[Debian-med-packaging] Bug#1086370: prime-phylo: FTBFS: fatal error: mpicxx.h: No such file or directory
Santiago Vila
sanvila at debian.org
Wed Oct 30 11:20:43 GMT 2024
Package: src:prime-phylo
Version: 1.0.11-12
Severity: serious
Tags: ftbfs
Dear maintainer:
During a rebuild of all packages in unstable, your package failed to build:
--------------------------------------------------------------------------------
[...]
debian/rules binary
dh binary --buildsystem=cmake
dh_update_autotools_config -O--buildsystem=cmake
dh_autoreconf -O--buildsystem=cmake
debian/rules override_dh_auto_configure
make[1]: Entering directory '/<<PKGBUILDDIR>>'
dh_auto_configure -- \
-Dofficial_binary_packaging=on \
-Dprime_dynamic=on \
-DCMAKE_INSTALL_PREFIX=/usr \
-DCMAKE_INSTALL_RPATH=/usr/lib/prime-phylo \
-DCMAKE_BUILD_TYPE=RELEASE
cd obj-x86_64-linux-gnu && DEB_PYTHON_INSTALL_LAYOUT=deb PKG_CONFIG=/usr/bin/pkg-config cmake -DCMAKE_INSTALL_PREFIX=/usr -DCMAKE_BUILD_TYPE=None -DCMAKE_INSTALL_SYSCONFDIR=/etc -DCMAKE_INSTALL_LOCALSTATEDIR=/var -DCMAKE_EXPORT_NO_PACKAGE_REGISTRY=ON -DCMAKE_FIND_USE_PACKAGE_REGISTRY=OFF -DCMAKE_FIND_PACKAGE_NO_PACKAGE_REGISTRY=ON -DFETCHCONTENT_FULLY_DISCONNECTED=ON -DCMAKE_INSTALL_RUNSTATEDIR=/run -DCMAKE_SKIP_INSTALL_ALL_DEPENDENCY=ON "-GUnix Makefiles" -DCMAKE_VERBOSE_MAKEFILE=ON -DCMAKE_INSTALL_LIBDIR=lib/x86_64-linux-gnu -Dofficial_binary_packaging=on -Dprime_dynamic=on -DCMAKE_INSTALL_PREFIX=/usr -DCMAKE_INSTALL_RPATH=/usr/lib/prime-phylo -DCMAKE_BUILD_TYPE=RELEASE ..
CMake Deprecation Warning at CMakeLists.txt:5 (cmake_minimum_required):
Compatibility with CMake < 3.5 will be removed from a future version of
CMake.
Update the VERSION argument <min> value or use a ...<max> suffix to tell
CMake that the project does not need compatibility with older versions.
-- The CXX compiler identification is GNU 14.2.0
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Check for working CXX compiler: /usr/bin/c++ - skipped
-- Detecting CXX compile features
-- Detecting CXX compile features - done
-- The Fortran compiler identification is GNU 14.2.0
-- Detecting Fortran compiler ABI info
-- Detecting Fortran compiler ABI info - done
-- Check for working Fortran compiler: /usr/bin/gfortran - skipped
-- The C compiler identification is GNU 14.2.0
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Check for working C compiler: /usr/bin/cc - skipped
-- Detecting C compile features
-- Detecting C compile features - done
-- Looking for Fortran sgemm
-- Looking for Fortran sgemm - not found
-- Performing Test CMAKE_HAVE_LIBC_PTHREAD
-- Performing Test CMAKE_HAVE_LIBC_PTHREAD - Success
-- Found Threads: TRUE
-- Looking for Fortran sgemm
-- Looking for Fortran sgemm - found
-- Found BLAS: /usr/lib/x86_64-linux-gnu/libblas.so
hittade /usr/lib/x86_64-linux-gnu/libblas.so
-- Looking for Fortran cheev
-- Looking for Fortran cheev - not found
-- Looking for Fortran cheev
-- Looking for Fortran cheev - found
-- Found LAPACK: /usr/lib/x86_64-linux-gnu/liblapack.so;/usr/lib/x86_64-linux-gnu/libblas.so
-- Found BISON: /usr/bin/bison (found version "3.8.2")
-- Found FLEX: /usr/bin/flex (found version "2.6.4")
-- Found MPI_C: /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so (found version "3.1")
-- Found MPI_CXX: /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so (found version "3.1")
-- Found MPI_Fortran: /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi_usempif08.so (found version "3.1")
-- Found MPI: TRUE (found version "3.1")
CMake Warning (dev) at src/cxx/CMakeLists.txt:92 (find_package):
Policy CMP0167 is not set: The FindBoost module is removed. Run "cmake
--help-policy CMP0167" for policy details. Use the cmake_policy command to
set the policy and suppress this warning.
This warning is for project developers. Use -Wno-dev to suppress it.
-- Found Boost: /usr/lib/x86_64-linux-gnu/cmake/Boost-1.83.0/BoostConfig.cmake (found suitable version "1.83.0", minimum required is "1.40.0") found components: mpi serialization
-- Found LibXml2: /usr/lib/x86_64-linux-gnu/libxml2.so (found version "2.9.14")
mpilib is /usr/lib/x86_64-linux-gnu/openmpi/include;/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi
included path is
CMake Warning (dev) at src/cxx/CMakeLists.txt:366 (get_target_property):
Policy CMP0026 is not set: Disallow use of the LOCATION target property.
Run "cmake --help-policy CMP0026" for policy details. Use the cmake_policy
command to set the policy and suppress this warning.
The LOCATION property should not be read from target "primeDTLSR". Use the
target name directly with add_custom_command, or use the generator
expression $<TARGET_FILE>, as appropriate.
Call Stack (most recent call first):
src/cxx/applications/primeDTLSR/CMakeLists.txt:30 (prime_add_tests)
This warning is for project developers. Use -Wno-dev to suppress it.
CMake Warning (dev) at src/cxx/CMakeLists.txt:366 (get_target_property):
Policy CMP0026 is not set: Disallow use of the LOCATION target property.
Run "cmake --help-policy CMP0026" for policy details. Use the cmake_policy
command to set the policy and suppress this warning.
The LOCATION property should not be read from target "primeDLRS". Use the
target name directly with add_custom_command, or use the generator
expression $<TARGET_FILE>, as appropriate.
Call Stack (most recent call first):
src/cxx/applications/primeDLRS/CMakeLists.txt:27 (prime_add_tests)
This warning is for project developers. Use -Wno-dev to suppress it.
CMake Warning (dev) at src/cxx/CMakeLists.txt:366 (get_target_property):
Policy CMP0026 is not set: Disallow use of the LOCATION target property.
Run "cmake --help-policy CMP0026" for policy details. Use the cmake_policy
command to set the policy and suppress this warning.
The LOCATION property should not be read from target "showtree". Use the
target name directly with add_custom_command, or use the generator
expression $<TARGET_FILE>, as appropriate.
Call Stack (most recent call first):
src/cxx/tools/showtree/CMakeLists.txt:12 (prime_add_tests)
This warning is for project developers. Use -Wno-dev to suppress it.
CMake Warning (dev) at CMakeLists.txt:120 (if):
Policy CMP0053 is not set: Simplify variable reference and escape sequence
evaluation. Run "cmake --help-policy CMP0053" for policy details. Use the
cmake_policy command to set the policy and suppress this warning.
For input:
'@CMAKE_SOURCE_DIR@/excluded_from_release'
the old evaluation rules produce:
'/<<PKGBUILDDIR>>/excluded_from_release'
but the new evaluation rules produce:
'@CMAKE_SOURCE_DIR@/excluded_from_release'
Using the old result for compatibility since the policy is not set.
This warning is for project developers. Use -Wno-dev to suppress it.
-- Configuring done (2.3s)
CMake Warning (dev) at src/cxx/tools/tree2leafnames/CMakeLists.txt:4 (add_executable):
Policy CMP0115 is not set: Source file extensions must be explicit. Run
"cmake --help-policy CMP0115" for policy details. Use the cmake_policy
command to set the policy and suppress this warning.
File:
/<<PKGBUILDDIR>>/src/cxx/tools/tree2leafnames/tree2leafnames.cc
This warning is for project developers. Use -Wno-dev to suppress it.
-- Generating done (0.0s)
CMake Warning:
Manually-specified variables were not used by the project:
CMAKE_EXPORT_NO_PACKAGE_REGISTRY
CMAKE_FIND_PACKAGE_NO_PACKAGE_REGISTRY
CMAKE_INSTALL_LIBDIR
CMAKE_INSTALL_LOCALSTATEDIR
CMAKE_INSTALL_RUNSTATEDIR
CMAKE_INSTALL_SYSCONFDIR
FETCHCONTENT_FULLY_DISCONNECTED
-- Build files have been written to: /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
dh_auto_build -O--buildsystem=cmake
cd obj-x86_64-linux-gnu && make -j2 "INSTALL=install --strip-program=true" VERBOSE=1
make[1]: Entering directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu'
/usr/bin/cmake -S/<<PKGBUILDDIR>> -B/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu --check-build-system CMakeFiles/Makefile.cmake 0
/usr/bin/cmake -E cmake_progress_start /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/CMakeFiles /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu//CMakeFiles/progress.marks
make -f CMakeFiles/Makefile2 all
make[2]: Entering directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu'
make -f src/cxx/libraries/sfile/CMakeFiles/prime-phylo-sfile.dir/build.make src/cxx/libraries/sfile/CMakeFiles/prime-phylo-sfile.dir/depend
make[3]: Entering directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu'
[ 1%] [FLEX][MyScanner2] Building scanner with flex 2.6.4
[ 1%] [BISON][MyParser2] Building parser with bison 3.8.2
cd /<<PKGBUILDDIR>>/src/cxx/libraries/sfile && /usr/bin/bison -d -d -o /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/src/cxx/libraries/sfile/gb.tab.c gb.y
cd /<<PKGBUILDDIR>>/src/cxx/libraries/sfile && /usr/bin/flex -o/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/src/cxx/libraries/sfile/lexer.c seqreader.l
gb.y: warning: 1 nonterminal useless in grammar [-Wother]
gb.y: warning: 1 rule useless in grammar [-Wother]
gb.y:259.1-12: warning: nonterminal useless in grammar: darwin_entry [-Wother]
259 | darwin_entry : TEXT {$$ = NULL; /* Not implemented yet */}
| ^~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/cxx/libraries/sfile /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/src/cxx/libraries/sfile /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/src/cxx/libraries/sfile/CMakeFiles/prime-phylo-sfile.dir/DependInfo.cmake "--color="
make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu'
make -f src/cxx/libraries/sfile/CMakeFiles/prime-phylo-sfile.dir/build.make src/cxx/libraries/sfile/CMakeFiles/prime-phylo-sfile.dir/build
make[3]: Entering directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu'
[ 2%] Building C object src/cxx/libraries/sfile/CMakeFiles/prime-phylo-sfile.dir/gbread.c.o
[ 2%] Building C object src/cxx/libraries/sfile/CMakeFiles/prime-phylo-sfile.dir/sfile.c.o
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/src/cxx/libraries/sfile && /usr/bin/cc -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_sfile_EXPORTS -I/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/src/cxx/libraries/sfile -I/<<PKGBUILDDIR>>/src/cxx/libraries/sfile -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/<<PKGBUILDDIR>>/src/cxx/libraries/prime -I/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/<<PKGBUILDDIR>>/src/cxx/libraries -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/sfile/CMakeFiles/prime-phylo-sfile.dir/sfile.c.o -MF CMakeFiles/prime-phylo-sfile.dir/sfile.c.o.d -o CMakeFiles/prime-phylo-sfile.dir/sfile.c.o -c /<<PKGBUILDDIR>>/src/cxx/libraries/sfile/sfile.c
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/src/cxx/libraries/sfile && /usr/bin/cc -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_sfile_EXPORTS -I/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/src/cxx/libraries/sfile -I/<<PKGBUILDDIR>>/src/cxx/libraries/sfile -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/<<PKGBUILDDIR>>/src/cxx/libraries/prime -I/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/<<PKGBUILDDIR>>/src/cxx/libraries -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/sfile/CMakeFiles/prime-phylo-sfile.dir/gbread.c.o -MF CMakeFiles/prime-phylo-sfile.dir/gbread.c.o.d -o CMakeFiles/prime-phylo-sfile.dir/gbread.c.o -c /<<PKGBUILDDIR>>/src/cxx/libraries/sfile/gbread.c
/<<PKGBUILDDIR>>/src/cxx/libraries/sfile/sfile.c: In function ‘seq_print’:
/<<PKGBUILDDIR>>/src/cxx/libraries/sfile/sfile.c:265:14: warning: format ‘%d’ expects argument of type ‘int’, but argument 2 has type ‘long int’ [-Wformat=]
265 | printf("%9d", char_counter + 1);
| ^~~~~ ~~~~~~~~~~~~~~~~
| |
| long int
/<<PKGBUILDDIR>>/src/cxx/libraries/sfile/sfile.c:212:15: warning: variable ‘date’ set but not used [-Wunused-but-set-variable]
212 | char *top, *date;
| ^~~~
[ 3%] Building C object src/cxx/libraries/sfile/CMakeFiles/prime-phylo-sfile.dir/lexer.c.o
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/src/cxx/libraries/sfile && /usr/bin/cc -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_sfile_EXPORTS -I/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/src/cxx/libraries/sfile -I/<<PKGBUILDDIR>>/src/cxx/libraries/sfile -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/<<PKGBUILDDIR>>/src/cxx/libraries/prime -I/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/<<PKGBUILDDIR>>/src/cxx/libraries -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/sfile/CMakeFiles/prime-phylo-sfile.dir/lexer.c.o -MF CMakeFiles/prime-phylo-sfile.dir/lexer.c.o.d -o CMakeFiles/prime-phylo-sfile.dir/lexer.c.o -c /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/src/cxx/libraries/sfile/lexer.c
/<<PKGBUILDDIR>>/src/cxx/libraries/sfile/sfile.c: In function ‘seq_add_comment’:
/<<PKGBUILDDIR>>/src/cxx/libraries/sfile/sfile.c:303:20: warning: array subscript ‘struct comment[0]’ is partly outside array bounds of ‘unsigned char[8]’ [-Warray-bounds=]
303 | tmp->text = strdup(s);
| ^~
/<<PKGBUILDDIR>>/src/cxx/libraries/sfile/sfile.c:301:38: note: object of size 8 allocated by ‘malloc’
301 | tmp = (struct comment *) malloc(sizeof(struct comment *));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/cxx/libraries/sfile/sfile.c:304:20: warning: array subscript ‘struct comment[0]’ is partly outside array bounds of ‘unsigned char[8]’ [-Warray-bounds=]
304 | tmp->next = NULL;
| ^~
/<<PKGBUILDDIR>>/src/cxx/libraries/sfile/sfile.c:301:38: note: object of size 8 allocated by ‘malloc’
301 | tmp = (struct comment *) malloc(sizeof(struct comment *));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
seqreader.l: In function ‘seq_read’:
seqreader.l:270:9: warning: unused variable ‘code’ [-Wunused-variable]
/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/src/cxx/libraries/sfile/lexer.c: At top level:
/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/src/cxx/libraries/sfile/lexer.c:1864:16: warning: ‘input’ defined but not used [-Wunused-function]
1864 | static int input (void)
| ^~~~~
/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/src/cxx/libraries/sfile/lexer.c:1821:17: warning: ‘yyunput’ defined but not used [-Wunused-function]
1821 | static void yyunput (int c, char * yy_bp )
| ^~~~~~~
[ 3%] Building C object src/cxx/libraries/sfile/CMakeFiles/prime-phylo-sfile.dir/gb.tab.c.o
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/src/cxx/libraries/sfile && /usr/bin/cc -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_sfile_EXPORTS -I/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/src/cxx/libraries/sfile -I/<<PKGBUILDDIR>>/src/cxx/libraries/sfile -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/<<PKGBUILDDIR>>/src/cxx/libraries/prime -I/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/<<PKGBUILDDIR>>/src/cxx/libraries -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/sfile/CMakeFiles/prime-phylo-sfile.dir/gb.tab.c.o -MF CMakeFiles/prime-phylo-sfile.dir/gb.tab.c.o.d -o CMakeFiles/prime-phylo-sfile.dir/gb.tab.c.o -c /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/src/cxx/libraries/sfile/gb.tab.c
gb.y: In function ‘add_to_seq’:
gb.y:403:9: warning: unused variable ‘new_buf’ [-Wunused-variable]
[ 4%] Linking C shared library libprime-phylo-sfile.so
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/src/cxx/libraries/sfile && /usr/bin/cmake -E cmake_link_script CMakeFiles/prime-phylo-sfile.dir/link.txt --verbose=1
/usr/bin/cc -fPIC -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -fexceptions -g -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libprime-phylo-sfile.so -o libprime-phylo-sfile.so "CMakeFiles/prime-phylo-sfile.dir/gbread.c.o" "CMakeFiles/prime-phylo-sfile.dir/sfile.c.o" "CMakeFiles/prime-phylo-sfile.dir/lexer.c.o" "CMakeFiles/prime-phylo-sfile.dir/gb.tab.c.o" -Wl,-rpath,::::::::::::::::::::
make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu'
[ 4%] Built target prime-phylo-sfile
make -f src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/build.make src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/depend
make[3]: Entering directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu'
[ 5%] [BISON][MyParser] Building parser with bison 3.8.2
[ 5%] [FLEX][MyScanner] Building scanner with flex 2.6.4
cd /<<PKGBUILDDIR>>/src/cxx/libraries/prime && /usr/bin/flex -Pyytree_ -o/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/src/cxx/libraries/prime/lexer.c NHX.l
cd /<<PKGBUILDDIR>>/src/cxx/libraries/prime && /usr/bin/bison -d -y -p yytree_ -d -o /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/src/cxx/libraries/prime/NHXparse.c NHXparse.y
NHXparse.y:108.1-7: warning: POSIX Yacc does not support %expect [-Wyacc]
108 | %expect 4
| ^~~~~~~
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/cxx/libraries/prime /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/src/cxx/libraries/prime /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/DependInfo.cmake "--color="
make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu'
make -f src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/build.make src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/build
make[3]: Entering directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu'
[ 6%] Building C object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/NHXnode.c.o
[ 6%] Building C object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/NHXtree.c.o
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/cc -DBOOST_MPI_DYN_LINK -DBOOST_MPI_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/<<PKGBUILDDIR>>/src/cxx/libraries/prime -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/<<PKGBUILDDIR>>/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/x86_64-linux-gnu/openmpi/include -isystem /usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/NHXtree.c.o -MF CMakeFiles/prime-phylo.dir/NHXtree.c.o.d -o CMakeFiles/prime-phylo.dir/NHXtree.c.o -c /<<PKGBUILDDIR>>/src/cxx/libraries/prime/NHXtree.c
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/cc -DBOOST_MPI_DYN_LINK -DBOOST_MPI_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/<<PKGBUILDDIR>>/src/cxx/libraries/prime -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/<<PKGBUILDDIR>>/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/x86_64-linux-gnu/openmpi/include -isystem /usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/NHXnode.c.o -MF CMakeFiles/prime-phylo.dir/NHXnode.c.o.d -o CMakeFiles/prime-phylo.dir/NHXnode.c.o -c /<<PKGBUILDDIR>>/src/cxx/libraries/prime/NHXnode.c
/<<PKGBUILDDIR>>/src/cxx/libraries/prime/NHXnode.c: In function ‘NHX_debug_print’:
/<<PKGBUILDDIR>>/src/cxx/libraries/prime/NHXnode.c:155:32: warning: format ‘%d’ expects argument of type ‘int’, but argument 3 has type ‘double’ [-Wformat=]
155 | fprintf(stderr, "BW:\t%d\n", l->arg.t);
| ~^ ~~~~~~~~
| | |
| int double
| %f
[ 7%] Building C object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/NHXannotation.c.o
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/cc -DBOOST_MPI_DYN_LINK -DBOOST_MPI_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/<<PKGBUILDDIR>>/src/cxx/libraries/prime -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/<<PKGBUILDDIR>>/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/x86_64-linux-gnu/openmpi/include -isystem /usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/NHXannotation.c.o -MF CMakeFiles/prime-phylo.dir/NHXannotation.c.o.d -o CMakeFiles/prime-phylo.dir/NHXannotation.c.o -c /<<PKGBUILDDIR>>/src/cxx/libraries/prime/NHXannotation.c
[ 7%] Building C object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/lexer.c.o
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/cc -DBOOST_MPI_DYN_LINK -DBOOST_MPI_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/<<PKGBUILDDIR>>/src/cxx/libraries/prime -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/<<PKGBUILDDIR>>/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/x86_64-linux-gnu/openmpi/include -isystem /usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/lexer.c.o -MF CMakeFiles/prime-phylo.dir/lexer.c.o.d -o CMakeFiles/prime-phylo.dir/lexer.c.o -c /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/src/cxx/libraries/prime/lexer.c
/<<PKGBUILDDIR>>/src/cxx/libraries/prime/NHXannotation.c: In function ‘new_annotation’:
/<<PKGBUILDDIR>>/src/cxx/libraries/prime/NHXannotation.c:80:3: warning: ‘__builtin_strncpy’ specified bound 5 equals destination size [-Wstringop-truncation]
80 | strncpy(a->anno_type, tag, MAX_ANNOTATION_ID_LENGTH);
| ^
/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/src/cxx/libraries/prime/lexer.c:1597:16: warning: ‘input’ defined but not used [-Wunused-function]
1597 | static int input (void)
| ^~~~~
/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/src/cxx/libraries/prime/lexer.c:1554:17: warning: ‘yyunput’ defined but not used [-Wunused-function]
1554 | static void yyunput (int c, char * yy_bp )
| ^~~~~~~
[ 8%] Building C object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/NHXparse.c.o
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/cc -DBOOST_MPI_DYN_LINK -DBOOST_MPI_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/<<PKGBUILDDIR>>/src/cxx/libraries/prime -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/<<PKGBUILDDIR>>/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/x86_64-linux-gnu/openmpi/include -isystem /usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/NHXparse.c.o -MF CMakeFiles/prime-phylo.dir/NHXparse.c.o.d -o CMakeFiles/prime-phylo.dir/NHXparse.c.o -c /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/src/cxx/libraries/prime/NHXparse.c
NHXparse.y: In function ‘read_tree_string’:
NHXparse.y:402:20: warning: passing argument 1 of ‘read_from_string’ discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers]
NHXparse.y:19:36: note: expected ‘char *’ but argument is of type ‘const char *’
[ 8%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/AnError.cc.o
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_MPI_DYN_LINK -DBOOST_MPI_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/<<PKGBUILDDIR>>/src/cxx/libraries/prime -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/<<PKGBUILDDIR>>/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/x86_64-linux-gnu/openmpi/include -isystem /usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/AnError.cc.o -MF CMakeFiles/prime-phylo.dir/AnError.cc.o.d -o CMakeFiles/prime-phylo.dir/AnError.cc.o -c /<<PKGBUILDDIR>>/src/cxx/libraries/prime/AnError.cc
[ 9%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/Beep.cc.o
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_MPI_DYN_LINK -DBOOST_MPI_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/<<PKGBUILDDIR>>/src/cxx/libraries/prime -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/<<PKGBUILDDIR>>/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/x86_64-linux-gnu/openmpi/include -isystem /usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/Beep.cc.o -MF CMakeFiles/prime-phylo.dir/Beep.cc.o.d -o CMakeFiles/prime-phylo.dir/Beep.cc.o -c /<<PKGBUILDDIR>>/src/cxx/libraries/prime/Beep.cc
[ 10%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/BeepOption.cc.o
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_MPI_DYN_LINK -DBOOST_MPI_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/<<PKGBUILDDIR>>/src/cxx/libraries/prime -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/<<PKGBUILDDIR>>/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/x86_64-linux-gnu/openmpi/include -isystem /usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/BeepOption.cc.o -MF CMakeFiles/prime-phylo.dir/BeepOption.cc.o.d -o CMakeFiles/prime-phylo.dir/BeepOption.cc.o -c /<<PKGBUILDDIR>>/src/cxx/libraries/prime/BeepOption.cc
[ 10%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/Hacks.cc.o
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_MPI_DYN_LINK -DBOOST_MPI_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/<<PKGBUILDDIR>>/src/cxx/libraries/prime -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/<<PKGBUILDDIR>>/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/x86_64-linux-gnu/openmpi/include -isystem /usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/Hacks.cc.o -MF CMakeFiles/prime-phylo.dir/Hacks.cc.o.d -o CMakeFiles/prime-phylo.dir/Hacks.cc.o -c /<<PKGBUILDDIR>>/src/cxx/libraries/prime/Hacks.cc
[ 11%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/ODESolver.cc.o
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_MPI_DYN_LINK -DBOOST_MPI_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/<<PKGBUILDDIR>>/src/cxx/libraries/prime -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/<<PKGBUILDDIR>>/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/x86_64-linux-gnu/openmpi/include -isystem /usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/ODESolver.cc.o -MF CMakeFiles/prime-phylo.dir/ODESolver.cc.o.d -o CMakeFiles/prime-phylo.dir/ODESolver.cc.o -c /<<PKGBUILDDIR>>/src/cxx/libraries/prime/ODESolver.cc
In file included from /<<PKGBUILDDIR>>/src/cxx/libraries/prime/ODESolver.cc:4:
/<<PKGBUILDDIR>>/src/cxx/libraries/prime/ODESolver.hh:359:27: warning: ‘constexpr’ needed for in-class initialization of static data member ‘const beep::Real beep::ODESolver::C2’ of non-integral type [-fpermissive]
359 | static const Real C2 = 1.0 / 5.0;
| ^~
/<<PKGBUILDDIR>>/src/cxx/libraries/prime/ODESolver.hh:360:27: warning: ‘constexpr’ needed for in-class initialization of static data member ‘const beep::Real beep::ODESolver::C3’ of non-integral type [-fpermissive]
360 | static const Real C3 = 3.0 / 10.0;
| ^~
/<<PKGBUILDDIR>>/src/cxx/libraries/prime/ODESolver.hh:361:27: warning: ‘constexpr’ needed for in-class initialization of static data member ‘const beep::Real beep::ODESolver::C4’ of non-integral type [-fpermissive]
361 | static const Real C4 = 4.0 / 5.0;
| ^~
/<<PKGBUILDDIR>>/src/cxx/libraries/prime/ODESolver.hh:362:27: warning: ‘constexpr’ needed for in-class initialization of static data member ‘const beep::Real beep::ODESolver::C5’ of non-integral type [-fpermissive]
362 | static const Real C5 = 8.0 / 9.0;
| ^~
/<<PKGBUILDDIR>>/src/cxx/libraries/prime/ODESolver.hh:363:27: warning: ‘constexpr’ needed for in-class initialization of static data member ‘const beep::Real beep::ODESolver::A21’ of non-integral type [-fpermissive]
363 | static const Real A21 = 1.0 / 5.0;
| ^~~
/<<PKGBUILDDIR>>/src/cxx/libraries/prime/ODESolver.hh:364:27: warning: ‘constexpr’ needed for in-class initialization of static data member ‘const beep::Real beep::ODESolver::A31’ of non-integral type [-fpermissive]
364 | static const Real A31 = 3.0 / 40.0;
| ^~~
/<<PKGBUILDDIR>>/src/cxx/libraries/prime/ODESolver.hh:365:27: warning: ‘constexpr’ needed for in-class initialization of static data member ‘const beep::Real beep::ODESolver::A32’ of non-integral type [-fpermissive]
365 | static const Real A32 = 9.0 / 40.0;
| ^~~
/<<PKGBUILDDIR>>/src/cxx/libraries/prime/ODESolver.hh:366:27: warning: ‘constexpr’ needed for in-class initialization of static data member ‘const beep::Real beep::ODESolver::A41’ of non-integral type [-fpermissive]
366 | static const Real A41 = 44.0 / 45.0;
| ^~~
/<<PKGBUILDDIR>>/src/cxx/libraries/prime/ODESolver.hh:367:27: warning: ‘constexpr’ needed for in-class initialization of static data member ‘const beep::Real beep::ODESolver::A42’ of non-integral type [-fpermissive]
367 | static const Real A42 = -56.0 / 15.0;
| ^~~
/<<PKGBUILDDIR>>/src/cxx/libraries/prime/ODESolver.hh:368:27: warning: ‘constexpr’ needed for in-class initialization of static data member ‘const beep::Real beep::ODESolver::A43’ of non-integral type [-fpermissive]
368 | static const Real A43 = 32.0 / 9.0;
| ^~~
/<<PKGBUILDDIR>>/src/cxx/libraries/prime/ODESolver.hh:369:27: warning: ‘constexpr’ needed for in-class initialization of static data member ‘const beep::Real beep::ODESolver::A51’ of non-integral type [-fpermissive]
369 | static const Real A51 = 19372.0 / 6561.0;
| ^~~
/<<PKGBUILDDIR>>/src/cxx/libraries/prime/ODESolver.hh:370:23: warning: ‘constexpr’ needed for in-class initialization of static data member ‘const beep::Real beep::ODESolver::A52’ of non-integral type [-fpermissive]
370 | static const Real A52 = -25360.0 / 2187.0;
| ^~~
/<<PKGBUILDDIR>>/src/cxx/libraries/prime/ODESolver.hh:371:23: warning: ‘constexpr’ needed for in-class initialization of static data member ‘const beep::Real beep::ODESolver::A53’ of non-integral type [-fpermissive]
371 | static const Real A53 = 64448.0 / 6561.0;
| ^~~
/<<PKGBUILDDIR>>/src/cxx/libraries/prime/ODESolver.hh:372:23: warning: ‘constexpr’ needed for in-class initialization of static data member ‘const beep::Real beep::ODESolver::A54’ of non-integral type [-fpermissive]
372 | static const Real A54 = -212.0 / 729.0;
| ^~~
/<<PKGBUILDDIR>>/src/cxx/libraries/prime/ODESolver.hh:373:23: warning: ‘constexpr’ needed for in-class initialization of static data member ‘const beep::Real beep::ODESolver::A61’ of non-integral type [-fpermissive]
373 | static const Real A61 = 9017.0 / 3168.0;
| ^~~
/<<PKGBUILDDIR>>/src/cxx/libraries/prime/ODESolver.hh:374:23: warning: ‘constexpr’ needed for in-class initialization of static data member ‘const beep::Real beep::ODESolver::A62’ of non-integral type [-fpermissive]
374 | static const Real A62 = -355.0 / 33.0;
| ^~~
/<<PKGBUILDDIR>>/src/cxx/libraries/prime/ODESolver.hh:375:23: warning: ‘constexpr’ needed for in-class initialization of static data member ‘const beep::Real beep::ODESolver::A63’ of non-integral type [-fpermissive]
375 | static const Real A63 = 46732.0 / 5247.0;
| ^~~
/<<PKGBUILDDIR>>/src/cxx/libraries/prime/ODESolver.hh:376:23: warning: ‘constexpr’ needed for in-class initialization of static data member ‘const beep::Real beep::ODESolver::A64’ of non-integral type [-fpermissive]
376 | static const Real A64 = 49.0 / 176.0;
| ^~~
/<<PKGBUILDDIR>>/src/cxx/libraries/prime/ODESolver.hh:377:23: warning: ‘constexpr’ needed for in-class initialization of static data member ‘const beep::Real beep::ODESolver::A65’ of non-integral type [-fpermissive]
377 | static const Real A65 = -5103.0 / 18656.0;
| ^~~
/<<PKGBUILDDIR>>/src/cxx/libraries/prime/ODESolver.hh:378:23: warning: ‘constexpr’ needed for in-class initialization of static data member ‘const beep::Real beep::ODESolver::A71’ of non-integral type [-fpermissive]
378 | static const Real A71 = 35.0 / 384.0;
| ^~~
/<<PKGBUILDDIR>>/src/cxx/libraries/prime/ODESolver.hh:379:23: warning: ‘constexpr’ needed for in-class initialization of static data member ‘const beep::Real beep::ODESolver::A73’ of non-integral type [-fpermissive]
379 | static const Real A73 = 500.0 / 1113.0;
| ^~~
/<<PKGBUILDDIR>>/src/cxx/libraries/prime/ODESolver.hh:380:23: warning: ‘constexpr’ needed for in-class initialization of static data member ‘const beep::Real beep::ODESolver::A74’ of non-integral type [-fpermissive]
380 | static const Real A74 = 125.0 / 192.0;
| ^~~
/<<PKGBUILDDIR>>/src/cxx/libraries/prime/ODESolver.hh:381:23: warning: ‘constexpr’ needed for in-class initialization of static data member ‘const beep::Real beep::ODESolver::A75’ of non-integral type [-fpermissive]
381 | static const Real A75 = -2187.0 / 6784.0;
| ^~~
/<<PKGBUILDDIR>>/src/cxx/libraries/prime/ODESolver.hh:382:23: warning: ‘constexpr’ needed for in-class initialization of static data member ‘const beep::Real beep::ODESolver::A76’ of non-integral type [-fpermissive]
382 | static const Real A76 = 11.0 / 84.0;
| ^~~
/<<PKGBUILDDIR>>/src/cxx/libraries/prime/ODESolver.hh:383:23: warning: ‘constexpr’ needed for in-class initialization of static data member ‘const beep::Real beep::ODESolver::E1’ of non-integral type [-fpermissive]
383 | static const Real E1 = 71.0 / 57600.0;
| ^~
/<<PKGBUILDDIR>>/src/cxx/libraries/prime/ODESolver.hh:384:23: warning: ‘constexpr’ needed for in-class initialization of static data member ‘const beep::Real beep::ODESolver::E3’ of non-integral type [-fpermissive]
384 | static const Real E3 = -71.0 / 16695.0;
| ^~
/<<PKGBUILDDIR>>/src/cxx/libraries/prime/ODESolver.hh:385:23: warning: ‘constexpr’ needed for in-class initialization of static data member ‘const beep::Real beep::ODESolver::E4’ of non-integral type [-fpermissive]
385 | static const Real E4 = 71.0 / 1920.0;
| ^~
/<<PKGBUILDDIR>>/src/cxx/libraries/prime/ODESolver.hh:386:23: warning: ‘constexpr’ needed for in-class initialization of static data member ‘const beep::Real beep::ODESolver::E5’ of non-integral type [-fpermissive]
386 | static const Real E5 = -17253.0 / 339200.0;
| ^~
/<<PKGBUILDDIR>>/src/cxx/libraries/prime/ODESolver.hh:387:23: warning: ‘constexpr’ needed for in-class initialization of static data member ‘const beep::Real beep::ODESolver::E6’ of non-integral type [-fpermissive]
387 | static const Real E6 = 22.0 / 525.0;
| ^~
/<<PKGBUILDDIR>>/src/cxx/libraries/prime/ODESolver.hh:388:23: warning: ‘constexpr’ needed for in-class initialization of static data member ‘const beep::Real beep::ODESolver::E7’ of non-integral type [-fpermissive]
388 | static const Real E7 = -1.0 / 40.0;
| ^~
/<<PKGBUILDDIR>>/src/cxx/libraries/prime/ODESolver.hh:391:23: warning: ‘constexpr’ needed for in-class initialization of static data member ‘const beep::Real beep::ODESolver::D1’ of non-integral type [-fpermissive]
391 | static const Real D1 = -12715105075.0 / 11282082432.0;
| ^~
/<<PKGBUILDDIR>>/src/cxx/libraries/prime/ODESolver.hh:392:23: warning: ‘constexpr’ needed for in-class initialization of static data member ‘const beep::Real beep::ODESolver::D3’ of non-integral type [-fpermissive]
392 | static const Real D3 = 87487479700.0 / 32700410799.0;
| ^~
/<<PKGBUILDDIR>>/src/cxx/libraries/prime/ODESolver.hh:393:23: warning: ‘constexpr’ needed for in-class initialization of static data member ‘const beep::Real beep::ODESolver::D4’ of non-integral type [-fpermissive]
393 | static const Real D4 = -10690763975.0 / 1880347072.0;
| ^~
/<<PKGBUILDDIR>>/src/cxx/libraries/prime/ODESolver.hh:394:23: warning: ‘constexpr’ needed for in-class initialization of static data member ‘const beep::Real beep::ODESolver::D5’ of non-integral type [-fpermissive]
394 | static const Real D5 = 701980252875.0 / 199316789632.0;
| ^~
/<<PKGBUILDDIR>>/src/cxx/libraries/prime/ODESolver.hh:395:23: warning: ‘constexpr’ needed for in-class initialization of static data member ‘const beep::Real beep::ODESolver::D6’ of non-integral type [-fpermissive]
395 | static const Real D6 = -1453857185.0 / 822651844.0;
| ^~
/<<PKGBUILDDIR>>/src/cxx/libraries/prime/ODESolver.hh:396:23: warning: ‘constexpr’ needed for in-class initialization of static data member ‘const beep::Real beep::ODESolver::D7’ of non-integral type [-fpermissive]
396 | static const Real D7 = 69997945.0 / 29380423.0;
| ^~
[ 11%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/PRNG.cc.o
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_MPI_DYN_LINK -DBOOST_MPI_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/<<PKGBUILDDIR>>/src/cxx/libraries/prime -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/<<PKGBUILDDIR>>/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/x86_64-linux-gnu/openmpi/include -isystem /usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/PRNG.cc.o -MF CMakeFiles/prime-phylo.dir/PRNG.cc.o.d -o CMakeFiles/prime-phylo.dir/PRNG.cc.o -c /<<PKGBUILDDIR>>/src/cxx/libraries/prime/PRNG.cc
[ 12%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/PrimeOptionMap.cc.o
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_MPI_DYN_LINK -DBOOST_MPI_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/<<PKGBUILDDIR>>/src/cxx/libraries/prime -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/<<PKGBUILDDIR>>/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/x86_64-linux-gnu/openmpi/include -isystem /usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/PrimeOptionMap.cc.o -MF CMakeFiles/prime-phylo.dir/PrimeOptionMap.cc.o.d -o CMakeFiles/prime-phylo.dir/PrimeOptionMap.cc.o -c /<<PKGBUILDDIR>>/src/cxx/libraries/prime/PrimeOptionMap.cc
[ 12%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/ProbabilityModel.cc.o
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_MPI_DYN_LINK -DBOOST_MPI_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/<<PKGBUILDDIR>>/src/cxx/libraries/prime -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/<<PKGBUILDDIR>>/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/x86_64-linux-gnu/openmpi/include -isystem /usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/ProbabilityModel.cc.o -MF CMakeFiles/prime-phylo.dir/ProbabilityModel.cc.o.d -o CMakeFiles/prime-phylo.dir/ProbabilityModel.cc.o -c /<<PKGBUILDDIR>>/src/cxx/libraries/prime/ProbabilityModel.cc
In file included from /<<PKGBUILDDIR>>/src/cxx/libraries/prime/PrimeOptionMap.cc:3:
/<<PKGBUILDDIR>>/src/cxx/libraries/prime/PrimeOption.hh: In member function ‘void beep::UserSubstitutionMatrixOption::parseParams(std::string&, unsigned int, std::vector<beep::UserSubstMatrixParams>&)’:
/<<PKGBUILDDIR>>/src/cxx/libraries/prime/PrimeOption.hh:405:30: warning: catching polymorphic type ‘class std::exception’ by value [-Wcatch-value=]
405 | catch(std::exception e)
| ^
/<<PKGBUILDDIR>>/src/cxx/libraries/prime/PrimeOption.hh:423:30: warning: catching polymorphic type ‘class std::exception’ by value [-Wcatch-value=]
423 | catch(std::exception e)
| ^
[ 13%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/DiscreteGamma.cc.o
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_MPI_DYN_LINK -DBOOST_MPI_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/<<PKGBUILDDIR>>/src/cxx/libraries/prime -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/<<PKGBUILDDIR>>/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/x86_64-linux-gnu/openmpi/include -isystem /usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/DiscreteGamma.cc.o -MF CMakeFiles/prime-phylo.dir/DiscreteGamma.cc.o.d -o CMakeFiles/prime-phylo.dir/DiscreteGamma.cc.o -c /<<PKGBUILDDIR>>/src/cxx/libraries/prime/DiscreteGamma.cc
[ 14%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/Probability.cc.o
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_MPI_DYN_LINK -DBOOST_MPI_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/<<PKGBUILDDIR>>/src/cxx/libraries/prime -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/<<PKGBUILDDIR>>/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/x86_64-linux-gnu/openmpi/include -isystem /usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/Probability.cc.o -MF CMakeFiles/prime-phylo.dir/Probability.cc.o.d -o CMakeFiles/prime-phylo.dir/Probability.cc.o -c /<<PKGBUILDDIR>>/src/cxx/libraries/prime/Probability.cc
[ 14%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/Tokenizer.cc.o
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_MPI_DYN_LINK -DBOOST_MPI_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/<<PKGBUILDDIR>>/src/cxx/libraries/prime -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/<<PKGBUILDDIR>>/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/x86_64-linux-gnu/openmpi/include -isystem /usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/Tokenizer.cc.o -MF CMakeFiles/prime-phylo.dir/Tokenizer.cc.o.d -o CMakeFiles/prime-phylo.dir/Tokenizer.cc.o -c /<<PKGBUILDDIR>>/src/cxx/libraries/prime/Tokenizer.cc
[ 15%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/TimeEstimator.cc.o
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_MPI_DYN_LINK -DBOOST_MPI_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/<<PKGBUILDDIR>>/src/cxx/libraries/prime -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/<<PKGBUILDDIR>>/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/x86_64-linux-gnu/openmpi/include -isystem /usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/TimeEstimator.cc.o -MF CMakeFiles/prime-phylo.dir/TimeEstimator.cc.o.d -o CMakeFiles/prime-phylo.dir/TimeEstimator.cc.o -c /<<PKGBUILDDIR>>/src/cxx/libraries/prime/TimeEstimator.cc
[ 15%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/BranchSwapping.cc.o
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_MPI_DYN_LINK -DBOOST_MPI_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/<<PKGBUILDDIR>>/src/cxx/libraries/prime -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/<<PKGBUILDDIR>>/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/x86_64-linux-gnu/openmpi/include -isystem /usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/BranchSwapping.cc.o -MF CMakeFiles/prime-phylo.dir/BranchSwapping.cc.o.d -o CMakeFiles/prime-phylo.dir/BranchSwapping.cc.o -c /<<PKGBUILDDIR>>/src/cxx/libraries/prime/BranchSwapping.cc
[ 16%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/DiscTree.cc.o
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_MPI_DYN_LINK -DBOOST_MPI_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/<<PKGBUILDDIR>>/src/cxx/libraries/prime -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/<<PKGBUILDDIR>>/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/x86_64-linux-gnu/openmpi/include -isystem /usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/DiscTree.cc.o -MF CMakeFiles/prime-phylo.dir/DiscTree.cc.o.d -o CMakeFiles/prime-phylo.dir/DiscTree.cc.o -c /<<PKGBUILDDIR>>/src/cxx/libraries/prime/DiscTree.cc
[ 17%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/EdgeDiscPtMaps.cc.o
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_MPI_DYN_LINK -DBOOST_MPI_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/<<PKGBUILDDIR>>/src/cxx/libraries/prime -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/<<PKGBUILDDIR>>/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/x86_64-linux-gnu/openmpi/include -isystem /usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/EdgeDiscPtMaps.cc.o -MF CMakeFiles/prime-phylo.dir/EdgeDiscPtMaps.cc.o.d -o CMakeFiles/prime-phylo.dir/EdgeDiscPtMaps.cc.o -c /<<PKGBUILDDIR>>/src/cxx/libraries/prime/EdgeDiscPtMaps.cc
[ 17%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/EdgeDiscTree.cc.o
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_MPI_DYN_LINK -DBOOST_MPI_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/<<PKGBUILDDIR>>/src/cxx/libraries/prime -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/<<PKGBUILDDIR>>/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/x86_64-linux-gnu/openmpi/include -isystem /usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/EdgeDiscTree.cc.o -MF CMakeFiles/prime-phylo.dir/EdgeDiscTree.cc.o.d -o CMakeFiles/prime-phylo.dir/EdgeDiscTree.cc.o -c /<<PKGBUILDDIR>>/src/cxx/libraries/prime/EdgeDiscTree.cc
In file included from /<<PKGBUILDDIR>>/src/cxx/libraries/prime/EdgeDiscPtMaps.cc:6:
/<<PKGBUILDDIR>>/src/cxx/libraries/prime/EdgeDiscPtMapIterator.hh:31:43: warning: ‘template<class _Category, class _Tp, class _Distance, class _Pointer, class _Reference> struct std::iterator’ is deprecated [-Wdeprecated-declarations]
31 | class EdgeDiscPtMapIterator : public std::iterator<std::forward_iterator_tag, T>
| ^~~~~~~~
In file included from /usr/include/c++/14/bits/stl_iterator_base_funcs.h:66,
from /usr/include/c++/14/string:47,
from /<<PKGBUILDDIR>>/src/cxx/libraries/prime/AnError.hh:1,
from /<<PKGBUILDDIR>>/src/cxx/libraries/prime/EdgeDiscPtMaps.cc:3:
/usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here
127 | struct _GLIBCXX17_DEPRECATED iterator
| ^~~~~~~~
/<<PKGBUILDDIR>>/src/cxx/libraries/prime/EdgeDiscPtMapIterator.hh: In constructor ‘beep::EdgeDiscPtMapIterator<T>::EdgeDiscPtMapIterator(beep::EdgeDiscPtMap<T>*, beep::EdgeDiscretizer::Point)’:
/<<PKGBUILDDIR>>/src/cxx/libraries/prime/EdgeDiscPtMapIterator.hh:42:22: warning: ‘template<class _Category, class _Tp, class _Distance, class _Pointer, class _Reference> struct std::iterator’ is deprecated [-Wdeprecated-declarations]
42 | std::iterator<std::forward_iterator_tag, T>(),
| ^~~~~~~~
/usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here
127 | struct _GLIBCXX17_DEPRECATED iterator
| ^~~~~~~~
/<<PKGBUILDDIR>>/src/cxx/libraries/prime/EdgeDiscPtMapIterator.hh: In constructor ‘beep::EdgeDiscPtMapIterator<T>::EdgeDiscPtMapIterator()’:
/<<PKGBUILDDIR>>/src/cxx/libraries/prime/EdgeDiscPtMapIterator.hh:54:22: warning: ‘template<class _Category, class _Tp, class _Distance, class _Pointer, class _Reference> struct std::iterator’ is deprecated [-Wdeprecated-declarations]
54 | std::iterator<std::forward_iterator_tag, T>(),
| ^~~~~~~~
/usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here
127 | struct _GLIBCXX17_DEPRECATED iterator
| ^~~~~~~~
/<<PKGBUILDDIR>>/src/cxx/libraries/prime/EdgeDiscPtMapIterator.hh: In copy constructor ‘beep::EdgeDiscPtMapIterator<T>::EdgeDiscPtMapIterator(const beep::EdgeDiscPtMapIterator<T>&)’:
/<<PKGBUILDDIR>>/src/cxx/libraries/prime/EdgeDiscPtMapIterator.hh:64:22: warning: ‘template<class _Category, class _Tp, class _Distance, class _Pointer, class _Reference> struct std::iterator’ is deprecated [-Wdeprecated-declarations]
64 | std::iterator<std::forward_iterator_tag, T>(),
| ^~~~~~~~
/usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here
127 | struct _GLIBCXX17_DEPRECATED iterator
| ^~~~~~~~
[ 18%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/EpochPtMaps.cc.o
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_MPI_DYN_LINK -DBOOST_MPI_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/<<PKGBUILDDIR>>/src/cxx/libraries/prime -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/<<PKGBUILDDIR>>/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/x86_64-linux-gnu/openmpi/include -isystem /usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/EpochPtMaps.cc.o -MF CMakeFiles/prime-phylo.dir/EpochPtMaps.cc.o.d -o CMakeFiles/prime-phylo.dir/EpochPtMaps.cc.o -c /<<PKGBUILDDIR>>/src/cxx/libraries/prime/EpochPtMaps.cc
[ 18%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/EpochPtSet.cc.o
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_MPI_DYN_LINK -DBOOST_MPI_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/<<PKGBUILDDIR>>/src/cxx/libraries/prime -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/<<PKGBUILDDIR>>/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/x86_64-linux-gnu/openmpi/include -isystem /usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/EpochPtSet.cc.o -MF CMakeFiles/prime-phylo.dir/EpochPtSet.cc.o.d -o CMakeFiles/prime-phylo.dir/EpochPtSet.cc.o -c /<<PKGBUILDDIR>>/src/cxx/libraries/prime/EpochPtSet.cc
In file included from /<<PKGBUILDDIR>>/src/cxx/libraries/prime/EpochPtMaps.hh:9,
from /<<PKGBUILDDIR>>/src/cxx/libraries/prime/EpochPtMaps.cc:5:
/<<PKGBUILDDIR>>/src/cxx/libraries/prime/EpochTree.hh:54:27: warning: ‘constexpr’ needed for in-class initialization of static data member ‘const beep::Real beep::EpochTree::MIN_SPLICE_DELTA’ of non-integral type [-fpermissive]
54 | static const Real MIN_SPLICE_DELTA = 0.0001;
| ^~~~~~~~~~~~~~~~
[ 19%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/EpochTree.cc.o
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_MPI_DYN_LINK -DBOOST_MPI_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/<<PKGBUILDDIR>>/src/cxx/libraries/prime -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/<<PKGBUILDDIR>>/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/x86_64-linux-gnu/openmpi/include -isystem /usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/EpochTree.cc.o -MF CMakeFiles/prime-phylo.dir/EpochTree.cc.o.d -o CMakeFiles/prime-phylo.dir/EpochTree.cc.o -c /<<PKGBUILDDIR>>/src/cxx/libraries/prime/EpochTree.cc
In file included from /<<PKGBUILDDIR>>/src/cxx/libraries/prime/EpochTree.cc:7:
/<<PKGBUILDDIR>>/src/cxx/libraries/prime/EpochTree.hh:54:27: warning: ‘constexpr’ needed for in-class initialization of static data member ‘const beep::Real beep::EpochTree::MIN_SPLICE_DELTA’ of non-integral type [-fpermissive]
54 | static const Real MIN_SPLICE_DELTA = 0.0001;
| ^~~~~~~~~~~~~~~~
[ 19%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/InvMRCA.cc.o
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_MPI_DYN_LINK -DBOOST_MPI_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/<<PKGBUILDDIR>>/src/cxx/libraries/prime -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/<<PKGBUILDDIR>>/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/x86_64-linux-gnu/openmpi/include -isystem /usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/InvMRCA.cc.o -MF CMakeFiles/prime-phylo.dir/InvMRCA.cc.o.d -o CMakeFiles/prime-phylo.dir/InvMRCA.cc.o -c /<<PKGBUILDDIR>>/src/cxx/libraries/prime/InvMRCA.cc
[ 20%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/Node.cc.o
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_MPI_DYN_LINK -DBOOST_MPI_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/<<PKGBUILDDIR>>/src/cxx/libraries/prime -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/<<PKGBUILDDIR>>/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/x86_64-linux-gnu/openmpi/include -isystem /usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/Node.cc.o -MF CMakeFiles/prime-phylo.dir/Node.cc.o.d -o CMakeFiles/prime-phylo.dir/Node.cc.o -c /<<PKGBUILDDIR>>/src/cxx/libraries/prime/Node.cc
[ 21%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/NodeMap.cc.o
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_MPI_DYN_LINK -DBOOST_MPI_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/<<PKGBUILDDIR>>/src/cxx/libraries/prime -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/<<PKGBUILDDIR>>/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/x86_64-linux-gnu/openmpi/include -isystem /usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/NodeMap.cc.o -MF CMakeFiles/prime-phylo.dir/NodeMap.cc.o.d -o CMakeFiles/prime-phylo.dir/NodeMap.cc.o -c /<<PKGBUILDDIR>>/src/cxx/libraries/prime/NodeMap.cc
[ 21%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/NodeNodeMap.cc.o
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_MPI_DYN_LINK -DBOOST_MPI_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/<<PKGBUILDDIR>>/src/cxx/libraries/prime -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/<<PKGBUILDDIR>>/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/x86_64-linux-gnu/openmpi/include -isystem /usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/NodeNodeMap.cc.o -MF CMakeFiles/prime-phylo.dir/NodeNodeMap.cc.o.d -o CMakeFiles/prime-phylo.dir/NodeNodeMap.cc.o -c /<<PKGBUILDDIR>>/src/cxx/libraries/prime/NodeNodeMap.cc
In file included from /<<PKGBUILDDIR>>/src/cxx/libraries/prime/NodeMap.cc:3:
/<<PKGBUILDDIR>>/src/cxx/libraries/prime/NodeMap.hh:28:15: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor]
28 | NodeMap<C>();
| ^
/<<PKGBUILDDIR>>/src/cxx/libraries/prime/NodeMap.hh:28:15: note: remove the ‘< >’
/<<PKGBUILDDIR>>/src/cxx/libraries/prime/NodeMap.hh:29:15: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor]
29 | NodeMap<C>(const Tree &G);
| ^
/<<PKGBUILDDIR>>/src/cxx/libraries/prime/NodeMap.hh:29:15: note: remove the ‘< >’
/<<PKGBUILDDIR>>/src/cxx/libraries/prime/NodeMap.hh:30:15: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor]
30 | NodeMap<C>(const Tree &G, const C defval);
| ^
/<<PKGBUILDDIR>>/src/cxx/libraries/prime/NodeMap.hh:30:15: note: remove the ‘< >’
/<<PKGBUILDDIR>>/src/cxx/libraries/prime/NodeMap.hh:31:15: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor]
31 | NodeMap<C>(const NodeMap<C> &nm);
| ^
/<<PKGBUILDDIR>>/src/cxx/libraries/prime/NodeMap.hh:31:15: note: remove the ‘< >’
/<<PKGBUILDDIR>>/src/cxx/libraries/prime/NodeMap.hh:32:5: warning: template-id not allowed for destructor in C++20 [-Wtemplate-id-cdtor]
32 | ~NodeMap<C>();
| ^
/<<PKGBUILDDIR>>/src/cxx/libraries/prime/NodeMap.hh:32:5: note: remove the ‘< >’
[ 22%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/RandomTreeGenerator.cc.o
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_MPI_DYN_LINK -DBOOST_MPI_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/<<PKGBUILDDIR>>/src/cxx/libraries/prime -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/<<PKGBUILDDIR>>/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/x86_64-linux-gnu/openmpi/include -isystem /usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/RandomTreeGenerator.cc.o -MF CMakeFiles/prime-phylo.dir/RandomTreeGenerator.cc.o.d -o CMakeFiles/prime-phylo.dir/RandomTreeGenerator.cc.o -c /<<PKGBUILDDIR>>/src/cxx/libraries/prime/RandomTreeGenerator.cc
[ 22%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/StrStrMap.cc.o
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_MPI_DYN_LINK -DBOOST_MPI_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/<<PKGBUILDDIR>>/src/cxx/libraries/prime -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/<<PKGBUILDDIR>>/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/x86_64-linux-gnu/openmpi/include -isystem /usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/StrStrMap.cc.o -MF CMakeFiles/prime-phylo.dir/StrStrMap.cc.o.d -o CMakeFiles/prime-phylo.dir/StrStrMap.cc.o -c /<<PKGBUILDDIR>>/src/cxx/libraries/prime/StrStrMap.cc
[ 23%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/Tree.cc.o
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_MPI_DYN_LINK -DBOOST_MPI_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/<<PKGBUILDDIR>>/src/cxx/libraries/prime -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/<<PKGBUILDDIR>>/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/x86_64-linux-gnu/openmpi/include -isystem /usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/Tree.cc.o -MF CMakeFiles/prime-phylo.dir/Tree.cc.o.d -o CMakeFiles/prime-phylo.dir/Tree.cc.o -c /<<PKGBUILDDIR>>/src/cxx/libraries/prime/Tree.cc
[ 23%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/TreeAnalysis.cc.o
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_MPI_DYN_LINK -DBOOST_MPI_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/<<PKGBUILDDIR>>/src/cxx/libraries/prime -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/<<PKGBUILDDIR>>/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/x86_64-linux-gnu/openmpi/include -isystem /usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/TreeAnalysis.cc.o -MF CMakeFiles/prime-phylo.dir/TreeAnalysis.cc.o.d -o CMakeFiles/prime-phylo.dir/TreeAnalysis.cc.o -c /<<PKGBUILDDIR>>/src/cxx/libraries/prime/TreeAnalysis.cc
In file included from /<<PKGBUILDDIR>>/src/cxx/libraries/prime/TreeAnalysis.cc:3:
/<<PKGBUILDDIR>>/src/cxx/libraries/prime/NodeMap.hh:28:15: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor]
28 | NodeMap<C>();
| ^
/<<PKGBUILDDIR>>/src/cxx/libraries/prime/NodeMap.hh:28:15: note: remove the ‘< >’
/<<PKGBUILDDIR>>/src/cxx/libraries/prime/NodeMap.hh:29:15: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor]
29 | NodeMap<C>(const Tree &G);
| ^
/<<PKGBUILDDIR>>/src/cxx/libraries/prime/NodeMap.hh:29:15: note: remove the ‘< >’
/<<PKGBUILDDIR>>/src/cxx/libraries/prime/NodeMap.hh:30:15: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor]
30 | NodeMap<C>(const Tree &G, const C defval);
| ^
/<<PKGBUILDDIR>>/src/cxx/libraries/prime/NodeMap.hh:30:15: note: remove the ‘< >’
/<<PKGBUILDDIR>>/src/cxx/libraries/prime/NodeMap.hh:31:15: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor]
31 | NodeMap<C>(const NodeMap<C> &nm);
| ^
/<<PKGBUILDDIR>>/src/cxx/libraries/prime/NodeMap.hh:31:15: note: remove the ‘< >’
/<<PKGBUILDDIR>>/src/cxx/libraries/prime/NodeMap.hh:32:5: warning: template-id not allowed for destructor in C++20 [-Wtemplate-id-cdtor]
32 | ~NodeMap<C>();
| ^
/<<PKGBUILDDIR>>/src/cxx/libraries/prime/NodeMap.hh:32:5: note: remove the ‘< >’
[ 24%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/TreeDiscretizer.cc.o
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_MPI_DYN_LINK -DBOOST_MPI_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/<<PKGBUILDDIR>>/src/cxx/libraries/prime -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/<<PKGBUILDDIR>>/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/x86_64-linux-gnu/openmpi/include -isystem /usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/TreeDiscretizer.cc.o -MF CMakeFiles/prime-phylo.dir/TreeDiscretizer.cc.o.d -o CMakeFiles/prime-phylo.dir/TreeDiscretizer.cc.o -c /<<PKGBUILDDIR>>/src/cxx/libraries/prime/TreeDiscretizer.cc
[ 25%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/TreeDiscretizers.cc.o
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_MPI_DYN_LINK -DBOOST_MPI_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/<<PKGBUILDDIR>>/src/cxx/libraries/prime -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/<<PKGBUILDDIR>>/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/x86_64-linux-gnu/openmpi/include -isystem /usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/TreeDiscretizers.cc.o -MF CMakeFiles/prime-phylo.dir/TreeDiscretizers.cc.o.d -o CMakeFiles/prime-phylo.dir/TreeDiscretizers.cc.o -c /<<PKGBUILDDIR>>/src/cxx/libraries/prime/TreeDiscretizers.cc
[ 25%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/TreeMCMC.cc.o
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_MPI_DYN_LINK -DBOOST_MPI_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/<<PKGBUILDDIR>>/src/cxx/libraries/prime -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/<<PKGBUILDDIR>>/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/x86_64-linux-gnu/openmpi/include -isystem /usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/TreeMCMC.cc.o -MF CMakeFiles/prime-phylo.dir/TreeMCMC.cc.o.d -o CMakeFiles/prime-phylo.dir/TreeMCMC.cc.o -c /<<PKGBUILDDIR>>/src/cxx/libraries/prime/TreeMCMC.cc
[ 26%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/TreeIO.cc.o
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_MPI_DYN_LINK -DBOOST_MPI_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/<<PKGBUILDDIR>>/src/cxx/libraries/prime -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/<<PKGBUILDDIR>>/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/x86_64-linux-gnu/openmpi/include -isystem /usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/TreeIO.cc.o -MF CMakeFiles/prime-phylo.dir/TreeIO.cc.o.d -o CMakeFiles/prime-phylo.dir/TreeIO.cc.o -c /<<PKGBUILDDIR>>/src/cxx/libraries/prime/TreeIO.cc
In file included from /<<PKGBUILDDIR>>/src/cxx/libraries/prime/ReconciliationModel.hh:10,
from /<<PKGBUILDDIR>>/src/cxx/libraries/prime/GuestTreeModel.hh:4,
from /<<PKGBUILDDIR>>/src/cxx/libraries/prime/TreeMCMC.hh:7,
from /<<PKGBUILDDIR>>/src/cxx/libraries/prime/TreeMCMC.cc:1:
/<<PKGBUILDDIR>>/src/cxx/libraries/prime/NodeMap.hh:28:15: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor]
28 | NodeMap<C>();
| ^
/<<PKGBUILDDIR>>/src/cxx/libraries/prime/NodeMap.hh:28:15: note: remove the ‘< >’
/<<PKGBUILDDIR>>/src/cxx/libraries/prime/NodeMap.hh:29:15: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor]
29 | NodeMap<C>(const Tree &G);
| ^
/<<PKGBUILDDIR>>/src/cxx/libraries/prime/NodeMap.hh:29:15: note: remove the ‘< >’
/<<PKGBUILDDIR>>/src/cxx/libraries/prime/NodeMap.hh:30:15: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor]
30 | NodeMap<C>(const Tree &G, const C defval);
| ^
/<<PKGBUILDDIR>>/src/cxx/libraries/prime/NodeMap.hh:30:15: note: remove the ‘< >’
/<<PKGBUILDDIR>>/src/cxx/libraries/prime/NodeMap.hh:31:15: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor]
31 | NodeMap<C>(const NodeMap<C> &nm);
| ^
/<<PKGBUILDDIR>>/src/cxx/libraries/prime/NodeMap.hh:31:15: note: remove the ‘< >’
/<<PKGBUILDDIR>>/src/cxx/libraries/prime/NodeMap.hh:32:5: warning: template-id not allowed for destructor in C++20 [-Wtemplate-id-cdtor]
32 | ~NodeMap<C>();
| ^
/<<PKGBUILDDIR>>/src/cxx/libraries/prime/NodeMap.hh:32:5: note: remove the ‘< >’
/<<PKGBUILDDIR>>/src/cxx/libraries/prime/TreeMCMC.cc: In constructor ‘beep::TreeMCMC::TreeMCMC(beep::MCMCModel&, beep::Tree&, const beep::Real&)’:
/<<PKGBUILDDIR>>/src/cxx/libraries/prime/TreeMCMC.cc:26:15: warning: passing NULL to non-pointer argument 1 of ‘beep::RealVector::RealVector(unsigned int)’ [-Wconversion-null]
26 | old_times(NULL),
| ^~~~
In file included from /<<PKGBUILDDIR>>/src/cxx/libraries/prime/BranchSwapping.hh:5,
from /<<PKGBUILDDIR>>/src/cxx/libraries/prime/TreeMCMC.hh:6:
/<<PKGBUILDDIR>>/src/cxx/libraries/prime/BeepVector.hh:257:25: note: declared here
257 | RealVector(unsigned n_elems) //!< All elems are initialized to zero.
| ~~~~~~~~~^~~~~~~
/<<PKGBUILDDIR>>/src/cxx/libraries/prime/TreeMCMC.cc:27:15: warning: passing NULL to non-pointer argument 1 of ‘beep::RealVector::RealVector(unsigned int)’ [-Wconversion-null]
27 | old_rates(NULL),
| ^~~~
/<<PKGBUILDDIR>>/src/cxx/libraries/prime/BeepVector.hh:257:25: note: declared here
257 | RealVector(unsigned n_elems) //!< All elems are initialized to zero.
| ~~~~~~~~~^~~~~~~
/<<PKGBUILDDIR>>/src/cxx/libraries/prime/TreeMCMC.cc:28:17: warning: passing NULL to non-pointer argument 1 of ‘beep::RealVector::RealVector(unsigned int)’ [-Wconversion-null]
28 | old_lengths(NULL),
| ^~~~
/<<PKGBUILDDIR>>/src/cxx/libraries/prime/BeepVector.hh:257:25: note: declared here
257 | RealVector(unsigned n_elems) //!< All elems are initialized to zero.
| ~~~~~~~~~^~~~~~~
[ 26%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/TreeInputOutput.cc.o
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_MPI_DYN_LINK -DBOOST_MPI_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/<<PKGBUILDDIR>>/src/cxx/libraries/prime -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/<<PKGBUILDDIR>>/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/x86_64-linux-gnu/openmpi/include -isystem /usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/TreeInputOutput.cc.o -MF CMakeFiles/prime-phylo.dir/TreeInputOutput.cc.o.d -o CMakeFiles/prime-phylo.dir/TreeInputOutput.cc.o -c /<<PKGBUILDDIR>>/src/cxx/libraries/prime/TreeInputOutput.cc
/<<PKGBUILDDIR>>/src/cxx/libraries/prime/TreeInputOutput.cc: In member function ‘void beep::TreeInputOutput::fromFileStream(FILE*, beep::inputFormats)’:
/<<PKGBUILDDIR>>/src/cxx/libraries/prime/TreeInputOutput.cc:118:29: warning: converting to non-pointer type ‘char’ from NULL [-Wconversion-null]
118 | buf[ bytes_read ]=NULL;
| ^~~~
[ 27%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/TreeIOTraits.cc.o
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_MPI_DYN_LINK -DBOOST_MPI_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/<<PKGBUILDDIR>>/src/cxx/libraries/prime -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/<<PKGBUILDDIR>>/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/x86_64-linux-gnu/openmpi/include -isystem /usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/TreeIOTraits.cc.o -MF CMakeFiles/prime-phylo.dir/TreeIOTraits.cc.o.d -o CMakeFiles/prime-phylo.dir/TreeIOTraits.cc.o -c /<<PKGBUILDDIR>>/src/cxx/libraries/prime/TreeIOTraits.cc
[ 28%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/TreePerturbationEvent.cc.o
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_MPI_DYN_LINK -DBOOST_MPI_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/<<PKGBUILDDIR>>/src/cxx/libraries/prime -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/<<PKGBUILDDIR>>/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/x86_64-linux-gnu/openmpi/include -isystem /usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/TreePerturbationEvent.cc.o -MF CMakeFiles/prime-phylo.dir/TreePerturbationEvent.cc.o.d -o CMakeFiles/prime-phylo.dir/TreePerturbationEvent.cc.o -c /<<PKGBUILDDIR>>/src/cxx/libraries/prime/TreePerturbationEvent.cc
[ 28%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/ConstRateModel.cc.o
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_MPI_DYN_LINK -DBOOST_MPI_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/<<PKGBUILDDIR>>/src/cxx/libraries/prime -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/<<PKGBUILDDIR>>/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/x86_64-linux-gnu/openmpi/include -isystem /usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/ConstRateModel.cc.o -MF CMakeFiles/prime-phylo.dir/ConstRateModel.cc.o.d -o CMakeFiles/prime-phylo.dir/ConstRateModel.cc.o -c /<<PKGBUILDDIR>>/src/cxx/libraries/prime/ConstRateModel.cc
[ 29%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/Density2P_common.cc.o
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_MPI_DYN_LINK -DBOOST_MPI_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/<<PKGBUILDDIR>>/src/cxx/libraries/prime -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/<<PKGBUILDDIR>>/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/x86_64-linux-gnu/openmpi/include -isystem /usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/Density2P_common.cc.o -MF CMakeFiles/prime-phylo.dir/Density2P_common.cc.o.d -o CMakeFiles/prime-phylo.dir/Density2P_common.cc.o -c /<<PKGBUILDDIR>>/src/cxx/libraries/prime/Density2P_common.cc
[ 29%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/Density2P_positive.cc.o
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_MPI_DYN_LINK -DBOOST_MPI_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/<<PKGBUILDDIR>>/src/cxx/libraries/prime -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/<<PKGBUILDDIR>>/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/x86_64-linux-gnu/openmpi/include -isystem /usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/Density2P_positive.cc.o -MF CMakeFiles/prime-phylo.dir/Density2P_positive.cc.o.d -o CMakeFiles/prime-phylo.dir/Density2P_positive.cc.o -c /<<PKGBUILDDIR>>/src/cxx/libraries/prime/Density2P_positive.cc
[ 30%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/Density2PMCMC.cc.o
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_MPI_DYN_LINK -DBOOST_MPI_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/<<PKGBUILDDIR>>/src/cxx/libraries/prime -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/<<PKGBUILDDIR>>/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/x86_64-linux-gnu/openmpi/include -isystem /usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/Density2PMCMC.cc.o -MF CMakeFiles/prime-phylo.dir/Density2PMCMC.cc.o.d -o CMakeFiles/prime-phylo.dir/Density2PMCMC.cc.o -c /<<PKGBUILDDIR>>/src/cxx/libraries/prime/Density2PMCMC.cc
In file included from /<<PKGBUILDDIR>>/src/cxx/libraries/prime/Density2P_common.cc:5:
/<<PKGBUILDDIR>>/src/cxx/libraries/prime/InvGaussDensity.hh:89:25: warning: ‘constexpr’ needed for in-class initialization of static data member ‘const double beep::InvGaussDensity::pi’ of non-integral type [-fpermissive]
89 | static const double pi = 3.14159265358979; //!< math.constant \f$\pi\f$
| ^~
In file included from /<<PKGBUILDDIR>>/src/cxx/libraries/prime/Density2P_common.cc:1:
/<<PKGBUILDDIR>>/src/cxx/libraries/prime/Density2P_common.hh:52:17: warning: ‘virtual beep::Probability beep::Density2P_common::operator()(const beep::Real&, const beep::Real&) const’ was hidden [-Woverloaded-virtual=]
52 | Probability operator()(const Real& x, const Real& interval) const;
| ^~~~~~~~
/<<PKGBUILDDIR>>/src/cxx/libraries/prime/InvGaussDensity.hh:55:17: note: by ‘virtual beep::Probability beep::InvGaussDensity::operator()(const beep::Real&) const’
55 | Probability operator()(const Real& x) const;
| ^~~~~~~~
In file included from /<<PKGBUILDDIR>>/src/cxx/libraries/prime/Density2P_common.cc:6:
/<<PKGBUILDDIR>>/src/cxx/libraries/prime/LogNormDensity.hh:81:23: warning: ‘constexpr’ needed for in-class initialization of static data member ‘const beep::Real beep::LogNormDensity::pi’ of non-integral type [-fpermissive]
81 | static const Real pi = 3.14159265358979; //! math. constant \f$ \pi \f$.
| ^~
/<<PKGBUILDDIR>>/src/cxx/libraries/prime/Density2P_common.hh:52:17: warning: ‘virtual beep::Probability beep::Density2P_common::operator()(const beep::Real&, const beep::Real&) const’ was hidden [-Woverloaded-virtual=]
52 | Probability operator()(const Real& x, const Real& interval) const;
| ^~~~~~~~
In file included from /<<PKGBUILDDIR>>/src/cxx/libraries/prime/Density2P_common.cc:7:
/<<PKGBUILDDIR>>/src/cxx/libraries/prime/GammaDensity.hh:55:17: note: by ‘virtual beep::Probability beep::GammaDensity::operator()(const beep::Real&) const’
55 | Probability operator()(const Real& x) const;
| ^~~~~~~~
/<<PKGBUILDDIR>>/src/cxx/libraries/prime/Density2P_common.hh:52:17: warning: ‘virtual beep::Probability beep::Density2P_common::operator()(const beep::Real&, const beep::Real&) const’ was hidden [-Woverloaded-virtual=]
52 | Probability operator()(const Real& x, const Real& interval) const;
| ^~~~~~~~
In file included from /<<PKGBUILDDIR>>/src/cxx/libraries/prime/Density2P_common.cc:8:
/<<PKGBUILDDIR>>/src/cxx/libraries/prime/UniformDensity.hh:63:17: note: by ‘virtual beep::Probability beep::UniformDensity::operator()(const beep::Real&) const’
63 | Probability operator()(const Real& x) const;
| ^~~~~~~~
[ 30%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/EdgeRateMCMC.cc.o
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_MPI_DYN_LINK -DBOOST_MPI_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/<<PKGBUILDDIR>>/src/cxx/libraries/prime -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/<<PKGBUILDDIR>>/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/x86_64-linux-gnu/openmpi/include -isystem /usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/EdgeRateMCMC.cc.o -MF CMakeFiles/prime-phylo.dir/EdgeRateMCMC.cc.o.d -o CMakeFiles/prime-phylo.dir/EdgeRateMCMC.cc.o -c /<<PKGBUILDDIR>>/src/cxx/libraries/prime/EdgeRateMCMC.cc
[ 31%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/EdgeRateMCMC_common.cc.o
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_MPI_DYN_LINK -DBOOST_MPI_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/<<PKGBUILDDIR>>/src/cxx/libraries/prime -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/<<PKGBUILDDIR>>/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/x86_64-linux-gnu/openmpi/include -isystem /usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/EdgeRateMCMC_common.cc.o -MF CMakeFiles/prime-phylo.dir/EdgeRateMCMC_common.cc.o.d -o CMakeFiles/prime-phylo.dir/EdgeRateMCMC_common.cc.o -c /<<PKGBUILDDIR>>/src/cxx/libraries/prime/EdgeRateMCMC_common.cc
[ 32%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/EdgeRateModel_common.cc.o
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_MPI_DYN_LINK -DBOOST_MPI_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/<<PKGBUILDDIR>>/src/cxx/libraries/prime -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/<<PKGBUILDDIR>>/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/x86_64-linux-gnu/openmpi/include -isystem /usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/EdgeRateModel_common.cc.o -MF CMakeFiles/prime-phylo.dir/EdgeRateModel_common.cc.o.d -o CMakeFiles/prime-phylo.dir/EdgeRateModel_common.cc.o -c /<<PKGBUILDDIR>>/src/cxx/libraries/prime/EdgeRateModel_common.cc
/<<PKGBUILDDIR>>/src/cxx/libraries/prime/EdgeRateMCMC_common.cc: In member function ‘void beep::EdgeRateMCMC_common<Templ_EdgeRateModel>::generateRates() [with Templ_EdgeRateModel = beep::gbmRateModel]’:
/<<PKGBUILDDIR>>/src/cxx/libraries/prime/EdgeRateMCMC_common.cc:104:30: warning: unused variable ‘fparam’ [-Wunused-variable]
104 | Real fparam = std::log(rate) - 0.5 * variance * (rtime - 3.0 * ltime);
| ^~~~~~
/<<PKGBUILDDIR>>/src/cxx/libraries/prime/EdgeRateMCMC_common.cc:105:30: warning: unused variable ‘rparam’ [-Wunused-variable]
105 | Real rparam = variance * (rtime + ltime);
| ^~~~~~
[ 32%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/EdgeWeightHandler.cc.o
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_MPI_DYN_LINK -DBOOST_MPI_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/<<PKGBUILDDIR>>/src/cxx/libraries/prime -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/<<PKGBUILDDIR>>/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/x86_64-linux-gnu/openmpi/include -isystem /usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/EdgeWeightHandler.cc.o -MF CMakeFiles/prime-phylo.dir/EdgeWeightHandler.cc.o.d -o CMakeFiles/prime-phylo.dir/EdgeWeightHandler.cc.o -c /<<PKGBUILDDIR>>/src/cxx/libraries/prime/EdgeWeightHandler.cc
[ 33%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/EdgeWeightMCMC.cc.o
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_MPI_DYN_LINK -DBOOST_MPI_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/<<PKGBUILDDIR>>/src/cxx/libraries/prime -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/<<PKGBUILDDIR>>/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/x86_64-linux-gnu/openmpi/include -isystem /usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/EdgeWeightMCMC.cc.o -MF CMakeFiles/prime-phylo.dir/EdgeWeightMCMC.cc.o.d -o CMakeFiles/prime-phylo.dir/EdgeWeightMCMC.cc.o -c /<<PKGBUILDDIR>>/src/cxx/libraries/prime/EdgeWeightMCMC.cc
In file included from /<<PKGBUILDDIR>>/src/cxx/libraries/prime/EdgeWeightHandler.cc:1:
/<<PKGBUILDDIR>>/src/cxx/libraries/prime/EdgeWeightHandler.hh:76:18: warning: ‘virtual void beep::EdgeWeightHandler::init(beep::EdgeWeightModel&)’ was hidden [-Woverloaded-virtual=]
76 | virtual void init(EdgeWeightModel& erm);
| ^~~~
/<<PKGBUILDDIR>>/src/cxx/libraries/prime/EdgeWeightHandler.hh:140:18: note: by ‘virtual void beep::EdgeTimeRateHandler::init(beep::EdgeRateModel&)’
140 | virtual void init(EdgeRateModel& erm);
| ^~~~
[ 33%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/GammaDensity.cc.o
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_MPI_DYN_LINK -DBOOST_MPI_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/<<PKGBUILDDIR>>/src/cxx/libraries/prime -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/<<PKGBUILDDIR>>/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/x86_64-linux-gnu/openmpi/include -isystem /usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/GammaDensity.cc.o -MF CMakeFiles/prime-phylo.dir/GammaDensity.cc.o.d -o CMakeFiles/prime-phylo.dir/GammaDensity.cc.o -c /<<PKGBUILDDIR>>/src/cxx/libraries/prime/GammaDensity.cc
/<<PKGBUILDDIR>>/src/cxx/libraries/prime/EdgeWeightMCMC.cc: In member function ‘void beep::EdgeWeightMCMC::showCurrentTree()’:
/<<PKGBUILDDIR>>/src/cxx/libraries/prime/EdgeWeightMCMC.cc:106:27: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare]
106 | for (int i = 0; i < t.size(); i++)
| ~~^~~~~~~~~~
In file included from /<<PKGBUILDDIR>>/src/cxx/libraries/prime/Density2P_positive.hh:4,
from /<<PKGBUILDDIR>>/src/cxx/libraries/prime/GammaDensity.hh:4,
from /<<PKGBUILDDIR>>/src/cxx/libraries/prime/GammaDensity.cc:1:
/<<PKGBUILDDIR>>/src/cxx/libraries/prime/Density2P_common.hh:52:17: warning: ‘virtual beep::Probability beep::Density2P_common::operator()(const beep::Real&, const beep::Real&) const’ was hidden [-Woverloaded-virtual=]
52 | Probability operator()(const Real& x, const Real& interval) const;
| ^~~~~~~~
/<<PKGBUILDDIR>>/src/cxx/libraries/prime/GammaDensity.hh:55:17: note: by ‘virtual beep::Probability beep::GammaDensity::operator()(const beep::Real&) const’
55 | Probability operator()(const Real& x) const;
| ^~~~~~~~
[ 34%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/InvGaussDensity.cc.o
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_MPI_DYN_LINK -DBOOST_MPI_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/<<PKGBUILDDIR>>/src/cxx/libraries/prime -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/<<PKGBUILDDIR>>/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/x86_64-linux-gnu/openmpi/include -isystem /usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/InvGaussDensity.cc.o -MF CMakeFiles/prime-phylo.dir/InvGaussDensity.cc.o.d -o CMakeFiles/prime-phylo.dir/InvGaussDensity.cc.o -c /<<PKGBUILDDIR>>/src/cxx/libraries/prime/InvGaussDensity.cc
[ 34%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/LengthRateModel.cc.o
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_MPI_DYN_LINK -DBOOST_MPI_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/<<PKGBUILDDIR>>/src/cxx/libraries/prime -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/<<PKGBUILDDIR>>/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/x86_64-linux-gnu/openmpi/include -isystem /usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/LengthRateModel.cc.o -MF CMakeFiles/prime-phylo.dir/LengthRateModel.cc.o.d -o CMakeFiles/prime-phylo.dir/LengthRateModel.cc.o -c /<<PKGBUILDDIR>>/src/cxx/libraries/prime/LengthRateModel.cc
In file included from /<<PKGBUILDDIR>>/src/cxx/libraries/prime/InvGaussDensity.cc:1:
/<<PKGBUILDDIR>>/src/cxx/libraries/prime/InvGaussDensity.hh:89:25: warning: ‘constexpr’ needed for in-class initialization of static data member ‘const double beep::InvGaussDensity::pi’ of non-integral type [-fpermissive]
89 | static const double pi = 3.14159265358979; //!< math.constant \f$\pi\f$
| ^~
In file included from /<<PKGBUILDDIR>>/src/cxx/libraries/prime/Density2P_positive.hh:4,
from /<<PKGBUILDDIR>>/src/cxx/libraries/prime/InvGaussDensity.hh:4:
/<<PKGBUILDDIR>>/src/cxx/libraries/prime/Density2P_common.hh:52:17: warning: ‘virtual beep::Probability beep::Density2P_common::operator()(const beep::Real&, const beep::Real&) const’ was hidden [-Woverloaded-virtual=]
52 | Probability operator()(const Real& x, const Real& interval) const;
| ^~~~~~~~
/<<PKGBUILDDIR>>/src/cxx/libraries/prime/InvGaussDensity.hh:55:17: note: by ‘virtual beep::Probability beep::InvGaussDensity::operator()(const beep::Real&) const’
55 | Probability operator()(const Real& x) const;
| ^~~~~~~~
[ 35%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/LogNormDensity.cc.o
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_MPI_DYN_LINK -DBOOST_MPI_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/<<PKGBUILDDIR>>/src/cxx/libraries/prime -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/<<PKGBUILDDIR>>/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/x86_64-linux-gnu/openmpi/include -isystem /usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/LogNormDensity.cc.o -MF CMakeFiles/prime-phylo.dir/LogNormDensity.cc.o.d -o CMakeFiles/prime-phylo.dir/LogNormDensity.cc.o -c /<<PKGBUILDDIR>>/src/cxx/libraries/prime/LogNormDensity.cc
[ 36%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/NormalDensity.cc.o
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_MPI_DYN_LINK -DBOOST_MPI_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/<<PKGBUILDDIR>>/src/cxx/libraries/prime -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/<<PKGBUILDDIR>>/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/x86_64-linux-gnu/openmpi/include -isystem /usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/NormalDensity.cc.o -MF CMakeFiles/prime-phylo.dir/NormalDensity.cc.o.d -o CMakeFiles/prime-phylo.dir/NormalDensity.cc.o -c /<<PKGBUILDDIR>>/src/cxx/libraries/prime/NormalDensity.cc
In file included from /<<PKGBUILDDIR>>/src/cxx/libraries/prime/LogNormDensity.cc:1:
/<<PKGBUILDDIR>>/src/cxx/libraries/prime/LogNormDensity.hh:81:23: warning: ‘constexpr’ needed for in-class initialization of static data member ‘const beep::Real beep::LogNormDensity::pi’ of non-integral type [-fpermissive]
81 | static const Real pi = 3.14159265358979; //! math. constant \f$ \pi \f$.
| ^~
In file included from /<<PKGBUILDDIR>>/src/cxx/libraries/prime/NormalDensity.cc:1:
/<<PKGBUILDDIR>>/src/cxx/libraries/prime/NormalDensity.hh:84:23: warning: ‘constexpr’ needed for in-class initialization of static data member ‘const beep::Real beep::NormalDensity::pi’ of non-integral type [-fpermissive]
84 | static const Real pi = 3.14159265358979; //! math. constant \f$ \pi \f$.
| ^~
In file included from /<<PKGBUILDDIR>>/src/cxx/libraries/prime/NormalDensity.hh:4:
/<<PKGBUILDDIR>>/src/cxx/libraries/prime/Density2P_common.hh:52:17: warning: ‘virtual beep::Probability beep::Density2P_common::operator()(const beep::Real&, const beep::Real&) const’ was hidden [-Woverloaded-virtual=]
52 | Probability operator()(const Real& x, const Real& interval) const;
| ^~~~~~~~
/<<PKGBUILDDIR>>/src/cxx/libraries/prime/NormalDensity.hh:54:17: note: by ‘virtual beep::Probability beep::NormalDensity::operator()(const beep::Real&) const’
54 | Probability operator()(const Real& x) const;
| ^~~~~~~~
[ 36%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/UniformDensity.cc.o
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_MPI_DYN_LINK -DBOOST_MPI_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/<<PKGBUILDDIR>>/src/cxx/libraries/prime -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/<<PKGBUILDDIR>>/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/x86_64-linux-gnu/openmpi/include -isystem /usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/UniformDensity.cc.o -MF CMakeFiles/prime-phylo.dir/UniformDensity.cc.o.d -o CMakeFiles/prime-phylo.dir/UniformDensity.cc.o -c /<<PKGBUILDDIR>>/src/cxx/libraries/prime/UniformDensity.cc
[ 37%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/VarRateModel.cc.o
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_MPI_DYN_LINK -DBOOST_MPI_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/<<PKGBUILDDIR>>/src/cxx/libraries/prime -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/<<PKGBUILDDIR>>/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/x86_64-linux-gnu/openmpi/include -isystem /usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/VarRateModel.cc.o -MF CMakeFiles/prime-phylo.dir/VarRateModel.cc.o.d -o CMakeFiles/prime-phylo.dir/VarRateModel.cc.o -c /<<PKGBUILDDIR>>/src/cxx/libraries/prime/VarRateModel.cc
In file included from /<<PKGBUILDDIR>>/src/cxx/libraries/prime/UniformDensity.hh:4,
from /<<PKGBUILDDIR>>/src/cxx/libraries/prime/UniformDensity.cc:1:
/<<PKGBUILDDIR>>/src/cxx/libraries/prime/Density2P_common.hh:52:17: warning: ‘virtual beep::Probability beep::Density2P_common::operator()(const beep::Real&, const beep::Real&) const’ was hidden [-Woverloaded-virtual=]
52 | Probability operator()(const Real& x, const Real& interval) const;
| ^~~~~~~~
/<<PKGBUILDDIR>>/src/cxx/libraries/prime/UniformDensity.hh:63:17: note: by ‘virtual beep::Probability beep::UniformDensity::operator()(const beep::Real&) const’
63 | Probability operator()(const Real& x) const;
| ^~~~~~~~
[ 37%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/SiteRateHandler.cc.o
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_MPI_DYN_LINK -DBOOST_MPI_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/<<PKGBUILDDIR>>/src/cxx/libraries/prime -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/<<PKGBUILDDIR>>/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/x86_64-linux-gnu/openmpi/include -isystem /usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/SiteRateHandler.cc.o -MF CMakeFiles/prime-phylo.dir/SiteRateHandler.cc.o.d -o CMakeFiles/prime-phylo.dir/SiteRateHandler.cc.o -c /<<PKGBUILDDIR>>/src/cxx/libraries/prime/SiteRateHandler.cc
[ 38%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/DummyMCMC.cc.o
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_MPI_DYN_LINK -DBOOST_MPI_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/<<PKGBUILDDIR>>/src/cxx/libraries/prime -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/<<PKGBUILDDIR>>/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/x86_64-linux-gnu/openmpi/include -isystem /usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/DummyMCMC.cc.o -MF CMakeFiles/prime-phylo.dir/DummyMCMC.cc.o.d -o CMakeFiles/prime-phylo.dir/DummyMCMC.cc.o -c /<<PKGBUILDDIR>>/src/cxx/libraries/prime/DummyMCMC.cc
In file included from /<<PKGBUILDDIR>>/src/cxx/libraries/prime/SiteRateHandler.cc:7:
/<<PKGBUILDDIR>>/src/cxx/libraries/prime/SiteRateHandler.hh:83:23: warning: ‘constexpr’ needed for in-class initialization of static data member ‘const beep::Real beep::SiteRateHandler::MAX’ of non-integral type [-fpermissive]
83 | static const Real MAX = 1e10; //!< rates do not change for alpha > MAX.
| ^~~
[ 38%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/MCMCModel.cc.o
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_MPI_DYN_LINK -DBOOST_MPI_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/<<PKGBUILDDIR>>/src/cxx/libraries/prime -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/<<PKGBUILDDIR>>/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/x86_64-linux-gnu/openmpi/include -isystem /usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/MCMCModel.cc.o -MF CMakeFiles/prime-phylo.dir/MCMCModel.cc.o.d -o CMakeFiles/prime-phylo.dir/MCMCModel.cc.o -c /<<PKGBUILDDIR>>/src/cxx/libraries/prime/MCMCModel.cc
[ 39%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/StdMCMCModel.cc.o
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_MPI_DYN_LINK -DBOOST_MPI_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/<<PKGBUILDDIR>>/src/cxx/libraries/prime -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/<<PKGBUILDDIR>>/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/x86_64-linux-gnu/openmpi/include -isystem /usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/StdMCMCModel.cc.o -MF CMakeFiles/prime-phylo.dir/StdMCMCModel.cc.o.d -o CMakeFiles/prime-phylo.dir/StdMCMCModel.cc.o -c /<<PKGBUILDDIR>>/src/cxx/libraries/prime/StdMCMCModel.cc
[ 40%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/MCMCObject.cc.o
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_MPI_DYN_LINK -DBOOST_MPI_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/<<PKGBUILDDIR>>/src/cxx/libraries/prime -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/<<PKGBUILDDIR>>/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/x86_64-linux-gnu/openmpi/include -isystem /usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/MCMCObject.cc.o -MF CMakeFiles/prime-phylo.dir/MCMCObject.cc.o.d -o CMakeFiles/prime-phylo.dir/MCMCObject.cc.o -c /<<PKGBUILDDIR>>/src/cxx/libraries/prime/MCMCObject.cc
In file included from /<<PKGBUILDDIR>>/src/cxx/libraries/prime/StdMCMCModel.cc:5:
/<<PKGBUILDDIR>>/src/cxx/libraries/prime/LogNormDensity.hh:81:23: warning: ‘constexpr’ needed for in-class initialization of static data member ‘const beep::Real beep::LogNormDensity::pi’ of non-integral type [-fpermissive]
81 | static const Real pi = 3.14159265358979; //! math. constant \f$ \pi \f$.
| ^~
In file included from /<<PKGBUILDDIR>>/src/cxx/libraries/prime/StdMCMCModel.cc:6:
/<<PKGBUILDDIR>>/src/cxx/libraries/prime/NormalDensity.hh:84:23: warning: ‘constexpr’ needed for in-class initialization of static data member ‘const beep::Real beep::NormalDensity::pi’ of non-integral type [-fpermissive]
84 | static const Real pi = 3.14159265358979; //! math. constant \f$ \pi \f$.
| ^~
In file included from /<<PKGBUILDDIR>>/src/cxx/libraries/prime/Density2P_positive.hh:4,
from /<<PKGBUILDDIR>>/src/cxx/libraries/prime/LogNormDensity.hh:4:
/<<PKGBUILDDIR>>/src/cxx/libraries/prime/Density2P_common.hh:52:17: warning: ‘virtual beep::Probability beep::Density2P_common::operator()(const beep::Real&, const beep::Real&) const’ was hidden [-Woverloaded-virtual=]
52 | Probability operator()(const Real& x, const Real& interval) const;
| ^~~~~~~~
/<<PKGBUILDDIR>>/src/cxx/libraries/prime/NormalDensity.hh:54:17: note: by ‘virtual beep::Probability beep::NormalDensity::operator()(const beep::Real&) const’
54 | Probability operator()(const Real& x) const;
| ^~~~~~~~
/<<PKGBUILDDIR>>/src/cxx/libraries/prime/Density2P_common.hh:52:17: warning: ‘virtual beep::Probability beep::Density2P_common::operator()(const beep::Real&, const beep::Real&) const’ was hidden [-Woverloaded-virtual=]
52 | Probability operator()(const Real& x, const Real& interval) const;
| ^~~~~~~~
In file included from /<<PKGBUILDDIR>>/src/cxx/libraries/prime/StdMCMCModel.cc:7:
/<<PKGBUILDDIR>>/src/cxx/libraries/prime/UniformDensity.hh:63:17: note: by ‘virtual beep::Probability beep::UniformDensity::operator()(const beep::Real&) const’
63 | Probability operator()(const Real& x) const;
| ^~~~~~~~
[ 40%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/SimpleMCMC.cc.o
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_MPI_DYN_LINK -DBOOST_MPI_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/<<PKGBUILDDIR>>/src/cxx/libraries/prime -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/<<PKGBUILDDIR>>/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/x86_64-linux-gnu/openmpi/include -isystem /usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/SimpleMCMC.cc.o -MF CMakeFiles/prime-phylo.dir/SimpleMCMC.cc.o.d -o CMakeFiles/prime-phylo.dir/SimpleMCMC.cc.o -c /<<PKGBUILDDIR>>/src/cxx/libraries/prime/SimpleMCMC.cc
[ 41%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/SimpleMCMCPostSample.cc.o
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_MPI_DYN_LINK -DBOOST_MPI_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/<<PKGBUILDDIR>>/src/cxx/libraries/prime -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/<<PKGBUILDDIR>>/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/x86_64-linux-gnu/openmpi/include -isystem /usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/SimpleMCMCPostSample.cc.o -MF CMakeFiles/prime-phylo.dir/SimpleMCMCPostSample.cc.o.d -o CMakeFiles/prime-phylo.dir/SimpleMCMCPostSample.cc.o -c /<<PKGBUILDDIR>>/src/cxx/libraries/prime/SimpleMCMCPostSample.cc
/<<PKGBUILDDIR>>/src/cxx/libraries/prime/SimpleMCMC.cc: In member function ‘virtual void beep::SimpleMCMC::iterate(unsigned int, unsigned int)’:
/<<PKGBUILDDIR>>/src/cxx/libraries/prime/SimpleMCMC.cc:78:14: warning: variable ‘check_number_nonupdate’ set but not used [-Wunused-but-set-variable]
78 | unsigned check_number_nonupdate = 0;
| ^~~~~~~~~~~~~~~~~~~~~~
[ 41%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/SimpleML.cc.o
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_MPI_DYN_LINK -DBOOST_MPI_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/<<PKGBUILDDIR>>/src/cxx/libraries/prime -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/<<PKGBUILDDIR>>/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/x86_64-linux-gnu/openmpi/include -isystem /usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/SimpleML.cc.o -MF CMakeFiles/prime-phylo.dir/SimpleML.cc.o.d -o CMakeFiles/prime-phylo.dir/SimpleML.cc.o -c /<<PKGBUILDDIR>>/src/cxx/libraries/prime/SimpleML.cc
[ 42%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/mcmc/MCMCSampler.cc.o
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_MPI_DYN_LINK -DBOOST_MPI_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/<<PKGBUILDDIR>>/src/cxx/libraries/prime -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/<<PKGBUILDDIR>>/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/x86_64-linux-gnu/openmpi/include -isystem /usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/mcmc/MCMCSampler.cc.o -MF CMakeFiles/prime-phylo.dir/mcmc/MCMCSampler.cc.o.d -o CMakeFiles/prime-phylo.dir/mcmc/MCMCSampler.cc.o -c /<<PKGBUILDDIR>>/src/cxx/libraries/prime/mcmc/MCMCSampler.cc
[ 43%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/mcmc/GSRSampler.cc.o
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_MPI_DYN_LINK -DBOOST_MPI_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/<<PKGBUILDDIR>>/src/cxx/libraries/prime -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/<<PKGBUILDDIR>>/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/x86_64-linux-gnu/openmpi/include -isystem /usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/mcmc/GSRSampler.cc.o -MF CMakeFiles/prime-phylo.dir/mcmc/GSRSampler.cc.o.d -o CMakeFiles/prime-phylo.dir/mcmc/GSRSampler.cc.o -c /<<PKGBUILDDIR>>/src/cxx/libraries/prime/mcmc/GSRSampler.cc
[ 43%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/mcmc/PosteriorSampler.cc.o
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_MPI_DYN_LINK -DBOOST_MPI_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/<<PKGBUILDDIR>>/src/cxx/libraries/prime -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/<<PKGBUILDDIR>>/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/x86_64-linux-gnu/openmpi/include -isystem /usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/mcmc/PosteriorSampler.cc.o -MF CMakeFiles/prime-phylo.dir/mcmc/PosteriorSampler.cc.o.d -o CMakeFiles/prime-phylo.dir/mcmc/PosteriorSampler.cc.o -c /<<PKGBUILDDIR>>/src/cxx/libraries/prime/mcmc/PosteriorSampler.cc
[ 44%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/SimpleObserver.cc.o
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_MPI_DYN_LINK -DBOOST_MPI_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/<<PKGBUILDDIR>>/src/cxx/libraries/prime -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/<<PKGBUILDDIR>>/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/x86_64-linux-gnu/openmpi/include -isystem /usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/SimpleObserver.cc.o -MF CMakeFiles/prime-phylo.dir/SimpleObserver.cc.o.d -o CMakeFiles/prime-phylo.dir/SimpleObserver.cc.o -c /<<PKGBUILDDIR>>/src/cxx/libraries/prime/SimpleObserver.cc
[ 44%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/MpiMCMC.cc.o
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_MPI_DYN_LINK -DBOOST_MPI_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/<<PKGBUILDDIR>>/src/cxx/libraries/prime -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/<<PKGBUILDDIR>>/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/x86_64-linux-gnu/openmpi/include -isystem /usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/MpiMCMC.cc.o -MF CMakeFiles/prime-phylo.dir/MpiMCMC.cc.o.d -o CMakeFiles/prime-phylo.dir/MpiMCMC.cc.o -c /<<PKGBUILDDIR>>/src/cxx/libraries/prime/MpiMCMC.cc
/<<PKGBUILDDIR>>/src/cxx/libraries/prime/MpiMCMC.cc:11:10: fatal error: mpicxx.h: No such file or directory
11 | #include "mpicxx.h"
| ^~~~~~~~~~
compilation terminated.
make[3]: *** [src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/build.make:1029: src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/MpiMCMC.cc.o] Error 1
make[3]: *** Waiting for unfinished jobs....
make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu'
make[2]: *** [CMakeFiles/Makefile2:314: src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/all] Error 2
make[2]: Leaving directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu'
make[1]: *** [Makefile:159: all] Error 2
make[1]: Leaving directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu'
dh_auto_build: error: cd obj-x86_64-linux-gnu && make -j2 "INSTALL=install --strip-program=true" VERBOSE=1 returned exit code 2
make: *** [debian/rules:12: binary] Error 25
dpkg-buildpackage: error: debian/rules binary subprocess returned exit status 2
--------------------------------------------------------------------------------
The above is just how the build ends and not necessarily the most relevant part.
If required, the full build log is available here:
https://people.debian.org/~sanvila/build-logs/202410/
About the archive rebuild: The build was made on virtual machines from AWS,
using sbuild and a reduced chroot with only build-essential packages.
If you could not reproduce the bug please contact me privately, as I
am willing to provide ssh access to a virtual machine where the bug is
fully reproducible.
If this is really a bug in one of the build-depends, please use
reassign and affects, so that this is still visible in the BTS web
page for this package.
Thanks.
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