Install log for 'mappoly'

* installing to library ‘/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages’
* installing *source* package ‘mappoly’ ...
** this is package ‘mappoly’ version ‘0.4.2’
** package ‘mappoly’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C compiler: ‘Debian clang version 23.1.0 (2)’
using C++ compiler: ‘Debian clang version 23.1.0 (2)’
make[1]: Entering directory '/home/hornik/tmp/scratch/RtmpzBwMvM/R.INSTALL39f18d22af453/mappoly/src'
clang++-23 -std=gnu++20 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG  -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/RcppParallel/include' -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O3 -Wall -pedantic   -c RcppExports.cpp -o RcppExports.o
clang++-23 -std=gnu++20 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG  -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/RcppParallel/include' -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O3 -Wall -pedantic   -c calc_genoprob.cpp -o calc_genoprob.o
clang++-23 -std=gnu++20 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG  -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/RcppParallel/include' -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O3 -Wall -pedantic   -c calc_genoprob_based_on_phased_marker_blocks.cpp -o calc_genoprob_based_on_phased_marker_blocks.o
clang++-23 -std=gnu++20 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG  -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/RcppParallel/include' -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O3 -Wall -pedantic   -c calc_loglike_given_map.cpp -o calc_loglike_given_map.o
clang++-23 -std=gnu++20 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG  -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/RcppParallel/include' -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O3 -Wall -pedantic   -c combinatorial.cpp -o combinatorial.o
clang++-23 -std=gnu++20 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG  -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/RcppParallel/include' -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O3 -Wall -pedantic   -c est_hmm_map_based_on_phased_mrk_blocks.cpp -o est_hmm_map_based_on_phased_mrk_blocks.o
clang++-23 -std=gnu++20 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG  -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/RcppParallel/include' -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O3 -Wall -pedantic   -c est_map_hmm_given_dose.cpp -o est_map_hmm_given_dose.o
clang++-23 -std=gnu++20 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG  -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/RcppParallel/include' -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O3 -Wall -pedantic   -c est_map_hmm_given_prior.cpp -o est_map_hmm_given_prior.o
clang++-23 -std=gnu++20 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG  -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/RcppParallel/include' -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O3 -Wall -pedantic   -c genotypic_counts.cpp -o genotypic_counts.o
clang++-23 -std=gnu++20 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG  -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/RcppParallel/include' -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O3 -Wall -pedantic   -c hmm_elements.cpp -o hmm_elements.o
clang++-23 -std=gnu++20 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG  -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/RcppParallel/include' -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O3 -Wall -pedantic   -c hmm_single_parent.cpp -o hmm_single_parent.o
clang-23 -std=gnu23 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG  -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/RcppParallel/include' -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O3 -Wall -pedantic -c mappoly_init.c -o mappoly_init.o
clang++-23 -std=gnu++20 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG  -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/RcppParallel/include' -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O3 -Wall -pedantic   -c pairwise_estimation.cpp -o pairwise_estimation.o
clang++-23 -std=gnu++20 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG  -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/RcppParallel/include' -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O3 -Wall -pedantic   -c pairwise_estimation_rcppparallel.cpp -o pairwise_estimation_rcppparallel.o
In file included from pairwise_estimation_rcppparallel.cpp:41:
In file included from /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/RcppParallel/include/RcppParallel.h:24:
In file included from /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/RcppParallel/include/RcppParallel/TBB.h:16:
In file included from /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/RcppParallel/include/tbb/parallel_for.h:17:
In file included from /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/RcppParallel/include/tbb/../oneapi/tbb/parallel_for.h:23:
/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/RcppParallel/include/tbb/../oneapi/tbb/detail/_task.h:89:13: warning: unused function template 'suspend_callback' [-Wunused-template]
   89 | static void suspend_callback(void* user_callback, suspend_point sp) {
      |             ^~~~~~~~~~~~~~~~
In file included from pairwise_estimation_rcppparallel.cpp:41:
In file included from /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/RcppParallel/include/RcppParallel.h:24:
In file included from /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/RcppParallel/include/RcppParallel/TBB.h:16:
In file included from /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/RcppParallel/include/tbb/parallel_for.h:17:
In file included from /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/RcppParallel/include/tbb/../oneapi/tbb/parallel_for.h:27:
In file included from /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/RcppParallel/include/tbb/../oneapi/tbb/partitioner.h:47:
/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/RcppParallel/include/tbb/../oneapi/tbb/task_group.h:130:15: warning: unused function template 'task_ptr_or_nullptr' [-Wunused-template]
  130 |     d1::task* task_ptr_or_nullptr(F&& f){
      |               ^~~~~~~~~~~~~~~~~~~
2 warnings generated.
clang++-23 -std=gnu++20 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG  -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/RcppParallel/include' -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O3 -Wall -pedantic   -c read_mappoly_vcf.cpp -o read_mappoly_vcf.o
clang++-23 -std=gnu++20 -shared -L/home/hornik/tmp/R.check/r-devel-clang/Work/build/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.check/r-devel-clang/Work/build/lib -lR
make[1]: Leaving directory '/home/hornik/tmp/scratch/RtmpzBwMvM/R.INSTALL39f18d22af453/mappoly/src'
make[1]: Entering directory '/home/hornik/tmp/scratch/RtmpzBwMvM/R.INSTALL39f18d22af453/mappoly/src'
make[1]: Leaving directory '/home/hornik/tmp/scratch/RtmpzBwMvM/R.INSTALL39f18d22af453/mappoly/src'
installing to /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/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)