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Using Homebrew's yaml-cpp (0.8.0) fails to link on macOS when using cmake #134

Open
scharlton2 opened this issue Oct 23, 2023 · 0 comments
Open

Using Homebrew's yaml-cpp (0.8.0) fails to link on macOS when using cmake #134

scharlton2 opened this issue Oct 23, 2023 · 0 comments

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@scharlton2
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Building with PHREEQCRM_WITH_YAML_CPP:BOOL=ON on macOS and using brew to install yaml-cpp (0.8.0) fails to link

Note: the autotools build on macOS builds fine using the brew's installation

see https://github.com/scharlton2/phreeqcrm/actions/runs/6593929938/job/17917210378

autotools (macos-latest)

✔️ Build with autotools 

  make -j4
  shell: /bin/bash -e {0}
  env:
    NAME: PhreeqcRM
    BUILD_TYPE: Release
    VER_STRING: 3.7.6-16656
Making all in database
make[1]: Nothing to be done for `all'.
Making all in doc
make[1]: Nothing to be done for `all'.
Making all in Doxygen
make[1]: Nothing to be done for `all'.
Making all in Tests
make[1]: Nothing to be done for `all'.
  CXX      src/IPhreeqcPhast/IPhreeqc/phreeqcpp/PHRQ_io_output.lo
  CXX      src/IPhreeqcPhast/IPhreeqc/phreeqcpp/pitzer_structures.lo
  CXX      src/IPhreeqcPhast/IPhreeqc/phreeqcpp/pitzer.lo
  CXX      src/IPhreeqcPhast/IPhreeqc/phreeqcpp/PPassemblage.lo
  CXX      src/IPhreeqcPhast/IPhreeqc/phreeqcpp/PPassemblageComp.lo
  CXX      src/IPhreeqcPhast/IPhreeqc/phreeqcpp/prep.lo
  CXX      src/IPhreeqcPhast/IPhreeqc/phreeqcpp/Pressure.lo
  CXX      src/IPhreeqcPhast/IPhreeqc/phreeqcpp/print.lo
  CXX      src/IPhreeqcPhast/IPhreeqc/phreeqcpp/Reaction.lo
  CXX      src/IPhreeqcPhast/IPhreeqc/phreeqcpp/read.lo
  CXX      src/IPhreeqcPhast/IPhreeqc/phreeqcpp/ReadClass.lo
  CXX      src/IPhreeqcPhast/IPhreeqc/phreeqcpp/readtr.lo
  CXX      src/IPhreeqcPhast/IPhreeqc/phreeqcpp/runner.lo
  CXX      src/IPhreeqcPhast/IPhreeqc/phreeqcpp/SelectedOutput.lo
  CXX      src/IPhreeqcPhast/IPhreeqc/phreeqcpp/Serializer.lo
  CXX      src/IPhreeqcPhast/IPhreeqc/phreeqcpp/sit.lo
  CXX      src/IPhreeqcPhast/IPhreeqc/phreeqcpp/smalldense.lo
  CXX      src/IPhreeqcPhast/IPhreeqc/phreeqcpp/Solution.lo
  CXX      src/IPhreeqcPhast/IPhreeqc/phreeqcpp/SolutionIsotope.lo
  CXX      src/IPhreeqcPhast/IPhreeqc/phreeqcpp/spread.lo
  CXX      src/IPhreeqcPhast/IPhreeqc/phreeqcpp/SS.lo
  CXX      src/IPhreeqcPhast/IPhreeqc/phreeqcpp/SSassemblage.lo
  CXX      src/IPhreeqcPhast/IPhreeqc/phreeqcpp/SScomp.lo
  CXX      src/IPhreeqcPhast/IPhreeqc/phreeqcpp/step.lo
  CXX      src/IPhreeqcPhast/IPhreeqc/phreeqcpp/StorageBin.lo
  CXX      src/IPhreeqcPhast/IPhreeqc/phreeqcpp/StorageBinList.lo
  CXX      src/IPhreeqcPhast/IPhreeqc/phreeqcpp/structures.lo
  CXX      src/IPhreeqcPhast/IPhreeqc/phreeqcpp/sundialsmath.lo
  CXX      src/IPhreeqcPhast/IPhreeqc/phreeqcpp/Surface.lo
  CXX      src/IPhreeqcPhast/IPhreeqc/phreeqcpp/SurfaceCharge.lo
  CXX      src/IPhreeqcPhast/IPhreeqc/phreeqcpp/SurfaceComp.lo
  CXX      src/IPhreeqcPhast/IPhreeqc/phreeqcpp/System.lo
  CXX      src/IPhreeqcPhast/IPhreeqc/phreeqcpp/tally.lo
  CXX      src/IPhreeqcPhast/IPhreeqc/phreeqcpp/Temperature.lo
  CXX      src/IPhreeqcPhast/IPhreeqc/phreeqcpp/tidy.lo
  CXX      src/IPhreeqcPhast/IPhreeqc/phreeqcpp/transport.lo
  CXX      src/IPhreeqcPhast/IPhreeqc/phreeqcpp/Use.lo
  CXX      src/IPhreeqcPhast/IPhreeqc/phreeqcpp/UserPunch.lo
  CXX      src/IPhreeqcPhast/IPhreeqc/phreeqcpp/utilities.lo
  CC       src/IPhreeqcPhast/IPhreeqc/Var.lo
  CXX      src/PhreeqcRM.lo
  CXX      src/RM_interface_C.lo
  CXX      src/RM_interface_F.lo
  CXX      src/VarManager.lo
  CXX      src/YAML_interface_F.lo
  CXX      src/YAMLPhreeqcRM.lo
  CXX      src/BMI_interface_F.lo
  CXX      src/BMIVariant.lo
  CXX      src/BMIPhreeqcRM.lo
  CXX      src/IPhreeqcPhast/IPhreeqc/CSelectedOutput.lo
  CXX      src/IPhreeqcPhast/IPhreeqc/IPhreeqc_interface_F.lo
  CXX      src/IPhreeqcPhast/IPhreeqc/IPhreeqc.lo
  CXX      src/IPhreeqcPhast/IPhreeqc/IPhreeqcLib.lo
  CXX      src/IPhreeqcPhast/IPhreeqc/phreeqcpp/advection.lo
  CXX      src/IPhreeqcPhast/IPhreeqc/phreeqcpp/basicsubs.lo
  CXX      src/IPhreeqcPhast/IPhreeqc/phreeqcpp/cl1.lo
  CXX      src/IPhreeqcPhast/IPhreeqc/phreeqcpp/common/Parser.lo
  CXX      src/IPhreeqcPhast/IPhreeqc/phreeqcpp/common/PHRQ_base.lo
  CXX      src/IPhreeqcPhast/IPhreeqc/phreeqcpp/common/PHRQ_io.lo
  CXX      src/IPhreeqcPhast/IPhreeqc/phreeqcpp/common/Utils.lo
  CXX      src/IPhreeqcPhast/IPhreeqc/phreeqcpp/cvdense.lo
  CXX      src/IPhreeqcPhast/IPhreeqc/phreeqcpp/cvode.lo
  CXX      src/IPhreeqcPhast/IPhreeqc/phreeqcpp/cxxKinetics.lo
  CXX      src/IPhreeqcPhast/IPhreeqc/phreeqcpp/cxxMix.lo
  CXX      src/IPhreeqcPhast/IPhreeqc/phreeqcpp/dense.lo
  CXX      src/IPhreeqcPhast/IPhreeqc/phreeqcpp/Dictionary.lo
  CXX      src/IPhreeqcPhast/IPhreeqc/phreeqcpp/dumper.lo
  CXX      src/IPhreeqcPhast/IPhreeqc/phreeqcpp/Exchange.lo
  CXX      src/IPhreeqcPhast/IPhreeqc/phreeqcpp/ExchComp.lo
  CXX      src/IPhreeqcPhast/IPhreeqc/phreeqcpp/GasComp.lo
  CXX      src/IPhreeqcPhast/IPhreeqc/phreeqcpp/gases.lo
  CXX      src/IPhreeqcPhast/IPhreeqc/phreeqcpp/GasPhase.lo
  CXX      src/IPhreeqcPhast/IPhreeqc/phreeqcpp/input.lo
  CXX      src/IPhreeqcPhast/IPhreeqc/phreeqcpp/integrate.lo
  CXX      src/IPhreeqcPhast/IPhreeqc/phreeqcpp/inverse.lo
  CXX      src/IPhreeqcPhast/IPhreeqc/phreeqcpp/ISolution.lo
  CXX      src/IPhreeqcPhast/IPhreeqc/phreeqcpp/ISolutionComp.lo
  CXX      src/IPhreeqcPhast/IPhreeqc/phreeqcpp/isotopes.lo
  CXX      src/IPhreeqcPhast/IPhreeqc/phreeqcpp/kinetics.lo
  CXX      src/IPhreeqcPhast/IPhreeqc/phreeqcpp/KineticsComp.lo
  CXX      src/IPhreeqcPhast/IPhreeqc/phreeqcpp/mainsubs.lo
  CXX      src/IPhreeqcPhast/IPhreeqc/phreeqcpp/model.lo
  CXX      src/IPhreeqcPhast/IPhreeqc/phreeqcpp/NameDouble.lo
  CXX      src/IPhreeqcPhast/IPhreeqc/phreeqcpp/NumKeyword.lo
  CXX      src/IPhreeqcPhast/IPhreeqc/phreeqcpp/nvector_serial.lo
  CXX      src/IPhreeqcPhast/IPhreeqc/phreeqcpp/nvector.lo
  CXX      src/IPhreeqcPhast/IPhreeqc/phreeqcpp/parse.lo
  CXX      src/IPhreeqcPhast/IPhreeqc/phreeqcpp/PBasic.lo
  CXX      src/IPhreeqcPhast/IPhreeqc/phreeqcpp/phqalloc.lo
  CXX      src/IPhreeqcPhast/IPhreeqc/phreeqcpp/Phreeqc.lo
  CXX      src/IPhreeqcPhast/IPhreeqc/phreeqcpp/PhreeqcKeywords/Keywords.lo
  CXX      src/IPhreeqcPhast/IPhreeqcPhast.lo
  CXX      src/IPhreeqcPhast/IPhreeqcPhastLib.lo
  CXXLD    libphreeqcrm.la
ld: warning: -undefined dynamic_lookup may not work with chained fixups

✔️ Make check 

Run make check -j4
  make check -j4
  shell: /bin/bash -e {0}
  env:
    NAME: PhreeqcRM
    BUILD_TYPE: Release
    VER_STRING: 3.7.6-16656
Making check in database
make[1]: Nothing to be done for `check'.
Making check in doc
make[1]: Nothing to be done for `check'.
Making check in Doxygen
make[1]: Nothing to be done for `check'.
Making check in Tests
/Applications/Xcode_14.2.app/Contents/Developer/usr/bin/make  TestRM TestRMdtor TestBMIdtor
  CC       Advect_c.o
  CXX      AdvectBMI_cpp.o
  CXX      AdvectBMI_cpp_test.o
  CXX      Advect_cpp.o
  CC       Gas_c.o
  CXX      Gas_cpp.o
  CXX      main.o
  CC       SimpleAdvect_c.o
  CXX      SimpleAdvect_cpp.o
  CC       Species_c.o
  CXX      Species_cpp.o
  CXX      TestAllMethods_cpp.o
  CXX      WriteYAMLFile_cpp.o
  CXX      WriteYAMLFile_cpp_test.o
  PPFC     ../src/RM_interface.o
  PPFC     ../src/IPhreeqcPhast/IPhreeqc/IPhreeqc_interface.o
  PPFC     ../src/YAML_interface.o
  CXX      TestRMdtor.o
  CXX      TestBMIdtor.o
  PPFC     WriteYAMLFile_f90.o
  PPFC     WriteYAMLFile_f90_test.o
  PPFC     ../src/BMI_interface.o
  PPFC     Advect_f90.o
  PPFC     Species_f90.o
  GEN      TestRMdtor
  PPFC     AdvectBMI_f90_test.o
  PPFC     TestAllMethods_f90.o
  GEN      TestBMIdtor
  PPFC     AdvectBMI_f90.o
  PPFC     Gas_f90.o
  PPFC     SimpleAdvect_f90.o
  GEN      TestRM
ld: warning: could not create compact unwind for _Advect_f90: stack subq instruction is too different from dwarf stack size
ld: warning: could not create compact unwind for _Species_f90: stack subq instruction is too different from dwarf stack size
/Applications/Xcode_14.2.app/Contents/Developer/usr/bin/make  check-TESTS
PASS: TestBMIdtor
PASS: TestRMdtor
PASS: TestRM
============================================================================
Testsuite summary for PhreeqcRM 3.7.6-16656
============================================================================
# TOTAL: 3
# PASS:  3
# SKIP:  0
# XFAIL: 0
# FAIL:  0
# XPASS: 0
# ERROR: 0
============================================================================
make[1]: Nothing to be done for `check-am'.

macos-11 shared-OFF yaml=ON

✔️ Install ninja yaml-cpp (macOS) 

Run brew install ninja yaml-cpp
  brew install ninja yaml-cpp
  ls -alR /usr/local/Cellar/
  shell: /bin/bash -e {0}
  env:
    NAME: PhreeqcRM
    BUILD_TYPE: Release
    VER_STRING: 3.7.6-16656
    FC: gfortran
    CC: gcc
    CXX: g++
==> Downloading https://ghcr.io/v2/homebrew/core/ninja/manifests/1.11.1-1
==> Fetching ninja
==> Downloading https://ghcr.io/v2/homebrew/core/ninja/blobs/sha256:3f625fc538dbceeecebb5088bda7b3d2daa8477adb3f9653f01e3eff76983b8d
==> Downloading https://ghcr.io/v2/homebrew/core/yaml-cpp/manifests/0.8.0
==> Fetching yaml-cpp
==> Downloading https://ghcr.io/v2/homebrew/core/yaml-cpp/blobs/sha256:34e2ea6e7e4c5db76bdbe1eb799025c0143c3cda82ad561bf6354ba79e014427
==> Pouring ninja--1.11.1.big_sur.bottle.1.tar.gz
==> Caveats
Bash completion has been installed to:
  /usr/local/etc/bash_completion.d

Emacs Lisp files have been installed to:
  /usr/local/share/emacs/site-lisp/ninja
==> Summary
🍺  /usr/local/Cellar/ninja/1.11.1: 10 files, 453.5KB
==> Pouring yaml-cpp--0.8.0.big_sur.bottle.tar.gz
🍺  /usr/local/Cellar/yaml-cpp/0.8.0: 49 files, 437.5KB
==> Caveats
==> ninja
Bash completion has been installed to:
  /usr/local/etc/bash_completion.d

Emacs Lisp files have been installed to:
  /usr/local/share/emacs/site-lisp/ninja
...

❌ Build with CMake 

  cmake --build /Users/runner/work/phreeqcrm/phreeqcrm/build --config Release
  shell: /bin/bash -e {0}
  env:
    NAME: PhreeqcRM
    BUILD_TYPE: Release
    VER_STRING: 3.7.6-16656
    FC: gfortran
    CC: gcc
    CXX: g++
    pythonLocation: /Users/runner/hostedtoolcache/Python/3.8.18/x64
    PKG_CONFIG_PATH: /Users/runner/hostedtoolcache/Python/3.8.18/x64/lib/pkgconfig
    Python_ROOT_DIR: /Users/runner/hostedtoolcache/Python/3.8.18/x64
    Python2_ROOT_DIR: /Users/runner/hostedtoolcache/Python/3.8.18/x64
    Python3_ROOT_DIR: /Users/runner/hostedtoolcache/Python/3.8.18/x64
[1/237] Building CXX object CMakeFiles/PhreeqcRM.dir/src/BMIVariant.cpp.o
[2/237] Building CXX object CMakeFiles/PhreeqcRM.dir/src/IPhreeqcPhast/IPhreeqc/CSelectedOutput.cpp.o
[3/237] Building CXX object CMakeFiles/PhreeqcRM.dir/src/IPhreeqcPhast/IPhreeqc/IPhreeqc_interface_F.cpp.o
[4/237] Building CXX object CMakeFiles/PhreeqcRM.dir/src/BMI_interface_F.cpp.o
[5/237] Building CXX object CMakeFiles/PhreeqcRM.dir/src/IPhreeqcPhast/IPhreeqc/IPhreeqcLib.cpp.o
[6/237] Building CXX object CMakeFiles/PhreeqcRM.dir/src/IPhreeqcPhast/IPhreeqc/phreeqcpp/advection.cpp.o
[7/237] Building CXX object CMakeFiles/PhreeqcRM.dir/src/IPhreeqcPhast/IPhreeqc/phreeqcpp/cl1.cpp.o
[8/237] Building CXX object CMakeFiles/PhreeqcRM.dir/src/BMIPhreeqcRM.cpp.o
[9/237] Building CXX object CMakeFiles/PhreeqcRM.dir/src/IPhreeqcPhast/IPhreeqc/phreeqcpp/common/PHRQ_base.cxx.o
[10/237] Building CXX object CMakeFiles/PhreeqcRM.dir/src/IPhreeqcPhast/IPhreeqc/IPhreeqc.cpp.o
[11/237] Building CXX object CMakeFiles/PhreeqcRM.dir/src/IPhreeqcPhast/IPhreeqc/phreeqcpp/common/Parser.cxx.o
[12/237] Building CXX object CMakeFiles/PhreeqcRM.dir/src/IPhreeqcPhast/IPhreeqc/phreeqcpp/common/Utils.cxx.o
[13/237] Building CXX object CMakeFiles/PhreeqcRM.dir/src/IPhreeqcPhast/IPhreeqc/phreeqcpp/common/PHRQ_io.cpp.o
[14/237] Building CXX object CMakeFiles/PhreeqcRM.dir/src/IPhreeqcPhast/IPhreeqc/phreeqcpp/basicsubs.cpp.o
[15/237] Building CXX object CMakeFiles/PhreeqcRM.dir/src/IPhreeqcPhast/IPhreeqc/phreeqcpp/dense.cpp.o
[16/237] Building CXX object CMakeFiles/PhreeqcRM.dir/src/IPhreeqcPhast/IPhreeqc/phreeqcpp/cvdense.cpp.o
[17/237] Building CXX object CMakeFiles/PhreeqcRM.dir/src/IPhreeqcPhast/IPhreeqc/phreeqcpp/Dictionary.cpp.o
[18/237] Building CXX object CMakeFiles/PhreeqcRM.dir/src/IPhreeqcPhast/IPhreeqc/phreeqcpp/dumper.cpp.o
[19/237] Building CXX object CMakeFiles/PhreeqcRM.dir/src/IPhreeqcPhast/IPhreeqc/phreeqcpp/cvode.cpp.o
[20/237] Building CXX object CMakeFiles/PhreeqcRM.dir/src/IPhreeqcPhast/IPhreeqc/phreeqcpp/cxxMix.cxx.o
[21/237] Building CXX object CMakeFiles/PhreeqcRM.dir/src/IPhreeqcPhast/IPhreeqc/phreeqcpp/cxxKinetics.cxx.o
[22/237] Building CXX object CMakeFiles/PhreeqcRM.dir/src/IPhreeqcPhast/IPhreeqc/phreeqcpp/GasComp.cxx.o
[23/237] Building CXX object CMakeFiles/PhreeqcRM.dir/src/IPhreeqcPhast/IPhreeqc/phreeqcpp/ExchComp.cxx.o
[24/237] Building CXX object CMakeFiles/PhreeqcRM.dir/src/IPhreeqcPhast/IPhreeqc/phreeqcpp/gases.cpp.o
[25/237] Building CXX object CMakeFiles/PhreeqcRM.dir/src/IPhreeqcPhast/IPhreeqc/phreeqcpp/Exchange.cxx.o
[26/237] Building CXX object CMakeFiles/PhreeqcRM.dir/src/IPhreeqcPhast/IPhreeqc/phreeqcpp/input.cpp.o
[27/237] Building CXX object CMakeFiles/PhreeqcRM.dir/src/IPhreeqcPhast/IPhreeqc/phreeqcpp/GasPhase.cxx.o
[28/237] Building CXX object CMakeFiles/PhreeqcRM.dir/src/IPhreeqcPhast/IPhreeqc/phreeqcpp/ISolution.cxx.o
[29/237] Building CXX object CMakeFiles/PhreeqcRM.dir/src/IPhreeqcPhast/IPhreeqc/phreeqcpp/ISolutionComp.cxx.o
[30/237] Building CXX object CMakeFiles/PhreeqcRM.dir/src/IPhreeqcPhast/IPhreeqc/phreeqcpp/integrate.cpp.o
[31/237] Building CXX object CMakeFiles/PhreeqcRM.dir/src/IPhreeqcPhast/IPhreeqc/phreeqcpp/isotopes.cpp.o
[32/237] Building CXX object CMakeFiles/PhreeqcRM.dir/src/IPhreeqcPhast/IPhreeqc/phreeqcpp/KineticsComp.cxx.o
[33/237] Building CXX object CMakeFiles/PhreeqcRM.dir/src/IPhreeqcPhast/IPhreeqc/phreeqcpp/inverse.cpp.o
[34/237] Building CXX object CMakeFiles/PhreeqcRM.dir/src/IPhreeqcPhast/IPhreeqc/phreeqcpp/NumKeyword.cxx.o
[35/237] Building CXX object CMakeFiles/PhreeqcRM.dir/src/IPhreeqcPhast/IPhreeqc/phreeqcpp/nvector_serial.cpp.o
[36/237] Building CXX object CMakeFiles/PhreeqcRM.dir/src/IPhreeqcPhast/IPhreeqc/phreeqcpp/nvector.cpp.o
[37/237] Building CXX object CMakeFiles/PhreeqcRM.dir/src/IPhreeqcPhast/IPhreeqc/phreeqcpp/kinetics.cpp.o
[38/237] Building CXX object CMakeFiles/PhreeqcRM.dir/src/IPhreeqcPhast/IPhreeqc/phreeqcpp/NameDouble.cxx.o
[39/237] Building CXX object CMakeFiles/PhreeqcRM.dir/src/IPhreeqcPhast/IPhreeqc/phreeqcpp/parse.cpp.o
[40/237] Building CXX object CMakeFiles/PhreeqcRM.dir/src/IPhreeqcPhast/IPhreeqc/phreeqcpp/mainsubs.cpp.o
[41/237] Building CXX object CMakeFiles/PhreeqcRM.dir/src/IPhreeqcPhast/IPhreeqc/phreeqcpp/phqalloc.cpp.o
[42/237] Building CXX object CMakeFiles/PhreeqcRM.dir/src/IPhreeqcPhast/IPhreeqc/phreeqcpp/PhreeqcKeywords/Keywords.cpp.o
[43/237] Building CXX object CMakeFiles/PhreeqcRM.dir/src/IPhreeqcPhast/IPhreeqc/phreeqcpp/model.cpp.o
[44/237] Building CXX object CMakeFiles/PhreeqcRM.dir/src/IPhreeqcPhast/IPhreeqc/phreeqcpp/PHRQ_io_output.cpp.o
[45/237] Building CXX object CMakeFiles/PhreeqcRM.dir/src/IPhreeqcPhast/IPhreeqc/phreeqcpp/pitzer_structures.cpp.o
[46/237] Building CXX object CMakeFiles/PhreeqcRM.dir/src/IPhreeqcPhast/IPhreeqc/phreeqcpp/PBasic.cpp.o
[47/237] Building CXX object CMakeFiles/PhreeqcRM.dir/src/IPhreeqcPhast/IPhreeqc/phreeqcpp/PPassemblage.cxx.o
[48/237] Building CXX object CMakeFiles/PhreeqcRM.dir/src/IPhreeqcPhast/IPhreeqc/phreeqcpp/PPassemblageComp.cxx.o
[49/237] Building CXX object CMakeFiles/PhreeqcRM.dir/src/IPhreeqcPhast/IPhreeqc/phreeqcpp/pitzer.cpp.o
[50/237] Building CXX object CMakeFiles/PhreeqcRM.dir/src/IPhreeqcPhast/IPhreeqc/phreeqcpp/Pressure.cxx.o
[51/237] Building CXX object CMakeFiles/PhreeqcRM.dir/src/IPhreeqcPhast/IPhreeqc/phreeqcpp/Phreeqc.cpp.o
[52/237] Building CXX object CMakeFiles/PhreeqcRM.dir/src/IPhreeqcPhast/IPhreeqc/phreeqcpp/Reaction.cxx.o
[53/237] Building CXX object CMakeFiles/PhreeqcRM.dir/src/IPhreeqcPhast/IPhreeqc/phreeqcpp/print.cpp.o
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[55/237] Building CXX object CMakeFiles/PhreeqcRM.dir/src/IPhreeqcPhast/IPhreeqc/phreeqcpp/runner.cpp.o
[56/237] Building CXX object CMakeFiles/PhreeqcRM.dir/src/IPhreeqcPhast/IPhreeqc/phreeqcpp/SelectedOutput.cpp.o
[57/237] Building CXX object CMakeFiles/PhreeqcRM.dir/src/IPhreeqcPhast/IPhreeqc/phreeqcpp/readtr.cpp.o
[58/237] Building CXX object CMakeFiles/PhreeqcRM.dir/src/IPhreeqcPhast/IPhreeqc/phreeqcpp/smalldense.cpp.o
[59/237] Building CXX object CMakeFiles/PhreeqcRM.dir/src/IPhreeqcPhast/IPhreeqc/phreeqcpp/ReadClass.cxx.o
[60/237] Building CXX object CMakeFiles/PhreeqcRM.dir/src/IPhreeqcPhast/IPhreeqc/phreeqcpp/SolutionIsotope.cxx.o
[61/237] Building CXX object CMakeFiles/PhreeqcRM.dir/src/IPhreeqcPhast/IPhreeqc/phreeqcpp/Serializer.cxx.o
[62/237] Building CXX object CMakeFiles/PhreeqcRM.dir/src/IPhreeqcPhast/IPhreeqc/phreeqcpp/Solution.cxx.o
[63/237] Building CXX object CMakeFiles/PhreeqcRM.dir/src/IPhreeqcPhast/IPhreeqc/phreeqcpp/sit.cpp.o
[64/237] Building CXX object CMakeFiles/PhreeqcRM.dir/src/IPhreeqcPhast/IPhreeqc/phreeqcpp/spread.cpp.o
[65/237] Building CXX object CMakeFiles/PhreeqcRM.dir/src/IPhreeqcPhast/IPhreeqc/phreeqcpp/SScomp.cxx.o
[66/237] Building CXX object CMakeFiles/PhreeqcRM.dir/src/IPhreeqcPhast/IPhreeqc/phreeqcpp/SS.cxx.o
[67/237] Building CXX object CMakeFiles/PhreeqcRM.dir/src/IPhreeqcPhast/IPhreeqc/phreeqcpp/SSassemblage.cxx.o
[68/237] Building CXX object CMakeFiles/PhreeqcRM.dir/src/IPhreeqcPhast/IPhreeqc/phreeqcpp/read.cpp.o
[69/237] Building CXX object CMakeFiles/PhreeqcRM.dir/src/IPhreeqcPhast/IPhreeqc/phreeqcpp/StorageBinList.cpp.o
[70/237] Building CXX object CMakeFiles/PhreeqcRM.dir/src/IPhreeqcPhast/IPhreeqc/phreeqcpp/sundialsmath.cpp.o
[71/237] Building CXX object CMakeFiles/PhreeqcRM.dir/src/IPhreeqcPhast/IPhreeqc/phreeqcpp/step.cpp.o
[72/237] Building CXX object CMakeFiles/PhreeqcRM.dir/src/IPhreeqcPhast/IPhreeqc/phreeqcpp/SurfaceCharge.cxx.o
[73/237] Building CXX object CMakeFiles/PhreeqcRM.dir/src/IPhreeqcPhast/IPhreeqc/phreeqcpp/SurfaceComp.cxx.o
[74/237] Building CXX object CMakeFiles/PhreeqcRM.dir/src/IPhreeqcPhast/IPhreeqc/phreeqcpp/Surface.cxx.o
[75/237] Building CXX object CMakeFiles/PhreeqcRM.dir/src/IPhreeqcPhast/IPhreeqc/phreeqcpp/System.cxx.o
[76/237] Building CXX object CMakeFiles/PhreeqcRM.dir/src/IPhreeqcPhast/IPhreeqc/phreeqcpp/StorageBin.cxx.o
[77/237] Building CXX object CMakeFiles/PhreeqcRM.dir/src/IPhreeqcPhast/IPhreeqc/phreeqcpp/Temperature.cxx.o
[78/237] Building CXX object CMakeFiles/PhreeqcRM.dir/src/IPhreeqcPhast/IPhreeqc/phreeqcpp/Use.cpp.o
[79/237] Building CXX object CMakeFiles/PhreeqcRM.dir/src/IPhreeqcPhast/IPhreeqc/phreeqcpp/tally.cpp.o
[80/237] Building CXX object CMakeFiles/PhreeqcRM.dir/src/IPhreeqcPhast/IPhreeqc/phreeqcpp/structures.cpp.o
[81/237] Building C object CMakeFiles/PhreeqcRM.dir/src/IPhreeqcPhast/IPhreeqc/Var.c.o
[82/237] Building CXX object CMakeFiles/PhreeqcRM.dir/src/IPhreeqcPhast/IPhreeqc/phreeqcpp/UserPunch.cpp.o
[83/237] Building CXX object CMakeFiles/PhreeqcRM.dir/src/IPhreeqcPhast/IPhreeqcPhastLib.cpp.o
[84/237] Building CXX object CMakeFiles/PhreeqcRM.dir/src/IPhreeqcPhast/IPhreeqcPhast.cxx.o
[85/237] Building CXX object CMakeFiles/PhreeqcRM.dir/src/IPhreeqcPhast/IPhreeqc/phreeqcpp/utilities.cpp.o
[86/237] Building CXX object CMakeFiles/PhreeqcRM.dir/src/IPhreeqcPhast/IPhreeqc/phreeqcpp/tidy.cpp.o
[87/237] Building CXX object CMakeFiles/PhreeqcRM.dir/src/RM_interface_C.cpp.o
[88/237] Building CXX object CMakeFiles/PhreeqcRM.dir/src/RM_interface_F.cpp.o
[89/237] Building CXX object CMakeFiles/PhreeqcRM.dir/src/YAML_interface_F.cpp.o
[90/237] Building Fortran preprocessed Tests/CMakeFiles/FortranAdvect.dir/Advect_f90.F90-pp.f90
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[93/237] Building Fortran preprocessed Tests/CMakeFiles/FortranAdvect.dir/Gas_f90.F90-pp.f90
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[99/237] Building Fortran preprocessed Tests/CMakeFiles/FortranAdvect.dir/__/src/RM_interface.F90-pp.f90
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[102/237] Building Fortran preprocessed Tests/CMakeFiles/FortranAdvect.dir/__/src/YAML_interface.F90-pp.f90
[103/237] Generating Fortran dyndep file Tests/CMakeFiles/FortranAdvect.dir/Fortran.dd
[104/237] Building Fortran object Tests/CMakeFiles/FortranAdvect.dir/__/src/IPhreeqcPhast/IPhreeqc/IPhreeqc_interface.F90.o
[105/237] Building CXX object CMakeFiles/PhreeqcRM.dir/src/IPhreeqcPhast/IPhreeqc/phreeqcpp/transport.cpp.o
[106/237] Building Fortran object Tests/CMakeFiles/FortranAdvect.dir/__/src/YAML_interface.F90.o
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[108/237] Building Fortran object Tests/CMakeFiles/FortranAdvect.dir/WriteYAMLFile_f90_test.F90.o
[109/237] Building Fortran object Tests/CMakeFiles/FortranAdvect.dir/__/src/RM_interface.F90.o
[110/237] Building Fortran object Tests/CMakeFiles/FortranAdvect.dir/Advect_f90.F90.o
[111/237] Building Fortran object Tests/CMakeFiles/FortranAdvect.dir/Gas_f90.F90.o
[112/237] Building Fortran object Tests/CMakeFiles/FortranAdvect.dir/SimpleAdvect_f90.F90.o
[113/237] Building CXX object CMakeFiles/PhreeqcRM.dir/src/VarManager.cpp.o
[114/237] Building CXX object CMakeFiles/PhreeqcRM.dir/src/YAMLPhreeqcRM.cpp.o
[115/237] Building Fortran object Tests/CMakeFiles/FortranAdvect.dir/__/src/BMI_interface.F90.o
[116/237] Building Fortran object Tests/CMakeFiles/FortranAdvect.dir/Species_f90.F90.o
[117/237] Building Fortran object Tests/CMakeFiles/FortranAdvect.dir/AdvectBMI_f90.F90.o
[118/237] Building Fortran object Tests/CMakeFiles/FortranAdvect.dir/AdvectBMI_f90_test.F90.o
[119/237] Building C object Tests/CMakeFiles/TestRM.dir/Advect_c.c.o
[120/237] Building Fortran object Tests/CMakeFiles/FortranAdvect.dir/TestAllMethods_f90.F90.o
[121/237] Building CXX object Tests/CMakeFiles/TestRM.dir/AdvectBMI_cpp.cpp.o
[122/237] Building C object Tests/CMakeFiles/TestRM.dir/Gas_c.c.o
[123/237] Building CXX object Tests/CMakeFiles/TestRM.dir/main.cpp.o
[124/237] Building C object Tests/CMakeFiles/TestRM.dir/SimpleAdvect_c.c.o
[125/237] Building CXX object Tests/CMakeFiles/TestRM.dir/Gas_cpp.cpp.o
[126/237] Building C object Tests/CMakeFiles/TestRM.dir/Species_c.c.o
[127/237] Building CXX object Tests/CMakeFiles/TestRM.dir/Advect_cpp.cpp.o
[128/237] Building CXX object Tests/CMakeFiles/TestRM.dir/SimpleAdvect_cpp.cpp.o
[129/237] Building CXX object Tests/CMakeFiles/TestRM.dir/AdvectBMI_cpp_test.cpp.o
[130/237] Building CXX object Tests/CMakeFiles/TestRM.dir/Species_cpp.cpp.o
[131/237] Building CXX object CMakeFiles/PhreeqcRM.dir/src/PhreeqcRM.cpp.o
[132/237] Building CXX object Tests/CMakeFiles/TestRM.dir/WriteYAMLFile_cpp.cpp.o
[133/237] Building CXX object Tests/CMakeFiles/TestRM.dir/WriteYAMLFile_cpp_test.cpp.o
[134/237] Building CXX object Tests/CMakeFiles/TestRMdtor.dir/TestRMdtor.cpp.o
[135/237] Building CXX object Tests/CMakeFiles/TestBMIdtor.dir/TestBMIdtor.cpp.o
[136/237] Linking CXX static library libPhreeqcRM.a
[137/237] Linking CXX static library Tests/libFortranAdvect.a
[138/237] Linking CXX executable Tests/TestRMdtor
FAILED: Tests/TestRMdtor 
: && /usr/local/bin/g++ -O3 -DNDEBUG -isysroot /Applications/Xcode_13.2.1.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX12.1.sdk -mmacosx-version-min=11.7 -Wl,-search_paths_first -Wl,-headerpad_max_install_names  Tests/CMakeFiles/TestRMdtor.dir/TestRMdtor.cpp.o -o Tests/TestRMdtor  -Wl,-rpath,/usr/local/lib  libPhreeqcRM.a  /usr/local/lib/libyaml-cpp.0.8.0.dylib  /usr/local/Cellar/gcc@12/12.3.0/lib/gcc/12/libgomp.dylib  -lemutls_w && :
Undefined symbols for architecture x86_64:
  "__ZN4YAML8LoadFileERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE", referenced from:
      __ZN9PhreeqcRM20GetGridCellCountYAMLEPKc in libPhreeqcRM.a(PhreeqcRM.cpp.o)
      __ZN9PhreeqcRM14InitializeYAMLENSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE in libPhreeqcRM.a(PhreeqcRM.cpp.o)
ld: symbol(s) not found for architecture x86_64
collect2: error: ld returned 1 exit status
[139/237] Linking CXX executable Tests/TestBMIdtor
FAILED: Tests/TestBMIdtor 
: && /usr/local/bin/g++ -O3 -DNDEBUG -isysroot /Applications/Xcode_13.2.1.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX12.1.sdk -mmacosx-version-min=11.7 -Wl,-search_paths_first -Wl,-headerpad_max_install_names  Tests/CMakeFiles/TestBMIdtor.dir/TestBMIdtor.cpp.o -o Tests/TestBMIdtor  -Wl,-rpath,/usr/local/lib  libPhreeqcRM.a  /usr/local/lib/libyaml-cpp.0.8.0.dylib  /usr/local/Cellar/gcc@12/12.3.0/lib/gcc/12/libgomp.dylib  -lemutls_w && :
Undefined symbols for architecture x86_64:
  "__ZN4YAML8LoadFileERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE", referenced from:
      __ZN12BMIPhreeqcRM10InitializeENSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE in libPhreeqcRM.a(BMIPhreeqcRM.cpp.o)
      __ZN9PhreeqcRM20GetGridCellCountYAMLEPKc in libPhreeqcRM.a(PhreeqcRM.cpp.o)
      __ZN9PhreeqcRM14InitializeYAMLENSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE in libPhreeqcRM.a(PhreeqcRM.cpp.o)
ld: symbol(s) not found for architecture x86_64
collect2: error: ld returned 1 exit status
[140/237] Building CXX object Tests/CMakeFiles/TestRM.dir/TestAllMethods_cpp.cpp.o
[141/237] Swig compile /Users/runner/work/phreeqcrm/phreeqcrm/phreeqcrm-3.7.6-16656/swig/python/../PhreeqcRM.i for python
/usr/local/Cellar/swig/4.1.1/share/swig/4.1.1/python/pyiterators.swg:431: Warning 490: Fragment 'NumPy_Backward_Compatibility' not found.
/usr/local/Cellar/swig/4.1.1/share/swig/4.1.1/python/pyiterators.swg:447: Warning 490: Fragment 'NumPy_Backward_Compatibility' not found.
ninja: build stopped: subcommand failed.
Error: Process completed with exit code 1.
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