Hello, I am experiencing issues when installing AFNI. I was wondering if you can help with this, please.
I followed the steps listed here to install AFNI.
I get errors when I run this line:
tcsh OS_notes.macos_12_intel_b_user.tcsh
The error seems to be the following:
-- current AFNI: AFNI_24.1.22, anyos_text, Jun 21 2024
-- cleaning old build root dir, /Users/francesca/afni_build
-- backing up dir build_src
-- preparing build_root dir, /Users/francesca/afni_build
-- have default git tag LAST_TAG, will checkout AFNI_24.1.22
-- checking out git tag AFNI_24.1.22
-- using repo branch (detached), tag AFNI_24.1.22
-- removing old atlas dir, prev/afni_atlases_dist
-- moving old atlas dir afni_atlases_dist to prev/afni_atlases_dist
-- downloading AFNI atlas package, afni_atlases_dist.tgz
-- unpacking atlas package, afni_atlases_dist
-- removing old NiiVue backup, prev/niivue_afni.umd.js
-- moving old niivue niivue_afni.umd.js to prev/niivue_afni.umd.js
-- downloading NiiVue, niivue_afni.umd.js
-- preparing to run 'make' build of package macos_12_x86_64
-- copying README files
-- copying Makefile.macos_12_x86_64 to Makefile
-- building make target 'itall'
-- consider monitoring the build in a separate window with:
cd /Users/francesca
tail -f /Users/francesca/afni_build/build_src/log_make.txt
# use ctrl-c to terminate 'tail' command (not the build)
++ building (please be patient)...
** error: failed run_cmd: make AFNI_WHOMADEIT=build itall >& log_make.txt
-- status: building FAILURE
see 'make' log file /Users/francesca/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
--------------------------------------------------
** warning: in conda environment
CONDA_SHLVL = 0, CONDA_DEFAULT_ENV = base
-- shell/system command history is in:
/Users/francesca/afni_build/hist_commands.txt
++ screen text history is in:
/Users/francesca/afni_build/hist_messages.txt
rehash
setenv R_LIBS /Users/francesca/sw/R-4.4.1
echo export R_LIBS=/Users/francesca/sw/R-4.4.1
echo export R_LIBS=/Users/francesca/sw/R-4.4.1
echo setenv R_LIBS /Users/francesca/sw/R-4.4.1
mkdir -p /Users/francesca/sw/R-4.4.1
rPkgsInstall -pkgs ALL
tee out.rPkgsInstall.txt
** ERROR: Failed to load R_io.so