* installing *source* package 'HDclust' ...
** package 'HDclust' successfully unpacked and MD5 sums checked
** using staged installation
**********************************************
WARNING: this package has a configure script
It probably needs manual configuration
**********************************************
** libs
using C++ compiler: 'g++.exe (GCC) 13.2.0'
make[1]: Entering directory '/d/temp/RtmpAj5hhs/R.INSTALL2d1e4170c22e/HDclust/src'
g++ -std=gnu++17 -I"D:/RCompile/recent/R-4.4.0/include" -DNDEBUG -I'D:/RCompile/CRANpkg/lib/4.4/Rcpp/include' -I'D:/RCompile/CRANpkg/lib/4.4/RcppProgress/include' -I"d:/rtools44/x86_64-w64-mingw32.static.posix/include" -pedantic -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++17 -I"D:/RCompile/recent/R-4.4.0/include" -DNDEBUG -I'D:/RCompile/CRANpkg/lib/4.4/Rcpp/include' -I'D:/RCompile/CRANpkg/lib/4.4/RcppProgress/include' -I"d:/rtools44/x86_64-w64-mingw32.static.posix/include" -pedantic -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c cluster.cpp -o cluster.o
g++ -std=gnu++17 -I"D:/RCompile/recent/R-4.4.0/include" -DNDEBUG -I'D:/RCompile/CRANpkg/lib/4.4/Rcpp/include' -I'D:/RCompile/CRANpkg/lib/4.4/RcppProgress/include' -I"d:/rtools44/x86_64-w64-mingw32.static.posix/include" -pedantic -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c estimate.cpp -o estimate.o
estimate.cpp:1030: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas]
1030 | #pragma omp parallel private(i, ii, j, k, m, mu, mom2, l1img, a, thetalog, betalog)
|
estimate.cpp:1064: warning: ignoring '#pragma omp master' [-Wunknown-pragmas]
1064 | #pragma omp master
|
estimate.cpp:1081: warning: ignoring '#pragma omp barrier' [-Wunknown-pragmas]
1081 | #pragma omp barrier
|
estimate.cpp:1083: warning: ignoring '#pragma omp for' [-Wunknown-pragmas]
1083 | #pragma omp for private(t, l)
|
estimate.cpp:1092: warning: ignoring '#pragma omp atomic' [-Wunknown-pragmas]
1092 | #pragma omp atomic
|
estimate.cpp:1096: warning: ignoring '#pragma omp atomic' [-Wunknown-pragmas]
1096 | #pragma omp atomic
|
estimate.cpp:1100: warning: ignoring '#pragma omp atomic' [-Wunknown-pragmas]
1100 | #pragma omp atomic
|
estimate.cpp:1106: warning: ignoring '#pragma omp atomic' [-Wunknown-pragmas]
1106 | #pragma omp atomic
|
estimate.cpp:1112: warning: ignoring '#pragma omp atomic' [-Wunknown-pragmas]
1112 | #pragma omp atomic
|
estimate.cpp:1117: warning: ignoring '#pragma omp master' [-Wunknown-pragmas]
1117 | #pragma omp master
|
estimate.cpp:1188: warning: ignoring '#pragma omp barrier' [-Wunknown-pragmas]
1188 | #pragma omp barrier
|
estimate.cpp:1192: warning: ignoring '#pragma omp master' [-Wunknown-pragmas]
1192 | #pragma omp master
|
estimate.cpp:1266: warning: ignoring '#pragma omp barrier' [-Wunknown-pragmas]
1266 | #pragma omp barrier
|
estimate.cpp: In function 'void findbuddy(int*, int*, int*, int, int**, double*, int**, int, int, int)':
estimate.cpp:1689:25: warning: 'v3' may be used uninitialized [-Wmaybe-uninitialized]
1689 | if (skipped[i]==0 && lhsum[i]>v3) {
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~
estimate.cpp:1678:10: note: 'v3' was declared here
1678 | double v3;
| ^~
estimate.cpp: In function 'int baumwelch(double**, int, CondChain*, double*, double*, double, double*)':
estimate.cpp:1295:11: warning: 'lhsum' may be used uninitialized [-Wmaybe-uninitialized]
1295 | *lhsumpt=lhsum;
| ~~~~~~~~^~~~~~
estimate.cpp:986:20: note: 'lhsum' was declared here
986 | double oldlhsum, lhsum;
| ^~~~~
estimate.cpp: In function 'void hmmfit_vb(double**, int, int, int*, int**, int***, int, int, int**, CondChain**, double*, double*, double, double*, int, int, int, int, int*, int, int, int)':
estimate.cpp:1917:17: warning: 'v0' may be used uninitialized [-Wmaybe-uninitialized]
1917 | lhsum1[k1]=v0; //no change occurred, record the best BIC
| ~~~~~~~~~~^~~
estimate.cpp:1787:27: note: 'v0' was declared here
1787 | double *lhsum, *lhsum1, v0,v1;
| ^~
g++ -std=gnu++17 -I"D:/RCompile/recent/R-4.4.0/include" -DNDEBUG -I'D:/RCompile/CRANpkg/lib/4.4/Rcpp/include' -I'D:/RCompile/CRANpkg/lib/4.4/RcppProgress/include' -I"d:/rtools44/x86_64-w64-mingw32.static.posix/include" -pedantic -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c matrix.cpp -o matrix.o
matrix.cpp: In function 'unsigned char ludcmp_float(float**, int, int*, float*)':
matrix.cpp:919:10: warning: 'vv' may be used uninitialized [-Wmaybe-uninitialized]
919 | vv[i]=1.0/big;
| ~~~~~^~~~~~~~
matrix.cpp:902:10: note: 'vv' was declared here
902 | float *vv;
| ^~
matrix.cpp:940:5: warning: 'imax' may be used uninitialized [-Wmaybe-uninitialized]
940 | if (j!=imax) {
| ^~
matrix.cpp:900:9: note: 'imax' was declared here
900 | int i,imax,j,k;
| ^~~~
matrix.cpp: In function 'unsigned char ludcmp_double(double**, int, int*, double*)':
matrix.cpp:984:10: warning: 'vv' may be used uninitialized [-Wmaybe-uninitialized]
984 | vv[i]=1.0/big;
| ~~~~~^~~~~~~~
matrix.cpp:967:11: note: 'vv' was declared here
967 | double *vv;
| ^~
matrix.cpp:1005:5: warning: 'imax' may be used uninitialized [-Wmaybe-uninitialized]
1005 | if (j!=imax) {
| ^~
matrix.cpp:965:9: note: 'imax' was declared here
965 | int i,imax,j,k;
| ^~~~
matrix.cpp: In function 'unsigned char mat_inv_float(float**, float**, int)':
matrix.cpp:1105:7: warning: 'col' may be used uninitialized [-Wmaybe-uninitialized]
1105 | free(col);
| ~~~~^~~~~
matrix.cpp:1073:13: note: 'col' was declared here
1073 | float d, *col;
| ^~~
matrix.cpp:1096:15: warning: 'indx' may be used uninitialized [-Wmaybe-uninitialized]
1096 | ludcmp_float(a,dim,indx,&d);
| ~~~~~~~~~~~~^~~~~~~~~~~~~~~
matrix.cpp:1074:12: note: 'indx' was declared here
1074 | int i,j,*indx;
| ^~~~
matrix.cpp: In function 'unsigned char mat_inv_double(double**, double**, int)':
matrix.cpp:1145:7: warning: 'col' may be used uninitialized [-Wmaybe-uninitialized]
1145 | free(col);
| ~~~~^~~~~
matrix.cpp:1113:14: note: 'col' was declared here
1113 | double d, *col;
| ^~~
matrix.cpp:1136:16: warning: 'indx' may be used uninitialized [-Wmaybe-uninitialized]
1136 | ludcmp_double(a,dim,indx,&d);
| ~~~~~~~~~~~~~^~~~~~~~~~~~~~~
matrix.cpp:1114:12: note: 'indx' was declared here
1114 | int i,j,*indx;
| ^~~~
matrix.cpp: In function 'unsigned char mat_det_inv_double(double**, double**, double*, int)':
matrix.cpp:1291:7: warning: 'col' may be used uninitialized [-Wmaybe-uninitialized]
1291 | free(col);
| ~~~~^~~~~
matrix.cpp:1244:14: note: 'col' was declared here
1244 | double d, *col;
| ^~~
matrix.cpp:1270:18: warning: 'indx' may be used uninitialized [-Wmaybe-uninitialized]
1270 | m=ludcmp_double(a,dim,indx,&d);
| ~~~~~~~~~~~~~^~~~~~~~~~~~~~~
matrix.cpp:1245:14: note: 'indx' was declared here
1245 | int i,j,m,*indx;
| ^~~~
matrix.cpp: In function 'unsigned char mat_det_inv_float(float**, float**, float*, int)':
matrix.cpp:1367:7: warning: 'col' may be used uninitialized [-Wmaybe-uninitialized]
1367 | free(col);
| ~~~~^~~~~
matrix.cpp:1321:13: note: 'col' was declared here
1321 | float d, *col;
| ^~~
matrix.cpp:1347:17: warning: 'indx' may be used uninitialized [-Wmaybe-uninitialized]
1347 | m=ludcmp_float(a,dim,indx,&d);
| ~~~~~~~~~~~~^~~~~~~~~~~~~~~
matrix.cpp:1322:14: note: 'indx' was declared here
1322 | int i,j,m,*indx;
| ^~~~
matrix.cpp: In function 'float mat_det_ludcmp_float(float**, int)':
matrix.cpp:1185:15: warning: 'indx' may be used uninitialized [-Wmaybe-uninitialized]
1185 | ludcmp_float(a,dim,indx,&d);
| ~~~~~~~~~~~~^~~~~~~~~~~~~~~
matrix.cpp:1154:13: note: 'indx' was declared here
1154 | int i,j, *indx;
| ^~~~
matrix.cpp: In function 'double mat_det_ludcmp_double(double**, int)':
matrix.cpp:1227:16: warning: 'indx' may be used uninitialized [-Wmaybe-uninitialized]
1227 | ludcmp_double(a,dim,indx,&d);
| ~~~~~~~~~~~~~^~~~~~~~~~~~~~~
matrix.cpp:1196:14: note: 'indx' was declared here
1196 | int i, j, *indx;
| ^~~~
g++ -std=gnu++17 -I"D:/RCompile/recent/R-4.4.0/include" -DNDEBUG -I'D:/RCompile/CRANpkg/lib/4.4/Rcpp/include' -I'D:/RCompile/CRANpkg/lib/4.4/RcppProgress/include' -I"d:/rtools44/x86_64-w64-mingw32.static.posix/include" -pedantic -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c modal.cpp -o modal.o
g++ -std=gnu++17 -I"D:/RCompile/recent/R-4.4.0/include" -DNDEBUG -I'D:/RCompile/CRANpkg/lib/4.4/Rcpp/include' -I'D:/RCompile/CRANpkg/lib/4.4/RcppProgress/include' -I"d:/rtools44/x86_64-w64-mingw32.static.posix/include" -pedantic -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c prob.cpp -o prob.o
g++ -std=gnu++17 -I"D:/RCompile/recent/R-4.4.0/include" -DNDEBUG -I'D:/RCompile/CRANpkg/lib/4.4/Rcpp/include' -I'D:/RCompile/CRANpkg/lib/4.4/RcppProgress/include' -I"d:/rtools44/x86_64-w64-mingw32.static.posix/include" -pedantic -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c rcpp_findModes.cpp -o rcpp_findModes.o
rcpp_findModes.cpp:145: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas]
145 | #pragma omp parallel
|
rcpp_findModes.cpp:149: warning: ignoring '#pragma omp for' [-Wunknown-pragmas]
149 | #pragma omp for
|
g++ -std=gnu++17 -I"D:/RCompile/recent/R-4.4.0/include" -DNDEBUG -I'D:/RCompile/CRANpkg/lib/4.4/Rcpp/include' -I'D:/RCompile/CRANpkg/lib/4.4/RcppProgress/include' -I"d:/rtools44/x86_64-w64-mingw32.static.posix/include" -pedantic -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c rcpp_testsync.cpp -o rcpp_testsync.o
rcpp_testsync.cpp:533: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas]
533 | #pragma omp parallel
|
rcpp_testsync.cpp:537: warning: ignoring '#pragma omp for' [-Wunknown-pragmas]
537 | #pragma omp for
|
g++ -std=gnu++17 -I"D:/RCompile/recent/R-4.4.0/include" -DNDEBUG -I'D:/RCompile/CRANpkg/lib/4.4/Rcpp/include' -I'D:/RCompile/CRANpkg/lib/4.4/RcppProgress/include' -I"d:/rtools44/x86_64-w64-mingw32.static.posix/include" -pedantic -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c rcpp_trainmaster.cpp -o rcpp_trainmaster.o
rcpp_trainmaster.cpp: In function 'Rcpp::S4 rcpp_trainHmmVb(Rcpp::NumericMatrix, const Rcpp::RObject&, const Rcpp::List&, const Rcpp::List&, Rcpp::IntegerVector, Rcpp::Function, Rcpp::Function, Rcpp::Function, bool)':
rcpp_trainmaster.cpp:213:14: warning: 'maxDim' may be used uninitialized [-Wmaybe-uninitialized]
213 | hmmfit_vb(u, nseq, dim, &nb, &bdim, &var, nperm, nperm0, vlist0,
| ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
214 | &md, loglikehd, &lhsum, (double)epsilon, wt, ninit0, ninit1,ninit2, randomseed,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
215 | Numst0, maxDim, minDim, relaxsearch); //output lhsum is BIC not loglikelihood
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
rcpp_trainmaster.cpp:57:7: note: 'maxDim' was declared here
57 | int maxDim;
| ^~~~~~
rcpp_trainmaster.cpp:213:14: warning: 'minDim' may be used uninitialized [-Wmaybe-uninitialized]
213 | hmmfit_vb(u, nseq, dim, &nb, &bdim, &var, nperm, nperm0, vlist0,
| ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
214 | &md, loglikehd, &lhsum, (double)epsilon, wt, ninit0, ninit1,ninit2, randomseed,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
215 | Numst0, maxDim, minDim, relaxsearch); //output lhsum is BIC not loglikelihood
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
rcpp_trainmaster.cpp:58:7: note: 'minDim' was declared here
58 | int minDim;
| ^~~~~~
rcpp_trainmaster.cpp:213:14: warning: 'relaxsearch' may be used uninitialized [-Wmaybe-uninitialized]
213 | hmmfit_vb(u, nseq, dim, &nb, &bdim, &var, nperm, nperm0, vlist0,
| ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
214 | &md, loglikehd, &lhsum, (double)epsilon, wt, ninit0, ninit1,ninit2, randomseed,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
215 | Numst0, maxDim, minDim, relaxsearch); //output lhsum is BIC not loglikelihood
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
rcpp_trainmaster.cpp:59:7: note: 'relaxsearch' was declared here
59 | int relaxsearch;
| ^~~~~~~~~~~
rcpp_trainmaster.cpp:208:17: warning: 'numst' may be used uninitialized [-Wmaybe-uninitialized]
208 | hmmfit_minit(u, nseq, nb, bdim, var, numst, &md, loglikehd, &lhsum, (double)epsilon, wt,
| ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
209 | ninit0, ninit1, ninit2, randomseed); //lhsum is loglikelihood
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
rcpp_trainmaster.cpp:68:8: note: 'numst' was declared here
68 | int *numst; // number of states in blocks
| ^~~~~
g++ -std=gnu++17 -I"D:/RCompile/recent/R-4.4.0/include" -DNDEBUG -I'D:/RCompile/CRANpkg/lib/4.4/Rcpp/include' -I'D:/RCompile/CRANpkg/lib/4.4/RcppProgress/include' -I"d:/rtools44/x86_64-w64-mingw32.static.posix/include" -pedantic -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c utils_rcpp.cpp -o utils_rcpp.o
utils_rcpp.cpp: In function 'void parseVbStructure(const Rcpp::S4&, CondChain*)':
utils_rcpp.cpp:57:3: warning: this 'for' clause does not guard... [-Wmisleading-indentation]
57 | for (int i = 0; i < md->nb; i++)
| ^~~
utils_rcpp.cpp:60:5: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'for'
60 | md->maxnumst = maxnumst;
| ^~
g++ -std=gnu++17 -shared -s -static-libgcc -o HDclust.dll tmp.def RcppExports.o cluster.o estimate.o matrix.o modal.o prob.o rcpp_findModes.o rcpp_testsync.o rcpp_trainmaster.o utils_rcpp.o -Ld:/rtools44/x86_64-w64-mingw32.static.posix/lib/x64 -Ld:/rtools44/x86_64-w64-mingw32.static.posix/lib -LD:/RCompile/recent/R-4.4.0/bin/x64 -lR
make[1]: Leaving directory '/d/temp/RtmpAj5hhs/R.INSTALL2d1e4170c22e/HDclust/src'
make[1]: Entering directory '/d/temp/RtmpAj5hhs/R.INSTALL2d1e4170c22e/HDclust/src'
make[1]: Leaving directory '/d/temp/RtmpAj5hhs/R.INSTALL2d1e4170c22e/HDclust/src'
installing to d:/Rcompile/CRANpkg/lib/4.4/00LOCK-HDclust/00new/HDclust/libs/x64
** R
** data
** 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
* MD5 sums
packaged installation of 'HDclust' as HDclust_1.0.3.zip
* DONE (HDclust)