libpba.so failed to build

[DeadDumpings]

I have been trying to install VisualSFM on MacOS Sierra V10.12.6 and have been running into some error with the installer script. I have enough programming experience to get me through the error that have been raised so far but the one that I have run into this time has really confused me and I don't understand. If any one has any ideas on what might fix this it would be much appreciated.

The terminal out put that I have received is as follows:

Jacks-Mac-mini:~ DeadDumlpings$ /Users/DeadDumlpings/Desktop/VisualSFM_OS_X_Installer-master/vsfm_os_x_installer.sh

Dan Monaghan's VSFM and PMVS installer for OS X

About to check to see if you have the Brew Package Manager
Great, you've got brew... Continuing
wget is already installed, OK
About to install xcode select
Hit Enter after it's installed
xcode-select: error: command line tools are already installed, use "Software Update" to install updates
Checking we have the right version of XQuartz

<string>2.7.8</string>

xquartz_version_result=0
Your version of XQuartz is 2.7.8 - perfect.

Ok, now you have to should have either...

1. Already had the correct version of XQuartz, so I'm continuing...

2. Had to have installed XQuartz and just logged out and back in...

Ready to continue the next installation of VSFM & PMVS (press ENTER)

Installing Brew packages... this can take quite a long time
Warning: jpeg 9c is already installed and up-to-date
To reinstall 9c, run brew reinstall jpeg
Warning: gdk-pixbuf 2.38.0 is already installed and up-to-date
To reinstall 2.38.0, run brew reinstall gdk-pixbuf
Warning: cairo 1.16.0 is already installed and up-to-date
To reinstall 1.16.0, run brew reinstall cairo
Warning: freetype 2.9.1 is already installed and up-to-date
To reinstall 2.9.1, run brew reinstall freetype
Warning: Already linked: /usr/local/Cellar/freetype/2.9.1
To relink: brew unlink freetype && brew link freetype
Warning: pango 1.42.4 is already installed and up-to-date
To reinstall 1.42.4, run brew reinstall pango
Warning: Already linked: /usr/local/Cellar/pixman/0.34.0_1
To relink: brew unlink pixman && brew link pixman
Warning: Already linked: /usr/local/Cellar/fontconfig/2.13.1
To relink: brew unlink fontconfig && brew link fontconfig
######################################################################## 100.0%
Warning: gtk+ 2.24.28 is already installed and up-to-date
To reinstall 2.24.28, run brew reinstall gtk+
Warning: glew 2.1.0 is already installed and up-to-date
To reinstall 2.1.0, run brew reinstall glew
Warning: gsl 2.5 is already installed and up-to-date
To reinstall 2.5, run brew reinstall gsl
Warning: boost 1.67.0_1 is already installed and up-to-date
To reinstall 1.67.0_1, run brew reinstall boost
Warning: intltool 0.51.0 is already installed and up-to-date
To reinstall 0.51.0, run brew reinstall intltool
Warning: cmake 3.12.3 is already installed and up-to-date
To reinstall 3.12.3, run brew reinstall cmake
Error: homebrew/versions was deprecated. This tap is now empty as all its formulae were migrated.
Warning: gcc@4.9 4.9.4_1 is already installed and up-to-date
To reinstall 4.9.4_1, run brew reinstall gcc@4.9
Warning: devil 1.8.0_1 is already installed and up-to-date
To reinstall 1.8.0_1, run brew reinstall devil
Warning: pkg-config 0.29.2 is already installed and up-to-date
To reinstall 0.29.2, run brew reinstall pkg-config
Zip file is present, so just unzipping, removing old dir to install so we don't have any conflicts
Archive: VisualSFM_osx_64bit.zip
creating: vsfm/
creating: vsfm/bin/
creating: vsfm/build/
creating: vsfm/lib/
inflating: vsfm/lib/blas.a
inflating: vsfm/lib/lapack.a
inflating: vsfm/lib/libf2c.a
inflating: vsfm/lib/libjpeg.a
inflating: vsfm/lib/VisualSFM.a
inflating: vsfm/makefile
inflating: vsfm/README
Changing VSFM GCC to Brews gcc-4.9
Changing /usr/x11/lib to OS X default /opt/x11/lib
About to make...
mkdir -p build
mkdir -p bin
cd build; ar -x ../lib/VisualSFM.a; cd ..;
g++-4.9 -w -o bin/VisualSFM build/. -L/usr/local/lib -L/opt/X11/lib -pthread -lGL -lGLU -lX11 -ldl -L/usr/local/Cellar/gtk+/2.24.28/lib -L/usr/local/Cellar/pango/1.42.4/lib -L/usr/local/Cellar/atk/2.30.0/lib -L/usr/local/Cellar/cairo/1.16.0/lib -L/usr/local/Cellar/gdk-pixbuf/2.38.0/lib -L/usr/local/Cellar/glib/2.58.1/lib -L/usr/local/Cellar/pango/1.42.4/lib -L/usr/local/Cellar/glib/2.58.1/lib -L/usr/local/Cellar/fontconfig/2.13.1/lib -L/usr/local/opt/freetype/lib -L/usr/local/Cellar/glib/2.58.1/lib -L/usr/local/opt/gettext/lib -lgtk-x11-2.0 -lgdk-x11-2.0 -lpangocairo-1.0 -latk-1.0 -lcairo -lgdk_pixbuf-2.0 -lgio-2.0 -lpangoft2-1.0 -lpango-1.0 -lgobject-2.0 -lfontconfig -lfreetype -lgthread-2.0 -lglib-2.0 -lintl -Wl,-framework -Wl,CoreFoundation lib/lapack.a lib/blas.a lib/libf2c.a lib/libjpeg.a
rm -f build/.
VSFM application built... moving on
Disable Cuda Flags
sed: makefile_no_gpu: No such file or directory
Changing march from native core2 in makefile
sed: makefile_no_gpu: No such file or directory
Changing to prefer GLUT
sed: makefile_no_gpu: No such file or directory
Removing -L/opt/local/lib from makefile
sed: makefile_no_gpu: No such file or directory
Changing /usr/x11/lib to OS X default /opt/x11/lib
sed: makefile_no_gpu: No such file or directory
Disable TestWin build for this OS X build
sed: makefile_no_gpu: No such file or directory
make: Nothing to be done for `SiftGPU'.
libsiftgpu.so built... moving on
Changing SiftGPU GCC to Brews gcc-4.9
Removing /usr/lib64 from makefile
Changing march from native core2 in makefile
Adding -L/usr/include/sys/ to compile Flags
patching file SparseBundleCPU.h
Reversed (or previously applied) patch detected! Assume -R? [n] n
Apply anyway? [n] n
Skipping patch.
1 out of 1 hunk ignored -- saving rejects to file SparseBundleCPU.h.rej
/Users/DeadDumlpings/pba
mkdir -p ./bin/out_no_gpu
mkdir -p ./bin
ar rcs ./bin/libpba_no_gpu.a ./bin/out_no_gpu/pba.o ./bin/out_no_gpu/ConfigBA.o ./bin/out_no_gpu/SparseBundleCPU.o
g++-4.9 -w -w -o ./bin/libpba_no_gpu.so ./bin/out_no_gpu/pba.o ./bin/out_no_gpu/ConfigBA.o ./bin/out_no_gpu/SparseBundleCPU.o -DPBA_NO_GPU -fPIC -L -L/usr/lib -L/usr/include/sys/ -L/usr/include/sys/ -L/usr/include/sys/ -L/usr/include/sys/ -L/usr/include/sys/ -L/usr/include/sys/ -L/usr/include/sys/ -L/usr/include/sys/ -L/usr/include/sys/ -L/usr/include/sys/ -L/usr/include/sys/ -L/usr/include/sys/ -L/usr/include/sys/ -L/usr/include/sys/ -L/usr/include/sys/ -L./bin -O2 -Wall -Wno-deprecated -pthread -march=core2 -mfpmath=sse -fpermissive -shared -fPIC
libpba.so built... moving on
/Users/DeadDumlpings/Desktop/VisualSFM_OS_X_Installer-master/vsfm_os_x_installer.sh: line 355: ../../patches/dpoint_err.patch: No such file or directory
Adding set CMAKE_EXE_LINKER_FLAGS -static-libgcc -static-libstdc++ to cmake flags
cat: ../../patches/cflag_var: No such file or directory
mkdir: build: File exists
/Users/DeadDumlpings/CMVS-PMVS-master/program/build
Found Eigen 3.2.3
-- Boost version: 1.67.0
Using system boost library: /usr/local/include
Using system JPEG library: /usr/local/lib/libjpeg.dylib
-- NLOPT: Version number 2.4.2 found in configure.ac
-- Configuring done
-- Generating done
-- Build files have been written to: /Users/DeadDumlpings/CMVS-PMVS-master/program/build
[ 2%] Built target cmvs_lib
[ 6%] Built target image_lib
[ 8%] Built target numeric_lib
[ 8%] Building CXX object base/pmvs/CMakeFiles/pmvs_lib.dir/filter.cc.o
In file included from /Users/DeadDumlpings/CMVS-PMVS-master/program/base/pmvs/filter.cc:6:
In file included from /Users/DeadDumlpings/CMVS-PMVS-master/program/base/pmvs/findMatch.h:7:
In file included from /Library/Developer/CommandLineTools/usr/include/c++/v1/iostream:38:
In file included from /Library/Developer/CommandLineTools/usr/include/c++/v1/ios:216:
In file included from /Library/Developer/CommandLineTools/usr/include/c++/v1/__locale:18:
In file included from /Library/Developer/CommandLineTools/usr/include/c++/v1/mutex:189:
In file included from /Library/Developer/CommandLineTools/usr/include/c++/v1/__mutex_base:17:
/Library/Developer/CommandLineTools/usr/include/c++/v1/__threading_support:156:1: error: unknown
type name 'mach_port_t'
mach_port_t __libcpp_thread_get_port();
^
/Library/Developer/CommandLineTools/usr/include/c++/v1/__threading_support:300:1: error: unknown
type name 'mach_port_t'
mach_port_t __libcpp_thread_get_port() {
^
/Library/Developer/CommandLineTools/usr/include/c++/v1/__threading_support:301:12: error: use of
undeclared identifier 'pthread_mach_thread_np'
return pthread_mach_thread_np(pthread_self());
^
3 errors generated.
make[2]: *** [base/pmvs/CMakeFiles/pmvs_lib.dir/filter.cc.o] Error 1
make[1]: *** [base/pmvs/CMakeFiles/pmvs_lib.dir/all] Error 2
make: *** [all] Error 2
libpba.so failed to build, halting....