Howdy-
I get the following warnings/messages in the terminal text whenever I run any @chauffeur_afni command, even just making an underlay of an anatomical (so there isn't any stat info (hence I don't get the FDR message):
*** can't get X11 colormap entry for overlay color DAFNI_DONT_ADJUST_FDR++
++
Hints disabled: X11 failure to create LiteClue window
The LiteClue thing seems to come from xutil.c.
The image still gets created and looks OK, but I have not seen these before, and hence thought I should seek expert opinions.
AFNI version info (afni -ver):
Precompiled binary macos_12_x86_64: Aug 31 2023 (Version AFNI_23.2.08 'Marcus Didius Severus Julianus')
Here is my afni_system_check.py -check_all output
-------------------------------- general ---------------------------------
architecture: 64bit
cpu type: i386
system: Darwin
release: 22.6.0
version: Darwin Kernel Version 22.6.0: Fri Sep 15 13:39:52 PDT 2023; root:xnu-8796.141.3.700.8~1/RELEASE_X86_64
distribution: 10.16
number of CPUs: 8
apparent login shell: bash
shell RC file: .bashrc (exists)
--------------------- AFNI and related program tests ---------------------
which afni : /Users/taylorpa3/abin/afni
afni version : Precompiled binary macos_12_x86_64: Aug 31 2023
: AFNI_23.2.08 'Marcus Didius Severus Julianus'
AFNI_version.txt : AFNI_23.2.08, macos_12_x86_64, Aug 31 2023, build
which python : /Users/taylorpa3/miniconda3/envs/py39_afni_mid/bin/python
python version : 3.9.16
which R : /usr/local/bin/R
R version : R version 4.2.3 (2023-03-15) -- "Shortstop Beagle"
instances of various programs found in PATH:
afni : 1 (/Users/taylorpa3/abin/afni)
R : 1 (/Library/Frameworks/R.framework/Versions/4.2/Resources/bin/R)
python : 1 (/Users/taylorpa3/miniconda3/envs/py39_afni_mid/bin/python3.9)
python2 : 0
python3 : 3
/Users/taylorpa3/miniconda3/envs/py39_afni_mid/bin/python3.9
/usr/local/Cellar/python@3.11/3.11.3/Frameworks/Python.framework/Versions/3.11/bin/python3.11
/usr/bin/python3
** have python3 but not python2
testing ability to start various programs...
afni : success
suma : success
3dSkullStrip : success
3dAllineate : success
3dRSFC : success
SurfMesh : success
3dClustSim : success
uber_subject.py : success
3dMVM : success
------------------------ dependent program tests -------------------------
checking for dependent programs...
which tcsh : /bin/tcsh
which Xvfb : /opt/X11/bin/Xvfb
checking for R packages...
rPkgsInstall -pkgs ALL -check : FAILURE
oo Warning:
These packages are not installed on the computer: afex!
These packages are not installed on the computer: phia!
These packages are not installed on the computer: snow!
These packages are not installed on the computer: lmerTest!
These packages are not installed on the computer: paran!
These packages are not installed on the computer: psych!
These packages are not installed on the computer: brms!
These packages are not installed on the computer: corrplot!
These packages are not installed on the computer: metafor!
R RHOME : /Library/Frameworks/R.framework/Resources
------------------------------ python libs -------------------------------
++ module loaded: matplotlib.pyplot
module file : /Users/taylorpa3/miniconda3/envs/py39_afni_mid/lib/python3.9/site-packages/matplotlib/pyplot.py
matplotlib version : 3.7.1
-- python binaries under /usr/local/bin:
/usr/local/bin/python3 (sym link to /usr/local/Cellar/python@3.11/3.11.3/Frameworks/Python.framework/Versions/3.11/bin/python3.11)
-------------------------------- env vars --------------------------------
PATH = /Users/taylorpa3/miniconda3/envs/py39_afni_mid/bin:/Users/taylorpa3/miniconda3/condabin:/usr/local/bin:/System/Cryptexes/App/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/opt/X11/bin:/var/run/com.apple.security.cryptexd/codex.system/bootstrap/usr/local/bin:/var/run/com.apple.security.cryptexd/codex.system/bootstrap/usr/bin:/var/run/com.apple.security.cryptexd/codex.system/bootstrap/usr/appleinternal/bin:/Users/taylorpa3/abin:/Users/taylorpa3/LAYNII:/Users/taylorpa3/abin:/Users/taylorpa3/LAYNII
PYTHONPATH (sub-shell) =
R_LIBS (sub-shell) =
LD_LIBRARY_PATH (sub-shell) =
DYLD_LIBRARY_PATH (sub-shell) = :/opt/X11/lib/flat_namespace
DYLD_FALLBACK_LIBRARY_PATH (sub-shell) =
----------------------------- eval dot files -----------------------------
----------- AFNI $HOME files -----------
.afnirc : found
.sumarc : found
.afni/help/all_progs.COMP : found
--------- shell startup files ----------
-- good: .tcshrc seems to contain 'source .cshrc'
-- considered operations: path, flatdir, apsearch
-- note: followers should not need edits, so edit flags should be 0
(have 1 follower(s), which can be ignored)
no modifications needed across 3 dot files
------------------------------ data checks -------------------------------
data dir : found AFNI_data6 under $HOME (476802M Avail)
top history: 20 Feb 2020 [rickr]: updated FT_analysis examples
data dir : found AFNI_demos under $HOME
top history: 22 Oct 2019 [discoraj]: added Cluster Explorer Demo
data dir : found suma_demo under $HOME
top history: ...s_New/data/Build_tmp on Mon Mar 4 11:56:45 EST 2013
data dir : found afni_handouts under $HOME
atlas : found TT_N27+tlrc under /Users/taylorpa3/REF_TEMPLATES
------------------------------ OS specific -------------------------------
XQuartz version : 2.8.5
which brew : /usr/local/bin/brew
brew version : Homebrew 4.0.22
** consider linking /usr/local/Cellar/gcc/13.1.0/lib/gcc/current/libgomp.1.dylib under /usr/local/lib
++ found valid link /usr/local/lib/libglib-2.0.dylib
to ../Cellar/glib/2.76.3/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 'bash'...
++ 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: =========================
* just be aware: login shell 'bash', but our code examples use 'tcsh'
* missing R packages (see rPkgsInstall)
thanks,
pt