* installing to library ‘/home/hornik/tmp/R.check/r-release-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 13.2.0-25) 13.2.0’
make[1]: Entering directory '/tmp/RtmpLTJoyf/R.INSTALL1c520f6d72614e/HDclust/src'
g++-13 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-release-gcc/Work/build/include" -DNDEBUG  -I'/home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-release-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-release-gcc/Work/build/include" -DNDEBUG  -I'/home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-release-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-release-gcc/Work/build/include" -DNDEBUG  -I'/home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-release-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-release-gcc/Work/build/include" -DNDEBUG  -I'/home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-release-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-release-gcc/Work/build/include" -DNDEBUG  -I'/home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-release-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-release-gcc/Work/build/include" -DNDEBUG  -I'/home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-release-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-release-gcc/Work/build/include" -DNDEBUG  -I'/home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-release-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-release-gcc/Work/build/include" -DNDEBUG  -I'/home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-release-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-release-gcc/Work/build/Packages/Rcpp/include/Rcpp/platform/compiler.h:100,
                 from /home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/Rcpp/include/Rcpp/r/headers.h:62,
                 from /home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/Rcpp/include/RcppCommon.h:30,
                 from /home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/Rcpp/include/Rcpp.h:27,
                 from rcpp_testsync.cpp:26:
/usr/include/stdlib.h:675:14: note: in a call to allocation function ‘void* calloc(size_t, size_t)’ declared here
  675 | extern void *calloc (size_t __nmemb, size_t __size)
      |              ^~~~~~
g++-13 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-release-gcc/Work/build/include" -DNDEBUG  -I'/home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-release-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-release-gcc/Work/build/include" -DNDEBUG  -I'/home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-release-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-release-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-release-gcc/Work/build/lib -lRblas -lgfortran -lm -lquadmath -fopenmp -L/home/hornik/tmp/R.check/r-release-gcc/Work/build/lib -lR
make[1]: Leaving directory '/tmp/RtmpLTJoyf/R.INSTALL1c520f6d72614e/HDclust/src'
make[1]: Entering directory '/tmp/RtmpLTJoyf/R.INSTALL1c520f6d72614e/HDclust/src'
make[1]: Leaving directory '/tmp/RtmpLTJoyf/R.INSTALL1c520f6d72614e/HDclust/src'
installing to /home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/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
* creating tarball
packaged installation of ‘HDclust’ as ‘HDclust_1.0.3_R_x86_64-pc-linux-gnu.tar.gz’
* DONE (HDclust)