LaTeX Warning: Citation undefined

It works for me after running

pdflatex file
bibtex file
pdflatex file
pdflatex file

I removed the ./ from the bibliography style as it is not installed in the current directory.

I saved the bibliography entry you posted as ref.bib in the current directory, and the code below as file.tex

\documentclass[a4paper,11pt]{article}
\usepackage[T1]{fontenc}
\usepackage[utf8]{inputenc}
\usepackage{lmodern}
\usepackage[hidelinks]{hyperref} % Hyperref package for url's and [hidelinks] option to remove collouring

\title{Test}
\author{Thanos}

\begin{document}

\maketitle
\tableofcontents

\begin{abstract}
  This is abstract
\end{abstract}

\section{Section 1}

Referecnce example~\cite{ref:thanos}

\bibliographystyle{IEEEtran}
\bibliography{ref}

\end{document}

David Carlisle's answer is very thorough, but I recently faced the same situation when I was working on a second paper, and wanted it to have the same format as my first paper. I copied over the .cls file, the .tex file and the .bib file and received the exact same error as OP.

LaTeX Warning: Citationref:thanos' on page 1 undefined on input line 21.

Following the previous answer's steps I was unable to resolve my issue. Turns out that in order to solve my problem I also needed to copy over the .bst file from my first paper's folder or the bibliography style file. Copying over the .bst file, I was able to resolve my issue.

I've recently experienced the same problem when typing my PhD thesis.

It has a master file and all the chapters and etc. are added with \input command.

Recently to speed up the compilation time, I started using \includeonly. I did not have this error until I replaced \input with \include to add the chapters. Then, I realized that \chapterbib is suitable to work with \include not with \input. So, when I was using \input, \chapterbib was idle and I never needed it because I print the bibliography at the end of the thesis, not separately for each chapter.

Long story short, I deactivated \chapterbib and it started to work normally again. Hope this can help to the ones experiencing the same difficulty.