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This page was generated on 2022-01-14 13:07:17 -0500 (Fri, 14 Jan 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_644.1.2 (2021-11-01) -- "Bird Hippie" 4327
tokay2Windows Server 2012 R2 Standardx644.1.2 (2021-11-01) -- "Bird Hippie" 4076
machv2macOS 10.14.6 Mojavex86_644.1.2 (2021-11-01) -- "Bird Hippie" 4137
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 tokay2


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? here for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 1944/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ternarynet 1.38.0  (landing page)
McCall N. Matthew
Snapshot Date: 2022-01-13 01:55:04 -0500 (Thu, 13 Jan 2022)
git_url: https://git.bioconductor.org/packages/ternarynet
git_branch: RELEASE_3_14
git_last_commit: a463985
git_last_commit_date: 2021-10-26 12:02:04 -0500 (Tue, 26 Oct 2021)
nebbiolo2Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: ternarynet
Version: 1.38.0
Command: C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:ternarynet.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings ternarynet_1.38.0.tar.gz
StartedAt: 2022-01-14 03:21:57 -0500 (Fri, 14 Jan 2022)
EndedAt: 2022-01-14 03:24:14 -0500 (Fri, 14 Jan 2022)
EllapsedTime: 136.6 seconds
RetCode: 0
Status:   OK  
CheckDir: ternarynet.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:ternarynet.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings ternarynet_1.38.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.14-bioc/meat/ternarynet.Rcheck'
* using R version 4.1.2 (2021-11-01)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'ternarynet/DESCRIPTION' ... OK
* this is package 'ternarynet' version '1.38.0'
* 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
* 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 i386 is not available
Note: information on .o files for x64 is not available
File 'C:/Users/biocbuild/bbs-3.14-bioc/R/library/ternarynet/libs/i386/ternarynet.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
  Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
  Found 'printf', possibly from 'printf' (C)
File 'C:/Users/biocbuild/bbs-3.14-bioc/R/library/ternarynet/libs/x64/ternarynet.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
  Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
  Found 'printf', possibly from 'printf' (C)

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. 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 files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
** running examples for arch 'x64' ... OK
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'test_smallmodel.R'
  Running 'test_smallmodel_2.R'
 OK
** running tests for arch 'x64' ...
  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
  'C:/Users/biocbuild/bbs-3.14-bioc/meat/ternarynet.Rcheck/00check.log'
for details.



Installation output

ternarynet.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.14/bioc/src/contrib/ternarynet_1.38.0.tar.gz && rm -rf ternarynet.buildbin-libdir && mkdir ternarynet.buildbin-libdir && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=ternarynet.buildbin-libdir ternarynet_1.38.0.tar.gz && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL ternarynet_1.38.0.zip && rm ternarynet_1.38.0.tar.gz ternarynet_1.38.0.zip
###
##############################################################################
##############################################################################


  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100 43109  100 43109    0     0   389k      0 --:--:-- --:--:-- --:--:--  389k

install for i386

* installing *source* package 'ternarynet' ...
** using staged installation
** libs
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c array.c -o array.o
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -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]
 #pragma omp parallel for
 
gn.c:493: warning: ignoring #pragma omp atomic [-Wunknown-pragmas]
 #pragma omp atomic
 
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c gn_Rwrap.c -o gn_Rwrap.o
In file included from C:/Users/BIOCBU~1/BBS-3~1.14-/R/include/R.h:71,
                 from gn_Rwrap.h:4,
                 from gn_Rwrap.c:1:
C:/Users/BIOCBU~1/BBS-3~1.14-/R/include/R_ext/Arith.h:58:18: warning: 'R_NaReal' redeclared without dllimport attribute: previous dllimport ignored [-Wattributes]
 #define NA_REAL  R_NaReal
                  ^~~~~~~~
C:/Users/BIOCBU~1/BBS-3~1.14-/R/include/Rmath.h:643:17: note: in expansion of macro 'NA_REAL'
 R_EXTERN double NA_REAL;
                 ^~~~~~~
In file included from gn_Rwrap.c:9:
C:/Users/BIOCBU~1/BBS-3~1.14-/R/include/Rmath.h:644:17: warning: 'R_PosInf' redeclared without dllimport attribute: previous dllimport ignored [-Wattributes]
 R_EXTERN double R_PosInf;
                 ^~~~~~~~
C:/Users/BIOCBU~1/BBS-3~1.14-/R/include/Rmath.h:645:17: warning: 'R_NegInf' redeclared without dllimport attribute: previous dllimport ignored [-Wattributes]
 R_EXTERN double R_NegInf;
                 ^~~~~~~~
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c init.c -o init.o
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG     -I"C:/extsoft/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]
     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;
                                      ^~~~~~~~~~~
tnetfit.cc:73:39: warning: unused variable 'tempi' [-Wunused-variable]
     int nOutcomes=3, l0, stage_count, tempi, jtrans, nTransition;
                                       ^~~~~
tnetfit.cc:311:19: warning: 'newScore' may be used uninitialized in this function [-Wmaybe-uninitialized]
     SET_VECTOR_ELT(Routput, 10, ScalarReal(newScore));
     ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
tnetfit.cc:207:25: warning: 'muci_old' may be used uninitialized in this function [-Wmaybe-uninitialized]
      convergence = (muci-muci_old)/sigma0;
                    ~~~~~^~~~~~~~~~
tnetfit.cc:202:36: warning: 'sigmaci' may be used uninitialized in this function [-Wmaybe-uninitialized]
    sigmaci = rho*sigmaRaw + (1-rho)*sigmaci;
                             ~~~~~~~^~~~~~~~
tnetfit.cc:207:18: warning: 'sigma0' may be used uninitialized in this function [-Wmaybe-uninitialized]
      convergence = (muci-muci_old)/sigma0;
      ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG     -I"C:/extsoft/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]
 int tableWidth = powi(nOutcomes,maxDegree);
     ^~~~~~~~~~
tnetfuncs.cc:435:5: warning: unused variable 'ipause' [-Wunused-variable]
 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]
  int ipause;
      ^~~~~~
tnetfuncs.cc:521:16: warning: unused variable 'i' [-Wunused-variable]
    int m1, m2, i;
                ^
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG     -I"C:/extsoft/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]
     int ipause;
         ^~~~~~
tnetpost.cc:27:9: warning: unused variable 'm0fit' [-Wunused-variable]
     int m0fit;
         ^~~~~
tnetpost.cc:28:32: warning: variable 'minScore' set but not used [-Wunused-but-set-variable]
     double newScore, oldScore, minScore, finalScore;
                                ^~~~~~~~
tnetpost.cc:28:42: warning: unused variable 'finalScore' [-Wunused-variable]
     double newScore, oldScore, minScore, finalScore;
                                          ^~~~~~~~~~
tnetpost.cc:30:9: warning: unused variable 'l0' [-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:30:26: warning: unused variable 'tempi' [-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:30:41: warning: unused variable 'nTransition' [-Wunused-variable]
     int l0, stage_count, tempi, jtrans, nTransition;
                                         ^~~~~~~~~~~
tnetpost.cc:36:21: warning: variable 'xSeedFit' set but not used [-Wunused-but-set-variable]
     int m0, mdelta, xSeedFit;
                     ^~~~~~~~
tnetpost.cc:38:9: warning: variable 'perturbationType' set but not used [-Wunused-but-set-variable]
     int perturbationType, scoreType, backupStage;
         ^~~~~~~~~~~~~~~~
tnetpost.cc:38:27: warning: variable 'scoreType' set but not used [-Wunused-but-set-variable]
     int perturbationType, scoreType, backupStage;
                           ^~~~~~~~~
tnetpost.cc:38:38: warning: variable 'backupStage' set but not used [-Wunused-but-set-variable]
     int perturbationType, scoreType, backupStage;
                                      ^~~~~~~~~~~
tnetpost.cc:39:9: warning: variable 'maxStage' set but not used [-Wunused-but-set-variable]
     int maxStage, maxTransition;
         ^~~~~~~~
tnetpost.cc:39:19: warning: variable 'maxTransition' set but not used [-Wunused-but-set-variable]
     int maxStage, maxTransition;
                   ^~~~~~~~~~~~~
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:40:34: warning: variable 'rho' set but not used [-Wunused-but-set-variable]
     double epsilon, chi0, delta, rho;
                                  ^~~
In file included from tnetpost.cc:14:
C:/Users/BIOCBU~1/BBS-3~1.14-/R/include/Rmath.h:208:15: warning: variable 'Rf_beta' set but not used [-Wunused-but-set-variable]
 #define beta  Rf_beta
               ^~~~~~~
tnetpost.cc:41:9: note: in expansion of macro 'beta'
     int beta;
         ^~~~
tnetpost.cc:44:9: warning: variable 'ne' set but not used [-Wunused-but-set-variable]
     int ne, maxDegree;
         ^~
tnetpost.cc:150:10: warning: variable 'minDump' set but not used [-Wunused-but-set-variable]
     bool minDump = true;
          ^~~~~~~
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c util.c -o util.o
C:/rtools40/mingw32/bin/g++ -std=gnu++11 -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:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.14-/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.14-bioc/meat/ternarynet.buildbin-libdir/00LOCK-ternarynet/00new/ternarynet/libs/i386
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'ternarynet'
    finding HTML links ... done
    attractorSummary                        html  
    graphPosterior                          html  
    parallelFit                             html  
    plotFit                                 html  
    plotPost                                html  
    plotTraces                              html  
    predictAttractor                        html  
    simulateSteadyState                     html  
    ternaryFit-class                        html  
    ternaryFitParameters-class              html  
    ternaryPost-class                       html  
    tnetfit                                 html  
    tnetpost                                html  
** 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

install for x64

* installing *source* package 'ternarynet' ...
** libs
"C:/rtools40/mingw64/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c array.c -o array.o
"C:/rtools40/mingw64/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -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]
 #pragma omp parallel for
 
gn.c:493: warning: ignoring #pragma omp atomic [-Wunknown-pragmas]
 #pragma omp atomic
 
"C:/rtools40/mingw64/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c gn_Rwrap.c -o gn_Rwrap.o
In file included from C:/Users/BIOCBU~1/BBS-3~1.14-/R/include/R.h:71,
                 from gn_Rwrap.h:4,
                 from gn_Rwrap.c:1:
C:/Users/BIOCBU~1/BBS-3~1.14-/R/include/R_ext/Arith.h:58:18: warning: 'R_NaReal' redeclared without dllimport attribute: previous dllimport ignored [-Wattributes]
 #define NA_REAL  R_NaReal
                  ^~~~~~~~
C:/Users/BIOCBU~1/BBS-3~1.14-/R/include/Rmath.h:643:17: note: in expansion of macro 'NA_REAL'
 R_EXTERN double NA_REAL;
                 ^~~~~~~
In file included from gn_Rwrap.c:9:
C:/Users/BIOCBU~1/BBS-3~1.14-/R/include/Rmath.h:644:17: warning: 'R_PosInf' redeclared without dllimport attribute: previous dllimport ignored [-Wattributes]
 R_EXTERN double R_PosInf;
                 ^~~~~~~~
C:/Users/BIOCBU~1/BBS-3~1.14-/R/include/Rmath.h:645:17: warning: 'R_NegInf' redeclared without dllimport attribute: previous dllimport ignored [-Wattributes]
 R_EXTERN double R_NegInf;
                 ^~~~~~~~
"C:/rtools40/mingw64/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c init.c -o init.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG     -I"C:/extsoft/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]
     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;
                                      ^~~~~~~~~~~
tnetfit.cc:73:39: warning: unused variable 'tempi' [-Wunused-variable]
     int nOutcomes=3, l0, stage_count, tempi, jtrans, nTransition;
                                       ^~~~~
tnetfit.cc:311:19: warning: 'newScore' may be used uninitialized in this function [-Wmaybe-uninitialized]
     SET_VECTOR_ELT(Routput, 10, ScalarReal(newScore));
     ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
tnetfit.cc:207:25: warning: 'muci_old' may be used uninitialized in this function [-Wmaybe-uninitialized]
      convergence = (muci-muci_old)/sigma0;
                    ~~~~~^~~~~~~~~~
tnetfit.cc:202:36: warning: 'sigmaci' may be used uninitialized in this function [-Wmaybe-uninitialized]
    sigmaci = rho*sigmaRaw + (1-rho)*sigmaci;
                             ~~~~~~~^~~~~~~~
tnetfit.cc:207:18: warning: 'sigma0' may be used uninitialized in this function [-Wmaybe-uninitialized]
      convergence = (muci-muci_old)/sigma0;
      ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG     -I"C:/extsoft/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]
 int tableWidth = powi(nOutcomes,maxDegree);
     ^~~~~~~~~~
tnetfuncs.cc:435:5: warning: unused variable 'ipause' [-Wunused-variable]
 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]
  int ipause;
      ^~~~~~
tnetfuncs.cc:521:16: warning: unused variable 'i' [-Wunused-variable]
    int m1, m2, i;
                ^
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG     -I"C:/extsoft/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]
     int ipause;
         ^~~~~~
tnetpost.cc:27:9: warning: unused variable 'm0fit' [-Wunused-variable]
     int m0fit;
         ^~~~~
tnetpost.cc:28:32: warning: variable 'minScore' set but not used [-Wunused-but-set-variable]
     double newScore, oldScore, minScore, finalScore;
                                ^~~~~~~~
tnetpost.cc:28:42: warning: unused variable 'finalScore' [-Wunused-variable]
     double newScore, oldScore, minScore, finalScore;
                                          ^~~~~~~~~~
tnetpost.cc:30:9: warning: unused variable 'l0' [-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:30:26: warning: unused variable 'tempi' [-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:30:41: warning: unused variable 'nTransition' [-Wunused-variable]
     int l0, stage_count, tempi, jtrans, nTransition;
                                         ^~~~~~~~~~~
tnetpost.cc:36:21: warning: variable 'xSeedFit' set but not used [-Wunused-but-set-variable]
     int m0, mdelta, xSeedFit;
                     ^~~~~~~~
tnetpost.cc:38:9: warning: variable 'perturbationType' set but not used [-Wunused-but-set-variable]
     int perturbationType, scoreType, backupStage;
         ^~~~~~~~~~~~~~~~
tnetpost.cc:38:27: warning: variable 'scoreType' set but not used [-Wunused-but-set-variable]
     int perturbationType, scoreType, backupStage;
                           ^~~~~~~~~
tnetpost.cc:38:38: warning: variable 'backupStage' set but not used [-Wunused-but-set-variable]
     int perturbationType, scoreType, backupStage;
                                      ^~~~~~~~~~~
tnetpost.cc:39:9: warning: variable 'maxStage' set but not used [-Wunused-but-set-variable]
     int maxStage, maxTransition;
         ^~~~~~~~
tnetpost.cc:39:19: warning: variable 'maxTransition' set but not used [-Wunused-but-set-variable]
     int maxStage, maxTransition;
                   ^~~~~~~~~~~~~
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:40:34: warning: variable 'rho' set but not used [-Wunused-but-set-variable]
     double epsilon, chi0, delta, rho;
                                  ^~~
In file included from tnetpost.cc:14:
C:/Users/BIOCBU~1/BBS-3~1.14-/R/include/Rmath.h:208:15: warning: variable 'Rf_beta' set but not used [-Wunused-but-set-variable]
 #define beta  Rf_beta
               ^~~~~~~
tnetpost.cc:41:9: note: in expansion of macro 'beta'
     int beta;
         ^~~~
tnetpost.cc:44:9: warning: variable 'ne' set but not used [-Wunused-but-set-variable]
     int ne, maxDegree;
         ^~
tnetpost.cc:150:10: warning: variable 'minDump' set but not used [-Wunused-but-set-variable]
     bool minDump = true;
          ^~~~~~~
"C:/rtools40/mingw64/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c util.c -o util.o
C:/rtools40/mingw64/bin/g++ -std=gnu++11 -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:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.14-/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.14-bioc/meat/ternarynet.buildbin-libdir/ternarynet/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'ternarynet' as ternarynet_1.38.0.zip
* DONE (ternarynet)
* installing to library 'C:/Users/biocbuild/bbs-3.14-bioc/R/library'
package 'ternarynet' successfully unpacked and MD5 sums checked

Tests output

ternarynet.Rcheck/tests_i386/test_smallmodel.Rout


R version 4.1.2 (2021-11-01) -- "Bird Hippie"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-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 
    1.4     0.1     1.5 

ternarynet.Rcheck/tests_x64/test_smallmodel.Rout


R version 4.1.2 (2021-11-01) -- "Bird Hippie"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (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 
   1.59    0.12    1.68 

ternarynet.Rcheck/tests_i386/test_smallmodel_2.Rout


R version 4.1.2 (2021-11-01) -- "Bird Hippie"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-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 
   1.81    0.10    1.90 

ternarynet.Rcheck/tests_x64/test_smallmodel_2.Rout


R version 4.1.2 (2021-11-01) -- "Bird Hippie"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (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 
   1.68    0.09    1.76 

Example timings

ternarynet.Rcheck/examples_i386/ternarynet-Ex.timings

nameusersystemelapsed
attractorSummary4.960.004.95
graphPosterior4.250.004.25
parallelFit0.140.000.14
plotFit3.890.003.89
plotPost4.330.004.33
plotTraces3.750.013.77
predictAttractor4.080.004.07
simulateSteadyState000
ternaryFit-class3.80.03.8
ternaryFitParameters-class000
ternaryPost-class3.780.003.78
tnetfit3.720.003.72
tnetpost3.750.003.75

ternarynet.Rcheck/examples_x64/ternarynet-Ex.timings

nameusersystemelapsed
attractorSummary3.450.003.46
graphPosterior3.250.003.25
parallelFit0.170.000.17
plotFit3.270.003.26
plotPost3.170.003.18
plotTraces3.640.013.65
predictAttractor3.030.003.03
simulateSteadyState000
ternaryFit-class3.170.003.17
ternaryFitParameters-class0.020.000.02
ternaryPost-class3.150.003.15
tnetfit3.330.003.33
tnetpost3.190.003.19