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-boun...@r-project.org on behalf of christopher.ee...@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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