[package - 123i386-default][science/avogadrolibs] Failed for avogadrolibs-1.95.1_2 in build

From: <pkg-fallout_at_FreeBSD.org>
Date: Sun, 09 Oct 2022 04:38:17 UTC
You are receiving this mail as a port that you maintain
is failing to build on the FreeBSD package build server.
Please investigate the failure and submit a PR to fix
build.

Maintainer:     yuri@FreeBSD.org
Log URL:        http://beefy5.nyi.freebsd.org/data/123i386-default/06ade0876922/logs/avogadrolibs-1.95.1_2.log
Build URL:      http://beefy5.nyi.freebsd.org/build.html?mastername=123i386-default&build=06ade0876922
Log:

=>> Building science/avogadrolibs
build started at Sun Oct  9 04:32:17 UTC 2022
port directory: /usr/ports/science/avogadrolibs
package name: avogadrolibs-1.95.1_2
building for: FreeBSD 123i386-default-job-06 12.3-RELEASE-p7 FreeBSD 12.3-RELEASE-p7 i386
maintained by: yuri@FreeBSD.org
Makefile ident: 
Poudriere version: 3.2.8-21-g883afb07
Host OSVERSION: 1400063
Jail OSVERSION: 1203000
Job Id: 06

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     MMTF=on: Enable optional features using mmtf
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     SPGLIB=on: Enable optional features using spglib
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===> Use 'make config' to modify these settings
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yuri@FreeBSD.org
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=======================<phase: check-sanity   >============================
===>  License GPLv2 accepted by the user
===========================================================================
=======================<phase: pkg-depends    >============================
===>   avogadrolibs-1.95.1_2 depends on file: /usr/local/sbin/pkg - not found
===>   Installing existing package /packages/All/pkg-1.18.4.pkg
[123i386-default-job-06] Installing pkg-1.18.4...
[123i386-default-job-06] Extracting pkg-1.18.4: .......... done
===>   avogadrolibs-1.95.1_2 depends on file: /usr/local/sbin/pkg - found
===>   Returning to build of avogadrolibs-1.95.1_2
===========================================================================
=======================<phase: fetch-depends  >============================
===========================================================================
=======================<phase: fetch          >============================
===>  License GPLv2 accepted by the user
===> Fetching all distfiles required by avogadrolibs-1.95.1_2 for building
===========================================================================
=======================<phase: checksum       >============================
===>  License GPLv2 accepted by the user
===> Fetching all distfiles required by avogadrolibs-1.95.1_2 for building
=> SHA256 Checksum OK for OpenChemistry-avogadrolibs-1.95.1_GH0.tar.gz.
=> SHA256 Checksum OK for OpenChemistry-molecules-b1e16c5_GH0.tar.gz.
=> SHA256 Checksum OK for OpenChemistry-crystals-c3e2468_GH0.tar.gz.
===========================================================================
=======================<phase: extract-depends>============================
===========================================================================
=======================<phase: extract        >============================
===>  License GPLv2 accepted by the user
===> Fetching all distfiles required by avogadrolibs-1.95.1_2 for building
===>  Extracting for avogadrolibs-1.95.1_2
=> SHA256 Checksum OK for OpenChemistry-avogadrolibs-1.95.1_GH0.tar.gz.
=> SHA256 Checksum OK for OpenChemistry-molecules-b1e16c5_GH0.tar.gz.
=> SHA256 Checksum OK for OpenChemistry-crystals-c3e2468_GH0.tar.gz.
===========================================================================
=======================<phase: patch-depends  >============================
===========================================================================
=======================<phase: patch          >============================
===>  Patching for avogadrolibs-1.95.1_2
<snip>
CMake Warning (dev) at /usr/local/share/cmake/Modules/FindPackageHandleStandardArgs.cmake:438 (message):
  The package name passed to `find_package_handle_standard_args` (SPGLIB)
  does not match the name of the calling package (Spglib).  This can lead to
  problems in calling code that expects `find_package` result variables
  (e.g., `_FOUND`) to follow a certain pattern.
Call Stack (most recent call first):
  cmake/FindSpglib.cmake:15 (find_package_handle_standard_args)
  avogadro/core/CMakeLists.txt:7 (find_package)
This warning is for project developers.  Use -Wno-dev to suppress it.

-- Found SPGLIB: /usr/local/include/spglib  
-- Performing Test CMAKE_HAVE_LIBC_PTHREAD
-- Performing Test CMAKE_HAVE_LIBC_PTHREAD - Failed
-- Looking for pthread_create in pthreads
-- Looking for pthread_create in pthreads - not found
-- Looking for pthread_create in pthread
-- Looking for pthread_create in pthread - found
-- Found Threads: TRUE  
-- Performing Test COMPILER_HAS_HIDDEN_VISIBILITY
-- Performing Test COMPILER_HAS_HIDDEN_VISIBILITY - Success
-- Performing Test COMPILER_HAS_HIDDEN_INLINE_VISIBILITY
-- Performing Test COMPILER_HAS_HIDDEN_INLINE_VISIBILITY - Success
-- Performing Test COMPILER_HAS_DEPRECATED_ATTR
-- Performing Test COMPILER_HAS_DEPRECATED_ATTR - Success
-- Found MMTF: /usr/local/include  
CMake Warning (dev) at /usr/local/share/cmake/Modules/FindOpenGL.cmake:315 (message):
  Policy CMP0072 is not set: FindOpenGL prefers GLVND by default when
  available.  Run "cmake --help-policy CMP0072" for policy details.  Use the
  cmake_policy command to set the policy and suppress this warning.

  FindOpenGL found both a legacy GL library:

    OPENGL_gl_LIBRARY: /usr/local/lib/libGL.so

  and GLVND libraries for OpenGL and GLX:

    OPENGL_opengl_LIBRARY: /usr/local/lib/libOpenGL.so
    OPENGL_glx_LIBRARY: /usr/local/lib/libGLX.so

  OpenGL_GL_PREFERENCE has not been set to "GLVND" or "LEGACY", so for
  compatibility with CMake 3.10 and below the legacy GL library will be used.
Call Stack (most recent call first):
  avogadro/rendering/CMakeLists.txt:6 (find_package)
This warning is for project developers.  Use -Wno-dev to suppress it.

-- Found OpenGL: /usr/local/lib/libOpenGL.so   
-- Found GLEW: /usr/local/include  
-- Found PythonInterp: /usr/local/bin/python3.9 (found suitable version "3.9.14", minimum required is "3") 
Avogadro Generators not found at /wrkdirs/usr/ports/science/avogadrolibs/work/avogadrolibs-1.95.1/../avogadrogenerators!
CMake Warning (dev) at /usr/local/share/cmake/Modules/FindPackageHandleStandardArgs.cmake:438 (message):
  The package name passed to `find_package_handle_standard_args` (LIBARCHIVE)
  does not match the name of the calling package (LibArchive).  This can lead
  to problems in calling code that expects `find_package` result variables
  (e.g., `_FOUND`) to follow a certain pattern.
Call Stack (most recent call first):
  cmake/FindLibArchive.cmake:17 (find_package_handle_standard_args)
  avogadro/qtplugins/plugindownloader/CMakeLists.txt:3 (find_package)
This warning is for project developers.  Use -Wno-dev to suppress it.

-- Found LIBARCHIVE: /usr/local/include  
msym include dir /usr/local/lib/cmake/libmsym/../../../include
CMake Warning (dev) at /usr/local/share/cmake/Modules/FindOpenGL.cmake:315 (message):
  Policy CMP0072 is not set: FindOpenGL prefers GLVND by default when
  available.  Run "cmake --help-policy CMP0072" for policy details.  Use the
  cmake_policy command to set the policy and suppress this warning.

  FindOpenGL found both a legacy GL library:

    OPENGL_gl_LIBRARY: /usr/local/lib/libGL.so

  and GLVND libraries for OpenGL and GLX:

    OPENGL_opengl_LIBRARY: /usr/local/lib/libOpenGL.so
    OPENGL_glx_LIBRARY: /usr/local/lib/libGLX.so

  OpenGL_GL_PREFERENCE has not been set to "GLVND" or "LEGACY", so for
  compatibility with CMake 3.10 and below the legacy GL library will be used.
Call Stack (most recent call first):
  avogadro/qtplugins/overlayaxes/CMakeLists.txt:3 (find_package)
This warning is for project developers.  Use -Wno-dev to suppress it.

-- Configuring done
-- Generating done
CMake Warning:
  Manually-specified variables were not used by the project:

    CMAKE_COLOR_MAKEFILE
    CMAKE_CXX_FLAGS_DEBUG
    CMAKE_C_FLAGS_DEBUG
    CMAKE_MODULE_LINKER_FLAGS
    CMAKE_VERBOSE_MAKEFILE


-- Build files have been written to: /wrkdirs/usr/ports/science/avogadrolibs/work/.build
===========================================================================
=======================<phase: build          >============================
===>  Building for avogadrolibs-1.95.1_2
[  0% 1/553] /usr/bin/c++  -I/wrkdirs/usr/ports/science/avogadrolibs/work/.build -I/wrkdirs/usr/ports/science/avogadrolibs/work/avogadrolibs-1.95.1 -isystem /wrkdirs/usr/ports/science/avogadrolibs/work/avogadrolibs-1.95.1/thirdparty/pugixml -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing  -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing  -isystem /usr/local/include -fvisibility=hidden -fvisibility-inlines-hidden -std=c++17 -MD -MT utilities/bodr/CMakeFiles/bodrparse.dir/bodrparse.cxx.o -MF utilities/bodr/CMakeFiles/bodrparse.dir/bodrparse.cxx.o.d -o utilities/bodr/CMakeFiles/bodrparse.dir/bodrparse.cxx.o -c /wrkdirs/usr/ports/science/avogadrolibs/work/avogadrolibs-1.95.1/utilities/bodr/bodrparse.cxx
[  0% 2/553] : && /usr/bin/c++ -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing  -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing  -isystem /usr/local/include -fstack-protector-strong utilities/bodr/CMakeFiles/bodrparse.dir/bodrparse.cxx.o -o bin/bodrparse   && :
[  0% 3/553] /usr/bin/c++  -I/wrkdirs/usr/ports/science/avogadrolibs/work/.build -I/wrkdirs/usr/ports/science/avogadrolibs/work/avogadrolibs-1.95.1 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing  -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing  -isystem /usr/local/include -fvisibility=hidden -fvisibility-inlines-hidden -std=c++17 -MD -MT utilities/encodefile/CMakeFiles/encodefile.dir/encodefile.cxx.o -MF utilities/encodefile/CMakeFiles/encodefile.dir/encodefile.cxx.o.d -o utilities/encodefile/CMakeFiles/encodefile.dir/encodefile.cxx.o -c /wrkdirs/usr/ports/science/avogadrolibs/work/avogadrolibs-1.95.1/utilities/encodefile/encodefile.cxx
[  0% 4/553] : && /usr/bin/c++ -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing  -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing  -isystem /usr/local/include -fstack-protector-strong utilities/encodefile/CMakeFiles/encodefile.dir/encodefile.cxx.o -o bin/encodefile   && :
[  0% 5/553] /usr/bin/c++  -I/wrkdirs/usr/ports/science/avogadrolibs/work/.build -I/wrkdirs/usr/ports/science/avogadrolibs/work/avogadrolibs-1.95.1 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing  -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing  -isystem /usr/local/include -fvisibility=hidden -fvisibility-inlines-hidden -std=c++17 -MD -MT utilities/resdata/CMakeFiles/resdataparse.dir/resdataparse.cxx.o -MF utilities/resdata/CMakeFiles/resdataparse.dir/resdataparse.cxx.o.d -o utilities/resdata/CMakeFiles/resdataparse.dir/resdataparse.cxx.o -c /wrkdirs/usr/ports/science/avogadrolibs/work/avogadrolibs-1.95.1/utilities/resdata/resdataparse.cxx
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[  3% 19/553] /usr/bin/c++ -DAvogadroCore_EXPORTS -I/wrkdirs/usr/ports/science/avogadrolibs/work/.build -I/wrkdirs/usr/ports/science/avogadrolibs/work/avogadrolibs-1.95.1 -I/wrkdirs/usr/ports/science/avogadrolibs/work/.build/avogadro/core -isystem /usr/local/include/eigen3 -isystem /usr/local/include/spglib -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing  -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing  -isystem /usr/local/include -fPIC -fvisibility=hidden -fvisibility-inlines-hidden -std=c++17 -MD -MT avogadro/core/CMakeFiles/AvogadroCore.dir/elements.cpp.o -MF avogadro/core/CMakeFiles/AvogadroCore.dir/elements.cpp.o.d -o avogadro/core/CMakeFiles/AvogadroCore.dir/elements.cpp.o -c /wrkdirs/usr/ports/science/avogadrolibs/work/avogadrolibs-1.95.1/avogadro/core/elements.cpp
[  3% 20/553] /usr/bin/c++ -DAvogadroCore_EXPORTS -I/wrkdirs/usr/ports/science/avogadrolibs/work/.build -I/wrkdirs/usr/ports/science/avogadrolibs/work/avogadrolibs-1.95.1 -I/wrkdirs/usr/ports/science/avogadrolibs/work/.build/avogadro/core -isystem /usr/local/include/eigen3 -isystem /usr/local/include/spglib -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing  -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing  -isystem /usr/local/include -fPIC -fvisibility=hidden -fvisibility-inlines-hidden -std=c++17 -MD -MT avogadro/core/CMakeFiles/AvogadroCore.dir/dihedraliterator.cpp.o -MF avogadro/core/CMakeFiles/AvogadroCore.dir/dihedraliterator.cpp.o.d -o avogadro/core/CMakeFiles/AvogadroCore.dir/dihedraliterator.cpp.o -c /wrkdirs/usr/ports/science/avogadrolibs/work/avogadrolibs-1.95.1/avogadro/core/dihedraliterator.cpp
[  3% 21/553] /usr/bin/c++ -DAvogadroCore_EXPORTS -I/wrkdirs/usr/ports/science/avogadrolibs/work/.build -I/wrkdirs/usr/ports/science/avogadrolibs/work/avogadrolibs-1.95.1 -I/wrkdirs/usr/ports/science/avogadrolibs/work/.build/avogadro/core -isystem /usr/local/include/eigen3 -isystem /usr/local/include/spglib -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing  -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing  -isystem /usr/local/include -fPIC -fvisibility=hidden -fvisibility-inlines-hidden -std=c++17 -MD -MT avogadro/core/CMakeFiles/AvogadroCore.dir/gaussianset.cpp.o -MF avogadro/core/CMakeFiles/AvogadroCore.dir/gaussianset.cpp.o.d -o avogadro/core/CMakeFiles/AvogadroCore.dir/gaussianset.cpp.o -c /wrkdirs/usr/ports/science/avogadrolibs/work/avogadrolibs-1.95.1/avogadro/core/gaussianset.cpp
[  3% 22/553] /usr/bin/c++ -DAvogadroCore_EXPORTS -I/wrkdirs/usr/ports/science/avogadrolibs/work/.build -I/wrkdirs/usr/ports/science/avogadrolibs/work/avogadrolibs-1.95.1 -I/wrkdirs/usr/ports/science/avogadrolibs/work/.build/avogadro/core -isystem /usr/local/include/eigen3 -isystem /usr/local/include/spglib -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing  -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing  -isystem /usr/local/include -fPIC -fvisibility=hidden -fvisibility-inlines-hidden -std=c++17 -MD -MT avogadro/core/CMakeFiles/AvogadroCore.dir/gaussiansettools.cpp.o -MF avogadro/core/CMakeFiles/AvogadroCore.dir/gaussiansettools.cpp.o.d -o avogadro/core/CMakeFiles/AvogadroCore.dir/gaussiansettools.cpp.o -c /wrkdirs/usr/ports/science/avogadrolibs/work/avogadrolibs-1.95.1/avogadro/core/gaussiansettools.cpp
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[  8% 46/553] /usr/bin/c++ -DAVO_USE_MMTF -DAvogadroIO_EXPORTS -I/wrkdirs/usr/ports/science/avogadrolibs/work/.build -I/wrkdirs/usr/ports/science/avogadrolibs/work/avogadrolibs-1.95.1 -I/wrkdirs/usr/ports/science/avogadrolibs/work/.build/avogadro/core -I/wrkdirs/usr/ports/science/avogadrolibs/work/.build/avogadro/io -isystem /usr/local/include/eigen3 -isystem /wrkdirs/usr/ports/science/avogadrolibs/work/avogadrolibs-1.95.1/thirdparty/pugixml -isystem /wrkdirs/usr/ports/science/avogadrolibs/work/avogadrolibs-1.95.1/thirdparty/struct -isystem /wrkdirs/usr/ports/science/avogadrolibs/work/avogadrolibs-1.95.1/thirdparty -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing  -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing  -isystem /usr/local/include -fPIC -fvisibility=hidden -fvisibility-inlines-hidden -std=c++17 -MD -MT avogadro/io/CMakeFiles/AvogadroIO.dir/dcdformat.cpp.o -MF avogadro/io/CMakeF
 iles/AvogadroIO.dir/dcdformat.cpp.o.d -o avogadro/io/CMakeFiles/AvogadroIO.dir/dcdformat.cpp.o -c /wrkdirs/usr/ports/science/avogadrolibs/work/avogadrolibs-1.95.1/avogadro/io/dcdformat.cpp
[  8% 47/553] /usr/bin/c++ -DAVO_USE_MMTF -DAvogadroIO_EXPORTS -I/wrkdirs/usr/ports/science/avogadrolibs/work/.build -I/wrkdirs/usr/ports/science/avogadrolibs/work/avogadrolibs-1.95.1 -I/wrkdirs/usr/ports/science/avogadrolibs/work/.build/avogadro/core -I/wrkdirs/usr/ports/science/avogadrolibs/work/.build/avogadro/io -isystem /usr/local/include/eigen3 -isystem /wrkdirs/usr/ports/science/avogadrolibs/work/avogadrolibs-1.95.1/thirdparty/pugixml -isystem /wrkdirs/usr/ports/science/avogadrolibs/work/avogadrolibs-1.95.1/thirdparty/struct -isystem /wrkdirs/usr/ports/science/avogadrolibs/work/avogadrolibs-1.95.1/thirdparty -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing  -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing  -isystem /usr/local/include -fPIC -fvisibility=hidden -fvisibility-inlines-hidden -std=c++17 -MD -MT avogadro/io/CMakeFiles/AvogadroIO.dir/fileformat.cpp.o -MF avogadro/io/CMake
 Files/AvogadroIO.dir/fileformat.cpp.o.d -o avogadro/io/CMakeFiles/AvogadroIO.dir/fileformat.cpp.o -c /wrkdirs/usr/ports/science/avogadrolibs/work/avogadrolibs-1.95.1/avogadro/io/fileformat.cpp
[  8% 48/553] /usr/bin/c++ -DAVO_USE_MMTF -DAvogadroIO_EXPORTS -I/wrkdirs/usr/ports/science/avogadrolibs/work/.build -I/wrkdirs/usr/ports/science/avogadrolibs/work/avogadrolibs-1.95.1 -I/wrkdirs/usr/ports/science/avogadrolibs/work/.build/avogadro/core -I/wrkdirs/usr/ports/science/avogadrolibs/work/.build/avogadro/io -isystem /usr/local/include/eigen3 -isystem /wrkdirs/usr/ports/science/avogadrolibs/work/avogadrolibs-1.95.1/thirdparty/pugixml -isystem /wrkdirs/usr/ports/science/avogadrolibs/work/avogadrolibs-1.95.1/thirdparty/struct -isystem /wrkdirs/usr/ports/science/avogadrolibs/work/avogadrolibs-1.95.1/thirdparty -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing  -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing  -isystem /usr/local/include -fPIC -fvisibility=hidden -fvisibility-inlines-hidden -std=c++17 -MD -MT avogadro/io/CMakeFiles/AvogadroIO.dir/fileformatmanager.cpp.o -MF avogadro/i
 o/CMakeFiles/AvogadroIO.dir/fileformatmanager.cpp.o.d -o avogadro/io/CMakeFiles/AvogadroIO.dir/fileformatmanager.cpp.o -c /wrkdirs/usr/ports/science/avogadrolibs/work/avogadrolibs-1.95.1/avogadro/io/fileformatmanager.cpp
In file included from /wrkdirs/usr/ports/science/avogadrolibs/work/avogadrolibs-1.95.1/avogadro/io/fileformatmanager.cpp:29:
/wrkdirs/usr/ports/science/avogadrolibs/work/avogadrolibs-1.95.1/avogadro/io/vaspformat.h:90:8: warning: 'read' overrides a member function but is not marked 'override' [-Winconsistent-missing-override]
  bool read(std::istream& inStream, Core::Molecule& mol);
       ^
/wrkdirs/usr/ports/science/avogadrolibs/work/avogadrolibs-1.95.1/avogadro/io/fileformat.h:126:16: note: overridden virtual function is here
  virtual bool read(std::istream& in, Core::Molecule& molecule) = 0;
               ^
In file included from /wrkdirs/usr/ports/science/avogadrolibs/work/avogadrolibs-1.95.1/avogadro/io/fileformatmanager.cpp:29:
/wrkdirs/usr/ports/science/avogadrolibs/work/avogadrolibs-1.95.1/avogadro/io/vaspformat.h:91:8: warning: 'write' overrides a member function but is not marked 'override' [-Winconsistent-missing-override]
  bool write(std::ostream& outStream, const Core::Molecule& mol);
       ^
/wrkdirs/usr/ports/science/avogadrolibs/work/avogadrolibs-1.95.1/avogadro/io/fileformat.h:134:16: note: overridden virtual function is here
  virtual bool write(std::ostream& out, const Core::Molecule& molecule) = 0;
               ^
2 warnings generated.
[  8% 49/553] /usr/bin/c++ -DAVO_USE_MMTF -DAvogadroIO_EXPORTS -I/wrkdirs/usr/ports/science/avogadrolibs/work/.build -I/wrkdirs/usr/ports/science/avogadrolibs/work/avogadrolibs-1.95.1 -I/wrkdirs/usr/ports/science/avogadrolibs/work/.build/avogadro/core -I/wrkdirs/usr/ports/science/avogadrolibs/work/.build/avogadro/io -isystem /usr/local/include/eigen3 -isystem /wrkdirs/usr/ports/science/avogadrolibs/work/avogadrolibs-1.95.1/thirdparty/pugixml -isystem /wrkdirs/usr/ports/science/avogadrolibs/work/avogadrolibs-1.95.1/thirdparty/struct -isystem /wrkdirs/usr/ports/science/avogadrolibs/work/avogadrolibs-1.95.1/thirdparty -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing  -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing  -isystem /usr/local/include -fPIC -fvisibility=hidden -fvisibility-inlines-hidden -std=c++17 -MD -MT avogadro/io/CMakeFiles/AvogadroIO.dir/gromacsformat.cpp.o -MF avogadro/io/CM
 akeFiles/AvogadroIO.dir/gromacsformat.cpp.o.d -o avogadro/io/CMakeFiles/AvogadroIO.dir/gromacsformat.cpp.o -c /wrkdirs/usr/ports/science/avogadrolibs/work/avogadrolibs-1.95.1/avogadro/io/gromacsformat.cpp
[  9% 50/553] /usr/bin/c++ -DAVO_USE_MMTF -DAvogadroIO_EXPORTS -I/wrkdirs/usr/ports/science/avogadrolibs/work/.build -I/wrkdirs/usr/ports/science/avogadrolibs/work/avogadrolibs-1.95.1 -I/wrkdirs/usr/ports/science/avogadrolibs/work/.build/avogadro/core -I/wrkdirs/usr/ports/science/avogadrolibs/work/.build/avogadro/io -isystem /usr/local/include/eigen3 -isystem /wrkdirs/usr/ports/science/avogadrolibs/work/avogadrolibs-1.95.1/thirdparty/pugixml -isystem /wrkdirs/usr/ports/science/avogadrolibs/work/avogadrolibs-1.95.1/thirdparty/struct -isystem /wrkdirs/usr/ports/science/avogadrolibs/work/avogadrolibs-1.95.1/thirdparty -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing  -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing  -isystem /usr/local/include -fPIC -fvisibility=hidden -fvisibility-inlines-hidden -std=c++17 -MD -MT avogadro/io/CMakeFiles/AvogadroIO.dir/mdlformat.cpp.o -MF avogadro/io/CMakeF
 iles/AvogadroIO.dir/mdlformat.cpp.o.d -o avogadro/io/CMakeFiles/AvogadroIO.dir/mdlformat.cpp.o -c /wrkdirs/usr/ports/science/avogadrolibs/work/avogadrolibs-1.95.1/avogadro/io/mdlformat.cpp
[  9% 51/553] /usr/bin/c++ -DAVO_USE_MMTF -DAvogadroIO_EXPORTS -I/wrkdirs/usr/ports/science/avogadrolibs/work/.build -I/wrkdirs/usr/ports/science/avogadrolibs/work/avogadrolibs-1.95.1 -I/wrkdirs/usr/ports/science/avogadrolibs/work/.build/avogadro/core -I/wrkdirs/usr/ports/science/avogadrolibs/work/.build/avogadro/io -isystem /usr/local/include/eigen3 -isystem /wrkdirs/usr/ports/science/avogadrolibs/work/avogadrolibs-1.95.1/thirdparty/pugixml -isystem /wrkdirs/usr/ports/science/avogadrolibs/work/avogadrolibs-1.95.1/thirdparty/struct -isystem /wrkdirs/usr/ports/science/avogadrolibs/work/avogadrolibs-1.95.1/thirdparty -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing  -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing  -isystem /usr/local/include -fPIC -fvisibility=hidden -fvisibility-inlines-hidden -std=c++17 -MD -MT avogadro/io/CMakeFiles/AvogadroIO.dir/vaspformat.cpp.o -MF avogadro/io/CMake
 Files/AvogadroIO.dir/vaspformat.cpp.o.d -o avogadro/io/CMakeFiles/AvogadroIO.dir/vaspformat.cpp.o -c /wrkdirs/usr/ports/science/avogadrolibs/work/avogadrolibs-1.95.1/avogadro/io/vaspformat.cpp
In file included from /wrkdirs/usr/ports/science/avogadrolibs/work/avogadrolibs-1.95.1/avogadro/io/vaspformat.cpp:17:
/wrkdirs/usr/ports/science/avogadrolibs/work/avogadrolibs-1.95.1/avogadro/io/vaspformat.h:90:8: warning: 'read' overrides a member function but is not marked 'override' [-Winconsistent-missing-override]
  bool read(std::istream& inStream, Core::Molecule& mol);
       ^
/wrkdirs/usr/ports/science/avogadrolibs/work/avogadrolibs-1.95.1/avogadro/io/fileformat.h:126:16: note: overridden virtual function is here
  virtual bool read(std::istream& in, Core::Molecule& molecule) = 0;
               ^
In file included from /wrkdirs/usr/ports/science/avogadrolibs/work/avogadrolibs-1.95.1/avogadro/io/vaspformat.cpp:17:
/wrkdirs/usr/ports/science/avogadrolibs/work/avogadrolibs-1.95.1/avogadro/io/vaspformat.h:91:8: warning: 'write' overrides a member function but is not marked 'override' [-Winconsistent-missing-override]
  bool write(std::ostream& outStream, const Core::Molecule& mol);
       ^
/wrkdirs/usr/ports/science/avogadrolibs/work/avogadrolibs-1.95.1/avogadro/io/fileformat.h:134:16: note: overridden virtual function is here
  virtual bool write(std::ostream& out, const Core::Molecule& molecule) = 0;
               ^
2 warnings generated.
[  9% 52/553] /usr/bin/c++ -DAVO_USE_MMTF -DAvogadroIO_EXPORTS -I/wrkdirs/usr/ports/science/avogadrolibs/work/.build -I/wrkdirs/usr/ports/science/avogadrolibs/work/avogadrolibs-1.95.1 -I/wrkdirs/usr/ports/science/avogadrolibs/work/.build/avogadro/core -I/wrkdirs/usr/ports/science/avogadrolibs/work/.build/avogadro/io -isystem /usr/local/include/eigen3 -isystem /wrkdirs/usr/ports/science/avogadrolibs/work/avogadrolibs-1.95.1/thirdparty/pugixml -isystem /wrkdirs/usr/ports/science/avogadrolibs/work/avogadrolibs-1.95.1/thirdparty/struct -isystem /wrkdirs/usr/ports/science/avogadrolibs/work/avogadrolibs-1.95.1/thirdparty -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing  -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing  -isystem /usr/local/include -fPIC -fvisibility=hidden -fvisibility-inlines-hidden -std=c++17 -MD -MT avogadro/io/CMakeFiles/AvogadroIO.dir/pdbformat.cpp.o -MF avogadro/io/CMakeF
 iles/AvogadroIO.dir/pdbformat.cpp.o.d -o avogadro/io/CMakeFiles/AvogadroIO.dir/pdbformat.cpp.o -c /wrkdirs/usr/ports/science/avogadrolibs/work/avogadrolibs-1.95.1/avogadro/io/pdbformat.cpp
[  9% 53/553] /usr/bin/c++ -DAVO_USE_MMTF -DAvogadroIO_EXPORTS -I/wrkdirs/usr/ports/science/avogadrolibs/work/.build -I/wrkdirs/usr/ports/science/avogadrolibs/work/avogadrolibs-1.95.1 -I/wrkdirs/usr/ports/science/avogadrolibs/work/.build/avogadro/core -I/wrkdirs/usr/ports/science/avogadrolibs/work/.build/avogadro/io -isystem /usr/local/include/eigen3 -isystem /wrkdirs/usr/ports/science/avogadrolibs/work/avogadrolibs-1.95.1/thirdparty/pugixml -isystem /wrkdirs/usr/ports/science/avogadrolibs/work/avogadrolibs-1.95.1/thirdparty/struct -isystem /wrkdirs/usr/ports/science/avogadrolibs/work/avogadrolibs-1.95.1/thirdparty -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing  -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing  -isystem /usr/local/include -fPIC -fvisibility=hidden -fvisibility-inlines-hidden -std=c++17 -MD -MT avogadro/io/CMakeFiles/AvogadroIO.dir/xyzformat.cpp.o -MF avogadro/io/CMakeF
 iles/AvogadroIO.dir/xyzformat.cpp.o.d -o avogadro/io/CMakeFiles/AvogadroIO.dir/xyzformat.cpp.o -c /wrkdirs/usr/ports/science/avogadrolibs/work/avogadrolibs-1.95.1/avogadro/io/xyzformat.cpp
[  9% 54/553] /usr/bin/c++ -DAVO_USE_MMTF -DAvogadroIO_EXPORTS -I/wrkdirs/usr/ports/science/avogadrolibs/work/.build -I/wrkdirs/usr/ports/science/avogadrolibs/work/avogadrolibs-1.95.1 -I/wrkdirs/usr/ports/science/avogadrolibs/work/.build/avogadro/core -I/wrkdirs/usr/ports/science/avogadrolibs/work/.build/avogadro/io -isystem /usr/local/include/eigen3 -isystem /wrkdirs/usr/ports/science/avogadrolibs/work/avogadrolibs-1.95.1/thirdparty/pugixml -isystem /wrkdirs/usr/ports/science/avogadrolibs/work/avogadrolibs-1.95.1/thirdparty/struct -isystem /wrkdirs/usr/ports/science/avogadrolibs/work/avogadrolibs-1.95.1/thirdparty -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing  -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing  -isystem /usr/local/include -fPIC -fvisibility=hidden -fvisibility-inlines-hidden -std=c++17 -MD -MT avogadro/io/CMakeFiles/AvogadroIO.dir/trrformat.cpp.o -MF avogadro/io/CMakeF
 iles/AvogadroIO.dir/trrformat.cpp.o.d -o avogadro/io/CMakeFiles/AvogadroIO.dir/trrformat.cpp.o -c /wrkdirs/usr/ports/science/avogadrolibs/work/avogadrolibs-1.95.1/avogadro/io/trrformat.cpp
[  9% 55/553] /usr/bin/c++ -DAVO_USE_MMTF -DAvogadroIO_EXPORTS -I/wrkdirs/usr/ports/science/avogadrolibs/work/.build -I/wrkdirs/usr/ports/science/avogadrolibs/work/avogadrolibs-1.95.1 -I/wrkdirs/usr/ports/science/avogadrolibs/work/.build/avogadro/core -I/wrkdirs/usr/ports/science/avogadrolibs/work/.build/avogadro/io -isystem /usr/local/include/eigen3 -isystem /wrkdirs/usr/ports/science/avogadrolibs/work/avogadrolibs-1.95.1/thirdparty/pugixml -isystem /wrkdirs/usr/ports/science/avogadrolibs/work/avogadrolibs-1.95.1/thirdparty/struct -isystem /wrkdirs/usr/ports/science/avogadrolibs/work/avogadrolibs-1.95.1/thirdparty -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing  -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing  -isystem /usr/local/include -fPIC -fvisibility=hidden -fvisibility-inlines-hidden -std=c++17 -MD -MT avogadro/io/CMakeFiles/AvogadroIO.dir/lammpsformat.cpp.o -MF avogadro/io/CMa
 keFiles/AvogadroIO.dir/lammpsformat.cpp.o.d -o avogadro/io/CMakeFiles/AvogadroIO.dir/lammpsformat.cpp.o -c /wrkdirs/usr/ports/science/avogadrolibs/work/avogadrolibs-1.95.1/avogadro/io/lammpsformat.cpp
[ 10% 56/553] /usr/bin/c++ -DAVO_USE_MMTF -DAvogadroIO_EXPORTS -I/wrkdirs/usr/ports/science/avogadrolibs/work/.build -I/wrkdirs/usr/ports/science/avogadrolibs/work/avogadrolibs-1.95.1 -I/wrkdirs/usr/ports/science/avogadrolibs/work/.build/avogadro/core -I/wrkdirs/usr/ports/science/avogadrolibs/work/.build/avogadro/io -isystem /usr/local/include/eigen3 -isystem /wrkdirs/usr/ports/science/avogadrolibs/work/avogadrolibs-1.95.1/thirdparty/pugixml -isystem /wrkdirs/usr/ports/science/avogadrolibs/work/avogadrolibs-1.95.1/thirdparty/struct -isystem /wrkdirs/usr/ports/science/avogadrolibs/work/avogadrolibs-1.95.1/thirdparty -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing  -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing  -isystem /usr/local/include -fPIC -fvisibility=hidden -fvisibility-inlines-hidden -std=c++17 -MD -MT avogadro/io/CMakeFiles/AvogadroIO.dir/mmtfformat.cpp.o -MF avogadro/io/CMake
 Files/AvogadroIO.dir/mmtfformat.cpp.o.d -o avogadro/io/CMakeFiles/AvogadroIO.dir/mmtfformat.cpp.o -c /wrkdirs/usr/ports/science/avogadrolibs/work/avogadrolibs-1.95.1/avogadro/io/mmtfformat.cpp
FAILED: avogadro/io/CMakeFiles/AvogadroIO.dir/mmtfformat.cpp.o 
/usr/bin/c++ -DAVO_USE_MMTF -DAvogadroIO_EXPORTS -I/wrkdirs/usr/ports/science/avogadrolibs/work/.build -I/wrkdirs/usr/ports/science/avogadrolibs/work/avogadrolibs-1.95.1 -I/wrkdirs/usr/ports/science/avogadrolibs/work/.build/avogadro/core -I/wrkdirs/usr/ports/science/avogadrolibs/work/.build/avogadro/io -isystem /usr/local/include/eigen3 -isystem /wrkdirs/usr/ports/science/avogadrolibs/work/avogadrolibs-1.95.1/thirdparty/pugixml -isystem /wrkdirs/usr/ports/science/avogadrolibs/work/avogadrolibs-1.95.1/thirdparty/struct -isystem /wrkdirs/usr/ports/science/avogadrolibs/work/avogadrolibs-1.95.1/thirdparty -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing  -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing  -isystem /usr/local/include -fPIC -fvisibility=hidden -fvisibility-inlines-hidden -std=c++17 -MD -MT avogadro/io/CMakeFiles/AvogadroIO.dir/mmtfformat.cpp.o -MF avogadro/io/CMakeFiles/Avogadro
 IO.dir/mmtfformat.cpp.o.d -o avogadro/io/CMakeFiles/AvogadroIO.dir/mmtfformat.cpp.o -c /wrkdirs/usr/ports/science/avogadrolibs/work/avogadrolibs-1.95.1/avogadro/io/mmtfformat.cpp
/wrkdirs/usr/ports/science/avogadrolibs/work/avogadrolibs-1.95.1/avogadro/io/mmtfformat.cpp:105:22: error: call to 'is_polymer' is ambiguous
    bool isPolymer = is_polymer(chainIndex, entityList);
                     ^~~~~~~~~~
/usr/local/include/mmtf/structure_data.hpp:432:6: note: candidate function
bool is_polymer(const unsigned int chain_index,
     ^
/wrkdirs/usr/ports/science/avogadrolibs/work/avogadrolibs-1.95.1/avogadro/io/mmtfformat.cpp:47:6: note: candidate function
bool is_polymer(const unsigned int chain_index,
     ^
1 error generated.
ninja: build stopped: subcommand failed.
*** Error code 1

Stop.
make: stopped in /usr/ports/science/avogadrolibs