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
>> 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
> about what they are doing. They do in some ways 'confuse' the
> the package author to know that the 'assignee' is the official
> are the people commenting on the package providing a consistent
> 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
> of assigned reviewer. I'd suggest you identify package(s) that
> interesting to you, and send email to me. I'll arrange for you to
> the assigned reviewer, and provide basic instructions and
> the future, you will be able to take on a package more directly.
>
> From the formal review process, incremental additional comments
> 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
> should more or less set out a contract -- do these things and your
> will meet reviewer requirements for inclusion in Bioconductor.
> it harder / more time consuming to review the package, because
> only the one chance to identify the most important points. Also,
> to follow through and confirm that yes, the appropriate changes
>
> It will be interesting to adjust the public review process, especially
> after the next release. For instance, one approach I like is to
> review with editable check boxes, with the package author editing the
> review with information about commits, etc, that satisfy the
> expressed. I don't really like the canned check-list in the joss
> mentions; they point to important areas but seem too generic 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
>>> have
>>> some amount of packages submitted in the last moment (and I am
>>> one of these). Is help with the reviews needed? If so, how do
>>> where to concentrate?
>>>
>>> Kasper
>>>
>>> [[alternative HTML version deleted]]
>>>
>>> _______________________________________________
>>> Bioc-devel at r-project.org <mailto:Bioc-devel at r-project.org>
>>
>> _______________________________________________
>> Bioc-devel at r-project.org <mailto:Bioc-devel at r-project.org>
>
> This email message may contain legally privileged
>
>
> _______________________________________________
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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
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