AFNI installation problem

Dear experts,

The below is the problem that I have met.
Thank you for your time to help me fix it!!

-------------------------------- general ---------------------------------
architecture: 64bit
system: Darwin
release: 17.7.0
version: Darwin Kernel Version 17.7.0: Thu Jun 21 22:53:14 PDT 2018; root:xnu-4570.71.2~1/RELEASE_X86_64
distribution: 10.13.6 x86_64
number of CPUs: 4
apparent login shell: tcsh
shell RC file: .cshrc (exists)

--------------------- AFNI and related program tests ---------------------
which afni : /Users/yao150/abin/afni
afni version : Precompiled binary macosx_10.7_Intel_64: May 25 2018
: AFNI_18.1.18
AFNI_version.txt : AFNI_18.1.18, macosx_10.7_Intel_64, May 25 2018
which python : /usr/bin/python
python version : 2.7.10
which R : /usr/local/bin/R
R version : R version 3.4.1 (2017-06-30) – “Single Candle”
which tcsh : /bin/tcsh

instances of various programs found in PATH:
afni : 1 (/Users/yao150/abin/afni)
R : 1 (/Library/Frameworks/R.framework/Versions/3.4/Resources/bin/R)
python : 1 (/usr/bin/python)
python2 : 0
python3 : 0

testing ability to start various programs…
afni : success
suma : FAILURE
dyld: Library not loaded: /sw/lib/libglib-2.0.0.dylib
Referenced from: /Users/yao150/abin/suma
Reason: image not found
3dSkullStrip : FAILURE
dyld: Library not loaded: /sw/lib/libglib-2.0.0.dylib
Referenced from: /Users/yao150/abin/3dSkullStrip
Reason: image not found
uber_subject.py : success
3dAllineate : FAILURE
dyld: Library not loaded: /usr/local/lib/libgomp.1.dylib
Referenced from: /Users/yao150/abin/3dAllineate
Reason: image not found
3dRSFC : success
SurfMesh : FAILURE
dyld: Library not loaded: /sw/lib/libglib-2.0.0.dylib
Referenced from: /Users/yao150/abin/SurfMesh
Reason: image not found
3dClustSim : FAILURE
dyld: Library not loaded: /usr/local/lib/libgomp.1.dylib
Referenced from: /Users/yao150/abin/3dClustSim
Reason: image not found

checking for R packages…
rPkgsInstall -pkgs ALL -check : FAILURE
This package has been verified on the computer: afex
This package has been verified on the computer: phia
This package has been verified on the computer: snow
This package has been verified on the computer: nlme
This package has been verified on the computer: lme4
This package has been verified on the computer: paran
This package has been verified on the computer: psych
This package has been verified on the computer: brms

    Warning message:
    In as.POSIXlt.POSIXct(x, tz) :
      unknown timezone 'zone/tz/2018e.1.0/zoneinfo/America/Indiana/Indianapolis'

checking for $HOME files…
.afnirc : found
.sumarc : missing
.afni/help/all_progs.COMP : found

------------------------------ python libs -------------------------------
** python module not found: PyQt4
– PyQt4 is no longer needed for an AFNI bootcamp

-------------------------------- env vars --------------------------------
PATH = /usr/local/bin:/usr/bin:/bin:/usr/sbin:/sbin:/opt/X11/bin:/Users/yao150/abin

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 : found AFNI_data6 under $HOME
top history: … Jun 2018 [gangc]: added 0.BGA and updated 2.3groups
data dir : found AFNI_demos under $HOME
top history: … [pault]: remove rank from FATCAT_DEMO, FAT_MVM_DEMO
data dir : found suma_demo under $HOME
top history: …/SUMA_data/Build_tmp on Wed Aug 20 10:04:23 EDT 2014
data dir : found afni_handouts under $HOME
atlas : found TT_N27+tlrc under /Users/yao150/abin

------------------------------ OS specific -------------------------------
which brew : /usr/local/bin/brew
brew version : Homebrew 1.7.2

– for PyQt4 under brew, consider running:
brew install cartr/qt4/pyqt
++ 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 ‘tcsh’…
++ found evar DYLD_LIBRARY_PATH = /opt/X11/lib/flat_namespace

========================= summary, please fix: =========================

  • AFNI programs show FAILURE
  • missing R packages (see rPkgsInstall)
  • consider running “suma -update_env” for .sumarc
  • consider installing gcc under homebrew
  • consider installing glib under homebrew

Following some steps from here that may have been updated since you were installing:
https://afni.nimh.nih.gov/pub/dist/doc/htmldoc/background_install/install_instructs/steps_mac.html

… can you run this:


cd 
curl -O https://afni.nimh.nih.gov/pub/dist/bin/macosx_10.7_local/@update.afni.binaries
tcsh @update.afni.binaries -defaults -package macosx_10.7_local

which will take care of a lot of the library errors you are seeing.

Then you should be able to run


sudo rPkgsInstall -pkgs ALL

more easily to install the R packages.

Let us know how that goes.

–pt

Hello,

Assuming the main thing you want to fix is the
set of library errors, it might make more sense
to use the ‘local’ package, rather than Intel_64.

Try: @update.afni.binaries -package macosx_10.7_local

  • rick

Dear experts,

Thank you for your quick response!
Now most problems has been fixed. However, the R packages still missing. Please see the report below!!

Thank you in advance!

-------------------------------- general ---------------------------------
architecture: 64bit
system: Darwin
release: 17.7.0
version: Darwin Kernel Version 17.7.0: Thu Jun 21 22:53:14 PDT 2018; root:xnu-4570.71.2~1/RELEASE_X86_64
distribution: 10.13.6 x86_64
number of CPUs: 4
apparent login shell: tcsh
shell RC file: .cshrc (exists)

--------------------- AFNI and related program tests ---------------------
which afni : /Users/yao150/abin/afni
afni version : Precompiled binary macosx_10.7_local: Aug 20 2018
: AFNI_18.2.13
AFNI_version.txt : AFNI_18.2.13, macosx_10.7_local, Aug 20 2018
which python : /usr/bin/python
python version : 2.7.10
which R : /usr/local/bin/R
R version : R version 3.4.1 (2017-06-30) – “Single Candle”
which tcsh : /bin/tcsh

instances of various programs found in PATH:
afni : 1 (/Users/yao150/abin/afni)
R : 1 (/Library/Frameworks/R.framework/Versions/3.4/Resources/bin/R)
python : 1 (/usr/bin/python)
python2 : 0
python3 : 0

testing ability to start various programs…
afni : success
suma : success
3dSkullStrip : success
uber_subject.py : success
3dAllineate : success
3dRSFC : success
SurfMesh : success
3dClustSim : success

checking for R packages…
rPkgsInstall -pkgs ALL -check : FAILURE
This package has been verified on the computer: afex
This package has been verified on the computer: phia
This package has been verified on the computer: snow
This package has been verified on the computer: nlme
This package has been verified on the computer: lme4
This package has been verified on the computer: paran
This package has been verified on the computer: psych
This package has been verified on the computer: brms

    Warning message:
    In as.POSIXlt.POSIXct(x, tz) :
      unknown timezone 'zone/tz/2018e.1.0/zoneinfo/America/Indiana/Indianapolis'

checking for $HOME files…
.afnirc : found
.sumarc : found
.afni/help/all_progs.COMP : found

------------------------------ python libs -------------------------------
** python module not found: PyQt4
– PyQt4 is no longer needed for an AFNI bootcamp

-------------------------------- env vars --------------------------------
PATH = /usr/local/bin:/usr/bin:/bin:/usr/sbin:/sbin:/opt/X11/bin:/Users/yao150/abin

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 : found AFNI_data6 under $HOME
top history: … Jun 2018 [gangc]: added 0.BGA and updated 2.3groups
data dir : found AFNI_demos under $HOME
top history: … [pault]: remove rank from FATCAT_DEMO, FAT_MVM_DEMO
data dir : found suma_demo under $HOME
top history: …/SUMA_data/Build_tmp on Wed Aug 20 10:04:23 EDT 2014
data dir : found afni_handouts under $HOME
atlas : found TT_N27+tlrc under /Users/yao150/abin

------------------------------ OS specific -------------------------------
which brew : /usr/local/bin/brew
brew version : Homebrew 1.7.2

– for PyQt4 under brew, consider running:
brew install cartr/qt4/pyqt
– consider installing gcc under homebrew
– consider installing glib under homebrew
++ 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 ‘tcsh’…
++ found evar DYLD_LIBRARY_PATH = /opt/X11/lib/flat_namespace

========================= summary, please fix: =========================

  • missing R packages (see rPkgsInstall)

Dear ptaylor,

After installed the “local” afni, the libraries problem fixed! Then I tried the “sudo rPkgsInstall -pkgs ALL” . The report also shows that the R packages missing. Below is the detail information!

Thank you in advance!
-------------------------------- general ---------------------------------
architecture: 64bit
system: Darwin
release: 17.7.0
version: Darwin Kernel Version 17.7.0: Thu Jun 21 22:53:14 PDT 2018; root:xnu-4570.71.2~1/RELEASE_X86_64
distribution: 10.13.6 x86_64
number of CPUs: 4
apparent login shell: tcsh
shell RC file: .cshrc (exists)

--------------------- AFNI and related program tests ---------------------
which afni : /Users/yao150/abin/afni
afni version : Precompiled binary macosx_10.7_local: Aug 20 2018
: AFNI_18.2.13
AFNI_version.txt : AFNI_18.2.13, macosx_10.7_local, Aug 20 2018
which python : /usr/bin/python
python version : 2.7.10
which R : /usr/local/bin/R
R version : R version 3.4.1 (2017-06-30) – “Single Candle”
which tcsh : /bin/tcsh

instances of various programs found in PATH:
afni : 1 (/Users/yao150/abin/afni)
R : 1 (/Library/Frameworks/R.framework/Versions/3.4/Resources/bin/R)
python : 1 (/usr/bin/python)
python2 : 0
python3 : 0

testing ability to start various programs…
afni : success
suma : success
3dSkullStrip : success
uber_subject.py : success
3dAllineate : success
3dRSFC : success
SurfMesh : success
3dClustSim : success

checking for R packages…
rPkgsInstall -pkgs ALL -check : FAILURE
This package has been verified on the computer: afex
This package has been verified on the computer: phia
This package has been verified on the computer: snow
This package has been verified on the computer: nlme
This package has been verified on the computer: lme4
This package has been verified on the computer: paran
This package has been verified on the computer: psych
This package has been verified on the computer: brms

    Warning message:
    In as.POSIXlt.POSIXct(x, tz) :
      unknown timezone 'zone/tz/2018e.1.0/zoneinfo/America/Indiana/Indianapolis'

checking for $HOME files…
.afnirc : found
.sumarc : found
.afni/help/all_progs.COMP : found

------------------------------ python libs -------------------------------
** python module not found: PyQt4
– PyQt4 is no longer needed for an AFNI bootcamp

-------------------------------- env vars --------------------------------
PATH = /usr/local/bin:/usr/bin:/bin:/usr/sbin:/sbin:/opt/X11/bin:/Users/yao150/abin

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 : found AFNI_data6 under $HOME
top history: … Jun 2018 [gangc]: added 0.BGA and updated 2.3groups
data dir : found AFNI_demos under $HOME
top history: … [pault]: remove rank from FATCAT_DEMO, FAT_MVM_DEMO
data dir : found suma_demo under $HOME
top history: …/SUMA_data/Build_tmp on Wed Aug 20 10:04:23 EDT 2014
data dir : found afni_handouts under $HOME
atlas : found TT_N27+tlrc under /Users/yao150/abin

------------------------------ OS specific -------------------------------
which brew : /usr/local/bin/brew
brew version : Homebrew 1.7.2

– for PyQt4 under brew, consider running:
brew install cartr/qt4/pyqt
– consider installing gcc under homebrew
– consider installing glib under homebrew
++ 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 ‘tcsh’…
++ found evar DYLD_LIBRARY_PATH = /opt/X11/lib/flat_namespace

========================= summary, please fix: =========================

  • missing R packages (see rPkgsInstall)