* 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++-13 -std=gnu++17 accepts -g... yes
checking how to run the C++ preprocessor... g++-13 -std=gnu++17 -E
checking for g++-13 -std=gnu++17 option to support OpenMP... -fopenmp
configure: creating ./config.status
config.status: creating src/Makevars
** libs
using C++ compiler: ‘g++-13 (GCC) 13.2.0’
make[1]: Entering directory '/data/gannet/ripley/R/packages/tests-devel/HDclust/src'
g++-13 -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppProgress/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -c RcppExports.cpp -o RcppExports.o
g++-13 -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppProgress/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -c cluster.cpp -o cluster.o
g++-13 -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppProgress/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -c estimate.cpp -o estimate.o
g++-13 -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppProgress/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -c matrix.cpp -o matrix.o
g++-13 -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppProgress/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -c modal.cpp -o modal.o
g++-13 -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppProgress/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -c prob.cpp -o prob.o
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 '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++-13 -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppProgress/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -c rcpp_findModes.cpp -o rcpp_findModes.o
matrix.cpp: In function 'unsigned char ludcmp_float(float**, int, int*, float*)':
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: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;
| ^~~~
g++-13 -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppProgress/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -c rcpp_testsync.cpp -o rcpp_testsync.o
g++-13 -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppProgress/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -c rcpp_trainmaster.cpp -o rcpp_trainmaster.o
g++-13 -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppProgress/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -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;
| ^~
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:573:22: warning: argument 1 range [18446744071562067968, 18446744073709551615] exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=]
573 | clsid=(int *)calloc(nseq,sizeof(int));
| ~~~~~~^~~~~~~~~~~~~~~~~~
In file included from /usr/local/gcc13/include/c++/13.2.0/bits/std_abs.h:38,
from /usr/local/gcc13/include/c++/13.2.0/cmath:49,
from /data/gannet/ripley/R/test-dev/Rcpp/include/Rcpp/platform/compiler.h:100,
from /data/gannet/ripley/R/test-dev/Rcpp/include/Rcpp/r/headers.h:62,
from /data/gannet/ripley/R/test-dev/Rcpp/include/RcppCommon.h:30,
from /data/gannet/ripley/R/test-dev/Rcpp/include/Rcpp.h:27,
from rcpp_testsync.cpp:26:
/usr/include/stdlib.h:543:14: note: in a call to allocation function 'void* calloc(size_t, size_t)' declared here
543 | extern void *calloc (size_t __nmemb, size_t __size)
| ^~~~~~
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++-13 -std=gnu++17 -shared -L/usr/local/gcc13/lib64 -L/usr/local/lib64 -L/usr/local/clang18/lib/x86_64-unknown-linux-gnu -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/data/gannet/ripley/R/R-devel/lib -lRblas -lgfortran -lm -lquadmath -fopenmp
make[1]: Leaving directory '/data/gannet/ripley/R/packages/tests-devel/HDclust/src'
make[1]: Entering directory '/data/gannet/ripley/R/packages/tests-devel/HDclust/src'
make[1]: Leaving directory '/data/gannet/ripley/R/packages/tests-devel/HDclust/src'
installing to /data/gannet/ripley/R/packages/tests-devel/HDclust.Rcheck/00LOCK-HDclust/00new/HDclust/libs
** 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
** 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)