We are happy to announce that we can finally answer the question on how to cite mlr properly in publications.
Our paper on mlr has been published in the open-access Journal of Machine Learning Research (JMLR) and can be downloaded on the journal home page.
The paper gives a brief overview of the features of mlr and also includes a comparison with similar toolkits.
For an in-depth understanding we still recommend our excellent online mlr tutorial which is now also available as a PDF on arxiv.org or as zipped HTML files for offline reading.
Once mlr 2.10 hits CRAN you can retrieve the citation information from within R: