McCall N. Matthew
| Snapshot Date: 2024-06-09 14:00 -0400 (Sun, 09 Jun 2024) |
| git_url: https://git.bioconductor.org/packages/ternarynet |
| git_branch: devel |
| git_last_commit: 4ec3c81 |
| git_last_commit_date: 2024-04-30 10:27:00 -0400 (Tue, 30 Apr 2024) |
| Back to Multiple platform build/check report for BioC 3.20: simplified long |
|
This page was generated on 2024-06-11 15:41 -0400 (Tue, 11 Jun 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.0 RC (2024-04-16 r86468) -- "Puppy Cup" | 4679 |
| palomino4 | Windows Server 2022 Datacenter | x64 | 4.4.0 RC (2024-04-16 r86468 ucrt) -- "Puppy Cup" | 4414 |
| merida1 | macOS 12.7.4 Monterey | x86_64 | 4.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup" | 4441 |
| kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup" | 4394 |
| 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 2087/2239 | 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 | | ||||||||
| palomino4 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| merida1 | macOS 12.7.4 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | OK | OK | OK | | ||||||||
|
To the developers/maintainers of the ternarynet package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/ternarynet.git to reflect on this report. See Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. |
| Package: ternarynet |
| Version: 1.49.0 |
| 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: 2024-06-10 11:07:35 -0400 (Mon, 10 Jun 2024) |
| EndedAt: 2024-06-10 11:12:05 -0400 (Mon, 10 Jun 2024) |
| EllapsedTime: 269.3 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 4.4.0 RC (2024-04-16 r86468 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
* 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 4.4.0 RC (2024-04-16 r86468 ucrt) -- "Puppy Cup"
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
1.25 5.37 6.70
ternarynet.Rcheck/tests/test_smallmodel_2.Rout
R version 4.4.0 RC (2024-04-16 r86468 ucrt) -- "Puppy Cup"
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
1.43 5.39 6.73
ternarynet.Rcheck/ternarynet-Ex.timings
| name | user | system | elapsed | |
| attractorSummary | 4.03 | 0.01 | 4.04 | |
| graphPosterior | 3.67 | 0.00 | 3.67 | |
| parallelFit | 0.28 | 0.48 | 0.77 | |
| plotFit | 4.01 | 0.18 | 4.22 | |
| plotPost | 4 | 0 | 4 | |
| plotTraces | 3.78 | 0.00 | 3.78 | |
| predictAttractor | 3.72 | 0.00 | 3.72 | |
| simulateSteadyState | 0 | 0 | 0 | |
| ternaryFit-class | 4.08 | 0.00 | 4.08 | |
| ternaryFitParameters-class | 0.02 | 0.00 | 0.01 | |
| ternaryPost-class | 3.98 | 0.00 | 3.99 | |
| tnetfit | 3.63 | 0.00 | 3.64 | |
| tnetpost | 4.57 | 0.00 | 4.57 | |