| Back to Multiple platform build/check report for BioC 3.15 |
|
This page was generated on 2022-10-19 13:20:58 -0400 (Wed, 19 Oct 2022).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 20.04.5 LTS) | x86_64 | 4.2.1 (2022-06-23) -- "Funny-Looking Kid" | 4386 |
| palomino3 | Windows Server 2022 Datacenter | x64 | 4.2.1 (2022-06-23 ucrt) -- "Funny-Looking Kid" | 4138 |
| merida1 | macOS 10.14.6 Mojave | x86_64 | 4.2.1 (2022-06-23) -- "Funny-Looking Kid" | 4205 |
| 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 | ||||
|
To the developers/maintainers of the ternarynet package: - Please 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 How and When does the builder pull? When will my changes propagate? for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 1995/2140 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| ternarynet 1.40.0 (landing page) McCall N. Matthew
| nebbiolo1 | Linux (Ubuntu 20.04.5 LTS) / x86_64 | OK | OK | OK |  | ||||||||
| palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| merida1 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | | ||||||||
| Package: ternarynet |
| Version: 1.40.0 |
| Command: /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD check --install=check:ternarynet.install-out.txt --library=/home/biocbuild/bbs-3.15-bioc/R/library --no-vignettes --timings ternarynet_1.40.0.tar.gz |
| StartedAt: 2022-10-18 22:08:03 -0400 (Tue, 18 Oct 2022) |
| EndedAt: 2022-10-18 22:08:49 -0400 (Tue, 18 Oct 2022) |
| EllapsedTime: 46.3 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: ternarynet.Rcheck |
| Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD check --install=check:ternarynet.install-out.txt --library=/home/biocbuild/bbs-3.15-bioc/R/library --no-vignettes --timings ternarynet_1.40.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.15-bioc/meat/ternarynet.Rcheck’ * using R version 4.2.1 (2022-06-23) * using platform: x86_64-pc-linux-gnu (64-bit) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘ternarynet/DESCRIPTION’ ... OK * this is package ‘ternarynet’ version ‘1.40.0’ * 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 * 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 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 in ‘inst/doc’ ... 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 ‘/home/biocbuild/bbs-3.15-bioc/meat/ternarynet.Rcheck/00check.log’ for details.
ternarynet.Rcheck/00install.out
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD INSTALL ternarynet
###
##############################################################################
##############################################################################
* installing to library ‘/home/biocbuild/bbs-3.15-bioc/R/library’
* installing *source* package ‘ternarynet’ ...
** using staged installation
** libs
gcc -I"/home/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c array.c -o array.o
gcc -I"/home/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -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"/home/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c gn_Rwrap.c -o gn_Rwrap.o
gcc -I"/home/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c init.c -o init.o
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -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:311:19: warning: ‘newScore’ may be used uninitialized in this function [-Wmaybe-uninitialized]
311 | SET_VECTOR_ELT(Routput, 10, ScalarReal(newScore));
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
tnetfit.cc:207:25: warning: ‘muci_old’ may be used uninitialized in this function [-Wmaybe-uninitialized]
207 | convergence = (muci-muci_old)/sigma0;
| ~~~~~^~~~~~~~~~
tnetfit.cc:202:36: warning: ‘sigmaci’ may be used uninitialized in this function [-Wmaybe-uninitialized]
202 | sigmaci = rho*sigmaRaw + (1-rho)*sigmaci;
| ~~~~~~~^~~~~~~~
tnetfit.cc:207:18: warning: ‘sigma0’ may be used uninitialized in this function [-Wmaybe-uninitialized]
207 | convergence = (muci-muci_old)/sigma0;
| ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -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:517:6: warning: unused variable ‘ipause’ [-Wunused-variable]
517 | int ipause;
| ^~~~~~
tnetfuncs.cc:521:16: warning: unused variable ‘i’ [-Wunused-variable]
521 | int m1, m2, i;
| ^
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -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-3.15-bioc/R/include/Rmath.h:210:15: 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"/home/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c util.c -o util.o
g++ -std=gnu++14 -shared -L/home/biocbuild/bbs-3.15-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-3.15-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.15-bioc/R/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 4.2.1 (2022-06-23) -- "Funny-Looking Kid"
Copyright (C) 2022 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)
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
1.160 0.076 1.224
ternarynet.Rcheck/tests/test_smallmodel_2.Rout
R version 4.2.1 (2022-06-23) -- "Funny-Looking Kid"
Copyright (C) 2022 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)
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
1.311 0.056 1.350
ternarynet.Rcheck/ternarynet-Ex.timings
| name | user | system | elapsed | |
| attractorSummary | 1.903 | 0.009 | 1.910 | |
| graphPosterior | 1.868 | 0.000 | 1.869 | |
| parallelFit | 0.240 | 0.028 | 0.268 | |
| plotFit | 1.874 | 0.008 | 1.882 | |
| plotPost | 1.880 | 0.008 | 1.887 | |
| plotTraces | 1.861 | 0.003 | 1.865 | |
| predictAttractor | 1.870 | 0.003 | 1.874 | |
| simulateSteadyState | 0.002 | 0.001 | 0.002 | |
| ternaryFit-class | 1.853 | 0.003 | 1.857 | |
| ternaryFitParameters-class | 0.001 | 0.001 | 0.001 | |
| ternaryPost-class | 1.863 | 0.004 | 1.867 | |
| tnetfit | 1.865 | 0.000 | 1.865 | |
| tnetpost | 1.893 | 0.003 | 1.897 | |