Okay, so looking at the log I see several problems. The easiest way to fix them all is going to be to uninstall Gregorio and start from scratch. There are two ways to do this:

1) Grab and run the Uninstall-Gregorio.pkg from a 4.1 release on the website. The one on this page should work: https://github.com/gregorio-project/gregorio/releases/tag/v4.1.4

Once you've done that, re-run system-setup.command to check that the system is clean. A clean system will have at most 1 entry for each of the files in the GregorioTeX Locations section (some will have 0 entries because they're looking for files from previous versions which have been obsoleted, see the attached log file for an example of a clean result) and that entry will have `2016` somewhere in it. If this isn't the case, use Terminal to remove the remaining extra entries (`rm /url/local/texlive/path/to/file`). Depending on permission settings, you may need to sudo this. (You can't do this from Finder because these are system folders which are hidden from it.)

2) You can also do the entire process from Terminal if you like. Just remove all the entries which don't have `2016` in them and the binary at `/usr/local/bin/gregorio`. Again, use system-setup.command when done to check that the system is really clean.



As the final step to cleaning your system, delete the `/Users/Shared/Gregorio` folder (either from Terminal or Finder). We save this step for last because it's where system-setup.command lives and we want to be able to use that script to check and make sure our system is clean.


Once you have cleaned up your system, you'll need to decide if you want to use 4.1 or 4.2. 4.1 is included in TeXLive 2016, so simply updating that with tlmgr or TeXLive Utility (on Mac) should get you the latest 4.1.5 version.

If you want 4.2, then download it from the website and follow the installation instructions.

--
✝✝✝✝✝✝✝✝✝✝✝✝✝✝✝✝✝✝✝✝✝✝✝✝✝
Br. Samuel, OSB
St. Anselm’s Abbey
Washington, DC
(R. Padraic Springuel)

PAX ☧ ΧΡΙΣΤΟΣ
###     Gregorio Unix Setup Results
####    Created: Ven  4 nov 2016 11:00:31 CET
-----------------------------------------------------------------------------


###     OS Version
Darwin Kernel Version 15.6.0: Mon Aug 29 20:21:34 PDT 2016; 
root:xnu-3248.60.11~1/RELEASE_X86_64


-----------------------------------------------------------------------------


###     LuaTeX Setup
####    Version

This is LuaTeX, Version 0.95.0 (TeX Live 2016)

Execute  'luatex --credits'  for credits and version details.

There is NO warranty. Redistribution of this software is covered by
the terms of the GNU General Public License, version 2 or (at your option)
any later version. For more information about these matters, see the file
named COPYING and the LuaTeX source.

LuaTeX is Copyright 2016 Taco Hoekwater and the LuaTeX Team.


####    Location

/Library/TeX/texbin/luatex


####    TEXMFLOCAL

/usr/local/texlive/texmf-local

#### TEXINPUTS.lualatex
.:{/Users/frromain/Library/texlive/2016/texmf-config,/Users/frromain/Library/texlive/2016/texmf-var,/Users/frromain/Library/texmf,!!/usr/local/texlive/2016/texmf-config,!!/usr/local/texlive/2016/texmf-var,!!/usr/local/texlive/texmf-local,!!/usr/local/texlive/2016/texmf-dist}/tex/{lualatex,latex,luatex,generic,}//

#### LUAINPUTS.lualatex
.:{/Users/frromain/Library/texlive/2016/texmf-config,/Users/frromain/Library/texlive/2016/texmf-var,/Users/frromain/Library/texmf,!!/usr/local/texlive/2016/texmf-config,!!/usr/local/texlive/2016/texmf-var,!!/usr/local/texlive/texmf-local,!!/usr/local/texlive/2016/texmf-dist}/scripts/{kpsewhich,unsetengine,}/{lua,}//:{/Users/frromain/Library/texlive/2016/texmf-config,/Users/frromain/Library/texlive/2016/texmf-var,/Users/frromain/Library/texmf,!!/usr/local/texlive/2016/texmf-config,!!/usr/local/texlive/2016/texmf-var,!!/usr/local/texlive/texmf-local,!!/usr/local/texlive/2016/texmf-dist}/tex/{lualatex,latex,luatex,generic,}//

#### shell_escape
p

#### Shell Escape Commands
bibtex,bibtex8,extractbb,gregorio,kpsewhich,makeindex,mpost,repstopdf,

#### openout_any
p

#### openin_any
a


-----------------------------------------------------------------------------


###     Gregorio Setup
####    Version

Gregorio 4.1.1 (kpathsea version 6.2.2).
Copyright (C) 2006-2016 Gregorio project authors (see CONTRIBUTORS.md)
License GPLv3+: GNU GPL version 3 or later <http://gnu.org/licenses/gpl.html>
This is free software: you are free to change and redistribute it.
There is NO WARRANTY, to the extent permitted by law.
####    Location

/Library/TeX/texbin/gregorio

####    GregorioTeX Locations

##### gregorio-vowels.dat
/usr/local/texlive/2016/texmf-dist/tex/luatex/gregoriotex/gregorio-vowels.dat
##### gregoriosyms.sty
/usr/local/texlive/2016/texmf-dist/tex/lualatex/gregoriotex/gregoriosyms.sty
##### gregoriotex-chars.tex
/usr/local/texlive/2016/texmf-dist/tex/luatex/gregoriotex/gregoriotex-chars.tex
##### gregoriotex-main.tex
/usr/local/texlive/2016/texmf-dist/tex/luatex/gregoriotex/gregoriotex-main.tex
##### gregoriotex-ictus.tex
##### gregoriotex-nabc.lua
/usr/local/texlive/2016/texmf-dist/tex/luatex/gregoriotex/gregoriotex-nabc.lua
##### gregoriotex-nabc.tex
/usr/local/texlive/2016/texmf-dist/tex/luatex/gregoriotex/gregoriotex-nabc.tex
##### gregoriotex-signs.lua
/usr/local/texlive/2016/texmf-dist/tex/luatex/gregoriotex/gregoriotex-signs.lua
##### gregoriotex-signs.tex
/usr/local/texlive/2016/texmf-dist/tex/luatex/gregoriotex/gregoriotex-signs.tex
##### gregoriotex-spaces.tex
/usr/local/texlive/2016/texmf-dist/tex/luatex/gregoriotex/gregoriotex-spaces.tex
##### gregoriotex-syllable.tex
/usr/local/texlive/2016/texmf-dist/tex/luatex/gregoriotex/gregoriotex-syllable.tex
##### gregoriotex-symbols.lua
/usr/local/texlive/2016/texmf-dist/tex/luatex/gregoriotex/gregoriotex-symbols.lua
##### gregoriotex-symbols.tex
/usr/local/texlive/2016/texmf-dist/tex/luatex/gregoriotex/gregoriotex-symbols.tex
##### gregoriotex.lua
/usr/local/texlive/2016/texmf-dist/tex/luatex/gregoriotex/gregoriotex.lua
##### gregoriotex.sty
/usr/local/texlive/2016/texmf-dist/tex/lualatex/gregoriotex/gregoriotex.sty
##### gregoriotex.tex
/usr/local/texlive/2016/texmf-dist/tex/luatex/gregoriotex/gregoriotex.tex
##### gsp-default.tex
/usr/local/texlive/2016/texmf-dist/tex/luatex/gregoriotex/gsp-default.tex
##### greciliae.ttf
/usr/local/texlive/2016/texmf-dist/fonts/truetype/public/gregoriotex/greciliae.ttf
##### greciliae-op.ttf
/usr/local/texlive/2016/texmf-dist/fonts/truetype/public/gregoriotex/greciliae-op.ttf
##### greextra.ttf
/usr/local/texlive/2016/texmf-dist/fonts/truetype/public/gregoriotex/greextra.ttf
##### gregorio.ttf
/usr/local/texlive/2016/texmf-dist/fonts/truetype/public/gregoriotex/gregorio.ttf
##### gregorio-op.ttf
/usr/local/texlive/2016/texmf-dist/fonts/truetype/public/gregoriotex/gregorio-op.ttf
##### gresym.ttf
##### parmesan.ttf
##### parmesan-op.ttf
##### gregall.ttf
/usr/local/texlive/2016/texmf-dist/fonts/truetype/public/gregoriotex/gregall.ttf
##### gregsmodern.ttf

####    kpsewhich --all -engine luatex -progname lualatex gregoriotex.sty
/usr/local/texlive/2016/texmf-dist/tex/lualatex/gregoriotex/gregoriotex.sty

####    kpsewhich --all -engine luatex gregoriotex.tex
/usr/local/texlive/2016/texmf-dist/tex/luatex/gregoriotex/gregoriotex.tex


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