Unable to reproduce Catalyst.jl Example

Most of the packages you are using are among the more popular / longer developed Julia libraries which someone who knows the broader Julia ecosystem would have heard of (and which typically get updated regularly). Most of them are also dependencies of various SciML libraries (or are SciML libraries themselves).

Looking at your list the only other that isn’t a more popular library is GraphViz.jl. It is then relatively straightforward for one to go look at the Project.toml for GraphViz.jl and PerceptualColourMaps.jl and see if it is dated and upper bounding the compatibility of its dependencies. One immediate issue with PerceptualColourMaps is that it uses ranges for compatibility, which means it is declaring an upper bound on the versions of its dependencies that it works with. That usually leads to problems if a package is not regularly updated since many Julia packages, especially SciML packages, release updates and bug fixes on a regular basis.

In the case of Catalyst, version 13 was a breaking change that simplified how one declares a reaction network, and hence your only installing older versions meant the current notation wasn’t supported (and you were looking at the current docs for examples instead of the docs for the version you had installed).