* 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) 12.3.0' make[1]: Entering directory '/d/temp/2024_11_13_01_50_00_32639/RtmpmQNlY3/R.INSTALL202fc618c78f2/HDclust/src' g++ -std=gnu++17 -I"D:/RCompile/recent/R-4.3.3/include" -DNDEBUG -I'D:/RCompile/CRANpkg/lib/4.3/Rcpp/include' -I'D:/RCompile/CRANpkg/lib/4.3/RcppProgress/include' -I"d:/rtools43/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-4.3.3/include" -DNDEBUG -I'D:/RCompile/CRANpkg/lib/4.3/Rcpp/include' -I'D:/RCompile/CRANpkg/lib/4.3/RcppProgress/include' -I"d:/rtools43/x86_64-w64-mingw32.static.posix/include" -pedantic -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c cluster.cpp -o cluster.o cluster.cpp: In function 'void centroid(double*, int, int, double*, int*, int)': cluster.cpp:68:30: warning: comparison of integer expressions of different signedness: 'int' and 'long long unsigned int' [-Wsign-compare] 68 | if (numcdwd < 0 || numcdwd > SIZE_MAX) { | ^ cluster.cpp: In function 'void encode(double*, int, int, double*, int*, int)': cluster.cpp:166:30: warning: comparison of integer expressions of different signedness: 'int' and 'long long unsigned int' [-Wsign-compare] 166 | if (numcdwd < 0 || numcdwd > SIZE_MAX) { | ^ cluster.cpp: In function 'double lloyd(double*, int, int, double*, int, double)': cluster.cpp:222:27: warning: comparison of integer expressions of different signedness: 'int' and 'long long unsigned int' [-Wsign-compare] 222 | if (numdata<0 || numdata>SIZE_MAX || numcdwd*dim<0 || numcdwd*dim > SIZE_MAX){ | ^ cluster.cpp:222:69: warning: comparison of integer expressions of different signedness: 'int' and 'long long unsigned int' [-Wsign-compare] 222 | if (numdata<0 || numdata>SIZE_MAX || numcdwd*dim<0 || numcdwd*dim > SIZE_MAX){ | ^ g++ -std=gnu++17 -I"D:/RCompile/recent/R-4.3.3/include" -DNDEBUG -I'D:/RCompile/CRANpkg/lib/4.3/Rcpp/include' -I'D:/RCompile/CRANpkg/lib/4.3/RcppProgress/include' -I"d:/rtools43/x86_64-w64-mingw32.static.posix/include" -pedantic -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c estimate.cpp -o estimate.o estimate.cpp:1071: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas] 1071 | #pragma omp parallel private(i, ii, j, k, m, mu, mom2, l1img, a, thetalog, betalog) | estimate.cpp:1108: warning: ignoring '#pragma omp master' [-Wunknown-pragmas] 1108 | #pragma omp master | estimate.cpp:1125: warning: ignoring '#pragma omp barrier' [-Wunknown-pragmas] 1125 | #pragma omp barrier | estimate.cpp:1127: warning: ignoring '#pragma omp for' [-Wunknown-pragmas] 1127 | #pragma omp for private(t, l) | estimate.cpp:1136: warning: ignoring '#pragma omp atomic' [-Wunknown-pragmas] 1136 | #pragma omp atomic | estimate.cpp:1140: warning: ignoring '#pragma omp atomic' [-Wunknown-pragmas] 1140 | #pragma omp atomic | estimate.cpp:1144: warning: ignoring '#pragma omp atomic' [-Wunknown-pragmas] 1144 | #pragma omp atomic | estimate.cpp:1150: warning: ignoring '#pragma omp atomic' [-Wunknown-pragmas] 1150 | #pragma omp atomic | estimate.cpp:1156: warning: ignoring '#pragma omp atomic' [-Wunknown-pragmas] 1156 | #pragma omp atomic | estimate.cpp:1161: warning: ignoring '#pragma omp master' [-Wunknown-pragmas] 1161 | #pragma omp master | estimate.cpp:1232: warning: ignoring '#pragma omp barrier' [-Wunknown-pragmas] 1232 | #pragma omp barrier | estimate.cpp:1236: warning: ignoring '#pragma omp master' [-Wunknown-pragmas] 1236 | #pragma omp master | estimate.cpp:1310: warning: ignoring '#pragma omp barrier' [-Wunknown-pragmas] 1310 | #pragma omp barrier | estimate.cpp: In function 'void initialize(double*, int, int, HmmModel*, int)': estimate.cpp:447:19: warning: comparison of integer expressions of different signedness: 'int' and 'long long unsigned int' [-Wsign-compare] 447 | if (nseq<0||nseq>SIZE_MAX) { | ^ estimate.cpp:451:32: warning: comparison of integer expressions of different signedness: 'int' and 'long long unsigned int' [-Wsign-compare] 451 | if (numst*dim <0|| numst*dim >SIZE_MAX) { | ^ estimate.cpp: In function 'void initialize2(double*, int, int, HmmModel*, double*)': estimate.cpp:623:19: warning: comparison of integer expressions of different signedness: 'int' and 'long long unsigned int' [-Wsign-compare] 623 | if (nseq<0||nseq>SIZE_MAX) { | ^ estimate.cpp: In function 'void initial_ccm(double**, int, CondChain*)': estimate.cpp:775:25: warning: comparison of integer expressions of different signedness: 'int' and 'long long unsigned int' [-Wsign-compare] 775 | if (nseq*m <0||nseq*m > SIZE_MAX) { | ^ estimate.cpp: In function 'void initial_ccm1(double**, int, CondChain*, int)': estimate.cpp:809:25: warning: comparison of integer expressions of different signedness: 'int' and 'long long unsigned int' [-Wsign-compare] 809 | if (nseq2*m<0||nseq2*m>SIZE_MAX || nseq<0 || nseq>SIZE_MAX) { | ^ estimate.cpp:809:52: warning: comparison of integer expressions of different signedness: 'int' and 'long long unsigned int' [-Wsign-compare] 809 | if (nseq2*m<0||nseq2*m>SIZE_MAX || nseq<0 || nseq>SIZE_MAX) { | ^ estimate.cpp: In function 'void initial_ccm2(double**, int, CondChain*, int)': estimate.cpp:858:23: warning: comparison of integer expressions of different signedness: 'int' and 'long long unsigned int' [-Wsign-compare] 858 | if (nseq*m<0||nseq*m>SIZE_MAX || n*m<0 || n*m>SIZE_MAX || nseq<0 || nseq>SIZE_MAX) { | ^ estimate.cpp:858:48: warning: comparison of integer expressions of different signedness: 'int' and 'long long unsigned int' [-Wsign-compare] 858 | if (nseq*m<0||nseq*m>SIZE_MAX || n*m<0 || n*m>SIZE_MAX || nseq<0 || nseq>SIZE_MAX) { | ^ estimate.cpp:858:75: warning: comparison of integer expressions of different signedness: 'int' and 'long long unsigned int' [-Wsign-compare] 858 | if (nseq*m<0||nseq*m>SIZE_MAX || n*m<0 || n*m>SIZE_MAX || nseq<0 || nseq>SIZE_MAX) { | ^ estimate.cpp: In function 'double comploglike(CondChain*, double**, int, double*, double*)': estimate.cpp:915:14: warning: comparison of integer expressions of different signedness: 'int' and 'long long unsigned int' [-Wsign-compare] 915 | if (m<0|| m>SIZE_MAX) { | ^ estimate.cpp: In function 'double classlikehd(CondChain*, double**, int, double***, double*)': estimate.cpp:953:13: warning: comparison of integer expressions of different signedness: 'int' and 'long long unsigned int' [-Wsign-compare] 953 | if (m<0||m>SIZE_MAX ) { | ^ estimate.cpp: In function 'int baumwelch(double**, int, CondChain*, double*, double*, double, double*)': estimate.cpp:1089:20: warning: comparison of integer expressions of different signedness: 'int' and 'long long unsigned int' [-Wsign-compare] 1089 | if (m<0|| m>SIZE_MAX ) { | ^ estimate.cpp: In function 'void ordervar2(double**, double***, int, int, int*, int**)': estimate.cpp:1401:21: warning: comparison of integer expressions of different signedness: 'int' and 'long long unsigned int' [-Wsign-compare] 1401 | if (nseq<0 || nseq>SIZE_MAX) { | ^ estimate.cpp: In function 'void hmmfit(double**, int, int, int*, int**, int*, CondChain*, double*, double*, double, double*)': estimate.cpp:1439:23: warning: comparison of integer expressions of different signedness: 'int' and 'long long unsigned int' [-Wsign-compare] 1439 | if (nseq<0 || nseq>SIZE_MAX) { | ^ estimate.cpp: In function 'void hmmfit_minit(double**, int, int, int*, int**, int*, CondChain**, double*, double*, double, double*, int, int, int, int)': estimate.cpp:1483:31: warning: comparison of integer expressions of different signedness: 'int' and 'long long unsigned int' [-Wsign-compare] 1483 | if (nseq*ninit<0||nseq*ninit>SIZE_MAX || nseq<0 || nseq>SIZE_MAX || ninit<0 || ninit>SIZE_MAX ) { | ^ estimate.cpp:1483:58: warning: comparison of integer expressions of different signedness: 'int' and 'long long unsigned int' [-Wsign-compare] 1483 | if (nseq*ninit<0||nseq*ninit>SIZE_MAX || nseq<0 || nseq>SIZE_MAX || ninit<0 || ninit>SIZE_MAX ) { | ^ estimate.cpp:1483:87: warning: comparison of integer expressions of different signedness: 'int' and 'long long unsigned int' [-Wsign-compare] 1483 | if (nseq*ninit<0||nseq*ninit>SIZE_MAX || nseq<0 || nseq>SIZE_MAX || ninit<0 || ninit>SIZE_MAX ) { | ^ estimate.cpp:1496:21: warning: comparison of integer expressions of different signedness: 'int' and 'long long unsigned int' [-Wsign-compare] 1496 | if (nseq<0||nseq>SIZE_MAX) { | ^ estimate.cpp: In function 'void hmmfit_minit2(double**, int, int, int*, int**, int*, CondChain**, double*, double*, double, double*, int, int, int, int)': estimate.cpp:1562:31: warning: comparison of integer expressions of different signedness: 'int' and 'long long unsigned int' [-Wsign-compare] 1562 | if (nseq*ninit<0||nseq*ninit>SIZE_MAX || nseq<0 || nseq>SIZE_MAX || ninit<0 || ninit>SIZE_MAX ) { | ^ estimate.cpp:1562:58: warning: comparison of integer expressions of different signedness: 'int' and 'long long unsigned int' [-Wsign-compare] 1562 | if (nseq*ninit<0||nseq*ninit>SIZE_MAX || nseq<0 || nseq>SIZE_MAX || ninit<0 || ninit>SIZE_MAX ) { | ^ estimate.cpp:1562:87: warning: comparison of integer expressions of different signedness: 'int' and 'long long unsigned int' [-Wsign-compare] 1562 | if (nseq*ninit<0||nseq*ninit>SIZE_MAX || nseq<0 || nseq>SIZE_MAX || ninit<0 || ninit>SIZE_MAX ) { | ^ estimate.cpp:1575:21: warning: comparison of integer expressions of different signedness: 'int' and 'long long unsigned int' [-Wsign-compare] 1575 | if (nseq<0||nseq>SIZE_MAX) { | ^ estimate.cpp: In function 'void findbuddy(int*, int*, int*, int, int**, double*, int**, int, int, int)': estimate.cpp:1758:25: warning: 'v3' may be used uninitialized [-Wmaybe-uninitialized] 1758 | if (skipped[i]==0 && lhsum[i]>v3) { | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~ estimate.cpp:1747:10: note: 'v3' was declared here 1747 | double v3; | ^~ estimate.cpp: In function 'int baumwelch(double**, int, CondChain*, double*, double*, double, double*)': estimate.cpp:1339:11: warning: 'lhsum' may be used uninitialized [-Wmaybe-uninitialized] 1339 | *lhsumpt=lhsum; | ~~~~~~~~^~~~~~ estimate.cpp:1027:20: note: 'lhsum' was declared here 1027 | 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:1986:17: warning: 'v0' may be used uninitialized [-Wmaybe-uninitialized] 1986 | lhsum1[k1]=v0; //no change occurred, record the best BIC | ~~~~~~~~~~^~~ estimate.cpp:1856:27: note: 'v0' was declared here 1856 | double *lhsum, *lhsum1, v0,v1; | ^~ g++ -std=gnu++17 -I"D:/RCompile/recent/R-4.3.3/include" -DNDEBUG -I'D:/RCompile/CRANpkg/lib/4.3/Rcpp/include' -I'D:/RCompile/CRANpkg/lib/4.3/RcppProgress/include' -I"d:/rtools43/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:948:17: warning: 'imax' may be used uninitialized [-Wmaybe-uninitialized] 948 | dum = a[imax][k]; | ^~~~ matrix.cpp:906:9: note: 'imax' was declared here 906 | int i,imax,j,k; | ^~~~ matrix.cpp: In function 'unsigned char ludcmp_double(double**, int, int*, double*)': matrix.cpp:1013:17: warning: 'imax' may be used uninitialized [-Wmaybe-uninitialized] 1013 | dum = a[imax][k]; | ^~~~ matrix.cpp:971:9: note: 'imax' was declared here 971 | int i,imax,j,k; | ^~~~ In file included from D:/RCompile/recent/R-4.3.3/include/R.h:78, from D:/RCompile/CRANpkg/lib/4.3/Rcpp/include/Rcpp/r/headers.h:70, from D:/RCompile/CRANpkg/lib/4.3/Rcpp/include/RcppCommon.h:30, from D:/RCompile/CRANpkg/lib/4.3/Rcpp/include/Rcpp.h:27, from matrix.cpp:31: D:/RCompile/recent/R-4.3.3/include/R_ext/RS.h: In function 'float mat_det_ludcmp_float(float**, int)': D:/RCompile/recent/R-4.3.3/include/R_ext/RS.h:60:35: warning: 'indx' may be used uninitialized [-Wmaybe-uninitialized] 60 | #define R_Free(p) (R_chk_free( (void *)(p) ), (p) = NULL) | ^ matrix.cpp:1160:13: note: 'indx' was declared here 1160 | int i,j, *indx; | ^~~~ D:/RCompile/recent/R-4.3.3/include/R_ext/RS.h: In function 'double mat_det_ludcmp_double(double**, int)': D:/RCompile/recent/R-4.3.3/include/R_ext/RS.h:60:35: warning: 'indx' may be used uninitialized [-Wmaybe-uninitialized] 60 | #define R_Free(p) (R_chk_free( (void *)(p) ), (p) = NULL) | ^ matrix.cpp:1202:14: note: 'indx' was declared here 1202 | int i, j, *indx; | ^~~~ g++ -std=gnu++17 -I"D:/RCompile/recent/R-4.3.3/include" -DNDEBUG -I'D:/RCompile/CRANpkg/lib/4.3/Rcpp/include' -I'D:/RCompile/CRANpkg/lib/4.3/RcppProgress/include' -I"d:/rtools43/x86_64-w64-mingw32.static.posix/include" -pedantic -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c modal.cpp -o modal.o modal.cpp: In function 'void FindDifSeq(int**, int, int, int***, int*, int*)': modal.cpp:871:19: warning: comparison of integer expressions of different signedness: 'int' and 'long long unsigned int' [-Wsign-compare] 871 | if (nseq<0||nseq>SIZE_MAX) { | ^ g++ -std=gnu++17 -I"D:/RCompile/recent/R-4.3.3/include" -DNDEBUG -I'D:/RCompile/CRANpkg/lib/4.3/Rcpp/include' -I'D:/RCompile/CRANpkg/lib/4.3/RcppProgress/include' -I"d:/rtools43/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-4.3.3/include" -DNDEBUG -I'D:/RCompile/CRANpkg/lib/4.3/Rcpp/include' -I'D:/RCompile/CRANpkg/lib/4.3/RcppProgress/include' -I"d:/rtools43/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:156: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas] 156 | #pragma omp parallel | rcpp_findModes.cpp:163: warning: ignoring '#pragma omp for' [-Wunknown-pragmas] 163 | #pragma omp for | rcpp_findModes.cpp: In function 'Rcpp::S4 rcpp_findModes(Rcpp::NumericMatrix, Rcpp::S4, Rcpp::IntegerVector)': rcpp_findModes.cpp:60:19: warning: comparison of integer expressions of different signedness: 'int' and 'long long unsigned int' [-Wsign-compare] 60 | if (nseq<0||nseq>SIZE_MAX) { | ^ rcpp_findModes.cpp:132:21: warning: comparison of integer expressions of different signedness: 'int' and 'long long unsigned int' [-Wsign-compare] 132 | if (nseq<0 || nseq>SIZE_MAX){ | ^ rcpp_findModes.cpp:136:19: warning: comparison of integer expressions of different signedness: 'int' and 'long long unsigned int' [-Wsign-compare] 136 | if (nseq<0||nseq>SIZE_MAX|| md->nb < 0 || md->nb > SIZE_MAX) { | ^ rcpp_findModes.cpp:136:52: warning: comparison of integer expressions of different signedness: 'int' and 'long long unsigned int' [-Wsign-compare] 136 | if (nseq<0||nseq>SIZE_MAX|| md->nb < 0 || md->nb > SIZE_MAX) { | ^ rcpp_findModes.cpp:158:37: warning: comparison of integer expressions of different signedness: 'int' and 'long long unsigned int' [-Wsign-compare] 158 | if (md->maxnumst<0||md->maxnumst>SIZE_MAX) { | ^ rcpp_findModes.cpp:178:21: warning: comparison of integer expressions of different signedness: 'int' and 'long long unsigned int' [-Wsign-compare] 178 | if (nseq<0 || nseq>SIZE_MAX){ | ^ rcpp_findModes.cpp:186:27: warning: comparison of integer expressions of different signedness: 'int' and 'long long unsigned int' [-Wsign-compare] 186 | if (newnseq<0 || newnseq>SIZE_MAX){ | ^ rcpp_findModes.cpp:209:19: warning: comparison of integer expressions of different signedness: 'int' and 'long long unsigned int' [-Wsign-compare] 209 | if (dim<0 || dim>SIZE_MAX){ | ^ g++ -std=gnu++17 -I"D:/RCompile/recent/R-4.3.3/include" -DNDEBUG -I'D:/RCompile/CRANpkg/lib/4.3/Rcpp/include' -I'D:/RCompile/CRANpkg/lib/4.3/RcppProgress/include' -I"d:/rtools43/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:580: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas] 580 | #pragma omp parallel | rcpp_testsync.cpp:590: warning: ignoring '#pragma omp for' [-Wunknown-pragmas] 590 | #pragma omp for | rcpp_testsync.cpp: In function 'void parseRefClust(const Rcpp::List&, double***, double**, int*, int*, int***, int**)': rcpp_testsync.cpp:84:45: warning: comparison of integer expressions of different signedness: 'R_xlen_t' {aka 'long long int'} and 'long long unsigned int' [-Wsign-compare] 84 | if (rvseqid.size()<0||rvseqid.size()>SIZE_MAX) { | ^ rcpp_testsync.cpp:91:41: warning: comparison of integer expressions of different signedness: 'int' and 'long long unsigned int' [-Wsign-compare] 91 | if (rmode.nrow()<0||rmode.nrow()>SIZE_MAX) { | ^ rcpp_testsync.cpp:96:43: warning: comparison of integer expressions of different signedness: 'int' and 'long long unsigned int' [-Wsign-compare] 96 | if (rmode.ncol()<0||rmode.ncol()>SIZE_MAX) { | ^ rcpp_testsync.cpp:105:29: warning: comparison of integer expressions of different signedness: 'int' and 'long long unsigned int' [-Wsign-compare] 105 | if (*rnseq<0||*rnseq>SIZE_MAX) { | ^ rcpp_testsync.cpp:115:43: warning: comparison of integer expressions of different signedness: 'R_xlen_t' {aka 'long long int'} and 'long long unsigned int' [-Wsign-compare] 115 | if (rsigma.size()<0||rsigma.size()>SIZE_MAX) { | ^ rcpp_testsync.cpp: In function 'Rcpp::List augmentrefcls(int, int, double**, double*, int**, int*, int, int, int, int*, int*, double**, int, int**, int*, int*, int, int*, double***)': rcpp_testsync.cpp:239:24: warning: comparison of integer expressions of different signedness: 'int' and 'long long unsigned int' [-Wsign-compare] 239 | if (numcls<0|| numcls>SIZE_MAX || dim<0|| dim>SIZE_MAX ) { | ^ rcpp_testsync.cpp:239:48: warning: comparison of integer expressions of different signedness: 'int' and 'long long unsigned int' [-Wsign-compare] 239 | if (numcls<0|| numcls>SIZE_MAX || dim<0|| dim>SIZE_MAX ) { | ^ rcpp_testsync.cpp:303:23: warning: comparison of integer expressions of different signedness: 'int' and 'long long unsigned int' [-Wsign-compare] 303 | if (rnseq2<0||rnseq2>SIZE_MAX) { | ^ rcpp_testsync.cpp:317:37: warning: comparison of integer expressions of different signedness: 'int' and 'long long unsigned int' [-Wsign-compare] 317 | if (numcls+rncls<0||numcls+rncls>SIZE_MAX) { | ^ rcpp_testsync.cpp:330:23: warning: comparison of integer expressions of different signedness: 'int' and 'long long unsigned int' [-Wsign-compare] 330 | if (rnseq2<0||rnseq2>SIZE_MAX) { | ^ rcpp_testsync.cpp: In function 'int AdjustCluster(int*, int, int, double**, double**, int, int)': rcpp_testsync.cpp:374:21: warning: comparison of integer expressions of different signedness: 'int' and 'long long unsigned int' [-Wsign-compare] 374 | if (rncls<0||rncls>SIZE_MAX) { | ^ rcpp_testsync.cpp: In function 'Rcpp::S4 rcpp_clust(Rcpp::NumericMatrix, Rcpp::S4, Rcpp::Nullable<Rcpp::Vector<19> >, Rcpp::List, Rcpp::IntegerVector)': rcpp_testsync.cpp:438:19: warning: comparison of integer expressions of different signedness: 'int' and 'long long unsigned int' [-Wsign-compare] 438 | if (nseq<0||nseq>SIZE_MAX) { | ^ rcpp_testsync.cpp:552:19: warning: comparison of integer expressions of different signedness: 'int' and 'long long unsigned int' [-Wsign-compare] 552 | if (nseq<0||nseq>SIZE_MAX || md->nb<0 || md->nb>SIZE_MAX) { | ^ rcpp_testsync.cpp:552:50: warning: comparison of integer expressions of different signedness: 'int' and 'long long unsigned int' [-Wsign-compare] 552 | if (nseq<0||nseq>SIZE_MAX || md->nb<0 || md->nb>SIZE_MAX) { | ^ rcpp_testsync.cpp:559:26: warning: comparison of integer expressions of different signedness: 'int' and 'long long unsigned int' [-Wsign-compare] 559 | if (md->nb < 0||md->nb > SIZE_MAX) { | ^ rcpp_testsync.cpp:582:40: warning: comparison of integer expressions of different signedness: 'int' and 'long long unsigned int' [-Wsign-compare] 582 | if (md->maxnumst<0 || md->maxnumst >SIZE_MAX) { | ^ rcpp_testsync.cpp:585:39: warning: comparison of integer expressions of different signedness: 'int' and 'long long unsigned int' [-Wsign-compare] 585 | if (md->maxnumst <0||md->maxnumst >SIZE_MAX) { | ^ rcpp_testsync.cpp:626:19: warning: comparison of integer expressions of different signedness: 'int' and 'long long unsigned int' [-Wsign-compare] 626 | if (nseq<0||nseq>SIZE_MAX) { | ^ rcpp_testsync.cpp:667:24: warning: comparison of integer expressions of different signedness: 'int' and 'long long unsigned int' [-Wsign-compare] 667 | if (rncls<0||rncls > SIZE_MAX) { | ^ rcpp_testsync.cpp:708:19: warning: comparison of integer expressions of different signedness: 'int' and 'long long unsigned int' [-Wsign-compare] 708 | if (nseq<0||nseq>SIZE_MAX) { | ^ rcpp_testsync.cpp:714:24: warning: comparison of integer expressions of different signedness: 'int' and 'long long unsigned int' [-Wsign-compare] 714 | if (noref<0||noref > SIZE_MAX) { | ^ rcpp_testsync.cpp:732:22: warning: comparison of integer expressions of different signedness: 'int' and 'long long unsigned int' [-Wsign-compare] 732 | if (noref<0||noref > SIZE_MAX) { | ^ rcpp_testsync.cpp:754:26: warning: comparison of integer expressions of different signedness: 'int' and 'long long unsigned int' [-Wsign-compare] 754 | if (newnseq<0||newnseq > SIZE_MAX) { | ^ rcpp_testsync.cpp:766:18: warning: comparison of integer expressions of different signedness: 'int' and 'long long unsigned int' [-Wsign-compare] 766 | if (dim<0||dim > SIZE_MAX) { | ^ rcpp_testsync.cpp:786:26: warning: comparison of integer expressions of different signedness: 'int' and 'long long unsigned int' [-Wsign-compare] 786 | if (newnseq<0||newnseq > SIZE_MAX) { | ^ rcpp_testsync.cpp:835:24: warning: comparison of integer expressions of different signedness: 'int' and 'long long unsigned int' [-Wsign-compare] 835 | if (rncls<0||rncls > SIZE_MAX) { | ^ rcpp_testsync.cpp:877:30: warning: comparison of integer expressions of different signedness: 'int' and 'long long unsigned int' [-Wsign-compare] 877 | if (norefmode<0||norefmode > SIZE_MAX || newnseq <0||newnseq > SIZE_MAX) { | ^ rcpp_testsync.cpp:877:64: warning: comparison of integer expressions of different signedness: 'int' and 'long long unsigned int' [-Wsign-compare] 877 | if (norefmode<0||norefmode > SIZE_MAX || newnseq <0||newnseq > SIZE_MAX) { | ^ rcpp_testsync.cpp:948:35: warning: comparison of integer expressions of different signedness: 'int' and 'long long unsigned int' [-Wsign-compare] 948 | if (rncls+numcls<0||rncls+numcls>SIZE_MAX) { | ^ g++ -std=gnu++17 -I"D:/RCompile/recent/R-4.3.3/include" -DNDEBUG -I'D:/RCompile/CRANpkg/lib/4.3/Rcpp/include' -I'D:/RCompile/CRANpkg/lib/4.3/RcppProgress/include' -I"d:/rtools43/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:31:21: warning: comparison of integer expressions of different signedness: 'int' and 'long long unsigned int' [-Wsign-compare] 31 | if (nseq<0 || nseq>SIZE_MAX){ | ^ rcpp_trainmaster.cpp:98:15: warning: comparison of integer expressions of different signedness: 'int' and 'long long unsigned int' [-Wsign-compare] 98 | if (nb<0||nb>SIZE_MAX) { | ^ rcpp_trainmaster.cpp:157:29: warning: comparison of integer expressions of different signedness: 'int' and 'long long unsigned int' [-Wsign-compare] 157 | if (nperm0<0|| nperm0 > SIZE_MAX) { | ^ rcpp_trainmaster.cpp:200:21: warning: comparison of integer expressions of different signedness: 'int' and 'long long unsigned int' [-Wsign-compare] 200 | if (nseq<0 || nseq>SIZE_MAX){ | ^ rcpp_trainmaster.cpp:220:17: warning: 'numst' may be used uninitialized [-Wmaybe-uninitialized] 220 | hmmfit_minit(u, nseq, nb, bdim, var, numst, &md, loglikehd, &lhsum, (double)epsilon, wt, | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 221 | ninit0, ninit1, ninit2, randomseed); //lhsum is loglikelihood | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ rcpp_trainmaster.cpp:72:8: note: 'numst' was declared here 72 | int *numst; // number of states in blocks | ^~~~~ rcpp_trainmaster.cpp:225:14: warning: 'relaxsearch' may be used uninitialized [-Wmaybe-uninitialized] 225 | hmmfit_vb(u, nseq, dim, &nb, &bdim, &var, nperm, nperm0, vlist0, | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 226 | &md, loglikehd, &lhsum, (double)epsilon, wt, ninit0, ninit1,ninit2, randomseed, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 227 | Numst0, maxDim, minDim, relaxsearch); //output lhsum is BIC not loglikelihood | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ rcpp_trainmaster.cpp:63:7: note: 'relaxsearch' was declared here 63 | int relaxsearch; | ^~~~~~~~~~~ rcpp_trainmaster.cpp:225:14: warning: 'minDim' may be used uninitialized [-Wmaybe-uninitialized] 225 | hmmfit_vb(u, nseq, dim, &nb, &bdim, &var, nperm, nperm0, vlist0, | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 226 | &md, loglikehd, &lhsum, (double)epsilon, wt, ninit0, ninit1,ninit2, randomseed, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 227 | Numst0, maxDim, minDim, relaxsearch); //output lhsum is BIC not loglikelihood | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ rcpp_trainmaster.cpp:62:7: note: 'minDim' was declared here 62 | int minDim; | ^~~~~~ rcpp_trainmaster.cpp:225:14: warning: 'maxDim' may be used uninitialized [-Wmaybe-uninitialized] 225 | hmmfit_vb(u, nseq, dim, &nb, &bdim, &var, nperm, nperm0, vlist0, | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 226 | &md, loglikehd, &lhsum, (double)epsilon, wt, ninit0, ninit1,ninit2, randomseed, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 227 | Numst0, maxDim, minDim, relaxsearch); //output lhsum is BIC not loglikelihood | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ rcpp_trainmaster.cpp:61:7: note: 'maxDim' was declared here 61 | int maxDim; | ^~~~~~ g++ -std=gnu++17 -I"D:/RCompile/recent/R-4.3.3/include" -DNDEBUG -I'D:/RCompile/CRANpkg/lib/4.3/Rcpp/include' -I'D:/RCompile/CRANpkg/lib/4.3/RcppProgress/include' -I"d:/rtools43/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:43:25: warning: comparison of integer expressions of different signedness: 'int' and 'long long unsigned int' [-Wsign-compare] 43 | if (md->nb<0 || md->nb>SIZE_MAX) { | ^ utils_rcpp.cpp:70:26: warning: comparison of integer expressions of different signedness: 'int' and 'long long unsigned int' [-Wsign-compare] 70 | if (md->nb <0 || md->nb>SIZE_MAX) { | ^ utils_rcpp.cpp: In function 'void parseHmmChain(const Rcpp::List&, CondChain*)': utils_rcpp.cpp:97:26: warning: comparison of integer expressions of different signedness: 'int' and 'long long unsigned int' [-Wsign-compare] 97 | if (md->nb <0 || md->nb>SIZE_MAX) { | ^ 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:/rtools43/x86_64-w64-mingw32.static.posix/lib/x64 -Ld:/rtools43/x86_64-w64-mingw32.static.posix/lib -LD:/RCompile/recent/R-4.3.3/bin/x64 -lR make[1]: Leaving directory '/d/temp/2024_11_13_01_50_00_32639/RtmpmQNlY3/R.INSTALL202fc618c78f2/HDclust/src' make[1]: Entering directory '/d/temp/2024_11_13_01_50_00_32639/RtmpmQNlY3/R.INSTALL202fc618c78f2/HDclust/src' make[1]: Leaving directory '/d/temp/2024_11_13_01_50_00_32639/RtmpmQNlY3/R.INSTALL202fc618c78f2/HDclust/src' installing to d:/Rcompile/CRANpkg/lib/4.3/00LOCK-HDclust/00new/HDclust/libs/x64 ** R ** data *** moving datasets to lazyload DB ** 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_1.0.4.zip * DONE (HDclust)