I've seen that error myself and am working out a solution.

The problem isn't an error in the package file, but rather the way that TeXShop (and possibly other GUI-based apps) uses the PATH variable. When 4.2 is installed over TL2016, the Gregorio 4.1 executable in /Library/TeX/texbin is left alone (by the current installer) and the 4.2 executable is placed in /usr/local/bin. This is okay from the command line because /usr/local/bin normally has priority over /Library/TeX/texbin. However, TeXShop specifically searches /Library/TeX/texbin first and thus ends up using the 4.1 executable.

On the other hand, the 4.2 TeX files have been placed in texmf-local, which has priority over texmf-dist (where the 4.1 files included in TL2016 live). Thus the lua code which calls the executable (and which attaches the filename suffix) is the 4.2 version, even though, due to the above issue the 4.1 executable is being used.

Thus far I've modified the installer so that the 4.1 executable is renamed to gregorio-41, allowing the above issue to be avoided (progress here: https://github.com/rpspringuel/gregorio/tree/install_over_2016). I've got a similar work around built into the Windows installer now too (the problem was slightly different over there, but the solution was basically the same). I still have to work out what to do for someone not using the package installer. At the very least I plan to expand the version checking we do when the package is loaded during document compilation to include the executable, raising an error/warning as appropriate. I might also add a install-exec-local rule to Makefile.am which will automate the file renaming, especially if I find the same error occurring in Linux (which I haven't tested yet).
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Br. Samuel, OSB
St. Anselm’s Abbey
Washington, DC
(R. Padraic Springuel)

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