Submitting a paper based on another yet unpublished paper I am in computer science. I am currently working on an applied paper that is based on a certain algorithm, let's call it method A.

Method A has been explained deeply in a my previous paper, that now is under review. So it is in arxiv, anybody can read it, but it has not yet being published on a peer review journal or conference.

I am now going to submit the applied paper to a conference, and I have a doubt: even if the results are interesting, how affected are the chances of being accepted for the applied paper, by the fact hat Method A has not yet been reviewed/published?
This should not be a problem. The reviewers of the conference paper should focus on the application you treat, but since the paper is available as a preprint, they could also have a closer look at the method if they want to.