Quote
Last login: Mon Oct 28 23:24:06 on ttys000
z@Z tmp % tcsh -x ./@update.afni.binaries -local_package macos_10.12_local.tgz -do_extras
set prog = `basename $0`
basename ./@update.afni.binaries
set hostname = afni.nimh.nih.gov
set hostproto = https://
set hostsite = [
afni.nimh.nih.gov]
set sysname = `uname -s`
uname -s
if ( 0 ) then
goto POST_HIST
set aub_version = 3.7, January 22, 2019
set obsolete_list = ( linux_gcc32 linux_gcc33_64 linux_glibc22 NIH.openSUSE.11.4_64 linux_fedora_21_64 linux_fedora_25_64 solaris29_suncc solaris29_suncc_64 macosx_10.5_Intel_64 macosx_10.6_Intel_64 macosx_10.7_Intel_64 macosx_10.7_local macosx_10.8_gcc macosx_10.8_icc )
set abin =
set package =
set local_package =
set prog_list = ( )
set tmp_dir = .tmp.install
set make_backup = 1
set sys_ok = 0
set system_progs = ( apt-get at cc cpp cmp diff du gcc less man md5sum od passwd perl python scp srm sudo vi vim wc xterm yum )
set show_system_progs = 0
set show_obsoletes = 0
set show_obsoletes_grep = 0
if ( 3 == 0 ) then
set help = 0
endif
set testing = 0
set test_protos = 0
set use_curl = 0
set do_extras = 0
set do_apsearch = 0
set do_dotfiles = 0
set do_recur = 1
set quick = 0
set revert = 0
set cert_verify = 1
set use_curl = 0
set bad_opt =
set ac = 1
while ( 1 < = 3 )
if ( -local_package == -apsearch ) then
if ( -local_package == -bindir ) then
if ( -local_package == -curl ) then
if ( -local_package == -d || -local_package == -defaults ) then
if ( -local_package == -do_dotfiles ) then
if ( -local_package == -do_extras ) then
if ( -local_package == -help ) then
if ( -local_package == -help_sys_progs ) then
if ( -local_package == -hist ) then
if ( -local_package == -local_package ) then
@ ac ++
if ( 2 > 3 ) then
set local_package = macos_10.12_local.tgz
if ( ! -f macos_10.12_local.tgz && -f macos_10.12_local.tgz.tgz ) then
if ( ! -f macos_10.12_local.tgz ) then
else if ( macos_10.12_local.tgz == -package ) then
@ ac ++
end
while ( 3 < = 3 )
if ( -do_extras == -apsearch ) then
if ( -do_extras == -bindir ) then
if ( -do_extras == -curl ) then
if ( -do_extras == -d || -do_extras == -defaults ) then
if ( -do_extras == -do_dotfiles ) then
if ( -do_extras == -do_extras ) then
set do_apsearch = 1
set do_dotfiles = 1
else if ( -do_extras == -help ) then
@ ac ++
end
while ( 4 < = 3 )
set tmpsite = [
afni.nimh.nih.gov]
if ( [
afni.nimh.nih.gov] != [
afni.nimh.nih.gov] ) then
if ( 0 ) then
if ( != && 1 ) then
if ( 0 ) then
echo -- running @update.afni.binaries version 3.7, January 22, 2019
-- running @update.afni.binaries version 3.7, January 22, 2019
which afni
if ( 1 ) then
echo -- no current AFNI package found in path...
-- no current AFNI package found in path...
set cur_afni =
else
if ( == ) then
if ( == ) then
echo -- install dir: using default ~/abin
-- install dir: using default ~/abin
set abin = ~/abin
else
endif
if ( macos_10.12_local.tgz != ) then
if ( != ) then
if ( ! -f macos_10.12_local.tgz ) then
if ( macos_10.12_local.tgz == macos_10.12_local.tgz ) then
set local_package_dir = `pwd`
pwd
else if ( -d macos_10.12_local.tgz ) then
set package = macos_10.12_local
echo -- will install from local package file: macos_10.12_local.tgz
-- will install from local package file: macos_10.12_local.tgz
endif
if ( macos_10.12_local == ) then
which wget
set missing_wget = 0
which curl
set missing_curl = 0
if ( 0 ) echo -- wget, curl status = 0, 0
if ( 0 && 0 ) then
set get_prog = ( wget )
if ( 0 || 0 ) set get_prog = ( curl -O -f )
if ( ! 1 ) then
echo -- any downloads will be from [
afni.nimh.nih.gov] via wget
-- any downloads will be from [
afni.nimh.nih.gov] via wget
echo
if ( macos_10.12_local =~ *.tgz ) set package = macos_10
echo -- attempting to install package macos_10.12_local under
-- attempting to install package macos_10.12_local under
if ( 0 > 0 ) echo (including only 0 programs)
echo install dir: /Users/z/abin...
install dir: /Users/z/abin...
if ( -d /Users/z/abin ) then
if ( 0 == 1 ) then
echo ++ creating install dir
++ creating install dir
mkdir -pv /Users/z/abin
if ( 0 ) then
echo
sleep 1
endif
set date = `date +%Y_%m_%d`
date +%Y_%m_%d
set backup_dir = auto_backup.macos_10.12_local
cd /Users/z/abin
if ( ! -w . ) then
set nerr = 0
foreach cprog ( apt-get at cc cpp cmp diff du gcc less man md5sum od passwd perl python scp srm sudo vi vim wc xterm yum )
if ( -e apt-get ) then
end
if ( -e at ) then
end
if ( -e cc ) then
end
if ( -e cpp ) then
end
if ( -e cmp ) then
end
if ( -e diff ) then
end
if ( -e du ) then
end
if ( -e gcc ) then
end
if ( -e less ) then
end
if ( -e man ) then
end
if ( -e md5sum ) then
end
if ( -e od ) then
end
if ( -e passwd ) then
end
if ( -e perl ) then
end
if ( -e python ) then
end
if ( -e scp ) then
end
if ( -e srm ) then
end
if ( -e sudo ) then
end
if ( -e vi ) then
end
if ( -e vim ) then
end
if ( -e wc ) then
end
if ( -e xterm ) then
end
if ( -e yum ) then
end
if ( 0 > 0 && ! 0 ) then
if ( ! 0 && ( -f macos_10.12_local.tgz || -d macos_10.12_local ) ) then
if ( -d .tmp.install ) then
echo ++ working in new temp dir, .tmp.install
++ working in new temp dir, .tmp.install
mkdir .tmp.install
if ( 0 ) then
cd .tmp.install
if ( 1 ) then
set temp_prog =
tmp.@update.afni.binaries
set retry = 0
set bin_root = [
afni.nimh.nih.gov]
set get_package = [
afni.nimh.nih.gov]
echo ++ getting install prog: wget macos_10.12_local/@update.afni.binaries ...
++ getting install prog: wget macos_10.12_local/@update.afni.binaries ...
echo wget [
afni.nimh.nih.gov]
wget [
afni.nimh.nih.gov]
wget [
afni.nimh.nih.gov]
--2019-10-28 23:26:51-- [
afni.nimh.nih.gov]
Resolving afni.nimh.nih.gov (afni.nimh.nih.gov)... 156.40.187.114
Connecting to afni.nimh.nih.gov (afni.nimh.nih.gov)|156.40.187.114|:443... connected.
HTTP request sent, awaiting response... 200 OK
Length: 45323 (44K) [text/plain]
Saving to: ‘@update.afni.binaries’
@update.afni.binari 100%[===================>] 44.26K 80.1KB/s in 0.6s
2019-10-28 23:26:53 (80.1 KB/s) - ‘@update.afni.binaries’ saved [45323/45323]
if ( 0 ) then
grep upgrade the AFNI binaries @update.afni.binaries
if ( 0 ) then
endif
if ( 0 ) then
if ( ! -x @update.afni.binaries ) then
echo -- fixing lost permissions on @update.afni.binaries
-- fixing lost permissions on @update.afni.binaries
chmod +x @update.afni.binaries
endif
cmp -s @update.afni.binaries ../@update.afni.binaries
if ( 2 ) then
echo ++ using updated @update.afni.binaries, instead...
++ using updated @update.afni.binaries, instead...
echo
if ( -f ../tmp.@update.afni.binaries ) rm -f ../tmp.@update.afni.binaries
mv @update.afni.binaries ../tmp.@update.afni.binaries
cd ..
set args = ( -local_package macos_10.12_local.tgz -do_extras )
if ( macos_10.12_local.tgz != ) then
set ind = 1
while ( 1 < 3 )
if ( -local_package == -local_package ) then
@ ind += 1
set args[2] = /Users/z/Downloads/tmp/macos_10.12_local.tgz
break
endif
echo ++ running: tcsh
tmp.@update.afni.binaries -no_recur -local_package /Users/z/Downloads/tmp/macos_10.12_local.tgz -do_extras
++ running: tcsh
tmp.@update.afni.binaries -no_recur -local_package /Users/z/Downloads/tmp/macos_10.12_local.tgz -do_extras
tcsh
tmp.@update.afni.binaries -no_recur -local_package /Users/z/Downloads/tmp/macos_10.12_local.tgz -do_extras
-- running
tmp.@update.afni.binaries version 3.13, September 24, 2019
-- no current AFNI package found in path...
-- install dir: using default ~/abin
-- will install from local package file: macos_10.12_local.tgz
-- any downloads will be from [
afni.nimh.nih.gov] via wget
-- attempting to install package macos_10.12_local under
install dir: /Users/z/abin...
-- have install dir
deleting old temporary directory...
++ working in new temp dir, .tmp.install
-- skipping update of
tmp.@update.afni.binaries
++ update needed, installing...
++ extracting local package macos_10.12_local from /Users/z/Downloads/tmp/macos_10.12_local.tgz...
++ backing up current binaries to auto_backup.macos_10.12_local
++ installing new binaries...
++ adding /Users/z/abin to path in /Users/z/.cshrc ...
++ adding /Users/z/abin to PATH in /Users/z/.bashrc ...
-- seem be be sourcing .bashrc from /Users/z/.bash_profile
-- seem be be sourcing .bashrc from /Users/z/.profile
++ running apsearch -update_all_afni_help ...
Killed
done, yay (binaries are under /Users/z/abin)
set ss = 0
if ( ! 0 ) then
echo ...finished, removing temp version,
tmp.@update.afni.binaries
...finished, removing temp version,
tmp.@update.afni.binaries
rm -f
tmp.@update.afni.binaries
endif
exit 0
z@Z tmp % cd ~/abin
z@Z abin % ./afni
zsh: killed ./afni
z@Z abin % ./afni_system_check.py -check_all
-------------------------------- general ---------------------------------
architecture: 64bit
system: Darwin
release: 19.0.0
version: Darwin Kernel Version 19.0.0: Wed Sep 25 20:18:50 PDT 2019; root:xnu-6153.11.26~2/RELEASE_X86_64
distribution: 10.15 x86_64
number of CPUs: 12
apparent login shell: zsh
shell RC file: .zshenv (does not exist)
--------------------- AFNI and related program tests ---------------------
which afni :
:
AFNI_version.txt : AFNI_19.3.09, macos_10.12_local, Oct 25 2019
which python : /usr/bin/python
python version : 2.7.16
which R : /usr/local/bin/R
R version : R version 3.6.1 (2019-07-05) -- "Action of the Toes"
which tcsh : /bin/tcsh
instances of various programs found in PATH:
afni : 0
R : 1 (/Library/Frameworks/R.framework/Versions/3.6/Resources/bin/R)
python : 1 (/System/Library/Frameworks/Python.framework/Versions/2.7/bin/python2.7)
python2 : 1 (/System/Library/Frameworks/Python.framework/Versions/2.7/bin/python2.7)
python3 : 2
/usr/local/Cellar/python/3.7.4_1/Frameworks/Python.framework/Versions/3.7/bin/python3.7
/usr/bin/python3
testing ability to start various programs...
afni : FAILURE
/bin/sh: afni: command not found
suma : FAILURE
/bin/sh: suma: command not found
3dSkullStrip : FAILURE
/bin/sh: 3dSkullStrip: command not found
uber_subject.py : FAILURE
/bin/sh: uber_subject.py: command not found
3dAllineate : FAILURE
/bin/sh: 3dAllineate: command not found
3dRSFC : FAILURE
/bin/sh: 3dRSFC: command not found
SurfMesh : FAILURE
/bin/sh: SurfMesh: command not found
3dClustSim : FAILURE
/bin/sh: 3dClustSim: command not found
3dMVM : FAILURE
/bin/sh: 3dMVM: command not found
none working, testing programs under implied /Users/z/abin...
afni : FAILURE
suma : FAILURE
3dSkullStrip : FAILURE
uber_subject.py : success
3dAllineate : FAILURE
3dRSFC : FAILURE
SurfMesh : FAILURE
3dClustSim : FAILURE
3dMVM : success
checking for R packages...
rPkgsInstall -pkgs ALL -check : FAILURE
/bin/sh: rPkgsInstall: command not found
R RHOME : /Library/Frameworks/R.framework/Resources
checking for $HOME files...
.afnirc : missing
.sumarc : missing
.afni/help/all_progs.COMP : missing
------------------------------ python libs -------------------------------
** failed to load module PyQt4
-- PyQt4 is no longer needed for an AFNI bootcamp
++ module loaded: matplotlib.pyplot
module file : /System/Library/Frameworks/Python.framework/Versions/2.7/Extras/lib/python/matplotlib/pyplot.pyc
-- python binaries under /usr/local/bin:
/usr/local/bin/python3 (sym link to /usr/local/Cellar/python/3.7.4_1/Frameworks/Python.framework/Versions/3.7/bin/python3.7)
/usr/local/bin/python3.7 (sym link to /usr/local/Cellar/python/3.7.4_1/Frameworks/Python.framework/Versions/3.7/bin/python3.7)
-------------------------------- env vars --------------------------------
PATH = /usr/local/ants/bin/:/usr/local/fsl/bin:/usr/local/bin:/usr/bin:/bin:/usr/sbin:/sbin:/Library/Apple/usr/bin:/Library/Apple/bin:/Library/TeX/texbin:/opt/X11/bin:/Users/z/Documents/OneDrive/Sync/Scripts
PYTHONPATH =
R_LIBS =
LD_LIBRARY_PATH =
DYLD_LIBRARY_PATH (sub-shell) = :/opt/X11/lib/flat_namespace
DYLD_FALLBACK_LIBRARY_PATH (sub-shell) =
------------------------------ data checks -------------------------------
data dir : missing AFNI_data6
data dir : missing AFNI_demos
data dir : missing suma_demo
data dir : missing afni_handouts
atlas : did not find TT_N27+tlrc
------------------------------ OS specific -------------------------------
XQuartz version : 2.7.11
which brew : /usr/local/bin/brew
brew version : Homebrew 2.1.15
-- for PyQt4 under brew, consider running:
brew install cartr/qt4/pyqt
++ found valid link /usr/local/lib/libglib-2.0.dylib
to ../Cellar/glib/2.62.2/lib/libglib-2.0.dylib
++ found 1 dylib files under '/opt/X11/lib/flat_namespace'
-- found 'libXt' dylib files:
/opt/X11/lib/flat_namespace/libXt.6.dylib
-- recent OS X, cheating to check DYLD_LIBRARY_PATH in cur shell 'zsh'...
++ found evar DYLD_LIBRARY_PATH = :/opt/X11/lib/flat_namespace
-- recent OS X, cheating to check DYLD_LIBRARY_PATH in shell 'tcsh'...
++ found evar DYLD_LIBRARY_PATH = /opt/X11/lib/flat_namespace
========================= summary, please fix: =========================
* login shell 'zsh', trusting user to translate code examples from 'tcsh'
* shell zsh : MISSING env shell setup file .zshenv
* failure under initial "AFNI and related program tests"
* AFNI programs show FAILURE
* consider adding /Users/z/abin to your PATH
* missing R packages (see rPkgsInstall)
* please run: cp /Users/z/abin/AFNI.afnirc ~/.afnirc
* please run: "suma -update_env" for .sumarc
* please run: apsearch -update_all_afni_help
* insufficient data for AFNI bootcamp
* possibly missing atlases
* consider installing gcc under homebrew
z@Z abin %
