Code dependencies and operational dependencies
Drew DeVault recently wrote Dependencies and maintainers, which I will summarize as both suggesting that dependencies should be minimized and being a call to become involved in your dependencies. I have various thoughts on this general issue (cf), but perhaps I have an unusual perspective as someone who is primarily a system administrator instead of a developer. As part of that perspective, I think it's useful to think about two sorts of dependencies, what I will call code dependencies and operational dependencies.
Code dependencies are the Python modules, Go packages (or modules these days), Rust crates, C libraries, Node packages, or whatever in your language that you choose to use or that get pulled in as indirect dependencies. You can keep track of at least your direct code dependencies (you're setting them up, after all), and hopefully you can trace through them to find indirect ones. If there are too many indirect dependencies and levels of indirection, this may be a sign (Drew DeVault would likely suggest that you take it as a bad one).
Operational dependencies are everything that you need to operate and even build your program and your system. If you have a web site, for example, your web server is at least an operation dependency. Everyone has an operational dependency on their operating system's kernel, and often on many other operating system components. People using interpreted languages (Ruby, Python, Node, etc) have an operational dependency on the language interpreter; people compiling programs have an operational dependency on GCC, clang/LLVM, the Rust compiler, the Go compiler, and so on. Operational dependencies have internal code dependencies, making you transitively dependent on them too. If you operate a web server that does HTTPS, whether Apache or nginx, it probably has a code dependency on some SSL library, most likely OpenSSL, making OpenSSL an indirect operational dependency for you.
Things can be both code dependencies and operational dependencies, because they're directly used by you and also used by other systems that you need. Some things are so commonly used and so much a part of the 'platform' that you'll likely consider them operational dependencies instead of code dependencies even if they're directly incorporated into your programs; the most significant example of this is your system's C library and, on Unix systems, the runtime dynamic linker.
(System administrators are often quite conscious of operational dependencies because much of our job is managing them. Other people can often assume that they are just there and work.)