Dear list,
Is there a recommended way to compile FSL from source on OS X Mavericks (10.9)?
I have tried compiling FSL on Mavericks, however the build fails. Looking at the log file, I think is because several libraries (newmat, niftiio and others) rely on ginstall. Apple no longer ship GCC and its tools with 10.9 so there is no ginstall on my system, just install. While "gcc" is symlinked to clang on Mavericks, no such symlink exists by default for ginstall. Despite failing to copy the files to the correct location some of these libraries claim to build successfully.
I have copied and pasted some relevant lines from build.log below - the full file exceeds the lists attachment limit.
Thanks,
Toby
Dr Tobias Wood
Department of Neuroimaging, IoP, King's College London
build.log sample:
Making project newmat
/Users/Tobias/Code/fslbuild/fsl/config/common/rules.mk:320: depend.mk: No such file or directory
Building dependency file depend.mk
/bin/rm -f /tmp/fslgrot *.o *.a *.exe core depend.mk
/bin/rm -f /tmp/fslgrot tmt example nl_ex sl_ex garch test_exc
/Users/Tobias/Code/fslbuild/fsl/config/common/rules.mk:320: depend.mk: No such file or directory
Building dependency file depend.mk
/bin/cp bandmat.cpp bandmat.cxx
c++ -Wall -ansi -pedantic -O3 -fexpensive-optimizations -I. -I/Users/Tobias/Code/fslbuild/fsl/extras/include -I/Users/Tobias/Code/fslbuild/fsl/include -c bandmat.cxx
/bin/rm -f bandmat.cxx
/bin/cp cholesky.cpp cholesky.cxx
c++ -Wall -ansi -pedantic -O3 -fexpensive-optimizations -I. -I/Users/Tobias/Code/fslbuild/fsl/extras/include -I/Users/Tobias/Code/fslbuild/fsl/include -c cholesky.cxx
/bin/rm -f cholesky.cxx
/bin/cp evalue.cpp evalue.cxx
c++ -Wall -ansi -pedantic -O3 -fexpensive-optimizations -I. -I/Users/Tobias/Code/fslbuild/fsl/extras/include -I/Users/Tobias/Code/fslbuild/fsl/include -c evalue.cxx
/bin/rm -f evalue.cxx
/bin/cp fft.cpp fft.cxx
c++ -Wall -ansi -pedantic -O3 -fexpensive-optimizations -I. -I/Users/Tobias/Code/fslbuild/fsl/extras/include -I/Users/Tobias/Code/fslbuild/fsl/include -c fft.cxx
/bin/rm -f fft.cxx
/bin/cp hholder.cpp hholder.cxx
c++ -Wall -ansi -pedantic -O3 -fexpensive-optimizations -I. -I/Users/Tobias/Code/fslbuild/fsl/extras/include -I/Users/Tobias/Code/fslbuild/fsl/include -c hholder.cxx
/bin/rm -f hholder.cxx
/bin/cp jacobi.cpp jacobi.cxx
c++ -Wall -ansi -pedantic -O3 -fexpensive-optimizations -I. -I/Users/Tobias/Code/fslbuild/fsl/extras/include -I/Users/Tobias/Code/fslbuild/fsl/include -c jacobi.cxx
/bin/rm -f jacobi.cxx
/bin/cp myexcept.cpp myexcept.cxx
c++ -Wall -ansi -pedantic -O3 -fexpensive-optimizations -I. -I/Users/Tobias/Code/fslbuild/fsl/extras/include -I/Users/Tobias/Code/fslbuild/fsl/include -c myexcept.cxx
/bin/rm -f myexcept.cxx
/bin/cp newmat1.cpp newmat1.cxx
c++ -Wall -ansi -pedantic -O3 -fexpensive-optimizations -I. -I/Users/Tobias/Code/fslbuild/fsl/extras/include -I/Users/Tobias/Code/fslbuild/fsl/include -c newmat1.cxx
/bin/rm -f newmat1.cxx
/bin/cp newmat2.cpp newmat2.cxx
c++ -Wall -ansi -pedantic -O3 -fexpensive-optimizations -I. -I/Users/Tobias/Code/fslbuild/fsl/extras/include -I/Users/Tobias/Code/fslbuild/fsl/include -c newmat2.cxx
/bin/rm -f newmat2.cxx
/bin/cp newmat3.cpp newmat3.cxx
c++ -Wall -ansi -pedantic -O3 -fexpensive-optimizations -I. -I/Users/Tobias/Code/fslbuild/fsl/extras/include -I/Users/Tobias/Code/fslbuild/fsl/include -c newmat3.cxx
/bin/rm -f newmat3.cxx
/bin/cp newmat4.cpp newmat4.cxx
c++ -Wall -ansi -pedantic -O3 -fexpensive-optimizations -I. -I/Users/Tobias/Code/fslbuild/fsl/extras/include -I/Users/Tobias/Code/fslbuild/fsl/include -c newmat4.cxx
/bin/rm -f newmat4.cxx
/bin/cp newmat5.cpp newmat5.cxx
c++ -Wall -ansi -pedantic -O3 -fexpensive-optimizations -I. -I/Users/Tobias/Code/fslbuild/fsl/extras/include -I/Users/Tobias/Code/fslbuild/fsl/include -c newmat5.cxx
/bin/rm -f newmat5.cxx
/bin/cp newmat6.cpp newmat6.cxx
c++ -Wall -ansi -pedantic -O3 -fexpensive-optimizations -I. -I/Users/Tobias/Code/fslbuild/fsl/extras/include -I/Users/Tobias/Code/fslbuild/fsl/include -c newmat6.cxx
/bin/rm -f newmat6.cxx
/bin/cp newmat7.cpp newmat7.cxx
c++ -Wall -ansi -pedantic -O3 -fexpensive-optimizations -I. -I/Users/Tobias/Code/fslbuild/fsl/extras/include -I/Users/Tobias/Code/fslbuild/fsl/include -c newmat7.cxx
/bin/rm -f newmat7.cxx
/bin/cp newmat8.cpp newmat8.cxx
c++ -Wall -ansi -pedantic -O3 -fexpensive-optimizations -I. -I/Users/Tobias/Code/fslbuild/fsl/extras/include -I/Users/Tobias/Code/fslbuild/fsl/include -c newmat8.cxx
/bin/rm -f newmat8.cxx
/bin/cp newmat9.cpp newmat9.cxx
c++ -Wall -ansi -pedantic -O3 -fexpensive-optimizations -I. -I/Users/Tobias/Code/fslbuild/fsl/extras/include -I/Users/Tobias/Code/fslbuild/fsl/include -c newmat9.cxx
/bin/rm -f newmat9.cxx
/bin/cp newmatex.cpp newmatex.cxx
c++ -Wall -ansi -pedantic -O3 -fexpensive-optimizations -I. -I/Users/Tobias/Code/fslbuild/fsl/extras/include -I/Users/Tobias/Code/fslbuild/fsl/include -c newmatex.cxx
/bin/rm -f newmatex.cxx
/bin/cp newmatnl.cpp newmatnl.cxx
c++ -Wall -ansi -pedantic -O3 -fexpensive-optimizations -I. -I/Users/Tobias/Code/fslbuild/fsl/extras/include -I/Users/Tobias/Code/fslbuild/fsl/include -c newmatnl.cxx
/bin/rm -f newmatnl.cxx
/bin/cp newmatrm.cpp newmatrm.cxx
c++ -Wall -ansi -pedantic -O3 -fexpensive-optimizations -I. -I/Users/Tobias/Code/fslbuild/fsl/extras/include -I/Users/Tobias/Code/fslbuild/fsl/include -c newmatrm.cxx
/bin/rm -f newmatrm.cxx
/bin/cp solution.cpp solution.cxx
c++ -Wall -ansi -pedantic -O3 -fexpensive-optimizations -I. -I/Users/Tobias/Code/fslbuild/fsl/extras/include -I/Users/Tobias/Code/fslbuild/fsl/include -c solution.cxx
/bin/rm -f solution.cxx
/bin/cp sort.cpp sort.cxx
c++ -Wall -ansi -pedantic -O3 -fexpensive-optimizations -I. -I/Users/Tobias/Code/fslbuild/fsl/extras/include -I/Users/Tobias/Code/fslbuild/fsl/include -c sort.cxx
/bin/rm -f sort.cxx
/bin/cp submat.cpp submat.cxx
c++ -Wall -ansi -pedantic -O3 -fexpensive-optimizations -I. -I/Users/Tobias/Code/fslbuild/fsl/extras/include -I/Users/Tobias/Code/fslbuild/fsl/include -c submat.cxx
/bin/rm -f submat.cxx
/bin/cp svd.cpp svd.cxx
c++ -Wall -ansi -pedantic -O3 -fexpensive-optimizations -I. -I/Users/Tobias/Code/fslbuild/fsl/extras/include -I/Users/Tobias/Code/fslbuild/fsl/include -c svd.cxx
/bin/rm -f svd.cxx
/bin/cp newfft.cpp newfft.cxx
c++ -Wall -ansi -pedantic -O3 -fexpensive-optimizations -I. -I/Users/Tobias/Code/fslbuild/fsl/extras/include -I/Users/Tobias/Code/fslbuild/fsl/include -c newfft.cxx
/bin/rm -f newfft.cxx
ar cr libnewmat.a bandmat.o cholesky.o evalue.o fft.o hholder.o jacobi.o myexcept.o newmat1.o newmat2.o newmat3.o newmat4.o newmat5.o newmat6.o newmat7.o newmat8.o newmat9.o newmatex.o newmatnl.o newmatrm.o solution.o sort.o submat.o svd.o newfft.o
ranlib libnewmat.a
make[2]: Nothing to be done for `all'.
Installing stable binaries
Installing stable header files
/bin/sh: ginstall: command not found
ginstall -p -m 0664 boolean.h /Users/Tobias/Code/fslbuild/fsl/extras/include/newmat/
/bin/sh: ginstall: command not found
ginstall -p -m 0664 controlw.h /Users/Tobias/Code/fslbuild/fsl/extras/include/newmat/
/bin/sh: ginstall: command not found
ginstall -p -m 0664 include.h /Users/Tobias/Code/fslbuild/fsl/extras/include/newmat/
/bin/sh: ginstall: command not found
ginstall -p -m 0664 myexcept.h /Users/Tobias/Code/fslbuild/fsl/extras/include/newmat/
/bin/sh: ginstall: command not found
ginstall -p -m 0664 newmat.h /Users/Tobias/Code/fslbuild/fsl/extras/include/newmat/
/bin/sh: ginstall: command not found
ginstall -p -m 0664 newmatap.h /Users/Tobias/Code/fslbuild/fsl/extras/include/newmat/
/bin/sh: ginstall: command not found
ginstall -p -m 0664 newmatio.h /Users/Tobias/Code/fslbuild/fsl/extras/include/newmat/
/bin/sh: ginstall: command not found
ginstall -p -m 0664 newmatnl.h /Users/Tobias/Code/fslbuild/fsl/extras/include/newmat/
/bin/sh: ginstall: command not found
ginstall -p -m 0664 newmatrc.h /Users/Tobias/Code/fslbuild/fsl/extras/include/newmat/
/bin/sh: ginstall: command not found
ginstall -p -m 0664 newmatrm.h /Users/Tobias/Code/fslbuild/fsl/extras/include/newmat/
/bin/sh: ginstall: command not found
ginstall -p -m 0664 precisio.h /Users/Tobias/Code/fslbuild/fsl/extras/include/newmat/
/bin/sh: ginstall: command not found
ginstall -p -m 0664 solution.h /Users/Tobias/Code/fslbuild/fsl/extras/include/newmat/
/bin/sh: ginstall: command not found
ginstall -p -m 0664 tmt.h /Users/Tobias/Code/fslbuild/fsl/extras/include/newmat/
Installing stable library archives
/bin/sh: ginstall: command not found
ginstall -p -m 0664 libnewmat.a /Users/Tobias/Code/fslbuild/fsl/extras/lib
error: /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/ranlib: can't open file: /Users/Tobias/Code/fslbuild/fsl/extras/lib/libnewmat.a (No such file or directory)
Installing tcl scripts
Installing (userguide) documents
/bin/chmod -R ug+w /Users/Tobias/Code/fslbuild/fsl/extras/doc/newmat/
Installing reference documents
/bin/chmod -R ug+w /Users/Tobias/Code/fslbuild/fsl/extras/refdoc/newmat/
/bin/rm -f /tmp/fslgrot *.o *.a *.exe core depend.mk
/bin/rm -f /tmp/fslgrot tmt example nl_ex sl_ex garch test_exc
-------------------------
Successfully made newmat
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