Re: [Bioc-devel] Problems pushing to release version of package

[Russell Bainer]

Thank you very much!

My apologies to Lori for missing her email.

-R

On Wed, Oct 19, 2022 at 2:09 PM Steve Lianoglou 
wrote:

> Howdy,
>
> On Wed, Oct 19, 2022 at 1:55 PM Russell Bainer 
> wrote:
>
>> Hi Everyone,
>>
>> I am trying to update an error in the release version of my package, but
>> after following the instructions here:
>>
>>
>> https://contributions.bioconductor.org/git-version-control.html#sync-existing-repositories
>>
>> I am unable to push upstream:
>>
>>  git push upstream RELEASE_3_15
>> > Warning: remote port forwarding failed for listen port 52698
>>
>
> As of 2 days ago (Lori sent an email out then), the 3_15 branch is frozen,
> so I'm guessing this is what you're tripping up on. You can now only push
> to master in prep for the 3.16 release.
>
> -steve
>
>

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[Bioc-devel] Problems pushing to release version of package

[Russell Bainer]

Hi Everyone,

I am trying to update an error in the release version of my package, but
after following the instructions here:

https://contributions.bioconductor.org/git-version-control.html#sync-existing-repositories

I am unable to push upstream:

 git push upstream RELEASE_3_15
> Warning: remote port forwarding failed for listen port 52698
> Enumerating objects: 32, done.
> Counting objects: 100% (27/27), done.
> Delta compression using up to 8 threads
> Compressing objects: 100% (14/14), done.
> Writing objects: 100% (14/14), 1.31 KiB | 1.31 MiB/s, done.
> Total 14 (delta 11), reused 0 (delta 0), pack-reused 0
> remote: FATAL: W refs/heads/RELEASE_3_15 packages/gCrisprTools r.bainer
> DENIED by fallthru
> remote: error: hook declined to update refs/heads/RELEASE_3_15
> To git.bioconductor.org:packages/gCrisprTools.git
>  ! [remote rejected] RELEASE_3_15 -> RELEASE_3_15 (hook declined)


Can anyone advise on what I am doing wrong here? Sorry if this solution is
well known but I'm following Nitesh's recommendation
to someone who was
experiencing something similar.

Many Thanks,

-R

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Re: [Bioc-devel] Best practices for joint release/update of BioC packages

[Russell Bainer]

Steve, I'll not have you malign my collaborators like that. :)

Thanks Nitesh for your clear and sensible suggestions. As Steve has surely
had time to speak the name of Webster lake by now, I'll plan to leave
things as-is and will coordinate with him about sparrow's acceptance status
to make sure that gCrisprTools continues to play nice with the final
version.

Best,

-R

On Wed, Aug 25, 2021 at 9:01 AM Steve Lianoglou 
wrote:

> Hello friends,
>
> I'm the derelict collaborator :-)
>
> I'll be submitting my package faster than you can (correctly) pronounce
> Lake Chargoggagoggmanchauggagoggchaubunagungamaugg
> https://en.wikipedia.org/wiki/Lake_Chaubunagungamaug
>
> -steve
>
>
> On Wed, Aug 25, 2021 at 8:48 AM Nitesh Turaga 
> wrote:
>
>> Hi Russell,
>>
>> The deprecation usually occurs around the time of release (October 2021,
>> but I don't have an exact date yet).
>>
>> If your collaborator has submitted the package to Bioconductor or CRAN,
>> and it gets accepted, and you can make everything build and check cleanly
>> before the release time, I think you should be ok. It might mean that he
>> submits the package 'sparrow' soon for review.
>>
>> The best way to do this (IMHO) is, wait for your collaborator's code to
>> get into Bioconductor/CRAN and plan the major release around that. If it
>> happens after this release, then do a major version update for the next
>> release cycle (April 2022 - approx). This will add all the significant
>> updates in your package only in the major version update to 2.0.0. In the
>> meantime, you may consider fixing/hiding parts of the code why are failing
>> for October 2021 release.
>>
>> Another "non-traditional" way is to add your collaborator as an Author on
>> your package and ingest parts that improve your package significantly as
>> code within your package. So this will attribute the authorship of the code
>> to your collaborator appropriately. Of course, this will not allow for
>> modular and independent development of two separate packages adding a lot
>> of complexity. (We should not consider this method for the sake of good
>> software engineering practices)
>>
>> I’m hoping other members on the team / community can provide better
>> suggestions.
>>
>> Best,
>>
>>
>> Nitesh Turaga
>> Scientist II, Department of Data Science,
>> Bioconductor Core Team Member
>> Dana Farber Cancer Institute
>>
>> > On Aug 24, 2021, at 7:07 PM, Russell Bainer 
>> wrote:
>> >
>> > Hello All,
>> >
>> > I am planning a major update to my BioC package in the next release (
>> >
>> https://www.bioconductor.org/packages/release/bioc/html/gCrisprTools.html
>> ),
>> > and some of the new functionality depends on another package that is
>> being
>> > submitted for acceptance by a collaborator.
>> >
>> > All of the code in my package passes R/BioC check using the package in
>> my
>> > collaborator's github repo, but as his code has not yet been
>> incorporated
>> > into BioC my current build is failing.
>> >
>> > What is the recommended way to deal with a situation like this?
>> Obviously I
>> > want to avoid deprecation of my own package, and obviously I could just
>> > hide all of the parts of the update that depend on external code. But I
>> > also think that my collaborator's work adds significantly to the
>> utility of
>> > my package, and I want to ensure that their contributions are properly
>> > highlighted/celebrated in my 2.0 release.
>> >
>> > Thanks in advance for the input.
>> >
>> > -R
>> >
>> >   [[alternative HTML version deleted]]
>> >
>> > ___
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>>
>> ___
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>>
>

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[Bioc-devel] Best practices for joint release/update of BioC packages

[Russell Bainer]

Hello All,

I am planning a major update to my BioC package in the next release (
https://www.bioconductor.org/packages/release/bioc/html/gCrisprTools.html),
and some of the new functionality depends on another package that is being
submitted for acceptance by a collaborator.

All of the code in my package passes R/BioC check using the package in my
collaborator's github repo, but as his code has not yet been incorporated
into BioC my current build is failing.

What is the recommended way to deal with a situation like this? Obviously I
want to avoid deprecation of my own package, and obviously I could just
hide all of the parts of the update that depend on external code. But I
also think that my collaborator's work adds significantly to the utility of
my package, and I want to ensure that their contributions are properly
highlighted/celebrated in my 2.0 release.

Thanks in advance for the input.

-R

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Re: [Bioc-devel] Change associated email/github

[Russell Bainer]

Thanks very much for the response. Can you recommend a way to do password
recovery? I no longer have access to the registered email address, and I'm
afraid that I registered long enough ago that I don't have the password
that I used.


On Tue, Mar 17, 2020 at 2:05 PM Turaga, Nitesh <
nitesh.tur...@roswellpark.org> wrote:

> Hi,
>
> There are a couple of things you'd have to do,
>
> 1. In the BiocCredentials app, you'd have to change your email address
> registered. And update your SSH keys if needed, add your personal Github ID
> as well.
>
> 2. In the DESCRIPTION file of the package, you'd have to change your email
> address to reflect where you'll be able to receive emails as a maintainer.
>
> 3. Update your email address on Bioc-devel mailing list if it is not
> already registered.
>
> Best,
>
> Nitesh
>
> > On Mar 17, 2020, at 1:34 PM, Russell Bainer 
> wrote:
> >
> > I'd like to change the email address associated with my
> > Bioconductor account, and also update the ownership of my packages to my
> > personal Github account (I originally registered both of these with my
> > employer, and I have since left the company). Could you please direct me
> to
> > documentation that will help me do this?
> >
> > Thanks very much
> >
> > -R
> >
> >   [[alternative HTML version deleted]]
> >
> > ___
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>
>
>
> This email message may contain legally privileged and/or confidential
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> agent responsible for the delivery of this message to the intended
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> received this message in error, please notify the sender immediately by
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>

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[Bioc-devel] Change associated email/github

[Russell Bainer]

I'd like to change the email address associated with my
Bioconductor account, and also update the ownership of my packages to my
personal Github account (I originally registered both of these with my
employer, and I have since left the company). Could you please direct me to
documentation that will help me do this?

Thanks very much

-R

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Re: [Bioc-devel] transfer maintainer status of gCrisprTools

[Russell Bainer]

Great, thanks!

-R

On Tue, Nov 26, 2019 at 1:07 PM Turaga, Nitesh <
nitesh.tur...@roswellpark.org> wrote:

> Hi,
>
> You should be able to access your package once you activate your
> BiocCredentials account and activate it.
>
> Best
>
> Nitesh
>
> > On Nov 26, 2019, at 3:54 PM, Russell Bainer 
> wrote:
> >
> > Hello Nitesh,
> >
> > Please associate it with russ.bai...@gmail.com.
> >
> > Thanks very much. I think that I will also need to associate my github
> account (RussBainer), but i see that there is a FAQ about that and will
> contact you in due course if I'm not able to access it.
> >
> > Best Regards,
> >
> > -Russ
> >
> > On Tue, Nov 26, 2019 at 12:09 PM Turaga, Nitesh <
> nitesh.tur...@roswellpark.org> wrote:
> > Hi,
> >
> > Which email would Russ like to use as his email account with
> BiocCredentials?
> >
> > Best,
> >
> > Nitesh
> >
> > > On Nov 22, 2019, at 5:11 PM, Peter Haverty <
> peterhave...@ucdavis-alumni.com> wrote:
> > >
> > > I'd like to transfer gCrisprTools to Russ Bainer (
> russ.bai...@gmail.com,
> > > rbai...@mazetx.com). How do I do that?
> > >
> > >   [[alternative HTML version deleted]]
> > >
> > > ___
> > > Bioc-devel@r-project.org mailing list
> > > https://stat.ethz.ch/mailman/listinfo/bioc-devel
> >
> >
> >
> > This email message may contain legally privileged and/or confidential
> information.  If you are not the intended recipient(s), or the employee or
> agent responsible for the delivery of this message to the intended
> recipient(s), you are hereby notified that any disclosure, copying,
> distribution, or use of this email message is prohibited.  If you have
> received this message in error, please notify the sender immediately by
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>
>
>
> This email message may contain legally privileged and/or confidential
> information.  If you are not the intended recipient(s), or the employee or
> agent responsible for the delivery of this message to the intended
> recipient(s), you are hereby notified that any disclosure, copying,
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> received this message in error, please notify the sender immediately by
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>

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Re: [Bioc-devel] transfer maintainer status of gCrisprTools

[Russell Bainer]

Hello Nitesh,

Please associate it with russ.bai...@gmail.com.

Thanks very much. I think that I will also need to associate my github
account (RussBainer), but i see that there is a FAQ about that and will
contact you in due course if I'm not able to access it.

Best Regards,

-Russ

On Tue, Nov 26, 2019 at 12:09 PM Turaga, Nitesh <
nitesh.tur...@roswellpark.org> wrote:

> Hi,
>
> Which email would Russ like to use as his email account with
> BiocCredentials?
>
> Best,
>
> Nitesh
>
> > On Nov 22, 2019, at 5:11 PM, Peter Haverty <
> peterhave...@ucdavis-alumni.com> wrote:
> >
> > I'd like to transfer gCrisprTools to Russ Bainer (russ.bai...@gmail.com,
> > rbai...@mazetx.com). How do I do that?
> >
> >   [[alternative HTML version deleted]]
> >
> > ___
> > Bioc-devel@r-project.org mailing list
> > https://stat.ethz.ch/mailman/listinfo/bioc-devel
>
>
>
> This email message may contain legally privileged and/or confidential
> information.  If you are not the intended recipient(s), or the employee or
> agent responsible for the delivery of this message to the intended
> recipient(s), you are hereby notified that any disclosure, copying,
> distribution, or use of this email message is prohibited.  If you have
> received this message in error, please notify the sender immediately by
> e-mail and delete this email message from your computer. Thank you.
>

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