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### Running command:
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### F:\biocbuild\bbs-3.16-bioc\R\bin\R.exe CMD INSTALL ternarynet
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* installing to library 'F:/biocbuild/bbs-3.16-bioc/R/library'
* installing *source* package 'ternarynet' ...
** using staged installation
** libs
gcc -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c array.c -o array.o
gcc -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I"C:/rtools42/x86_64-w64-mingw32.static.posix/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]
486 | #pragma omp parallel for
|
gn.c:493: warning: ignoring '#pragma omp atomic' [-Wunknown-pragmas]
493 | #pragma omp atomic
|
gcc -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c gn_Rwrap.c -o gn_Rwrap.o
In file included from F:/biocbuild/bbs-3.16-bioc/R/include/R.h:71,
from gn_Rwrap.h:4,
from gn_Rwrap.c:1:
F:/biocbuild/bbs-3.16-bioc/R/include/R_ext/Arith.h:58:18: warning: 'R_NaReal' redeclared without dllimport attribute: previous dllimport ignored [-Wattributes]
58 | #define NA_REAL R_NaReal
| ^~~~~~~~
F:/biocbuild/bbs-3.16-bioc/R/include/Rmath.h:645:17: note: in expansion of macro 'NA_REAL'
645 | R_EXTERN double NA_REAL;
| ^~~~~~~
In file included from gn_Rwrap.c:9:
F:/biocbuild/bbs-3.16-bioc/R/include/Rmath.h:646:17: warning: 'R_PosInf' redeclared without dllimport attribute: previous dllimport ignored [-Wattributes]
646 | R_EXTERN double R_PosInf;
| ^~~~~~~~
F:/biocbuild/bbs-3.16-bioc/R/include/Rmath.h:647:17: warning: 'R_NegInf' redeclared without dllimport attribute: previous dllimport ignored [-Wattributes]
647 | R_EXTERN double R_NegInf;
| ^~~~~~~~
gcc -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c init.c -o init.o
g++ -std=gnu++14 -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I"C:/rtools42/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:311:19: warning: 'newScore' may be used uninitialized in this function [-Wmaybe-uninitialized]
311 | SET_VECTOR_ELT(Routput, 10, ScalarReal(newScore));
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
tnetfit.cc:207:25: warning: 'muci_old' may be used uninitialized in this function [-Wmaybe-uninitialized]
207 | convergence = (muci-muci_old)/sigma0;
| ~~~~~^~~~~~~~~~
tnetfit.cc:202:36: warning: 'sigmaci' may be used uninitialized in this function [-Wmaybe-uninitialized]
202 | sigmaci = rho*sigmaRaw + (1-rho)*sigmaci;
| ~~~~~~~^~~~~~~~
tnetfit.cc:207:18: warning: 'sigma0' may be used uninitialized in this function [-Wmaybe-uninitialized]
207 | convergence = (muci-muci_old)/sigma0;
| ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~
g++ -std=gnu++14 -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I"C:/rtools42/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:517:6: warning: unused variable 'ipause' [-Wunused-variable]
517 | int ipause;
| ^~~~~~
tnetfuncs.cc:521:16: warning: unused variable 'i' [-Wunused-variable]
521 | int m1, m2, i;
| ^
g++ -std=gnu++14 -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I"C:/rtools42/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-3.16-bioc/R/include/Rmath.h:210:15: warning: variable 'Rf_beta' set but not used [-Wunused-but-set-variable]
210 | #define beta Rf_beta
| ^~~~~~~
tnetpost.cc:41:9: note: in expansion of macro 'beta'
41 | int beta;
| ^~~~
tnetpost.cc:44:9: warning: variable 'ne' set but not used [-Wunused-but-set-variable]
44 | int ne, maxDegree;
| ^~
tnetpost.cc:150:10: warning: variable 'minDump' set but not used [-Wunused-but-set-variable]
150 | bool minDump = true;
| ^~~~~~~
gcc -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c util.c -o util.o
g++ -std=gnu++14 -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:/rtools42/x86_64-w64-mingw32.static.posix/lib/x64 -LC:/rtools42/x86_64-w64-mingw32.static.posix/lib -LF:/biocbuild/bbs-3.16-bioc/R/bin/x64 -lR
installing to F:/biocbuild/bbs-3.16-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)
