Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-12-23 12:08 -0500 (Mon, 23 Dec 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4744 |
palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" | 4487 |
merida1 | macOS 12.7.5 Monterey | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4515 |
kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4467 |
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 2132/2289 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
ternarynet 1.50.0 (landing page) McCall N. Matthew
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | |||||||||
palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | |||||||||
merida1 | macOS 12.7.5 Monterey / x86_64 | OK | OK | OK | OK | |||||||||
kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | OK | OK | OK | |||||||||
To the developers/maintainers of the ternarynet package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/ternarynet.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: ternarynet |
Version: 1.50.0 |
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:ternarynet.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings ternarynet_1.50.0.tar.gz |
StartedAt: 2024-12-21 11:44:12 -0500 (Sat, 21 Dec 2024) |
EndedAt: 2024-12-21 11:45:21 -0500 (Sat, 21 Dec 2024) |
EllapsedTime: 69.3 seconds |
RetCode: 0 |
Status: OK |
CheckDir: ternarynet.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:ternarynet.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings ternarynet_1.50.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/ternarynet.Rcheck’ * using R version 4.4.2 (2024-10-31) * using platform: aarch64-apple-darwin20 * R was compiled by Apple clang version 14.0.0 (clang-1400.0.29.202) GNU Fortran (GCC) 12.2.0 * running under: macOS Ventura 13.7.1 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘ternarynet/DESCRIPTION’ ... OK * this is package ‘ternarynet’ version ‘1.50.0’ * checking package namespace information ... OK * checking package dependencies ... NOTE Package which this enhances but not available for checking: ‘Rmpi’ * 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 ‘ternarynet’ can be installed ... OK * used C compiler: ‘Apple clang version 15.0.0 (clang-1500.0.40.1)’ * used C++ compiler: ‘Apple clang version 15.0.0 (clang-1500.0.40.1)’ * used SDK: ‘MacOSX11.3.sdk’ * checking installed package size ... OK * 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 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 line endings in shell scripts ... 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 compiled code ... NOTE Note: information on .o files is not available * checking sizes of PDF files under ‘inst/doc’ ... OK * checking files in ‘vignettes’ ... OK * checking examples ... OK * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘test_smallmodel.R’ Running ‘test_smallmodel_2.R’ OK * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... 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 ‘/Users/biocbuild/bbs-3.20-bioc/meat/ternarynet.Rcheck/00check.log’ for details.
ternarynet.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL ternarynet ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library’ * installing *source* package ‘ternarynet’ ... ** using staged installation ** libs using C compiler: ‘Apple clang version 15.0.0 (clang-1500.0.40.1)’ using C++ compiler: ‘Apple clang version 15.0.0 (clang-1500.0.40.1)’ using SDK: ‘MacOSX11.3.sdk’ clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c array.c -o array.o clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c gn.c -o gn.o clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c gn_Rwrap.c -o gn_Rwrap.o clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c init.c -o init.o clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c tnetfit.cc -o tnetfit.o tnetfit.cc:24:9: warning: variable 'perturbationType' set but not used [-Wunused-but-set-variable] int perturbationType, scoreType, backupStage, maxStage, maxTransition; ^ tnetfit.cc:24:27: warning: variable 'scoreType' set but not used [-Wunused-but-set-variable] int perturbationType, scoreType, backupStage, maxStage, maxTransition; ^ tnetfit.cc:24:38: warning: variable 'backupStage' set but not used [-Wunused-but-set-variable] int perturbationType, scoreType, backupStage, maxStage, maxTransition; ^ tnetfit.cc:73:39: warning: unused variable 'tempi' [-Wunused-variable] int nOutcomes=3, l0, stage_count, tempi, jtrans, nTransition; ^ tnetfit.cc:99:9: warning: variable 'acceptCount' set but not used [-Wunused-but-set-variable] int acceptCount; ^ 5 warnings generated. clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c tnetfuncs.cc -o tnetfuncs.o tnetfuncs.cc:427:5: warning: unused variable 'tableWidth' [-Wunused-variable] int tableWidth = powi(nOutcomes,maxDegree); ^ tnetfuncs.cc:435:5: warning: unused variable 'ipause' [-Wunused-variable] int ipause; ^ tnetfuncs.cc:517:6: warning: unused variable 'ipause' [-Wunused-variable] int ipause; ^ tnetfuncs.cc:521:16: warning: unused variable 'i' [-Wunused-variable] int m1, m2, i; ^ 4 warnings generated. clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c tnetpost.cc -o tnetpost.o tnetpost.cc:25:9: warning: unused variable 'ipause' [-Wunused-variable] int ipause; ^ tnetpost.cc:27:9: warning: unused variable 'm0fit' [-Wunused-variable] int m0fit; ^ tnetpost.cc:28:32: warning: variable 'minScore' set but not used [-Wunused-but-set-variable] double newScore, oldScore, minScore, finalScore; ^ tnetpost.cc:28:42: warning: unused variable 'finalScore' [-Wunused-variable] double newScore, oldScore, minScore, finalScore; ^ tnetpost.cc:30:9: warning: unused variable 'l0' [-Wunused-variable] int l0, stage_count, tempi, jtrans, nTransition; ^ tnetpost.cc:30:13: warning: unused variable 'stage_count' [-Wunused-variable] int l0, stage_count, tempi, jtrans, nTransition; ^ tnetpost.cc:30:26: warning: unused variable 'tempi' [-Wunused-variable] int l0, stage_count, tempi, jtrans, nTransition; ^ tnetpost.cc:30:33: warning: unused variable 'jtrans' [-Wunused-variable] int l0, stage_count, tempi, jtrans, nTransition; ^ tnetpost.cc:30:41: warning: unused variable 'nTransition' [-Wunused-variable] int l0, stage_count, tempi, jtrans, nTransition; ^ tnetpost.cc:33:9: warning: variable 'acceptCount' set but not used [-Wunused-but-set-variable] int acceptCount; ^ tnetpost.cc:36:21: warning: variable 'xSeedFit' set but not used [-Wunused-but-set-variable] int m0, mdelta, xSeedFit; ^ tnetpost.cc:38:9: warning: variable 'perturbationType' set but not used [-Wunused-but-set-variable] int perturbationType, scoreType, backupStage; ^ tnetpost.cc:38:27: warning: variable 'scoreType' set but not used [-Wunused-but-set-variable] int perturbationType, scoreType, backupStage; ^ tnetpost.cc:38:38: warning: variable 'backupStage' set but not used [-Wunused-but-set-variable] int perturbationType, scoreType, backupStage; ^ tnetpost.cc:39:9: warning: variable 'maxStage' set but not used [-Wunused-but-set-variable] int maxStage, maxTransition; ^ tnetpost.cc:39:19: warning: variable 'maxTransition' set but not used [-Wunused-but-set-variable] int maxStage, maxTransition; ^ tnetpost.cc:40:12: warning: variable 'epsilon' set but not used [-Wunused-but-set-variable] double epsilon, chi0, delta, rho; ^ tnetpost.cc:40:21: warning: variable 'chi0' set but not used [-Wunused-but-set-variable] double epsilon, chi0, delta, rho; ^ tnetpost.cc:40:27: warning: variable 'delta' set but not used [-Wunused-but-set-variable] double epsilon, chi0, delta, rho; ^ tnetpost.cc:40:34: warning: variable 'rho' set but not used [-Wunused-but-set-variable] double epsilon, chi0, delta, rho; ^ tnetpost.cc:44:9: warning: variable 'ne' set but not used [-Wunused-but-set-variable] int ne, maxDegree; ^ tnetpost.cc:150:10: warning: variable 'minDump' set but not used [-Wunused-but-set-variable] bool minDump = true; ^ tnetpost.cc:41:9: warning: variable 'Rf_beta' set but not used [-Wunused-but-set-variable] int beta; ^ /Library/Frameworks/R.framework/Resources/include/Rmath.h:210:15: note: expanded from macro 'beta' #define beta Rf_beta ^ 23 warnings generated. clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c util.c -o util.o clang++ -arch arm64 -std=gnu++17 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/arm64/lib -o ternarynet.so array.o gn.o gn_Rwrap.o init.o tnetfit.o tnetfuncs.o tnetpost.o util.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation installing to /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/00LOCK-ternarynet/00new/ternarynet/libs ** R ** 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 (ternarynet)
ternarynet.Rcheck/tests/test_smallmodel.Rout
R version 4.4.2 (2024-10-31) -- "Pile of Leaves" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: aarch64-apple-darwin20 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(ternarynet) > > smallmodel_score <- function() { + + library(ternarynet) + + i_exp <- as.integer(c(0,0,0, 0,0,0, 0,0,0, 0,0,0, + 1,1,1, 1,1,1, 1,1,1, 1,1,1, + 2,2,2, 2,2,2, 2,2,2, 2,2,2, + 3,3,3, 3,3,3, 3,3,3, 3,3,3, + 4,4,4, 4,4,4, 4,4,4, 4,4,4, + 5,5,5, 5,5,5, 5,5,5, 5,5,5, + 6,6,6, 6,6,6, 6,6,6, 6,6,6, + 7,7,7, 7,7,7, 7,7,7, 7,7,7)) + + i_node <- as.integer(c(0,0,0, 1,1,1, 2,2,2, 3,3,3, + 0,0,0, 1,1,1, 2,2,2, 3,3,3, + 0,0,0, 1,1,1, 2,2,2, 3,3,3, + 0,0,0, 1,1,1, 2,2,2, 3,3,3, + 0,0,0, 1,1,1, 2,2,2, 3,3,3, + 0,0,0, 1,1,1, 2,2,2, 3,3,3, + 0,0,0, 1,1,1, 2,2,2, 3,3,3, + 0,0,0, 1,1,1, 2,2,2, 3,3,3)) + + outcome <- as.integer(c(-1,0,1, -1,0,1, -1,0,1, -1,0,1, + -1,0,1, -1,0,1, -1,0,1, -1,0,1, + -1,0,1, -1,0,1, -1,0,1, -1,0,1, + -1,0,1, -1,0,1, -1,0,1, -1,0,1, + -1,0,1, -1,0,1, -1,0,1, -1,0,1, + -1,0,1, -1,0,1, -1,0,1, -1,0,1, + -1,0,1, -1,0,1, -1,0,1, -1,0,1, + -1,0,1, -1,0,1, -1,0,1, -1,0,1)) + + value <- c(0,1,2, 0,1,2, 0,1,2, 0,1,2, + 2,1,0, 0,1,2, 0,1,2, 0,1,2, + 2,1,0, 2,1,0, 0,1,2, 0,1,2, + 2,1,0, 2,1,0, 2,1,0, 0,1,2, + 2,1,0, 2,1,0, 2,1,0, 2,1,0, + 0,1,2, 2,1,0, 2,1,0, 2,1,0, + 0,1,2, 0,1,2, 2,1,0, 2,1,0, + 0,1,2, 0,1,2, 0,1,2, 2,1,0) + + is_perturbation <- c(TRUE,TRUE,TRUE, FALSE,FALSE,FALSE, FALSE,FALSE,FALSE, FALSE,FALSE,FALSE, + FALSE,FALSE,FALSE, TRUE,TRUE,TRUE, FALSE,FALSE,FALSE, FALSE,FALSE,FALSE, + FALSE,FALSE,FALSE, FALSE,FALSE,FALSE, TRUE,TRUE,TRUE, FALSE,FALSE,FALSE, + FALSE,FALSE,FALSE, FALSE,FALSE,FALSE, FALSE,FALSE,FALSE, TRUE,TRUE,TRUE, + TRUE,TRUE,TRUE, FALSE,FALSE,FALSE, FALSE,FALSE,FALSE, FALSE,FALSE,FALSE, + FALSE,FALSE,FALSE, TRUE,TRUE,TRUE, FALSE,FALSE,FALSE, FALSE,FALSE,FALSE, + FALSE,FALSE,FALSE, FALSE,FALSE,FALSE, TRUE,TRUE,TRUE, FALSE,FALSE,FALSE, + FALSE,FALSE,FALSE, FALSE,FALSE,FALSE, FALSE,FALSE,FALSE, TRUE,TRUE,TRUE) + + indata <- data.frame(i_exp,i_node,outcome,value,is_perturbation) + + results <- parallelFit(indata, + max_parents=1, + n_cycles=1000000, + n_write=10, + T_lo=0.001, + T_hi=1.0, + target_score=0, + n_proc=1, + logfile='try.log') + + lowest_temp_results <- results[[1]] + + lowest_temp_results$unnormalized_score + + } > > test_that("smallmodel", { + expect_true(smallmodel_score() == 0) + }) Test passed 😀 > > proc.time() user system elapsed 1.510 0.132 1.660
ternarynet.Rcheck/tests/test_smallmodel_2.Rout
R version 4.4.2 (2024-10-31) -- "Pile of Leaves" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: aarch64-apple-darwin20 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(ternarynet) > > smallmodel_2_score <- function() { + + library(ternarynet) + + i_exp <- as.integer(c(0,0,0, 0,0,0, 0,0,0, + 1,1,1, 1,1,1, 1,1,1, + 2,2,2, 2,2,2, 2,2,2, + 3,3,3, 3,3,3, 3,3,3, + 4,4,4, 4,4,4, 4,4,4, + 5,5,5, 5,5,5, 5,5,5, + 6,6,6, 6,6,6, 6,6,6, + 7,7,7, 7,7,7, 7,7,7, + 8,8,8, 8,8,8, 8,8,8, + 9,9,9, 9,9,9, 9,9,9, + 10,10,10, 10,10,10, 10,10,10, + 11,11,11, 11,11,11, 11,11,11, + 12,12,12, 12,12,12, 12,12,12, + 13,13,13, 13,13,13, 13,13,13, + 14,14,14, 14,14,14, 14,14,14, + 15,15,15, 15,15,15, 15,15,15, + 16,16,16, 16,16,16, 16,16,16, + 17,17,17, 17,17,17, 17,17,17)) + + i_node <- as.integer(c(0,0,0, 1,1,1, 2,2,2, + 0,0,0, 1,1,1, 2,2,2, + 0,0,0, 1,1,1, 2,2,2, + 0,0,0, 1,1,1, 2,2,2, + 0,0,0, 1,1,1, 2,2,2, + 0,0,0, 1,1,1, 2,2,2, + 0,0,0, 1,1,1, 2,2,2, + 0,0,0, 1,1,1, 2,2,2, + 0,0,0, 1,1,1, 2,2,2, + 0,0,0, 1,1,1, 2,2,2, + 0,0,0, 1,1,1, 2,2,2, + 0,0,0, 1,1,1, 2,2,2, + 0,0,0, 1,1,1, 2,2,2, + 0,0,0, 1,1,1, 2,2,2, + 0,0,0, 1,1,1, 2,2,2, + 0,0,0, 1,1,1, 2,2,2, + 0,0,0, 1,1,1, 2,2,2, + 0,0,0, 1,1,1, 2,2,2)) + + outcome <- as.integer(c(-1,0,1, -1,0,1, -1,0,1, + -1,0,1, -1,0,1, -1,0,1, + -1,0,1, -1,0,1, -1,0,1, + -1,0,1, -1,0,1, -1,0,1, + -1,0,1, -1,0,1, -1,0,1, + -1,0,1, -1,0,1, -1,0,1, + -1,0,1, -1,0,1, -1,0,1, + -1,0,1, -1,0,1, -1,0,1, + -1,0,1, -1,0,1, -1,0,1, + -1,0,1, -1,0,1, -1,0,1, + -1,0,1, -1,0,1, -1,0,1, + -1,0,1, -1,0,1, -1,0,1, + -1,0,1, -1,0,1, -1,0,1, + -1,0,1, -1,0,1, -1,0,1, + -1,0,1, -1,0,1, -1,0,1, + -1,0,1, -1,0,1, -1,0,1, + -1,0,1, -1,0,1, -1,0,1, + -1,0,1, -1,0,1, -1,0,1)) + + value <- c(2,1,0, 1,0,1, 2,1,0, + 1,0,1, 2,1,0, 0,1,2, + 1,0,1, 1,0,1, 2,1,0, + 0,1,2, 1,0,1, 0,1,2, + 1,0,1, 0,1,2, 2,1,0, + 1,0,1, 1,0,1, 0,1,2, + 2,1,0, 1,0,1, 2,1,0, + 0,1,2, 1,0,1, 0,1,2, + 1,0,1, 2,1,0, 0,1,2, + 1,0,1, 0,1,2, 2,1,0, + 2,1,0, 2,1,0, 1,0,1, + 0,1,2, 0,1,2, 1,0,1, + 2,1,0, 0,1,2, 2,1,0, + 0,1,2, 2,1,0, 0,1,2, + 2,1,0, 1,0,1, 0,1,2, + 0,1,2, 1,0,1, 2,1,0, + 1,0,1, 2,1,0, 2,1,0, + 1,0,1, 0,1,2, 0,1,2) + + is_perturbation <- c(TRUE,TRUE,TRUE, FALSE,FALSE,FALSE, FALSE,FALSE,FALSE, + FALSE,FALSE,FALSE, TRUE,TRUE,TRUE, FALSE,FALSE,FALSE, + FALSE,FALSE,FALSE, FALSE,FALSE,FALSE, TRUE,TRUE,TRUE, + TRUE,TRUE,TRUE, FALSE,FALSE,FALSE, FALSE,FALSE,FALSE, + FALSE,FALSE,FALSE, TRUE,TRUE,TRUE, FALSE,FALSE,FALSE, + FALSE,FALSE,FALSE, FALSE,FALSE,FALSE, TRUE,TRUE,TRUE, + TRUE,TRUE,TRUE, FALSE,FALSE,FALSE, TRUE,TRUE,TRUE, + TRUE,TRUE,TRUE, FALSE,FALSE,FALSE, TRUE,TRUE,TRUE, + FALSE,FALSE,FALSE, TRUE,TRUE,TRUE, TRUE,TRUE,TRUE, + FALSE,FALSE,FALSE, TRUE,TRUE,TRUE, TRUE,TRUE,TRUE, + TRUE,TRUE,TRUE, TRUE,TRUE,TRUE, FALSE,FALSE,FALSE, + TRUE,TRUE,TRUE, TRUE,TRUE,TRUE, FALSE,FALSE,FALSE, + TRUE,TRUE,TRUE, TRUE,TRUE,TRUE, FALSE,FALSE,FALSE, + TRUE,TRUE,TRUE, TRUE,TRUE,TRUE, FALSE,FALSE,FALSE, + TRUE,TRUE,TRUE, FALSE,FALSE,FALSE, TRUE,TRUE,TRUE, + TRUE,TRUE,TRUE, FALSE,FALSE,FALSE, TRUE,TRUE,TRUE, + FALSE,FALSE,FALSE, TRUE,TRUE,TRUE, TRUE,TRUE,TRUE, + FALSE,FALSE,FALSE, TRUE,TRUE,TRUE, TRUE,TRUE,TRUE) + + indata <- data.frame(i_exp,i_node,outcome,value,is_perturbation) + + results <- parallelFit(indata, + max_parents=2, + n_cycles=1000000, + n_write=10, + T_lo=0.001, + T_hi=2.0, + target_score=0, + n_proc=1, + logfile='try2.log') + + lowest_temp_results <- results[[1]] + + lowest_temp_results$unnormalized_score + + } > > test_that("smallmodel_2", { + expect_true(smallmodel_2_score() == 0) + }) Test passed 🌈 > > proc.time() user system elapsed 1.788 0.128 1.945
ternarynet.Rcheck/ternarynet-Ex.timings
name | user | system | elapsed | |
attractorSummary | 2.928 | 0.010 | 2.972 | |
graphPosterior | 2.914 | 0.010 | 2.950 | |
parallelFit | 0.314 | 0.013 | 0.332 | |
plotFit | 3.019 | 0.019 | 3.064 | |
plotPost | 2.948 | 0.013 | 3.033 | |
plotTraces | 2.916 | 0.010 | 2.950 | |
predictAttractor | 2.923 | 0.009 | 2.958 | |
simulateSteadyState | 0.001 | 0.000 | 0.002 | |
ternaryFit-class | 2.918 | 0.009 | 2.954 | |
ternaryFitParameters-class | 0.001 | 0.000 | 0.001 | |
ternaryPost-class | 2.916 | 0.011 | 2.990 | |
tnetfit | 2.876 | 0.009 | 2.919 | |
tnetpost | 2.916 | 0.009 | 2.961 | |