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caravagnalab / rRACES

R wrapper for the RACES package
GNU General Public License v3.0
2 stars 1 forks source link

Installation issue? #23

Closed riccardobergamin closed 11 months ago

riccardobergamin commented 11 months ago

Installation issue

> devtools::install_github("caravagnalab/rRACES")
Using github PAT from envvar GITHUB_PAT
Downloading GitHub repo caravagnalab/rRACES@HEAD
✔  checking for file ‘/private/var/folders/b1/qw7wc3td0szcvw17h0698lmm0000gn/T/RtmpIwp3pQ/remotes109f54a35960/caravagnalab-rRACES-534d467/DESCRIPTION’ ...
─  preparing ‘rRACES’:
✔  checking DESCRIPTION meta-information ...
─  cleaning src
─  running ‘cleanup’
─  checking for LF line-endings in source and make files and shell scripts
─  checking for empty or unneeded directories
─  building ‘rRACES_0.0.1.tar.gz’

* installing *source* package ‘rRACES’ ...
** using staged installation
++ set -e
++ which cmake
/usr/local/bin/cmake
++ rm -rf _builds _include RACES
++ git clone https://github.com/albertocasagrande/RACES.git
Cloning into 'RACES'...
++ cd RACES
++ git checkout 4d45d78c0af
Note: switching to '4d45d78c0af'.

You are in 'detached HEAD' state. You can look around, make experimental
changes and commit them, and you can discard any commits you make in this
state without impacting any branches by switching back to a branch.

If you want to create a new branch to retain commits you create, you may
do so (now or later) by using -c with the switch command. Example:

  git switch -c <new-branch-name>

Or undo this operation with:

  git switch -

Turn off this advice by setting config variable advice.detachedHead to false

HEAD is now at 4d45d78 Fixed missing  method in `TissueStatistics` - implemented missing `contains_data_for(const Species&) const`
++ cmake -H./RACES/ -B_builds -DCMAKE_BUILD_TYPE=Release -DCMAKE_INSTALL_PREFIX=_install -DCMAKE_SHARED_LIBRARY_PREFIX_CXX= -DONLY_LIBRARIES=1 -DAVOID_OPTIONAL_LIBS=1
-- The CXX compiler identification is AppleClang 12.0.0.12000032
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Check for working CXX compiler: /Library/Developer/CommandLineTools/usr/bin/c++ - skipped
-- Detecting CXX compile features
-- Detecting CXX compile features - done
Avoiding optional libraries
Downloading "p-ranav/indicators" library...
done
Using "p-ranav/indicators"
Building exclusively RACES libraries
-- Configuring done (0.7s)
-- Generating done (0.0s)
-- Build files have been written to: /private/var/folders/b1/qw7wc3td0szcvw17h0698lmm0000gn/T/Rtmp5a0lKE/R.INSTALL10e43c70fb23/rRACES/_builds
++ cmake --build _builds --target install --config Release
[  2%] Building CXX object CMakeFiles/objlib.dir/src/basic_IO.cpp.o
[  4%] Building CXX object CMakeFiles/objlib.dir/src/archive.cpp.o
[  7%] Building CXX object CMakeFiles/objlib.dir/src/driver_genotype.cpp.o
/private/var/folders/b1/qw7wc3td0szcvw17h0698lmm0000gn/T/Rtmp5a0lKE/R.INSTALL10e43c70fb23/rRACES/RACES/src/driver_genotype.cpp:225:22: warning: loop variable 'b_value' is always a copy because the range of type 'const Races::Drivers::MethylationSignature' (aka 'const vector<bool>') does not return a reference [-Wrange-loop-analysis]
    for (const bool& b_value: methylation_signature) {
                     ^
/private/var/folders/b1/qw7wc3td0szcvw17h0698lmm0000gn/T/Rtmp5a0lKE/R.INSTALL10e43c70fb23/rRACES/RACES/src/driver_genotype.cpp:225:10: note: use non-reference type 'bool'
    for (const bool& b_value: methylation_signature) {
         ^~~~~~~~~~~~~~~~~~~~
1 warning generated.
[  9%] Building CXX object CMakeFiles/objlib.dir/src/species.cpp.o
[ 11%] Building CXX object CMakeFiles/objlib.dir/src/position.cpp.o
[ 14%] Building CXX object CMakeFiles/objlib.dir/src/ending_conditions.cpp.o
[ 16%] Building CXX object CMakeFiles/objlib.dir/src/simulation.cpp.o
[ 19%] Building CXX object CMakeFiles/objlib.dir/src/tissue.cpp.o
[ 21%] Building CXX object CMakeFiles/objlib.dir/src/cell.cpp.o
[ 23%] Building CXX object CMakeFiles/objlib.dir/src/cell_event.cpp.o
[ 26%] Building CXX object CMakeFiles/objlib.dir/src/simulation_event.cpp.o
[ 28%] Building CXX object CMakeFiles/objlib.dir/src/driver_mutation.cpp.o
[ 30%] Building CXX object CMakeFiles/objlib.dir/src/rate_update.cpp.o
[ 33%] Building CXX object CMakeFiles/objlib.dir/src/tissue_sample.cpp.o
[ 35%] Building CXX object CMakeFiles/objlib.dir/src/sample_specification.cpp.o
[ 38%] Building CXX object CMakeFiles/objlib.dir/src/sampling.cpp.o
[ 40%] Building CXX object CMakeFiles/objlib.dir/src/event_wrapper.cpp.o
[ 42%] Building CXX object CMakeFiles/objlib.dir/src/timed_event.cpp.o
[ 45%] Building CXX object CMakeFiles/objlib.dir/src/logger.cpp.o
[ 47%] Building CXX object CMakeFiles/objlib.dir/src/binary_logger.cpp.o
In file included from /private/var/folders/b1/qw7wc3td0szcvw17h0698lmm0000gn/T/Rtmp5a0lKE/R.INSTALL10e43c70fb23/rRACES/RACES/src/binary_logger.cpp:36:
In file included from /private/var/folders/b1/qw7wc3td0szcvw17h0698lmm0000gn/T/Rtmp5a0lKE/R.INSTALL10e43c70fb23/rRACES/RACES/include/binary_logger.hpp:38:
In file included from /private/var/folders/b1/qw7wc3td0szcvw17h0698lmm0000gn/T/Rtmp5a0lKE/R.INSTALL10e43c70fb23/rRACES/RACES/include/logger.hpp:37:
In file included from /private/var/folders/b1/qw7wc3td0szcvw17h0698lmm0000gn/T/Rtmp5a0lKE/R.INSTALL10e43c70fb23/rRACES/RACES/include/cell.hpp:36:
/private/var/folders/b1/qw7wc3td0szcvw17h0698lmm0000gn/T/Rtmp5a0lKE/R.INSTALL10e43c70fb23/rRACES/RACES/include/archive.hpp:1093:19: warning: loop variable 'value' is always a copy because the range of type 'const vector<bool, std::__1::allocator<bool> >' does not return a reference [-Wrange-loop-analysis]
    for (const T& value : container) {
                  ^
/private/var/folders/b1/qw7wc3td0szcvw17h0698lmm0000gn/T/Rtmp5a0lKE/R.INSTALL10e43c70fb23/rRACES/RACES/include/driver_genotype.hpp:274:17: note: in instantiation of function template specialization 'operator&<Races::Archive::Binary::Out, vector, bool, std::__1::allocator<bool>, true>' requested here
                & methylation_signature 
                ^
/private/var/folders/b1/qw7wc3td0szcvw17h0698lmm0000gn/T/Rtmp5a0lKE/R.INSTALL10e43c70fb23/rRACES/RACES/include/archive.hpp:692:11: note: in instantiation of function template specialization 'Races::Drivers::EpigeneticGenotype::save<Races::Archive::Binary::Out, true>' requested here
    value.save(archive);
          ^
/private/var/folders/b1/qw7wc3td0szcvw17h0698lmm0000gn/T/Rtmp5a0lKE/R.INSTALL10e43c70fb23/rRACES/RACES/include/species.hpp:415:17: note: in instantiation of function template specialization 'operator&<Races::Archive::Binary::Out, Races::Drivers::EpigeneticGenotype, true>' requested here
        archive & static_cast<const EpigeneticGenotype &>(*this);
                ^
/private/var/folders/b1/qw7wc3td0szcvw17h0698lmm0000gn/T/Rtmp5a0lKE/R.INSTALL10e43c70fb23/rRACES/RACES/include/archive.hpp:692:11: note: in instantiation of function template specialization 'Races::Drivers::Simulation::Species::save<Races::Archive::Binary::Out, true>' requested here
    value.save(archive);
          ^
/private/var/folders/b1/qw7wc3td0szcvw17h0698lmm0000gn/T/Rtmp5a0lKE/R.INSTALL10e43c70fb23/rRACES/RACES/include/archive.hpp:1094:17: note: in instantiation of function template specialization 'operator&<Races::Archive::Binary::Out, Races::Drivers::Simulation::Species, true>' requested here
        archive & value;
                ^
/private/var/folders/b1/qw7wc3td0szcvw17h0698lmm0000gn/T/Rtmp5a0lKE/R.INSTALL10e43c70fb23/rRACES/RACES/include/tissue.hpp:781:17: note: (skipping 1 context in backtrace; use -ftemplate-backtrace-limit=0 to see all)
                & species
                ^
/private/var/folders/b1/qw7wc3td0szcvw17h0698lmm0000gn/T/Rtmp5a0lKE/R.INSTALL10e43c70fb23/rRACES/RACES/include/archive.hpp:692:11: note: in instantiation of function template specialization 'Races::Drivers::Simulation::Tissue::save<Races::Archive::Binary::Out, true>' requested here
    value.save(archive);
          ^
/private/var/folders/b1/qw7wc3td0szcvw17h0698lmm0000gn/T/Rtmp5a0lKE/R.INSTALL10e43c70fb23/rRACES/RACES/include/archive.hpp:1094:17: note: in instantiation of function template specialization 'operator&<Races::Archive::Binary::Out, Races::Drivers::Simulation::Tissue, true>' requested here
        archive & value;
                ^
/private/var/folders/b1/qw7wc3td0szcvw17h0698lmm0000gn/T/Rtmp5a0lKE/R.INSTALL10e43c70fb23/rRACES/RACES/include/simulation.hpp:731:17: note: in instantiation of function template specialization 'operator&<Races::Archive::Binary::Out, vector, Races::Drivers::Simulation::Tissue, std::__1::allocator<Races::Drivers::Simulation::Tissue>, true>' requested here
        archive & tissues
                ^
/private/var/folders/b1/qw7wc3td0szcvw17h0698lmm0000gn/T/Rtmp5a0lKE/R.INSTALL10e43c70fb23/rRACES/RACES/include/archive.hpp:692:11: note: in instantiation of function template specialization 'Races::Drivers::Simulation::Simulation::save<Races::Archive::Binary::Out, true>' requested here
    value.save(archive);
          ^
/private/var/folders/b1/qw7wc3td0szcvw17h0698lmm0000gn/T/Rtmp5a0lKE/R.INSTALL10e43c70fb23/rRACES/RACES/src/binary_logger.cpp:232:13: note: in instantiation of function template specialization 'operator&<Races::Archive::Binary::Out, Races::Drivers::Simulation::Simulation, true>' requested here
    archive & simulation;
            ^
/private/var/folders/b1/qw7wc3td0szcvw17h0698lmm0000gn/T/Rtmp5a0lKE/R.INSTALL10e43c70fb23/rRACES/RACES/include/archive.hpp:1093:10: note: use non-reference type 'bool'
    for (const T& value : container) {
         ^~~~~~~~~~~~~~~~
1 warning generated.
[ 50%] Building CXX object CMakeFiles/objlib.dir/src/statistics.cpp.o
[ 52%] Building CXX object CMakeFiles/objlib.dir/src/palette.cpp.o
[ 54%] Building CXX object CMakeFiles/objlib.dir/src/plot_2D.cpp.o
[ 57%] Building CXX object CMakeFiles/objlib.dir/src/progress_bar.cpp.o
[ 59%] Building CXX object CMakeFiles/objlib.dir/src/context.cpp.o
[ 61%] Building CXX object CMakeFiles/objlib.dir/src/snv_signature.cpp.o
[ 64%] Building CXX object CMakeFiles/objlib.dir/src/snv.cpp.o
[ 66%] Building CXX object CMakeFiles/objlib.dir/src/allele.cpp.o
[ 69%] Building CXX object CMakeFiles/objlib.dir/src/genomic_region.cpp.o
[ 71%] Building CXX object CMakeFiles/objlib.dir/src/genomic_position.cpp.o
[ 73%] Building CXX object CMakeFiles/objlib.dir/src/fasta_reader.cpp.o
[ 76%] Building CXX object CMakeFiles/objlib.dir/src/fasta_utils.cpp.o
[ 78%] Building CXX object CMakeFiles/objlib.dir/src/genome_mutations.cpp.o
[ 80%] Building CXX object CMakeFiles/objlib.dir/src/cna.cpp.o
[ 83%] Building CXX object CMakeFiles/objlib.dir/src/mutation_engine.cpp.o
In file included from /private/var/folders/b1/qw7wc3td0szcvw17h0698lmm0000gn/T/Rtmp5a0lKE/R.INSTALL10e43c70fb23/rRACES/RACES/src/mutation_engine.cpp:31:
/private/var/folders/b1/qw7wc3td0szcvw17h0698lmm0000gn/T/Rtmp5a0lKE/R.INSTALL10e43c70fb23/rRACES/RACES/include/mutation_engine.hpp:494:29: warning: loop variable 'child' of type 'const Races::Drivers::PhylogeneticForest::const_node' creates a copy from type 'const Races::Drivers::PhylogeneticForest::const_node' [-Wrange-loop-analysis]
            for (const auto child: node.children()) {
                            ^
/private/var/folders/b1/qw7wc3td0szcvw17h0698lmm0000gn/T/Rtmp5a0lKE/R.INSTALL10e43c70fb23/rRACES/RACES/include/mutation_engine.hpp:494:18: note: use reference type 'const Races::Drivers::PhylogeneticForest::const_node &' to prevent copying
            for (const auto child: node.children()) {
                 ^~~~~~~~~~~~~~~~~
                            &
1 warning generated.
[ 85%] Building CXX object CMakeFiles/objlib.dir/src/mutational_properties.cpp.o
[ 88%] Building CXX object CMakeFiles/objlib.dir/src/read_simulator.cpp.o
[ 90%] Building CXX object CMakeFiles/objlib.dir/src/position_set.cpp.o
[ 92%] Building CXX object CMakeFiles/objlib.dir/src/phyloXML.cpp.o
[ 95%] Building CXX object CMakeFiles/objlib.dir/src/phylogenetic_forest.cpp.o
[ 95%] Built target objlib
[ 97%] Linking CXX shared library RACES.dylib
[ 97%] Built target libRACES
[100%] Linking CXX static library libRACES.a
[100%] Built target libRACES_static
Install the project...
-- Install configuration: "Release"
-- Installing: /private/var/folders/b1/qw7wc3td0szcvw17h0698lmm0000gn/T/Rtmp5a0lKE/R.INSTALL10e43c70fb23/rRACES/_install/lib/RACES.0.1.0.dylib
-- Installing: /private/var/folders/b1/qw7wc3td0szcvw17h0698lmm0000gn/T/Rtmp5a0lKE/R.INSTALL10e43c70fb23/rRACES/_install/lib/RACES.dylib
-- Installing: /private/var/folders/b1/qw7wc3td0szcvw17h0698lmm0000gn/T/Rtmp5a0lKE/R.INSTALL10e43c70fb23/rRACES/_install/include/variables.hpp
-- Installing: /private/var/folders/b1/qw7wc3td0szcvw17h0698lmm0000gn/T/Rtmp5a0lKE/R.INSTALL10e43c70fb23/rRACES/_install/include/basic_IO.hpp
-- Installing: /private/var/folders/b1/qw7wc3td0szcvw17h0698lmm0000gn/T/Rtmp5a0lKE/R.INSTALL10e43c70fb23/rRACES/_install/include/archive.hpp
-- Installing: /private/var/folders/b1/qw7wc3td0szcvw17h0698lmm0000gn/T/Rtmp5a0lKE/R.INSTALL10e43c70fb23/rRACES/_install/include/driver_genotype.hpp
-- Installing: /private/var/folders/b1/qw7wc3td0szcvw17h0698lmm0000gn/T/Rtmp5a0lKE/R.INSTALL10e43c70fb23/rRACES/_install/include/driver_genotype_id.hpp
-- Installing: /private/var/folders/b1/qw7wc3td0szcvw17h0698lmm0000gn/T/Rtmp5a0lKE/R.INSTALL10e43c70fb23/rRACES/_install/include/species.hpp
-- Installing: /private/var/folders/b1/qw7wc3td0szcvw17h0698lmm0000gn/T/Rtmp5a0lKE/R.INSTALL10e43c70fb23/rRACES/_install/include/position.hpp
-- Installing: /private/var/folders/b1/qw7wc3td0szcvw17h0698lmm0000gn/T/Rtmp5a0lKE/R.INSTALL10e43c70fb23/rRACES/_install/include/simulation.hpp
-- Installing: /private/var/folders/b1/qw7wc3td0szcvw17h0698lmm0000gn/T/Rtmp5a0lKE/R.INSTALL10e43c70fb23/rRACES/_install/include/tissue.hpp
-- Installing: /private/var/folders/b1/qw7wc3td0szcvw17h0698lmm0000gn/T/Rtmp5a0lKE/R.INSTALL10e43c70fb23/rRACES/_install/include/cell.hpp
-- Installing: /private/var/folders/b1/qw7wc3td0szcvw17h0698lmm0000gn/T/Rtmp5a0lKE/R.INSTALL10e43c70fb23/rRACES/_install/include/cell_event.hpp
-- Installing: /private/var/folders/b1/qw7wc3td0szcvw17h0698lmm0000gn/T/Rtmp5a0lKE/R.INSTALL10e43c70fb23/rRACES/_install/include/simulation_event.hpp
-- Installing: /private/var/folders/b1/qw7wc3td0szcvw17h0698lmm0000gn/T/Rtmp5a0lKE/R.INSTALL10e43c70fb23/rRACES/_install/include/driver_mutation.hpp
-- Installing: /private/var/folders/b1/qw7wc3td0szcvw17h0698lmm0000gn/T/Rtmp5a0lKE/R.INSTALL10e43c70fb23/rRACES/_install/include/rate_update.hpp
-- Installing: /private/var/folders/b1/qw7wc3td0szcvw17h0698lmm0000gn/T/Rtmp5a0lKE/R.INSTALL10e43c70fb23/rRACES/_install/include/tissue_sample.hpp
-- Installing: /private/var/folders/b1/qw7wc3td0szcvw17h0698lmm0000gn/T/Rtmp5a0lKE/R.INSTALL10e43c70fb23/rRACES/_install/include/sample_specification.hpp
-- Installing: /private/var/folders/b1/qw7wc3td0szcvw17h0698lmm0000gn/T/Rtmp5a0lKE/R.INSTALL10e43c70fb23/rRACES/_install/include/sampling.hpp
-- Installing: /private/var/folders/b1/qw7wc3td0szcvw17h0698lmm0000gn/T/Rtmp5a0lKE/R.INSTALL10e43c70fb23/rRACES/_install/include/event_wrapper.hpp
-- Installing: /private/var/folders/b1/qw7wc3td0szcvw17h0698lmm0000gn/T/Rtmp5a0lKE/R.INSTALL10e43c70fb23/rRACES/_install/include/timed_event.hpp
-- Installing: /private/var/folders/b1/qw7wc3td0szcvw17h0698lmm0000gn/T/Rtmp5a0lKE/R.INSTALL10e43c70fb23/rRACES/_install/include/logger.hpp
-- Installing: /private/var/folders/b1/qw7wc3td0szcvw17h0698lmm0000gn/T/Rtmp5a0lKE/R.INSTALL10e43c70fb23/rRACES/_install/include/binary_logger.hpp
-- Installing: /private/var/folders/b1/qw7wc3td0szcvw17h0698lmm0000gn/T/Rtmp5a0lKE/R.INSTALL10e43c70fb23/rRACES/_install/include/statistics.hpp
-- Installing: /private/var/folders/b1/qw7wc3td0szcvw17h0698lmm0000gn/T/Rtmp5a0lKE/R.INSTALL10e43c70fb23/rRACES/_install/include/palette.hpp
-- Installing: /private/var/folders/b1/qw7wc3td0szcvw17h0698lmm0000gn/T/Rtmp5a0lKE/R.INSTALL10e43c70fb23/rRACES/_install/include/plot_2D.hpp
-- Installing: /private/var/folders/b1/qw7wc3td0szcvw17h0698lmm0000gn/T/Rtmp5a0lKE/R.INSTALL10e43c70fb23/rRACES/_install/include/progress_bar.hpp
-- Installing: /private/var/folders/b1/qw7wc3td0szcvw17h0698lmm0000gn/T/Rtmp5a0lKE/R.INSTALL10e43c70fb23/rRACES/_install/include/phyloXML.hpp
-- Installing: /private/var/folders/b1/qw7wc3td0szcvw17h0698lmm0000gn/T/Rtmp5a0lKE/R.INSTALL10e43c70fb23/rRACES/_install/include/phylogenetic_forest.hpp
-- Up-to-date: /private/var/folders/b1/qw7wc3td0szcvw17h0698lmm0000gn/T/Rtmp5a0lKE/R.INSTALL10e43c70fb23/rRACES/_install/include/palette.hpp
-- Up-to-date: /private/var/folders/b1/qw7wc3td0szcvw17h0698lmm0000gn/T/Rtmp5a0lKE/R.INSTALL10e43c70fb23/rRACES/_install/include/statistics.hpp
-- Installing: /private/var/folders/b1/qw7wc3td0szcvw17h0698lmm0000gn/T/Rtmp5a0lKE/R.INSTALL10e43c70fb23/rRACES/_install/include/tissue_plotter.hpp
-- Installing: /private/var/folders/b1/qw7wc3td0szcvw17h0698lmm0000gn/T/Rtmp5a0lKE/R.INSTALL10e43c70fb23/rRACES/_install/include/time.hpp
-- Up-to-date: /private/var/folders/b1/qw7wc3td0szcvw17h0698lmm0000gn/T/Rtmp5a0lKE/R.INSTALL10e43c70fb23/rRACES/_install/include/simulation.hpp
-- Installing: /private/var/folders/b1/qw7wc3td0szcvw17h0698lmm0000gn/T/Rtmp5a0lKE/R.INSTALL10e43c70fb23/rRACES/_install/include/ending_conditions.hpp
-- Installing: /private/var/folders/b1/qw7wc3td0szcvw17h0698lmm0000gn/T/Rtmp5a0lKE/R.INSTALL10e43c70fb23/rRACES/_install/include/context.hpp
-- Installing: /private/var/folders/b1/qw7wc3td0szcvw17h0698lmm0000gn/T/Rtmp5a0lKE/R.INSTALL10e43c70fb23/rRACES/_install/include/context_index.hpp
-- Installing: /private/var/folders/b1/qw7wc3td0szcvw17h0698lmm0000gn/T/Rtmp5a0lKE/R.INSTALL10e43c70fb23/rRACES/_install/include/snv_signature.hpp
-- Installing: /private/var/folders/b1/qw7wc3td0szcvw17h0698lmm0000gn/T/Rtmp5a0lKE/R.INSTALL10e43c70fb23/rRACES/_install/include/snv.hpp
-- Installing: /private/var/folders/b1/qw7wc3td0szcvw17h0698lmm0000gn/T/Rtmp5a0lKE/R.INSTALL10e43c70fb23/rRACES/_install/include/allele.hpp
-- Installing: /private/var/folders/b1/qw7wc3td0szcvw17h0698lmm0000gn/T/Rtmp5a0lKE/R.INSTALL10e43c70fb23/rRACES/_install/include/genomic_region.hpp
-- Installing: /private/var/folders/b1/qw7wc3td0szcvw17h0698lmm0000gn/T/Rtmp5a0lKE/R.INSTALL10e43c70fb23/rRACES/_install/include/genomic_position.hpp
-- Installing: /private/var/folders/b1/qw7wc3td0szcvw17h0698lmm0000gn/T/Rtmp5a0lKE/R.INSTALL10e43c70fb23/rRACES/_install/include/fasta_reader.hpp
-- Installing: /private/var/folders/b1/qw7wc3td0szcvw17h0698lmm0000gn/T/Rtmp5a0lKE/R.INSTALL10e43c70fb23/rRACES/_install/include/fasta_utils.hpp
-- Installing: /private/var/folders/b1/qw7wc3td0szcvw17h0698lmm0000gn/T/Rtmp5a0lKE/R.INSTALL10e43c70fb23/rRACES/_install/include/cna.hpp
-- Installing: /private/var/folders/b1/qw7wc3td0szcvw17h0698lmm0000gn/T/Rtmp5a0lKE/R.INSTALL10e43c70fb23/rRACES/_install/include/mutation_engine.hpp
-- Installing: /private/var/folders/b1/qw7wc3td0szcvw17h0698lmm0000gn/T/Rtmp5a0lKE/R.INSTALL10e43c70fb23/rRACES/_install/include/mutational_properties.hpp
-- Installing: /private/var/folders/b1/qw7wc3td0szcvw17h0698lmm0000gn/T/Rtmp5a0lKE/R.INSTALL10e43c70fb23/rRACES/_install/include/read_simulator.hpp
-- Installing: /private/var/folders/b1/qw7wc3td0szcvw17h0698lmm0000gn/T/Rtmp5a0lKE/R.INSTALL10e43c70fb23/rRACES/_install/include/position_set.hpp
-- Up-to-date: /private/var/folders/b1/qw7wc3td0szcvw17h0698lmm0000gn/T/Rtmp5a0lKE/R.INSTALL10e43c70fb23/rRACES/_install/include/phyloXML.hpp
-- Up-to-date: /private/var/folders/b1/qw7wc3td0szcvw17h0698lmm0000gn/T/Rtmp5a0lKE/R.INSTALL10e43c70fb23/rRACES/_install/include/phylogenetic_forest.hpp
-- Installing: /private/var/folders/b1/qw7wc3td0szcvw17h0698lmm0000gn/T/Rtmp5a0lKE/R.INSTALL10e43c70fb23/rRACES/_install/include/indicators.hpp
-- Installing: /private/var/folders/b1/qw7wc3td0szcvw17h0698lmm0000gn/T/Rtmp5a0lKE/R.INSTALL10e43c70fb23/rRACES/_install/lib/libRACES.a
-- Up-to-date: /private/var/folders/b1/qw7wc3td0szcvw17h0698lmm0000gn/T/Rtmp5a0lKE/R.INSTALL10e43c70fb23/rRACES/_install/include/variables.hpp
-- Up-to-date: /private/var/folders/b1/qw7wc3td0szcvw17h0698lmm0000gn/T/Rtmp5a0lKE/R.INSTALL10e43c70fb23/rRACES/_install/include/basic_IO.hpp
-- Up-to-date: /private/var/folders/b1/qw7wc3td0szcvw17h0698lmm0000gn/T/Rtmp5a0lKE/R.INSTALL10e43c70fb23/rRACES/_install/include/archive.hpp
-- Up-to-date: /private/var/folders/b1/qw7wc3td0szcvw17h0698lmm0000gn/T/Rtmp5a0lKE/R.INSTALL10e43c70fb23/rRACES/_install/include/driver_genotype.hpp
-- Up-to-date: /private/var/folders/b1/qw7wc3td0szcvw17h0698lmm0000gn/T/Rtmp5a0lKE/R.INSTALL10e43c70fb23/rRACES/_install/include/driver_genotype_id.hpp
-- Up-to-date: /private/var/folders/b1/qw7wc3td0szcvw17h0698lmm0000gn/T/Rtmp5a0lKE/R.INSTALL10e43c70fb23/rRACES/_install/include/species.hpp
-- Up-to-date: /private/var/folders/b1/qw7wc3td0szcvw17h0698lmm0000gn/T/Rtmp5a0lKE/R.INSTALL10e43c70fb23/rRACES/_install/include/position.hpp
-- Up-to-date: /private/var/folders/b1/qw7wc3td0szcvw17h0698lmm0000gn/T/Rtmp5a0lKE/R.INSTALL10e43c70fb23/rRACES/_install/include/simulation.hpp
-- Up-to-date: /private/var/folders/b1/qw7wc3td0szcvw17h0698lmm0000gn/T/Rtmp5a0lKE/R.INSTALL10e43c70fb23/rRACES/_install/include/tissue.hpp
-- Up-to-date: /private/var/folders/b1/qw7wc3td0szcvw17h0698lmm0000gn/T/Rtmp5a0lKE/R.INSTALL10e43c70fb23/rRACES/_install/include/cell.hpp
-- Up-to-date: /private/var/folders/b1/qw7wc3td0szcvw17h0698lmm0000gn/T/Rtmp5a0lKE/R.INSTALL10e43c70fb23/rRACES/_install/include/cell_event.hpp
-- Up-to-date: /private/var/folders/b1/qw7wc3td0szcvw17h0698lmm0000gn/T/Rtmp5a0lKE/R.INSTALL10e43c70fb23/rRACES/_install/include/simulation_event.hpp
-- Up-to-date: /private/var/folders/b1/qw7wc3td0szcvw17h0698lmm0000gn/T/Rtmp5a0lKE/R.INSTALL10e43c70fb23/rRACES/_install/include/driver_mutation.hpp
-- Up-to-date: /private/var/folders/b1/qw7wc3td0szcvw17h0698lmm0000gn/T/Rtmp5a0lKE/R.INSTALL10e43c70fb23/rRACES/_install/include/rate_update.hpp
-- Up-to-date: /private/var/folders/b1/qw7wc3td0szcvw17h0698lmm0000gn/T/Rtmp5a0lKE/R.INSTALL10e43c70fb23/rRACES/_install/include/tissue_sample.hpp
-- Up-to-date: /private/var/folders/b1/qw7wc3td0szcvw17h0698lmm0000gn/T/Rtmp5a0lKE/R.INSTALL10e43c70fb23/rRACES/_install/include/sample_specification.hpp
-- Up-to-date: /private/var/folders/b1/qw7wc3td0szcvw17h0698lmm0000gn/T/Rtmp5a0lKE/R.INSTALL10e43c70fb23/rRACES/_install/include/sampling.hpp
-- Up-to-date: /private/var/folders/b1/qw7wc3td0szcvw17h0698lmm0000gn/T/Rtmp5a0lKE/R.INSTALL10e43c70fb23/rRACES/_install/include/event_wrapper.hpp
-- Up-to-date: /private/var/folders/b1/qw7wc3td0szcvw17h0698lmm0000gn/T/Rtmp5a0lKE/R.INSTALL10e43c70fb23/rRACES/_install/include/timed_event.hpp
-- Up-to-date: /private/var/folders/b1/qw7wc3td0szcvw17h0698lmm0000gn/T/Rtmp5a0lKE/R.INSTALL10e43c70fb23/rRACES/_install/include/logger.hpp
-- Up-to-date: /private/var/folders/b1/qw7wc3td0szcvw17h0698lmm0000gn/T/Rtmp5a0lKE/R.INSTALL10e43c70fb23/rRACES/_install/include/binary_logger.hpp
-- Up-to-date: /private/var/folders/b1/qw7wc3td0szcvw17h0698lmm0000gn/T/Rtmp5a0lKE/R.INSTALL10e43c70fb23/rRACES/_install/include/statistics.hpp
-- Up-to-date: /private/var/folders/b1/qw7wc3td0szcvw17h0698lmm0000gn/T/Rtmp5a0lKE/R.INSTALL10e43c70fb23/rRACES/_install/include/palette.hpp
-- Up-to-date: /private/var/folders/b1/qw7wc3td0szcvw17h0698lmm0000gn/T/Rtmp5a0lKE/R.INSTALL10e43c70fb23/rRACES/_install/include/plot_2D.hpp
-- Up-to-date: /private/var/folders/b1/qw7wc3td0szcvw17h0698lmm0000gn/T/Rtmp5a0lKE/R.INSTALL10e43c70fb23/rRACES/_install/include/progress_bar.hpp
-- Up-to-date: /private/var/folders/b1/qw7wc3td0szcvw17h0698lmm0000gn/T/Rtmp5a0lKE/R.INSTALL10e43c70fb23/rRACES/_install/include/phyloXML.hpp
-- Up-to-date: /private/var/folders/b1/qw7wc3td0szcvw17h0698lmm0000gn/T/Rtmp5a0lKE/R.INSTALL10e43c70fb23/rRACES/_install/include/phylogenetic_forest.hpp
-- Up-to-date: /private/var/folders/b1/qw7wc3td0szcvw17h0698lmm0000gn/T/Rtmp5a0lKE/R.INSTALL10e43c70fb23/rRACES/_install/include/palette.hpp
-- Up-to-date: /private/var/folders/b1/qw7wc3td0szcvw17h0698lmm0000gn/T/Rtmp5a0lKE/R.INSTALL10e43c70fb23/rRACES/_install/include/statistics.hpp
-- Up-to-date: /private/var/folders/b1/qw7wc3td0szcvw17h0698lmm0000gn/T/Rtmp5a0lKE/R.INSTALL10e43c70fb23/rRACES/_install/include/tissue_plotter.hpp
-- Up-to-date: /private/var/folders/b1/qw7wc3td0szcvw17h0698lmm0000gn/T/Rtmp5a0lKE/R.INSTALL10e43c70fb23/rRACES/_install/include/time.hpp
-- Up-to-date: /private/var/folders/b1/qw7wc3td0szcvw17h0698lmm0000gn/T/Rtmp5a0lKE/R.INSTALL10e43c70fb23/rRACES/_install/include/simulation.hpp
-- Up-to-date: /private/var/folders/b1/qw7wc3td0szcvw17h0698lmm0000gn/T/Rtmp5a0lKE/R.INSTALL10e43c70fb23/rRACES/_install/include/ending_conditions.hpp
-- Up-to-date: /private/var/folders/b1/qw7wc3td0szcvw17h0698lmm0000gn/T/Rtmp5a0lKE/R.INSTALL10e43c70fb23/rRACES/_install/include/context.hpp
-- Up-to-date: /private/var/folders/b1/qw7wc3td0szcvw17h0698lmm0000gn/T/Rtmp5a0lKE/R.INSTALL10e43c70fb23/rRACES/_install/include/context_index.hpp
-- Up-to-date: /private/var/folders/b1/qw7wc3td0szcvw17h0698lmm0000gn/T/Rtmp5a0lKE/R.INSTALL10e43c70fb23/rRACES/_install/include/snv_signature.hpp
-- Up-to-date: /private/var/folders/b1/qw7wc3td0szcvw17h0698lmm0000gn/T/Rtmp5a0lKE/R.INSTALL10e43c70fb23/rRACES/_install/include/snv.hpp
-- Up-to-date: /private/var/folders/b1/qw7wc3td0szcvw17h0698lmm0000gn/T/Rtmp5a0lKE/R.INSTALL10e43c70fb23/rRACES/_install/include/allele.hpp
-- Up-to-date: /private/var/folders/b1/qw7wc3td0szcvw17h0698lmm0000gn/T/Rtmp5a0lKE/R.INSTALL10e43c70fb23/rRACES/_install/include/genomic_region.hpp
-- Up-to-date: /private/var/folders/b1/qw7wc3td0szcvw17h0698lmm0000gn/T/Rtmp5a0lKE/R.INSTALL10e43c70fb23/rRACES/_install/include/genomic_position.hpp
-- Up-to-date: /private/var/folders/b1/qw7wc3td0szcvw17h0698lmm0000gn/T/Rtmp5a0lKE/R.INSTALL10e43c70fb23/rRACES/_install/include/fasta_reader.hpp
-- Up-to-date: /private/var/folders/b1/qw7wc3td0szcvw17h0698lmm0000gn/T/Rtmp5a0lKE/R.INSTALL10e43c70fb23/rRACES/_install/include/fasta_utils.hpp
-- Up-to-date: /private/var/folders/b1/qw7wc3td0szcvw17h0698lmm0000gn/T/Rtmp5a0lKE/R.INSTALL10e43c70fb23/rRACES/_install/include/cna.hpp
-- Up-to-date: /private/var/folders/b1/qw7wc3td0szcvw17h0698lmm0000gn/T/Rtmp5a0lKE/R.INSTALL10e43c70fb23/rRACES/_install/include/mutation_engine.hpp
-- Up-to-date: /private/var/folders/b1/qw7wc3td0szcvw17h0698lmm0000gn/T/Rtmp5a0lKE/R.INSTALL10e43c70fb23/rRACES/_install/include/mutational_properties.hpp
-- Up-to-date: /private/var/folders/b1/qw7wc3td0szcvw17h0698lmm0000gn/T/Rtmp5a0lKE/R.INSTALL10e43c70fb23/rRACES/_install/include/read_simulator.hpp
-- Up-to-date: /private/var/folders/b1/qw7wc3td0szcvw17h0698lmm0000gn/T/Rtmp5a0lKE/R.INSTALL10e43c70fb23/rRACES/_install/include/position_set.hpp
-- Up-to-date: /private/var/folders/b1/qw7wc3td0szcvw17h0698lmm0000gn/T/Rtmp5a0lKE/R.INSTALL10e43c70fb23/rRACES/_install/include/phyloXML.hpp
-- Up-to-date: /private/var/folders/b1/qw7wc3td0szcvw17h0698lmm0000gn/T/Rtmp5a0lKE/R.INSTALL10e43c70fb23/rRACES/_install/include/phylogenetic_forest.hpp
-- Up-to-date: /private/var/folders/b1/qw7wc3td0szcvw17h0698lmm0000gn/T/Rtmp5a0lKE/R.INSTALL10e43c70fb23/rRACES/_install/include/indicators.hpp
++ cp _install/lib/libRACES.so src/
cp: _install/lib/libRACES.so: No such file or directory
++ echo 'Failed: libRACES.so -> src'
Failed: libRACES.so -> src
++ cp _install/lib/RACES.dylib src/libRACES.so
++ cp _install/lib/libRACES.a src/libRACES.so
++ /Library/Frameworks/R.framework/Resources/bin/R --vanilla --silent -e 'Rcpp::compileAttributes()'
> Rcpp::compileAttributes()
> 
> 
** libs
clang++ -mmacosx-version-min=10.13 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rcpp/include' -I/usr/local/include  -I../_install/include/ -fPIC  -Wall -g -O2  -c RcppExports.cpp -o RcppExports.o
clang++ -mmacosx-version-min=10.13 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rcpp/include' -I/usr/local/include  -I../_install/include/ -fPIC  -Wall -g -O2  -c drivers.cpp -o drivers.o
In file included from drivers.cpp:23:
In file included from ../_install/include/simulation.hpp:40:
In file included from ../_install/include/tissue.hpp:41:
../_install/include/archive.hpp:143:28: error: 'path' is unavailable: introduced in macOS 10.15
    Basic(std::filesystem::path filename, std::ios_base::openmode mode);
                           ^
/Library/Developer/CommandLineTools/usr/bin/../include/c++/v1/filesystem:738:24: note: 'path' has been explicitly marked unavailable here
class _LIBCPP_TYPE_VIS path {
                       ^
In file included from drivers.cpp:23:
In file included from ../_install/include/simulation.hpp:40:
In file included from ../_install/include/tissue.hpp:41:
../_install/include/archive.hpp:151:39: error: 'path' is unavailable: introduced in macOS 10.15
    inline void open(std::filesystem::path filename, std::ios_base::openmode mode)
                                      ^
/Library/Developer/CommandLineTools/usr/bin/../include/c++/v1/filesystem:738:24: note: 'path' has been explicitly marked unavailable here
class _LIBCPP_TYPE_VIS path {
                       ^
In file included from drivers.cpp:23:
In file included from ../_install/include/simulation.hpp:40:
In file included from ../_install/include/tissue.hpp:41:
../_install/include/archive.hpp:153:12: error: 'open' is unavailable: introduced in macOS 10.15
        fs.open(filename, mode);
           ^
/Library/Developer/CommandLineTools/usr/bin/../include/c++/v1/fstream:1610:10: note: 'open' has been explicitly marked unavailable here
    void open(const filesystem::path& __p, ios_base::openmode __mode = ios_base::in|ios_base::out)
         ^
In file included from drivers.cpp:23:
In file included from ../_install/include/simulation.hpp:40:
In file included from ../_install/include/tissue.hpp:41:
../_install/include/archive.hpp:219:35: error: 'path' is unavailable: introduced in macOS 10.15
    explicit Out(std::filesystem::path filename);
                                  ^
/Library/Developer/CommandLineTools/usr/bin/../include/c++/v1/filesystem:738:24: note: 'path' has been explicitly marked unavailable here
class _LIBCPP_TYPE_VIS path {
                       ^
In file included from drivers.cpp:23:
In file included from ../_install/include/simulation.hpp:40:
In file included from ../_install/include/tissue.hpp:41:
../_install/include/archive.hpp:230:26: error: 'path' is unavailable: introduced in macOS 10.15
    Out(std::filesystem::path filename, std::ios_base::openmode mode);
                         ^
/Library/Developer/CommandLineTools/usr/bin/../include/c++/v1/filesystem:738:24: note: 'path' has been explicitly marked unavailable here
class _LIBCPP_TYPE_VIS path {
                       ^
In file included from drivers.cpp:23:
In file included from ../_install/include/simulation.hpp:40:
In file included from ../_install/include/tissue.hpp:41:
../_install/include/archive.hpp:240:39: error: 'path' is unavailable: introduced in macOS 10.15
    inline void open(std::filesystem::path filename, std::ios_base::openmode mode)
                                      ^
/Library/Developer/CommandLineTools/usr/bin/../include/c++/v1/filesystem:738:24: note: 'path' has been explicitly marked unavailable here
class _LIBCPP_TYPE_VIS path {
                       ^
In file included from drivers.cpp:23:
In file included from ../_install/include/simulation.hpp:40:
In file included from ../_install/include/tissue.hpp:41:
../_install/include/archive.hpp:242:21: error: 'path' is unavailable: introduced in macOS 10.15
        Basic::open(filename, mode | std::fstream::out);
                    ^
/Library/Developer/CommandLineTools/usr/bin/../include/c++/v1/filesystem:763:29: note: 'path' has been explicitly marked unavailable here
  _LIBCPP_INLINE_VISIBILITY path(const path& __p) : __pn_(__p.__pn_) {}
                            ^
In file included from drivers.cpp:23:
In file included from ../_install/include/simulation.hpp:40:
In file included from ../_install/include/tissue.hpp:41:
../_install/include/archive.hpp:242:21: error: '~path' is unavailable: introduced in macOS 10.15
        Basic::open(filename, mode | std::fstream::out);
                    ^
/Library/Developer/CommandLineTools/usr/bin/../include/c++/v1/filesystem:790:3: note: '~path' has been explicitly marked unavailable here
  ~path() = default;
  ^
In file included from drivers.cpp:23:
In file included from ../_install/include/simulation.hpp:40:
In file included from ../_install/include/tissue.hpp:41:
../_install/include/archive.hpp:269:34: error: 'path' is unavailable: introduced in macOS 10.15
    explicit In(std::filesystem::path filename);
                                 ^
/Library/Developer/CommandLineTools/usr/bin/../include/c++/v1/filesystem:738:24: note: 'path' has been explicitly marked unavailable here
class _LIBCPP_TYPE_VIS path {
                       ^
In file included from drivers.cpp:23:
In file included from ../_install/include/simulation.hpp:40:
In file included from ../_install/include/tissue.hpp:41:
../_install/include/archive.hpp:280:25: error: 'path' is unavailable: introduced in macOS 10.15
    In(std::filesystem::path filename, std::ios_base::openmode mode);
                        ^
/Library/Developer/CommandLineTools/usr/bin/../include/c++/v1/filesystem:738:24: note: 'path' has been explicitly marked unavailable here
class _LIBCPP_TYPE_VIS path {
                       ^
In file included from drivers.cpp:23:
In file included from ../_install/include/simulation.hpp:40:
In file included from ../_install/include/tissue.hpp:41:
../_install/include/archive.hpp:290:39: error: 'path' is unavailable: introduced in macOS 10.15
    inline void open(std::filesystem::path filename, std::ios_base::openmode mode)
                                      ^
/Library/Developer/CommandLineTools/usr/bin/../include/c++/v1/filesystem:738:24: note: 'path' has been explicitly marked unavailable here
class _LIBCPP_TYPE_VIS path {
                       ^
In file included from drivers.cpp:23:
In file included from ../_install/include/simulation.hpp:40:
In file included from ../_install/include/tissue.hpp:41:
../_install/include/archive.hpp:292:21: error: 'path' is unavailable: introduced in macOS 10.15
        Basic::open(filename, mode | std::fstream::in);
                    ^
/Library/Developer/CommandLineTools/usr/bin/../include/c++/v1/filesystem:763:29: note: 'path' has been explicitly marked unavailable here
  _LIBCPP_INLINE_VISIBILITY path(const path& __p) : __pn_(__p.__pn_) {}
                            ^
In file included from drivers.cpp:23:
In file included from ../_install/include/simulation.hpp:40:
In file included from ../_install/include/tissue.hpp:41:
../_install/include/archive.hpp:292:21: error: '~path' is unavailable: introduced in macOS 10.15
        Basic::open(filename, mode | std::fstream::in);
                    ^
/Library/Developer/CommandLineTools/usr/bin/../include/c++/v1/filesystem:790:3: note: '~path' has been explicitly marked unavailable here
  ~path() = default;
  ^
In file included from drivers.cpp:23:
In file included from ../_install/include/simulation.hpp:40:
In file included from ../_install/include/tissue.hpp:41:
../_install/include/archive.hpp:416:35: error: 'path' is unavailable: introduced in macOS 10.15
    explicit Out(std::filesystem::path filename);
                                  ^
/Library/Developer/CommandLineTools/usr/bin/../include/c++/v1/filesystem:738:24: note: 'path' has been explicitly marked unavailable here
class _LIBCPP_TYPE_VIS path {
                       ^
In file included from drivers.cpp:23:
In file included from ../_install/include/simulation.hpp:40:
In file included from ../_install/include/tissue.hpp:41:
../_install/include/archive.hpp:427:26: error: 'path' is unavailable: introduced in macOS 10.15
    Out(std::filesystem::path filename, std::ios_base::openmode mode);
                         ^
/Library/Developer/CommandLineTools/usr/bin/../include/c++/v1/filesystem:738:24: note: 'path' has been explicitly marked unavailable here
class _LIBCPP_TYPE_VIS path {
                       ^
In file included from drivers.cpp:23:
In file included from ../_install/include/simulation.hpp:40:
In file included from ../_install/include/tissue.hpp:41:
../_install/include/archive.hpp:436:39: error: 'path' is unavailable: introduced in macOS 10.15
    inline void open(std::filesystem::path filename)
                                      ^
/Library/Developer/CommandLineTools/usr/bin/../include/c++/v1/filesystem:738:24: note: 'path' has been explicitly marked unavailable here
class _LIBCPP_TYPE_VIS path {
                       ^
In file included from drivers.cpp:23:
In file included from ../_install/include/simulation.hpp:40:
In file included from ../_install/include/tissue.hpp:41:
../_install/include/archive.hpp:449:39: error: 'path' is unavailable: introduced in macOS 10.15
    inline void open(std::filesystem::path filename, std::ios_base::openmode mode)
                                      ^
/Library/Developer/CommandLineTools/usr/bin/../include/c++/v1/filesystem:738:24: note: 'path' has been explicitly marked unavailable here
class _LIBCPP_TYPE_VIS path {
                       ^
In file included from drivers.cpp:23:
In file included from ../_install/include/simulation.hpp:40:
In file included from ../_install/include/tissue.hpp:41:
../_install/include/archive.hpp:438:14: error: 'path' is unavailable: introduced in macOS 10.15
        open(filename, std::fstream::binary);
             ^
/Library/Developer/CommandLineTools/usr/bin/../include/c++/v1/filesystem:763:29: note: 'path' has been explicitly marked unavailable here
  _LIBCPP_INLINE_VISIBILITY path(const path& __p) : __pn_(__p.__pn_) {}
                            ^
In file included from drivers.cpp:23:
In file included from ../_install/include/simulation.hpp:40:
In file included from ../_install/include/tissue.hpp:41:
../_install/include/archive.hpp:438:14: error: '~path' is unavailable: introduced in macOS 10.15
        open(filename, std::fstream::binary);
             ^
/Library/Developer/CommandLineTools/usr/bin/../include/c++/v1/filesystem:790:3: note: '~path' has been explicitly marked unavailable here
  ~path() = default;
  ^
fatal error: too many errors emitted, stopping now [-ferror-limit=]
20 errors generated.
make: *** [drivers.o] Error 1
ERROR: compilation failed for package ‘rRACES’
* removing ‘/Library/Frameworks/R.framework/Versions/4.2/Resources/library/rRACES’
Messaggio di avvertimento:
In i.p(...) :
  l'installazione del pacchetto ‘/var/folders/b1/qw7wc3td0szcvw17h0698lmm0000gn/T//RtmpIwp3pQ/file109f7168f69e/rRACES_0.0.1.tar.gz’ ha uno stato di uscita non-zero
riccardobergamin commented 11 months ago

Note that

(base) riccardobergamin@cli-10-106-5-182 ~ %  brew install cmake
 brew install gcc
 brew install boost
 brew install nlohmann-json
 brew install boost-python3
 brew install sdl2_image
 brew install sdl2_ttf
Running `brew update --auto-update`...
==> Auto-updated Homebrew!
Updated 1 tap (homebrew/core).
==> New Formulae
immer               pmix                sigma-cli           zug

You have 13 outdated formulae installed.

Warning: Treating cmake as a formula. For the cask, use homebrew/cask/cmake
Warning: cmake 3.27.7 is already installed and up-to-date.
To reinstall 3.27.7, run:
  brew reinstall cmake
Warning: gcc 13.2.0 is already installed and up-to-date.
To reinstall 13.2.0, run:
  brew reinstall gcc
Warning: boost 1.83.0 is already installed and up-to-date.
To reinstall 1.83.0, run:
  brew reinstall boost
Warning: nlohmann-json 3.11.2 is already installed and up-to-date.
To reinstall 3.11.2, run:
  brew reinstall nlohmann-json
Warning: boost-python3 1.83.0 is already installed and up-to-date.
To reinstall 1.83.0, run:
  brew reinstall boost-python3
Warning: sdl2_image 2.6.3_2 is already installed and up-to-date.
To reinstall 2.6.3_2, run:
  brew reinstall sdl2_image
Warning: sdl2_ttf 2.20.2 is already installed and up-to-date.
To reinstall 2.20.2, run:
  brew reinstall sdl2_ttf
(base) riccardobergamin@cli-10-106-5-182 ~ %
albertocasagrande commented 11 months ago

@riccardobergamin you are using an old version of Apple clang++ during the compilation

-- The CXX compiler identification is AppleClang 12.0.0.12000032

For some reason, it struggles with std::filesystem::path.

You may use gcc since you installed it, but my suggestion is to upgrade the Apple compiler since most of the brew packages are compiled by using it.

So, try the following command:

sudo xcode-select --install

Let me know if this solves the issue.

riccardobergamin commented 11 months ago

i updated the compiler, now i have MBPdiRiccardo3:RACES riccardobergamin$ clang --version Apple clang version 15.0.0 (clang-1500.0.40.1) Target: x86_64-apple-darwin22.6.0 Thread model: posix InstalledDir: /Library/Developer/CommandLineTools/usr/bin

But i still have the installation error in R:

── R CMD build ────────────────────────────────────────────────────────────────────────────────────────────── ✔ checking for file ‘/private/var/folders/nw/qhmvcddx03zdqs89f9h32q6c0000gn/T/RtmpVwOXid/remotes133f38435ecb/caravagnalab-rRACES-abee6e6/DESCRIPTION’ (448ms) ─ preparing ‘rRACES’: ✔ checking DESCRIPTION meta-information ... ─ cleaning src ─ running ‘cleanup’ ─ checking for LF line-endings in source and make files and shell scripts (1m 39.5s) ─ checking for empty or unneeded directories Removed empty directory ‘rRACES/_builds/CMakeFiles/3.27.7/CompilerIdCXX/tmp’ Removed empty directory ‘rRACES/_builds/CMakeFiles/CMakeScratch’ Removed empty directory ‘rRACES/_builds/CMakeFiles/pkgRedirects’ ─ building ‘rRACES_0.0.1.tar.gz’

You are in 'detached HEAD' state. You can look around, make experimental changes and commit them, and you can discard any commits you make in this state without impacting any branches by switching back to a branch.

If you want to create a new branch to retain commits you create, you may do so (now or later) by using -c with the switch command. Example:

git switch -c

Or undo this operation with:

git switch -

Turn off this advice by setting config variable advice.detachedHead to false

HEAD is now at 6636290 Closes #8 - fixed out_of_range exception in test_archive - fixed never ending execution of test_fasta_reader - fixed wrong attribute names in CellEventType - fixed a bug in PythonEndTest - cleaned up all the compilation warning ++ rm -rf .git ++ /Library/Frameworks/R.framework/Resources/bin/R --vanilla --silent -e 'Rcpp::compileAttributes()'

Rcpp::compileAttributes()

** libs clang++ -mmacosx-version-min=10.13 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rcpp/include' -I/usr/local/include -I../_install/include/ -fPIC -Wall -g -O2 -c RcppExports.cpp -o RcppExports.o clang++ -mmacosx-version-min=10.13 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rcpp/include' -I/usr/local/include -I../_install/include/ -fPIC -Wall -g -O2 -c drivers.cpp -o drivers.o In file included from drivers.cpp:23: In file included from ../_install/include/simulation.hpp:40: In file included from ../_install/include/tissue.hpp:41: ../_install/include/archive.hpp:143:28: error: 'path' is unavailable: introduced in macOS 10.15 Basic(std::filesystem::path filename, std::ios_base::openmode mode); ^ /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/filesystem/path.h:442:24: note: 'path' has been explicitly marked unavailable here class _LIBCPP_TYPE_VIS path { ^ In file included from drivers.cpp:23: In file included from ../_install/include/simulation.hpp:40: In file included from ../_install/include/tissue.hpp:41: ../_install/include/archive.hpp:151:39: error: 'path' is unavailable: introduced in macOS 10.15 inline void open(std::filesystem::path filename, std::ios_base::openmode mode) ^ /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/filesystem/path.h:442:24: note: 'path' has been explicitly marked unavailable here class _LIBCPP_TYPE_VIS path { ^ In file included from drivers.cpp:23: In file included from ../_install/include/simulation.hpp:40: In file included from ../_install/include/tissue.hpp:41: ../_install/include/archive.hpp:153:12: error: 'open' is unavailable: introduced in macOS 10.15 fs.open(filename, mode); ^ /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/fstream:1601:10: note: 'open' has been explicitly marked unavailable here void open(const filesystem::path& p, ios_base::openmode mode = ios_base::in|ios_base::out) ^ In file included from drivers.cpp:23: In file included from ../_install/include/simulation.hpp:40: In file included from ../_install/include/tissue.hpp:41: ../_install/include/archive.hpp:219:35: error: 'path' is unavailable: introduced in macOS 10.15 explicit Out(std::filesystem::path filename); ^ /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/filesystem/path.h:442:24: note: 'path' has been explicitly marked unavailable here class _LIBCPP_TYPE_VIS path { ^ In file included from drivers.cpp:23: In file included from ../_install/include/simulation.hpp:40: In file included from ../_install/include/tissue.hpp:41: ../_install/include/archive.hpp:230:26: error: 'path' is unavailable: introduced in macOS 10.15 Out(std::filesystem::path filename, std::ios_base::openmode mode); ^ /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__filesystem/path.h:442:24: note: 'path' has been explicitly marked unavailable here class _LIBCPP_TYPE_VIS path { ^ In file included from drivers.cpp:23: In file included from ../_install/include/simulation.hpp:40: In file included from ../_install/include/tissue.hpp:41: ../_install/include/archive.hpp:240:39: error: 'path' is unavailable: introduced in macOS 10.15 inline void open(std::filesystem::path filename, std::ios_base::openmode mode) ^ /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/filesystem/path.h:442:24: note: 'path' has been explicitly marked unavailable here class _LIBCPP_TYPE_VIS path { ^ In file included from drivers.cpp:23: In file included from ../_install/include/simulation.hpp:40: In file included from ../_install/include/tissue.hpp:41: ../_install/include/archive.hpp:242:21: error: 'path' is unavailable: introduced in macOS 10.15 Basic::open(filename, mode | std::fstream::out); ^ /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/filesystem/path.h:472:25: note: 'path' has been explicitly marked unavailable here _LIBCPP_HIDE_FROM_ABI path(const path& p) : pn(p.pn) {} ^ In file included from drivers.cpp:23: In file included from ../_install/include/simulation.hpp:40: In file included from ../_install/include/tissue.hpp:41: ../_install/include/archive.hpp:242:21: error: '~path' is unavailable: introduced in macOS 10.15 Basic::open(filename, mode | std::fstream::out); ^ /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__filesystem/path.h:505:3: note: '~path' has been explicitly marked unavailable here ~path() = default; ^ In file included from drivers.cpp:23: In file included from ../_install/include/simulation.hpp:40: In file included from ../_install/include/tissue.hpp:41: ../_install/include/archive.hpp:269:34: error: 'path' is unavailable: introduced in macOS 10.15 explicit In(std::filesystem::path filename); ^ /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/filesystem/path.h:442:24: note: 'path' has been explicitly marked unavailable here class _LIBCPP_TYPE_VIS path { ^ In file included from drivers.cpp:23: In file included from ../_install/include/simulation.hpp:40: In file included from ../_install/include/tissue.hpp:41: ../_install/include/archive.hpp:280:25: error: 'path' is unavailable: introduced in macOS 10.15 In(std::filesystem::path filename, std::ios_base::openmode mode); ^ /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/filesystem/path.h:442:24: note: 'path' has been explicitly marked unavailable here class _LIBCPP_TYPE_VIS path { ^ In file included from drivers.cpp:23: In file included from ../_install/include/simulation.hpp:40: In file included from ../_install/include/tissue.hpp:41: ../_install/include/archive.hpp:290:39: error: 'path' is unavailable: introduced in macOS 10.15 inline void open(std::filesystem::path filename, std::ios_base::openmode mode) ^ /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/filesystem/path.h:442:24: note: 'path' has been explicitly marked unavailable here class _LIBCPP_TYPE_VIS path { ^ In file included from drivers.cpp:23: In file included from ../_install/include/simulation.hpp:40: In file included from ../_install/include/tissue.hpp:41: ../_install/include/archive.hpp:292:21: error: 'path' is unavailable: introduced in macOS 10.15 Basic::open(filename, mode | std::fstream::in); ^ /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/filesystem/path.h:472:25: note: 'path' has been explicitly marked unavailable here _LIBCPP_HIDE_FROMABI path(const path& p) : pn(p.pn_) {} ^ In file included from drivers.cpp:23: In file included from ../_install/include/simulation.hpp:40: In file included from ../_install/include/tissue.hpp:41: ../_install/include/archive.hpp:292:21: error: '~path' is unavailable: introduced in macOS 10.15 Basic::open(filename, mode | std::fstream::in); ^ /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/filesystem/path.h:505:3: note: '~path' has been explicitly marked unavailable here ~path() = default; ^ In file included from drivers.cpp:23: In file included from ../_install/include/simulation.hpp:40: In file included from ../_install/include/tissue.hpp:41: ../_install/include/archive.hpp:416:35: error: 'path' is unavailable: introduced in macOS 10.15 explicit Out(std::filesystem::path filename); ^ /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/filesystem/path.h:442:24: note: 'path' has been explicitly marked unavailable here class _LIBCPP_TYPE_VIS path { ^ In file included from drivers.cpp:23: In file included from ../_install/include/simulation.hpp:40: In file included from ../_install/include/tissue.hpp:41: ../_install/include/archive.hpp:427:26: error: 'path' is unavailable: introduced in macOS 10.15 Out(std::filesystem::path filename, std::ios_base::openmode mode); ^ /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/filesystem/path.h:442:24: note: 'path' has been explicitly marked unavailable here class _LIBCPP_TYPE_VIS path { ^ In file included from drivers.cpp:23: In file included from ../_install/include/simulation.hpp:40: In file included from ../_install/include/tissue.hpp:41: ../_install/include/archive.hpp:436:39: error: 'path' is unavailable: introduced in macOS 10.15 inline void open(std::filesystem::path filename) ^ /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/filesystem/path.h:442:24: note: 'path' has been explicitly marked unavailable here class _LIBCPP_TYPE_VIS path { ^ In file included from drivers.cpp:23: In file included from ../_install/include/simulation.hpp:40: In file included from ../_install/include/tissue.hpp:41: ../_install/include/archive.hpp:449:39: error: 'path' is unavailable: introduced in macOS 10.15 inline void open(std::filesystem::path filename, std::ios_base::openmode mode) ^ /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/filesystem/path.h:442:24: note: 'path' has been explicitly marked unavailable here class _LIBCPP_TYPE_VIS path { ^ In file included from drivers.cpp:23: In file included from ../_install/include/simulation.hpp:40: In file included from ../_install/include/tissue.hpp:41: ../_install/include/archive.hpp:438:14: error: 'path' is unavailable: introduced in macOS 10.15 open(filename, std::fstream::binary); ^ /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/filesystem/path.h:472:25: note: 'path' has been explicitly marked unavailable here _LIBCPP_HIDE_FROM_ABI path(const path& p) : _pn(p.pn_) {} ^ In file included from drivers.cpp:23: In file included from ../_install/include/simulation.hpp:40: In file included from ../_install/include/tissue.hpp:41: ../_install/include/archive.hpp:438:14: error: '~path' is unavailable: introduced in macOS 10.15 open(filename, std::fstream::binary); ^ /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__filesystem/path.h:505:3: note: '~path' has been explicitly marked unavailable here ~path() = default; ^ fatal error: too many errors emitted, stopping now [-ferror-limit=] 20 errors generated. make: *** [drivers.o] Error 1 ERROR: compilation failed for package ‘rRACES’

  • removing ‘/Library/Frameworks/R.framework/Versions/4.2/Resources/library/rRACES’ Messaggio di avvertimento: In i.p(...) : l'installazione del pacchetto ‘/var/folders/nw/qhmvcddx03zdqs89f9h32q6c0000gn/T//RtmpVwOXid/file133f4f047e48/rRACES_0.0.1.tar.gz’ ha uno stato di uscita non-zero
albertocasagrande commented 11 months ago

Can you try the following commands and post the console output?

git clone https://github.com/albertocasagrande/RACES.git
cd RACES
cmake .
make -j
riccardobergamin commented 11 months ago

yes, sure. I get:

riccardobergamin$ git clone https://github.com/albertocasagrande/RACES.git Cloning into 'RACES'... remote: Enumerating objects: 2146, done. remote: Counting objects: 100% (914/914), done. remote: Compressing objects: 100% (565/565), done. remote: Total 2146 (delta 677), reused 564 (delta 343), pack-reused 1232 Receiving objects: 100% (2146/2146), 1.32 MiB | 2.30 MiB/s, done. Resolving deltas: 100% (1603/1603), done. (base) MBPdiRiccardo3:~ riccardobergamin$ cd RACES (base) MBPdiRiccardo3:RACES riccardobergamin$ cmake . -- The CXX compiler identification is AppleClang 15.0.0.15000040 -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Check for working CXX compiler: /Library/Developer/CommandLineTools/usr/bin/c++ - skipped -- Detecting CXX compile features -- Detecting CXX compile features - done SDL2_ttf found SDL2_image found Matplot++ found Downloading "p-ranav/indicators" library... done Using "p-ranav/indicators" Building executable, Python wrapper, and tests -- Found Boost: /usr/local/lib/cmake/Boost-1.83.0/BoostConfig.cmake (found version "1.83.0") found components: program_options -- Found nlohmann_json: /usr/local/share/cmake/nlohmann_json/nlohmann_jsonConfig.cmake (found suitable version "3.11.2", minimum required is "3.2.0") -- Found Python: /Library/Python/miniconda3/bin/python3.9 (found version "3.9.12") found components: Interpreter Development Development.Module Development.Embed -- Found Boost: /usr/local/lib/cmake/Boost-1.83.0/BoostConfig.cmake (found version "1.83.0") found components: python Python bindings will be compiled python-test will not be executed: pytest package not available -- Found Boost: /usr/local/lib/cmake/Boost-1.83.0/BoostConfig.cmake (found version "1.83.0") found components: unit_test_framework C++ code will tested Downloading SBS profile example from sanger... -- Configuring done (8.0s) -- Generating done (0.1s) -- Build files have been written to: /Users/riccardobergamin/RACES (base) MBPdiRiccardo3:RACES riccardobergamin$ make -j [ 1%] Building CXX object CMakeFiles/objlib.dir/src/basic_IO.cpp.o [ 2%] Building CXX object CMakeFiles/objlib.dir/src/archive.cpp.o [ 3%] Building CXX object CMakeFiles/objlib.dir/src/driver_genotype.cpp.o [ 5%] Building CXX object CMakeFiles/objlib.dir/src/species.cpp.o [ 6%] Building CXX object CMakeFiles/objlib.dir/src/position.cpp.o [ 7%] Building CXX object CMakeFiles/objlib.dir/src/ending_conditions.cpp.o [ 8%] Building CXX object CMakeFiles/objlib.dir/src/simulation.cpp.o [ 10%] Building CXX object CMakeFiles/objlib.dir/src/cell.cpp.o [ 11%] Building CXX object CMakeFiles/objlib.dir/src/tissue.cpp.o [ 12%] Building CXX object CMakeFiles/objlib.dir/src/progress_bar.cpp.o [ 14%] Building CXX object CMakeFiles/objlib.dir/src/tissue_sample.cpp.o [ 15%] Building CXX object CMakeFiles/objlib.dir/src/snv_signature.cpp.o [ 16%] Building CXX object CMakeFiles/objlib.dir/src/event_wrapper.cpp.o [ 17%] Building CXX object CMakeFiles/objlib.dir/src/sample_specification.cpp.o [ 19%] Building CXX object CMakeFiles/objlib.dir/src/cell_event.cpp.o [ 20%] Building CXX object CMakeFiles/objlib.dir/src/rate_update.cpp.o [ 21%] Building CXX object CMakeFiles/objlib.dir/src/simulation_event.cpp.o [ 23%] Building CXX object CMakeFiles/objlib.dir/src/driver_mutation.cpp.o [ 24%] Building CXX object CMakeFiles/objlib.dir/src/plot_2D.cpp.o [ 25%] Building CXX object CMakeFiles/objlib.dir/src/logger.cpp.o [ 26%] Building CXX object CMakeFiles/objlib.dir/src/snv.cpp.o [ 28%] Building CXX object CMakeFiles/objlib.dir/src/cna.cpp.o [ 29%] Building CXX object CMakeFiles/objlib.dir/src/palette.cpp.o [ 30%] Building CXX object CMakeFiles/objlib.dir/src/timed_event.cpp.o [ 32%] Building CXX object CMakeFiles/objlib.dir/src/context.cpp.o [ 33%] Building CXX object CMakeFiles/objlib.dir/src/statistics.cpp.o [ 34%] Building CXX object CMakeFiles/objlib.dir/src/genomic_region.cpp.o [ 35%] Building CXX object CMakeFiles/objlib.dir/src/binary_logger.cpp.o [ 38%] Building CXX object CMakeFiles/objlib.dir/src/read_simulator.cpp.o [ 39%] Building CXX object CMakeFiles/objlib.dir/src/fasta_reader.cpp.o [ 41%] Building CXX object CMakeFiles/objlib.dir/src/allele.cpp.o [ 42%] Building CXX object CMakeFiles/objlib.dir/src/genomic_position.cpp.o [ 43%] Building CXX object CMakeFiles/objlib.dir/src/phyloXML.cpp.o [ 44%] Building CXX object CMakeFiles/objlib.dir/src/fasta_utils.cpp.o [ 46%] Building CXX object CMakeFiles/objlib.dir/src/mutation_engine.cpp.o [ 47%] Building CXX object CMakeFiles/objlib.dir/src/SDL_plot.cpp.o [ 48%] Building CXX object CMakeFiles/objlib.dir/src/position_set.cpp.o [ 51%] Building CXX object CMakeFiles/objlib.dir/src/phylogenetic_forest.cpp.o [ 50%] Building CXX object CMakeFiles/objlib.dir/src/sampling.cpp.o [ 52%] Building CXX object CMakeFiles/objlib.dir/src/mutational_properties.cpp.o [ 52%] Building CXX object CMakeFiles/objlib.dir/src/genome_mutations.cpp.o [ 52%] Built target objlib [ 55%] Linking CXX static library libRACES.a [ 55%] Linking CXX shared library libRACES.dylib [ 55%] Built target libRACES [ 55%] Built target libRACES_static [ 56%] Building CXX object CMakeFiles/tissue_sampler.dir/src/tissue_sampler.cpp.o [ 57%] Building CXX object CMakeFiles/phylo_builder.dir/src/phylo_builder.cpp.o [ 60%] Building CXX object CMakeFiles/sample_context_index.dir/src/sample_context_index.cpp.o [ 60%] Building CXX object CMakeFiles/build_context_index.dir/src/build_context_index.cpp.o [ 61%] Building CXX object CMakeFiles/passengers_sim.dir/src/json_config.cpp.o [ 62%] Building CXX object python/CMakeFiles/pyRACES.dir/src/genotype.cpp.o [ 64%] Building CXX object python/CMakeFiles/pyRACES.dir/src/bindings.cpp.o [ 65%] Building CXX object tests/CMakeFiles/test_snv_signature.dir/snv_signature.cpp.o [ 66%] Building CXX object CMakeFiles/tissue_sampler.dir/src/json_config.cpp.o [ 67%] Building CXX object CMakeFiles/phylo_builder.dir/src/json_config.cpp.o [ 69%] Building CXX object python/CMakeFiles/pyRACES.dir/src/simulation_wrapper.cpp.o [ 70%] Building CXX object CMakeFiles/phylo_builder.dir/src/common.cpp.o [ 71%] Building CXX object tests/CMakeFiles/test_context_index.dir/context_index.cpp.o [ 73%] Building CXX object tests/CMakeFiles/test_fasta_reader.dir/fasta_reader.cpp.o [ 74%] Building CXX object tests/CMakeFiles/test_archive.dir/archive.cpp.o [ 75%] Building CXX object CMakeFiles/tissue_sampler.dir/src/common.cpp.o [ 76%] Building CXX object python/CMakeFiles/pyRACES.dir/src/epigenetic_rates.cpp.o [ 78%] Building CXX object CMakeFiles/passengers_sim.dir/src/passengers_sim.cpp.o [ 79%] Building CXX object CMakeFiles/passengers_sim.dir/src/common.cpp.o [ 80%] Building CXX object tests/CMakeFiles/test_genome_mutations.dir/genome_mutations.cpp.o [ 82%] Building CXX object CMakeFiles/drivers_sim.dir/src/drivers_sim.cpp.o [ 83%] Building CXX object CMakeFiles/drivers_sim.dir/src/common.cpp.o [ 84%] Building CXX object CMakeFiles/drivers_sim.dir/src/json_config.cpp.o [ 85%] Linking CXX executable test_fasta_reader [ 85%] Built target test_fasta_reader [ 87%] Linking CXX executable test_snv_signature [ 88%] Linking CXX executable test_context_index [ 88%] Built target test_snv_signature [ 88%] Built target test_context_index [ 89%] Linking CXX executable test_genome_mutations [ 89%] Built target test_genome_mutations [ 91%] Linking CXX executable sample_context_index [ 91%] Built target sample_context_index [ 92%] Linking CXX executable build_context_index [ 92%] Built target build_context_index [ 93%] Linking CXX executable test_archive [ 93%] Built target test_archive [ 94%] Linking CXX shared module RACES.so [ 94%] Built target pyRACES [ 96%] Linking CXX executable phylo_builder [ 97%] Linking CXX executable tissue_sampler [ 97%] Built target phylo_builder [ 97%] Built target tissue_sampler [ 98%] Linking CXX executable drivers_sim [ 98%] Built target drivers_sim [100%] Linking CXX executable passengers_sim [100%] Built target passengers_sim

albertocasagrande commented 11 months ago

I noticed that you have an already configured source in the R devtools cache. Try the following command in the command line:

git clone https://github.com/caravagnalab/rRACES.git
R CMD build rRACES
R CMD install rRACES_*.tar.gz
riccardobergamin commented 11 months ago

(base) MBPdiRiccardo3:~ riccardobergamin$ R CMD build rRACES

albertocasagrande commented 11 months ago

What are the results of the following shell commands?

clang++ --version
which clang++
echo $CXX
riccardobergamin commented 11 months ago

(base) MBPdiRiccardo3:~ riccardobergamin$ clang++ --version Apple clang version 15.0.0 (clang-1500.0.40.1) Target: x86_64-apple-darwin22.6.0 Thread model: posix InstalledDir: /Library/Developer/CommandLineTools/usr/bin (base) MBPdiRiccardo3:~ riccardobergamin$ which clang++ /usr/bin/clang++ (base) MBPdiRiccardo3:~ riccardobergamin$

albertocasagrande commented 11 months ago

What about echo $CXX?

riccardobergamin commented 11 months ago

it does not give output

(base) MBPdiRiccardo3:~ riccardobergamin$ echo $CXX

albertocasagrande commented 11 months ago

ls -la /Library/Developer/CommandLineTools/SDKs/

riccardobergamin commented 11 months ago

(base) MBPdiRiccardo3:~ riccardobergamin$ ls -la /Library/Developer/CommandLineTools/SDKs/ total 0 drwxr-xr-x 10 root wheel 320 2 Nov 16:45 . drwxr-xr-x 5 root admin 160 2 Nov 16:45 .. lrwxr-xr-x 1 root wheel 14 2 Nov 16:45 MacOSX.sdk -> MacOSX14.0.sdk drwxr-xr-x 7 root wheel 224 2 Nov 16:42 MacOSX12.3.sdk lrwxr-xr-x 1 root wheel 14 2 Nov 16:41 MacOSX12.sdk -> MacOSX12.3.sdk drwxr-xr-x 7 root wheel 224 12 Nov 2022 MacOSX13.1.sdk drwxr-xr-x 7 root wheel 224 2 Nov 16:45 MacOSX13.3.sdk lrwxr-xr-x 1 root wheel 14 2 Nov 16:44 MacOSX13.sdk -> MacOSX13.3.sdk drwxr-xr-x 7 root wheel 224 31 Ago 21:12 MacOSX14.0.sdk lrwxr-xr-x 1 root wheel 14 2 Nov 16:43 MacOSX14.sdk -> MacOSX14.0.sdk

albertocasagrande commented 11 months ago 
R CMD config CXX
R CMD config MAKE
R CMD config CXXFLAGS
R CMD config CXX17FLAGS
R CMD config SHLIB_CXXFLAGS
riccardobergamin commented 11 months ago

(base) MBPdiRiccardo3:~ riccardobergamin$ R CMD config CXX clang++ -mmacosx-version-min=10.13 -std=gnu++14 (base) MBPdiRiccardo3:~ riccardobergamin$ R CMD config MAKE make (base) MBPdiRiccardo3:~ riccardobergamin$ R CMD config CXXFLAGS -Wall -g -O2 (base) MBPdiRiccardo3:~ riccardobergamin$ R CMD config CXX17FLAGS -Wall -g -O2 (base) MBPdiRiccardo3:~ riccardobergamin$ R CMD config SHLIB_CXXFLAGS

albertocasagrande commented 11 months ago 
grep "CXX ="  /Library/Frameworks/R.framework/Resources/etc/Makeconf
riccardobergamin commented 11 months ago 
(base) MBPdiRiccardo3:~ riccardobergamin$ grep CXX /Library/Frameworks/R.framework/Resources/etc/Makeconf
# configure  'CC=clang -mmacosx-version-min=10.13' 'CXX=clang++ -mmacosx-version-min=10.13' 'OBJC=clang -mmacosx-version-min=10.13' 'FC=gfortran -mmacosx-version-min=10.13' 'F77=gfortran -mmacosx-version-min=10.13' 'CFLAGS=-Wall -g -O2' 'CXXFLAGS=-Wall -g -O2' 'OBJCFLAGS=-Wall -g -O2' 'FCFLAGS=-Wall -g -O2' 'F77FLAGS=-Wall -g -O2' '--enable-memory-profiling' '--x-libraries=/opt/X11/lib' '--x-includes=/opt/X11/include' '--enable-R-framework' '--build=x86_64-apple-darwin17.0' 'build_alias=x86_64-apple-darwin17.0' 'PKG_CONFIG_PATH=/usr/lib/pkgconfig:/usr/local/lib/pkgconfig:/opt/X11/lib/pkgconfig'
CXX = clang++ -mmacosx-version-min=10.13 -std=gnu++14
CXXFLAGS = -Wall -g -O2 $(LTO)
CXXPICFLAGS = -fPIC
CXX11 = clang++ -mmacosx-version-min=10.13
CXX11FLAGS = -Wall -g -O2 $(LTO)
CXX11PICFLAGS = -fPIC
CXX11STD = -std=gnu++11
CXX14 = clang++ -mmacosx-version-min=10.13
CXX14FLAGS = -Wall -g -O2 $(LTO)
CXX14PICFLAGS = -fPIC
CXX14STD = -std=gnu++14
CXX17 = clang++ -mmacosx-version-min=10.13
CXX17FLAGS = -Wall -g -O2 $(LTO)
CXX17PICFLAGS = -fPIC
CXX17STD = -std=gnu++17
CXX20 = clang++ -mmacosx-version-min=10.13
CXX20FLAGS = -Wall -g -O2 $(LTO)
CXX20PICFLAGS = -fPIC
CXX20STD = -std=gnu++2a
CXX_VISIBILITY = 
OBJCXX = clang++ -mmacosx-version-min=10.13
SHLIB_CXXFLAGS = 
SHLIB_CXXLD = $(CXX)
SHLIB_CXXLDFLAGS = -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress# $(CXXFLAGS) $(CXXPICFLAGS) $(LTO_LD)
SHLIB_CXX11LD = $(CXX11) $(CXX11STD)
SHLIB_CXX11LDFLAGS = -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress# $(CXX11FLAGS) $(CXX11PICFLAGS) $(LTO_LD)
SHLIB_CXX14LD = $(CXX14) $(CXX14STD)
SHLIB_CXX14LDFLAGS = -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress# $(CXX14FLAGS) $(CXX14PICFLAGS) $(LTO_LD)
SHLIB_CXX17LD = $(CXX17) $(CXX17STD)
SHLIB_CXX17LDFLAGS = -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress# $(CXX17FLAGS) $(CXX17PICFLAGS) $(LTO_LD)
SHLIB_CXX20LD = $(CXX20) $(CXX20STD)
SHLIB_CXX20LDFLAGS = -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress# $(CXX20FLAGS) $(CXX20PICFLAGS) $(LTO_LD)
SHLIB_OPENMP_CXXFLAGS = 
R_XTRA_CXXFLAGS = 
## SHLIB_CFLAGS SHLIB_CXXFLAGS SHLIB_FFLAGS are apparently currently unused
## SHLIB_CXXFLAGS is undocumented, there is no SHLIB_FCFLAGS
ALL_CXXFLAGS =  $(PKG_CXXFLAGS) $(CXXPICFLAGS) $(SHLIB_CXXFLAGS) $(CXXFLAGS)
ALL_OBJCXXFLAGS = $(PKG_OBJCXXFLAGS) $(CXXPICFLAGS) $(SHLIB_CXXFLAGS) $(OBJCXXFLAGS)
    $(CXX) $(ALL_CPPFLAGS) $(ALL_CXXFLAGS) -c $< -o $@
    $(CXX) $(ALL_CPPFLAGS) $(ALL_CXXFLAGS) -c $< -o $@
    @$(CXX) -M $(ALL_CPPFLAGS) $< > $@
    @$(CXX) -M $(ALL_CPPFLAGS) $< > $@
    $(OBJCXX) $(ALL_CPPFLAGS) $(ALL_OBJCXXFLAGS) -c $< -o $@
    $(OBJCXX) $(ALL_CPPFLAGS) $(ALL_OBJCXXFLAGS) -c $< -o $@
albertocasagrande commented 11 months ago 
cp  /Library/Frameworks/R.framework/Resources/etc/Makeconf ~/Makeconf.backup
cat ~/Makeconf.backup| awk '{ if ($0 ~ /^CXX = /) { sub("gnu\\+\\+14","gnu++17");}; print; }'  > Makeconf
sudo mv Makeconf  /Library/Frameworks/R.framework/Resources/etc/Makeconf

and try to install the package again

riccardobergamin commented 11 months ago

R CMD build rRACES

albertocasagrande commented 11 months ago

Do you have a file ~/.R/Makeconf? What is the output of which R? Can you attach your /Library/Frameworks/R.framework/Resources/etc/Makeconf to the reply?

riccardobergamin commented 11 months ago 
# etc/Makeconf.  Generated from Makeconf.in by configure.
#
# ${R_HOME}/etc/Makeconf
#
# R was configured using the following call
# (not including env. vars and site configuration)
# configure  'CC=clang -mmacosx-version-min=10.13' 'CXX=clang++ -mmacosx-version-min=10.13' 'OBJC=clang -mmacosx-version-min=10.13' 'FC=gfortran -mmacosx-version-min=10.13' 'F77=gfortran -mmacosx-version-min=10.13' 'CFLAGS=-Wall -g -O2' 'CXXFLAGS=-Wall -g -O2' 'OBJCFLAGS=-Wall -g -O2' 'FCFLAGS=-Wall -g -O2' 'F77FLAGS=-Wall -g -O2' '--enable-memory-profiling' '--x-libraries=/opt/X11/lib' '--x-includes=/opt/X11/include' '--enable-R-framework' '--build=x86_64-apple-darwin17.0' 'build_alias=x86_64-apple-darwin17.0' 'PKG_CONFIG_PATH=/usr/lib/pkgconfig:/usr/local/lib/pkgconfig:/opt/X11/lib/pkgconfig'

## This fails if it contains spaces, or if it is quoted
include $(R_SHARE_DIR)/make/vars.mk

AR = ar
BLAS_LIBS = -L"$(R_HOME)/lib$(R_ARCH)" -lRblas
C_VISIBILITY = 
CC = clang -mmacosx-version-min=10.13
CFLAGS = -Wall -g -O2 $(LTO)
CPICFLAGS = -fPIC
CPPFLAGS = -I/usr/local/include
CXX = clang++ -mmacosx-version-min=10.13 -std=gnu++17
CXXFLAGS = -Wall -g -O2 $(LTO)
CXXPICFLAGS = -fPIC
CXX11 = clang++ -mmacosx-version-min=10.13
CXX11FLAGS = -Wall -g -O2 $(LTO)
CXX11PICFLAGS = -fPIC
CXX11STD = -std=gnu++11
CXX14 = clang++ -mmacosx-version-min=10.13
CXX14FLAGS = -Wall -g -O2 $(LTO)
CXX14PICFLAGS = -fPIC
CXX14STD = -std=gnu++14
CXX17 = clang++ -mmacosx-version-min=10.13
CXX17FLAGS = -Wall -g -O2 $(LTO)
CXX17PICFLAGS = -fPIC
CXX17STD = -std=gnu++17
CXX20 = clang++ -mmacosx-version-min=10.13
CXX20FLAGS = -Wall -g -O2 $(LTO)
CXX20PICFLAGS = -fPIC
CXX20STD = -std=gnu++2a
CXX_VISIBILITY = 
DYLIB_EXT = .dylib
DYLIB_LD = $(CC)
DYLIB_LDFLAGS = -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress# $(CFLAGS) $(CPICFLAGS) 
## should be used by packages for dylibs, but at the time of writing was not
DYLIB_LINK = $(DYLIB_LD) $(DYLIB_LDFLAGS) $(LDFLAGS)
ECHO = echo
ECHO_C = \c
ECHO_N = 
ECHO_T = 
F_VISIBILITY = 
## FC is the compiler used for all Fortran as from R 3.6.0
FC = gfortran -mmacosx-version-min=10.13
FCFLAGS = -Wall -g -O2 $(LTO_FC)
## additional libs needed when linking with $(FC), e.g. on some Oracle compilers
FCLIBS_XTRA = 
FFLAGS = -Wall -g -O2 $(LTO_FC)
FLIBS =  -L/usr/local/gfortran/lib/gcc/x86_64-apple-darwin18/8.2.0 -L/usr/local/gfortran/lib -lgfortran -lquadmath -lm
FPICFLAGS = -fPIC
FPIEFLAGS = -fPIE
FOUNDATION_CPPFLAGS = 
FOUNDATION_LIBS = -framework Foundation
JAR = /usr/bin/jar
JAVA = /usr/bin/java
JAVAC = /usr/bin/javac
JAVAH = /usr/bin/javah
## JAVA_HOME might be used in the next three.  
## They are for packages 'JavaGD' and 'rJava'
JAVA_HOME = /Library/Java/JavaVirtualMachines/jdk1.8.0_241.jdk/Contents/Home/jre
JAVA_CPPFLAGS = -I$(JAVA_HOME)/../include -I$(JAVA_HOME)/../include/darwin
JAVA_LIBS = -L$(JAVA_HOME)/lib/server -ljvm
JAVA_LD_LIBRARY_PATH = $(JAVA_HOME)/lib/server
LAPACK_LIBS = -L"$(R_HOME)/lib$(R_ARCH)" -lRlapack
LDFLAGS = -L/usr/local/lib
## we only need this is if it is external, as otherwise link to R
LIBINTL=   -Wl,-framework -Wl,CoreFoundation
LIBM = 
LIBR0 = -L"$(R_HOME)/lib$(R_ARCH)"
LIBR1 = -lR
LIBR = -F/Library/Frameworks/R.framework/.. -framework R
LIBS = -L/usr/local/lib -lpcre2-8 -llzma -lbz2 -lz -licucore -ldl -lm -liconv
## needed by R CMD config
LIBnn = lib
LIBTOOL = $(SHELL) "$(R_HOME)/bin/libtool"
## set for --enable-lto, --enable-lto=check
LTO = 
LTO_FC = 
LTO_LD = 
## set for --enable-lto=R, used in INSTALL
LTO_OPT = 
LTO_FC_OPT = 
## needed to build applications linking to static libR
MAIN_LD = $(CC)
MAIN_LDFLAGS = 
MAIN_LINK = $(MAIN_LD) $(MAIN_LDFLAGS) $(LDFLAGS)
MKINSTALLDIRS = "$(R_HOME)/bin/mkinstalldirs"
NM = /usr/bin/nm -B
OBJC = clang -mmacosx-version-min=10.13
OBJCFLAGS = -Wall -g -O2 -fobjc-exceptions $(LTO)
OBJC_LIBS = -lobjc 
OBJCXX = clang++ -mmacosx-version-min=10.13
R_ARCH = 
RANLIB = ranlib
SAFE_FFLAGS = -Wall -g -O2 -msse2 -mfpmath=sse
SED = /usr/bin/sed
SHELL = /bin/sh
SHLIB_CFLAGS = 
SHLIB_CXXFLAGS = 
SHLIB_CXXLD = $(CXX)
SHLIB_CXXLDFLAGS = -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress# $(CXXFLAGS) $(CXXPICFLAGS) $(LTO_LD)
SHLIB_CXX11LD = $(CXX11) $(CXX11STD)
SHLIB_CXX11LDFLAGS = -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress# $(CXX11FLAGS) $(CXX11PICFLAGS) $(LTO_LD)
SHLIB_CXX14LD = $(CXX14) $(CXX14STD)
SHLIB_CXX14LDFLAGS = -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress# $(CXX14FLAGS) $(CXX14PICFLAGS) $(LTO_LD)
SHLIB_CXX17LD = $(CXX17) $(CXX17STD)
SHLIB_CXX17LDFLAGS = -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress# $(CXX17FLAGS) $(CXX17PICFLAGS) $(LTO_LD)
SHLIB_CXX20LD = $(CXX20) $(CXX20STD)
SHLIB_CXX20LDFLAGS = -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress# $(CXX20FLAGS) $(CXX20PICFLAGS) $(LTO_LD)
SHLIB_EXT = .so
SHLIB_FCLD = $(FC)
SHLIB_FCLDFLAGS = -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress# $(FCFLAGS) $(FPICFLAGS)
SHLIB_FFLAGS = 
SHLIB_LD = $(CC)
## used for add-on packages linked by C
SHLIB_LDFLAGS = -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress# $(CFLAGS) $(CPICFLAGS) $(LTO_LD)
## used for standard packages
SHLIB_LDFLAGS_R = -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress# $(CFLAGS) $(CPICFLAGS) $(LTO_LD)
SHLIB_LIBADD = 
## We want to ensure libR is picked up from $(R_HOME)/lib
## before e.g. /usr/local/lib if a version is already installed.
SHLIB_LINK = $(SHLIB_LD) $(SHLIB_LDFLAGS) $(LIBR0) $(LDFLAGS)
SHLIB_OPENMP_CFLAGS = 
SHLIB_OPENMP_CXXFLAGS = 
SHLIB_OPENMP_FFLAGS = 
STRIP_STATIC_LIB = strip -S
STRIP_SHARED_LIB = strip -x
TCLTK_CPPFLAGS = -I/usr/local/include -I/usr/local/include -I/opt/X11/include
TCLTK_LIBS = -L/usr/local/lib -ltcl8.6 -L/usr/local/lib -ltk8.6 -L/opt/X11/lib -lX11 -Wl,-weak-lXss -lXext
YACC = bison -y

## for linking to libR.a
STATIC_LIBR = #  "$(R_HOME)/lib$(R_ARCH)/libR.a"  $(BLAS_LIBS) $(FLIBS)  $(LIBINTL) -lreadline -lncurses  $(LIBS)

## These are recorded as macros for legacy use in packages
## set on AIX, formerly for old glibc (-D__NO_MATH_INLINES)
R_XTRA_CFLAGS = 
##  was formerly set on HP-UX
R_XTRA_CPPFLAGS =  -I"$(R_INCLUDE_DIR)" -DNDEBUG
## currently unset
R_XTRA_CXXFLAGS = 
## used for gfortran >= 7 in R > 3.6.0
R_XTRA_FFLAGS = -fno-optimize-sibling-calls

## SHLIB_CFLAGS SHLIB_CXXFLAGS SHLIB_FFLAGS are apparently currently unused
## SHLIB_CXXFLAGS is undocumented, there is no SHLIB_FCFLAGS
ALL_CFLAGS =  $(PKG_CFLAGS) $(CPICFLAGS) $(SHLIB_CFLAGS) $(CFLAGS)
ALL_CPPFLAGS =  -I"$(R_INCLUDE_DIR)" -DNDEBUG $(PKG_CPPFLAGS) $(CLINK_CPPFLAGS) $(CPPFLAGS) 
ALL_CXXFLAGS =  $(PKG_CXXFLAGS) $(CXXPICFLAGS) $(SHLIB_CXXFLAGS) $(CXXFLAGS)
ALL_OBJCFLAGS = $(PKG_OBJCFLAGS) $(CPICFLAGS) $(SHLIB_CFLAGS) $(OBJCFLAGS)
ALL_OBJCXXFLAGS = $(PKG_OBJCXXFLAGS) $(CXXPICFLAGS) $(SHLIB_CXXFLAGS) $(OBJCXXFLAGS)
ALL_FFLAGS = -fno-optimize-sibling-calls $(PKG_FFLAGS) $(FPICFLAGS) $(SHLIB_FFLAGS) $(FFLAGS)
## can be overridden by R CMD SHLIB
P_FCFLAGS = $(PKG_FFLAGS)
ALL_FCFLAGS = -fno-optimize-sibling-calls $(P_FCFLAGS) $(FPICFLAGS) $(SHLIB_FFLAGS) $(FCFLAGS)
## LIBR here as a couple of packages use this without SHLIB_LINK
ALL_LIBS = $(PKG_LIBS) $(SHLIB_LIBADD) $(LIBR) $(LIBINTL)

.SUFFIXES:
.SUFFIXES: .c .cc .cpp .d .f .f90 .f95 .m .mm .M .o

.c.o:
    $(CC) $(ALL_CPPFLAGS) $(ALL_CFLAGS) -c $< -o $@
.c.d:
    @echo "making $@ from $<"
    @$(CC) -MM $(ALL_CPPFLAGS) $< > $@
.cc.o:
    $(CXX) $(ALL_CPPFLAGS) $(ALL_CXXFLAGS) -c $< -o $@
.cpp.o:
    $(CXX) $(ALL_CPPFLAGS) $(ALL_CXXFLAGS) -c $< -o $@
.cc.d:
    @echo "making $@ from $<"
    @$(CXX) -M $(ALL_CPPFLAGS) $< > $@
.cpp.d:
    @echo "making $@ from $<"
    @$(CXX) -M $(ALL_CPPFLAGS) $< > $@
.m.o:
    $(OBJC) $(ALL_CPPFLAGS) $(ALL_OBJCFLAGS) -c $< -o $@
.m.d:
    @echo "making $@ from $<"
    @$(OBJC) -MM $(ALL_CPPFLAGS) $< > $@
.mm.o:
    $(OBJCXX) $(ALL_CPPFLAGS) $(ALL_OBJCXXFLAGS) -c $< -o $@
.M.o:
    $(OBJCXX) $(ALL_CPPFLAGS) $(ALL_OBJCXXFLAGS) -c $< -o $@
.f.o:
    $(FC) $(ALL_FFLAGS) -c $< -o $@
.f95.o:
    $(FC) $(ALL_FCFLAGS) -c  $< -o $@
.f90.o:
    $(FC) $(ALL_FCFLAGS) -c  $< -o $@
albertocasagrande commented 11 months ago

Download this file and execute

sudo mv ~/Downloads/Makeconf.txt /Library/Frameworks/R.framework/Resources/etc/Makeconf

and try to compile rRACES for the last time.

riccardobergamin commented 11 months ago

It works but it takes time to create vignettes i think

riccardobergamin commented 11 months ago

Thank you !!!

albertocasagrande commented 11 months ago

@riccardobergamin Thank you for your patience. Let us know if you have any other issues.