Following acknowledgement by the editor in chief, submissions are considered by the executive editors. Some will be rejected without review as insufficiently relevant for our readership, or of too poor technical quality, for example submissions not following the author guidelines. There are also many resources indicating how package authors may improve their code, for example Bioconductor notes for developers.
If the submission is considered worth sending for review, a handling editor is assigned, and reviewers are identified, invited, and begin work on assessing the submission. When their reports are available, the handling editor may decide to reject, to consult a rejection decision with other editors, to ask for revisions based on the reviews, or to accept. This reviewing process may iterate several times before submissions are either rejected or accepted. If revised submissions are not received within three months of the corresponding author being asked to make revisions, the submission may be considered withdrawn by the editors and rejected.
Accepted articles appear online in order of processing. The handling editor and editor in chief may ask for technical or other revisions to the files making up the submission before it appears online. It is important to keep the LaTeX files as simple as possible, and markup instructions in the author guidelines must be followed.
When an issue is to be published, the stock of accepted articles is split among all the editors for proof reading and copy-editing. We are not able to help with language issues, so authors must be prepared to find help themselves if necessary. It is important to follow the requirements in the proofreading checklist when responding to the copy editor, who will not be the same editor as your handling editor. It is also important to work quickly and carefully, as inadequate responsiveness will lead to articles being left online only without an issue number and issue page numbers, or in extremity acceptance may be withdrawn and the article rejected as technically inadequate.