* 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/Rtmp6jv2La/R.INSTALL1f5dc29c750d/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/Rtmp6jv2La/R.INSTALL1f5dc29c750d/HDclust/src' make[1]: Entering directory '/d/temp/Rtmp6jv2La/R.INSTALL1f5dc29c750d/HDclust/src' make[1]: Leaving directory '/d/temp/Rtmp6jv2La/R.INSTALL1f5dc29c750d/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)