA"
[1] "Checking intervention: intOverA"
[1] "Checking intervention: intOverTotPop"
[1] 0.45 0.45 0.45
[1] "Checking intervention: intOverTotPop"
[1] "Checking intervention: intOverA"
[1] "Checking intervention: intOverB"
[1] "Checking intervention: intOverC"
[1] "Checking intervention: intOverD"
Init Mutant with birth == 1.0
Init Mutant with birth == 1.0
[1] "Checking intervention: intOverA"
[1] "Checking intervention: intOverB"
[1] "Checking intervention: intOverC"
[1] "Checking intervention: intOverD"
Init Mutant with birth == 1.0
Init Mutant with birth == 1.0
[1] "Checking user variable: user_var_1"
[1] "Checking rule: rule_1"
[1] "Checking rule: rule_2"
[1] "Checking rule: rule_3"
[1] "Checking intervention: intOverTotPop"
[1] "Checking intervention: intOverTotPop2"
[1] "Checking intervention: intOverTotPop3"
[1] "Checking user variable: user_var_1"
[1] "Checking rule: rule_1"
[1] "Checking rule: rule_2"
[1] "Checking rule: rule_3"
[1] "Checking intervention: intOverTotPop"
Ending interventions tests Tue Jul 23 02:31:00 2024
Took 5.5
Starting test.magellan at Tue Jul 23 02:31:00 2024
Ending test.magellan at Tue Jul 23 02:31:01 2024
Took 0.25
Starting test.modules-root-no-root at Tue Jul 23 02:31:01 2024
Ending test.modules-root-no-root at Tue Jul 23 02:31:01 2024
Took 0.15
Starting at mutPropGrowth Tue Jul 23 02:31:01 2024
Ended test.mutPropGrowth: Tue Jul 23 02:31:09 2024
Took 8.64
Starting test.mutator-oncoSimulSample.R test at Tue Jul 23 02:31:09 2024
Finished test.mutator-oncoSimulSample.R test at Tue Jul 23 02:31:16 2024
Took 7.15 seconds
Starting test.mutator.R test at Tue Jul 23 02:31:16 2024[1] 6.36836e-10
[1] 2.581706e-13
Finished test.mutator.R test at Tue Jul 23 02:31:35 2024
Took 18.39
Starting test.mutatorFDF.R test at Tue Jul 23 02:31:35 2024
Starting test.no-v1 at Tue Jul 23 02:31:36 2024
Ending test.no-v1 at Tue Jul 23 02:31:36 2024
Took 0.02
Starting oncoSimulIndiv-miscell tests Tue Jul 23 02:31:36 2024
Ending oncoSimulIndiv-miscell tests Tue Jul 23 02:31:47 2024
Took 10.68
Starting oncoSimulSample-failures tests Tue Jul 23 02:31:47 2024
Ending oncoSimulSample-failures tests Tue Jul 23 02:31:51 2024
Took 3.91
Starting oncoSimulSample-limits tests Tue Jul 23 02:31:51 2024
Ending oncoSimulSample-limits tests Tue Jul 23 02:31:51 2024
Took 0.11
Starting per-gene-mutation rates at Tue Jul 23 02:31:51 2024
Ending per-gene-mutation rates at Tue Jul 23 02:32:18 2024
Took 26.81
Starting plotFitnessLandscape at Tue Jul 23 02:32:18 2024
Ending plotFitnessLandscape at Tue Jul 23 02:32:22 2024
Took 4.15
Starting poset-transformations tests Tue Jul 23 02:32:22 2024
Ending poset-transformations tests Tue Jul 23 02:32:41 2024
Took 19.42
Starting sample-prob Tue Jul 23 02:32:41 2024
[1] 3.742537e-23
[1] 2.066097e-15
[1] 2.940663e-09
[1] 3.348438e-11
[1] 1.747831e-09
[1] 1.048821e-11
[1] 1.688059e-11
[1] 1.867064e-14
[1] 1.437166e-09
[1] 1.031616e-10
[1] 1.265176e-05
[1] 1.670858e-09
Ending sample-prob tests Tue Jul 23 02:32:47 2024
Took 6.29
Starting samplePop tests Tue Jul 23 02:32:47 2024
Ending samplePop tests Tue Jul 23 02:32:53 2024
Took 5.96
Starting simuls-runs-examples tests Tue Jul 23 02:32:53 2024
Ending simuls-runs-examples tests Tue Jul 23 02:32:59 2024
Took 5.82
Starting user variable tests Tue Jul 23 02:32:59 2024
[1] "Checking user variable: user_var_1"
[1] "Checking rule: rule_1"
Ending user variable tests Tue Jul 23 02:32:59 2024
Took 0.11
Starting warning-mutPropGrowth tests Tue Jul 23 02:32:59 2024
Ending warning-mutPropGrowth tests Tue Jul 23 02:33:00 2024
Took 0.43
Starting wide2long tests Tue Jul 23 02:33:00 2024
Ending wide2long tests Tue Jul 23 02:33:00 2024
Took 0.2
[ FAIL 0 | WARN 18 | SKIP 5 | PASS 8417 ]
══ Skipped tests (5) ═══════════════════════════════════════════════════════════
• empty test (5): 'test.FDF-letter-fitness-order.R:376:1',
'test.ZZ-dummy-skip-warn-test.R:8:1', 'test.ZZ-dummy-skip-warn-test.R:12:1',
'test.fixation.R:4:1', 'test.init-mutant.R:1097:1'
[ FAIL 0 | WARN 18 | SKIP 5 | PASS 8417 ]
>
> proc.time()
user system elapsed
252.088 37.655 235.140
OncoSimulR.Rcheck/OncoSimulR-Ex.timings
| name | user | system | elapsed | |
| OncoSimulWide2Long | 0.237 | 0.008 | 0.304 | |
| POM | 0.985 | 0.119 | 0.834 | |
| allFitnessEffects | 3.341 | 0.332 | 4.341 | |
| benchmarks | 0.008 | 0.008 | 0.039 | |
| createInterventions | 0.461 | 0.012 | 0.944 | |
| createUserVars | 0.653 | 0.004 | 0.780 | |
| evalAllGenotypes | 0.443 | 0.020 | 0.505 | |
| example-missing-drivers | 0.483 | 0.011 | 0.632 | |
| examplePosets | 0.478 | 0.048 | 0.632 | |
| examplesFitnessEffects | 0.068 | 0.004 | 0.072 | |
| freq-dep-simul-examples | 0.016 | 0.000 | 0.017 | |
| mcfLs | 0 | 0 | 0 | |
| oncoSimulIndiv | 1.551 | 0.162 | 1.843 | |
| plot.fitnessEffects | 0.460 | 0.040 | 0.512 | |
| plot.oncosimul | 0.704 | 0.024 | 0.832 | |
| plotClonePhylog | 2.975 | 0.156 | 3.376 | |
| plotFitnessLandscape | 2.396 | 0.108 | 2.504 | |
| plotPoset | 0.195 | 0.000 | 0.259 | |
| poset | 0.222 | 0.008 | 0.230 | |
| rfitness | 1.098 | 0.475 | 1.609 | |
| samplePop | 0.054 | 0.115 | 0.105 | |
| simOGraph | 0.088 | 0.020 | 0.108 | |
| to_Magellan | 0.252 | 0.027 | 0.278 | |
| vignette_pre_computed | 0.014 | 0.000 | 0.013 | |