Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-08-19 11:41 -0400 (Mon, 19 Aug 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
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nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4703 |
palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" | 4440 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4472 |
kjohnson3 | macOS 13.6.5 Ventura | arm64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4420 |
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4413 |
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 2103/2255 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
ternarynet 1.49.0 (landing page) McCall N. Matthew
| 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 | OK | OK | OK | ![]() | ||||||||
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | 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: 1.49.0 |
Command: F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:ternarynet.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings ternarynet_1.49.0.tar.gz |
StartedAt: 2024-08-19 05:54:28 -0400 (Mon, 19 Aug 2024) |
EndedAt: 2024-08-19 05:56:05 -0400 (Mon, 19 Aug 2024) |
EllapsedTime: 96.4 seconds |
RetCode: 0 |
Status: OK |
CheckDir: ternarynet.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:ternarynet.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings ternarynet_1.49.0.tar.gz ### ############################################################################## ############################################################################## * using log directory 'F:/biocbuild/bbs-3.20-bioc/meat/ternarynet.Rcheck' * using R version 4.4.1 (2024-06-14 ucrt) * using platform: x86_64-w64-mingw32 * R was compiled by gcc.exe (GCC) 13.2.0 GNU Fortran (GCC) 13.2.0 * running under: Windows Server 2022 x64 (build 20348) * using session charset: UTF-8 * using option '--no-vignettes' * checking for file 'ternarynet/DESCRIPTION' ... OK * this is package 'ternarynet' version '1.49.0' * 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 whether package 'ternarynet' can be installed ... OK * used C compiler: 'gcc.exe (GCC) 13.2.0' * used C++ compiler: 'G__~1.EXE (GCC) 13.2.0' * 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 for x64 is not available File 'F:/biocbuild/bbs-3.20-bioc/R/library/ternarynet/libs/x64/ternarynet.dll': Found '_exit', possibly from '_exit' (C) Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran) Found 'exit', possibly from 'exit' (C), 'stop' (Fortran) Compiled code should not call entry points which might terminate R nor write to stdout/stderr instead of to the console, nor use Fortran I/O nor system RNGs nor [v]sprintf. The detected symbols are linked into the code but might come from libraries and not actually be called. See 'Writing portable packages' in the 'Writing R Extensions' manual. * checking sizes of PDF files under 'inst/doc' ... OK * checking files in 'vignettes' ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed graphPosterior 5.08 0 5.07 * 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: 1 NOTE See 'F:/biocbuild/bbs-3.20-bioc/meat/ternarynet.Rcheck/00check.log' for details.
ternarynet.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD INSTALL ternarynet ### ############################################################################## ############################################################################## * installing to library 'F:/biocbuild/bbs-3.20-bioc/R/library' * installing *source* package 'ternarynet' ... ** using staged installation ** libs using C compiler: 'gcc.exe (GCC) 13.2.0' using C++ compiler: 'G__~1.EXE (GCC) 13.2.0' gcc -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c array.c -o array.o gcc -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c gn.c -o gn.o gn.c: In function 'score': gn.c:486: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas] 486 | #pragma omp parallel for | gn.c:493: warning: ignoring '#pragma omp atomic' [-Wunknown-pragmas] 493 | #pragma omp atomic | gcc -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c gn_Rwrap.c -o gn_Rwrap.o In file included from F:/biocbuild/bbs-3.20-bioc/R/include/R.h:69, from gn_Rwrap.h:4, from gn_Rwrap.c:1: F:/biocbuild/bbs-3.20-bioc/R/include/R_ext/Arith.h:58:25: warning: 'R_NaReal' redeclared without dllimport attribute: previous dllimport ignored [-Wattributes] 58 | #define NA_REAL R_NaReal | ^~~~~~~~ F:/biocbuild/bbs-3.20-bioc/R/include/Rmath.h:644:17: note: in expansion of macro 'NA_REAL' 644 | R_EXTERN double NA_REAL; | ^~~~~~~ In file included from gn_Rwrap.c:9: F:/biocbuild/bbs-3.20-bioc/R/include/Rmath.h:645:17: warning: 'R_PosInf' redeclared without dllimport attribute: previous dllimport ignored [-Wattributes] 645 | R_EXTERN double R_PosInf; | ^~~~~~~~ F:/biocbuild/bbs-3.20-bioc/R/include/Rmath.h:646:17: warning: 'R_NegInf' redeclared without dllimport attribute: previous dllimport ignored [-Wattributes] 646 | R_EXTERN double R_NegInf; | ^~~~~~~~ gcc -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c init.c -o init.o g++ -std=gnu++17 -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c tnetfit.cc -o tnetfit.o tnetfit.cc: In function 'SEXPREC* tnetfit(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP)': tnetfit.cc:24:9: warning: variable 'perturbationType' set but not used [-Wunused-but-set-variable] 24 | int perturbationType, scoreType, backupStage, maxStage, maxTransition; | ^~~~~~~~~~~~~~~~ tnetfit.cc:24:27: warning: variable 'scoreType' set but not used [-Wunused-but-set-variable] 24 | int perturbationType, scoreType, backupStage, maxStage, maxTransition; | ^~~~~~~~~ tnetfit.cc:24:38: warning: variable 'backupStage' set but not used [-Wunused-but-set-variable] 24 | int perturbationType, scoreType, backupStage, maxStage, maxTransition; | ^~~~~~~~~~~ tnetfit.cc:73:39: warning: unused variable 'tempi' [-Wunused-variable] 73 | int nOutcomes=3, l0, stage_count, tempi, jtrans, nTransition; | ^~~~~ tnetfit.cc:207:25: warning: 'sigma0' may be used uninitialized [-Wmaybe-uninitialized] 207 | convergence = (muci-muci_old)/sigma0; | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ tnetfit.cc:98:12: note: 'sigma0' was declared here 98 | double sigma0, sigmaci, sigmaRaw, muci, muci_old, convergence; | ^~~~~~ tnetfit.cc:202:43: warning: 'sigmaci' may be used uninitialized [-Wmaybe-uninitialized] 202 | sigmaci = rho*sigmaRaw + (1-rho)*sigmaci; | ~~~~~~~^~~~~~~~ tnetfit.cc:98:20: note: 'sigmaci' was declared here 98 | double sigma0, sigmaci, sigmaRaw, muci, muci_old, convergence; | ^~~~~~~ tnetfit.cc:207:32: warning: 'muci_old' may be used uninitialized [-Wmaybe-uninitialized] 207 | convergence = (muci-muci_old)/sigma0; | ~~~~~^~~~~~~~~~ tnetfit.cc:98:45: note: 'muci_old' was declared here 98 | double sigma0, sigmaci, sigmaRaw, muci, muci_old, convergence; | ^~~~~~~~ tnetfit.cc:311:19: warning: 'newScore' may be used uninitialized [-Wmaybe-uninitialized] 311 | SET_VECTOR_ELT(Routput, 10, ScalarReal(newScore)); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ tnetfit.cc:77:12: note: 'newScore' was declared here 77 | double newScore, oldScore, difference, minScore = 999999999; | ^~~~~~~~ g++ -std=gnu++17 -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c tnetfuncs.cc -o tnetfuncs.o tnetfuncs.cc: In function 'double AttractorDistanceForced(int, int, int, int, double, int*, int*, int*, const double*, const int*)': tnetfuncs.cc:427:5: warning: unused variable 'tableWidth' [-Wunused-variable] 427 | int tableWidth = powi(nOutcomes,maxDegree); | ^~~~~~~~~~ tnetfuncs.cc:435:5: warning: unused variable 'ipause' [-Wunused-variable] 435 | int ipause; | ^~~~~~ tnetfuncs.cc: In function 'double initialTemp(double, int, int, int, int, int, double, double, double, int, const double*, int*, int*, int*, const double*, const int*)': tnetfuncs.cc:517:13: warning: unused variable 'ipause' [-Wunused-variable] 517 | int ipause; | ^~~~~~ tnetfuncs.cc:521:21: warning: unused variable 'i' [-Wunused-variable] 521 | int m1, m2, i; | ^ g++ -std=gnu++17 -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c tnetpost.cc -o tnetpost.o tnetpost.cc: In function 'SEXPREC* tnetpost(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP)': tnetpost.cc:25:9: warning: unused variable 'ipause' [-Wunused-variable] 25 | int ipause; | ^~~~~~ tnetpost.cc:27:9: warning: unused variable 'm0fit' [-Wunused-variable] 27 | int m0fit; | ^~~~~ tnetpost.cc:28:32: warning: variable 'minScore' set but not used [-Wunused-but-set-variable] 28 | double newScore, oldScore, minScore, finalScore; | ^~~~~~~~ tnetpost.cc:28:42: warning: unused variable 'finalScore' [-Wunused-variable] 28 | double newScore, oldScore, minScore, finalScore; | ^~~~~~~~~~ tnetpost.cc:30:9: warning: unused variable 'l0' [-Wunused-variable] 30 | int l0, stage_count, tempi, jtrans, nTransition; | ^~ tnetpost.cc:30:13: warning: unused variable 'stage_count' [-Wunused-variable] 30 | int l0, stage_count, tempi, jtrans, nTransition; | ^~~~~~~~~~~ tnetpost.cc:30:26: warning: unused variable 'tempi' [-Wunused-variable] 30 | int l0, stage_count, tempi, jtrans, nTransition; | ^~~~~ tnetpost.cc:30:33: warning: unused variable 'jtrans' [-Wunused-variable] 30 | int l0, stage_count, tempi, jtrans, nTransition; | ^~~~~~ tnetpost.cc:30:41: warning: unused variable 'nTransition' [-Wunused-variable] 30 | int l0, stage_count, tempi, jtrans, nTransition; | ^~~~~~~~~~~ tnetpost.cc:36:21: warning: variable 'xSeedFit' set but not used [-Wunused-but-set-variable] 36 | int m0, mdelta, xSeedFit; | ^~~~~~~~ tnetpost.cc:38:9: warning: variable 'perturbationType' set but not used [-Wunused-but-set-variable] 38 | int perturbationType, scoreType, backupStage; | ^~~~~~~~~~~~~~~~ tnetpost.cc:38:27: warning: variable 'scoreType' set but not used [-Wunused-but-set-variable] 38 | int perturbationType, scoreType, backupStage; | ^~~~~~~~~ tnetpost.cc:38:38: warning: variable 'backupStage' set but not used [-Wunused-but-set-variable] 38 | int perturbationType, scoreType, backupStage; | ^~~~~~~~~~~ tnetpost.cc:39:9: warning: variable 'maxStage' set but not used [-Wunused-but-set-variable] 39 | int maxStage, maxTransition; | ^~~~~~~~ tnetpost.cc:39:19: warning: variable 'maxTransition' set but not used [-Wunused-but-set-variable] 39 | int maxStage, maxTransition; | ^~~~~~~~~~~~~ tnetpost.cc:40:12: warning: variable 'epsilon' set but not used [-Wunused-but-set-variable] 40 | double epsilon, chi0, delta, rho; | ^~~~~~~ tnetpost.cc:40:21: warning: variable 'chi0' set but not used [-Wunused-but-set-variable] 40 | double epsilon, chi0, delta, rho; | ^~~~ tnetpost.cc:40:27: warning: variable 'delta' set but not used [-Wunused-but-set-variable] 40 | double epsilon, chi0, delta, rho; | ^~~~~ tnetpost.cc:40:34: warning: variable 'rho' set but not used [-Wunused-but-set-variable] 40 | double epsilon, chi0, delta, rho; | ^~~ In file included from tnetpost.cc:14: F:/biocbuild/bbs-3.20-bioc/R/include/Rmath.h:210:25: warning: variable 'Rf_beta' set but not used [-Wunused-but-set-variable] 210 | #define beta Rf_beta | ^~~~~~~ tnetpost.cc:41:9: note: in expansion of macro 'beta' 41 | int beta; | ^~~~ tnetpost.cc:44:9: warning: variable 'ne' set but not used [-Wunused-but-set-variable] 44 | int ne, maxDegree; | ^~ tnetpost.cc:150:10: warning: variable 'minDump' set but not used [-Wunused-but-set-variable] 150 | bool minDump = true; | ^~~~~~~ gcc -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c util.c -o util.o g++ -std=gnu++17 -shared -s -static-libgcc -o ternarynet.dll tmp.def array.o gn.o gn_Rwrap.o init.o tnetfit.o tnetfuncs.o tnetpost.o util.o -LC:/rtools44/x86_64-w64-mingw32.static.posix/lib/x64 -LC:/rtools44/x86_64-w64-mingw32.static.posix/lib -LF:/biocbuild/bbs-3.20-bioc/R/bin/x64 -lR installing to F:/biocbuild/bbs-3.20-bioc/R/library/00LOCK-ternarynet/00new/ternarynet/libs/x64 ** 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 ** 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 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: x86_64-w64-mingw32/x64 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 1.50 0.17 1.65
ternarynet.Rcheck/tests/test_smallmodel_2.Rout
R version 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: x86_64-w64-mingw32/x64 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 1.70 0.23 1.92
ternarynet.Rcheck/ternarynet-Ex.timings
name | user | system | elapsed | |
attractorSummary | 4.70 | 0.00 | 4.71 | |
graphPosterior | 5.08 | 0.00 | 5.07 | |
parallelFit | 0.28 | 0.03 | 0.31 | |
plotFit | 4.92 | 0.02 | 4.99 | |
plotPost | 4.81 | 0.00 | 4.81 | |
plotTraces | 4.11 | 0.00 | 4.11 | |
predictAttractor | 4.89 | 0.00 | 4.89 | |
simulateSteadyState | 0 | 0 | 0 | |
ternaryFit-class | 4.46 | 0.00 | 4.45 | |
ternaryFitParameters-class | 0 | 0 | 0 | |
ternaryPost-class | 4.31 | 0.00 | 4.32 | |
tnetfit | 4.58 | 0.00 | 4.57 | |
tnetpost | 4.22 | 0.00 | 4.22 | |