Re: [Bioc-devel] Missed deadline

[Gabe Becker]

Kenneth,

I agree with Kasper. I generally like the approach of getting the software
out there sooner rather than later. Especially if the paper you are talking
about is a method paper about the software algorithm, rather than a result
paper. In that case, getting it into a public, DOI'ed repository quickly
protects you from being scooped (if that is a concern of yours, it's
generally not a super large one of mine).

This will also give the community and package reviewers a chance to give
you feedback, resulting in the paper being written about a better piece of
software when it does happen. Just like manuscripts, no (ok, *vanishingly
few *but almost surely not yours or mine) software is perfect after its
first development pass, so i'd strongly advise you not to think of your
software as 'complete' the moment you hit submit. Consider it an important
part of the development process.

Best,
~G

On Wed, Apr 4, 2018 at 4:34 AM, Kasper Daniel Hansen <
kasperdanielhan...@gmail.com> wrote:

> This is a subjective question. As a paper reviewer I like to see the
> package accepted. That increases trust.  As a package reviewer I like some
> idea of what the package actually does, so a statement like "we implement X
> which is described in (XX, in preparation), is also irritating.
>
> Unless you're trying to not show anything prior to publication (which
> happens) I like submitting the package first.
>
> On Wed, Apr 4, 2018 at 12:31 PM, Kenneth Condon 
> wrote:
>
>> Hi Gabe & Levi,
>>
>> Here is my current plan:
>>
>> 1 - complete the requirements checklist (
>> http://www.bioconductor.org/developers/package-submission/)
>> 2 - get feedback the in-house NGS team, and then from the rest of in-house
>> bioinformatics (others who use R more may spot some issues)
>> 3 - set up pull requests release on github for community testing
>> 4 - advertise github repo on bioconductor and biostars forums
>> 5 - compare to other packages
>> 6 - write paper (decide which journal)
>> 7 - have submission of paper + package ready for October deadline.
>>
>> Regarding the sequence of events - do other authors usually release on
>> bioconductor before submission of a paper or at the same time?
>> What would you recommend?
>>
>> Thanks for the help
>>
>> Kenneth
>>
>> On Tue, Apr 3, 2018 at 4:56 PM, Gabe Becker  wrote:
>>
>> > Indeed, and to be a bit more explicit about Levi's point, you *can*
>> > publish your package to bioconductor any time after the deadline, it
>> will
>> > simply go to the development repo for ~6 months, which, as he points
>> out,
>> > may not be a bad thing if it's not ready yet.
>> >
>> > On Tue, Apr 3, 2018 at 8:06 AM, Levi Waldron <
>> lwaldron.resea...@gmail.com>
>> > wrote:
>> >
>> >> On Tue, Apr 3, 2018 at 5:32 AM, Kenneth Condon 
>> >> wrote:
>> >>
>> >> > Have I missed the deadline for the latest release? I have created a
>> >> > package, that runs great but there are a number of errors still from
>> R
>> >> CMD
>> >> > check that I am sorting out.
>> >> >
>> >> > This is my first R package so I'm not sure if development is far
>> enough
>> >> > along, although I suspect it might be.
>> >> >
>> >>
>> >> IMHO, when you're not sure a package is mature enough, and especially
>> for
>> >> a
>> >> first package, it's actually better to miss the release deadline and
>> allow
>> >> bioc-devel users test your package for 6 months before entering the
>> >> release
>> >> cycle. Making significant bug fixes and other changes becomes more
>> >> complicated and more of a pain for you and your users once you are in
>> the
>> >> release...
>> >>
>> >> [[alternative HTML version deleted]]
>> >>
>> >> ___
>> >> Bioc-devel@r-project.org mailing list
>> >> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>> >>
>> >>
>> >
>> >
>> > --
>> > Gabriel Becker, Ph.D
>> > Scientist
>> > Bioinformatics and Computational Biology
>> > Genentech Research
>> >
>>
>> [[alternative HTML version deleted]]
>>
>> ___
>> Bioc-devel@r-project.org mailing list
>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>>
>
>


-- 
Gabriel Becker, Ph.D
Scientist
Bioinformatics and Computational Biology
Genentech Research

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Re: [Bioc-devel] Missed deadline

[Kasper Daniel Hansen]

This is a subjective question. As a paper reviewer I like to see the
package accepted. That increases trust.  As a package reviewer I like some
idea of what the package actually does, so a statement like "we implement X
which is described in (XX, in preparation), is also irritating.

Unless you're trying to not show anything prior to publication (which
happens) I like submitting the package first.

On Wed, Apr 4, 2018 at 12:31 PM, Kenneth Condon 
wrote:

> Hi Gabe & Levi,
>
> Here is my current plan:
>
> 1 - complete the requirements checklist (
> http://www.bioconductor.org/developers/package-submission/)
> 2 - get feedback the in-house NGS team, and then from the rest of in-house
> bioinformatics (others who use R more may spot some issues)
> 3 - set up pull requests release on github for community testing
> 4 - advertise github repo on bioconductor and biostars forums
> 5 - compare to other packages
> 6 - write paper (decide which journal)
> 7 - have submission of paper + package ready for October deadline.
>
> Regarding the sequence of events - do other authors usually release on
> bioconductor before submission of a paper or at the same time?
> What would you recommend?
>
> Thanks for the help
>
> Kenneth
>
> On Tue, Apr 3, 2018 at 4:56 PM, Gabe Becker  wrote:
>
> > Indeed, and to be a bit more explicit about Levi's point, you *can*
> > publish your package to bioconductor any time after the deadline, it will
> > simply go to the development repo for ~6 months, which, as he points out,
> > may not be a bad thing if it's not ready yet.
> >
> > On Tue, Apr 3, 2018 at 8:06 AM, Levi Waldron <
> lwaldron.resea...@gmail.com>
> > wrote:
> >
> >> On Tue, Apr 3, 2018 at 5:32 AM, Kenneth Condon 
> >> wrote:
> >>
> >> > Have I missed the deadline for the latest release? I have created a
> >> > package, that runs great but there are a number of errors still from R
> >> CMD
> >> > check that I am sorting out.
> >> >
> >> > This is my first R package so I'm not sure if development is far
> enough
> >> > along, although I suspect it might be.
> >> >
> >>
> >> IMHO, when you're not sure a package is mature enough, and especially
> for
> >> a
> >> first package, it's actually better to miss the release deadline and
> allow
> >> bioc-devel users test your package for 6 months before entering the
> >> release
> >> cycle. Making significant bug fixes and other changes becomes more
> >> complicated and more of a pain for you and your users once you are in
> the
> >> release...
> >>
> >> [[alternative HTML version deleted]]
> >>
> >> ___
> >> Bioc-devel@r-project.org mailing list
> >> https://stat.ethz.ch/mailman/listinfo/bioc-devel
> >>
> >>
> >
> >
> > --
> > Gabriel Becker, Ph.D
> > Scientist
> > Bioinformatics and Computational Biology
> > Genentech Research
> >
>
> [[alternative HTML version deleted]]
>
> ___
> Bioc-devel@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>

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Re: [Bioc-devel] Missed deadline

[Kenneth Condon]

Hi Gabe & Levi,

Here is my current plan:

1 - complete the requirements checklist (
http://www.bioconductor.org/developers/package-submission/)
2 - get feedback the in-house NGS team, and then from the rest of in-house
bioinformatics (others who use R more may spot some issues)
3 - set up pull requests release on github for community testing
4 - advertise github repo on bioconductor and biostars forums
5 - compare to other packages
6 - write paper (decide which journal)
7 - have submission of paper + package ready for October deadline.

Regarding the sequence of events - do other authors usually release on
bioconductor before submission of a paper or at the same time?
What would you recommend?

Thanks for the help

Kenneth

On Tue, Apr 3, 2018 at 4:56 PM, Gabe Becker  wrote:

> Indeed, and to be a bit more explicit about Levi's point, you *can*
> publish your package to bioconductor any time after the deadline, it will
> simply go to the development repo for ~6 months, which, as he points out,
> may not be a bad thing if it's not ready yet.
>
> On Tue, Apr 3, 2018 at 8:06 AM, Levi Waldron 
> wrote:
>
>> On Tue, Apr 3, 2018 at 5:32 AM, Kenneth Condon 
>> wrote:
>>
>> > Have I missed the deadline for the latest release? I have created a
>> > package, that runs great but there are a number of errors still from R
>> CMD
>> > check that I am sorting out.
>> >
>> > This is my first R package so I'm not sure if development is far enough
>> > along, although I suspect it might be.
>> >
>>
>> IMHO, when you're not sure a package is mature enough, and especially for
>> a
>> first package, it's actually better to miss the release deadline and allow
>> bioc-devel users test your package for 6 months before entering the
>> release
>> cycle. Making significant bug fixes and other changes becomes more
>> complicated and more of a pain for you and your users once you are in the
>> release...
>>
>> [[alternative HTML version deleted]]
>>
>> ___
>> Bioc-devel@r-project.org mailing list
>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>>
>>
>
>
> --
> Gabriel Becker, Ph.D
> Scientist
> Bioinformatics and Computational Biology
> Genentech Research
>

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Re: [Bioc-devel] Missed deadline

[Levi Waldron]

ONE more note that Gabe reminded me of! As soon as your package is accepted
into bioc-devel, it will be accessible via
https://bioconductor.org/packages/mypackage/. Once it enters the release
branch, that URL will instead point to the release page.

On Tue, Apr 3, 2018 at 11:56 AM, Gabe Becker  wrote:

> Indeed, and to be a bit more explicit about Levi's point, you *can*
> publish your package to bioconductor any time after the deadline, it will
> simply go to the development repo for ~6 months, which, as he points out,
> may not be a bad thing if it's not ready yet.
>
> On Tue, Apr 3, 2018 at 8:06 AM, Levi Waldron 
> wrote:
>
>> On Tue, Apr 3, 2018 at 5:32 AM, Kenneth Condon 
>> wrote:
>>
>> > Have I missed the deadline for the latest release? I have created a
>> > package, that runs great but there are a number of errors still from R
>> CMD
>> > check that I am sorting out.
>> >
>> > This is my first R package so I'm not sure if development is far enough
>> > along, although I suspect it might be.
>> >
>>
>> IMHO, when you're not sure a package is mature enough, and especially for
>> a
>> first package, it's actually better to miss the release deadline and allow
>> bioc-devel users test your package for 6 months before entering the
>> release
>> cycle. Making significant bug fixes and other changes becomes more
>> complicated and more of a pain for you and your users once you are in the
>> release...
>>
>> [[alternative HTML version deleted]]
>>
>> ___
>> Bioc-devel@r-project.org mailing list
>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>>
>>
>
>
> --
> Gabriel Becker, Ph.D
> Scientist
> Bioinformatics and Computational Biology
> Genentech Research
>



-- 
Levi Waldron
http://www.waldronlab.org
Assistant Professor of Biostatistics CUNY School of Public Health
US: +1 646-364-9616   Skype:
levi.waldron

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Re: [Bioc-devel] Missed deadline

[Gabe Becker]

Indeed, and to be a bit more explicit about Levi's point, you *can* publish
your package to bioconductor any time after the deadline, it will simply go
to the development repo for ~6 months, which, as he points out, may not be
a bad thing if it's not ready yet.

On Tue, Apr 3, 2018 at 8:06 AM, Levi Waldron 
wrote:

> On Tue, Apr 3, 2018 at 5:32 AM, Kenneth Condon 
> wrote:
>
> > Have I missed the deadline for the latest release? I have created a
> > package, that runs great but there are a number of errors still from R
> CMD
> > check that I am sorting out.
> >
> > This is my first R package so I'm not sure if development is far enough
> > along, although I suspect it might be.
> >
>
> IMHO, when you're not sure a package is mature enough, and especially for a
> first package, it's actually better to miss the release deadline and allow
> bioc-devel users test your package for 6 months before entering the release
> cycle. Making significant bug fixes and other changes becomes more
> complicated and more of a pain for you and your users once you are in the
> release...
>
> [[alternative HTML version deleted]]
>
> ___
> Bioc-devel@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>
>


-- 
Gabriel Becker, Ph.D
Scientist
Bioinformatics and Computational Biology
Genentech Research

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Re: [Bioc-devel] Missed deadline

[Levi Waldron]

On Tue, Apr 3, 2018 at 5:32 AM, Kenneth Condon 
wrote:

> Have I missed the deadline for the latest release? I have created a
> package, that runs great but there are a number of errors still from R CMD
> check that I am sorting out.
>
> This is my first R package so I'm not sure if development is far enough
> along, although I suspect it might be.
>

IMHO, when you're not sure a package is mature enough, and especially for a
first package, it's actually better to miss the release deadline and allow
bioc-devel users test your package for 6 months before entering the release
cycle. Making significant bug fixes and other changes becomes more
complicated and more of a pain for you and your users once you are in the
release...

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Re: [Bioc-devel] Missed deadline

[Shepherd, Lori]

The deadline to submit new packages for this release was yesterday.  You could 
still submit the package for review but there is no guarantee it will make it 
through the review process in time to be included as reviewers will focus on 
packages that made the deadline.  The last day for the newly submitted packages 
to not only build and check without any WARNING or ERRORS but also to go 
through the official review and be accepted is two weeks away.  Beyond that, 
packages accepted after this date will be included in the release later this 
year.


Lori Shepherd

Bioconductor Core Team

Roswell Park Cancer Institute

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263


From: Bioc-devel <bioc-devel-boun...@r-project.org> on behalf of Kenneth Condon 
<roonysga...@gmail.com>
Sent: Tuesday, April 3, 2018 5:32:28 AM
To: bioc-devel@r-project.org
Cc: roonysga...@gmail.com
Subject: [Bioc-devel] Missed deadline

Hello,

Have I missed the deadline for the latest release? I have created a
package, that runs great but there are a number of errors still from R CMD
check that I am sorting out.

This is my first R package so I'm not sure if development is far enough
along, although I suspect it might be.

Could someone advise me please

Regards,
Kenneth

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[Bioc-devel] Missed deadline

[Kenneth Condon]

Hello,

Have I missed the deadline for the latest release? I have created a
package, that runs great but there are a number of errors still from R CMD
check that I am sorting out.

This is my first R package so I'm not sure if development is far enough
along, although I suspect it might be.

Could someone advise me please

Regards,
Kenneth

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