Problem with Installation on Intel Core i7, macOS Ventura 13.6 system

Installation Issues
1

Hi all,

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ld: warning: -multiply_defined is obsolete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.

Thank you so much!

2

Hello,

Do you have an older version of homebrew, or was it just installed vie the quick setup commands?
What is the output from:

ls -l /usr/local/bin/gcc*

Thanks,

  • rick
3

Hi!

Thanks for your reply, I used the quick setup commands.

Version of homebrew:
Homebrew 4.1.16-2-g23ee8af

Output:

ls -l /usr/local/bin/gcc*
lrwxr-xr-x  1 dir_support  admin  31 Oct 12 14:37 /usr/local/bin/gcc-13 -> ../Cellar/gcc/13.2.0/bin/gcc-13
lrwxr-xr-x  1 dir_support  admin  34 Oct 12 14:37 /usr/local/bin/gcc-ar-13 -> ../Cellar/gcc/13.2.0/bin/gcc-ar-13
lrwxr-xr-x  1 dir_support  admin  34 Oct 12 14:37 /usr/local/bin/gcc-nm-13 -> ../Cellar/gcc/13.2.0/bin/gcc-nm-13
lrwxr-xr-x  1 dir_support  admin  38 Oct 12 14:37 /usr/local/bin/gcc-ranlib-13 -> ../Cellar/gcc/13.2.0/bin/gcc-ranlib-13
4

Hello @radchat,

Would you please try reinstalling the CommandLineTools, before trying the build again? First run:

xcode-select -p

and verify that it shows the output: /Library/Developer/CommandLineTools
If so, remove that directory tree, and reinstall:

sudo rm -rf /Library/Developer/CommandLineTools
xcode-select --install

Please let us know how that goes. If it goes well, you can try building AFNI again:

build_afni.py -build_root ~/afni_build -package  macos_12_x86_64

Thanks,

  • rick
5

Hi @rickr,

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:

** error: failed run_cmd: make AFNI_WHOMADEIT=build itall >& log_make.txt
-- status: building FAILURE
   see 'make' log file /Users/chatterjeer4/afni_build/build_src/log_make.txt
** error: tail from log_make.txt:
   --------------------------------------------------
   /usr/local/bin/gcc-13 -O2 -DDARWIN -m64 -Wcomment -Wformat -DUSE_TRACING -DHAVE_XDBE -DDONT_USE_MCW_MALLOC  -c afni_whelp.c -I. -I/usr/local/include -I/opt/X11/include -I/usr/local/include/netpbm -I/usr/include -Icoxplot -Inifti/nifti2 -Inifti/niftilib -Inifti/nifticdf -Inifti/znzlib -I3DEdge/src -Irickr -Ileej3 -DHAVE_ZLIB -DHAVE_GIFTI  -If2c
   (cd leej3; \
   /usr/local/bin/gcc-13 -O2 -DDARWIN -m64 -Wcomment -Wformat -DUSE_TRACING -DHAVE_XDBE -DDONT_USE_MCW_MALLOC  -c whats_my_exepath.c; \
   /bin/cp -f whats_my_exepath.o ..; \
   cd ..)
   /bin/rm -f afni
   /usr/local/bin/gcc-13 -O2 -DDARWIN -m64 -Wcomment -Wformat -DUSE_TRACING -DHAVE_XDBE -DDONT_USE_MCW_MALLOC  -DWHATS_MY_EXEPATH -o afni afni.o afni_func.o afni_widg.o afni_warp.o afni_fimmer.o afni_slice_short.o afni_slice_float.o afni_filer.o afni_slice_byte.o  afni_slice_complex.o afni_pcor.o afni_pcor_float.o afni_transforms.o pbar.o afni_graph.o afni_plugin.o afni_cluster.o parser.o parser_int.o afni_plugout.o afni_fimfunc.o afni_setup.o afni_receive.o mcw_graf.o afni_splash.o afni_pplug_env.o afni_pplug_2dfunc.o afni_friends.o afni_ttren.o afni_pplug_1dfunc.o afni_driver.o afni_niml.o afni_sumafunc.o afni_slice_rgbyte.o afni_version.o afni_lock.o afni_vol2surf.o afni_pplug_instacorr.o afni_pplug_instacalc.o afni_pplug_tstat.o afni_whelp.o whats_my_exepath.o  -m64 -dynamic -L. -L/usr/local/lib -L/opt/X11/lib -L/usr/local/lib -Wl,-x -Wl,-multiply_defined -Wl,warning -Wl,-bind_at_load  -lmrix -lcoxplot -lmri  libXmHTML.a libjpeg.a -lmri -lf2c -lXm -ljpeg -lXt -lXft -lfontconfig -lpng16 -liconv -lXmu -lXp -lXpm -lXext -lX11 -lz -lexpat  -lm -lc -lm -lc
   ld: file not found: libjpeg.a
   collect2: error: ld returned 1 exit status
   make: *** [afni] Error 1
   ---------------------------

Thanks again! Appreciate it.

Best,
Radhika

6

Those binaries have been updated in the distribution, so in the future you should be able to update them via:

@update.afni.binaries -d

Maybe later we can look at compiling locally again. It would be good to figure this issue out.

Thanks,

  • rick
7

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