[Bioc-devel] package review help
Martin Morgan
martin.morgan at roswellpark.org
Sat Oct 1 11:51:00 CEST 2016
On 09/30/2016 11:44 PM, Robert M. Flight wrote:
> Regarding Cytoscape, at least, I know RCytoscape and categoryCompare use
> active Cytoscape sessions during vignette builds, but the build
> maintainers need to know about it. I also don't know if the review
> builds would have access to that.
Yes, this is one of those cases where the additional infrastructure to
support an active Cytoscape session adds complexity to the
administration of the build system. Looking forward, I don't think new
packages should rely on this kind of service during package build and
check. Rather, the package should check for appropriate pre-conditions
to the functions that they implement. This is a challenge for all
heavily visual applications.
Martin
>
> Robert
>
>
> On Fri, Sep 30, 2016, 9:53 PM Vincent Carey <stvjc at channing.harvard.edu
> <mailto:stvjc at channing.harvard.edu>> wrote:
>
> i would have comments on StarTrek. if you would like me to be
> reviewer of
> that i can do it.
>
> a query on policy
>
> how do you propose to handle needlessly repeated code?
>
> the code given below is repeated many many times with slight
> variations for
> selected KEGG_path. i would ask the author
> to implement DRY (don't repeat yourself), find a functional approach
> to the
> repeated element, and
> simplify. i can imagine that damping enthusiasm of the contributor
> but I
> think it is worth holding back
> until such a thing is accomplished. too meddlesome?
>
> if (KEGG_path=="Carb_met") {
> pathways.list <- keggList("pathway", "hsa")## returns the list of human
> pathways
> mer<-select_path_carb(Carbohydrate)
> common<-intersect(pathways.list,mer)
> lo<-list()
> for (i in 1:length(pathways.list)){
> if (length(intersect(pathways.list[[i]],common)!=0)){
> lo[[i]]<-pathways.list[[i]]
> names(lo)[[i]]<-names(pathways.list)[[i]]
> }
> }
> pathways.list<-lo[lapply(lo,length)!=0]
> pathway.codes <- sub("path:", "", names(pathways.list))
> a<-do.call("rbind", pathways.list)
> }
>
> Another issue the author seems to raise is the need for "open cytoscape
> session" for meaningful tests.
> I think this will never happen on the build system. So the author
> has to
> emulate the cytoscape behavior
> perhaps with some static objects that cytoscape might return on
> interaction.
>
>
>
> On Fri, Sep 30, 2016 at 5:22 PM, Martin Morgan <
> martin.morgan at roswellpark.org
> <mailto:martin.morgan at roswellpark.org>> wrote:
>
> > On 09/30/2016 12:05 PM, Michael Lawrence wrote:
> >
> >> I have been chipping in here and there, but I'm not sure if I'm
> >> causing more confusion than help. I just select packages that
> interest
> >> me and contribute bite size pieces, but I would be happy to assume a
> >> more formal role. It takes very little of my time.
> >>
> >> One suggestion is that reviews should be incremental, i.e., provide
> >> obvious feedback first, let the package authors respond, then dig
> >> deeper for more detailed comments.
> >>
> >
> > Michael, I've found your comments / reviews really helpful. They are
> > generally on-target and constructive, and help spur the authors to
> think
> > about what they are doing. They do in some ways 'confuse' the
> issue (how is
> > the package author to know that the 'assignee' is the official
> reviewer?
> > are the people commenting on the package providing a consistent
> message?),
> > but definitely a plus. I encourage others to participate in the public
> > review process in this way, too.
> >
> > It would be great to hear from people who would like to take on
> the role
> > of assigned reviewer. I'd suggest you identify package(s) that
> would be
> > interesting to you, and send email to me. I'll arrange for you to
> become
> > the assigned reviewer, and provide basic instructions and
> guidelines. In
> > the future, you will be able to take on a package more directly.
> >
> > From the formal review process, incremental additional comments
> are not a
> > good way to go, because the package author can feel like they are on a
> > never-ending treadmill of requirements. Instead I think the formal
> review
> > should more or less set out a contract -- do these things and your
> package
> > will meet reviewer requirements for inclusion in Bioconductor.
> This makes
> > it harder / more time consuming to review the package, because
> there is
> > only the one chance to identify the most important points. Also,
> one needs
> > to follow through and confirm that yes, the appropriate changes
> were made.
> >
> > It will be interesting to adjust the public review process, especially
> > after the next release. For instance, one approach I like is to
> provide a
> > review with editable check boxes, with the package author editing the
> > review with information about commits, etc, that satisfy the
> concerns being
> > expressed. I don't really like the canned check-list in the joss
> link Tim
> > mentions; they point to important areas but seem too generic to
> lead to
> > constructive changes to individual packages.
> >
> > Martin
> >
> >
> >> Michael
> >>
> >> On Fri, Sep 30, 2016 at 8:49 AM, Kasper Daniel Hansen
> >> <kasperdanielhansen at gmail.com
> <mailto:kasperdanielhansen at gmail.com>> wrote:
> >>
> >>> One of the advantages of the Github review process is open
> review. We
> >>> have
> >>> some amount of packages submitted in the last moment (and I am
> guilty of
> >>> one of these). Is help with the reviews needed? If so, how do
> we know
> >>> where to concentrate?
> >>>
> >>> Kasper
> >>>
> >>> [[alternative HTML version deleted]]
> >>>
> >>> _______________________________________________
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> >>>
> >>
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> >>
> >>
> >
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> >
> > _______________________________________________
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>
>
>
> --
>
> Vincent J. Carey, Ph.D.
> Professor of Medicine
> Channing Division of Network Medicine
> Brigham and Women's Hospital
> Harvard Medical School
> 181 Longwood Avenue
> Boston, MA 02115 USA
>
> [[alternative HTML version deleted]]
>
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