Re: [Bioc-devel] What should I do if I need to ask my package to be deprecated?

[Kern, Lori]

Thank you for letting us know. I will begin the deprecation process for the 
package.

Cheers

Get Outlook for iOS

From: Bioc-devel  on behalf of Kozo Nishida 

Sent: Thursday, February 25, 2021 5:00:18 PM
To: bioc-devel@r-project.org 
Subject: [Bioc-devel] What should I do if I need to ask my package to be 
deprecated?

Hello,

Can I ask my package MSEADbi to be deprecated?
https://secure-web.cisco.com/1k5L1s41pbEp75fIRd4yxYx_PXFvf0mnOmvT3o9wrlyM2u5K44MTwvZGR0ecC7aq0qlIhu2AOJZyW4xgaE8jQnyQFkVh_kJsvSxYvel4QuHY523awMKvXW6CCCo8nBb9fq_MYZlzjRlk6SK92nT_HB7FjV8XW_dhTSBVr-DMOa09kbkuF8-DpnsC98vX0m3ayjN9RQE7996hI5PD4Bvx8IhqzOL3N269jq5Bp1Z1IeaiFrRsAfaMnEMJLHkG1be7quWjcFCY6al6VYsPY5nqvK3M7QezQVHaf1Mpvj-ynzXbmjBGXLApvVDT9y1SZ84Wa/https%3A%2F%2Fbioconductor.org%2Fpackages%2Frelease%2Fbioc%2Fhtml%2FMSEADbi.html

I have developed an alternative (AnnotationHub) package to MSEADbi
(called AHPathbankDbs
https://secure-web.cisco.com/1ZVXn-bPXajcvw-mLAqfJ-0ANAP2YqH2SByLRfbYC_R26MiFH9X5qZZOdIQEiTD8NgdStmAZI-b4r1H4hikpzJ3LOdqJzn1VzLplVuSh7aytveMf3wqkrPHO4_ADXEQRk477wrwYopoaagBJRvBS-E2t89EEW5vUKL17VPRY8lIwjOQunZ0X9N7v1pmSyT0iLovKRbFWH8mYTJ1z8X0vbV97D5dMFYwYxw61J-fYMBaiFjBz8is-OrnN78jO202GmKTer1Bls-Ee_DTf9ICQlVFEL6qsXEgiMeoK0AdVl4JUvX9ao7tnkuh5oTT8ZuBZ8/https%3A%2F%2Fgithub.com%2FBioconductor%2FContributions%2Fissues%2F1825
 )
So the MSEADbi package will not be maintained.

MSEADbi is not AnnotationHub package and the implementation style
is not up to date.
I was unaware of the existence of the AnnotationHub package
when I developed MSEADbi.

What kind of procedure should I take in such a case?


Thanks,
Kozo Nishida

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recipient(s), you are hereby notified that any disclosure, copying, 
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[Bioc-devel] What should I do if I need to ask my package to be deprecated?

[Kozo Nishida]

Hello,

Can I ask my package MSEADbi to be deprecated?
https://bioconductor.org/packages/release/bioc/html/MSEADbi.html

I have developed an alternative (AnnotationHub) package to MSEADbi
(called AHPathbankDbs
https://github.com/Bioconductor/Contributions/issues/1825 )
So the MSEADbi package will not be maintained.

MSEADbi is not AnnotationHub package and the implementation style
is not up to date.
I was unaware of the existence of the AnnotationHub package
when I developed MSEADbi.

What kind of procedure should I take in such a case?


Thanks,
Kozo Nishida

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[Bioc-devel] Please change maintainer of chipenrich and chipenrich.data packages

[Raymond Cavalcante]

Hello,

Could we please change the maintainer of the chipenrich and chipenrich.data
packages to Kai Wang (wangd...@umich.edu)? I have instructed the new
maintainer to setup an account at https://support.bioconductor.org/, and
I'll change the DESCRIPTION files shortly. Are there any other steps?

FWIW, at this page
https://bioconductor.org/developers/how-to/git/change-maintainer/ there is
a reference to maintai...@bioconductor.org. This was the first addressed I
tried, but got various bounce backs. Perhaps the change maintainer page
should be updated?

Thanks,
Raymond Cavalcante


Raymond Cavalcante, PhD
Bioinformatics Analyst
Epigenomics Core and Bioinformatics Core
Biomedical Research Core Facilities
University of Michigan Medical School

rcava...@umich.edu
rcava...@med.umich.edu

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Re: [Bioc-devel] Rsync to Bioconductor

[Henrik Bengtsson]

FYI, I just sent an email to 'maintai...@bioconductor.org' regarding
this but it bounced with the below errors (I've truncated your
address):

From: Mail Delivery System 
Date: Thu, Feb 25, 2021 at 12:39 PM
Subject: Undelivered Mail Returned to Sender
To: ...


This is the mail system at host delivery.bioconductor.org.

I'm sorry to have to inform you that your message could not
be delivered to one or more recipients. It's attached below.

For further assistance, please send mail to postmaster.

If you do so, please include this problem report. You can
delete your own text from the attached returned message.

   The mail system

: host mx1.roswellpark.iphmx.com[68.232.137.170]
said: 550 #5.7.1 Your access to submit messages to this e-mail system has
been rejected. (in reply to DATA command)

: host mx1.roswellpark.iphmx.com[68.232.137.170]
said: 550 #5.7.1 Your access to submit messages to this e-mail system has
been rejected. (in reply to DATA command)

: host
mx1.roswellpark.iphmx.com[68.232.137.170] said: 550 #5.7.1 Your access to
submit messages to this e-mail system has been rejected. (in reply to DATA
command)

: host mx1.roswellpark.iphmx.com[68.232.137.170]
said: 550 #5.7.1 Your access to submit messages to this e-mail system has
been rejected. (in reply to DATA command)

/Henrik

On Wed, Feb 24, 2021 at 8:03 AM Kern, Lori
 wrote:
>
> In the next few weeks we will be limiting the ability to rsync to 
> Bioconductor resources.  If you currently are using rsync please reach out to 
> maintai...@bioconductor.org as we will need additional information to 
> continue to allow rsync on your machines.
>
> Cheers,
>
>
> Lori Shepherd
>
> Bioconductor Core Team
>
> Roswell Park Comprehensive Cancer Center
>
> Department of Biostatistics & Bioinformatics
>
> Elm & Carlton Streets
>
> Buffalo, New York 14263
>
>
> 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.
> [[alternative HTML version deleted]]
>
> ___
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Re: [Bioc-devel] EXTERNAL: Re: Encountering Issues with Github sync

[Marcel Ramos]

Hi Krithika,

Regarding Step #10:

It is a good idea to have a release branch checkout in your GitHub 
(origin) repository
in case you need to commit bug fixes to that branch:

http://bioconductor.org/developers/how-to/git/bug-fix-in-release-and-devel/ 


Best,

Marcel

On 2/25/21 3:02 PM, Krithika Bhuvaneshwar wrote:
> Thank you for catching that !  That was very helpful
>
> I have now completed Steps# 1 - 7 and Step # 9 from here:
> *http://bioconductor.org/developers/how-to/git/sync-existing-repositories/
> 
> *(I think Step # 8 does not apply to me)
>
> I don't exactly understand what Step # 10 is. Is this what I should do , or
> can I skip this ? Please advise.
>
>
> *10. Repeat for the release branch, replacing master with the name of the
> release branch, e.g., RELEASE_3_6. It may be necessary to create the
> release branch in the local repository.*
>
> git checkout RELEASE_13_3
>   git merge upstream/RELEASE_13_3
>   git merge origin/RELEASE_13_3
>   git push upstream RELEASE_13_3
>   git push origin RELEASE_13_3
>
>
> Thanks,
> Krithika
>
>
>
> On Thu, Feb 25, 2021 at 12:33 PM Martin Morgan 
> wrote:
>
>> The Bioconductor remote should not include 'ICBI,
>>
>>  git remote remove upstream
>>  git remote add upstream g...@git.bioconductor.org:packages/CINdex.git
>>
>> On 2/25/21, 11:40 AM, "Bioc-devel on behalf of Krithika Bhuvaneshwar" <
>> bioc-devel-boun...@r-project.org on behalf of kb...@georgetown.edu> wrote:
>>
>>  Hello,
>>
>>  We are the package maintaines for the CINdex package.  We have made
>> changes
>>  in our package to address the build errors for the upcoming release.
>> The
>>  latest code is here in our Gtithub account *
>> https://github.com/ICBI/CINdex
>>    . *I'm trying to sync it with the
>> BioC
>>  Github repo, but encountering errors. Would appreciate some help
>>
>>  These are the steps I did:
>>
>>  1) Updated code so that there are no build errors. Updated version
>>  information in DESCRIPTION File (changed from 1.19.0 to 1.19.1). The
>> latest
>>  code is here in our Gtithub account *https://github.com/ICBI/CINdex
>>   *
>>
>>  2)  I generated new ssh keys , and then added the ssh information from
>> my
>>  *id_rsa.pub* file in this link.
>>  https://git.bioconductor.org/BiocCredentials/account_activation/
>>
>>  3) I'm currently following the steps mentioned here:
>>  bioconductor.org/developers/how-to/git/sync-existing-repositories/.
>> *I have
>>  an error when I try git fetch*
>>
>>  #Configure the “remotes” of the GitHub clone. --- completed step
>>  git remote add upstream g...@git.bioconductor.org:
>> packages/ICBI/CINdex.git
>>
>>  $ git remote -v
>>  origin https://github.com/ICBI/CINdex (fetch)
>>  origin https://github.com/ICBI/CINdex (push)
>>  upstream g...@git.bioconductor.org:packages/ICBI/CINdex.git (fetch)
>>  upstream g...@git.bioconductor.org:packages/ICBI/CINdex.git (push)
>>
>>  $ git fetch --all
>>  Fetching origin
>>  Fetching upstream
>>  FATAL: R any packages/ICBI/CINdex k.bhuvaneshwar DENIED by fallthru
>>  (or you mis-spelled the reponame)
>>  fatal: Could not read from remote repository.
>>
>>  Please make sure you have the correct access rights
>>  and the repository exists.
>>  error: Could not fetch upstream
>>
>>  Thanks,
>>  Krithika
>>  kb...@georgetown.edu
>>
>>  [[alternative HTML version deleted]]
>>
>>  ___
>>  Bioc-devel@r-project.org mailing list
>>  https://stat.ethz.ch/mailman/listinfo/bioc-devel
>>
>   [[alternative HTML version deleted]]
>
> ___
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---
Marcel Ramos
Bioconductor Core Team
Roswell Park Comprehensive Cancer Center
Dept. of Biostatistics & Bioinformatics
Elm St. & Carlton St.
Buffalo, New York 14263



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Re: [Bioc-devel] Encountering Issues with Github sync

[Krithika Bhuvaneshwar]

Thank you for catching that !  That was very helpful

I have now completed Steps# 1 - 7 and Step # 9 from here:
*http://bioconductor.org/developers/how-to/git/sync-existing-repositories/

*(I think Step # 8 does not apply to me)

I don't exactly understand what Step # 10 is. Is this what I should do , or
can I skip this ? Please advise.


*10. Repeat for the release branch, replacing master with the name of the
release branch, e.g., RELEASE_3_6. It may be necessary to create the
release branch in the local repository.*

git checkout RELEASE_13_3
 git merge upstream/RELEASE_13_3
 git merge origin/RELEASE_13_3
 git push upstream RELEASE_13_3
 git push origin RELEASE_13_3


Thanks,
Krithika



On Thu, Feb 25, 2021 at 12:33 PM Martin Morgan 
wrote:

> The Bioconductor remote should not include 'ICBI,
>
> git remote remove upstream
> git remote add upstream g...@git.bioconductor.org:packages/CINdex.git
>
> On 2/25/21, 11:40 AM, "Bioc-devel on behalf of Krithika Bhuvaneshwar" <
> bioc-devel-boun...@r-project.org on behalf of kb...@georgetown.edu> wrote:
>
> Hello,
>
> We are the package maintaines for the CINdex package.  We have made
> changes
> in our package to address the build errors for the upcoming release.
> The
> latest code is here in our Gtithub account *
> https://github.com/ICBI/CINdex
>   . *I'm trying to sync it with the
> BioC
> Github repo, but encountering errors. Would appreciate some help
>
> These are the steps I did:
>
> 1) Updated code so that there are no build errors. Updated version
> information in DESCRIPTION File (changed from 1.19.0 to 1.19.1). The
> latest
> code is here in our Gtithub account *https://github.com/ICBI/CINdex
>  *
>
> 2)  I generated new ssh keys , and then added the ssh information from
> my
> *id_rsa.pub* file in this link.
> https://git.bioconductor.org/BiocCredentials/account_activation/
>
> 3) I'm currently following the steps mentioned here:
> bioconductor.org/developers/how-to/git/sync-existing-repositories/.
> *I have
> an error when I try git fetch*
>
> #Configure the “remotes” of the GitHub clone. --- completed step
> git remote add upstream g...@git.bioconductor.org:
> packages/ICBI/CINdex.git
>
> $ git remote -v
> origin https://github.com/ICBI/CINdex (fetch)
> origin https://github.com/ICBI/CINdex (push)
> upstream g...@git.bioconductor.org:packages/ICBI/CINdex.git (fetch)
> upstream g...@git.bioconductor.org:packages/ICBI/CINdex.git (push)
>
> $ git fetch --all
> Fetching origin
> Fetching upstream
> FATAL: R any packages/ICBI/CINdex k.bhuvaneshwar DENIED by fallthru
> (or you mis-spelled the reponame)
> fatal: Could not read from remote repository.
>
> Please make sure you have the correct access rights
> and the repository exists.
> error: Could not fetch upstream
>
> Thanks,
> Krithika
> kb...@georgetown.edu
>
> [[alternative HTML version deleted]]
>
> ___
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> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>

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Re: [Bioc-devel] Encountering Issues with Github sync

[Martin Morgan]

The Bioconductor remote should not include 'ICBI,

git remote remove upstream
git remote add upstream g...@git.bioconductor.org:packages/CINdex.git

On 2/25/21, 11:40 AM, "Bioc-devel on behalf of Krithika Bhuvaneshwar" 
 wrote:

Hello,

We are the package maintaines for the CINdex package.  We have made changes
in our package to address the build errors for the upcoming release. The
latest code is here in our Gtithub account *https://github.com/ICBI/CINdex
  . *I'm trying to sync it with the BioC
Github repo, but encountering errors. Would appreciate some help

These are the steps I did:

1) Updated code so that there are no build errors. Updated version
information in DESCRIPTION File (changed from 1.19.0 to 1.19.1). The latest
code is here in our Gtithub account *https://github.com/ICBI/CINdex
 *

2)  I generated new ssh keys , and then added the ssh information from my
*id_rsa.pub* file in this link.
https://git.bioconductor.org/BiocCredentials/account_activation/

3) I'm currently following the steps mentioned here:
bioconductor.org/developers/how-to/git/sync-existing-repositories/. *I have
an error when I try git fetch*

#Configure the “remotes” of the GitHub clone. --- completed step
git remote add upstream g...@git.bioconductor.org:packages/ICBI/CINdex.git

$ git remote -v
origin https://github.com/ICBI/CINdex (fetch)
origin https://github.com/ICBI/CINdex (push)
upstream g...@git.bioconductor.org:packages/ICBI/CINdex.git (fetch)
upstream g...@git.bioconductor.org:packages/ICBI/CINdex.git (push)

$ git fetch --all
Fetching origin
Fetching upstream
FATAL: R any packages/ICBI/CINdex k.bhuvaneshwar DENIED by fallthru
(or you mis-spelled the reponame)
fatal: Could not read from remote repository.

Please make sure you have the correct access rights
and the repository exists.
error: Could not fetch upstream

Thanks,
Krithika
kb...@georgetown.edu

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[Bioc-devel] Encountering Issues with Github sync

[Krithika Bhuvaneshwar]

Hello,

We are the package maintaines for the CINdex package.  We have made changes
in our package to address the build errors for the upcoming release. The
latest code is here in our Gtithub account *https://github.com/ICBI/CINdex
  . *I'm trying to sync it with the BioC
Github repo, but encountering errors. Would appreciate some help

These are the steps I did:

1) Updated code so that there are no build errors. Updated version
information in DESCRIPTION File (changed from 1.19.0 to 1.19.1). The latest
code is here in our Gtithub account *https://github.com/ICBI/CINdex
 *

2)  I generated new ssh keys , and then added the ssh information from my
*id_rsa.pub* file in this link.
https://git.bioconductor.org/BiocCredentials/account_activation/

3) I'm currently following the steps mentioned here:
bioconductor.org/developers/how-to/git/sync-existing-repositories/. *I have
an error when I try git fetch*

#Configure the “remotes” of the GitHub clone. --- completed step
git remote add upstream g...@git.bioconductor.org:packages/ICBI/CINdex.git

$ git remote -v
origin https://github.com/ICBI/CINdex (fetch)
origin https://github.com/ICBI/CINdex (push)
upstream g...@git.bioconductor.org:packages/ICBI/CINdex.git (fetch)
upstream g...@git.bioconductor.org:packages/ICBI/CINdex.git (push)

$ git fetch --all
Fetching origin
Fetching upstream
FATAL: R any packages/ICBI/CINdex k.bhuvaneshwar DENIED by fallthru
(or you mis-spelled the reponame)
fatal: Could not read from remote repository.

Please make sure you have the correct access rights
and the repository exists.
error: Could not fetch upstream

Thanks,
Krithika
kb...@georgetown.edu

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Re: [Bioc-devel] Bioconductor 3.13 release date

[Martin Morgan]

This information has not yet been determined. Usually we try to sync with R, 
especially in the spring when there is a new, rather than patch, release of R. 
R has not announced when their release is (see 
https://developer.r-project.org/), so we haven't started our own release 
process. Likely it will be toward the end of April -- historical dates are at 
https://bioconductor.org/about/release-announcements/. 

Martin

On 2/25/21, 6:52 AM, "Bioc-devel on behalf of Fabricio de Almeida" 
 wrote:

Hi all,

I will submit a package to Bioconductor in the next few days, but I would 
like to know the submission deadline for my package to be included in the next 
Bioc release.

Last year, new Bioconductor versions were released on April 28 and October 
28. What about this year? I searched it everywhere, but didn't find the answer.

Best,


=


Fabr�cio de Almeida Silva

Undergraduate degree in Biological Sciences (UENF)

MSc. candidate in Plant Biotechnology (PGBV/UENF - RJ/Brazil)

Laborat�rio de Qu�mica e Fun��o de Prote�nas e Pept�deos (LQFPP/CBB/UENF - 
RJ/Brazil)

Lattes CNPq: http://lattes.cnpq.br/3119358824056108

Personal website: https://almeidasilvaf.github.io/almeida-silvaf/

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[Bioc-devel] Bioconductor 3.13 release date

[Fabricio de Almeida]

Hi all,

I will submit a package to Bioconductor in the next few days, but I would like 
to know the submission deadline for my package to be included in the next Bioc 
release.

Last year, new Bioconductor versions were released on April 28 and October 28. 
What about this year? I searched it everywhere, but didn't find the answer.

Best,


=


Fabr�cio de Almeida Silva

Undergraduate degree in Biological Sciences (UENF)

MSc. candidate in Plant Biotechnology (PGBV/UENF - RJ/Brazil)

Laborat�rio de Qu�mica e Fun��o de Prote�nas e Pept�deos (LQFPP/CBB/UENF - 
RJ/Brazil)

Lattes CNPq: http://lattes.cnpq.br/3119358824056108

Personal website: https://almeidasilvaf.github.io/almeida-silvaf/

[[alternative HTML version deleted]]

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