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.