I would really appreciate any advice or help in getting AFNI installed. I have been using the Quick Setup guideline for General Users, but I keep getting the following error when I try to run part E tcsh OS_notes.macos_12_intel_b_user.tcsh:
error: failed run_cmd: make AFNI_WHOMADEIT=build itall >& log_make.txt
-- status: building FAILURE
see 'make' log file /Users/chatt/afni_build/build_src/log_make.txt
** error: tail from log_make.txt:
I did some debugging and found this configuration error message in the log_make.txt which I think might be causing the problem but am not sure what to do next.
ld: warning: -multiply_defined is obsolete
( cd jpeg-6b ; /bin/rm -f Makefile jconfig.h ; \
chmod ugo+x ./configure ; ./configure 'CC=/usr/local/bin/gcc-13' 'LDFLAGS=-L. -L/usr/local/lib -L/opt/X11/lib -L/usr/local/lib -Wl,-x -Wl,-multiply_defined -Wl,warning -Wl,-bind_at_load ' ; \
make ; /bin/mv -f cjpeg djpeg libjpeg.a .. ; \
make clean ; /bin/rm -f Makefile )
checking for gcc... /usr/local/bin/gcc-13
checking whether the C compiler (/usr/local/bin/gcc-13 -L. -L/usr/local/lib -L/opt/X11/lib -L/usr/local/lib -Wl,-x -Wl,-multiply_defined -Wl,warning -Wl,-bind_at_load ) works... no
configure: error: installation or configuration problem: C compiler cannot create executables.
make[1]: *** No targets specified and no makefile found. Stop.
If anyone has any advice on how to proceed, please let me know. I tried a couple of things like changing the gcc to gcc-13 which did not work.
Thanks for your help. I didn't see this earlier and just tried this now. I've been using the precompiled binaries that you installed last week and it's working well so far, but I am sure something will be outdated eventually.
I was able to successfully re-install the CommandLineTools, but I still got the following error when trying to build AFNI again:
Hi Rick,
Oh, awesome. Yes, I agree, once I start using AFNI regularly I may want to compile it locally. I'll let you know.
Thanks! I appreciate all your help!
Best,
Radhika
The
National Institute of Mental Health (NIMH) is part of the National Institutes of
Health (NIH), a component of the U.S. Department of Health and Human
Services.