[Bioc-devel] Question

[Michael Lawrence]

Another concern with kent utils (as opposed to kent lib) is the
non-open-source licensing.

Michael

On Sat, Aug 18, 2018 at 10:11 AM, Tim Triche, Jr. <tim.triche using gmail.com> wrote:
> Vince beat me to it. Don’t use Kent utils unless you have to. If you have something like a bigBed parser, I could perhaps help clean it up. But if you’re doing anything that could possibly be done in Rsamtools or rtracklayer, I would join Vince in urging you to use their functions. You will have less maintenance burden if you do.
>
> This list exists in part to keep package developers from immiserating themselves through misplaced enthusiasm 😉
>
> --t
>
>> On Aug 18, 2018, at 12:46 PM, Vincent Carey <stvjc using channing.harvard.edu> wrote:
>>
>>> On Sat, Aug 18, 2018 at 12:17 PM, Ghiwa Khalil <gk39 using aub.edu.lb> wrote:
>>>
>>> Hello,
>>>
>>> We are writing a package with 2 main functions, one of these functions
>>> requires kent utils to be installed.
>>>
>>> Since kent utils is supported by only specific operating systems, is it
>>> recommended to have it in an R package?
>>>
>>> If we remove this function then our package will only be based on one
>>> function, we are not sure if it is clever to submit a package with one
>>> function. We were thinking to keep the function based on kent utils and
>>> consider it as an option for users able to use it.
>>>
>>>
>>> Any thoughts on this issue?
>>>
>>
>> It is best to have packages that run on all platforms.  The number of
>> functions
>> in a package is not an important determinant of usefulness.
>>
>> What exactly do you require from the "kent utils"?  Have you checked
>> rtracklayer
>> for relevant functionality?
>>
>> You would get best guidance if you identified a github repo where your
>> package is being developed.  If you are concerned about exposure, you can
>> invite a developer as a confidential evaluator/consultant.  I would be
>> willing
>> to play this role if necessary.
>>
>> Sincerely,
>> Vincent Carey
>>
>>>
>>>
>>> Thank you.
>>>
>>> Regards
>>>
>>>        [[alternative HTML version deleted]]
>>>
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>>>
>>
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>>
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