Install log for 'TreeDist'

* installing to library ‘/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages’
* installing *source* package ‘TreeDist’ ...
** this is package ‘TreeDist’ version ‘2.12.0’
** package ‘TreeDist’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
specified C++17
using C++ compiler: ‘Debian clang version 21.1.8 (3+b1)’
using C++17
make[1]: Entering directory '/home/hornik/tmp/scratch/Rtmpt7dpTI/R.INSTALLb6078465c65e3/TreeDist/src'
clang++-21 -std=gnu++17 -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/TreeTools/include' -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O3 -Wall -pedantic   -c RcppExports.cpp -o RcppExports.o
clang++-21 -std=gnu++17 -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/TreeTools/include' -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O3 -Wall -pedantic   -c binary_entropy_counts.cpp -o binary_entropy_counts.o
clang++-21 -std=gnu++17 -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/TreeTools/include' -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O3 -Wall -pedantic   -c day_1985.cpp -o day_1985.o
clang++-21 -std=gnu++17 -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/TreeTools/include' -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O3 -Wall -pedantic   -c hmi.cpp -o hmi.o
clang++-21 -std=gnu++17 -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/TreeTools/include' -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O3 -Wall -pedantic   -c hpart.cpp -o hpart.o
clang++-21 -std=gnu++17 -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/TreeTools/include' -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O3 -Wall -pedantic   -c hpart_relabel.cpp -o hpart_relabel.o
clang++-21 -std=gnu++17 -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/TreeTools/include' -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O3 -Wall -pedantic   -c lap.cpp -o lap.o
clang++-21 -std=gnu++17 -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/TreeTools/include' -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O3 -Wall -pedantic   -c mast.cpp -o mast.o
clang++-21 -std=gnu++17 -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/TreeTools/include' -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O3 -Wall -pedantic   -c nni_distance.cpp -o nni_distance.o
clang++-21 -std=gnu++17 -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/TreeTools/include' -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O3 -Wall -pedantic   -c path_vector.cpp -o path_vector.o
clang++-21 -std=gnu++17 -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/TreeTools/include' -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O3 -Wall -pedantic   -c reduce_tree.cpp -o reduce_tree.o
clang++-21 -std=gnu++17 -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/TreeTools/include' -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O3 -Wall -pedantic   -c spr.cpp -o spr.o
clang++-21 -std=gnu++17 -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/TreeTools/include' -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O3 -Wall -pedantic   -c spr_lookup.cpp -o spr_lookup.o
clang++-21 -std=gnu++17 -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/TreeTools/include' -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O3 -Wall -pedantic   -c tree_distance_functions.cpp -o tree_distance_functions.o
clang++-21 -std=gnu++17 -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/TreeTools/include' -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O3 -Wall -pedantic   -c tree_distances.cpp -o tree_distances.o
clang++-21 -std=gnu++17 -shared -L/home/hornik/tmp/R.check/r-devel-clang/Work/build/lib -Wl,-O1 -o TreeDist.so RcppExports.o binary_entropy_counts.o day_1985.o hmi.o hpart.o hpart_relabel.o lap.o mast.o nni_distance.o path_vector.o reduce_tree.o spr.o spr_lookup.o tree_distance_functions.o tree_distances.o -L/home/hornik/tmp/R.check/r-devel-clang/Work/build/lib -lR
tree_distances.o: in function `Rcpp::demangler_one[abi:cxx11](char const*)':
/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/Rcpp/include/Rcpp/exceptions_impl.h:43:(.text+0x3897): relocation truncated to fit: R_X86_64_PC32 against `.bss'
tree_distances.o: in function `std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >::size() const':
/usr/lib/gcc/x86_64-linux-gnu/15/../../../../include/c++/15/bits/basic_string.h:1165:(.text+0x38a6): relocation truncated to fit: R_X86_64_PC32 against `.bss'
/usr/lib/gcc/x86_64-linux-gnu/15/../../../../include/c++/15/bits/basic_string.h:1165:(.text+0x38ad): relocation truncated to fit: R_X86_64_PC32 against `.bss'
/usr/lib/gcc/x86_64-linux-gnu/15/../../../../include/c++/15/bits/basic_string.h:1165:(.text+0x396b): relocation truncated to fit: R_X86_64_PC32 against `.bss'
tree_distances.o: in function `std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >::_M_local_data()':
/usr/lib/gcc/x86_64-linux-gnu/15/../../../../include/c++/15/bits/basic_string.h:(.text+0x3989): relocation truncated to fit: R_X86_64_PC32 against `.bss'
tree_distances.o: in function `std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >::size() const':
/usr/lib/gcc/x86_64-linux-gnu/15/../../../../include/c++/15/bits/basic_string.h:1165:(.text+0x3a77): relocation truncated to fit: R_X86_64_PC32 against `.bss'
tree_distances.o: in function `Rcpp::demangler_one[abi:cxx11](char const*)':
/usr/lib/gcc/x86_64-linux-gnu/15/../../../../include/c++/15/bits/basic_string.h:2462:(.text+0x3a9b): relocation truncated to fit: R_X86_64_PC32 against `.bss'
tree_distances.o: in function `std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >::_M_data() const':
/usr/lib/gcc/x86_64-linux-gnu/15/../../../../include/c++/15/bits/basic_string.h:239:(.text+0x3acd): relocation truncated to fit: R_X86_64_PC32 against `.bss'
tree_distances.o: in function `std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >::size() const':
/usr/lib/gcc/x86_64-linux-gnu/15/../../../../include/c++/15/bits/basic_string.h:1165:(.text+0x3ad4): relocation truncated to fit: R_X86_64_PC32 against `.bss'
tree_distances.o: in function `Rcpp::demangler_one[abi:cxx11](char const*)':
/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/Rcpp/include/Rcpp/exceptions_impl.h:43:(.text+0x3b54): relocation truncated to fit: R_X86_64_PC32 against `.bss'
tree_distances.o: in function `std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >::_Alloc_hider::_Alloc_hider(char*, std::allocator<char>&&)':
/usr/lib/gcc/x86_64-linux-gnu/15/../../../../include/c++/15/bits/basic_string.h:209:(.text+0x3b68): additional relocation overflows omitted from the output
clang++-21: error: linker command failed with exit code 1 (use -v to see invocation)
make[1]: *** [/home/hornik/tmp/R.check/r-devel-clang/Work/build/share/make/shlib.mk:10: TreeDist.so] Error 1
make[1]: Leaving directory '/home/hornik/tmp/scratch/Rtmpt7dpTI/R.INSTALLb6078465c65e3/TreeDist/src'
ERROR: compilation failed for package ‘TreeDist’
* removing ‘/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/TreeDist’