Multiple platform build/check report for BioC 3.22 - CHECK results for ternarynet on nebbiolo2

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo2	Linux (Ubuntu 24.04.3 LTS)	x86_64	4.5.1 Patched (2025-08-23 r88802) -- "Great Square Root"	4898
lconway	macOS 12.7.6 Monterey	x86_64	4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root"	4688
kjohnson3	macOS 13.7.7 Ventura	arm64	4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root"	4634
taishan	Linux (openEuler 24.03 LTS)	aarch64	4.5.0 (2025-04-11) -- "How About a Twenty-Six"	4658
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*

CHECK results for ternarynet on nebbiolo2

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.

raw results

Summary

Package: ternarynet

Version: 1.53.0

Command: /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:ternarynet.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings ternarynet_1.53.0.tar.gz

StartedAt: 2025-10-24 04:41:24 -0400 (Fri, 24 Oct 2025)

EndedAt: 2025-10-24 04:42:12 -0400 (Fri, 24 Oct 2025)

EllapsedTime: 48.0 seconds

RetCode: 0

Status: OK

CheckDir: ternarynet.Rcheck

Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:ternarynet.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings ternarynet_1.53.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/ternarynet.Rcheck’
* using R version 4.5.1 Patched (2025-08-23 r88802)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
    GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.3 LTS
* using session charset: UTF-8
* checking for file ‘ternarynet/DESCRIPTION’ ... OK
* this is package ‘ternarynet’ version ‘1.53.0’
* 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 ‘ternarynet’ can be installed ... OK
* used C compiler: ‘gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’
* used C++ compiler: ‘g++ (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’
* 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 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 ... 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 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 re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 1 NOTE
See
  ‘/home/biocbuild/bbs-3.22-bioc/meat/ternarynet.Rcheck/00check.log’
for details.

Installation output

ternarynet.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD INSTALL ternarynet
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.22-bioc/R/site-library’
* installing *source* package ‘ternarynet’ ...
** this is package ‘ternarynet’ version ‘1.53.0’
** using staged installation
** libs
using C compiler: ‘gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’
using C++ compiler: ‘g++ (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security -c array.c -o array.o
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security -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 -std=gnu2x -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security -c gn_Rwrap.c -o gn_Rwrap.o
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security -c init.c -o init.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -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"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -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"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -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:
/home/biocbuild/bbs-3.22-bioc/R/include/Rmath.h:221:25: warning: variable ‘Rf_beta’ set but not used [-Wunused-but-set-variable]
  221 | #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 -std=gnu2x -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security -c util.c -o util.o
g++ -std=gnu++17 -shared -L/home/biocbuild/bbs-3.22-bioc/R/lib -L/usr/local/lib -o ternarynet.so array.o gn.o gn_Rwrap.o init.o tnetfit.o tnetfuncs.o tnetpost.o util.o -L/home/biocbuild/bbs-3.22-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.22-bioc/R/site-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)

Tests output

ternarynet.Rcheck/tests/test_smallmodel.Rout


R version 4.5.1 Patched (2025-08-23 r88802) -- "Great Square Root"
Copyright (C) 2025 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(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 
  1.243   0.084   1.314

ternarynet.Rcheck/tests/test_smallmodel_2.Rout


R version 4.5.1 Patched (2025-08-23 r88802) -- "Great Square Root"
Copyright (C) 2025 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(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 
  1.381   0.077   1.445

Example timings

ternarynet.Rcheck/ternarynet-Ex.timings

name	user	system	elapsed
attractorSummary	1.760	0.005	1.765
graphPosterior	1.738	0.000	1.738
parallelFit	0.225	0.011	0.236
plotFit	1.839	0.016	1.855
plotPost	1.770	0.009	1.778
plotTraces	1.750	0.006	1.756
predictAttractor	1.746	0.002	1.748
simulateSteadyState	0.001	0.000	0.001
ternaryFit-class	1.743	0.000	1.744
ternaryFitParameters-class	0.002	0.000	0.001
ternaryPost-class	1.743	0.003	1.746
tnetfit	1.741	0.001	1.742
tnetpost	1.744	0.000	1.744