3dttest++ categorical covariates of no interest

AFNI Message Board
1

Hello AFNI Gurus,

I am interested in examining whole brain activity associated with a quantitative covariate of interest (“DESB”) while controlling for both categorical (e.g., sex, data collection site) and quantitative (e.g., age, “PCL5”, “CTQ”) covariates of no-interest. I also have two within-subjects conditions in my task (“fearful faces”, “neutral faces”). I first ran this analysis using 3dMVM, however, I hit a snag once I wanted to correct for multiple comparisons using 3dClustSim. The data were processed originally in SPM12, and I do not have access to the appropriate residual file to estimate smoothness with 3dFWHMx for 3dClustSim. To get around this, I decided to run my group analysis using a paired t-test in 3dttest++ with the -Clustsim option instead.

Per 3dttest++ instructions, I have coded the categorical covariates numerically using, e.g., 1=Male, 2=Female (see below for an excerpt of my covariates file). Is this the correct numerical coding for categorical variables of no interest in 3dttest++? Or do these need to be dummy coded instead?

Furthermore, I do not want the program to center the categorical covariates, so I have set the covariates -center option to “NONE”, and I instead mean centered the quantitative covariates before entering them into my covariates file for use with 3dttest++. Is this the correct course of action?

Thanks for your time and help!
Best,
Lauren

Excerpt from Covariate File Used with 3dttest++:


Subj	              Site  Sex	Age	       PCL5	DES 	CTQ
sub-100203	2	2	11.34	30.86	1.64	        -8.95
sub-100311	4	2	-1.66	-24.14	-0.36	-9.95
sub-100325	2	1	5.34	         17.86	1.64	        14.05
sub-100458	3	2	17.34	32.86	2.64	         -7.95
sub-100459	3	2	-8.66	-9.14	-1.36	-1.95
sub-100491	1	2	-5.66	-13.14	-1.36	-6.95
sub-100676	2	2	-9.66	-17.14	0.64	         2.05
sub-100814	1	1	-3.66	-6.14	-0.36	0.05
sub-100926	1	1	0.34	         -1.14	-1.36	20.05
sub-101028	2	2	19.34	-10.14	-1.36	-6.95
sub-101045	2	2	-8.66	-3.14	-1.36	-9.95
sub-101345	1	1	-0.66	-1.14	-1.36	-7.95
sub-101394	4	2	-12.66	-24.14	-1.36	5.05
...
2

I do not have access to the appropriate residual file to estimate smoothness with 3dFWHMx for 3dClustSim.

You could use the -resid option in 3dMVM to generate the residuals for ACF estimation, which is arguably a better approach than the individual-level residuals.

I also have two within-subjects conditions in my task (“fearful faces”, “neutral faces”).

To use 3dttest++, you already obtained the contrast or interaction effect between the two within-subject factors as input for 3dttest++?

For categorical variables (i.e., Site, Sex), code the two levels as 1 and -1 (or 0.5 and -0.5). See discussion here:

https://stats.idre.ucla.edu/r/library/r-library-contrast-coding-systems-for-categorical-variables/

For the centering issue, your specification seems fine.

3

Thank you so much, Gang!

I went ahead and tried to implement the -resid option in 3dMVM, but with this new option my script now crashes:


oo Warning: 
   Failed to load R_io.so with this error message:

Error in dyn.load(ll) : 
  unable to load shared object '/Users/laurenlebois/abin/R_io.so':
  dlopen(/Users/laurenlebois/abin/R_io.so, 6): Library not loaded: /sw/lib/libjpeg.9.dylib
  Referenced from: /Users/laurenlebois/abin/R_io.so
  Reason: Incompatible library version: R_io.so requires version 12.0.0 or later, but libjpeg.9.dylib provides version 11.0.0
Calls: source ... withVisible -> eval -> eval -> set_R_io -> dyn.load
Execution halted

Any advice on how to address this? I’ve checked several other threads about this, but my error seems slightly different.

In case it is helpful, I ran afni_system_check.py output, and get the following


~ % afni_system_check.py -check_all
-------------------------------- general ---------------------------------
architecture:         64bit 
system:               Darwin
release:              18.7.0
version:              Darwin Kernel Version 18.7.0: Tue Aug 20 16:57:14 PDT 2019; root:xnu-4903.271.2~2/RELEASE_X86_64
distribution:         10.14.6 x86_64
number of CPUs:       8
apparent login shell: csh
shell RC file:        .cshrc (exists)

--------------------- AFNI and related program tests ---------------------
which afni           : /Users/laurenlebois/abin/afni
afni version         : Precompiled binary macos_10.12_local: Mar 30 2020 
                     : AFNI_20.0.24 'Galba'
AFNI_version.txt     : AFNI_20.0.24, macos_10.12_local, Mar 30 2020
which python         : /sw/bin/python
python version       : 2.7.11
which R              : /usr/local/bin/R
R version            : R version 3.5.3 (2019-03-11) -- "Great Truth"
which tcsh           : /bin/tcsh

instances of various programs found in PATH:
    afni    : 1   (/Users/laurenlebois/abin/afni)
    R       : 1   (/Library/Frameworks/R.framework/Versions/3.5/Resources/bin/R)
    python  : 2 
      /sw/bin/python2.7
      /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
    3dMVM                : FAILURE
        Error in dyn.load(ll) : 
          unable to load shared object '/Users/laurenlebois/abin/R_io.so':
          dlopen(/Users/laurenlebois/abin/R_io.so, 6): Library not loaded: /sw/lib/libjpeg.9.dylib
          Referenced from: /Users/laurenlebois/abin/R_io.so
          Reason: Incompatible library version: R_io.so requires version 12.0.0 or later, but libjpeg.9.dylib provides version 11.0.0
        Calls: source ... withVisible -> eval -> eval -> set_R_io -> dyn.load
        Execution halted

checking for R packages...
    rPkgsInstall -pkgs ALL -check : success

R RHOME : /Library/Frameworks/R.framework/Resources

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

------------------------------ python libs -------------------------------
++ module loaded: PyQt4
   module file : /usr/local/lib/python2.7/site-packages/PyQt4/__init__.pyc

** failed to load module matplotlib.pyplot
-- matplotlib.pyplot is not required, but is desirable

-- python binaries under /sw/bin:
    /sw/bin/python       (sym link to /sw/bin/python2.7)
    /sw/bin/python2.7   

-------------------------------- env vars --------------------------------
PATH = /opt/local/bin:/opt/local/sbin:/usr/local/fsl/bin:/opt/local/bin:/opt/local/sbin:/sw/bin:/sw/sbin:/Applications/freesurfer/bin:/Applications/freesurfer/fsfast/bin:/Applications/freesurfer/tktools:/usr/local/fsl/bin:/Applications/freesurfer/mni/bin:/sw/bin:/opt/local/bin:/opt/local/sbin:/usr/local/fsl/bin:/opt/local/bin:/opt/local/sbin:/Applications/freesurfer/bin:/Applications/freesurfer/fsfast/bin:/Applications/freesurfer/tktools:/usr/local/fsl/bin:/Applications/freesurfer/mni/bin:/sw/bin:/usr/local/bin:/usr/bin:/bin:/usr/sbin:/sbin:/opt/X11/bin:/Users/laurenlebois/abin:/Users/laurenlebois/Programs_Misc:/Users/laurenlebois/scripts:/opt/local/bin:opt/local/sbin:/bin:/Applications/gedit.app/Contents/MacOS:/opt/local/bin:/opt/local/sbin:/Users/laurenlebois/osx:/usr/local/bin:/usr/local/bin:/usr/bin:/bin:/usr/sbin:/sbin:/opt/X11/bin:/Users/laurenlebois/abin:/Applications/mricron:/Applications/mricron/dcm2niix:/Applications/freesurfer:/Applications/R:/opt/X11/bin:/Users/laurenlebois/abin:/Users/laurenlebois/Programs_Misc:/Users/laurenlebois/scripts:/opt/local/bin:opt/local/sbin:/bin:/Applications/gedit.app/Contents/MacOS:/opt/local/bin:/opt/local/sbin:/Users/laurenlebois/osx:/usr/local/bin:/opt/local/bin:/opt/local/sbin:/usr/local/fsl/bin:/opt/local/bin:/opt/local/sbin:/Applications/freesurfer/bin:/Applications/freesurfer/fsfast/bin:/Applications/freesurfer/tktools:/usr/local/fsl/bin:/Applications/freesurfer/mni/bin:/sw/bin:/usr/local/bin:/usr/bin:/bin:/usr/sbin:/sbin:/opt/X11/bin:/Users/laurenlebois/abin:/Users/laurenlebois/Programs_Misc:/Users/laurenlebois/scripts:/opt/local/bin:opt/local/sbin:/bin:/Applications/gedit.app/Contents/MacOS:/opt/local/bin:/opt/local/sbin:/Users/laurenlebois/osx:/usr/local/bin:/usr/local/bin:/usr/bin:/bin:/usr/sbin:/sbin:/opt/X11/bin:/Users/laurenlebois/abin:/Applications/mricron:/Applications/mricron/dcm2niix:/Applications/freesurfer:/Applications/R:/opt/X11/bin:/Users/laurenlebois/abin:/Applications/mricron:/Applications/mricron/dcm2niix:/Applications/freesurfer:/Applications/R

PYTHONPATH = /usr/local/lib/python2.7/site-packages

R_LIBS = 
LD_LIBRARY_PATH = 
DYLD_LIBRARY_PATH (sub-shell) = /opt/X11/lib/flat_namespace
DYLD_FALLBACK_LIBRARY_PATH (sub-shell) = FSL_DIR           /usr/local/fsl

------------------------------ data checks -------------------------------
data dir : found AFNI_data6   under $HOME
           top history: ... [rickr]: updated FT_white.nii w/out 16 (brain stem)
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 : missing afni_handouts
atlas    : found TT_N27+tlrc  under .

------------------------------ OS specific -------------------------------
XQuartz version      : 2.7.11

which fink           : /sw/bin/fink
fink version         : Package manager version: 0.39.2
which brew           : /usr/local/bin/brew
brew version         : Homebrew 2.2.11
which port           : /opt/local/bin/port
port version         : Error: Current platform "darwin 18" does not match expected platform "darwin 14"

++ found 'brew' at /usr/local/bin/brew
++ 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 'csh'...
++ found evar DYLD_LIBRARY_PATH = /opt/X11/lib/flat_namespace

=========================  summary, please fix:  =========================
*  AFNI programs show FAILURE
*  insufficient data for AFNI bootcamp

Best,
LL

4

This is a knotty issue. Is it possible that you have an outdated XCode for the new OS? Run the following command at the terminal:

system_profiler SPDeveloperToolsDataType

Update your XCode if outdated.

5

Hi Gang,

In response to your suggestion, I updated my XCode, XCode Command Tools, and Fink. However, I’m still getting the R_io error…

In case it’s helpful: After the XCode, XCode Command Tools and Fink updates, running the system_profiler SPDeveloperToolsDataType command at the terminal reveals the following:


~ % system_profiler SPDeveloperToolsDataType
Developer:

    Developer Tools:

      Version: 10.3 (10G8)
      Location: /Applications/Xcode.app
      Applications:
          Xcode: 10.3 (14492.2)
          Instruments: 10.2.1 (64492.2)
      SDKs:
          iOS:
              12.4: (16G73)
          iOS Simulator:
              12.4: (16G73)
          macOS:
              10.14: (18G74)
          tvOS:
              12.4: (16M567)
          tvOS Simulator:
              12.4: (16M567)
          watchOS:
              5.3: (16U567)
          watchOS Simulator:
              5.3: (16U567)

Running afni_system_check.py is nearly the same as before with the same error, but updated fink version:


~ % afni_system_check.py -check_all
-------------------------------- general ---------------------------------
architecture:         64bit 
system:               Darwin
release:              18.7.0
version:              Darwin Kernel Version 18.7.0: Tue Aug 20 16:57:14 PDT 2019; root:xnu-4903.271.2~2/RELEASE_X86_64
distribution:         10.14.6 x86_64
number of CPUs:       8
apparent login shell: csh
shell RC file:        .cshrc (exists)

--------------------- AFNI and related program tests ---------------------
which afni           : /Users/laurenlebois/abin/afni
afni version         : Precompiled binary macos_10.12_local: Mar 30 2020 
                     : AFNI_20.0.24 'Galba'
AFNI_version.txt     : AFNI_20.0.24, macos_10.12_local, Mar 30 2020
which python         : /sw/bin/python
python version       : 2.7.11
which R              : /usr/local/bin/R
R version            : R version 3.5.3 (2019-03-11) -- "Great Truth"
which tcsh           : /bin/tcsh

instances of various programs found in PATH:
    afni    : 1   (/Users/laurenlebois/abin/afni)
    R       : 1   (/Library/Frameworks/R.framework/Versions/3.5/Resources/bin/R)
    python  : 2 
      /sw/bin/python2.7
      /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
    3dMVM                : FAILURE
        Error in dyn.load(ll) : 
          unable to load shared object '/Users/laurenlebois/abin/R_io.so':
          dlopen(/Users/laurenlebois/abin/R_io.so, 6): Library not loaded: /sw/lib/libjpeg.9.dylib
          Referenced from: /Users/laurenlebois/abin/R_io.so
          Reason: Incompatible library version: R_io.so requires version 12.0.0 or later, but libjpeg.9.dylib provides version 11.0.0
        Calls: source ... withVisible -> eval -> eval -> set_R_io -> dyn.load
        Execution halted

checking for R packages...
    rPkgsInstall -pkgs ALL -check : success

R RHOME : /Library/Frameworks/R.framework/Resources

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

------------------------------ python libs -------------------------------
++ module loaded: PyQt4
   module file : /usr/local/lib/python2.7/site-packages/PyQt4/__init__.pyc

** failed to load module matplotlib.pyplot
-- matplotlib.pyplot is not required, but is desirable

-- python binaries under /sw/bin:
    /sw/bin/python       (sym link to /sw/bin/python2.7)
    /sw/bin/python2.7   

-------------------------------- env vars --------------------------------
PATH = /opt/local/bin:/opt/local/sbin:/usr/local/fsl/bin:/opt/local/bin:/opt/local/sbin:/sw/bin:/sw/sbin:/Applications/freesurfer/bin:/Applications/freesurfer/fsfast/bin:/Applications/freesurfer/tktools:/usr/local/fsl/bin:/Applications/freesurfer/mni/bin:/sw/bin:/opt/local/bin:/opt/local/sbin:/usr/local/fsl/bin:/opt/local/bin:/opt/local/sbin:/Applications/freesurfer/bin:/Applications/freesurfer/fsfast/bin:/Applications/freesurfer/tktools:/usr/local/fsl/bin:/Applications/freesurfer/mni/bin:/sw/bin:/usr/local/bin:/usr/bin:/bin:/usr/sbin:/sbin:/opt/X11/bin:/Users/laurenlebois/abin:/Users/laurenlebois/Programs_Misc:/Users/laurenlebois/scripts:/opt/local/bin:opt/local/sbin:/bin:/Applications/gedit.app/Contents/MacOS:/opt/local/bin:/opt/local/sbin:/Users/laurenlebois/osx:/usr/local/bin:/usr/local/bin:/usr/bin:/bin:/usr/sbin:/sbin:/opt/X11/bin:/Users/laurenlebois/abin:/Applications/mricron:/Applications/mricron/dcm2niix:/Applications/freesurfer:/Applications/R:/opt/X11/bin:/Users/laurenlebois/abin:/Users/laurenlebois/Programs_Misc:/Users/laurenlebois/scripts:/opt/local/bin:opt/local/sbin:/bin:/Applications/gedit.app/Contents/MacOS:/opt/local/bin:/opt/local/sbin:/Users/laurenlebois/osx:/usr/local/bin:/opt/local/bin:/opt/local/sbin:/usr/local/fsl/bin:/opt/local/bin:/opt/local/sbin:/Applications/freesurfer/bin:/Applications/freesurfer/fsfast/bin:/Applications/freesurfer/tktools:/usr/local/fsl/bin:/Applications/freesurfer/mni/bin:/sw/bin:/usr/local/bin:/usr/bin:/bin:/usr/sbin:/sbin:/opt/X11/bin:/Users/laurenlebois/abin:/Users/laurenlebois/Programs_Misc:/Users/laurenlebois/scripts:/opt/local/bin:opt/local/sbin:/bin:/Applications/gedit.app/Contents/MacOS:/opt/local/bin:/opt/local/sbin:/Users/laurenlebois/osx:/usr/local/bin:/usr/local/bin:/usr/bin:/bin:/usr/sbin:/sbin:/opt/X11/bin:/Users/laurenlebois/abin:/Applications/mricron:/Applications/mricron/dcm2niix:/Applications/freesurfer:/Applications/R:/opt/X11/bin:/Users/laurenlebois/abin:/Applications/mricron:/Applications/mricron/dcm2niix:/Applications/freesurfer:/Applications/R

PYTHONPATH = /usr/local/lib/python2.7/site-packages

R_LIBS = 
LD_LIBRARY_PATH = 
DYLD_LIBRARY_PATH (sub-shell) = /opt/X11/lib/flat_namespace
DYLD_FALLBACK_LIBRARY_PATH (sub-shell) = FSL_DIR           /usr/local/fsl

------------------------------ data checks -------------------------------
data dir : found AFNI_data6   under $HOME
           top history: ... [rickr]: updated FT_white.nii w/out 16 (brain stem)
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 : missing afni_handouts
atlas    : found TT_N27+tlrc  under .


------------------------------ OS specific -------------------------------
XQuartz version      : 2.7.11

which fink           : /sw/bin/fink
fink version         : Package manager version: 0.45.1
which brew           : /usr/local/bin/brew
brew version         : Homebrew 2.2.11
which port           : /opt/local/bin/port
port version         : Error: Current platform "darwin 18" does not match expected platform "darwin 14"

++ found 'brew' at /usr/local/bin/brew
++ 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 'csh'...
++ found evar DYLD_LIBRARY_PATH = /opt/X11/lib/flat_namespace

=========================  summary, please fix:  =========================
*  AFNI programs show FAILURE
*  insufficient data for AFNI bootcamp

Any advice greatly appreciated.
Best,
Lauren

6

Lauren, unfortunately I don’t know what caused the issue. Hopefully someone could help you soon.

7

Hi Gang & all,

No worries - I followed up with Rick over email. Here is a summary of our discoveries:

Rick recommended to first test the output of the following:

"This should fail, but still, what is the complete output of:
3dMVM -help

Also, what is the output from:
otool -L ~/abin/R_io.so
ls -l ~/abin/lib*.dylib

To some degree, you shouldn’t need fink unless, for example, you want to be able to run the uber_*.py programs that require PyQt4. But either way, I would expect R_io.so to find libjpeg.9.dylib from your abin. Let’s see what you say about the above commands."

These commands had the following output:

Here is the output of 3dMVM -help:

~ % 3dMVM -help
updating R_LD_LIBRARY_PATH …

oo Warning:
Failed to load R_io.so with this error message:

Error in dyn.load(ll) :
unable to load shared object ‘/Users/laurenlebois/abin/R_io.so’:
dlopen(/Users/laurenlebois/abin/R_io.so, 6): Library not loaded: /sw/lib/libjpeg.9.dylib
Referenced from: /Users/laurenlebois/abin/R_io.so
Reason: Incompatible library version: R_io.so requires version 12.0.0 or later, but libjpeg.9.dylib provides version 11.0.0
Calls: source … withVisible → eval → eval → set_R_io → dyn.load
Execution halted

Here is the output from the otool -L ~/abin/R_io.so :

~ % otool -L ~/abin/R_io.so
/Users/laurenlebois/abin/R_io.so:
R_io.so (compatibility version 0.0.0, current version 0.0.0)
/sw/Library/Frameworks/R.framework/Versions/3.3/Resources/lib/libR.dylib (compatibility version 3.3.0, current version 3.3.2)
/sw/lib/libjpeg.9.dylib (compatibility version 12.0.0, current version 12.0.0)
/sw/lib/libXt.6.dylib (compatibility version 7.0.0, current version 7.0.0)
/opt/X11/lib/libXft.2.dylib (compatibility version 6.0.0, current version 6.2.0)
/opt/X11/lib/libfontconfig.1.dylib (compatibility version 11.0.0, current version 11.2.0)
/opt/X11/lib/libpng16.16.dylib (compatibility version 43.0.0, current version 43.0.0)
/sw/lib/libiconv.2.dylib (compatibility version 8.0.0, current version 8.1.0)
/opt/X11/lib/libXmu.6.dylib (compatibility version 9.0.0, current version 9.0.0)
/opt/X11/lib/libXp.6.dylib (compatibility version 9.0.0, current version 9.0.0)
/opt/X11/lib/libXpm.4.dylib (compatibility version 16.0.0, current version 16.0.0)
/opt/X11/lib/libXext.6.dylib (compatibility version 11.0.0, current version 11.0.0)
/opt/X11/lib/libX11.6.dylib (compatibility version 10.0.0, current version 10.0.0)
/usr/lib/libz.1.dylib (compatibility version 1.0.0, current version 1.2.8)
/usr/lib/libexpat.1.dylib (compatibility version 7.0.0, current version 8.0.0)
/sw/lib/python2.7/config/libpython2.7.dylib (compatibility version 2.7.0, current version 2.7.0)
/usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version 1238.60.2)
/sw/lib/libintl.8.dylib (compatibility version 10.0.0, current version 10.5.0)
/System/Library/Frameworks/CoreFoundation.framework/Versions/A/CoreFoundation (compatibility version 150.0.0, current version 1349.8.0)
/sw/lib/gcc7/lib/libgcc_s.1.dylib (compatibility version 1.0.0, current version 1.0.0)

Here is the output from ls -l ~/abin/lib*.dylib :

~ % ls -l ~/abin/lib*.dylib
-rwxr-xr-x 1 laurenlebois staff 3035636 Mar 30 23:25 /Users/laurenlebois/abin/libXm.4.dylib
-rwxr-xr-x 1 laurenlebois staff 77656 Mar 30 23:25 /Users/laurenlebois/abin/libbz2.1.dylib
-rwxr-xr-x 1 laurenlebois staff 867420 Mar 30 23:25 /Users/laurenlebois/abin/libfreetype.6.dylib
-rw-r–r-- 1 laurenlebois staff 255712 Mar 30 23:25 /Users/laurenlebois/abin/libgcc_s.1.dylib
-rwxr-xr-x 1 laurenlebois staff 841172 Mar 30 23:25 /Users/laurenlebois/abin/libglib-2.0.0.dylib
-rwxr-xr-x 1 laurenlebois staff 257608 Mar 30 23:25 /Users/laurenlebois/abin/libgomp.1.dylib
-rwxr-xr-x 1 laurenlebois staff 2763820 Mar 30 23:25 /Users/laurenlebois/abin/libgsl.0.dylib
-rwxr-xr-x 1 laurenlebois staff 313404 Mar 30 23:25 /Users/laurenlebois/abin/libgslcblas.0.dylib
-rw-r–r-- 1 laurenlebois staff 1124448 Mar 30 23:25 /Users/laurenlebois/abin/libiconv.2.dylib
-rw-r–r-- 1 laurenlebois staff 46084 Mar 30 23:25 /Users/laurenlebois/abin/libintl.8.dylib
-rwxr-xr-x 1 laurenlebois staff 284432 Mar 30 23:25 /Users/laurenlebois/abin/libjpeg.9.dylib
-rwxr-xr-x 1 laurenlebois staff 253372 Mar 30 23:25 /Users/laurenlebois/abin/libpng16.16.dylib
-rwxr-xr-x 1 laurenlebois staff 2040952 Mar 30 23:25 /Users/laurenlebois/abin/libpython2.7.dylib

According to Rick, this revealed that:
“There is some aspect of this that is not working the way I would expect. Have R_LD_LIBRARY_PATH set, R_io.so should be finding libjpeg.9.dylib in your abin, yet it is complaining about the fink version.”

Recommended a test of this theory: “I would like you to temporarily rename your /sw directory, try the command again, and then change the sw name back. That will enable us to see how it behaves as if you did not have fink installed.”
sudo mv /sw /sw.rename
3dMVM -help
sudo mv /sw.rename /sw

This test showed that if I renamed my sw directory, R_io.so did appear to find libjpeg.9.dylib in my abin (3dMVM -help worked).

Rick said, that this means “R_LD_LIBRARY_PATH variable is not working the way it should (or at least not the way the name suggests it should)…This little aspect will make dealing with R more difficult for us. R_LD_LIBRARY_PATH suggests that our libraries get priority, but it seems it is more like LD_FALLBACK_LIBRARY_PATH, unfortunately.”

For the time being, I decided to keep my fink tree (/sw) renamed so I could successfully run 3dMVM, and since I don’t use the uber_* programs that require the fink tree.

8

Thanks for sharing the information, Laurent!