Build error for lfortran

[kjelljorner]

When trying to install lfortran on Mac M1 Monterey I get this error message. Also, seems like lfortran 0.15 is now available so the recipe could be updated as well.

(base) kjelljorner@dhcp-45 lfortran-0.15.0 % brew install lfortran                                             
==> Downloading https://lfortran.github.io/tarballs/release/lfortran-0.14.0.tar.gz
Already downloaded: /Users/kjelljorner/Library/Caches/Homebrew/downloads/a2cafbbe75c0ad045754d066d39f2f76dbaf1edffdf9831bc80f23435d63af5f--lfortran-0.14.0.tar.gz
==> Installing lfortran from fortran-lang/fortran
==> cmake -DCMAKE_CXX_FLAGS_RELEASE=-O3 -funroll-loops -DNDEBUG -DWITH_LLVM=ON -G Ninja -B build
==> cmake --build build
Last 15 lines from /Users/kjelljorner/Library/Logs/Homebrew/lfortran/02.cmake:
  "VTT for std::__1::basic_ofstream<char, std::__1::char_traits<char> >", referenced from:
      LFortran::write_file(std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> > const&, std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> > const&) in liblfortran_lib.a(evaluator.cpp.o)
  "vtable for std::__1::basic_ifstream<char, std::__1::char_traits<char> >", referenced from:
      LFortran::read_file(std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> > const&) in liblfortran_lib.a(utils.cpp.o)
      LFortran::read_line_from_file(std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> >, unsigned int) in liblfortran_lib.a(stacktrace.cpp.o)
      LFortran::get_local_info_dwarfdump(std::__1::vector<LFortran::StacktraceItem, std::__1::allocator<LFortran::StacktraceItem> >&) in liblfortran_lib.a(stacktrace.cpp.o)
  NOTE: a missing vtable usually means the first non-inline virtual member function has no definition.
  "vtable for std::__1::basic_ofstream<char, std::__1::char_traits<char> >", referenced from:
      LFortran::write_file(std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> > const&, std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> > const&) in liblfortran_lib.a(evaluator.cpp.o)
  NOTE: a missing vtable usually means the first non-inline virtual member function has no definition.
ld: symbol(s) not found for architecture arm64
clang: error: linker command failed with exit code 1 (use -v to see invocation)
[70/86] /opt/homebrew/Library/Homebrew/shims/mac/super/clang++ -DHAVE_TARGET_AARCH64=1 -I/tmp/lfortran-20220603-47415-1fci7r4/lfortran-0.14.0/build/src -I/tmp/lfortran-20220603-47415-1fci7r4/lfortran-0.14.0/src -O3 -funroll-loops -DNDEBUG -arch arm64 -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk -fPIE -fno-rtti -std=gnu++17 -MD -MT src/bin/CMakeFiles/cpptranslate.dir/cpptranslate.cpp.o -MF src/bin/CMakeFiles/cpptranslate.dir/cpptranslate.cpp.o.d -o src/bin/CMakeFiles/cpptranslate.dir/cpptranslate.cpp.o -c /tmp/lfortran-20220603-47415-1fci7r4/lfortran-0.14.0/src/bin/cpptranslate.cpp
[71/86] /opt/homebrew/Library/Homebrew/shims/mac/super/clang++ -DHAVE_TARGET_AARCH64=1 -I/tmp/lfortran-20220603-47415-1fci7r4/lfortran-0.14.0/src/bin/tpl -I/tmp/lfortran-20220603-47415-1fci7r4/lfortran-0.14.0/build/src -I/tmp/lfortran-20220603-47415-1fci7r4/lfortran-0.14.0/src -O3 -funroll-loops -DNDEBUG -arch arm64 -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk -fPIE -fno-rtti -std=gnu++17 -MD -MT src/bin/CMakeFiles/lfortran.dir/lfortran.cpp.o -MF src/bin/CMakeFiles/lfortran.dir/lfortran.cpp.o.d -o src/bin/CMakeFiles/lfortran.dir/lfortran.cpp.o -c /tmp/lfortran-20220603-47415-1fci7r4/lfortran-0.14.0/src/bin/lfortran.cpp
ninja: build stopped: subcommand failed.

[certik]

Not sure where this might be coming from. Here is a Spack build that works for me on M1:

• LFortran: add new package spack/spack#30901

The above error looks like some C++ runtime library issue?

[kjelljorner]

Building with GCC gives similar errors

Last 15 lines from /Users/kjelljorner/Library/Logs/Homebrew/lfortran/02.cmake:
  "__ZTv0_n24_NSt3__114basic_iostreamIcNS_11char_traitsIcEEED0Ev", referenced from:
      __ZTCNSt3__118basic_stringstreamIcNS_11char_traitsIcEENS_9allocatorIcEEEE0_NS_14basic_iostreamIcS2_EE in libLLVMInstrumentation.a(InstrOrderFile.cpp.o)
      __ZTCNSt3__118basic_stringstreamIcNS_11char_traitsIcEENS_9allocatorIcEEEE0_NS_14basic_iostreamIcS2_EE in libLLVMAnalysis.a(InlineAdvisor.cpp.o)
      __ZTCNSt3__118basic_stringstreamIcNS_11char_traitsIcEENS_9allocatorIcEEEE0_NS_14basic_iostreamIcS2_EE in libLLVMTransformUtils.a(ImportedFunctionsInliningStatistics.cpp.o)
      __ZTCNSt3__118basic_stringstreamIcNS_11char_traitsIcEENS_9allocatorIcEEEE0_NS_14basic_iostreamIcS2_EE in libLLVMTextAPI.a(InterfaceFile.cpp.o)
  "__ZTv0_n24_NSt3__114basic_iostreamIcNS_11char_traitsIcEEED1Ev", referenced from:
      __ZTCNSt3__118basic_stringstreamIcNS_11char_traitsIcEENS_9allocatorIcEEEE0_NS_14basic_iostreamIcS2_EE in libLLVMInstrumentation.a(InstrOrderFile.cpp.o)
      __ZTCNSt3__118basic_stringstreamIcNS_11char_traitsIcEENS_9allocatorIcEEEE0_NS_14basic_iostreamIcS2_EE in libLLVMAnalysis.a(InlineAdvisor.cpp.o)
      __ZTCNSt3__118basic_stringstreamIcNS_11char_traitsIcEENS_9allocatorIcEEEE0_NS_14basic_iostreamIcS2_EE in libLLVMTransformUtils.a(ImportedFunctionsInliningStatistics.cpp.o)
      __ZTCNSt3__118basic_stringstreamIcNS_11char_traitsIcEENS_9allocatorIcEEEE0_NS_14basic_iostreamIcS2_EE in libLLVMTextAPI.a(InterfaceFile.cpp.o)
ld: symbol(s) not found for architecture arm64
collect2: error: ld returned 1 exit status

[awvwgk]

For LFortran 0.14.0 there is an error on MacOS/Arm64, which got LFortran rejected from homebrew-core (see Homebrew/homebrew-core#92088). Seems like this is fixed with 0.15.0, so maybe an update of the formula would be the best fix.

[kjelljorner]

Modifying the recipe to load 0.15.0 with

url "https://lfortran.github.io/tarballs/release/lfortran-0.15.0.tar.gz"
sha256 "8712c1b0c886f08937ff4c277ff3fa5c05e4dead1bafe55e3bd789be96470127"

still gives an error for me

Last 15 lines from /Users/kjelljorner/Library/Logs/Homebrew/lfortran/02.cmake:
      LFortran::read_file(std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> > const&, std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> >&) in libasr.a(utils2.cpp.o)
      LFortran::read_line_from_file(std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> >, unsigned int) in libasr.a(stacktrace.cpp.o)
      LFortran::get_local_info_dwarfdump(std::__1::vector<LFortran::StacktraceItem, std::__1::allocator<LFortran::StacktraceItem> >&) in libasr.a(stacktrace.cpp.o)
      LFortran::read_file(std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> > const&) in libasr.a(string_utils.cpp.o)
  NOTE: a missing vtable usually means the first non-inline virtual member function has no definition.
  "vtable for std::__1::basic_ofstream<char, std::__1::char_traits<char> >", referenced from:
      LFortran::X86Assembler::save_asm(std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> > const&) in test_asm.cpp.o
      LFortran::write_file(std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> > const&, std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> > const&) in libasr.a(evaluator.cpp.o)
      LFortran::X86Assembler::save_binary(std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> > const&) in libasr.a(x86_assembler.cpp.o)
  NOTE: a missing vtable usually means the first non-inline virtual member function has no definition.
ld: symbol(s) not found for architecture arm64

[certik]

I use M1 as my main development machine for LFortran, so everything should work. I've never seen this error. Can you post the full log: the output of cmake and the full ninja build? I am happy to fix it upstream (if this is some bug in LFortran) and make a new release.

[kjelljorner]

Here's the full stderr and stdout of HOMEBREW_MAKE_JOBS=1 brew install lfortran --verbose > brew.out 2> brew.err. Included are also the logs created by homebrew and mentioned at the end of the output file. Hope that helps.

Logs:
     /Users/kjelljorner/Library/Logs/Homebrew/lfortran/02.cmake.cc
     /Users/kjelljorner/Library/Logs/Homebrew/lfortran/00.options.out
     /Users/kjelljorner/Library/Logs/Homebrew/lfortran/01.cmake.cc
     /Users/kjelljorner/Library/Logs/Homebrew/lfortran/01.cmake
     /Users/kjelljorner/Library/Logs/Homebrew/lfortran/02.cmake
     /Users/kjelljorner/Library/Logs/Homebrew/lfortran/build

Archive.zip

[certik]

Ok, so it seems you are missing a C++ standard library in the Homebrew's own clang. Here is an example of the invocation:

: && /opt/homebrew/Library/Homebrew/shims/mac/super/clang++ -O3 -funroll-loops -DNDEBUG -arch arm64 -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk -Wl,-search_paths_first -Wl,-headerpad_max_install_names  src/lfortran/tests/CMakeFiles/x.dir/x.cpp.o -o src/lfortran/tests/x  src/lfortran/liblfortran_lib.a  src/runtime/legacy/liblfortran_runtime_static.a  /opt/homebrew/opt/llvm@11/lib/libLLVMMCJIT.a  /opt/homebrew/opt/llvm@11/lib/libLLVMOrcJIT.a  /opt/homebrew/opt/llvm@11/lib/libLLVMExecutionEngine.a  /opt/homebrew/opt/llvm@11/lib/libLLVMRuntimeDyld.a  /opt/homebrew/opt/llvm@11/lib/libLLVMJITLink.a  /opt/homebrew/opt/llvm@11/lib/libLLVMOrcError.a  /opt/homebrew/opt/llvm@11/lib/libLLVMPasses.a  /opt/homebrew/opt/llvm@11/lib/libLLVMCoroutines.a  /opt/homebrew/opt/llvm@11/lib/libLLVMipo.a  /opt/homebrew/opt/llvm@11/lib/libLLVMInstrumentation.a  /opt/homebrew/opt/llvm@11/lib/libLLVMVectorize.a  /opt/homebrew/opt/llvm@11/lib/libLLVMFrontendOpenMP.a  /opt/homebrew/opt/llvm@11/lib/libLLVMIRReader.a  /opt/homebrew/opt/llvm@11/lib/libLLVMLinker.a  /opt/homebrew/opt/llvm@11/lib/libLLVMAsmParser.a  /opt/homebrew/opt/llvm@11/lib/libLLVMAArch64AsmParser.a  /opt/homebrew/opt/llvm@11/lib/libLLVMAArch64CodeGen.a  /opt/homebrew/opt/llvm@11/lib/libLLVMAsmPrinter.a  /opt/homebrew/opt/llvm@11/lib/libLLVMDebugInfoDWARF.a  /opt/homebrew/opt/llvm@11/lib/libLLVMCFGuard.a  /opt/homebrew/opt/llvm@11/lib/libLLVMGlobalISel.a  /opt/homebrew/opt/llvm@11/lib/libLLVMSelectionDAG.a  /opt/homebrew/opt/llvm@11/lib/libLLVMCodeGen.a  /opt/homebrew/opt/llvm@11/lib/libLLVMTarget.a  /opt/homebrew/opt/llvm@11/lib/libLLVMBitWriter.a  /opt/homebrew/opt/llvm@11/lib/libLLVMScalarOpts.a  /opt/homebrew/opt/llvm@11/lib/libLLVMAggressiveInstCombine.a  /opt/homebrew/opt/llvm@11/lib/libLLVMInstCombine.a  /opt/homebrew/opt/llvm@11/lib/libLLVMTransformUtils.a  /opt/homebrew/opt/llvm@11/lib/libLLVMAnalysis.a  /opt/homebrew/opt/llvm@11/lib/libLLVMObject.a  /opt/homebrew/opt/llvm@11/lib/libLLVMBitReader.a  /opt/homebrew/opt/llvm@11/lib/libLLVMMCParser.a  /opt/homebrew/opt/llvm@11/lib/libLLVMTextAPI.a  /opt/homebrew/opt/llvm@11/lib/libLLVMProfileData.a  /opt/hom@@@
Undefined symbols for architecture arm64:^M
  "std::__1::basic_stringbuf<char, std::__1::char_traits<char>, std::__1::allocator<char> >::str(std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> > const&)", referenced from:^M
      LFortran::get_line(std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> >, int) in liblfortran_lib.a(parser.cpp.o)^M
ld: symbol(s) not found for architecture arm64^M
clang: error: linker command failed with exit code 1 (use -v to see invocation)^M

The line looks good to me. For comparison, here is such a line on my M1:

/Library/Developer/CommandLineTools/usr/bin/c++ -Wall -Wextra -g -ggdb -arch arm64 -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX12.1.sdk -Wl,-search_paths_first -Wl,-headerpad_max_install_names CMakeFiles/lfortran.dir/lfortran.cpp.o -o lfortran  ../lfortran/liblfortran_lib.a ../libasr/libasr.a ../runtime/legacy/liblfortran_runtime_static.a /Users/ondrej/mambaforge/envs/lf/lib/libz.a /Users/ondrej/mambaforge/envs/lf/lib/libLLVMMCJIT.a /Users/ondrej/mambaforge/envs/lf/lib/libLLVMOrcJIT.a /Users/ondrej/mambaforge/envs/lf/lib/libLLVMExecutionEngine.a /Users/ondrej/mambaforge/envs/lf/lib/libLLVMRuntimeDyld.a /Users/ondrej/mambaforge/envs/lf/lib/libLLVMJITLink.a /Users/ondrej/mambaforge/envs/lf/lib/libLLVMOrcError.a /Users/ondrej/mambaforge/envs/lf/lib/libLLVMPasses.a /Users/ondrej/mambaforge/envs/lf/lib/libLLVMCoroutines.a /Users/ondrej/mambaforge/envs/lf/lib/libLLVMipo.a /Users/ondrej/mambaforge/envs/lf/lib/libLLVMInstrumentation.a /Users/ondrej/mambaforge/envs/lf/lib/libLLVMVectorize.a /Users/ondrej/mambaforge/envs/lf/lib/libLLVMFrontendOpenMP.a /Users/ondrej/mambaforge/envs/lf/lib/libLLVMIRReader.a /Users/ondrej/mambaforge/envs/lf/lib/libLLVMLinker.a /Users/ondrej/mambaforge/envs/lf/lib/libLLVMAsmParser.a /Users/ondrej/mambaforge/envs/lf/lib/libLLVMAArch64AsmParser.a /Users/ondrej/mambaforge/envs/lf/lib/libLLVMAArch64CodeGen.a /Users/ondrej/mambaforge/envs/lf/lib/libLLVMAsmPrinter.a /Users/ondrej/mambaforge/envs/lf/lib/libLLVMDebugInfoDWARF.a /Users/ondrej/mambaforge/envs/lf/lib/libLLVMCFGuard.a /Users/ondrej/mambaforge/envs/lf/lib/libLLVMGlobalISel.a /Users/ondrej/mambaforge/envs/lf/lib/libLLVMSelectionDAG.a /Users/ondrej/mambaforge/envs/lf/lib/libLLVMCodeGen.a /Users/ondrej/mambaforge/envs/lf/lib/libLLVMTarget.a /Users/ondrej/mambaforge/envs/lf/lib/libLLVMBitWriter.a /Users/ondrej/mambaforge/envs/lf/lib/libLLVMScalarOpts.a /Users/ondrej/mambaforge/envs/lf/lib/libLLVMAggressiveInstCombine.a /Users/ondrej/mambaforge/envs/lf/lib/libLLVMInstCombine.a /Users/ondrej/mambaforge/envs/lf/lib/libLLVMTransformUtils.a /Users/ondrej/mambaforge/envs/lf/lib/libLLVMAnalysis.a /Users/ondrej/mambaforge/envs/lf/lib/libLLVMObject.a /Users/ondrej/mambaforge/envs/lf/lib/libLLVMBitReader.a /Users/ondrej/mambaforge/envs/lf/lib/libLLVMMCParser.a /Users/ondrej/mambaforge/envs/lf/lib/libLLVMTextAPI.a /Users/ondrej/mambaforge/envs/lf/lib/libLLVMProfileData.a /Users/ondrej/mambaforge/envs/lf/lib/libLLVMCore.a /Users/ondrej/mambaforge/envs/lf/lib/libLLVMRemarks.a /Users/ondrej/mambaforge/envs/lf/lib/libLLVMBitstreamReader.a /Users/ondrej/mambaforge/envs/lf/lib/libLLVMAArch64Disassembler.a /Users/ondrej/mambaforge/envs/lf/lib/libLLVMAArch64Desc.a /Users/ondrej/mambaforge/envs/lf/lib/libLLVMAArch64Info.a /Users/ondrej/mambaforge/envs/lf/lib/libLLVMAArch64Utils.a /Users/ondrej/mambaforge/envs/lf/lib/libLLVMMCDisassembler.a /Users/ondrej/mambaforge/envs/lf/lib/libLLVMMC.a /Users/ondrej/mambaforge/envs/lf/lib/libLLVMBinaryFormat.a /Users/ondrej/mambaforge/envs/lf/lib/libLLVMDebugInfoCodeView.a /Users/ondrej/mambaforge/envs/lf/lib/libLLVMDebugInfoMSF.a /Users/ondrej/mambaforge/envs/lf/lib/libLLVMSupport.a -lz -lm /Users/ondrej/mambaforge/envs/lf/lib/libLLVMDemangle.a 

They look pretty much the same.

On your computer, can you try to compile this simple program:

#include <iostream>
#include <string>

int main() {
    std::string x;
    x = "123";
    std::cout << x << std::endl;
    return 0;
}

with

/opt/homebrew/Library/Homebrew/shims/mac/super/clang++ a.cpp
./a.out

And see if it works?

[kjelljorner]

I get this with the homebrew clang

(base) kjelljorner@dhcp-45 c++ % /opt/homebrew/Library/Homebrew/shims/mac/super/clang++ a.cpp
clang++: The build tool has reset ENV; --env=std required.

and this with Apple clang

(base) kjelljorner@dhcp-45 c++ % c++ a.cpp
(base) kjelljorner@dhcp-45 c++ % ls
a.cpp a.out
(base) kjelljorner@dhcp-45 c++ % ./a.out 
123

[certik]

It looks like Homebrew has a modified clang++ compiler, or a wrapper script. It seems it does not link the C++ runtime library correctly. It would have to be investigated by creating a minimal reproducible example by executing the /opt/homebrew/Library/Homebrew/shims/mac/super/clang++ manually (not via cmake) to first compile the above simple file to an object file, then link to a binary and hopefully it fails in the same way. Then we can report it as a bug to Homebrew.

[kjelljorner]

Might be related to this issue: Homebrew/homebrew-core#96915.

[certik]

Is there a way to install homebrew without sudo? If it is, then I can install and help debug it. I just don't want to install anything that requires sudo for operation. So I use Conda and Spack frequently, both of which (now) work and do not require sudo.

[kjelljorner]

I haven't tried this myself, but it seems possible: https://www.scivision.dev/macos-homebrew-non-sudo/

[awvwgk]

Resolved with #11