* installing *source* package ‘signalHsmm’ ...
** this is package ‘signalHsmm’ version ‘1.5’
** package ‘signalHsmm’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C++ compiler: ‘g++ (GCC) 16.1.1 20260515 (Red Hat 16.1.1-2)’
make[1]: Entering directory '/data/localhost/ripley/R/packages/tests-devel/signalHsmm/src'
g++ -std=gnu++20 -I"/data/localhost/ripley/R/R-devel/include" -DNDEBUG  -I'/data/localhost/ripley/R/test-dev/Rcpp/include' -I/usr/local/include    -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++ -std=gnu++20 -I"/data/localhost/ripley/R/R-devel/include" -DNDEBUG  -I'/data/localhost/ripley/R/test-dev/Rcpp/include' -I/usr/local/include    -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 duration_viterbi.cpp -o duration_viterbi.o
duration_viterbi.cpp: In function ‘Rcpp::List duration_viterbi(Rcpp::NumericVector, Rcpp::NumericVector, Rcpp::NumericMatrix, Rcpp::NumericMatrix, Rcpp::NumericMatrix)’:
duration_viterbi.cpp:50:26: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare]
   50 |   for(unsigned int j=0; j<nstates; j++) {
      |                         ~^~~~~~~~
g++ -std=gnu++20 -shared -L/usr/local/lib64 -o signalHsmm.so RcppExports.o duration_viterbi.o
make[1]: Leaving directory '/data/localhost/ripley/R/packages/tests-devel/signalHsmm/src'
make[1]: Entering directory '/data/localhost/ripley/R/packages/tests-devel/signalHsmm/src'
make[1]: Leaving directory '/data/localhost/ripley/R/packages/tests-devel/signalHsmm/src'
installing to /data/localhost/ripley/R/packages/tests-devel/signalHsmm.Rcheck/00LOCK-signalHsmm/00new/signalHsmm/libs
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
Warning in structure(list(`1` = c("R", "N", "D", "Q", "E", "H", "K"), `2` = c("G",  :
  Replacing special names ‘.Names’ is deprecated; use ‘names’ instead.
Warning in structure(c(0, 0, 0, 0, 1, 0, 0, 0, 0, 1, 0, 0, 0, 0, 1, 0),  :
  Replacing special names ‘.Dim’ is deprecated; use ‘dim’ instead.
Warning in structure(c(0.282182230869001, 0.0128884115403133, 0.20406633561323,  :
  Replacing special names ‘.Dim’ is deprecated; use ‘dim’ instead.
Warning in structure(c(-1.11328712008703, -1.1685797676654, -1.34674657905895,  :
  Replacing special names ‘.Names’ is deprecated; use ‘names’ instead.
Warning in structure(c(0.0946771378708551, 0.18804537521815, 0.191972076788831,  :
  Replacing special names ‘.Dim’, ‘.Dimnames’ is deprecated; use ‘dim’, ‘dimnames’ instead.
Warning in structure(list(aa_group = structure(list(`1` = c("R", "N", "D",  :
  Replacing special names ‘.Names’ is deprecated; use ‘names’ instead.
** help
*** installing help indices
** building package indices
** 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 (signalHsmm)