* 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) 13.3.0'
make[1]: Entering directory '/d/temp/2024_12_08_01_50_01_8405/RtmpemI2hV/R.INSTALL22d94125f3bc8/HDclust/src'
g++ -std=gnu++17 -I"D:/RCompile/recent/R-4.4.2/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-4.4.2/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
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-4.4.2/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: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-4.4.2/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:946:5: warning: 'imax' may be used uninitialized [-Wmaybe-uninitialized]
946 | if (j!=imax) {
| ^~
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:1011:5: warning: 'imax' may be used uninitialized [-Wmaybe-uninitialized]
1011 | if (j!=imax) {
| ^~
matrix.cpp:971:9: note: 'imax' was declared here
971 | int i,imax,j,k;
| ^~~~
matrix.cpp: In function 'float mat_det_ludcmp_float(float**, int)':
matrix.cpp:1191:15: warning: 'indx' may be used uninitialized [-Wmaybe-uninitialized]
1191 | ludcmp_float(a,dim,indx,&d);
| ~~~~~~~~~~~~^~~~~~~~~~~~~~~
matrix.cpp:1160:13: note: 'indx' was declared here
1160 | int i,j, *indx;
| ^~~~
matrix.cpp: In function 'double mat_det_ludcmp_double(double**, int)':
matrix.cpp:1233:16: warning: 'indx' may be used uninitialized [-Wmaybe-uninitialized]
1233 | ludcmp_double(a,dim,indx,&d);
| ~~~~~~~~~~~~~^~~~~~~~~~~~~~~
matrix.cpp:1202:14: note: 'indx' was declared here
1202 | int i, j, *indx;
| ^~~~
g++ -std=gnu++17 -I"D:/RCompile/recent/R-4.4.2/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
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-4.4.2/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-4.4.2/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: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-4.4.2/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: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-4.4.2/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: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: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;
| ^~~~~~
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: '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: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
| ^~~~~
g++ -std=gnu++17 -I"D:/RCompile/recent/R-4.4.2/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: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:/rtools44/x86_64-w64-mingw32.static.posix/lib/x64 -Ld:/rtools44/x86_64-w64-mingw32.static.posix/lib -LD:/RCompile/recent/R-4.4.2/bin/x64 -lR
make[1]: Leaving directory '/d/temp/2024_12_08_01_50_01_8405/RtmpemI2hV/R.INSTALL22d94125f3bc8/HDclust/src'
make[1]: Entering directory '/d/temp/2024_12_08_01_50_01_8405/RtmpemI2hV/R.INSTALL22d94125f3bc8/HDclust/src'
make[1]: Leaving directory '/d/temp/2024_12_08_01_50_01_8405/RtmpemI2hV/R.INSTALL22d94125f3bc8/HDclust/src'
installing to d:/Rcompile/CRANpkg/lib/4.4/00LOCK-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)