[Bioc-devel] Package Submission Limbo

[Martin Morgan]

Sorry that your packages have not been reviewed more promptly.

We try to have an initial review in two weeks, how long a full review takes depends on many factors, including complexity of the review process. Your own packages were I believe handled relatively efficiently initially. The release at the end of April) is a major activity for us, and necessarily slows the overall process down.

We are exploring processes to reduce the reviewer burden so that packages like yours are added to Bioconductor more promptly; a major concern is to do so in a manner that does not compromise the overall quality of accepted packages.

Martin

On 5/30/20, 4:52 PM, "Bioc-devel on behalf of Chris Eeles" <bioc-devel-bounces using r-project.org on behalf of christopher.eeles using outlook.com> wrote:

    Hello Bioconductor team and community,

    My name is Christopher Eeles and I am a software developer in the Benjamin Haibe-Kains laboratory at Princess Margaret Cancer Research Centre in Toronto, Ontario, Canada.

    I am concerned due to inaction on the part of my reviewer for two of my package submissions, and am not sure how to move forward.

    Initially, I submitted three packages - CoreGx, ToxicoGx and RadioGx - on April 4th, 2020 hoping to get included in the May Bioconductor release. It became apparent that approval would not be possible in time, as such I requested to expedite acceptance of CoreGx (on which the latter two packages depend) so it could be included. My reviewer obliged and I am thankful for that.

    I was told to resubmit ToxicoGx and RadioGx on separate issues and that the review process would continue from where it was for the resubmissions. This occurred on April 25th, 2020. Before resubmission I had replied to a round of reviewer comments and was waiting for a reply before making more changes.

    However, since resubmission I have received no further reviewer comments and no reply to my code updates since the last review. RadioGx will be a part of a workshop our lab is putting together for Bioconductor conference in July, but without acceptance of the package it will have to be installed from GitHub.

    Additionally, ToxicoGx is the package that was used to curate data for our web application, ToxicoDB, which has been accepted to the NAR web server edition. We had assumed that the package would be accepted by now and have had criticism from our NAR reviewers about it's lack of availability. Both of these packages were available on CRAN before our submission to Bioconductor.

    My question is, how do I move forward? Without response from my reviewer I do not know which conditions I need to meet for package acceptance? I am available to respond to criticism.

    Initial submission of these packages occurred almost 2 months ago, and it has been over a month since the resubmissions. Is this normal? Are there extenuating circumstances of which I am unaware?

    Our lab put a lot of time and effort into these packages and wish to share them with the Bioconductor community. Does anyone have advice on what I can do to get the ball rolling again?

    Thanks for your assistance.

    Best,
    ---
    Christopher Eeles
    Software Developer
    BHK Laboratory<http://www.bhklab.ca/>
    Princess Margaret Cancer Centre<https://www.pmgenomics.ca/pmgenomics/>
    University Health Network<http://www.uhn.ca/>




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