* installing to library ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages’
* installing *source* package ‘HDclust’ ...
** package ‘HDclust’ successfully unpacked and MD5 sums checked
** using staged installation
checking whether the C++ compiler works... yes
checking for C++ compiler default output file name... a.out
checking for suffix of executables...
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether we are using the GNU C++ compiler... yes
checking whether g++-14 -std=gnu++17 accepts -g... yes
checking how to run the C++ preprocessor... g++-14 -std=gnu++17 -E
checking for g++-14 -std=gnu++17 option to support OpenMP... -fopenmp
configure: creating ./config.status
config.status: creating src/Makevars
** libs
using C++ compiler: ‘g++-14 (Debian 14.2.0-8) 14.2.0’
make[1]: Entering directory '/home/hornik/tmp/scratch/Rtmp12LLOh/R.INSTALL1c7052481d41ad/HDclust/src'
g++-14 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppProgress/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -c RcppExports.cpp -o RcppExports.o
g++-14 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppProgress/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -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 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 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 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 unsigned int’ [-Wsign-compare]
222 | if (numdata<0 || numdata>SIZE_MAX || numcdwd*dim<0 || numcdwd*dim > SIZE_MAX){
| ^
g++-14 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppProgress/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -c estimate.cpp -o estimate.o
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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 ‘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++-14 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppProgress/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -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;
| ^~~~
g++-14 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppProgress/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -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 unsigned int’ [-Wsign-compare]
871 | if (nseq<0||nseq>SIZE_MAX) {
| ^
g++-14 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppProgress/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -c prob.cpp -o prob.o
g++-14 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppProgress/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -c rcpp_findModes.cpp -o rcpp_findModes.o
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 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 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 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 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 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 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 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 unsigned int’ [-Wsign-compare]
209 | if (dim<0 || dim>SIZE_MAX){
| ^
g++-14 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppProgress/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -c rcpp_testsync.cpp -o rcpp_testsync.o
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 int’} and ‘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 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 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 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 int’} and ‘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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 unsigned int’ [-Wsign-compare]
948 | if (rncls+numcls<0||rncls+numcls>SIZE_MAX) {
| ^
g++-14 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppProgress/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -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 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 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 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 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++-14 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppProgress/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -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 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 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 unsigned int’ [-Wsign-compare]
97 | if (md->nb <0 || md->nb>SIZE_MAX) {
| ^
g++-14 -std=gnu++17 -shared -L/home/hornik/tmp/R.check/r-patched-gcc/Work/build/lib -Wl,-O1 -o HDclust.so RcppExports.o cluster.o estimate.o matrix.o modal.o prob.o rcpp_findModes.o rcpp_testsync.o rcpp_trainmaster.o utils_rcpp.o -llapack -L/home/hornik/tmp/R.check/r-patched-gcc/Work/build/lib -lRblas -lgfortran -lm -lquadmath -fopenmp -L/home/hornik/tmp/R.check/r-patched-gcc/Work/build/lib -lR
make[1]: Leaving directory '/home/hornik/tmp/scratch/Rtmp12LLOh/R.INSTALL1c7052481d41ad/HDclust/src'
make[1]: Entering directory '/home/hornik/tmp/scratch/Rtmp12LLOh/R.INSTALL1c7052481d41ad/HDclust/src'
make[1]: Leaving directory '/home/hornik/tmp/scratch/Rtmp12LLOh/R.INSTALL1c7052481d41ad/HDclust/src'
installing to /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/00LOCK-HDclust/00new/HDclust/libs
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package ‘HDclust’
finding HTML links ... done
HDclust-package html
HMM-class html
HMMVB-class html
HMMVBBIC-class html
HMMVBclust-class html
VB-class html
clustControl html
clustModes html
getBIC html
getBdim html
getClsid html
getClustParam html
getDiagCov html
getDim html
getHmmChain html
getHmmParam html
getLoglikehd html
getNb html
getNumst html
getOptHMMVB html
getPrenumst html
getSize html
getVarorder html
getVb html
hmm html
hmmvbBIC html
hmmvbClust html
hmmvbFindModes html
hmmvbTrain html
mkhmmvb html
sim2 html
sim3 html
trainControl html
vb html
vbSearchControl html
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (HDclust)