* installing *source* package ‘simer’ ...
** using staged installation
** libs
using C++ compiler: ‘Debian clang version 16.0.6 (15)’
using C++11
clang++-16  -std=gnu++11 -I"/home/hornik/tmp/R/include" -DNDEBUG  -I'/home/hornik/lib/R/Library/4.4/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.4/x86_64-linux-gnu/RcppArmadillo/include' -I'/home/hornik/lib/R/Library/4.4/x86_64-linux-gnu/RcppProgress/include' -I'/home/hornik/lib/R/Library/4.4/x86_64-linux-gnu/BH/include' -I'/home/hornik/lib/R/Library/4.4/x86_64-linux-gnu/bigmemory/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3  -DARMA_64BIT_WORD=1 -fopenmp -fpic  -g -O3 -Wall -pedantic -Wno-error=enum-constexpr-conversion -c RcppExports.cpp -o RcppExports.o
clang++-16  -std=gnu++11 -I"/home/hornik/tmp/R/include" -DNDEBUG  -I'/home/hornik/lib/R/Library/4.4/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.4/x86_64-linux-gnu/RcppArmadillo/include' -I'/home/hornik/lib/R/Library/4.4/x86_64-linux-gnu/RcppProgress/include' -I'/home/hornik/lib/R/Library/4.4/x86_64-linux-gnu/BH/include' -I'/home/hornik/lib/R/Library/4.4/x86_64-linux-gnu/bigmemory/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3  -DARMA_64BIT_WORD=1 -fopenmp -fpic  -g -O3 -Wall -pedantic -Wno-error=enum-constexpr-conversion -c data_converter.cpp -o data_converter.o
In file included from data_converter.cpp:2:
/home/hornik/lib/R/Library/4.4/x86_64-linux-gnu/BH/include/boost/bind.hpp:36:1: warning: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use <boost/bind/bind.hpp> + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior. [-W#pragma-messages]
BOOST_PRAGMA_MESSAGE(
^
/home/hornik/lib/R/Library/4.4/x86_64-linux-gnu/BH/include/boost/config/pragma_message.hpp:24:34: note: expanded from macro 'BOOST_PRAGMA_MESSAGE'
# define BOOST_PRAGMA_MESSAGE(x) _Pragma(BOOST_STRINGIZE(message(x)))
                                 ^
<scratch space>:2:2: note: expanded from here
 message("The practice of declaring the Bind placeholders (_1, _2, ...) " "in the global namespace is deprecated. Please use " "<boost/bind/bind.hpp> + using namespace boost::placeholders, " "or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.")
 ^
data_converter.cpp:131:10: warning: variable 'n_bytes_read' set but not used [-Wunused-but-set-variable]
  size_t n_bytes_read = static_cast<size_t>(fread(buffer, 1, 3, fin));
         ^
2 warnings generated.
clang++-16  -std=gnu++11 -I"/home/hornik/tmp/R/include" -DNDEBUG  -I'/home/hornik/lib/R/Library/4.4/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.4/x86_64-linux-gnu/RcppArmadillo/include' -I'/home/hornik/lib/R/Library/4.4/x86_64-linux-gnu/RcppProgress/include' -I'/home/hornik/lib/R/Library/4.4/x86_64-linux-gnu/BH/include' -I'/home/hornik/lib/R/Library/4.4/x86_64-linux-gnu/bigmemory/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3  -DARMA_64BIT_WORD=1 -fopenmp -fpic  -g -O3 -Wall -pedantic -Wno-error=enum-constexpr-conversion -c emma.cpp -o emma.o
clang++-16  -std=gnu++11 -I"/home/hornik/tmp/R/include" -DNDEBUG  -I'/home/hornik/lib/R/Library/4.4/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.4/x86_64-linux-gnu/RcppArmadillo/include' -I'/home/hornik/lib/R/Library/4.4/x86_64-linux-gnu/RcppProgress/include' -I'/home/hornik/lib/R/Library/4.4/x86_64-linux-gnu/BH/include' -I'/home/hornik/lib/R/Library/4.4/x86_64-linux-gnu/bigmemory/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3  -DARMA_64BIT_WORD=1 -fopenmp -fpic  -g -O3 -Wall -pedantic -Wno-error=enum-constexpr-conversion -c genotype.cpp -o genotype.o
clang++-16  -std=gnu++11 -I"/home/hornik/tmp/R/include" -DNDEBUG  -I'/home/hornik/lib/R/Library/4.4/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.4/x86_64-linux-gnu/RcppArmadillo/include' -I'/home/hornik/lib/R/Library/4.4/x86_64-linux-gnu/RcppProgress/include' -I'/home/hornik/lib/R/Library/4.4/x86_64-linux-gnu/BH/include' -I'/home/hornik/lib/R/Library/4.4/x86_64-linux-gnu/bigmemory/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3  -DARMA_64BIT_WORD=1 -fopenmp -fpic  -g -O3 -Wall -pedantic -Wno-error=enum-constexpr-conversion -c impute.cpp -o impute.o
impute.cpp:97:14: warning: unused variable 'r' [-Wunused-variable]
      size_t r = (block_start + j) / n;
             ^
impute.cpp:82:10: warning: variable 'n_bytes_read' set but not used [-Wunused-but-set-variable]
  size_t n_bytes_read = static_cast<size_t>(fread(buffer, 1, 3, fin));
         ^
2 warnings generated.
clang++-16  -std=gnu++11 -I"/home/hornik/tmp/R/include" -DNDEBUG  -I'/home/hornik/lib/R/Library/4.4/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.4/x86_64-linux-gnu/RcppArmadillo/include' -I'/home/hornik/lib/R/Library/4.4/x86_64-linux-gnu/RcppProgress/include' -I'/home/hornik/lib/R/Library/4.4/x86_64-linux-gnu/BH/include' -I'/home/hornik/lib/R/Library/4.4/x86_64-linux-gnu/bigmemory/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3  -DARMA_64BIT_WORD=1 -fopenmp -fpic  -g -O3 -Wall -pedantic -Wno-error=enum-constexpr-conversion -c pedigree.cpp -o pedigree.o
pedigree.cpp:195:11: warning: use of bitwise '|' with boolean operands [-Wbitwise-instead-of-logical]
      if ((sirState[i] == "Match") | (sirState[i] == "Found")) {
          ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
                                   ||
pedigree.cpp:195:11: note: cast one or both operands to int to silence this warning
pedigree.cpp:200:11: warning: use of bitwise '|' with boolean operands [-Wbitwise-instead-of-logical]
      if ((damState[i] == "Match") | (damState[i] == "Found")) {
          ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
                                   ||
pedigree.cpp:200:11: note: cast one or both operands to int to silence this warning
pedigree.cpp:218:15: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
          if (((sirState[i] == "Match") | (sirState[i] == "Found")) & ((damState[i] == "Match") | (damState[i] == "Found"))) {
              ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
                                                                    &&
pedigree.cpp:218:15: note: cast one or both operands to int to silence this warning
pedigree.cpp:218:72: warning: use of bitwise '|' with boolean operands [-Wbitwise-instead-of-logical]
          if (((sirState[i] == "Match") | (sirState[i] == "Found")) & ((damState[i] == "Match") | (damState[i] == "Found"))) {
                                                                      ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
                                                                                                ||
pedigree.cpp:218:72: note: cast one or both operands to int to silence this warning
pedigree.cpp:218:16: warning: use of bitwise '|' with boolean operands [-Wbitwise-instead-of-logical]
          if (((sirState[i] == "Match") | (sirState[i] == "Found")) & ((damState[i] == "Match") | (damState[i] == "Found"))) {
              ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
                                        ||
pedigree.cpp:218:16: note: cast one or both operands to int to silence this warning
pedigree.cpp:195:11: warning: use of bitwise '|' with boolean operands [-Wbitwise-instead-of-logical]
      if ((sirState[i] == "Match") | (sirState[i] == "Found")) {
          ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
                                   ||
pedigree.cpp:247:12: note: in instantiation of function template specialization 'PedigreeCorrector<char>' requested here
    return PedigreeCorrector<char>(xpMat, rawGenoID, rawPed, candSirID, candDamID, exclThres, assignThres, birthDate, threads, verbose);
           ^
pedigree.cpp:195:11: note: cast one or both operands to int to silence this warning
      if ((sirState[i] == "Match") | (sirState[i] == "Found")) {
          ^
pedigree.cpp:200:11: warning: use of bitwise '|' with boolean operands [-Wbitwise-instead-of-logical]
      if ((damState[i] == "Match") | (damState[i] == "Found")) {
          ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
                                   ||
pedigree.cpp:200:11: note: cast one or both operands to int to silence this warning
pedigree.cpp:218:15: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
          if (((sirState[i] == "Match") | (sirState[i] == "Found")) & ((damState[i] == "Match") | (damState[i] == "Found"))) {
              ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
                                                                    &&
pedigree.cpp:218:15: note: cast one or both operands to int to silence this warning
pedigree.cpp:218:72: warning: use of bitwise '|' with boolean operands [-Wbitwise-instead-of-logical]
          if (((sirState[i] == "Match") | (sirState[i] == "Found")) & ((damState[i] == "Match") | (damState[i] == "Found"))) {
                                                                      ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
                                                                                                ||
pedigree.cpp:218:72: note: cast one or both operands to int to silence this warning
pedigree.cpp:218:16: warning: use of bitwise '|' with boolean operands [-Wbitwise-instead-of-logical]
          if (((sirState[i] == "Match") | (sirState[i] == "Found")) & ((damState[i] == "Match") | (damState[i] == "Found"))) {
              ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
                                        ||
pedigree.cpp:218:16: note: cast one or both operands to int to silence this warning
pedigree.cpp:195:11: warning: use of bitwise '|' with boolean operands [-Wbitwise-instead-of-logical]
      if ((sirState[i] == "Match") | (sirState[i] == "Found")) {
          ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
                                   ||
pedigree.cpp:249:12: note: in instantiation of function template specialization 'PedigreeCorrector<short>' requested here
    return PedigreeCorrector<short>(xpMat, rawGenoID, rawPed, candSirID, candDamID, exclThres, assignThres, birthDate, threads, verbose);
           ^
pedigree.cpp:195:11: note: cast one or both operands to int to silence this warning
      if ((sirState[i] == "Match") | (sirState[i] == "Found")) {
          ^
pedigree.cpp:200:11: warning: use of bitwise '|' with boolean operands [-Wbitwise-instead-of-logical]
      if ((damState[i] == "Match") | (damState[i] == "Found")) {
          ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
                                   ||
pedigree.cpp:200:11: note: cast one or both operands to int to silence this warning
pedigree.cpp:218:15: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
          if (((sirState[i] == "Match") | (sirState[i] == "Found")) & ((damState[i] == "Match") | (damState[i] == "Found"))) {
              ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
                                                                    &&
pedigree.cpp:218:15: note: cast one or both operands to int to silence this warning
pedigree.cpp:218:72: warning: use of bitwise '|' with boolean operands [-Wbitwise-instead-of-logical]
          if (((sirState[i] == "Match") | (sirState[i] == "Found")) & ((damState[i] == "Match") | (damState[i] == "Found"))) {
                                                                      ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
                                                                                                ||
pedigree.cpp:218:72: note: cast one or both operands to int to silence this warning
pedigree.cpp:218:16: warning: use of bitwise '|' with boolean operands [-Wbitwise-instead-of-logical]
          if (((sirState[i] == "Match") | (sirState[i] == "Found")) & ((damState[i] == "Match") | (damState[i] == "Found"))) {
              ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
                                        ||
pedigree.cpp:218:16: note: cast one or both operands to int to silence this warning
pedigree.cpp:195:11: warning: use of bitwise '|' with boolean operands [-Wbitwise-instead-of-logical]
      if ((sirState[i] == "Match") | (sirState[i] == "Found")) {
          ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
                                   ||
pedigree.cpp:251:12: note: in instantiation of function template specialization 'PedigreeCorrector<int>' requested here
    return PedigreeCorrector<int>(xpMat, rawGenoID, rawPed, candSirID, candDamID, exclThres, assignThres, birthDate, threads, verbose);
           ^
pedigree.cpp:195:11: note: cast one or both operands to int to silence this warning
      if ((sirState[i] == "Match") | (sirState[i] == "Found")) {
          ^
pedigree.cpp:200:11: warning: use of bitwise '|' with boolean operands [-Wbitwise-instead-of-logical]
      if ((damState[i] == "Match") | (damState[i] == "Found")) {
          ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
                                   ||
pedigree.cpp:200:11: note: cast one or both operands to int to silence this warning
pedigree.cpp:218:15: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
          if (((sirState[i] == "Match") | (sirState[i] == "Found")) & ((damState[i] == "Match") | (damState[i] == "Found"))) {
              ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
                                                                    &&
pedigree.cpp:218:15: note: cast one or both operands to int to silence this warning
pedigree.cpp:218:72: warning: use of bitwise '|' with boolean operands [-Wbitwise-instead-of-logical]
          if (((sirState[i] == "Match") | (sirState[i] == "Found")) & ((damState[i] == "Match") | (damState[i] == "Found"))) {
                                                                      ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
                                                                                                ||
pedigree.cpp:218:72: note: cast one or both operands to int to silence this warning
pedigree.cpp:218:16: warning: use of bitwise '|' with boolean operands [-Wbitwise-instead-of-logical]
          if (((sirState[i] == "Match") | (sirState[i] == "Found")) & ((damState[i] == "Match") | (damState[i] == "Found"))) {
              ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
                                        ||
pedigree.cpp:218:16: note: cast one or both operands to int to silence this warning
pedigree.cpp:195:11: warning: use of bitwise '|' with boolean operands [-Wbitwise-instead-of-logical]
      if ((sirState[i] == "Match") | (sirState[i] == "Found")) {
          ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
                                   ||
pedigree.cpp:253:12: note: in instantiation of function template specialization 'PedigreeCorrector<double>' requested here
    return PedigreeCorrector<double>(xpMat, rawGenoID, rawPed, candSirID, candDamID, exclThres, assignThres, birthDate, threads, verbose);
           ^
pedigree.cpp:195:11: note: cast one or both operands to int to silence this warning
      if ((sirState[i] == "Match") | (sirState[i] == "Found")) {
          ^
pedigree.cpp:200:11: warning: use of bitwise '|' with boolean operands [-Wbitwise-instead-of-logical]
      if ((damState[i] == "Match") | (damState[i] == "Found")) {
          ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
                                   ||
pedigree.cpp:200:11: note: cast one or both operands to int to silence this warning
pedigree.cpp:218:15: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
          if (((sirState[i] == "Match") | (sirState[i] == "Found")) & ((damState[i] == "Match") | (damState[i] == "Found"))) {
              ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
                                                                    &&
pedigree.cpp:218:15: note: cast one or both operands to int to silence this warning
pedigree.cpp:218:72: warning: use of bitwise '|' with boolean operands [-Wbitwise-instead-of-logical]
          if (((sirState[i] == "Match") | (sirState[i] == "Found")) & ((damState[i] == "Match") | (damState[i] == "Found"))) {
                                                                      ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
                                                                                                ||
pedigree.cpp:218:72: note: cast one or both operands to int to silence this warning
pedigree.cpp:218:16: warning: use of bitwise '|' with boolean operands [-Wbitwise-instead-of-logical]
          if (((sirState[i] == "Match") | (sirState[i] == "Found")) & ((damState[i] == "Match") | (damState[i] == "Found"))) {
              ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
                                        ||
pedigree.cpp:218:16: note: cast one or both operands to int to silence this warning
25 warnings generated.
clang++-16 -std=gnu++11 -shared -L/home/hornik/tmp/R/lib -Wl,-O1 -o simer.so RcppExports.o data_converter.o emma.o genotype.o impute.o pedigree.o -fopenmp -llapack -L/home/hornik/tmp/R/lib -lRblas -lgfortran -lm -lquadmath -L/home/hornik/tmp/R/lib -lR
installing to /srv/hornik/tmp/CRAN/simer.Rcheck/00LOCK-simer/00new/simer/libs
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** 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 (simer)