* 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++-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 (Debian 13.2.0-23) 13.2.0’
make[1]: Entering directory '/tmp/RtmpZmKlQM/R.INSTALL3e045f53203508/HDclust/src'
g++-13 -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++-13 -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
g++-13 -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 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"/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: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"/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
g++-13 -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++-13 -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
g++-13 -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 ‘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/include/c++/13/bits/std_abs.h:38,
from /usr/include/c++/13/cmath:49,
from /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include/Rcpp/platform/compiler.h:100,
from /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include/Rcpp/r/headers.h:62,
from /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include/RcppCommon.h:30,
from /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include/Rcpp.h:27,
from rcpp_testsync.cpp:26:
/usr/include/stdlib.h:556:14: note: in a call to allocation function ‘void* calloc(size_t, size_t)’ declared here
556 | extern void *calloc (size_t __nmemb, size_t __size)
| ^~~~~~
g++-13 -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: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 -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:57:3: warning: this ‘for’ clause does not guard... [-Wmisleading-indentation]
57 | for (int i = 0; i < md->nb; i++)
| ^~~
utils_rcpp.cpp:60:5: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘for’
60 | md->maxnumst = maxnumst;
| ^~
g++-13 -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 '/tmp/RtmpZmKlQM/R.INSTALL3e045f53203508/HDclust/src'
make[1]: Entering directory '/tmp/RtmpZmKlQM/R.INSTALL3e045f53203508/HDclust/src'
make[1]: Leaving directory '/tmp/RtmpZmKlQM/R.INSTALL3e045f53203508/HDclust/src'
installing to /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/00LOCK-HDclust/00new/HDclust/libs
** R
** data
** 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)