| Back to Multiple platform build/check report for BioC 3.13 |
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This page was generated on 2021-10-15 15:06:25 -0400 (Fri, 15 Oct 2021).
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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. |
| Package 1906/2041 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| ternarynet 1.36.0 (landing page) McCall N. Matthew
| nebbiolo1 | Linux (Ubuntu 20.04.2 LTS) / x86_64 | OK | OK | OK |  | ||||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | | ||||||||
| machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | | ||||||||
| Package: ternarynet |
| Version: 1.36.0 |
| Command: C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:ternarynet.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings ternarynet_1.36.0.tar.gz |
| StartedAt: 2021-10-15 06:32:01 -0400 (Fri, 15 Oct 2021) |
| EndedAt: 2021-10-15 06:34:14 -0400 (Fri, 15 Oct 2021) |
| EllapsedTime: 133.6 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: ternarynet.Rcheck |
| Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:ternarynet.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings ternarynet_1.36.0.tar.gz ### ############################################################################## ############################################################################## * using log directory 'C:/Users/biocbuild/bbs-3.13-bioc/meat/ternarynet.Rcheck' * using R version 4.1.1 (2021-08-10) * 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 '1.36.0' * 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-3.13-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-3.13-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-3.13-bioc/meat/ternarynet.Rcheck/00check.log' for details.
ternarynet.Rcheck/00install.out
##############################################################################
##############################################################################
###
### Running command:
###
### C:\cygwin\bin\curl.exe -O http://155.52.207.165/BBS/3.13/bioc/src/contrib/ternarynet_1.36.0.tar.gz && rm -rf ternarynet.buildbin-libdir && mkdir ternarynet.buildbin-libdir && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=ternarynet.buildbin-libdir ternarynet_1.36.0.tar.gz && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL ternarynet_1.36.0.zip && rm ternarynet_1.36.0.tar.gz ternarynet_1.36.0.zip
###
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% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0
100 41751 100 41751 0 0 267k 0 --:--:-- --:--:-- --:--:-- 270k
install for i386
* installing *source* package 'ternarynet' ...
** using staged installation
** libs
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/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-3~1.13-/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:506: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
#pragma omp parallel for
gn.c:513: warning: ignoring #pragma omp atomic [-Wunknown-pragmas]
#pragma omp atomic
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/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-3~1.13-/R/include/R.h:82,
from gn_Rwrap.h:4,
from gn_Rwrap.c:1:
C:/Users/BIOCBU~1/BBS-3~1.13-/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-3~1.13-/R/include/Rmath.h:647:17: 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-3~1.13-/R/include/Rmath.h:648:17: warning: 'R_PosInf' redeclared without dllimport attribute: previous dllimport ignored [-Wattributes]
R_EXTERN double R_PosInf;
^~~~~~~~
C:/Users/BIOCBU~1/BBS-3~1.13-/R/include/Rmath.h:649:17: 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-3~1.13-/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-3~1.13-/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-3~1.13-/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-3~1.13-/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-3~1.13-/R/include/Rmath.h:212:15: 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-3~1.13-/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-3~1.13-/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.13-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-3~1.13-/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-3~1.13-/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:506: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
#pragma omp parallel for
gn.c:513: warning: ignoring #pragma omp atomic [-Wunknown-pragmas]
#pragma omp atomic
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/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-3~1.13-/R/include/R.h:82,
from gn_Rwrap.h:4,
from gn_Rwrap.c:1:
C:/Users/BIOCBU~1/BBS-3~1.13-/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-3~1.13-/R/include/Rmath.h:647:17: 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-3~1.13-/R/include/Rmath.h:648:17: warning: 'R_PosInf' redeclared without dllimport attribute: previous dllimport ignored [-Wattributes]
R_EXTERN double R_PosInf;
^~~~~~~~
C:/Users/BIOCBU~1/BBS-3~1.13-/R/include/Rmath.h:649:17: 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-3~1.13-/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-3~1.13-/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-3~1.13-/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-3~1.13-/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-3~1.13-/R/include/Rmath.h:212:15: 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-3~1.13-/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-3~1.13-/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.13-bioc/meat/ternarynet.buildbin-libdir/ternarynet/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'ternarynet' as ternarynet_1.36.0.zip
* DONE (ternarynet)
* installing to library 'C:/Users/biocbuild/bbs-3.13-bioc/R/library'
package 'ternarynet' successfully unpacked and MD5 sums checked
|
ternarynet.Rcheck/tests_i386/test_smallmodel.Rout
R version 4.1.1 (2021-08-10) -- "Kick Things"
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=100000,
+ 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
1.40 0.09 1.46
|
ternarynet.Rcheck/tests_x64/test_smallmodel.Rout
R version 4.1.1 (2021-08-10) -- "Kick Things"
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=100000,
+ 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
1.34 0.09 1.42
|
|
ternarynet.Rcheck/tests_i386/test_smallmodel_2.Rout
R version 4.1.1 (2021-08-10) -- "Kick Things"
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=100000,
+ 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
1.40 0.07 1.45
|
ternarynet.Rcheck/tests_x64/test_smallmodel_2.Rout
R version 4.1.1 (2021-08-10) -- "Kick Things"
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=100000,
+ 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
1.48 0.06 1.53
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ternarynet.Rcheck/examples_i386/ternarynet-Ex.timings
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ternarynet.Rcheck/examples_x64/ternarynet-Ex.timings
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