Current Solution as of <2022-03-02 Wed>. The solution only works on doom emacs only, I found that pdf-tools must be install with init.el. I had (package! pdf-tools) and :tools pdf. Dependencies conflict is caused by endable pdf-tools two different ways as shown. I solved the problem by remove (package! pdf-tools) from packages.el and only keep :tools pdf. Abit of backstory, I first encounter the problem at a very early stage of using doom emacs (first 2 weeks.