McCall N. Matthew
| Snapshot Date: 2024-03-01 14:00:22 -0500 (Fri, 01 Mar 2024) |
| git_url: https://git.bioconductor.org/packages/ternarynet |
| git_branch: devel |
| git_last_commit: ad33b27 |
| git_last_commit_date: 2024-02-24 09:23:37 -0500 (Sat, 24 Feb 2024) |
| Back to Multiple platform build/check report for BioC 3.19: simplified long |
|
This page was generated on 2024-03-04 11:40:04 -0500 (Mon, 04 Mar 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | R Under development (unstable) (2024-01-16 r85808) -- "Unsuffered Consequences" | 4676 |
| palomino3 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2024-01-14 r85805 ucrt) -- "Unsuffered Consequences" | 4414 |
| merida1 | macOS 12.7.1 Monterey | x86_64 | R Under development (unstable) (2024-01-16 r85808) -- "Unsuffered Consequences" | 4441 |
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | R Under development (unstable) (2024-01-16 r85812) -- "Unsuffered Consequences" | 4417 |
| 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 2103/2251 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| ternarynet 1.47.2 (landing page) McCall N. Matthew
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| merida1 | macOS 12.7.1 Monterey / x86_64 | 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: 1.47.2 |
| 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_1.47.2.tar.gz |
| StartedAt: 2024-03-02 11:41:00 -0500 (Sat, 02 Mar 2024) |
| EndedAt: 2024-03-02 11:43:21 -0500 (Sat, 02 Mar 2024) |
| EllapsedTime: 141.0 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: ternarynet.Rcheck |
| Warnings: 0 |
##############################################################################
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###
### 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_1.47.2.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.19-bioc/meat/ternarynet.Rcheck’
* using R Under development (unstable) (2024-01-16 r85808)
* using platform: x86_64-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 Monterey 12.7.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘ternarynet/DESCRIPTION’ ... OK
* this is package ‘ternarynet’ version ‘1.47.2’
* 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 14.0.0 (clang-1400.0.29.202)’
* used C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
* 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 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 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
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
plotFit 6.711 0.072 7.805
plotPost 6.521 0.047 7.522
attractorSummary 6.521 0.042 7.622
predictAttractor 6.515 0.047 7.471
tnetpost 6.498 0.048 7.720
ternaryFit-class 6.491 0.043 7.469
ternaryPost-class 6.491 0.042 7.481
plotTraces 6.484 0.044 7.473
graphPosterior 6.478 0.048 7.603
tnetfit 6.477 0.042 7.497
* 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-3.19-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-x86_64/Resources/library’
* installing *source* package ‘ternarynet’ ...
** using staged installation
** libs
using C compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
using C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
using SDK: ‘MacOSX11.3.sdk’
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c array.c -o array.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c gn.c -o gn.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c gn_Rwrap.c -o gn_Rwrap.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c init.c -o init.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c tnetfit.cc -o tnetfit.o
tnetfit.cc:73:39: warning: unused variable 'tempi' [-Wunused-variable]
int nOutcomes=3, l0, stage_count, tempi, jtrans, nTransition;
^
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;
^
4 warnings generated.
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c tnetfuncs.cc -o tnetfuncs.o
tnetfuncs.cc:435:5: warning: unused variable 'ipause' [-Wunused-variable]
int ipause;
^
tnetfuncs.cc:427:5: warning: unused variable 'tableWidth' [-Wunused-variable]
int tableWidth = powi(nOutcomes,maxDegree);
^
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 x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c tnetpost.cc -o tnetpost.o
tnetpost.cc:28:32: warning: variable 'minScore' set but not used [-Wunused-but-set-variable]
double newScore, oldScore, minScore, finalScore;
^
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
^
tnetpost.cc:27:9: warning: unused variable 'm0fit' [-Wunused-variable]
int m0fit;
^
tnetpost.cc:30:9: warning: unused variable 'l0' [-Wunused-variable]
int l0, stage_count, tempi, jtrans, nTransition;
^
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:28:42: warning: unused variable 'finalScore' [-Wunused-variable]
double newScore, oldScore, minScore, finalScore;
^
tnetpost.cc:40:34: warning: variable 'rho' set but not used [-Wunused-but-set-variable]
double epsilon, chi0, delta, rho;
^
tnetpost.cc:30:41: warning: unused variable 'nTransition' [-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:30:26: warning: unused variable 'tempi' [-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:150:10: warning: variable 'minDump' set but not used [-Wunused-but-set-variable]
bool minDump = true;
^
tnetpost.cc:44:9: warning: variable 'ne' set but not used [-Wunused-but-set-variable]
int ne, maxDegree;
^
tnetpost.cc:36:21: warning: variable 'xSeedFit' set but not used [-Wunused-but-set-variable]
int m0, mdelta, xSeedFit;
^
tnetpost.cc:38:27: warning: variable 'scoreType' set but not used [-Wunused-but-set-variable]
int perturbationType, scoreType, backupStage;
^
tnetpost.cc:38:9: warning: variable 'perturbationType' set but not used [-Wunused-but-set-variable]
int perturbationType, scoreType, backupStage;
^
tnetpost.cc:25:9: warning: unused variable 'ipause' [-Wunused-variable]
int ipause;
^
tnetpost.cc:39:19: warning: variable 'maxTransition' set but not used [-Wunused-but-set-variable]
int maxStage, maxTransition;
^
tnetpost.cc:39:9: warning: variable 'maxStage' set but not used [-Wunused-but-set-variable]
int maxStage, maxTransition;
^
tnetpost.cc:38:38: warning: variable 'backupStage' set but not used [-Wunused-but-set-variable]
int perturbationType, scoreType, backupStage;
^
22 warnings generated.
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c util.c -o util.o
clang++ -arch x86_64 -std=gnu++17 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/x86_64/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-x86_64/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 Under development (unstable) (2024-01-16 r85808) -- "Unsuffered Consequences"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-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
2.977 0.254 3.562
ternarynet.Rcheck/tests/test_smallmodel_2.Rout
R Under development (unstable) (2024-01-16 r85808) -- "Unsuffered Consequences"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-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
3.233 0.258 3.941
ternarynet.Rcheck/ternarynet-Ex.timings
| name | user | system | elapsed | |
| attractorSummary | 6.521 | 0.042 | 7.622 | |
| graphPosterior | 6.478 | 0.048 | 7.603 | |
| parallelFit | 0.428 | 0.032 | 0.532 | |
| plotFit | 6.711 | 0.072 | 7.805 | |
| plotPost | 6.521 | 0.047 | 7.522 | |
| plotTraces | 6.484 | 0.044 | 7.473 | |
| predictAttractor | 6.515 | 0.047 | 7.471 | |
| simulateSteadyState | 0.003 | 0.002 | 0.005 | |
| ternaryFit-class | 6.491 | 0.043 | 7.469 | |
| ternaryFitParameters-class | 0.002 | 0.002 | 0.004 | |
| ternaryPost-class | 6.491 | 0.042 | 7.481 | |
| tnetfit | 6.477 | 0.042 | 7.497 | |
| tnetpost | 6.498 | 0.048 | 7.720 | |