downloading reverse dependencies ...
downloading cAIC4_1.1.tar.gz ... ok
downloading GEVACO_1.0.1.tar.gz ... ok
downloading qtlpoly_0.2.4.tar.gz ... ok
downloading refund_0.1-38.tar.gz ... ok
downloading simr_1.0.8.tar.gz ... ok
downloading iccbeta_1.2.0.tar.gz ... ok
downloading MVA_1.0-9.tar.gz ... ok

installing dependencies ‘HSAUR2’, ‘mappoly’, ‘RLRsim’

begin installing package ‘mappoly’
begin installing package ‘HSAUR2’
begin installing package ‘RLRsim’
* installing *source* package ‘HSAUR2’ ...
** this is package ‘HSAUR2’ version ‘1.1-21’
** package ‘HSAUR2’ successfully unpacked and MD5 sums checked
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** 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
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (HSAUR2)
* installing *source* package ‘RLRsim’ ...
** this is package ‘RLRsim’ version ‘3.1-9’
** using staged installation
** libs
using C compiler: ‘gcc-15 (Debian 15.2.0-7) 15.2.0’
using C++ compiler: ‘g++-15 (Debian 15.2.0-7) 15.2.0’
make[1]: Entering directory '/home/hornik/tmp/scratch/Rtmp5Hpz1U/R.INSTALL1b4c801869564e/RLRsim/src'
g++-15 -std=gnu++17 -I"/home/hornik/tmp/R/include" -DNDEBUG  -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3   -fpic  -g -O2 -Wall -pedantic -mtune=native   -c RLRsim.cpp -o RLRsim.o
In file included from /home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include/RcppCommon.h:192,
                 from /home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include/Rcpp.h:27,
                 from RLRsim.cpp:3:
In function ‘SEXPREC* Rcpp::internal::primitive_wrap__impl__cast(const T&, Rcpp::traits::false_type) [with T = double]’,
    inlined from ‘SEXPREC* Rcpp::internal::primitive_wrap__impl(const T&, Rcpp::traits::r_type_primitive_tag) [with T = double]’ at /home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include/Rcpp/internal/wrap.h:471:46,
    inlined from ‘SEXPREC* Rcpp::internal::primitive_wrap(const T&) [with T = double]’ at /home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include/Rcpp/internal/wrap.h:495:40,
    inlined from ‘SEXPREC* Rcpp::internal::wrap_dispatch(const T&, Rcpp::traits::wrap_type_primitive_tag) [with T = double]’ at /home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include/Rcpp/internal/wrap.h:744:34,
    inlined from ‘SEXPREC* Rcpp::wrap(const T&) [with T = double]’ at /home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include/Rcpp/internal/wrap_end.h:30:38,
    inlined from ‘static SEXPREC* Rcpp::internal::generic_element_converter<RTYPE>::get(const T&) [with T = double; int RTYPE = 19]’ at /home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include/Rcpp/vector/converter.h:80:23,
    inlined from ‘static void Rcpp::Vector<RTYPE, StoragePolicy>::replace_element__dispatch__isArgument(Rcpp::traits::false_type, iterator, SEXP, R_xlen_t, const U&) [with U = Rcpp::traits::named_object<double>; int RTYPE = 19; StoragePolicy = Rcpp::PreserveStorage]’ at /home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include/Rcpp/vector/Vector.h:530:13,
    inlined from ‘static void Rcpp::Vector<RTYPE, StoragePolicy>::replace_element__dispatch(Rcpp::traits::true_type, iterator, SEXP, R_xlen_t, const U&) [with U = Rcpp::traits::named_object<double>; int RTYPE = 19; StoragePolicy = Rcpp::PreserveStorage]’ at /home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include/Rcpp/vector/Vector.h:523:46,
    inlined from ‘static void Rcpp::Vector<RTYPE, StoragePolicy>::replace_element(iterator, SEXP, R_xlen_t, const U&) [with U = Rcpp::traits::named_object<double>; int RTYPE = 19; StoragePolicy = Rcpp::PreserveStorage]’ at /home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include/Rcpp/vector/Vector.h:512:34,
    inlined from ‘static void Rcpp::Vector<RTYPE, StoragePolicy>::replace_element_impl(iterator&, Rcpp::Shield<SEXPREC*>&, int&, const T&) [with T = Rcpp::traits::named_object<double>; int RTYPE = 19; StoragePolicy = Rcpp::PreserveStorage]’ at /home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include/Rcpp/vector/Vector.h:1164:24,
    inlined from ‘static void Rcpp::Vector<RTYPE, StoragePolicy>::replace_element_impl(iterator&, Rcpp::Shield<SEXPREC*>&, int&, const T&, const TArgs& ...) [with T = Rcpp::traits::named_object<Rcpp::Vector<14, Rcpp::PreserveStorage> >; TArgs = {Rcpp::traits::named_object<double>}; int RTYPE = 19; StoragePolicy = Rcpp::PreserveStorage]’ at /home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include/Rcpp/vector/Vector.h:1170:29,
    inlined from ‘static void Rcpp::Vector<RTYPE, StoragePolicy>::replace_element_impl(iterator&, Rcpp::Shield<SEXPREC*>&, int&, const T&, const TArgs& ...) [with T = Rcpp::traits::named_object<Rcpp::Vector<14, Rcpp::PreserveStorage> >; TArgs = {Rcpp::traits::named_object<Rcpp::Vector<14, Rcpp::PreserveStorage> >, Rcpp::traits::named_object<double>}; int RTYPE = 19; StoragePolicy = Rcpp::PreserveStorage]’ at /home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include/Rcpp/vector/Vector.h:1170:29,
    inlined from ‘static void Rcpp::Vector<RTYPE, StoragePolicy>::replace_element_impl(iterator&, Rcpp::Shield<SEXPREC*>&, int&, const T&, const TArgs& ...) [with T = Rcpp::traits::named_object<Rcpp::Matrix<14> >; TArgs = {Rcpp::traits::named_object<Rcpp::Vector<14, Rcpp::PreserveStorage> >, Rcpp::traits::named_object<Rcpp::Vector<14, Rcpp::PreserveStorage> >, Rcpp::traits::named_object<double>}; int RTYPE = 19; StoragePolicy = Rcpp::PreserveStorage]’ at /home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include/Rcpp/vector/Vector.h:1170:29,
    inlined from ‘static void Rcpp::Vector<RTYPE, StoragePolicy>::replace_element_impl(iterator&, Rcpp::Shield<SEXPREC*>&, int&, const T&, const TArgs& ...) [with T = Rcpp::traits::named_object<Rcpp::Matrix<14> >; TArgs = {Rcpp::traits::named_object<Rcpp::Matrix<14, Rcpp::PreserveStorage> >, Rcpp::traits::named_object<Rcpp::Vector<14, Rcpp::PreserveStorage> >, Rcpp::traits::named_object<Rcpp::Vector<14, Rcpp::PreserveStorage> >, Rcpp::traits::named_object<double>}; int RTYPE = 19; StoragePolicy = Rcpp::PreserveStorage]’ at /home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include/Rcpp/vector/Vector.h:1170:29,
    inlined from ‘static void Rcpp::Vector<RTYPE, StoragePolicy>::replace_element_impl(iterator&, Rcpp::Shield<SEXPREC*>&, int&, const T&, const TArgs& ...) [with T = Rcpp::traits::named_object<Rcpp::Matrix<14> >; TArgs = {Rcpp::traits::named_object<Rcpp::Matrix<14, Rcpp::PreserveStorage> >, Rcpp::traits::named_object<Rcpp::Matrix<14, Rcpp::PreserveStorage> >, Rcpp::traits::named_object<Rcpp::Vector<14, Rcpp::PreserveStorage> >, Rcpp::traits::named_object<Rcpp::Vector<14, Rcpp::PreserveStorage> >, Rcpp::traits::named_object<double>}; int RTYPE = 19; StoragePolicy = Rcpp::PreserveStorage]’ at /home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include/Rcpp/vector/Vector.h:1170:29,
    inlined from ‘static void Rcpp::Vector<RTYPE, StoragePolicy>::replace_element_impl(iterator&, Rcpp::Shield<SEXPREC*>&, int&, const T&, const TArgs& ...) [with T = Rcpp::traits::named_object<Rcpp::Vector<13> >; TArgs = {Rcpp::traits::named_object<Rcpp::Matrix<14, Rcpp::PreserveStorage> >, Rcpp::traits::named_object<Rcpp::Matrix<14, Rcpp::PreserveStorage> >, Rcpp::traits::named_object<Rcpp::Matrix<14, Rcpp::PreserveStorage> >, Rcpp::traits::named_object<Rcpp::Vector<14, Rcpp::PreserveStorage> >, Rcpp::traits::named_object<Rcpp::Vector<14, Rcpp::PreserveStorage> >, Rcpp::traits::named_object<double>}; int RTYPE = 19; StoragePolicy = Rcpp::PreserveStorage]’ at /home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include/Rcpp/vector/Vector.h:1170:29,
    inlined from ‘static void Rcpp::Vector<RTYPE, StoragePolicy>::replace_element_impl(iterator&, Rcpp::Shield<SEXPREC*>&, int&, const T&, const TArgs& ...) [with T = Rcpp::traits::named_object<Rcpp::Vector<14, Rcpp::PreserveStorage> >; TArgs = {Rcpp::traits::named_object<Rcpp::Vector<13, Rcpp::PreserveStorage> >, Rcpp::traits::named_object<Rcpp::Matrix<14, Rcpp::PreserveStorage> >, Rcpp::traits::named_object<Rcpp::Matrix<14, Rcpp::PreserveStorage> >, Rcpp::traits::named_object<Rcpp::Matrix<14, Rcpp::PreserveStorage> >, Rcpp::traits::named_object<Rcpp::Vector<14, Rcpp::PreserveStorage> >, Rcpp::traits::named_object<Rcpp::Vector<14, Rcpp::PreserveStorage> >, Rcpp::traits::named_object<double>}; int RTYPE = 19; StoragePolicy = Rcpp::PreserveStorage]’ at /home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include/Rcpp/vector/Vector.h:1170:29,
    inlined from ‘static Rcpp::Vector<RTYPE, StoragePolicy> Rcpp::Vector<RTYPE, StoragePolicy>::create__dispatch(Rcpp::traits::true_type, const T& ...) [with T = {Rcpp::traits::named_object<Rcpp::Vector<14, Rcpp::PreserveStorage> >, Rcpp::traits::named_object<Rcpp::Vector<13, Rcpp::PreserveStorage> >, Rcpp::traits::named_object<Rcpp::Matrix<14, Rcpp::PreserveStorage> >, Rcpp::traits::named_object<Rcpp::Matrix<14, Rcpp::PreserveStorage> >, Rcpp::traits::named_object<Rcpp::Matrix<14, Rcpp::PreserveStorage> >, Rcpp::traits::named_object<Rcpp::Vector<14, Rcpp::PreserveStorage> >, Rcpp::traits::named_object<Rcpp::Vector<14, Rcpp::PreserveStorage> >, Rcpp::traits::named_object<double>}; int RTYPE = 19; StoragePolicy = Rcpp::PreserveStorage]’ at /home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include/Rcpp/vector/Vector.h:1146:29,
    inlined from ‘static Rcpp::Vector<RTYPE, StoragePolicy> Rcpp::Vector<RTYPE, StoragePolicy>::create(const T& ...) [with T = {Rcpp::traits::named_object<Rcpp::Vector<14, Rcpp::PreserveStorage> >, Rcpp::traits::named_object<Rcpp::Vector<13, Rcpp::PreserveStorage> >, Rcpp::traits::named_object<Rcpp::Matrix<14, Rcpp::PreserveStorage> >, Rcpp::traits::named_object<Rcpp::Matrix<14, Rcpp::PreserveStorage> >, Rcpp::traits::named_object<Rcpp::Matrix<14, Rcpp::PreserveStorage> >, Rcpp::traits::named_object<Rcpp::Vector<14, Rcpp::PreserveStorage> >, Rcpp::traits::named_object<Rcpp::Vector<14, Rcpp::PreserveStorage> >, Rcpp::traits::named_object<double>}; int RTYPE = 19; StoragePolicy = Rcpp::PreserveStorage]’ at /home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include/Rcpp/vector/Vector.h:1128:50,
    inlined from ‘Rcpp::List RLRsimCpp(int, int, int, int, int, int, Rcpp::NumericVector, Rcpp::NumericVector, double, Rcpp::NumericVector, bool)’ at RLRsim.cpp:105:23:
/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include/Rcpp/internal/wrap.h:448:41: warning: ‘ChiK’ may be used uninitialized [-Wmaybe-uninitialized]
  448 |             r_vector_start<RTYPE>(x)[0] = object;
      |             ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~
RLRsim.cpp: In function ‘Rcpp::List RLRsimCpp(int, int, int, int, int, int, Rcpp::NumericVector, Rcpp::NumericVector, double, Rcpp::NumericVector, bool)’:
RLRsim.cpp:36:23: note: ‘ChiK’ was declared here
   36 |     double  LR, N, D, ChiK, ChiSum ;
      |                       ^~~~
g++-15 -std=gnu++17 -I"/home/hornik/tmp/R/include" -DNDEBUG  -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3   -fpic  -g -O2 -Wall -pedantic -mtune=native   -c RcppExports.cpp -o RcppExports.o
gcc-15 -I"/home/hornik/tmp/R/include" -DNDEBUG  -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3   -fpic  -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native  -c init.c -o init.o
g++-15 -std=gnu++17 -shared -L/home/hornik/tmp/R/lib -Wl,-O1 -o RLRsim.so RLRsim.o RcppExports.o init.o -L/home/hornik/tmp/R/lib -lR
make[1]: Leaving directory '/home/hornik/tmp/scratch/Rtmp5Hpz1U/R.INSTALL1b4c801869564e/RLRsim/src'
installing to /home/hornik/tmp/CRAN_recheck/Library/00LOCK-RLRsim/00new/RLRsim/libs
** R
** 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 (RLRsim)
* installing *source* package ‘mappoly’ ...
** this is package ‘mappoly’ version ‘0.4.1’
** package ‘mappoly’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C compiler: ‘gcc-15 (Debian 15.2.0-7) 15.2.0’
using C++ compiler: ‘g++-15 (Debian 15.2.0-7) 15.2.0’
make[1]: Entering directory '/home/hornik/tmp/scratch/Rtmp2SIoe6/R.INSTALL1b4c7e60ada50/mappoly/src'
g++-15 -std=gnu++17 -I"/home/hornik/tmp/R/include" -DNDEBUG  -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/RcppParallel/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3   -fpic  -g -O2 -Wall -pedantic -mtune=native   -c RcppExports.cpp -o RcppExports.o
g++-15 -std=gnu++17 -I"/home/hornik/tmp/R/include" -DNDEBUG  -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/RcppParallel/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3   -fpic  -g -O2 -Wall -pedantic -mtune=native   -c calc_genoprob.cpp -o calc_genoprob.o
g++-15 -std=gnu++17 -I"/home/hornik/tmp/R/include" -DNDEBUG  -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/RcppParallel/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3   -fpic  -g -O2 -Wall -pedantic -mtune=native   -c calc_genoprob_based_on_phased_marker_blocks.cpp -o calc_genoprob_based_on_phased_marker_blocks.o
g++-15 -std=gnu++17 -I"/home/hornik/tmp/R/include" -DNDEBUG  -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/RcppParallel/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3   -fpic  -g -O2 -Wall -pedantic -mtune=native   -c calc_loglike_given_map.cpp -o calc_loglike_given_map.o
g++-15 -std=gnu++17 -I"/home/hornik/tmp/R/include" -DNDEBUG  -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/RcppParallel/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3   -fpic  -g -O2 -Wall -pedantic -mtune=native   -c combinatorial.cpp -o combinatorial.o
g++-15 -std=gnu++17 -I"/home/hornik/tmp/R/include" -DNDEBUG  -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/RcppParallel/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3   -fpic  -g -O2 -Wall -pedantic -mtune=native   -c est_hmm_map_based_on_phased_mrk_blocks.cpp -o est_hmm_map_based_on_phased_mrk_blocks.o
g++-15 -std=gnu++17 -I"/home/hornik/tmp/R/include" -DNDEBUG  -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/RcppParallel/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3   -fpic  -g -O2 -Wall -pedantic -mtune=native   -c est_map_hmm_given_dose.cpp -o est_map_hmm_given_dose.o
g++-15 -std=gnu++17 -I"/home/hornik/tmp/R/include" -DNDEBUG  -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/RcppParallel/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3   -fpic  -g -O2 -Wall -pedantic -mtune=native   -c est_map_hmm_given_prior.cpp -o est_map_hmm_given_prior.o
g++-15 -std=gnu++17 -I"/home/hornik/tmp/R/include" -DNDEBUG  -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/RcppParallel/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3   -fpic  -g -O2 -Wall -pedantic -mtune=native   -c genotypic_counts.cpp -o genotypic_counts.o
g++-15 -std=gnu++17 -I"/home/hornik/tmp/R/include" -DNDEBUG  -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/RcppParallel/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3   -fpic  -g -O2 -Wall -pedantic -mtune=native   -c hmm_elements.cpp -o hmm_elements.o
g++-15 -std=gnu++17 -I"/home/hornik/tmp/R/include" -DNDEBUG  -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/RcppParallel/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3   -fpic  -g -O2 -Wall -pedantic -mtune=native   -c hmm_single_parent.cpp -o hmm_single_parent.o
gcc-15 -I"/home/hornik/tmp/R/include" -DNDEBUG  -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/RcppParallel/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3   -fpic  -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native  -c mappoly_init.c -o mappoly_init.o
g++-15 -std=gnu++17 -I"/home/hornik/tmp/R/include" -DNDEBUG  -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/RcppParallel/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3   -fpic  -g -O2 -Wall -pedantic -mtune=native   -c pairwise_estimation.cpp -o pairwise_estimation.o
g++-15 -std=gnu++17 -I"/home/hornik/tmp/R/include" -DNDEBUG  -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/RcppParallel/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3   -fpic  -g -O2 -Wall -pedantic -mtune=native   -c pairwise_estimation_rcppparallel.cpp -o pairwise_estimation_rcppparallel.o
g++-15 -std=gnu++17 -I"/home/hornik/tmp/R/include" -DNDEBUG  -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/RcppParallel/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3   -fpic  -g -O2 -Wall -pedantic -mtune=native   -c read_mappoly_vcf.cpp -o read_mappoly_vcf.o
g++-15 -std=gnu++17 -shared -L/home/hornik/tmp/R/lib -Wl,-O1 -o mappoly.so RcppExports.o calc_genoprob.o calc_genoprob_based_on_phased_marker_blocks.o calc_loglike_given_map.o combinatorial.o est_hmm_map_based_on_phased_mrk_blocks.o est_map_hmm_given_dose.o est_map_hmm_given_prior.o genotypic_counts.o hmm_elements.o hmm_single_parent.o mappoly_init.o pairwise_estimation.o pairwise_estimation_rcppparallel.o read_mappoly_vcf.o -L/home/hornik/tmp/R/lib -lR
make[1]: Leaving directory '/home/hornik/tmp/scratch/Rtmp2SIoe6/R.INSTALL1b4c7e60ada50/mappoly/src'
installing to /home/hornik/tmp/CRAN_recheck/Library/00LOCK-mappoly/00new/mappoly/libs
** R
** data
*** moving datasets to lazyload DB
** 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 (mappoly)

checking RLRsim_3.1-9.tar.gz ...
checking cAIC4_1.1.tar.gz ...
checking GEVACO_1.0.1.tar.gz ...
checking qtlpoly_0.2.4.tar.gz ...
checking refund_0.1-38.tar.gz ...
checking simr_1.0.8.tar.gz ...
checking iccbeta_1.2.0.tar.gz ...
checking MVA_1.0-9.tar.gz ...

Depends:
Package: RLRsim
  Depends: R (>= 2.14.0)
  Imports: Rcpp (>= 0.11.1), lme4 (>= 1.1), mgcv, nlme
  LinkingTo: Rcpp

Timings:
         user system elapsed
RLRsim 47.087  5.245  54.207

Results:
Check status summary:
                  WARNING OK
  Source packages       0  1
  Reverse depends       1  6

Check results summary:
RLRsim ... OK
rdepends_cAIC4 ... OK
rdepends_GEVACO ... OK
rdepends_iccbeta ... WARNING
* checking whether package ‘iccbeta’ can be installed ... [13s/13s] WARNING
* checking C++ specification ... NOTE
rdepends_MVA ... OK
rdepends_qtlpoly ... OK
rdepends_refund ... OK
rdepends_simr ... OK

Check results changes:
Package: GEVACO
Check: CRAN incoming feasibility
Old result: NOTE

Package: iccbeta
Check: CRAN incoming feasibility
Old result: NOTE