It doesn’t reproduce for me (MacOS installation from relocatable application bundle):
$ cat test.yaml
key: "E5410"
$ swipl
Welcome to SWI-Prolog (threaded, 64 bits, version 9.1.17)
SWI-Prolog comes with ABSOLUTELY NO WARRANTY. This is free software.
Please run ?- license. for legal details.
For online help and background, visit https://www.swi-prolog.org
For built-in help, use ?- help(Topic). or ?- apropos(Word).
?- yaml_read("test.yaml", T).
T = yaml{key:"E5410"}.
You should at least include the SWI-Prolog version and OS if you report a bug. You should also report if you have a non-default configuration.
The R solution to this (since there are endless ways to configure and botch your R environment) is the command-line option --vanilla:
--vanilla
Combine --no-save, --no-restore, --no-site-file, --no-init-file and --no-environ
I couldn’t find one single flag to do this in SWI-Prolog.
This is (AFAIK) an old bug. Get the 9.1.17 series. Not sure whether it is patched in 9.0.4.
The version 9.1.17 indicates a hash if it is not compiled from a tagged git version and DIRTY if some file is different from the git repo. To disable extensions, use
swipl -f none --no-packs ...
The first disables your ~/.config/swi-prolog/init.pl (or the OS alternative) and the second does not attach your extension packs. This stuff was first of all added to prevent user extensions messing up building from source