Re: [Bioc-devel] monocle package on Bioconductor

[Nitesh Turaga]

Hi,

As the error message says, there is a version number issue. You can only bump 
the ‘patch’ version i.e x.y.z -> x.y.z+1.

You cannot bump the “minor” version number. 

> http://bioconductor.org/developers/how-to/version-numbering/

Please send these questions to bioc-d...@r-project.org, where there is a 
community to help you.


Best,

Nitesh Turaga
Scientist II, Department of Data Science,
Bioconductor Core Team Member
Dana Farber Cancer Institute

"I don’t expect you to respond to my email outside your work hours"





> On Jun 7, 2022, at 7:17 PM, Brent G Ewing  wrote:
> 
> Hi Nitesh,
> 
> You helped me to fix a problem with the monocle package about a year ago. I 
> fixed another problem recently and I appear to have created a mess with the 
> version in the DESCRIPTION file, which prevents me from pushing the change to 
> the Bioconductor git repository.
> 
> I have looked at the online information for Bioconductor package 
> submitters/maintainers and I find myself confused.
> 
> The error that the repository returns is
> 
> $ git push origin master
> Enter passphrase for key '/home/brent/.ssh/id_rsa': 
> X11 forwarding request failed on channel 0
> Enumerating objects: 14, done.
> Counting objects: 100% (14/14), done.
> Delta compression using up to 4 threads
> Compressing objects: 100% (9/9), done.
> Writing objects: 100% (9/9), 777 bytes | 777.00 KiB/s, done.
> Total 9 (delta 6), reused 0 (delta 0), pack-reused 0
> remote: Error: Illegal version bump from '2.25.0' to '2.26.0'.
> remote: 
> remote: Check http://bioconductor.org/developers/how-to/version-numbering/
> remote: for details.
> remote: 
> To git.bioconductor.org:packages/monocle
>  ! [remote rejected] master -> master (pre-receive hook declined)
> error: failed to push some refs to 'git.bioconductor.org:packages/monocle'
> 
> I notice that the online documentation refers to a develop branch but the 
> repository has no develop branch, and I believe that I want to push the 
> changes to the master branch anyway. I see that the existing head on the 
> master branch has a version that's recommended, or perhaps required, for a 
> develop branch. So I tried increasing the version to an even number for y but 
> I get the above error.
> 
> Are you in a position to assist me? If so, are you willing to assist me?
> 
> I apprciate your patience and guidance.
> 
> Thank you.
> 
> Ever grateful,
> Brent

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Re: [Bioc-devel] MetaboSignal problems reported in the Multiple platform build/check report for BioC 3.15

[Nitesh Turaga]

Hi Andrea,

Please try again, I’ve fixed your email in the system. 

Try to activate your account with this email 
"andrea.rodriguez-martine...@imperial.ac.uk”. The previous email for some 
reason had ‘@ic.ac.uk’. 

Best,

Nitesh 

Nitesh Turaga
Scientist II, Department of Data Science,
Bioconductor Core Team Member
Dana Farber Cancer Institute

> On Jun 6, 2022, at 8:08 AM, Rodriguez Martinez, Andrea 
>  wrote:
> 
> Hi Lori
> 
> I also tried activating my account with my current email but it didnt 
> recognise the email account 
> 
> Best
> 
> Andrea
> 
> From: Kern, Lori 
> Sent: 06 June 2022 13:05
> To: Rodriguez Martinez, Andrea ; 
> bioc-devel@r-project.org 
> Subject: Re: MetaboSignal problems reported in the Multiple platform 
> build/check report for BioC 3.15
> 
> The email in the GitCredentials is andrea.rodriguez-martine...@ic.ac.uk
> 
> Please remember you will have to activate your account first.
> 
> https://git.bioconductor.org/BiocCredentials/account_activation/
> 
> When you activate the account there should be a verification email that often 
> goes into people's spam folders so also please check there.  If you continue 
> to have trouble activating and adding keys please reach back out.
> 
> 
> 
> Lori Shepherd - Kern
> 
> Bioconductor Core Team
> 
> Roswell Park Comprehensive Cancer Center
> 
> Department of Biostatistics & Bioinformatics
> 
> Elm & Carlton Streets
> 
> Buffalo, New York 14263
> 
> 
> From: Bioc-devel  on behalf of Rodriguez 
> Martinez, Andrea 
> Sent: Sunday, June 5, 2022 2:38 PM
> To: bioc-devel@r-project.org 
> Subject: [Bioc-devel] Fw: MetaboSignal problems reported in the Multiple 
> platform build/check report for BioC 3.15
> 
> Hi
> 
> Many thanks for contacting us regarding the issues with our package. We have 
> made the needed changes; but I'm having issues commiting/pushing the changes. 
> I'm now using a new computer where unfortunately I don't have my bioconductor 
> credentials. I tried resetting password here: 
> https://secure-web.cisco.com/1oT1_7Qu35F7hM2kS7Cpd956bpqpE0ll3ZvoqJiS2Hx-xq3XLUNBH7LhrINgpAWqe3DIfc1l7SVJf0RaawGKBJInsxl-zJwiXVbZvQ3Fks7MIoWTg2vOiFmc0ok2DFKT5MAbtXpQJ2-OsObYf0VlEcRu8dUMdT2MWkgvQl9kUlsyIg3n8rxafb4elm4LPV0iswG_cjbJi9Nvgz2ujNNf2y1xH2kdo37ha1EI0FBlCqsi0dVZOOViICtsBkMoOOmIj_quKvH04yqZ1cNUOkd2bx-ZJSaavVlNHMbsV06yOAbCnjNqMZJzTZH1YMqabe0rl/https%3A%2F%2Fgit.bioconductor.org%2FBiocCredentials%2Flogin%2F%3Fnext%3D%2FBiocCredentials%2F%3B
>  but my email doesn't seem to be recognised? could you please let me know to 
> which email is my account linked?
> 
> Thanks
> 
> Andrea
> Bioconductor Git 
> Credentials<https://secure-web.cisco.com/1KokUeE9EPVqY-SMAv7Z_bIyNXRqgseKzk7ntVkasnfKEuhj8FuD3mIznapNL04ou6KmTM5y5UcqIFdObrJ-NcBkiJWkxuPx_oK4MUd3qqAmbmvuTc4EKAACU83r2OrnBnUs4wUv9XV-pzZ7xk__g0NvzOMZ4xnym_iPypsm14SmZTHLnmiX_QudREG20m4jrUuSNSw3TFNpWX3pWkf5e7ZOxpTGT34R9W2F1AfUa-YNE6pYUaFA-ulQtpvHA93D_uIDhwtDByDhdv7p1RCDxzA6z00DPfatGvyIjbzXitUUcy3Sk8z6i8_Qg-M_5tQ3z/https%3A%2F%2Fgit.bioconductor.org%2FBiocCredentials%2Flogin%2F%3Fnext%3D%2FBiocCredentials%2F>
> Bioconductor Git Credentials. Welcome! This site allows package authors to 
> manage their credentials for the Bioconductor Git repository.
> git.bioconductor.org
> 
> 
> From: bbs-nore...@bioconductor.org 
> Sent: 03 June 2022 18:00
> To: Rodriguez Martinez, Andrea 
> Subject: MetaboSignal problems reported in the Multiple platform build/check 
> report for BioC 3.15
> 
> 
> ***
> This email originates from outside Imperial. Do not click on links and 
> attachments unless you recognise the sender.
> If you trust the sender, add them to your safe senders list 
> https://secure-web.cisco.com/1YdB8ZzSCwoNIAEfbZHz_8mUpowu1vk-MjQdA6ZIP4yGq20zHQ8c69TUu5w0XGJcrs1575Rr6JkiFZd2AV2ib-JXpiVqqdCd6IMjEVP5lvszkp-K6HwHJM31-vV1tViPnWdAEi78Zu1kEKdIW8UdZTfmTu9R9OUDqc36dQVt6Xlev6rOOZae_QpfWw6h8HFt3GN4KkCWj9QeCsjf1wFSRfjOb2RGu3kDGqro52btWFeaURxs6p0x8SV79DL3XTjzLhHLjTk9fJMYqjbRitrHmNLp-QjBqWf6c3Bb-joZziE3oXyzqN30GyfSDYJ878S4e/https%3A%2F%2Fspam.ic.ac.uk%2FSpamConsole%2FSenders.aspx
>  to disable email stamping for this address.
> ***
> [This is an automatically generated email. Please don't reply.]
> 
> Hi MetaboSignal maintainer,
> 
> According to the Multiple platform build/check report for BioC 3.15,
> the MetaboSignal package has the following problem(s):
> 
>  o ERROR for 'R CMD build' on nebbiolo1. See the details here:
>  
> https://secure-web.cisco.com/1YYc3F7pJ-eBcOENIZ8o7MNbYJNJSKg3Iau9VaHknfnPRekk94bU_LGDwEXfHTRwslOkAxaVIr7-MdZQceM1SlnfsO8EQGOertDF2c4Eaci959_S-toXxE

Re: [Bioc-devel] Maintainer change pRolocGUI

[Nitesh Turaga]

Dear Laurent,

I’m adding Lisa to the package.

Dear Lisa, you’d need to activate your BiocCredentials account and add SSH keys 
to access the package. The link for activation is 
https://git.bioconductor.org/BiocCredentials/account_activation. 

Once you do that you’ll gain access.

Best,

Nitesh

Nitesh Turaga
Scientist II, Department of Data Science,
Bioconductor Core Team Member
Dana Farber Cancer Institute

> On May 17, 2022, at 5:36 AM, Laurent Gatto  wrote:
> 
> Would it be possible to give Lisa Breckels  write access to 
> the pRolocGUI git repo, as she will be taking over maintenance of the package.
> 
> Thank you in advance.
> 
> Laurent 
> 
> 
> 
> 
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Re: [Bioc-devel] Add Maintainer to `tripr` package

[Nitesh Turaga]

Hi Nikolaos

The maintainer for the Bioconductor access has been changed.

Please list this (inab.bioinformat...@lists.certh.gr) as the maintainer email 
with your “Name” on the maintainer field. Please also make sure to populate the 
authors field with the Names of people and not groups.

Please update both and confirm with are reply.

Best,

Nitesh



Nitesh Turaga
Scientist II, Department of Data Science,
Bioconductor Core Team Member
Dana Farber Cancer Institute

> On May 13, 2022, at 6:28 AM, Nikolaos Pechlivanis  wrote:
> 
> Dear Mrs. Kern,
> 
> Thank you for your previous email. I apologize for the late answer.
> 
> During the last few months, there have been some changes in the team's
> structure, and we need to update our submitted package maintainer rights.
> There are two packages in Bioconductor maintained by our group; tripr
> <https://bioconductor.org/packages/release/bioc/html/tripr.html> (with
> maintainer Iason Ofeidis ) and lineagespot
> <https://bioconductor.org/packages/release/bioc/html/lineagespot.html> (with
> maintainer Nikolaos Pechlivanis ).
> 
> We have created a new GitHub profile as an administrator account, and we
> would like to change both packages' maintainers to this account.
> Below you can find the new account details:
> 
> 
> *Email: inab.bioinformatics@lists.certh.grGitHub
> username: inabbioinformatics *
> 
> At the moment, there is only one SSH key related to this account:
> *https://github.com/inabbioinformatics.keys
> <https://github.com/inabbioinformatics.keys>*
> 
> Thank you in advance for your time and help. Please let me know if there
> are any problems.
> 
> Kind regards,
> Nikolaos Pechlivanis
> 
> On Mon, May 9, 2022 at 2:32 PM Kern, Lori 
> wrote:
> 
>> Nikolaos -- For the BiocCredentials app *nikopech* is already associated
>> with nikos...@certh.gr
>> <https://git.bioconductor.org/BiocCredentials/admin/gitapp/biocuser/1847/?_changelist_filters=q%3Dnikopech>;
>> if you no longer have access to that email and would like help switching
>> the email on BiocCredentials where you can manage ssh access keys please
>> let us know.
>> 
>> You should have push access provided ssh keys on the BiocCredentials
>> account are up-to-date.
>> 
>> Lori Shepherd - Kern
>> 
>> Bioconductor Core Team
>> 
>> Roswell Park Comprehensive Cancer Center
>> 
>> Department of Biostatistics & Bioinformatics
>> 
>> Elm & Carlton Streets
>> 
>> Buffalo, New York 14263
>> --
>> *From:* Nikolaos Pechlivanis 
>> *Sent:* Monday, May 9, 2022 3:51 AM
>> *To:* maintai...@bioconductor.org 
>> *Cc:* bioc-devel@r-project.org ;
>> jaso...@certh.gr 
>> *Subject:* Re: Add Maintainer to `tripr` package
>> 
>> Dear,
>> 
>> I am sending a request for a change in the Bioconductor package *tripr*
>> <https://secure-web.cisco.com/1YObg9QtpymS9My69qysXwuTWjqceinBEJ0bvawMBM8df9_pC45GtYmrVpDkQYX-wu2lf2EAEjzjrTL4bhp-iwKZQHcpNZE6VpwqpG-w09t6bMQtoZUWXptcvQQDAs8YbVeXIOMsGhP4TyjQf-_8VOOIkDskzqvhIjmwCX4Qiycic80GlsmsSzAfrEXDToKWIYv9-IGBQNEOEx1cLOX91aKa9zS2xYj5CJmdSSYlKSBasGJfHxxDaqLC_kVUCQefhGc2Tq3AUO3e9jaPwHSInyGjbONsfXseUhQrAlyse9bEIEwaEBpGhPrLf1jszMZ70/https%3A%2F%2Fbioconductor.org%2Fpackages%2Frelease%2Fbioc%2Fhtml%2Ftripr.html>
>> maintainer, following the guidelines in
>> https://bioconductor.org/developers/how-to/git/change-maintainer
>> <https://secure-web.cisco.com/1dfMz17oqERDEJOURYBWU_hxB3AbA0GbRseTTvNLQ601GG3UX1JZqAXHohu9GoMg6UvDSqebSlDYO7SC3nutSY9plixTiQ0rlN11DUQOagjH9-2O6ShFFZIztXIIg4DLQ2QwnPO3-8N6000p-06StZxyb1yCub0_3YkkJpfA18HarmBfPCjEhY8qBOiGk1CYWAmblbyCGNWQ7JmyrKsEz9cO3CYqs-Afg4cR5VUnQ30J2DKU1WBQs05lhLkYeQzKUapalIGMKgwVA9D-GAvWd6RKcxwVvMy5AeMDL3mmSn6vuuq3-MLgdmqnf4-aSP6dc/https%3A%2F%2Fbioconductor.org%2Fdevelopers%2Fhow-to%2Fgit%2Fchange-maintainer>
>> .
>> 
>> The original maintainer of the package is
>> 
>> 
>> 
>> *original maintainer: Email: jaso...@certh.gr  GitHub
>> username: iofeidis*
>> 
>> Yet, a few months ago, we asked to add a new maintainer to the package:
>> 
>> 
>> 
>> *new maintainer: Email: nikos...@gmail.com  GitHub
>> username: nikopech*
>> 
>> Could you please provide us with some instructions on how we need to
>> proceed?
>> 
>> Thank you in advance for your time.
>> 
>> Kind regards,
>> Pechlivanis Nikolaos
>> 
>> On Thu, Sep 30, 2021 at 10:49 AM Iasonas Ofeidis  wrote:
>> 
>> Hello,
>> 
>> I would like to add a new maintainer to the newly accepted package
>> `tripr`.
>> I am following the guideli

Re: [Bioc-devel] Maintainer change for pairkat package

[Nitesh Turaga]

Hi Cameron and Max,

Max should have access to the package with the registered BiocCredentials 
address. 

Best,

Nitesh 


Nitesh Turaga
Scientist II, Department of Data Science,
Bioconductor Core Team Member
Dana Farber Cancer Institute

> On Feb 10, 2022, at 1:06 PM, Cameron Severn  wrote:
> 
> Hello,
> 
> I am looking to change the transfer maintenance of "pairkat" to Max
> McGrath. max.mcgr...@ucdenver.edu. I have pushed a bumped version number
> with Max added to the description file. Please let me know if there is
> anything else I need to do to proceed.
> 
> Thanks!
> 
> Cameron Severn
> 
>   [[alternative HTML version deleted]]
> 
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Re: [Bioc-devel] Git recognizes me but denies access

[Nitesh Turaga]

Is this resolved Philipp? 

‘destiny’ seems to be failing on windows still 
http://bioconductor.org/checkResults/release/bioc-LATEST/destiny/. 

Best,

Nitesh 


Nitesh Turaga
Scientist II, Department of Data Science,
Bioconductor Core Team Member
Dana Farber Cancer Institute

> On Dec 19, 2021, at 7:17 AM, Philipp A.  wrote:
> 
> Seems like I fixed it! Is there anything else I have to do?
> 
> destiny is green now on your build bots (linux and mac, I don’t see windows
> there but there seems to be a build artifact on destiny’s landing page).
> 
> Seems like checking doesn’t use BiocCheck there, is that no longer used? If
> it were used, it would break because it doesn’t consider my .ipynb files to
> be vignettes.
> 
> Best, Phil
> 
> Am Mo., 13. Dez. 2021 um 19:55 Uhr schrieb Philipp A. :
> 
>> Am Mo., 13. Dez. 2021 um 14:24 Uhr schrieb Kern, Lori <
>> lori.sheph...@roswellpark.org>:
>> 
>>> I don't see any changes on the RELEASE_3_14 branch.  Please make sure to
>>> push to the RELEASE_3_14 branch […]
>>> 
>> 
>> Understood! Done, I cherry-picked all the commits over.
>> 
>> Am Mo., 13. Dez. 2021 um 19:39 Uhr schrieb Hervé Pagès <
>> hpages.on.git...@gmail.com>:
>> 
>>> Just in case someone is watching this thread and wondering what we're
>>> doing with the LaTeX environment on the build machines.
>>> […]
>>> All these installations are stock installations.
>> 
>> 
>> That’s extremely weird, as I also use stock TexLive to locally build
>> things, and everything works flawlessly.
>> 
>> Well, I circumvented the problem by building HTML vignettes instead, which
>> is probably more convenient for users anyway.
>> 
> 
>   [[alternative HTML version deleted]]
> 
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Re: [Bioc-devel] DeMixT Bioconductor maintainer

[Nitesh Turaga]

Hi Peng and Shuai,

Happy new year.

I’ve added Shuai as a maintainer to the package.

Shuai, you need to activate your BiocCredentials account with the email you 
gave. 

https://git.bioconductor.org/BiocCredentials/account_activation. 

Once you activate and add your SSH keys, you’ll have access. Please change the 
maintainer once this happens on the DESCRIPTION file.

Best,

Nitesh 

Nitesh Turaga
Scientist II, Department of Data Science,
Bioconductor Core Team Member
Dana Farber Cancer Institute

> On Dec 28, 2021, at 5:36 PM, Yang,Peng  wrote:
> 
> Hi Bioconductor team,
>  
> I would like to change maintainer for our DeMixT package.
> https://bioconductor.org/packages/release/bioc/html/DeMixT.html
>  
> Below is the contact information.
> maintainer: Shuai Guo
> email: shuai@uth.tmc.edu (cc'd in this email)
>  
> I will update the new maintainer information in DESCRIPTION, and push  
> to the Bioconductor (devel brunch) very soon.
>  
> Thanks,
> Peng

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Re: [Bioc-devel] No write permissions on PDATK

[Nitesh Turaga]

As far as password reset goes. Please check your spam as well.



Nitesh Turaga
Scientist II, Department of Data Science,
Bioconductor Core Team Member
Dana Farber Cancer Institute

> On Dec 17, 2021, at 11:58 AM, Chris Eeles  
> wrote:
> 
> Hello Core Team,
> 
> I am trying to push a fix for our package, PDATK, to Bioconductor but it 
> seems I have lost write permissions on the repo, as indicated by `ssh -T 
> g...@git.bioconductor.org<mailto:g...@git.bioconductor.org> | grep PDATK`. I 
> also tried to login to the BiocCredentials app, but it seems the password has 
> changed and I do not receive an email when I try to reset it.
> 
> Any help would be appreciated. My SSH key grants access to all other package 
> we maintain.
> 
> Best,
> ---
> Christopher Eeles
> Software Developer
> BHK 
> Laboratory<https://nam05.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.bhklab.ca%2F=02%7C01%7Ctao.qing%40yale.edu%7Ce130a2d3267b46a945ab08d79f7660ad%7Cdd8cbebb21394df8b4114e3e87abeb5c%7C0%7C0%7C637153203084194682=nGXPfLnlbcaLQdDOHFDmp4lZ7lD9H29uFeVCAqjT9Ds%3D=0>
> Princess Margaret Cancer 
> Centre<https://nam05.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.pmgenomics.ca%2Fpmgenomics%2F=02%7C01%7Ctao.qing%40yale.edu%7Ce130a2d3267b46a945ab08d79f7660ad%7Cdd8cbebb21394df8b4114e3e87abeb5c%7C0%7C0%7C637153203084194682=b2ZjA%2FPDKjTZmAWGbnQAY1SjVtCDQGQmXu2Thz%2FXQkI%3D=0>
> University Health 
> Network<https://nam05.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.uhn.ca%2F=02%7C01%7Ctao.qing%40yale.edu%7Ce130a2d3267b46a945ab08d79f7660ad%7Cdd8cbebb21394df8b4114e3e87abeb5c%7C0%7C0%7C637153203084204675=NH1nVdRr9SsFOtMYhC%2BaXpdZiC7Nm%2BaUt37NvDWBfCg%3D=0>
> 
> 
>   [[alternative HTML version deleted]]
> 
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Re: [Bioc-devel] No write permissions on PDATK

[Nitesh Turaga]

Hi,

Should be fixed.

Please check again now.

Best

Nitesh Turaga
Scientist II, Department of Data Science,
Bioconductor Core Team Member
Dana Farber Cancer Institute

> On Dec 17, 2021, at 11:58 AM, Chris Eeles  
> wrote:
> 
> PDATK

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Re: [Bioc-devel] Transfer Maintainership of GeoDiff

[Nitesh Turaga]

Hi,

I’ve added Nicole. She should have maintainer access. Please change the 
DESCRIPTION file.

Best,



Nitesh Turaga
Scientist II, Department of Data Science,
Bioconductor Core Team Member
Dana Farber Cancer Institute

> On Nov 15, 2021, at 1:59 PM, Nicole Ortogero  wrote:
> 
> Hi Bioconductor team,
>  
> I was wondering if this maintainer update has been made in the system yet.
>  
> Package: GeoDiff
> New Maintainer: Nicole Ortogero < nortog...@nanostring.com>
> Old Maintainer: Zhi Yang (see Zhi’s message below)
>  
> Thanks,
>  
> Nicole Ortogero, PhD  
> Bioinformatics Scientist II  
> NanoString Technologies, Inc. • nanostring.com
>   
>   
>   
>   
>   
>  
>  
>  
>  
> From: Zhi Yang  
> Sent: Monday, November 8, 2021 11:08 AM
> To: maintai...@bioconductor.org
> Cc: Nicole Ortogero 
> Subject: Transfer Maintainership of GeoDiff
>  
> Hello, 
>  
> We’d like to switch the maintainer for GeoDiff to be Nicole Ortogero 
> (nortog...@nanostring.com). We will soon update the description to reflect 
> the change.
>  
> Zhi Yang  
> Biostatistician II  
> NanoString Technologies, Inc. • nanostring.com
>   
>   
>   
>   
> 

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Re: [Bioc-devel] Activate account in Bioconductor Git Credentials

[Nitesh Turaga]

Hi Yihang,

You should have access now. Please activate your account at 
https://git.bioconductor.org/BiocCredentials/account_activation and add SSH 
keys.

You’ll be able to push to the package.

Make sure you are complaint with all the rules of contributions here, 

http://bioconductor.org/developers/how-to/version-numbering/

http://bioconductor.org/developers/

Best,



Nitesh Turaga
Scientist II, Department of Data Science,
Bioconductor Core Team Member
Dana Farber Cancer Institute

> On Nov 17, 2021, at 5:01 PM, Yihang Xin  wrote:
> 
> Hi Alex and Nitesh,
> 
> I would like access to the package on git.bioconductor now. Alex, can you 
> grant me the permission?
> 
> -Yihang
> 
> -- Forwarded message -
> From: Nitesh Turaga 
> Date: Wed, Nov 17, 2021 at 5:49 AM
> Subject: Re: [Bioc-devel] Activate account in Bioconductor Git Credentials
> To: Yihang Xin 
> Cc: Bioc-devel 
> 
> 
> Hi Yihang,
> 
> You are only listed as ‘contributor’ but not the maintainer of the package 
> according to both the link you sent and the Bioconductor package DESCRIPTION 
> which is on git.bioconductor.org. 
> 
> You need to get access permissions from Alex Pico, who is the maintainer of 
> the package. Ideally, Alex would make the final sync from Github to 
> Bioconductor once all your development is done on Github. 
> 
> If you would like access to the package on git.bioconductor even now, please 
> let me know and cc Alex. 
> 
> Best,
> 
> Nitesh 
> 
> Nitesh Turaga
> Scientist II, Department of Data Science,
> Bioconductor Core Team Member
> Dana Farber Cancer Institute
> 
> > On Nov 16, 2021, at 4:29 AM, Yihang Xin via Bioc-devel 
> >  wrote:
> > 
> > Hi,
> > 
> > I am currently maintain the RCy3 package in Bioconductor, and I am trying
> > to activate my account to add SSH keys. I think I have already added email
> > address in the DESCRIPTION file of the package I maintain. You can find it
> > here:
> > https://github.com/cytoscape/RCy3/blob/dfd6fdc28c0fc88c0b0719ef28fdea51c9a18c32/DESCRIPTION#L17
> > 
> > But the website shows that my email address "is not associated with a
> > maintainer of a Bioconductor package. Please check the spelling or contact
> > bioc-devel@r-project.org for help." Could you help me to activate my
> > account?
> > 
> > Best,
> > Yihang
> > 
> > *Yihang Xin [He, Him, His]*
> > Software Engineer II | Bioinformatics core
> > yihang@gladstone.ucsf.edu
> > Gladstone Institutes
> > 1650 Owens St, San Francisco, CA 94158
> > 
> >   [[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] Git recognizes me but denies access

[Nitesh Turaga]

Please activate your account flying-sh...@web.de for BiocCredentials. 

You should be good to go.


Nitesh Turaga
Scientist II, Department of Data Science,
Bioconductor Core Team Member
Dana Farber Cancer Institute

> On Nov 18, 2021, at 4:23 AM, Philipp A.  wrote:
> 
> My addresses are phil.ange...@gmail.com (not philipp) and flying-sh...@web.de.
> 
> I’ll add a key as soon as I’m able to log in.
> 
> Am Mo., 15. Nov. 2021 um 15:56 Uhr schrieb Nitesh Turaga 
> :
> You have to activate the account at 
> https://git.bioconductor.org/BiocCredentials/account_activation. Set a 
> password and add Ssh keys. 
> 
> Once again, the email you are trying to activate is 
> 'philipp.ange...@gmail.com’.
> 
> The problem seems to be non-matching key pairs. Add new SSH keys.
> 
> Best,
> 
> Nitesh 
> 
> 
> Nitesh Turaga
> Scientist II, Department of Data Science,
> Bioconductor Core Team Member
> Dana Farber Cancer Institute
> 
> > On Nov 15, 2021, at 9:54 AM, Nitesh Turaga  wrote:
> > 
> > Hi Philipp,
> > 
> > The email address that is registered to BiocCredentials right now is 
> > 'philipp.ange...@gmail.com'. It doesn’t look like an institutional email 
> > address. 
> > 
> > Could you please confirm the email change to flying-sh...@web.de ?? 
> > 
> > Best,
> > 
> > Nitesh 
> > 
> > Nitesh Turaga
> > Scientist II, Department of Data Science,
> > Bioconductor Core Team Member
> > Dana Farber Cancer Institute
> > 
> >> On Nov 15, 2021, at 2:36 AM, Carsten Marr 
> >>  wrote:
> >> 
> >> confirmed!
> >> 
> >> 
> >> best,
> >> c
> >> 
> >> 
> >> 
> >>> Am 13.11.2021 um 15:56 schrieb Philipp A. :
> >>> 
> >>> I no longer have control of this email address.
> >>> 
> >>> Please add the one I’m writing from to the account.
> >>> 
> >>> My supervisor (CC) from when I was at the institution can confirm that 
> >>> I’m the same person.
> >>> 
> >>> Best, Phil
> >>> 
> >>> Am Di., 9. Nov. 2021 um 16:24 Uhr schrieb Nitesh Turaga 
> >>> :
> >>> Dear Phil,
> >>> 
> >>> Please activate your account at 
> >>> https://git.bioconductor.org/BiocCredentials/account_activation. Add new 
> >>> SSH keys, because it’s possible you are not using the correct key-pairs. 
> >>> 
> >>> Nothing on our end seems out of place. 
> >>> 
> >>> The FAQ section from #13 onwards has other debugging options as well, 
> >>> https://bioconductor.org/developers/how-to/git/faq/.
> >>> 
> >>> Best,
> >>> 
> >>> Nitesh 
> >>> 
> >>> 
> >>> Nitesh Turaga
> >>> Scientist II, Department of Data Science,
> >>> Bioconductor Core Team Member
> >>> Dana Farber Cancer Institute
> >>> 
> >>>> On Nov 8, 2021, at 12:23 PM, Philipp A.  wrote:
> >>>> 
> >>>> Hi,
> >>>> 
> >>>> My package (destiny) has been deprecated because Bioconductor’s LaTeX
> >>>> environment keeps changing and breaking my docs.
> >>>> 
> >>>> I‘m trying to fix it once again, but I get:
> >>>> 
> >>>> $ git push upstream masterFATAL: W any packages/destiny p.angerer
> >>>> DENIED by fallthru
> >>>> 
> >>>> *Please note that this isn’t covered in the FAQ*:
> >>>> 
> >>>> “p.angerer” indicates that it recognizes me, but still doesn’t allow me 
> >>>> to
> >>>> push commits.
> >>>> 
> >>>> Best, Phil
> >>>> 
> >>>>  [[alternative HTML version deleted]]
> >>>> 
> >>>> ___
> >>>> Bioc-devel@r-project.org mailing list
> >>>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
> >>> 
> >> 
> >> ---
> >> Carsten Marr
> >> +49 89 3187 2158
> >> AIH Institute of AI for Health 
> >> Helmholtz Zentrum München 
> >> www.helmholtz-muenchen.de/aih/index.html
> >> 
> >> 
> >> 
> >> 
> >> 
> >> 
> >> 
> >> 
> >> 
> >> 
> >> Helmholtz Zentrum München 
> >> Deutsches Forschungszentrum für Gesundheit und Umwelt (GmbH) 
> >> Ingolstädter Landstr. 1 
> >> 85764 Neuherberg 
> >> www.helmholtz-muenchen.de 
> >> Aufsichtsratsvorsitzende: MinDir.in Prof. Dr. Veronika von Messling 
> >> Geschäftsführung: Prof. Dr. med. Dr. h.c. Matthias Tschöp, Kerstin Günther
> >> Registergericht: Amtsgericht München HRB 6466 
> >> USt-IdNr: DE 129521671
> >> 
> > 
> 

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Re: [Bioc-devel] Activate account in Bioconductor Git Credentials

[Nitesh Turaga]

Hi Yihang,

You are only listed as ‘contributor’ but not the maintainer of the package 
according to both the link you sent and the Bioconductor package DESCRIPTION 
which is on git.bioconductor.org. 

You need to get access permissions from Alex Pico, who is the maintainer of the 
package. Ideally, Alex would make the final sync from Github to Bioconductor 
once all your development is done on Github. 

If you would like access to the package on git.bioconductor even now, please 
let me know and cc Alex. 

Best,

Nitesh 

Nitesh Turaga
Scientist II, Department of Data Science,
Bioconductor Core Team Member
Dana Farber Cancer Institute

> On Nov 16, 2021, at 4:29 AM, Yihang Xin via Bioc-devel 
>  wrote:
> 
> Hi,
> 
> I am currently maintain the RCy3 package in Bioconductor, and I am trying
> to activate my account to add SSH keys. I think I have already added email
> address in the DESCRIPTION file of the package I maintain. You can find it
> here:
> https://github.com/cytoscape/RCy3/blob/dfd6fdc28c0fc88c0b0719ef28fdea51c9a18c32/DESCRIPTION#L17
> 
> But the website shows that my email address "is not associated with a
> maintainer of a Bioconductor package. Please check the spelling or contact
> bioc-devel@r-project.org for help." Could you help me to activate my
> account?
> 
> Best,
> Yihang
> 
> *Yihang Xin [He, Him, His]*
> Software Engineer II | Bioinformatics core
> yihang@gladstone.ucsf.edu
> Gladstone Institutes
> 1650 Owens St, San Francisco, CA 94158
> 
>   [[alternative HTML version deleted]]
> 
> ___
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Re: [Bioc-devel] Git recognizes me but denies access

[Nitesh Turaga]

Hi Philipp,

The email address that is registered to BiocCredentials right now is 
'philipp.ange...@gmail.com'. It doesn’t look like an institutional email 
address. 

Could you please confirm the email change to flying-sh...@web.de ?? 

Best,

Nitesh 

Nitesh Turaga
Scientist II, Department of Data Science,
Bioconductor Core Team Member
Dana Farber Cancer Institute

> On Nov 15, 2021, at 2:36 AM, Carsten Marr 
>  wrote:
> 
> confirmed!
> 
> 
> best,
> c
> 
> 
> 
>> Am 13.11.2021 um 15:56 schrieb Philipp A. :
>> 
>> I no longer have control of this email address.
>> 
>> Please add the one I’m writing from to the account.
>> 
>> My supervisor (CC) from when I was at the institution can confirm that I’m 
>> the same person.
>> 
>> Best, Phil
>> 
>> Am Di., 9. Nov. 2021 um 16:24 Uhr schrieb Nitesh Turaga 
>> :
>> Dear Phil,
>> 
>> Please activate your account at 
>> https://git.bioconductor.org/BiocCredentials/account_activation. Add new SSH 
>> keys, because it’s possible you are not using the correct key-pairs. 
>> 
>> Nothing on our end seems out of place. 
>> 
>> The FAQ section from #13 onwards has other debugging options as well, 
>> https://bioconductor.org/developers/how-to/git/faq/.
>> 
>> Best,
>> 
>> Nitesh 
>> 
>> 
>> Nitesh Turaga
>> Scientist II, Department of Data Science,
>> Bioconductor Core Team Member
>> Dana Farber Cancer Institute
>> 
>> > On Nov 8, 2021, at 12:23 PM, Philipp A.  wrote:
>> > 
>> > Hi,
>> > 
>> > My package (destiny) has been deprecated because Bioconductor’s LaTeX
>> > environment keeps changing and breaking my docs.
>> > 
>> > I‘m trying to fix it once again, but I get:
>> > 
>> > $ git push upstream masterFATAL: W any packages/destiny p.angerer
>> > DENIED by fallthru
>> > 
>> > *Please note that this isn’t covered in the FAQ*:
>> > 
>> > “p.angerer” indicates that it recognizes me, but still doesn’t allow me to
>> > push commits.
>> > 
>> > Best, Phil
>> > 
>> >   [[alternative HTML version deleted]]
>> > 
>> > ___
>> > Bioc-devel@r-project.org mailing list
>> > https://stat.ethz.ch/mailman/listinfo/bioc-devel
>> 
> 
> ---
> Carsten Marr
> +49 89 3187 2158
> AIH Institute of AI for Health 
> Helmholtz Zentrum München 
> www.helmholtz-muenchen.de/aih/index.html
> 
> 
> 
> 
> 
> 
> 
> 
> 
> 
> Helmholtz Zentrum München 
> Deutsches Forschungszentrum für Gesundheit und Umwelt (GmbH) 
> Ingolstädter Landstr. 1 
> 85764 Neuherberg 
> www.helmholtz-muenchen.de 
> Aufsichtsratsvorsitzende: MinDir.in Prof. Dr. Veronika von Messling 
> Geschäftsführung: Prof. Dr. med. Dr. h.c. Matthias Tschöp, Kerstin Günther
> Registergericht: Amtsgericht München HRB 6466 
> USt-IdNr: DE 129521671
> 

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Re: [Bioc-devel] Add or Transfer Maintainership of DecoupleR Package

[Nitesh Turaga]

Hi Jesús,

I’ve changed the maintainer to Pau. 

Please be sure to remove yourself from maintainer field in the DESCRIPTION of 
the package. 

Hello Pau,

You would need to activate your account at 
https://git.bioconductor.org/BiocCredentials/account_activation. Once you gain 
access to the account, please add your SSH keys and you’ll get access to the 
package.

Best regards,

Nitesh 

Nitesh Turaga
Scientist II, Department of Data Science,
Bioconductor Core Team Member
Dana Farber Cancer Institute

> On Nov 5, 2021, at 12:44 PM, Jesús Vélez Santiago  
> wrote:
> 
> Hi,
> 
> I would like to request to add a new maintainership or change the 
> maintainership completely for the decoupleR package 
> (https://www.bioconductor.org/packages/release/bioc/html/decoupleR.html). 
> 
> New maintainer information:
>   • Name: Pau Badia-i-Mompel
>   • email: pau.ba...@uni-heidelberg.de
> Do you think you can help us?
> 
> Thanks!
> 
> -- 
> Best regards
> 
> Jesús Vélez Santiago, B.S.
> Center for Genome Sciences, UNAM
> jvelezmagic.com

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Re: [Bioc-devel] Bioconductor Git Credentials

[Nitesh Turaga]

Hi Wubing,

You would need to activate your account first, at 
https://git.bioconductor.org/BiocCredentials/account_activation.

Then you are able to set your password.

You have never activated your account.

Best,

Nitesh 

Nitesh Turaga
Scientist II, Department of Data Science,
Bioconductor Core Team Member
Dana Farber Cancer Institute

> On Nov 9, 2021, at 6:06 PM, Wubing Zhang  wrote:
> 
> Hi,
> 
> I'm a maintainer of MAGeCKFlute R package (
> https://bioconductor.org/packages/release/bioc/html/MAGeCKFlute.html). I
> can't log in to the BiocCredentials
> <https://git.bioconductor.org/BiocCredentials> and can't update my package.
> When I try to activate my account, the system pops up a warning message "
> watson5bzh...@gmail.com is not associated with a maintainer of a
> Bioconductor package. Please check the spelling or contact
> bioc-devel@r-project.org for help." Could you please help me with this?
> 
> Thank you!
> Best,
> Wubing Zhang
> CLS11025, 3 Blackfan Circle, Boston 02115
> Department of Data Sciences
> Dana-Farber Cancer Institute
> Phone: +1 617 319 5887
> 
>   [[alternative HTML version deleted]]
> 
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Re: [Bioc-devel] Git recognizes me but denies access

[Nitesh Turaga]

Dear Phil,

Please activate your account at 
https://git.bioconductor.org/BiocCredentials/account_activation. Add new SSH 
keys, because it’s possible you are not using the correct key-pairs. 

Nothing on our end seems out of place. 

The FAQ section from #13 onwards has other debugging options as well, 
https://bioconductor.org/developers/how-to/git/faq/.

Best,

Nitesh 


Nitesh Turaga
Scientist II, Department of Data Science,
Bioconductor Core Team Member
Dana Farber Cancer Institute

> On Nov 8, 2021, at 12:23 PM, Philipp A.  wrote:
> 
> Hi,
> 
> My package (destiny) has been deprecated because Bioconductor’s LaTeX
> environment keeps changing and breaking my docs.
> 
> I‘m trying to fix it once again, but I get:
> 
> $ git push upstream masterFATAL: W any packages/destiny p.angerer
> DENIED by fallthru
> 
> *Please note that this isn’t covered in the FAQ*:
> 
> “p.angerer” indicates that it recognizes me, but still doesn’t allow me to
> push commits.
> 
> Best, Phil
> 
>   [[alternative HTML version deleted]]
> 
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Re: [Bioc-devel] bumphunter 1.35.0 - GENCODE FTP Server File Download Error

[Nitesh Turaga]

Dear Selvi,

It looks like a transient issue that happens on and off.

I’m not sure there is any special insight I can offer here. I do not think any 
action is needed on your end.

Best,

Nitesh 

Nitesh Turaga
Scientist II, Department of Data Science,
Bioconductor Core Team Member
Dana Farber Cancer Institute

> On Oct 25, 2021, at 12:00 PM, Tamilselvi Guharaj  
> wrote:
> 
> Dear Bioconductor Core Team,
> 
> The bumphunter package is exhibiting errors under the Linux and Windows
> platforms due to a file download failure from the GENCODE FTP server at the
> time of the daily multi-platform build/check testing for BioC 3.14.
> *https://bioc.ism.ac.jp/packages/checkResults/devel/bioc-LATEST/bumphunter/
> <https://bioc.ism.ac.jp/packages/checkResults/devel/bioc-LATEST/bumphunter/>*
> 
> *FTP Server File Download Error:*
> Error in `download.file(resource(con), destfile)`: cannot open URL '
> ftp://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_25/gencode.v25.annotation.gtf.gz
> '
> 
> The file is downloading fine on our end. We routinely see this error in the
> daily testing reports and it goes away in a day or two. But it seems to be
> persistent for the past five days or so.
> 
> Are such errors accepted or do we need to take any action from our end?
> 
> Thank you very much in advance for any input.
> 
> Thanks,
> Selvi
> 
>   [[alternative HTML version deleted]]
> 
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Re: [Bioc-devel] Release 3.14 process - stop all commits

[Nitesh Turaga]

Dear Bioconductor Community,

The push access to ‘master' and ‘RELEASE_3_14’ branches is now reinstated on 
the Bioconductor git server. You may now push to git repositories. 

Please be sure to ‘sync’ your package with the updates we have pushed to your 
package as part of the release process. 

To sync your packages, please follow 
http://bioconductor.org/developers/how-to/git/sync-existing-repositories/. 

If you have any questions, please send them to bioc-devel@r-project.org as a 
new email.

Best regards,

Nitesh Turaga
Scientist II, Department of Data Science,
Bioconductor Core Team Member
Dana Farber Cancer Institute

> On Oct 26, 2021, at 10:19 AM, Nitesh Turaga  wrote:
> 
> Dear Bioconductor Community,
> 
> I will be stopping all push access to the Bioconductor git server at 11am EST 
> today for about 2.5 - 3 hours.
> 
> During this time, a new branch will be added to your repositories 
> RELEASE_3_14. 
> 
> As soon as the release process is done, I will reply to this thread about 
> allowing commits to be pushed to the Bioconductor git server again.
> 
> Best regards,
> 
> Nitesh 
> 
> Nitesh Turaga
> Scientist II, Department of Data Science,
> Bioconductor Core Team Member
> Dana Farber Cancer Institute
> 

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[Bioc-devel] Release 3.14 process - stop all commits

[Nitesh Turaga]

Dear Bioconductor Community,

I will be stopping all push access to the Bioconductor git server at 11am EST 
today for about 2.5 - 3 hours.

During this time, a new branch will be added to your repositories RELEASE_3_14. 

As soon as the release process is done, I will reply to this thread about 
allowing commits to be pushed to the Bioconductor git server again.

Best regards,

Nitesh 

Nitesh Turaga
Scientist II, Department of Data Science,
Bioconductor Core Team Member
Dana Farber Cancer Institute

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Re: [Bioc-devel] hypeR Bioconductor package

[Nitesh Turaga]

The release branch has been frozen. 
http://bioconductor.org/developers/release-schedule/

Best,



Nitesh Turaga
Scientist II, Department of Data Science,
Bioconductor Core Team Member
Dana Farber Cancer Institute

> On Oct 25, 2021, at 10:28 AM, Federico, Anthony, Nicholas  
> wrote:
> 
> Hi Nitesh,
> 
> Any idea why this isn’t working?
> 
> ❯ git push upstream master:RELEASE_3_13 
> 
> Enumerating objects: 7, done.
> Counting objects: 100% (7/7), done.
> Delta compression using up to 4 threads
> Compressing objects: 100% (4/4), done.
> Writing objects: 100% (4/4), 383 bytes | 383.00 KiB/s, done.
> Total 4 (delta 3), reused 0 (delta 0), pack-reused 0
> 
> remote: Error: Illegal version bump from '1.8.0' to '2.0.0'.
> remote: 
> remote: Check http://bioconductor.org/developers/how-to/version-numbering/
> remote: for details.
> remote: 
> To git.bioconductor.org:packages/hypeR.git
> ! [remote rejected] master -> RELEASE_3_13 (pre-receive hook declined)
> error: failed to push some refs to 'git.bioconductor.org:packages/hypeR.git’
> 
> My understanding was an even “y” in x.y.z version was all that was required 
> for pushing to release branches.
> 
> Anthony
> 
>> On Oct 13, 2021, at 9:40 AM, Federico, Anthony, Nicholas  
>> wrote:
>> 
>> Hi Nitesh,
>> 
>> So it seems my key is ok:
>> 
>> ssh -T g...@git.bioconductor.org returns:
>> R Wpackages/hypeR
>> 
>> Do I need to create a new RELEASE branch on the upstream repository?
>> 
>> I noticed on the hypeR main repo, there is RELEASE_3_9 and RELEASE_3_10 - 
>> but they stopped ~ 2 years ago. 
>> 
>> Anthony
>> 
>>> On Oct 9, 2021, at 10:09 AM, Federico, Anthony, Nicholas  
>>> wrote:
>>> 
>>> I’ll try with a new key and let you know if it worked.
>>> 
>>> Anthony
>>> 
>>>> On Oct 9, 2021, at 10:08 AM, Anthony Federico  wrote:
>>>> 
>>>> Here is what I get:
>>>> 
>>>> ❯ git remote -v
>>>> origin  https://github.com/montilab/hypeR.git (fetch)
>>>> origin  https://github.com/montilab/hypeR.git (push)
>>>> upstreamg...@git.bioconductor.org:packages/hypeR.git (fetch)
>>>> upstreamg...@git.bioconductor.org:packages/hypeR.git (push)
>>>> 
>>>> Anthony
>>>> 
>>>>> On Oct 8, 2021, at 4:45 PM, Nitesh Turaga  wrote:
>>>>> 
>>>>> Hi,
>>>>> 
>>>>> What is your upstream remote set as?
>>>>> 
>>>>>   git remote -v
>>>>> 
>>>>> Please send results. It might just be you are using the wrong SSH key. A 
>>>>> good solution is to try with a new SSH key on your BiocCredentials app.
>>>>> 
>>>>> Best,
>>>>> 
>>>>> Nitesh
>>>>> 
>>>>> 
>>>>> Nitesh Turaga
>>>>> Scientist II, Department of Data Science,
>>>>> Bioconductor Core Team Member
>>>>> Dana Farber Cancer Institute
>>>>> 
>>>>>> On Oct 8, 2021, at 10:34 AM, Federico, Anthony, Nicholas  
>>>>>> wrote:
>>>>>> 
>>>>>> So here are my notes for this when pushing changes:
>>>>>> 
>>>>>> # Sync with bioconductor dev branch
>>>>>> git fetch --all
>>>>>> git checkout master
>>>>>> git merge upstream/master
>>>>>> git push upstream master
>>>>>> 
>>>>>> This worked for a while (past 3 years) but then at some point the 
>>>>>> Bioconductor branch on hypeR stopped getting updated. It seems like that 
>>>>>> last time it worked was in May of this year.
>>>>>> 
>>>>>> https://bioconductor.org/checkResults/release/bioc-LATEST/hypeR/
>>>>>> Snapshot Date: 2021-10-07 04:50:01 -0400 (Thu, 07 Oct 2021)
>>>>>> git_url: https://git.bioconductor.org/packages/hypeR
>>>>>> git_branch: RELEASE_3_13
>>>>>> git_last_commit: 23b7217
>>>>>> git_last_commit_date: 2021-05-19 12:41:30 -0400 (Wed, 19 May 2021)
>>>>>> 
>>>>>> Sorry for the confusion, my understanding of how to merge things 
>>>>>> upstream may just be lacking.
>>>>>> 
>>>>>> Anthony
>>>>>> 
>>>>>>> On Oct 6, 2021, at 11:11 AM, Nitesh Turaga  
>>>>>>&g

[Bioc-devel] Release 3.13 is frozen

[Nitesh Turaga]

Hello,

The release 3.13 branch of Bioconductor is now frozen. You will not be able to 
push to this RELEASE_3_13 branch of your package again.

Please review the release schedule 
http://bioconductor.org/developers/release-schedule/ for more information.

Best regards,


Nitesh Turaga
Scientist II, Department of Data Science,
Bioconductor Core Team Member
Dana Farber Cancer Institute

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Re: [Bioc-devel] Bioconductor Release 3.13 Code Freeze

[Nitesh Turaga]

Hi

The release 3.13 branch will be frozen after the next 2 hours. After today, you 
will not be able push to this branch.

Please refer to http://bioconductor.org/developers/release-schedule/. 

Best regards,


Nitesh Turaga
Scientist II, Department of Data Science,
Bioconductor Core Team Member
Dana Farber Cancer Institute

> On Oct 7, 2021, at 2:03 AM, Kern, Lori  wrote:
> 
> The release 3.13 branch will be frozen next Tuesday October 12th. After this 
> date there will be no updates to Bioconductor 3.13 packages in Bioconductor 
> EVER. Note this is one day later than previously announced due to the US 
> Holiday on October 11th.
> 
> 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] hypeR Bioconductor package

[Nitesh Turaga]

Hi,

What is your upstream remote set as?

git remote -v

Please send results. It might just be you are using the wrong SSH key. A good 
solution is to try with a new SSH key on your BiocCredentials app.

Best,

Nitesh


Nitesh Turaga
Scientist II, Department of Data Science,
Bioconductor Core Team Member
Dana Farber Cancer Institute

> On Oct 8, 2021, at 10:34 AM, Federico, Anthony, Nicholas  wrote:
> 
> So here are my notes for this when pushing changes:
> 
> # Sync with bioconductor dev branch
> git fetch --all
> git checkout master
> git merge upstream/master
> git push upstream master
> 
> This worked for a while (past 3 years) but then at some point the 
> Bioconductor branch on hypeR stopped getting updated. It seems like that last 
> time it worked was in May of this year.
> 
> https://bioconductor.org/checkResults/release/bioc-LATEST/hypeR/
> Snapshot Date: 2021-10-07 04:50:01 -0400 (Thu, 07 Oct 2021)
> git_url: https://git.bioconductor.org/packages/hypeR
> git_branch: RELEASE_3_13
> git_last_commit: 23b7217
> git_last_commit_date: 2021-05-19 12:41:30 -0400 (Wed, 19 May 2021)
> 
> Sorry for the confusion, my understanding of how to merge things upstream may 
> just be lacking.
> 
> Anthony
> 
>> On Oct 6, 2021, at 11:11 AM, Nitesh Turaga  wrote:
>> 
>> What are you trying exactly?
>> 
>> Please send the exact commands. 
>> 
>> Check -  http://bioconductor.org/developers/how-to/git/ and the FAQ 
>> http://bioconductor.org/developers/how-to/git/faq/.
>> 
>> Best,
>> 
>> Nitesh
>> 
>> 
>> 
>> 
>> On Wed, Oct 6, 2021, 4:38 AM Federico, Anthony, Nicholas  
>> wrote:
>> Hi,
>> 
>> I think I need some help, I somehow lost the ability to update the Bioc 
>> branch for hypeR. The GitHub main branch is passing my tests locally but 
>> whatever I try never seems to update the BioC servers.
>> 
>> Anthony
>> 
>>> On Oct 4, 2021, at 7:43 PM, nturaga.b...@gmail.com wrote:
>>> 
>>> hypeR Bioconductor Package Notification
>>> 
>>> Nitesh Turaga1
>>> 
>>> 1Dana Farber Cancer Institute, Boston, MA, USA
>>> 
>>> October 04, 2021
>>> 
>>> Package: hypeR
>>> 
>>> Hi Anthony Federico,
>>> 
>>> I am contacting you concerning the hypeR package, on the release and devel 
>>> branch of Bioconductor, for which you are listed as the maintainer.
>>> 
>>> The latest build/check report shows that your package is failing on one or 
>>> more platforms. Please resolve the issues before the next Bioconductor 
>>> release for your package’s continued inclusion in Bioconductor.
>>> 
>>> https://bioconductor.org/checkResults/release/bioc-LATEST/hypeR/https://bioconductor.org/checkResults/devel/bioc-LATEST/hypeR/
>>> 
>>> Please let me know if you have any questions.
>>> 
>>> Regards,
>>> 
>>> Nitesh
>>> 
>>> Bioconductor Core Team 
>>> Scientist II 
>>> Dana Farber Cancer Institute 
>>> Data Science 
>>> Boston, MA
>>> 
>> 
> 

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Re: [Bioc-devel] Can't push to upstream for ToxicoGx

[Nitesh Turaga]

Hi Chris,

Either way, this is a problem we have to solve post release. I’ve given the SSH 
key you are using access to that package as well.

It should work now. 

Best

Nitesh Turaga
Scientist II, Department of Data Science,
Bioconductor Core Team Member
Dana Farber Cancer Institute

> On Oct 6, 2021, at 10:52 AM, Chris Eeles  
> wrote:
> 
> Hello BioC core team,
> 
> I am having a weird issue with pushing a fix to the ToxicoGx repo. I tried 
> removing and re-adding the upstream branch, but the problem still persists.
> 
> I can fetch and pull from the remote using my SSH key, I can also access our 
> CoreGx repo (push and pull) using the same key.
> 
> However, when I try to push to upstream master I get this error:
> (py39) ceeles@EELESPC-DESK:~/development/ToxicoGx$ git push upstream master
> Enter passphrase for key '/home/ceeles/.ssh/bioc_rsa':
> FATAL: W any packages/ToxicoGx b.haibe-kains 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.
> 
> This is the same SSH key I have been using for years and I have pushed to 
> this repository in the past without issue.
> 
> Not sure what has gone wrong, some help would be appreciated as there is 
> currently and ERROR in the development branch.
> 
> Best,
> ---
> Christopher Eeles
> Software Developer
> BHK 
> Laboratory<https://nam05.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.bhklab.ca%2F=02%7C01%7Ctao.qing%40yale.edu%7Ce130a2d3267b46a945ab08d79f7660ad%7Cdd8cbebb21394df8b4114e3e87abeb5c%7C0%7C0%7C637153203084194682=nGXPfLnlbcaLQdDOHFDmp4lZ7lD9H29uFeVCAqjT9Ds%3D=0>
> Princess Margaret Cancer 
> Centre<https://nam05.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.pmgenomics.ca%2Fpmgenomics%2F=02%7C01%7Ctao.qing%40yale.edu%7Ce130a2d3267b46a945ab08d79f7660ad%7Cdd8cbebb21394df8b4114e3e87abeb5c%7C0%7C0%7C637153203084194682=b2ZjA%2FPDKjTZmAWGbnQAY1SjVtCDQGQmXu2Thz%2FXQkI%3D=0>
> University Health 
> Network<https://nam05.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.uhn.ca%2F=02%7C01%7Ctao.qing%40yale.edu%7Ce130a2d3267b46a945ab08d79f7660ad%7Cdd8cbebb21394df8b4114e3e87abeb5c%7C0%7C0%7C637153203084204675=NH1nVdRr9SsFOtMYhC%2BaXpdZiC7Nm%2BaUt37NvDWBfCg%3D=0>
> 
> 
>   [[alternative HTML version deleted]]
> 
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Re: [Bioc-devel] Can't push to upstream for ToxicoGx

[Nitesh Turaga]

Hi

Can you just try with a new SSH key? This is again related to using the wrong 
account.

benjamin.haibe.ka...@utoronto.ca is the email associated with the 
BiocCredentials account, and `ChristopherEeles` is the GitHub username / Bioc 
ID attached to it. 

Best,


Nitesh Turaga
Scientist II, Department of Data Science,
Bioconductor Core Team Member
Dana Farber Cancer Institute

> On Oct 6, 2021, at 10:52 AM, Chris Eeles  
> wrote:
> 
> Hello BioC core team,
> 
> I am having a weird issue with pushing a fix to the ToxicoGx repo. I tried 
> removing and re-adding the upstream branch, but the problem still persists.
> 
> I can fetch and pull from the remote using my SSH key, I can also access our 
> CoreGx repo (push and pull) using the same key.
> 
> However, when I try to push to upstream master I get this error:
> (py39) ceeles@EELESPC-DESK:~/development/ToxicoGx$ git push upstream master
> Enter passphrase for key '/home/ceeles/.ssh/bioc_rsa':
> FATAL: W any packages/ToxicoGx b.haibe-kains 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.
> 
> This is the same SSH key I have been using for years and I have pushed to 
> this repository in the past without issue.
> 
> Not sure what has gone wrong, some help would be appreciated as there is 
> currently and ERROR in the development branch.
> 
> Best,
> ---
> Christopher Eeles
> Software Developer
> BHK 
> Laboratory<https://nam05.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.bhklab.ca%2F=02%7C01%7Ctao.qing%40yale.edu%7Ce130a2d3267b46a945ab08d79f7660ad%7Cdd8cbebb21394df8b4114e3e87abeb5c%7C0%7C0%7C637153203084194682=nGXPfLnlbcaLQdDOHFDmp4lZ7lD9H29uFeVCAqjT9Ds%3D=0>
> Princess Margaret Cancer 
> Centre<https://nam05.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.pmgenomics.ca%2Fpmgenomics%2F=02%7C01%7Ctao.qing%40yale.edu%7Ce130a2d3267b46a945ab08d79f7660ad%7Cdd8cbebb21394df8b4114e3e87abeb5c%7C0%7C0%7C637153203084194682=b2ZjA%2FPDKjTZmAWGbnQAY1SjVtCDQGQmXu2Thz%2FXQkI%3D=0>
> University Health 
> Network<https://nam05.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.uhn.ca%2F=02%7C01%7Ctao.qing%40yale.edu%7Ce130a2d3267b46a945ab08d79f7660ad%7Cdd8cbebb21394df8b4114e3e87abeb5c%7C0%7C0%7C637153203084204675=NH1nVdRr9SsFOtMYhC%2BaXpdZiC7Nm%2BaUt37NvDWBfCg%3D=0>
> 
> 
>   [[alternative HTML version deleted]]
> 
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Re: [Bioc-devel] Don't have git access to my newly submitted git package

[Nitesh Turaga]

I think point #2 is the bigger issue. We are pressed for time as far as reviews 
go, and I’m happy to try and get sparrow reviewed, but cannot promise time for 
sparrow.shiny.

You are welcome to submit though, but there is no guarantee that I will be 
assigned to the package for review.



Nitesh Turaga
Scientist II, Department of Data Science,
Bioconductor Core Team Member
Dana Farber Cancer Institute

> On Oct 5, 2021, at 9:53 AM, Steve Lianoglou  wrote:
> 
> You are having it ;) I’m the one assigned to your package.
> 
> Oh, sweet!
> 
> My last commit looks like it has resulted in a successful build across the 
> board, so I guess the hard part begins now: sorry in advance for any 
> headaches this particular review may cause ;-)
> 
> It would be great if I could add as an additional package to this review the 
> "sibling" package {sparrow.shiny} of shiny modules and an app that enables 
> users to interactively explore gsea results that are produced by {sparrow}.
> 
> My reservations are these -- assuming the main {sparrow} package you are now 
> reviewing looks good for acceptance into bioc and release:
> 
> 1. Would any snafu's that arise in reviewing {sparrow.shiny} potentially hold 
> back {sparrow}'s inclusion into the upcoming bioc release?
> 
> 2. We are now past the official deadline of new package submission, so don't 
> want to try and take advantage of your time in this way.
> 
> Thanks again for your feedback and time,
> -steve
>  
> > On Oct 4, 2021, at 5:42 PM, Steve Lianoglou  wrote:
> > 
> > Hi Nitesh,
> > 
> > Thanks for working on this ... I've been able to push some changes I've 
> > made up to the upstream/master, so I think we should be ok for now.
> > 
> > Waiting till the next cycle is fine if you think that is the best approach. 
> > 
> > In all honesty, I'd prefer to attach the associated "shiny add-on package" 
> > to be reviewed with the main sparrow package I submitted last week, but I 
> > don't want to overwhelm the reviewers. Perhaps this is a conversation I can 
> > have directly with the person assigned to review my package via the github 
> > issues?
> > 
> > Thanks!
> > -steve
> >  
> > > On Oct 1, 2021, at 5:52 PM, Steve Lianoglou  wrote:
> > > 
> > > Hello folks,
> > > 
> > > I think I may have a similar problem accessing the git repos as was
> > > reported by Henrik back in August:
> > > https://marc.info/?l=bioc-devel=162937494630582=2
> > > 
> > > My recently submitted package (sparrow) was just accepted for review:
> > > https://github.com/Bioconductor/Contributions/issues/2342
> > > 
> > > I added the upstream bioc git repos, and have activated my account under:
> > > https://git.bioconductor.org/BiocCredentials/profile/
> > > 
> > > I have also confirmed that the public ssh-rsa key under my bioc profile is
> > > the one I have in ~/.ssh/id_rsa.pub
> > > 
> > > I want to start whacking away at the code so that the package passes on 
> > > the
> > > bioc build servers, but when I try to push a small change to the upstream
> > > repo, I get this:
> > > 
> > > ```
> > > $ git push upstream main
> > > FATAL: W any packages/sparrow s.lianoglou 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.
> > > ```
> > > 
> > > I went in to see what's cooking via ssh and see that I only have read
> > > access to the sparrow repository:
> > > 
> > > ```
> > > $ ssh -T g...@git.bioconductor.org | grep -E "sparrow"
> > > R   packages/sparrow
> > > ```
> > > 
> > > But I can also see that I have write access to some repositories I
> > > contributed to back in the day when I was a graduate student (ohhh good
> > > times):
> > > 
> > > ```
> > > $ ssh -T g...@git.bioconductor.org | grep -E "^ R W"
> > > R W packages/GenomicRanges
> > > R W packages/Gviz
> > > R W packages/IRanges
> > > ```
> > > 
> > > Is this likely something going wrong on my side, or is there something
> > > cooking on the bioc side?
> > > 
> > > Lastly, I would also like to submit a second "sibling" package along
> > > sparrow that (only) enhances sparrow by adding shiny modules and a fu

Re: [Bioc-devel] regain access to git repository

[Nitesh Turaga]

Just as a follow up to this thread,(this is an email copied from a 
communication with Noah). 

Hi Noah,

Can you tell me if your email n...@u.washington.edu is still active? If it is, 
please activate your BiocCredentials account and add your SSH 
keys,https://git.bioconductor.org/BiocCredentials/account_activation.

If not I’ll change it to n...@u.washington.edu. Just let me know.

Best



Nitesh Turaga
Scientist II, Department of Data Science,
Bioconductor Core Team Member
Dana Farber Cancer Institute

> On Oct 4, 2021, at 4:22 PM, Noah G. Hoffman  wrote:
> 
> Hello,
> 
> 
> 
> I am the author of two Bioconductor packages that I haven�t touched for a 
> long time - since before the migration to git, and I believe before the 
> existence of the BiocCredentials<https://git.bioconductor.org/BiocCredentials>
> 
> App. I have long since lost any credentials. Apologies if this is addressed 
> in the FAQ and I missed it, but how can I regain access to the repositories?
> 
> 
> 
> Thanks a lot,
> 
> Noah
> 
> 
> 
> From: Herv� Pag�s 
> Sent: Monday, October 4, 2021 6:48 PM
> To: Noah G. Hoffman 
> Subject: BioC 3.14 coming soon, package clstutils needs your attention!
> 
> Dear Noah,
> 
> The Bioconductor nightly builds are reporting a CHECK error on all
> platforms for the release (BioC 3.13) and devel (BioC 3.14) branches of
> the clstutils package:
> 
>   https://bioconductor.org/checkResults/3.13/bioc-LATEST/clstutils/
>   https://bioconductor.org/checkResults/3.14/bioc-LATEST/clstutils/
> 
> This is apparently caused by the recent removal of the RSVGTipsDevice
> package from CRAN:
> 
>   https://cran.r-project.org/package=RSVGTipsDevice
> 
> Please take the time to address the issue.
> 
> Keep in mind that the package needs to pass 'R CMD build' and 'R CMD
> check' with no error for the next Bioconductor release (BioC 3.14)
> scheduled for Wednesday Oct 27. Note that the deadline for packages
> passing 'R CMD build' and 'R CMD check' without errors or warnings is
> actually Friday October 22. See our release schedule here for more
> information:
> 
>   https://bioconductor.org/developers/release-schedule/
> 
> Don't hesitate to ask on the bioc-devel mailing list if you have
> questions or concerns about this.
> 
> Thank you for your contribution to Bioconductor.
> 
> Best,
> H.
> 
> --
> Herv� Pag�s
> 
> Bioconductor Core Team
> hpages.on.git...@gmail.com
> 
>   [[alternative HTML version deleted]]
> 
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Re: [Bioc-devel] Reset package

[Nitesh Turaga]

H Matineh,

This is taken care of, and your package has been reset.

Best,

Nitesh 


Nitesh Turaga
Scientist II, Department of Data Science,
Bioconductor Core Team Member
Dana Farber Cancer Institute

> On Oct 5, 2021, at 9:14 AM, matine rb  wrote:
> 
> Dear Bioconductor community,
> 
> My package HPiP (https://bioconductor.org/packages/devel/bioc/html/HPiP.html)
> has been cleaned for large files, May you please reset the repository on
> Bioconductor?
> 
> Matineh Rahmatbakhsh
> 
>   [[alternative HTML version deleted]]
> 
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Re: [Bioc-devel] Reset package

[Nitesh Turaga]

Hi,

I’ve taken care of the resetting of the repo on Bioconductor from your GitHub 
location  https://github.com/compbiomed/curatedTBData. 

Best,

Nitesh 

Nitesh Turaga
Scientist II, Department of Data Science,
Bioconductor Core Team Member
Dana Farber Cancer Institute

> On Oct 5, 2021, at 5:30 AM, Wang, Xutao  wrote:
> 
> Hi,
> 
> My package curatedTBData is currently under review and was asked to reduce 
> the package size. Now that the package has been cleaned for large files, 
> could you help me to reset the repository on Bioconductor?
> 
> Thanks,
> Xutao
> 
>   [[alternative HTML version deleted]]
> 
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Re: [Bioc-devel] Don't have git access to my newly submitted git package

[Nitesh Turaga]

Hi Steve,

You are having it ;) I’m the one assigned to your package.

Best,

Nitesh



Nitesh Turaga
Scientist II, Department of Data Science,
Bioconductor Core Team Member
Dana Farber Cancer Institute

> On Oct 4, 2021, at 5:42 PM, Steve Lianoglou  wrote:
> 
> Hi Nitesh,
> 
> Thanks for working on this ... I've been able to push some changes I've made 
> up to the upstream/master, so I think we should be ok for now.
> 
> Waiting till the next cycle is fine if you think that is the best approach. 
> 
> In all honesty, I'd prefer to attach the associated "shiny add-on package" to 
> be reviewed with the main sparrow package I submitted last week, but I don't 
> want to overwhelm the reviewers. Perhaps this is a conversation I can have 
> directly with the person assigned to review my package via the github issues?
> 
> Thanks!
> -steve
>  
> > On Oct 1, 2021, at 5:52 PM, Steve Lianoglou  wrote:
> > 
> > Hello folks,
> > 
> > I think I may have a similar problem accessing the git repos as was
> > reported by Henrik back in August:
> > https://marc.info/?l=bioc-devel=162937494630582=2
> > 
> > My recently submitted package (sparrow) was just accepted for review:
> > https://github.com/Bioconductor/Contributions/issues/2342
> > 
> > I added the upstream bioc git repos, and have activated my account under:
> > https://git.bioconductor.org/BiocCredentials/profile/
> > 
> > I have also confirmed that the public ssh-rsa key under my bioc profile is
> > the one I have in ~/.ssh/id_rsa.pub
> > 
> > I want to start whacking away at the code so that the package passes on the
> > bioc build servers, but when I try to push a small change to the upstream
> > repo, I get this:
> > 
> > ```
> > $ git push upstream main
> > FATAL: W any packages/sparrow s.lianoglou 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.
> > ```
> > 
> > I went in to see what's cooking via ssh and see that I only have read
> > access to the sparrow repository:
> > 
> > ```
> > $ ssh -T g...@git.bioconductor.org | grep -E "sparrow"
> > R   packages/sparrow
> > ```
> > 
> > But I can also see that I have write access to some repositories I
> > contributed to back in the day when I was a graduate student (ohhh good
> > times):
> > 
> > ```
> > $ ssh -T g...@git.bioconductor.org | grep -E "^ R W"
> > R W packages/GenomicRanges
> > R W packages/Gviz
> > R W packages/IRanges
> > ```
> > 
> > Is this likely something going wrong on my side, or is there something
> > cooking on the bioc side?
> > 
> > Lastly, I would also like to submit a second "sibling" package along
> > sparrow that (only) enhances sparrow by adding shiny modules and a full
> > shiny app to explore GSEA results.
> > 
> > I planned on doing that following the instructions here:
> > https://github.com/Bioconductor/Contributions#submitting-related-packages
> > 
> > But maybe I should wait until the next cycle (happy to do that)?
> > 
> > There is a package in bioc (gCrisprTools) with an update that relies on
> > some mojo in my sparrow package and don't want to jeopardize sparrow's
> > consideration for this release cycle by adding another package for review
> > on top of that.
> > 
> > https://stat.ethz.ch/pipermail/bioc-devel/2021-August/018402.html
> > 
> > Thanks in advance for your time and guidance,
> > -steve
> > 
> >   [[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] Don't have git access to my newly submitted git package

[Nitesh Turaga]

Hi Steve,

This is resolved now. You should see access to your package.

Waiting till the next cycle is fine if you think that is the best approach. 

Best,

Nitesh

Nitesh Turaga
Scientist II, Department of Data Science,
Bioconductor Core Team Member
Dana Farber Cancer Institute

> On Oct 1, 2021, at 5:52 PM, Steve Lianoglou  wrote:
> 
> Hello folks,
> 
> I think I may have a similar problem accessing the git repos as was
> reported by Henrik back in August:
> https://marc.info/?l=bioc-devel=162937494630582=2
> 
> My recently submitted package (sparrow) was just accepted for review:
> https://github.com/Bioconductor/Contributions/issues/2342
> 
> I added the upstream bioc git repos, and have activated my account under:
> https://git.bioconductor.org/BiocCredentials/profile/
> 
> I have also confirmed that the public ssh-rsa key under my bioc profile is
> the one I have in ~/.ssh/id_rsa.pub
> 
> I want to start whacking away at the code so that the package passes on the
> bioc build servers, but when I try to push a small change to the upstream
> repo, I get this:
> 
> ```
> $ git push upstream main
> FATAL: W any packages/sparrow s.lianoglou 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.
> ```
> 
> I went in to see what's cooking via ssh and see that I only have read
> access to the sparrow repository:
> 
> ```
> $ ssh -T g...@git.bioconductor.org | grep -E "sparrow"
> R   packages/sparrow
> ```
> 
> But I can also see that I have write access to some repositories I
> contributed to back in the day when I was a graduate student (ohhh good
> times):
> 
> ```
> $ ssh -T g...@git.bioconductor.org | grep -E "^ R W"
> R W packages/GenomicRanges
> R W packages/Gviz
> R W packages/IRanges
> ```
> 
> Is this likely something going wrong on my side, or is there something
> cooking on the bioc side?
> 
> Lastly, I would also like to submit a second "sibling" package along
> sparrow that (only) enhances sparrow by adding shiny modules and a full
> shiny app to explore GSEA results.
> 
> I planned on doing that following the instructions here:
> https://github.com/Bioconductor/Contributions#submitting-related-packages
> 
> But maybe I should wait until the next cycle (happy to do that)?
> 
> There is a package in bioc (gCrisprTools) with an update that relies on
> some mojo in my sparrow package and don't want to jeopardize sparrow's
> consideration for this release cycle by adding another package for review
> on top of that.
> 
> https://stat.ethz.ch/pipermail/bioc-devel/2021-August/018402.html
> 
> Thanks in advance for your time and guidance,
> -steve
> 
>   [[alternative HTML version deleted]]
> 
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Re: [Bioc-devel] access problems

[Nitesh Turaga]

Hi Leo,

The best way forward is just to add a new SSH key to your BiocCredentials 
account. The email registered is lsc...@essex.ac.uk. 

I see that you tried the password reset option. To help the issue, please try 
to “activate” your account 
https://git.bioconductor.org/BiocCredentials/account_activation. 

Best,

Nitesh



Nitesh Turaga
Scientist II, Department of Data Science,
Bioconductor Core Team Member
Dana Farber Cancer Institute

> On Sep 29, 2021, at 1:38 AM, Schalkwyk, Leonard  wrote:
> 
> I am the maintainer of the wateRmelon package. This message is coming from 
> the address named in its DESCRIPTION.
> 
> In the run-up to the new bioc version and a publication, I would like to push 
> our latest changes to the git repo but I’m having problems.  I previously had 
> ssh keys set up, and git.bioconductor.org is still in my known-hosts, but I’m 
> getting permission denied.
> 
> I also have a password in my keychain but it’s either out of date or 
> connected with an out of date email, and I’m not receiving password reset 
> emails.
> 
> Could I possibly have someone look at it and a password reset sent to this 
> address please.
> 
> Best wishes
> 
> Leo
> 
> Professor Leonard C Schalkwyk
> Head, School of Life Sciences
> University of Essex
> Colchester C04 3SQ
> UK
> 
>   [[alternative HTML version deleted]]
> 
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Re: [Bioc-devel] Add maintainer to scruff and celda

[Nitesh Turaga]

Hi,

Joshua campbell is the maintainer of these two packages already.

If that is not reflected in the description file of the package, it is up to 
Joshua to change it.

Best,

Nitesh

Nitesh Turaga
Scientist II, Department of Data Science,
Bioconductor Core Team Member
Dana Farber Cancer Institute

> On Oct 4, 2021, at 6:32 AM, Wang, Zhe  wrote:
> 
> Hi,
> 
> I sent this to 
> maintai...@bioconductor.org<mailto:maintai...@bioconductor.org> but no one 
> replied. I am the current maintainer of packages scruff 
> https://www.bioconductor.org/packages/release/bioc/html/scruff.html and celda 
> https://www.bioconductor.org/packages/release/bioc/html/celda.html. Please 
> add Joshua Campbell c...@bu.edu<mailto:c...@bu.edu> as a maintainer for these 
> two packages.
> 
> Thank you,
> Zhe Wang
> 
> 
>   [[alternative HTML version deleted]]
> 
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Re: [Bioc-devel] Submit a package via Gitlab

[Nitesh Turaga]

Hi Jiyuan,

You cannot submit a package through Gitlab.

Our submission process requires a Github based contribution.  If you have 
trouble importing your package, please checkout this article, 
https://docs.github.com/en/github/importing-your-projects-to-github/importing-source-code-to-github/importing-a-repository-with-github-importer
 which is quite helpful.

Best, 

Nitesh 

Nitesh Turaga
Scientist II, Department of Data Science,
Bioconductor Core Team Member
Dana Farber Cancer Institute

> On Sep 17, 2021, at 2:35 PM, Jiyuan Fang  wrote:
> 
> Dear Sir/Madam,
> 
> May I ask whether we can submit an R package to Bioconductor if it is in 
> Gitlab not Github?
> I tried once but failed as shown in the issue.
> 
> https://github.com/Bioconductor/Contributions/issues/2296
> 
> Best,
> Jiyuan
> 
>   [[alternative HTML version deleted]]
> 
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Re: [Bioc-devel] Regarding package IntramiRExploreR

[Nitesh Turaga]

Dear Surajit,

You should have access now with the new email. Please add SSH keys in the 
BiocCredentials app, and you’ll gain access.

Best,

Nitesh 


Nitesh Turaga
Scientist II, Department of Data Science,
Bioconductor Core Team Member
Dana Farber Cancer Institute

> On Sep 10, 2021, at 5:30 PM, Bhattacharya, Surajit 
>  wrote:
> 
> Hi All,
>  
> I am the  maintainer for a package IntramiRExploreR. Unfortunately I had a 
> change in institution and had lost access to my previous email, and had 
> forgotten to change my email. Can I please be reinstated as a maintainer 
> agai? My new email ID is sbhatta...@childrensnational.org. The github link 
> for the tool is https://github.com/sbhattacharya3/IntramiRExploreR.
>  
> Please let me know if you need any other information.
>  
> With Regards,
> Surajit Bhattacharya
> Research Postdoctoral Fellow
> Eric Vilain Lab
> Center for Genetic Medicine Research
> Children’s National Medical Center
>  
> Confidentiality Notice: This e-mail message, including any attachments, is 
> for the sole use of the intended recipient(s) and may contain confidential 
> and privileged information. Any unauthorized review, use, disclosure or 
> distribution is prohibited. If you are not the intended recipient, please 
> contact the sender by reply e-mail and destroy all copies of the original 
> message.

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Re: [Bioc-devel] pre-receive hook won't let me fix (very) old merge conflict

[Nitesh Turaga]

Hi Alyssa,

I can help you with this. Merge conflicts are hard to deal with for a few 
reasons, and this makes the hook design a little challenging. We want to keep 
the hook simple, and straightforward without adding too many edge cases into 
it. 

The reason for your issue, is because the conflicts in your code were 
introduced in the ‘pre-git’ era. I can disable the hook for your package and we 
can resolve it.

I’ll send you a private email to coordinate.

Best,

Nitesh 


Nitesh Turaga
Scientist II, Department of Data Science,
Bioconductor Core Team Member
Dana Farber Cancer Institute

> On Sep 1, 2021, at 12:33 AM, Alyssa Frazee  wrote:
> 
> Hello!
> 
> I have an old package up on Bioconductor, and as I was dusting it off
> fixing a build error this weekend, I ran into an issue where a commit with
> merge conflict markers (>>>>, , etc) was introduced into my repo in
> 2016. My new diff removes those characters and fixes the conflict, but I'm
> not able to push the fix to the g...@git.bioconductor.org remote because the
> diff itself contains those characters, which is not allowed by pre-receive
> hooks (even if they are being removed and not added):
> https://github.com/Bioconductor/git-hooks/blob/916f2fd1ddc5f461f14ba8d7cb9fc077aea37e44/prevent_merge_markers.py#L96
> 
> Is there a workaround for this? (any way to temporarily disable the hook to
> get out of a bad state? also open to other suggestions!)
> 
> Thanks so much!
> -Alyssa
> 
> details: package is polyester, commit containing the merge conflict
> characters is 2306e5b3e88c6156e091ff5cb9933a190f45d33c (2016-06-01) in the
> .travis.yml file, which isn't important for actual package
> functionality (but was being used on the github side).
> 
>   [[alternative HTML version deleted]]
> 
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Re: [Bioc-devel] lessons learned: negative experiences with git log

[Nitesh Turaga]

Hi Kasper,

Is this what you are looking for? (My understanding of your question is you 
want to see which files changed as part of a ‘merge’ commit)

The command below lists 5 commits 

-n : number of commits 

-m : This option makes diff output for merge commits to be shown in the 
default format. (More details here: https://git-scm.com/docs/git-show)

-—name-only: will display only the names of the files


Rgraphviz ❯❯❯ git log -m --name-only -n 5   


commit 50a89903830505a1a686570825304f7a30e194f1 (HEAD -> master, origin/master, 
origin/HEAD)
Author: kasperdanielhansen 
Date:   Thu Aug 12 21:19:44 2021 -0400

fixing seg fault

DESCRIPTION
src/doLayout.c

commit 43207afdc87afc04bbc8b2a1acbbdb3b531d25b3
Author: kasperdanielhansen 
Date:   Thu Aug 12 21:18:02 2021 -0400

removing testing vignette

vignettes/testing.Rmd

commit 955e30b3ae316265b4f5f130ab6f12c33081da54
Author: Kasper Daniel Hansen 
Date:   Wed Aug 11 08:52:11 2021 -0400

Fixing length condition error

DESCRIPTION
man/agopenSimple.Rd

commit 15204d879d974de8d40b0342b2f853c88f4bf9a3 (from 
7c1433d9f6025e3195f27ccc18a1439398221ffc)
Merge: 7c1433d b01ad95
Author: Kasper Daniel Hansen 
Date:   Wed Aug 11 08:26:09 2021 -0400

Merge remote-tracking branch 'upstream/master'

DESCRIPTION

commit 15204d879d974de8d40b0342b2f853c88f4bf9a3 (from 
b01ad9552737978b3b7db6815323a078ceafe041)
Merge: 7c1433d b01ad95
Author: Kasper Daniel Hansen 
Date:   Wed Aug 11 08:26:09 2021 -0400

Merge remote-tracking branch 'upstream/master'

R/plotGraph.R
src/doLayout.c
vignettes/testing.Rmd


As you can see above, the files which changed are listed. You can also see 
“only” merge commits and the files that change with this command,

git log --merges -m --name-only -n 5


Hope this helps. 


Best regards,

Nitesh



Nitesh Turaga
Scientist II, Department of Data Science,
Bioconductor Core Team Member
Dana Farber Cancer Institute

> On Aug 13, 2021, at 9:34 AM, Kasper Daniel Hansen 
>  wrote:
> 
> Here are my experiences as a novice in git.
> 
> Yesterday I was working on fixing a condition length error in Rgraphviz, a
> package which has not been touched in years. After I fixed this, I got a
> segmentation fault in examples / tests / vignettes; all over the place.
> 
> This could have been related to a small git snafu I had on my laptop
> because I had not synchronized  laptop / Github / bioc git for a _long_
> time (read: years).
> 
> No matter, I thought, git history will easily reveal this, and since there
> has been no changes to the package in years, it should be really easy to
> just list which file had changed. However, running
>  git log --name-status
> I got this
> 
>  START git log ==
> commit 955e30b3ae316265b4f5f130ab6f12c33081da54
> Author: Kasper Daniel Hansen 
> Date:   Wed Aug 11 08:52:11 2021 -0400
> 
>Fixing length condition error
> 
> :100644 100644 25e24de 3aee690 MDESCRIPTION
> :100644 100644 f8e077f b73b052 Mman/agopenSimple.Rd
> 
> commit 15204d879d974de8d40b0342b2f853c88f4bf9a3
> Merge: 7c1433d b01ad95
> Author: Kasper Daniel Hansen 
> Date:   Wed Aug 11 08:26:09 2021 -0400
> 
>Merge remote-tracking branch 'upstream/master'
> 
> commit b01ad9552737978b3b7db6815323a078ceafe041
> Author: Nitesh Turaga 
> Date:   Wed May 19 15:33:11 2021 +
> 
>bump x.y.z version to odd y following creation of RELEASE_3_13 branch
> 
> :100644 100644 78243eb 25e24de MDESCRIPTION
> == END git log ==
> 
> This suggests that no files apart from DESCRIPTION and a man page were
> touched recently (it looks the same if I go back longer). Look at the
> second message with "Merge remote-tracking". No files are listed!
> 
> It turns out that files were indeed touched as part of the "Merge
> remote-tracking ..." commit. I can see this by a
>  git diff b01ad9552737978b3b7db6815323a078ceafe041
> but in reality I had given up on git and did a standard recursive diff on
> the stable release tarball and my codebase.
> 
> I have not been able to figure out what options I need to give git log to
> display which files changed as part of that commit, and I find that
> perplexing and -- frankly -- pretty worrying.
> 
> Anyway, just some scary lessons on git log and merge.
> 
> Best
> 
> -- 
> Best,
> Kasper
> 
>   [[alternative HTML version deleted]]
> 
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Re: [Bioc-devel] Best practices for joint release/update of BioC packages

[Nitesh Turaga]

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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Re: [Bioc-devel] Git lfs support

[Nitesh Turaga]

Hi,

We don’t have LFS support on the Bioconductor git server.

I would suggest finding an alternative.

Best,




Nitesh Turaga
Scientist II, Department of Data Science,
Bioconductor Core Team Member
Dana Farber Cancer Institute

> On Aug 24, 2021, at 6:18 PM, Anatoly Sorokin  wrote:
> 
> Hi all,
> 
> we have developed a package that provides access to the data in the locally
> stored SQLite database. The GitHub Action successfully built the package,
> but in Bioconductor, it got an error. The only reason for the error is that
> the database itself is stored on GitHub via git-lfs, and the R code got an
> lfs placeholder instead of the actual database.
> 
> Is it possible to activate lfs within Bioconductor automatic building
> server? The database is tiny (80 Mb), but I don't want to have it as a
> regular git object.
> 
> Thank you,
> Anatoly
> 
>   [[alternative HTML version deleted]]
> 
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Re: [Bioc-devel] git: lost write access to some repos + what is my BiocCredentials email address?

[Nitesh Turaga]

Hi Henrik,

You should have access to these packages again. 

Please try again.

Best

Nitesh Turaga
Scientist II, Department of Data Science,
Bioconductor Core Team Member
Dana Farber Cancer Institute

> On Aug 19, 2021, at 8:08 AM, Henrik Bengtsson  
> wrote:
> 
> Hi,
> 
> I seem to have "lost" write access to several Bioconductor git
> repositories that I had git push access for before;
> 
> $ ssh -T g...@git.bioconductor.org | grep -E
> "(affxparser|aroma.light|illuminaio|QDNAseq)$"
> X11 forwarding request failed on channel 0
> R  packages/QDNAseq
> R  packages/affxparser
> R  packages/aroma.light
> R Wpackages/illuminaio
> 
> Using `ssh -v ...`, I see that my git+ssh "offers" the server an RSA
> public key (B...PwYDZ), which is accepted.  Since this gives me
> write access to one of the repositories, I either have lost write
> access to the others, or I somehow have ended up with different SSH
> keys associated with different repositories (since I had write
> permissions in the past).
> 
> For example, with:
> 
> $ git clone g...@git.bioconductor.org:packages/aroma.light
> $ cd aroma.light
> $ git remote -v
> origing...@git.bioconductor.org:packages/aroma.light (fetch)
> origing...@git.bioconductor.org:packages/aroma.light (push)
> 
> I get:
> 
> $ git push
> X11 forwarding request failed on channel 0
> FATAL: W any packages/aroma.light h.bengtsson 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.
> 
> I followed FAQ #15 to check what SSH key I have on BiocCredentials,
> but when I try to activate the account on
> https://git.bioconductor.org/BiocCredentials/account_activation/ using
> the email address I have in the DESCRIPTION file, I get
> "henr...@braju.com is not associated with a maintainer of a
> Bioconductor package. Please check the spelling or contact
> bioc-devel@r-project.org for help."(*) I suspect it's another email
> address I should use, possibly one from the SVN era. How can I find
> out which email address I should use?
> 
> (*) FYI, the webpage hint reading "Enter the email associated with
> your Bioconductor package" might be ambiguous; Is it really specific
> to a particular package?  Should it say something like "Enter the
> email associated with your Bioconductor developer account"?
> 
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Re: [Bioc-devel] Pushing an update to already released package

[Nitesh Turaga]

Hi

There are no notifications for every push. This is unrealistic, because there 
are hundreds of pushes if not thousands to our ecosystem each day.

Depending on your package and if you have your repository configured properly, 
you can check https://code.bioconductor.org/browse/. You could also check the 
RSS feed for our git server http://bioconductor.org/developers/gitlog/ 

There are other helpful FAQ here, 
http://bioconductor.org/developers/how-to/git/faq/. 

Nitesh Turaga
Scientist II, Department of Data Science,
Bioconductor Core Team Member
Dana Farber Cancer Institute

> On Jul 29, 2021, at 10:06 AM, Oluwafemi OLUSOJI via Bioc-devel 
>  wrote:
> 
> Hello All,
> 
> I just pushed an update to the upstream branch of a recently released
> package (cyanoFilter). I did not get any notification so I am not sure if
> this was the right thing to do.
> If not, what am I missing?
> 
> Regards,
> Daniel
> 
>   [[alternative HTML version deleted]]
> 
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Re: [Bioc-devel] EXTERNAL: R: Bioconductor package DaMiRseq

[Nitesh Turaga]

Hi,

Everything on our end looks good. I just checked.

It must be your SSH key or the permissions on your SSH key. Please try to go 
through the FAQ section, http://bioconductor.org/developers/how-to/git/faq/ 
specifically #13 onwards. 

You have access rights on our system. There is no problem there. If all else 
fails, generate a new SSH key and add it.

Best

Nitesh Turaga
Scientist II, Department of Data Science,
Bioconductor Core Team Member
Dana Farber Cancer Institute

> On Jul 29, 2021, at 3:20 AM, Mattia Chiesa  wrote:
> 
> Dear all,
> sorry to keep asking but I did not solve the problem yet and I cannot figure 
> out how to fix it.
> I copied the ssh key, generated, after activating the bioc credentials, in 
> the ~/.ssh/id_rsa.pub file.
> 
> Now, I can communicate with 'origin':
> $ git pull origin master
> From https://github.com/BioinfoMonzino/DaMiRseq
>  * branchmaster -> FETCH_HEAD
> Already up to date.
> 
> but not with 'upstream' that I need to modify the package, which is in ERROR 
> status :
> $ git pull upstream master
> kex_exchange_identification: read: Connection reset by peer
> Connection reset by 34.192.48.227 port 22
> fatal: Could not read from remote repository.
> 
> Please make sure you have the correct access rights
> and the repository exists.
> 
> These are my remote repos:
> $ git remote -v
> origin  https://github.com/BioinfoMonzino/DaMiRseq.git (fetch)
> origin  https://github.com/BioinfoMonzino/DaMiRseq.git (push)
> upstreamg...@git.bioconductor.org:packages/DaMiRseq.git (fetch)
> upstreamg...@git.bioconductor.org:packages/DaMiRseq.git (push)
> 
> Thanks in advance,
> Mattia
> 
> 
> 
> 
> Da: Mattia Chiesa 
> Inviato: mercoledì 28 luglio 2021 10:09
> A: bioc-devel@r-project.org ; 
> marcel.ra...@roswellpark.org 
> Oggetto: R: [Bioc-devel] EXTERNAL: R: Bioconductor package DaMiRseq
>  
> I fixed some Github stuffs, related to the generation of token for the 
> authentication, and now I can communicate with the DaMiRseq package at  
> https://github.com/BioinfoMonzino/DaMiRseq (origin master); however, I got 
> again the same (connection) problem when I try to push/pull with 
> git.bioconductor.org (upstream master).
> Therefore, I cannot modify DESCRPTION file in 
> https://code.bioconductor.org/browse/DaMiRseq/blob/master/DESCRIPTION
> 
> Mattia
> 
> 
> 
> 
> 
> Da: Bioc-devel  per conto di Marcel Ramos 
> 
> Inviato: martedì 27 luglio 2021 17:06
> A: bioc-devel@r-project.org 
> Oggetto: Re: [Bioc-devel] EXTERNAL: R: Bioconductor package DaMiRseq
>  
> Hi Mattia,
> 
> Make sure you are pushing to git.bioconductor.org in addition to GitHub. 
> I still see
> 
> Maintainer: Mattia Chiesa 
> 
> in the git.bioconductor.org repo:
> 
> https://code.bioconductor.org/browse/DaMiRseq/blob/master/DESCRIPTION
> 
> 
> Best,
> 
> Marcel
> 
> On 7/27/21 11:00 AM, Mattia Chiesa wrote:
> > Sorry Nitesh but maybe I missed something.
> > I activated Bioc Credential; I checked the ssh keys in .ssh/id_rsa.pub 
> > (before generating a newest one) and it was the same in my BiocCredential 
> > profile. I changed the mantainer's mail in DESCRIPTION directly by Github.  
> > But nothing changes: I've got again the error.
> >
> > 
> > Da: Nitesh Turaga 
> > Inviato: martedì 27 luglio 2021 16:10
> > A: Mattia Chiesa 
> > Cc: bioc-devel 
> > Oggetto: Re: [Bioc-devel] Bioconductor package DaMiRseq
> >
> > Please add your SSH keys and you’ll gain access to your package.
> >
> > Once you get access, change the maintainer email address in the DESCRIPTION 
> > file of the package.
> >
> > Best,
> >
> >
> > Nitesh Turaga
> > Scientist II, Department of Data Science,
> > Bioconductor Core Team Member
> > Dana Farber Cancer Institute
> >
> >> On Jul 27, 2021, at 10:09 AM, Mattia Chiesa  
> >> wrote:
> >>
> >> Yes I'm still using my istitutional mail. I've just activated the Bioc 
> >> Credintials.
> >> Da: Nitesh Turaga 
> >> Inviato: martedì 27 luglio 2021 16:01
> >> A: Mattia Chiesa 
> >> Oggetto: Re: [Bioc-devel] Bioconductor package DaMiRseq
> >>
> >> Hi
> >>
> >> I guess the question is are you still using the email I referred to in the 
> >> previous email? Do you still have access to it?
> >>
> >> If so, you can activate your BiocCredentials account with that.
> >>
> >> Nitesh Turaga
> >> Scientist II, Department of Data Science,
> >> Bioconductor Core Team Member
&

Re: [Bioc-devel] pre-receive hook declined

[Nitesh Turaga]

Hi,

This is because all commits to RELEASE_3_12 have been blocked during the 
release of Bioconductor 3.13.

You can now only commit/push to RELEASE_3_13 and devel.

Nitesh Turaga
Scientist II, Department of Data Science,
Bioconductor Core Team Member
Dana Farber Cancer Institute

> On Jul 27, 2021, at 3:44 PM, Clay Wright  wrote:
> 
> Hi,
> 
> I am now encountering the following similar error trying to push a bugfix
> to my package. Does my account also need a similar update to Victor and
> Mike? Or is this something on my end? I just finally updated my github
> personal access tokens, maybe that's the issue? I haven't tried a fresh
> clone of the repository yet.
> 
> 
> git push origin RELEASE_3_12
> 
> Enumerating objects: 17, done.
> Counting objects: 100% (17/17), done.
> Delta compression using up to 4 threads
> Compressing objects: 100% (12/12), done.
> Writing objects: 100% (12/12), 1.48 KiB | 151.00 KiB/s, done.
> Total 12 (delta 9), reused 0 (delta 0), pack-reused 0
> remote: FATAL: W refs/heads/RELEASE_3_12 packages/flowTime r.wright DENIED
> by fallthru
> remote: error: hook declined to update refs/heads/RELEASE_3_12
> To git.bioconductor.org:packages/flowTime.git
> ! [remote rejected] RELEASE_3_12 -> RELEASE_3_12 (hook declined)
> error: failed to push some refs to 'git.bioconductor.org:
> packages/flowTime.git'
> 
> 
> Thanks!
> Clay
> 
> 
> On Fri, Jul 2, 2021 at 1:30 PM Victor Yuan  wrote:
> 
>> It works for me as well now. Thanks!
>> 
>> On Thu, Jul 1, 2021 at 8:21 AM Michael Love 
>> wrote:
>> 
>>> That works for me. Thanks.
>>> 
>>> Mike
>>> 
>>> On Thu, Jul 1, 2021 at 2:07 PM Nitesh Turaga 
>>> wrote:
>>>> 
>>>> Hi
>>>> 
>>>> Please try again. You should not see this error anymore.
>>>> 
>>>> This was a mistake on our end.
>>>> 
>>>> Best,
>>>> 
>>>> Nitesh
>>>> 
>>>> 
>>>> 
>>>> Nitesh Turaga
>>>> Scientist II, Department of Data Science,
>>>> Bioconductor Core Team Member
>>>> Dana Farber Cancer Institute
>>>> 
>>>>> On Jul 1, 2021, at 1:49 AM, Michael Love <
>> michaelisaiahl...@gmail.com>
>>> wrote:
>>>>> 
>>>>> I'm getting a similar error, trying to push commits for a new package
>>>>> submission. So this is my first attempt to push to Bioc git servers
>>>>> for this package.
>>>>> 
>>>>> After following instructions from
>>>>> https://bioconductor.org/developers/how-to/git/new-package-workflow/
>>>>> ...
>>>>> 
>>>>> spatialDmelxsim git:(main) > git push upstream main:master
>>>>> Enumerating objects: 20, done.
>>>>> Counting objects: 100% (20/20), done.
>>>>> Delta compression using up to 8 threads
>>>>> Compressing objects: 100% (10/10), done.
>>>>> Writing objects: 100% (12/12), 1.60 KiB | 1.60 MiB/s, done.
>>>>> Total 12 (delta 5), reused 0 (delta 0), pack-reused 0
>>>>> remote: Traceback (most recent call last):
>>>>> remote:   File
>>> "hooks/pre-receive.h00-pre-receive-hook-dataexp-workflow",
>>>>> line 90, in 
>>>>> remote: apply_hooks(hooks_dict)
>>>>> remote:   File
>>> "hooks/pre-receive.h00-pre-receive-hook-dataexp-workflow",
>>>>> line 72, in apply_hooks
>>>>> remote: if hooks_dict["pre-receive-hook-merge-markers"]:  #
>> enable
>>> hook
>>>>> remote: KeyError: 'pre-receive-hook-merge-markers'
>>>>> To git.bioconductor.org:packages/spatialDmelxsim
>>>>> ! [remote rejected] main -> master (pre-receive hook declined)
>>>>> error: failed to push some refs to
>>>>> 'git.bioconductor.org:packages/spatialDmelxsim'
>>>> 
>>> 
>> 
>>[[alternative HTML version deleted]]
>> 
>> ___
>> Bioc-devel@r-project.org mailing list
>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>> 
> 
>   [[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] Bioconductor package DaMiRseq

[Nitesh Turaga]

Please add your SSH keys and you’ll gain access to your package.

Once you get access, change the maintainer email address in the DESCRIPTION 
file of the package. 

Best,


Nitesh Turaga
Scientist II, Department of Data Science,
Bioconductor Core Team Member
Dana Farber Cancer Institute

> On Jul 27, 2021, at 10:09 AM, Mattia Chiesa  wrote:
> 
> Yes I'm still using my istitutional mail. I've just activated the Bioc 
> Credintials.
> Da: Nitesh Turaga 
> Inviato: martedì 27 luglio 2021 16:01
> A: Mattia Chiesa 
> Oggetto: Re: [Bioc-devel] Bioconductor package DaMiRseq
>  
> Hi 
> 
> I guess the question is are you still using the email I referred to in the 
> previous email? Do you still have access to it?
> 
> If so, you can activate your BiocCredentials account with that. 
> 
> Nitesh Turaga
> Scientist II, Department of Data Science,
> Bioconductor Core Team Member
> Dana Farber Cancer Institute
> 
> > On Jul 27, 2021, at 9:47 AM, Mattia Chiesa  wrote:
> > 
> > Sorry, but I really do not remember. Probably Yes! when we moved from SVN 
> > to GIT, I used my istitutional mail. However, I have never had problems in 
> > the past updating my packages by GitBash.
> > How can I fix it now?
> > Thanks Nitesh
> > Mattia
> > 
> > 
> > 
> > Da: Nitesh Turaga 
> > Inviato: martedì 27 luglio 2021 15:38
> > A: Mattia Chiesa 
> > Cc: bioc-devel@r-project.org 
> > Oggetto: Re: [Bioc-devel] Bioconductor package DaMiRseq
> >  
> > Hi
> > 
> > Are you using mattia.chi...@cardiologicomonzino.it to activate your 
> > BiocCredentials account? 
> > 
> > It seems this email is not the same as the one on the maintainer on the 
> > DESCRIPTION file of the package. 
> > 
> > Best,
> > 
> > Nitesh 
> > 
> > Nitesh Turaga
> > Scientist II, Department of Data Science,
> > Bioconductor Core Team Member
> > Dana Farber Cancer Institute
> > 
> > > On Jul 27, 2021, at 9:25 AM, Mattia Chiesa  
> > > wrote:
> > > 
> > > Dear all,
> > > I need to update my package 
> > > (DaMiRseq<https://www.bioconductor.org/packages/release/bioc/html/DaMiRseq.html>)
> > >  in order to fix a bug that makes the package fail in devel and release.
> > > I tried, as usual, to pull the latest version of package with:
> > > git pull upstream master
> > > but a connection error occurs:
> > > ssh_exchange_identification: read: Connection reset by peer
> > > fatal: Could not read from remote repository.
> > > Please make sure you have the correct access rights
> > > and the repository exists.
> > > 
> > > I asked to Lori who kindly invites me to write you. What should I do?
> > > In addition, I cannot activate the Bioconductor Git Credentials,  even 
> > > though I mantain the package since 2017.
> > > 
> > > Thanks in advance,
> > > Mattia
> > > 
> > > 
> > > 
> > > Da: Kern, Lori 
> > > Inviato: marted� 27 luglio 2021 14:29
> > > A: Mattia Chiesa 
> > > Oggetto: Re: Bioconductor package DaMiRseq
> > > 
> > > Regardless of whether it stems from a dependency package or not,  your 
> > > package is still failing in release and devel which is problematic.  If 
> > > the change is intentional from a dependent package, you would still have 
> > > to modify your code.  If you find it is from a dependent package and 
> > > consider it a bug,  I encourage you to reach out to their maintainer 
> > > directly as well.
> > > 
> > > Please ask further git access issues on bioc-devel@r-project.org mailing 
> > > list as there are dedicated members of the team to assist with access. To 
> > > start,  make sure you have a valid ssh key on the computer you are using, 
> > > and that the key is uploaded to the git credentials app.  If you have not 
> > > activated the git credentials app, be sure to activate your account 
> > > first.  Links to the app and other useful git workflow can be found here:
> > > http://bioconductor.org/developers/how-to/git/new-package-workflow/
> > > 
> > > Cheers,
> > > 
> > > 
> > > 
> > > 
> > > 
> > > Lori Shepherd
> > > 
> > > Bioconductor Core Team
> > > 
> > > Roswell Park Comprehensive Cancer Center
> > > 
> > > Department of Biostatistics & Bioinformatics
> > > 
> > > Elm & Carlton Streets
> > > 
> 

Re: [Bioc-devel] Bioconductor package DaMiRseq

[Nitesh Turaga]

Hi

Are you using mattia.chi...@cardiologicomonzino.it to activate your 
BiocCredentials account? 

It seems this email is not the same as the one on the maintainer on the 
DESCRIPTION file of the package. 

Best,

Nitesh 

Nitesh Turaga
Scientist II, Department of Data Science,
Bioconductor Core Team Member
Dana Farber Cancer Institute

> On Jul 27, 2021, at 9:25 AM, Mattia Chiesa  wrote:
> 
> Dear all,
> I need to update my package 
> (DaMiRseq<https://www.bioconductor.org/packages/release/bioc/html/DaMiRseq.html>)
>  in order to fix a bug that makes the package fail in devel and release.
> I tried, as usual, to pull the latest version of package with:
> git pull upstream master
> but a connection error occurs:
> ssh_exchange_identification: read: Connection reset by peer
> fatal: Could not read from remote repository.
> Please make sure you have the correct access rights
> and the repository exists.
> 
> I asked to Lori who kindly invites me to write you. What should I do?
> In addition, I cannot activate the Bioconductor Git Credentials,  even though 
> I mantain the package since 2017.
> 
> Thanks in advance,
> Mattia
> 
> 
> 
> Da: Kern, Lori 
> Inviato: marted� 27 luglio 2021 14:29
> A: Mattia Chiesa 
> Oggetto: Re: Bioconductor package DaMiRseq
> 
> Regardless of whether it stems from a dependency package or not,  your 
> package is still failing in release and devel which is problematic.  If the 
> change is intentional from a dependent package, you would still have to 
> modify your code.  If you find it is from a dependent package and consider it 
> a bug,  I encourage you to reach out to their maintainer directly as well.
> 
> Please ask further git access issues on bioc-devel@r-project.org mailing list 
> as there are dedicated members of the team to assist with access. To start,  
> make sure you have a valid ssh key on the computer you are using, and that 
> the key is uploaded to the git credentials app.  If you have not activated 
> the git credentials app, be sure to activate your account first.  Links to 
> the app and other useful git workflow can be found here:
> http://bioconductor.org/developers/how-to/git/new-package-workflow/
> 
> Cheers,
> 
> 
> 
> 
> 
> Lori Shepherd
> 
> Bioconductor Core Team
> 
> Roswell Park Comprehensive Cancer Center
> 
> Department of Biostatistics & Bioinformatics
> 
> Elm & Carlton Streets
> 
> Buffalo, New York 14263
> 
> 
> From: Mattia Chiesa 
> Sent: Tuesday, July 27, 2021 5:06 AM
> To: Kern, Lori 
> Subject: R: Bioconductor package DaMiRseq
> 
> Dear Lori,
> Since I haven't modified DaMiRseq for several months, I think the the problem 
> could be related to some Damirseq dependencies.
> Anyway, I tried to go deep into the problem, but when I type:
> git pull upstream master
> a connection error occurs:
> ssh_exchange_identification: read: Connection reset by peer
> fatal: Could not read from remote repository.
> Please make sure you have the correct access rights
> and the repository exists.
> 
> It's the first time I have experinced this problem. What should I do?
> Thanks In advance.
> Mattia
> 
> 
> 
> Da: Kern, Lori 
> Inviato: luned� 26 luglio 2021 16:55
> A: mattia.chi...@hotmail.it 
> Oggetto: Bioconductor package DaMiRseq
> 
> We would like to bring to your attention that your package is failing to build
> or check on our release and devel build machines:
> 
> Devel:
> http://bioconductor.org/checkResults/3.14/bioc-LATEST/<http://secure-web.cisco.com/1UyHFFpElhlwoJASYNWNnZo294YfOAS2eA-p2cjmz_DSDOF7yfSSvnTsaWfgpR1F03jqoFKgAspBBEeYNfj1PZhObI9jNDtfIEciWCb5icLfNgkIPsjNScxTtUrhAiUJfpwX1edKaYyjjfRmcH0tpo8_bG7MbqZWqkyL1PcWBQwLbjU_fO4UKLxjBmK_VXNwz6SsMCrYCO27DgHBRWvvQi5im5uzCiGg1HlXwSSVi_1Y5fDp8kh52CbA_eo7SuaKaCcjsfEn5qVvTrl6YIlBCANzv2HubDATSyRHIu9nGNZG7mF3Ky8x4fk2dXP45/http%3A%2F%2Fbioconductor.org%2FcheckResults%2F3.14%2Fbioc-LATEST%2FCHETAH%2F>DaMiRseq
> 
> Release:
> http://bioconductor.org/checkResults/3.13/bioc-LATEST/<http://secure-web.cisco.com/1h7aSKHWtsfb4cOI13Zh8EU4a5W856Zce40L3uyRNdZTtbeGJQMra08tCbRLlaKugtrt2IECy6CVe6neRyat4TcRkKG4IEZyrSEipziS7yH_RNNvEAkRC8zauoM6Ai7f_9UZojDR7tXXczshLqKDLZteLqLDX9baox4e-VZG8wMfuKwpTvE6cNGtDHFMEZ3rzhOR1IT3M_3xSYbknmx0Q71qZxihn2YtiYhjU4Up9pe4bXUjhWRxl6LOhqp9PgND-GKfgV5YeyM3XFZKfynGIEcs8lF-8eZl1GbgEzIcKHUJ1FupgfLANKtUF7v_ibzB6/http%3A%2F%2Fbioconductor.org%2FcheckResults%2F3.13%2Fbioc-LATEST%2FCHETAH%2F>DaMiRseq
> 
> Would you mind taking a look at this? Don't hesitate to ask on the bioc-devel 
> mailing list if you have any question or need help.
> 
> This is very problematic.   If 

Re: [Bioc-devel] BentoBox and BentoBoxData git.bioconductor repositories

[Nitesh Turaga]

Hello,

Please take a look at http://bioconductor.org/developers/how-to/git/faq/ #13 
onwards to see if any of those issues fix your problem.

There is nothing wrong on our end.

Best,

Nitesh 

Nitesh Turaga
Scientist II, Department of Data Science,
Bioconductor Core Team Member
Dana Farber Cancer Institute

> On Jul 26, 2021, at 6:28 PM, Kramer, Nicole Emma  
> wrote:
> 
> I've also been having issues pushing to the BentoBoxData git.bioconductor.org 
> repo, but I do not have trouble with the BentoBox repo. Do I have the correct 
> permissions?
> 
> Thank you,
> Nicole
> 
> --
> Nicole Kramer
> Ph.D. Student in Bioinformatics and Computational Biology
> University of North Carolina at Chapel Hill
> nekra...@live.unc.edu
> From: Nitesh Turaga 
> Sent: Monday, July 26, 2021 4:48 PM
> To: Kramer, Nicole Emma 
> Cc: bioc-devel 
> Subject: Re: [Bioc-devel] BentoBox and BentoBoxData git.bioconductor 
> repositories
>  
> Hi Nicole,
> 
> Please sync your two repos now. You should be all set.
> 
> Best,
> 
> Nitesh Turaga
> Scientist II, Department of Data Science,
> Bioconductor Core Team Member
> Dana Farber Cancer Institute
> 
> > On Jul 26, 2021, at 12:44 PM, Kramer, Nicole Emma  
> > wrote:
> > 
> > Hi Nitesh,
> > 
> > Thank you so much!
> > 
> > Best,
> > Nicole
> > 
> > --
> > Nicole Kramer
> > Ph.D. Student in Bioinformatics and Computational Biology
> > University of North Carolina at Chapel Hill
> > nekra...@live.unc.edu
> > From: Nitesh Turaga 
> > Sent: Monday, July 26, 2021 11:21 AM
> > To: Kramer, Nicole Emma 
> > Cc: bioc-devel@r-project.org 
> > Subject: Re: [Bioc-devel] BentoBox and BentoBoxData git.bioconductor 
> > repositories
> >  
> > Hi Nicole,
> > 
> > Thank you for cleaning the repos. 
> > 
> > I will do the force push for you, but you will have to re-sync the Github 
> > repo once it’s done. 
> > 
> > I’ll email you as soon as I’m done with the force push.
> > 
> > Best,
> > 
> > Nitesh 
> > 
> > Nitesh Turaga
> > Scientist II, Department of Data Science,
> > Bioconductor Core Team Member
> > Dana Farber Cancer Institute
> > 
> > > On Jul 24, 2021, at 6:54 PM, Kramer, Nicole Emma  
> > > wrote:
> > > 
> > > Hello,
> > > 
> > > I am in the review process for the packages BentoBoxData and BentoBox and 
> > > I am attempting to make changes to these packages. However, they have 
> > > been cleaned for large data files and need to be reset at their 
> > > git.bioconductor.org locations. Would I be able to get these repos force 
> > > pushed?
> > > 
> > > Thank you,
> > > Nicole Kramer
> > > 
> > > 
> > > --
> > > 
> > > Nicole Kramer
> > > 
> > > Ph.D. Student in Bioinformatics and Computational Biology
> > > 
> > > University of North Carolina at Chapel Hill
> > > 
> > > nekra...@live.unc.edu
> > > 
> > >[[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] BentoBox and BentoBoxData git.bioconductor repositories

[Nitesh Turaga]

Hi Nicole,

Please sync your two repos now. You should be all set.

Best,

Nitesh Turaga
Scientist II, Department of Data Science,
Bioconductor Core Team Member
Dana Farber Cancer Institute

> On Jul 26, 2021, at 12:44 PM, Kramer, Nicole Emma  
> wrote:
> 
> Hi Nitesh,
> 
> Thank you so much!
> 
> Best,
> Nicole
> 
> --
> Nicole Kramer
> Ph.D. Student in Bioinformatics and Computational Biology
> University of North Carolina at Chapel Hill
> nekra...@live.unc.edu
> From: Nitesh Turaga 
> Sent: Monday, July 26, 2021 11:21 AM
> To: Kramer, Nicole Emma 
> Cc: bioc-devel@r-project.org 
> Subject: Re: [Bioc-devel] BentoBox and BentoBoxData git.bioconductor 
> repositories
>  
> Hi Nicole,
> 
> Thank you for cleaning the repos. 
> 
> I will do the force push for you, but you will have to re-sync the Github 
> repo once it’s done. 
> 
> I’ll email you as soon as I’m done with the force push.
> 
> Best,
> 
> Nitesh 
> 
> Nitesh Turaga
> Scientist II, Department of Data Science,
> Bioconductor Core Team Member
> Dana Farber Cancer Institute
> 
> > On Jul 24, 2021, at 6:54 PM, Kramer, Nicole Emma  
> > wrote:
> > 
> > Hello,
> > 
> > I am in the review process for the packages BentoBoxData and BentoBox and I 
> > am attempting to make changes to these packages. However, they have been 
> > cleaned for large data files and need to be reset at their 
> > git.bioconductor.org locations. Would I be able to get these repos force 
> > pushed?
> > 
> > Thank you,
> > Nicole Kramer
> > 
> > 
> > --
> > 
> > Nicole Kramer
> > 
> > Ph.D. Student in Bioinformatics and Computational Biology
> > 
> > University of North Carolina at Chapel Hill
> > 
> > nekra...@live.unc.edu
> > 
> >[[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] BentoBox and BentoBoxData git.bioconductor repositories

[Nitesh Turaga]

Hi Nicole,

Thank you for cleaning the repos. 

I will do the force push for you, but you will have to re-sync the Github repo 
once it’s done. 

I’ll email you as soon as I’m done with the force push.

Best,

Nitesh 

Nitesh Turaga
Scientist II, Department of Data Science,
Bioconductor Core Team Member
Dana Farber Cancer Institute

> On Jul 24, 2021, at 6:54 PM, Kramer, Nicole Emma  
> wrote:
> 
> Hello,
> 
> I am in the review process for the packages BentoBoxData and BentoBox and I 
> am attempting to make changes to these packages. However, they have been 
> cleaned for large data files and need to be reset at their 
> git.bioconductor.org locations. Would I be able to get these repos force 
> pushed?
> 
> Thank you,
> Nicole Kramer
> 
> 
> --
> 
> Nicole Kramer
> 
> Ph.D. Student in Bioinformatics and Computational Biology
> 
> University of North Carolina at Chapel Hill
> 
> nekra...@live.unc.edu
> 
>   [[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] Maintainer change

[Nitesh Turaga]

Hi Mikhail,

You now have access to both packages.

Please remove the previous maintainer in the DESCRIPTION file and add yourself 
as the new maintainer. 

Best,

Nitesh 

Nitesh Turaga
Scientist II, Department of Data Science,
Bioconductor Core Team Member
Dana Farber Cancer Institute

> On Jul 18, 2021, at 8:48 PM, Mikhail Dozmorov  
> wrote:
> 
> Please, add me, Mikhail Dozmorov, as a maintainer of the
> https://bioconductor.org/packages/preciseTAD/ and
> https://bioconductor.org/packages/preciseTADhub/ packages. The current
> maintainer cannot be reached.
> 
> Thanks,
> Mikhail
> 
> ---
> Mikhail Dozmorov, Ph.D.
> Department of Biostatistics, VCU
> 
>   [[alternative HTML version deleted]]
> 
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Re: [Bioc-devel] Git credentials

[Nitesh Turaga]

Hi Ludwig,

Could you please try to activate your account now?

I’ve changed your email.

Best,

Nitesh 

Nitesh Turaga
Scientist II, Department of Data Science,
Bioconductor Core Team Member
Dana Farber Cancer Institute

> On Jul 15, 2021, at 10:57 AM, Geistlinger, Ludwig 
>  wrote:
> 
> Hi I am trying to update my Bioc git credentials.
> 
> Under:
> 
> https://git.bioconductor.org/BiocCredentials/account_activation/
> 
> I am trying to activate my account using the email
> 
> ludwig_geistlin...@hms.harvard.edu
> 
> that is listed as the email in the maintainer field of my Bioc packages (eg 
> EnrichmentBrowser, GSEABenchmarker, CNVRanger).
> 
> However, I get a
> 
> ludwig_geistlin...@hms.harvard.edu is not associated with a maintainer of a 
> Bioconductor package. Please check the spelling or contact 
> bioc-devel@r-project.org for help.
> 
> Can you please advise how to proceed?
> 
> Thanks,
> Ludwig
> 
> ---
> Dr. Ludwig Geistlinger
> Center for Computational Biomedicine
> Harvard Medical School
> 
>   [[alternative HTML version deleted]]
> 
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Re: [Bioc-devel] Updating stable release

[Nitesh Turaga]

Hi Margaret,

Please follow the documentation on the website, 
http://bioconductor.org/developers/how-to/git/. 

http://bioconductor.org/developers/how-to/version-numbering/ 

Best,

Nitesh 


Nitesh Turaga
Scientist II, Department of Data Science,
Bioconductor Core Team Member
Dana Farber Cancer Institute

> On Jul 14, 2021, at 4:01 PM, James W. MacDonald  wrote:
> 
> The release version of your package is 1.8.0, and the devel is on increment 
> ahead (e.g., 1.9.x). You cannot increment the middle version number of your 
> release package because that makes it a devel package, hence the pre-release 
> hook denying your changes.
> 
> You should change the version to 1.8.1 for the release version.
> 
> Jim
> 
> 
> -Original Message-
> From: Bioc-devel  On Behalf Of margaret 
> linan
> Sent: Wednesday, July 14, 2021 12:56 PM
> To: bioc-devel 
> Subject: Re: [Bioc-devel] Updating stable release
> 
> Hi -
> 
> I successfully updated my devel PoTRA package recently, now I am trying to 
> push these same changes to the stable PoTRA package. I am encountering the 
> following issue (see highlight below).
> Note - in the github PoTRA repo, I have pulled and merged from head --> 
> RELEASE_3_13. Also the devel commit never had a problem with my version bump.
> 
> 
>>>>> git checkout master
> Already on 'master'
> Your branch is up to date with 'origin/master'.
> 
>>>>> git checkout RELEASE_3_13
> Switched to branch 'RELEASE_3_13'
> Your branch is up to date with 'origin/RELEASE_3_13'.
> 
>>>>> git push upstream RELEASE_3_13
> Enumerating objects: 1, done.
> Counting objects: 100% (1/1), done.
> Writing objects: 100% (1/1), 641 bytes | 641.00 KiB/s, done.
> Total 1 (delta 0), reused 0 (delta 0), pack-reused 0
> remote: Error: Illegal version bump from '1.8.0' to '1.9.1'.
> remote:
> remote: Check http://bioconductor.org/developers/how-to/version-numbering/
> remote: for details.
> remote:
> To git.bioconductor.org:packages/PoTRA.git
> ! [remote rejected] RELEASE_3_13 -> RELEASE_3_13 (pre-receive hook
> declined)
> error: failed to push some refs to 'git.bioconductor.org:packages/PoTRA.git'
> 
> Thanks,
> Margaret
> 
> 
> 
> 
> On Wed, Jul 14, 2021 at 9:01 AM Kern, Lori 
> wrote:
> 
>> In your steps you were good when you checked out RELEASE_3_13
>> 
>> So after git checkout RELEASE_3_13
>> 
>> apply the changes you did to fix master.  You can do this manually or 
>> you investigate how to use git cherry-pick
>> 
>> When you have changed the files remember to do a git commit that 
>> includes the version bump in the DESCRIPTION
>> 
>> You should push those changes with a git push upstream RELEASE_3_13
>> 
>> Please ask further questions on bioc-devel so other members of the 
>> team can also assist.
>> 
>> Cheers,
>> 
>> Lori Shepherd
>> 
>> Bioconductor Core Team
>> 
>> Roswell Park Comprehensive Cancer Center
>> 
>> Department of Biostatistics & Bioinformatics
>> 
>> Elm & Carlton Streets
>> 
>> Buffalo, New York 14263
>> --
>> *From:* margaret linan 
>> *Sent:* Wednesday, July 14, 2021 11:55 AM
>> *To:* Kern, Lori 
>> *Subject:* Re: [Bioc-devel] Updating stable release
>> 
>> Hi Lori,
>> 
>> I followed the instructions, but it seems that everything is 
>> up-to-date already, I also didn't see anything pushed to RELEASE_3_13. 
>> Here are my steps.
>> 
>>>>>> git fetch --all
>> Fetching origin
>> Fetching upstream
>> 
>>>>>> git checkout RELEASE_3_13
>> Switched to a new branch 'RELEASE_3_13'
>> Branch 'RELEASE_3_13' set up to track remote branch 'RELEASE_3_13' 
>> from 'upstream'.
>> 
>>>>>> git merge upstream/RELEASE_3_13
>> Already up to date.
>> 
>>>>>> git merge origin/RELEASE_3_13
>> merge: origin/RELEASE_3_13 - not something we can merge
>> 
>>>>>> git checkout master
>> Switched to branch 'master'
>> Your branch is up to date with 'origin/master'.
>> 
>>>>>> git checkout -b RELEASE_3_13 upstream/RELEASE_3_13
>> fatal: A branch named 'RELEASE_3_13' already exists.
>> 
>>>>>> git checkout master
>> Already on 'master'
>> Your branch is up to date with 'origin/master'.
>> 
>>>>>> git push upstream RELEASE_3_13
>> Everything up-to-date
>> 
>>>>>> git push origin RELEASE_3_13
>> Total 0 (delta 0), reused 0 (delta 0), pack-reus

Re: [Bioc-devel] Getting ready for package submission, running into a couple of errors/warnings that I can't figure out

[Nitesh Turaga]

Hi,

I will try to answer a couple of the questions you asked. I am not able to help 
with your question on ‘qpdf'. 

> On Jul 12, 2021, at 5:58 PM, Wight, Andrew E. 
>  wrote:
> 
> Good evening all - I'm getting my first package ready for submission to 
> Bioconductor, and I'm running into a couple of errors/warnings when I run R 
> CMD CHECK or BiocCheck. All of my current troubleshooting on these errors has 
> come up blank, so I'm hoping someone here can point me in the right direction.
> 
> I'm running R4.1 on Ubuntu 20.04, Bioconductor 3.13, and BiocCheck 1.28
> 
> 
>  1.  R CMD check warning: �qpdf� is needed for checks on size reduction of 
> PDFs
> 
> I am getting this warning with R CMD check despite the fact that I have 
> installed qpdf and it is visible to my R session. Stack Exchange suggested a 
> couple of fixes in .Renviron, none of which helped. This seems like a new 
> problem in R4.x, and possibly is only a problem with packages intended for 
> CRAN, but I wanted to make sure it wouldn't cause headaches during review.
> 
> 
>  1.  BiocCheck error: Maintainer must register at the support site; visit 
> https://support.bioconductor.org/accounts/signup/
> 
> I am registered on the support site as andrewe_wi...@dfci.harvard.edu, which 
> is the same email address as listed in my package's DESCRIPTION, so I'm not 
> sure what else to do here. I've been registered on the support site for 7 
> months now and have a verified email address.
> 

I don’t **think** local installation of BiocCheck has the ability to cross 
check the support site database of registered users. If you are registered, 
trust that once submitted this issue will not show up.  

>  1.  BiocCheckGitClone error: System Files found that should not be git 
> tracked:
>flowGate.Rproj
>.Rhistory
> 
> I accidentally tracked these two files ages past, but have long since added 
> them to .gitignore and deleted them with git rm --cached . I can 
> confirm that they are gone with git ls-files and git ls-files --cache; they 
> appear in neither of these lists when I run the command. To be certain, I 
> made a fresh clone of the repo on a new computer and ran BiocCheckGitClone, 
> but still got this error despite neither of these files showing up anywhere 
> in the git as far as I can tell.
> 

You would need to “purge” the file from your repository history. There is good 
documentation in a couple of places, for the tool called BFG repo cleaner.

- 
https://docs.github.com/en/github/authenticating-to-github/keeping-your-account-and-data-secure/removing-sensitive-data-from-a-repository#purging-a-file-from-your-repositorys-history

- https://rtyley.github.io/bfg-repo-cleaner/


> 
> My apologies for what seem like basic problems - these look like they should 
> be straightforward fixes (install qpdf, register for the site, and remove the 
> offending files), but none of those fixes worked and I'm not sure where to go 
> from here. Any insight anyone can give on how to fix these errors is greatly 
> appreciated!
> 
> Thanks,
> 
> -Andrew
> 
> 
> 
> 
> The information in this e-mail is intended only for th...{{dropped:17}}

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Re: [Bioc-devel] lack of ability to push changes to new bioc repo via git

[Nitesh Turaga]

Hi Ben,


Please activate your account at 
https://git.bioconductor.org/BiocCredentials/account_activation. Once you do 
that, you can add SSH keys and gain access to your package.

Best,


Nitesh Turaga
Scientist II, Department of Data Science,
Bioconductor Core Team Member
Dana Farber Cancer Institute

> On Jul 1, 2021, at 8:29 AM, Benjamin Story  wrote:
> 
> Dear Bioc,
> 
> For some reason my github public key isn’t working with the BioC git (see
> comment). I'm just trying to push some fixes to my package under review.
> 
> Here is the command I'm running:
> 
> git remote -v
> origin g...@github.com:benstory/mitoClone2 (fetch)
> origin g...@github.com:benstory/mitoClone2 (push)
> upstream g...@git.bioconductor.org:packages/mitoClone2.git (fetch)
> upstream g...@git.bioconductor.org:packages/mitoClone2.git (push)
> then
> git fetch --all
> Fetching origin
> Fetching upstream
> Permission denied (publickey).
> 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
> also
> I tried to login/reset here ((
> https://git.bioconductor.org/BiocCredentials/login/?next=/BiocCredentials/)
> but I think my e-mail is not currently associated with the package (i.e. i
> get the error when activating that my email *is not associated with a
> maintainer of a Bioconductor package*). Although it is listed in the
> DESCRIPTION https://github.com/Bioconductor/Contributions/issues/2158
> 
> Any help would be great.
> 
> Thanks for your time,
> Ben
> 
>   [[alternative HTML version deleted]]
> 
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Re: [Bioc-devel] pre-receive hook declined

[Nitesh Turaga]

Hi

Please try again. You should not see this error anymore.

This was a mistake on our end. 

Best,

Nitesh 



Nitesh Turaga
Scientist II, Department of Data Science,
Bioconductor Core Team Member
Dana Farber Cancer Institute

> On Jul 1, 2021, at 1:49 AM, Michael Love  wrote:
> 
> I'm getting a similar error, trying to push commits for a new package
> submission. So this is my first attempt to push to Bioc git servers
> for this package.
> 
> After following instructions from
> https://bioconductor.org/developers/how-to/git/new-package-workflow/
> ...
> 
> spatialDmelxsim git:(main) > git push upstream main:master
> Enumerating objects: 20, done.
> Counting objects: 100% (20/20), done.
> Delta compression using up to 8 threads
> Compressing objects: 100% (10/10), done.
> Writing objects: 100% (12/12), 1.60 KiB | 1.60 MiB/s, done.
> Total 12 (delta 5), reused 0 (delta 0), pack-reused 0
> remote: Traceback (most recent call last):
> remote:   File "hooks/pre-receive.h00-pre-receive-hook-dataexp-workflow",
> line 90, in 
> remote: apply_hooks(hooks_dict)
> remote:   File "hooks/pre-receive.h00-pre-receive-hook-dataexp-workflow",
> line 72, in apply_hooks
> remote: if hooks_dict["pre-receive-hook-merge-markers"]:  # enable hook
> remote: KeyError: 'pre-receive-hook-merge-markers'
> To git.bioconductor.org:packages/spatialDmelxsim
> ! [remote rejected] main -> master (pre-receive hook declined)
> error: failed to push some refs to
> 'git.bioconductor.org:packages/spatialDmelxsim'

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Re: [Bioc-devel] pre-receive hook declined

[Nitesh Turaga]

Hi,


Can you please try again??


It seems a minor issue on our end, which I just fixed.

Best,

Nitesh 

Nitesh Turaga
Scientist II, Department of Data Science,
Bioconductor Core Team Member
Dana Farber Cancer Institute

> On Jun 30, 2021, at 1:41 PM, Victor Yuan  wrote:
> 
> Hi I cannot seem to push to the remote g...@git.bioconductor.org:
> packages/GSE159526
> 
> I get a "pre-receive hook declined" error:
> 
> 
> $ git push upstream master
> Enumerating objects: 21, done.
> Counting objects: 100% (21/21), done.
> Delta compression using up to 12 threads
> Compressing objects: 100% (15/15), done.
> Writing objects: 100% (15/15), 1.55 KiB | 1.55 MiB/s, done.
> Total 15 (delta 9), reused 0 (delta 0), pack-reused 0
> remote: Traceback (most recent call last):
> remote:   File "hooks/pre-receive.h00-pre-receive-hook-dataexp-workflow",
> line 89, in 
> remote: apply_hooks(hooks_dict)
> remote:   File "hooks/pre-receive.h00-pre-receive-hook-dataexp-workflow",
> line 71, in apply_hooks
> remote: if hooks_dict["pre-receive-hook-merge-markers"]:  # enable hook
> remote: KeyError: 'pre-receive-hook-merge-markers'
> To git.bioconductor.org:packages/GSE159526
> ! [remote rejected] master -> master (pre-receive hook declined)
> error: failed to push some refs to 'git.bioconductor.org:packages/GSE159526'
> 
> 
> I checked, and my ssh keys are configured correctly.
> 
> https://github.com/Bioconductor/Contributions/issues/2170
> 
> Any help appreciated!
> Victor
> 
>   [[alternative HTML version deleted]]
> 
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[Bioc-devel] Reg: Git hook update on Experiment Data and workflow packages

[Nitesh Turaga]

Hello Maintainers,

We have recently come across some experiment data packages that had merge 
conflicts in them. 

As a precaution,  the git hook to prevent these merge conflicts has been 
enabled. This will keep merge conflict markers from entering the git 
repositories we maintain. 

Maintainers should be aware and make sure there are no merge conflict markers 
before making a commit to the git repositories. 

Some links about resolving merge conflicts: 

1. 
https://docs.github.com/en/github/collaborating-with-pull-requests/addressing-merge-conflicts/resolving-a-merge-conflict-using-the-command-line

2. https://www.atlassian.com/git/tutorials/using-branches/merge-conflicts

3. Bioconductor git hooks: https://github.com/Bioconductor/git-hooks

If you have any questions, please reply to this thread. 

Best regards,

Nitesh 


Nitesh Turaga
Scientist II, Department of Data Science,
Bioconductor Core Team Member
Dana Farber Cancer Institute

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Re: [Bioc-devel] Push bug fix to release branch

[Nitesh Turaga]

Hi Alan,


What you have written below looks correct to me. 


A simpler way to remember this is how the versioning works - (X.Y.Z) or 
(major.minor.patch). 

You only every update the “patch” or the “Z” number in the versioning system. 

Best,

Nitesh 


Nitesh Turaga
Scientist II, Department of Data Science,
Bioconductor Core Team Member
Dana Farber Cancer Institute

> On Jun 16, 2021, at 1:33 PM, Murphy, Alan E  wrote:
> 
> Hi,
> 
> I have a package EWCE(https://github.com/NathanSkene/EWCE) that was newly 
> published in Bioconductor in version 3.13. The release package version number 
> is 1.0.0.
> 
> However, I have identified a bug in the package and need to push the fix to 
> the current release version and the devel version. This is my first time 
> doing this so I want to make sure I understand how to do it correctly. I have 
> read the information 
> here(http://bioconductor.org/developers/how-to/git/bug-fix-in-release-and-devel/)
>  about bug fixes and 
> here(http://bioconductor.org/developers/how-to/version-numbering/) regarding 
> version numbering. Based on these, I do have a specific question. My current 
> master branch is at version 1.1.0 for the devel branch while the release_3_13 
> branch is version 1.0.0. Should I checkout out either branch separately, make 
> the fix and bump the versions (1.0.1 for release branch and 1.1.1 for the 
> master branch) and then push both upstream separately (git push upstream 
> /master) and afterwards push each to the repo (git push origin 
> /master)?
> 
> Thanks,
> Alan.
> 
> 
> Alan Murphy
> Bioinformatician
> Neurogenomics lab
> UK Dementia Research Institute
> Imperial College London
> 
>   [[alternative HTML version deleted]]
> 
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Re: [Bioc-devel] Help fixing version and resync existing package epidecodeR

[Nitesh Turaga]

Hi Kandarp,

Please email the bioc-devel@r-project.org for questions on git. 

You can try to use the documentation we have on our website, 
http://bioconductor.org/developers/how-to/git/sync-existing-repositories/. 


The problem is to sync your Github repo with the Bioconductor git repo, hence 
it’s solvable on your end. You’d need to make sure your reset your GitHub repo 
“ca8d4d8526a3374bb8830982405710740922fb57” and then merge with the Bioconductor 
repo.

I would suggest you follow the documentation as it’s much clearer. Please also 
remember the versioning scheme, 
http://bioconductor.org/developers/how-to/version-numbering/. You are only 
allowed to bump the “patch” version (major.minor.patch - versioning scheme). 

Best,

Nitesh 
 

> On Jun 2, 2021, at 4:11 PM, Kandarp Joshi  wrote:
> 
> Dear Nitesh,
> 
> My package epidecodeR was accepted in bioconductor last month. I have made 
> some changes to the package and am trying to push updates to bioconductor 
> git. However, I screwed up while trying to push and now my github and bio git 
> are out of sync and also I am getting an illegal version bump error. 
> 
> Can you please help me out in solving this error?
> 
> Git repo https://github.com/kandarpRJ/epidecodeR
> 
> package: https://bioconductor.org/packages/release/bioc/html/epidecodeR.html
> 
> 
> 
> -- 
> With regards,
> Dr. Kandarp Joshi
> Post doctoral fellow, GP Lab
> 
> Institute for Integrated Cell-Material Sciences (iCeMS)
> iCeMS Complex 2, Kyoto University
> Yoshida-Honmachi, Sakyo-ku
> Kyoto, 606-8501, Japan

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Re: [Bioc-devel] I don't have access to my package

[Nitesh Turaga]

Hi,

Your email is listed for access on the package, but jh...@genetics.utah.edu is 
listed as the email. 

You also haven’t activated your account on BiocCredentials or added and SSH key 
to it. 

Please activate your account at 
https://git.bioconductor.org/BiocCredentials/account_activation with the email 
from Utah.edu as I listed above and add your keys.

If that is not your email and you need the BYU email to be listed instead, let 
me know and I’ll change it.

Best,

Nitesh 

> On May 25, 2021, at 6:45 AM, Jonathon Hill  wrote:
> 
> Hi,
> 
> I am the listed maintainer for the sangerseqR package. However, I am unable 
> to access it to push a small bug fix. I am the owner of the GitHub repository 
> and the maintainer listed on the bioconductor website/DESCRIPTION file. 
> However, when I try to push the change to upstream, I get the following error:
> 
> FATAL: W any packages/sangerseqR kjohnsen 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.
> 
> 
> The username listed is a former student, but they never should have been 
> listed as the maintainer for this package (they are on another package we 
> made). How can I get access restored?
> 
> Thanks,
> 
> Jonathon Hill
> 
>   [[alternative HTML version deleted]]
> 
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[Bioc-devel] RELEASE_3_13 is now available for bioconductor_docker

[Nitesh Turaga]

Hello Developers,

The Bioconductor docker images have been updated to reflect the latest release. 
For more details on how to use the docker image, 
http://bioconductor.org/help/docker/ .

- 'bioconductor/bioconductor_docker:RELEASE_3_13' is the new image (Bioc 3.13 
and R version 4.1.0).

- 'bioconductor/Bioconductor_docker:devel' is upadated as well (Bioc  3.14 
“devel” and R version is 4.1.0).


NOTE: Singularity Hub has been archived in 2021. So we will not be hosting 
Singularity images on the hub anymore.  We do however still provide the 
bootstrap file (named Singularity, or Singularity.RELEASE_3_13) if users choose 
to use that. 

There is very good documentation about using Singularity directly from the 
docker images we provide in the following link, 
https://singularity.lbl.gov/archive/docs/v2-3/docs-docker.


If you face any issues with this image, please reply to this thread or open an 
issue here, https://github.com/Bioconductor/bioconductor_docker on the Github 
page.

Best regards,

Nitesh

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Re: [Bioc-devel] Access to schex

[Nitesh Turaga]

Hi Saskia,

I’ve updated your email address to saskia.frey...@perkins.uwa.edu.au. 

Please activate your BiocCredentials account again, from 
https://git.bioconductor.org/BiocCredentials/account_activation. 

Another thing that could be happening is the “permissions” on your keys. 
http://bioconductor.org/developers/how-to/git/faq/ please check FAQ number #14, 
#15 and  #16 to see if those might help as well. 

Hopefully this sorts it out.


Nitesh

> On May 20, 2021, at 10:03 PM, Saskia Freytag 
>  wrote:
> 
> Hi Nitesh,
> 
> I have added multiple keys (using both my maintainer addresses), but none of 
> them seem to change anything. Could it be that there is a problem with the 
> email addresses registered to the package? It may be that a year ago we 
> changed these to make them the same between RUVcorr and schex.
> 
> Cheers,
> 
> Saskia
> 
>> On 18 May 2021, at 7:46 am, Nitesh Turaga  wrote:
>> 
>> Hi Saskia ,
>>  
>> Please try to add new keys. It’s possible you aren’t using the correct key 
>> pair to access your package.
>>  
>> Best,
>>  
>> Nitesh 
>>  
>> From: Bioc-devel  on behalf of Saskia 
>> Freytag 
>> Date: Saturday, May 15, 2021 at 8:42 PM
>> To: bioc-devel@r-project.org 
>> Subject: [Bioc-devel] Access to schex
>> 
>> Hi,
>> 
>> I am the maintainer of the schex package. I tried to update the package but 
>> when I get to the step of pushing the changes to upstream, I get the 
>> following error message:
>> FATAL: W any packages/schex SaskiaFreytag 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.
>> Do I need to change my ssh keys in Bioccredentials or is there something 
>> deeper going on?
>> 
>> Cheers,
>> 
>> Saskia
>> 
>> [[alternative HTML version deleted]]
>> 
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Re: [Bioc-devel] Bioconductor git repository commits have resumed

[Nitesh Turaga]

You should also be able to see the RELEASE_3_13 branch on your package (example 
below is BiocGenerics) at,

https://code.bioconductor.org/browse/BiocGenerics/RELEASE_3_13/

Best,

Nitesh

From: Nitesh Turaga 
Date: Wednesday, May 19, 2021 at 7:31 AM
To: bioc-devel@r-project.org 
Subject: Bioconductor git repository commits have resumed
Dear Maintainers,

The commits to the Bioconductor repository have been resumed. The new branch 
RELEASE_3_13 has been created for all packages. Please be sure to check your 
package and sync it with your Github repositories 
(http://bioconductor.org/developers/how-to/git/) .

All maintainers should have access to the "master" (devel branch) and the 
RELEASE_3_13 branch of their packages.


Thank you for your contributions, and we are looking forward to more.

Best regards,

Nitesh Turaga




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[Bioc-devel] Bioconductor git repository commits have resumed

[Nitesh Turaga]

Dear Maintainers,

The commits to the Bioconductor repository have been resumed. The new branch 
RELEASE_3_13 has been created for all packages. Please be sure to check your 
package and sync it with your Github repositories 
(http://bioconductor.org/developers/how-to/git/) .

All maintainers should have access to the "master" (devel branch) and the 
RELEASE_3_13 branch of their packages.

Thank you for your contributions, and we are looking forward to more.

Best regards,

Nitesh Turaga



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[Bioc-devel] Creating Bioconductor 3.13 branch on May 19th 2021 - 11 AM EDT

[Nitesh Turaga]

Dear Maintainers,

Please keep in mind that we are on schedule for our release as given
in http://bioconductor.org/developers/release-schedule/.

Today (May 19th 2021) at 11:00am EDT, I will freeze the commits to
Bioconductor until further notice so we can create the RELEASE_3_13
branch for all packages (software, data experiment, workflow, and books). The
process will take about 2.5 - 3 hours once commits are stopped.

If there are any issues in the meantime, please reply to this thread and c.c 
bioc-devel@r-project.org<mailto:bioc-devel@r-project.org>.

Best regards,

Nitesh Turaga
Bioconductor Core Team


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Re: [Bioc-devel] Access to schex

[Nitesh Turaga]

Hi Saskia ,

Please try to add new keys. It�s possible you aren�t using the correct key pair 
to access your package.

Best,

Nitesh

From: Bioc-devel  on behalf of Saskia Freytag 

Date: Saturday, May 15, 2021 at 8:42 PM
To: bioc-devel@r-project.org 
Subject: [Bioc-devel] Access to schex
Hi,

I am the maintainer of the schex package. I tried to update the package but 
when I get to the step of pushing the changes to upstream, I get the following 
error message:
FATAL: W any packages/schex SaskiaFreytag 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.
Do I need to change my ssh keys in Bioccredentials or is there something deeper 
going on?

Cheers,

Saskia

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Re: [Bioc-devel] MSstatsPTM Maintainer Change

[Nitesh Turaga]

Hi,

You are already the maintainer of this package.

I don�t understand your request here. Did you have a problem pushing to the 
package?

Nitesh

From: Devon Kohler 
Date: Wednesday, May 12, 2021 at 12:46 PM
To: maintai...@bioconductor.org , 
bioc-devel@r-project.org 
Cc: Tsung-Heng Tsai 
Subject: MSstatsPTM Maintainer Change
Hello,

I am trying to change the maintainer of the package MSstatsPTM so that I can 
push a version update for release 3.13. Could you please add me as a 
maintainer? My email is 
kohle...@northeastern.edu and my github name 
is devonjkohler. I am currently the maintainer of MSstatsTMTPTM. I have linked 
the current maintainer of MSstatsPTM, Tsung-Heng Tsai.

Is there anyway this can happen tonight? Sorry about the last minute request, 
we were unaware that I was not able to push any changes to the package.

Thank you!
Devon Kohler

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Re: [Bioc-devel] Problems while activating my bioconductor git account

[Nitesh Turaga]

Hi,

I�ve changed the email to 
m...@sebastianbauer.info. You did used to have 
sebastian.ba...@charite.de.

Please activate now, and add your SSH keys to gain access to the package.

Best,

Nitesh


From: Bioc-devel  on behalf of Sebastian 
Bauer 
Date: Wednesday, May 12, 2021 at 7:16 AM
To: bioc-devel@r-project.org 
Subject: [Bioc-devel] Problems while activating my bioconductor git account
Dear Bioconductors,

(resent two days after my initial attempt)

I recently got an automated message reporting a problem concering the
'mgsa' package for which I'm listed as the maintainer. I would like to
check this out and apply a possibly fix if there is a problem. I haven't
done any contribution since quite a while and Bioconductor has undergone
some infrastructure changes in the meantime, in particullar, the switch
to git.

If I understood everything correctly, I have to activate my account via
https://git.bioconductor.org/BiocCredentials/account_activation/ before
being able to push something to the package source.

I'm getting following response from the Webserver:

"m...@sebastianbauer.info is not associated with a maintainer of a
Bioconductor package. Please check the spelling or contact
bioc-devel@r-project.org for help"

I'm quite sure that the spelling is correctly, so I'm trying now the
second option :)

If you look at
https://www.bioconductor.org/packages/release/bioc/html/mgsa.html then
clearly this mail address is associated to the package  (obviously, I
wouldn't get the error report then).

It may or may not have something to do with the fact that at the time I
contributed the package a decade ago, the email address I used was
sebastian.ba...@charite.de.

Any help how to get access to the source back is highly appreciated.

Bye
Sebastian

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Re: [Bioc-devel] BFG clean-up and reset for compartmap

[Nitesh Turaga]

cc-ing bioc-devel

From: Nitesh Turaga 
Date: Tuesday, May 11, 2021 at 10:13 AM
To: Johnson, Ben 
Subject: Re: BFG clean-up and reset for compartmap
That is exactly right.

I would also delete/archive non-bioconductor feature branches like dev, hg38 
etc. Only master and RELEASE_X_Y branches should be available.

Best,

Nitesh

From: Johnson, Ben 
Date: Tuesday, May 11, 2021 at 10:11 AM
To: Nitesh Turaga 
Subject: Re: BFG clean-up and reset for compartmap
Hi Nitesh,

Apologies for not having the github in the state it should be in. Just to 
clarify, I need to follow the steps outlined here 
(https://bioconductor.org/developers/how-to/git/sync-existing-repositories/) 
through the merges, run the BFG, and contact you again for the force reset?

Again, my apologies if these are all naïve. Thanks for your time!

Best,
Ben K Johnson

Postdoctoral Fellow
Department of Epigenetics
Van Andel Institute
333 Bostwick Ave. NE
Grand Rapids, MI 49503


From: Nitesh Turaga 
Date: Tuesday, May 11, 2021 at 2:06 PM
To: Johnson, Ben , bioc-devel@r-project.org 

Subject: [External] Re: BFG clean-up and reset for compartmap
Hi,

Thanks for sending the github repo.

I noticed that the repo is missing the RELEASE branches. You’ll have to sync 
this from the Bioconductor repo. I cannot merge just a orphan devel branch into 
what exists on git.bioconductor.org.

You’ll have to have sync your github repo, sync all the branches and run BFG.

Best,

Nitesh

From: Johnson, Ben 
Date: Tuesday, May 11, 2021 at 8:02 AM
To: Nitesh Turaga , bioc-devel@r-project.org 

Subject: Re: BFG clean-up and reset for compartmap
Hi Nitesh,

It would be https://github.com/biobenkj/compartmap. Thanks!

Best,
Ben K Johnson

Postdoctoral Fellow
Department of Epigenetics
Van Andel Institute
333 Bostwick Ave. NE
Grand Rapids, MI 49503


From: Nitesh Turaga 
Date: Tuesday, May 11, 2021 at 2:01 PM
To: Johnson, Ben , bioc-devel@r-project.org 

Subject: [External] Re: BFG clean-up and reset for compartmap
Hi,

What exactly is the github repo we have to pull from?

Nitesh

From: Bioc-devel  on behalf of Johnson, Ben 

Date: Monday, May 10, 2021 at 3:11 AM
To: bioc-devel@r-project.org 
Subject: [Bioc-devel] BFG clean-up and reset for compartmap
Hi all,

We had a couple manifest files that were needing to be cleaned out to pass 
BiocCheck and were removed using the BFG. I�d like to request a reset/force 
pull upstream into the BioC devel git server repo 
(g...@git.bioconductor.org:packages/compartmap<mailto:g...@git.bioconductor.org:packages/compartmap>)
 to commit various bugfixes and API changes for compartmap.

Thanks so much!

Best,
Ben K Johnson

Postdoctoral Fellow
Department of Epigenetics
Van Andel Institute
333 Bostwick Ave. NE
Grand Rapids, MI 49503


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CAUTION: This email was sent from outside of the organization 
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Re: [Bioc-devel] Maintainer change Bioconductor packages

[Nitesh Turaga]

Hi,

I added gene-expression to get package access.

Please activate the account 
https://git.bioconductor.org/BiocCredentials/account_activation. Add “new” SSH 
keys. Change the password.

gene-expression will then have access to the package, and like I mentioned 
before the changes on the package itself will be on your end to make.

Change the maintainer email, subscribe to bioc-devel etc.

Best,

Nitesh

From: Nitesh Turaga 
Date: Tuesday, May 11, 2021 at 7:59 AM
To: Pablo Moreno 
Cc: Suhaib Mohammed , maintai...@bioconductor.org 
, bioc-devel@r-project.org 
, gene-express...@ebi.ac.uk 

Subject: Re: Maintainer change Bioconductor packages
Hi,

I think this might be possible to try.

So the maintainer email again has to be changed from your end on the 
DESCRIPTION file.

As far as access goes, I can add 
gene-express...@ebi.ac.uk<mailto:gene-express...@ebi.ac.uk>, on the 
BiocCredentials system. You’ll have to activate the account and add SSH keys.

gene-express...@ebi.ac.uk<mailto:gene-express...@ebi.ac.uk> will also have to 
follow all the protocols of a maintainer, so someone will have to actively 
monitor it and subscribe to 
bioc-devel@r-project.org<mailto:bioc-devel@r-project.org> mailing list.

Best,

Nitesh


From: Pablo Moreno 
Date: Sunday, May 9, 2021 at 10:32 PM
To: Nitesh Turaga 
Cc: Suhaib Mohammed , maintai...@bioconductor.org 
, bioc-devel@r-project.org 
, gene-express...@ebi.ac.uk 

Subject: Re: Maintainer change Bioconductor packages
Dear Nitesh,

I think that in the rush of Suhaib leaving, we didn’t finalise this process.

Is it acceptable to have a group email/account as maintainer? We would have 
gene-express...@ebi.ac.uk, which email gets to all the Expression Atlas team 
members. Then we wouldn’t need to repeat the process if any of us leaves.

Thanks,
Pablo

> On 28 Jan 2021, at 18:27, Nitesh Turaga  wrote:
>
> Hi Suhaib,
>
> You are correct, the maintainer needs to be changed if you are unable to 
> maintain the package further. You need to nominate another maintainer for the 
> packages you listed.
>
> Once the new maintainer steps in,
>
> 1. Change the Maintainer or Authors@R field in the DESCRIPTION file of the 
> package to reflect the change.
>
> 2. Maintainer has to have a BiocCredentials account.
>
> 3. Maintainer has to be subscripted to bioc-devel@r-project.org mailing list.
>
> Best,
>
> Nitesh
>
>
> On 1/28/21, 7:00 AM, "Suhaib Mohammed"  wrote:
>
>To whom ever it may concern,
>
>I have been maintaining the Bioconductor R packages (ExpressionAtlas and
>ArrayExpress) of Gene Expression Atlas team at the EMBL-EBI. As I will
>be leaving EBI, I understand the maintainer needs to be changed. Could
>you point to the procedure for changing the maintainer ?
>
>Expression Atlas -
>https://bioconductor.org/packages/release/bioc/html/ExpressionAtlas.html
>Array Express -
>https://bioconductor.org/packages/release/bioc/html/ArrayExpress.html
>
>Many thanks,
>Suhaib
>
>--
>Suhaib Mohammed, Ph.D.
>Senior Bioinformatician
>European Bioinformatics Institute (EMBL-EBI)
>European Molecular Biology Laboratory
>Wellcome Trust Genome Campus
>Hinxton, Cambridge CB10 1SD
>United Kingdom
>tel : +44-1223494296
>email: suh...@ebi.ac.uk
>

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Re: [Bioc-devel] BFG clean-up and reset for compartmap

[Nitesh Turaga]

Hi,

Thanks for sending the github repo.

I noticed that the repo is missing the RELEASE branches. You’ll have to sync 
this from the Bioconductor repo. I cannot merge just a orphan devel branch into 
what exists on git.bioconductor.org.

You’ll have to have sync your github repo, sync all the branches and run BFG.

Best,

Nitesh

From: Johnson, Ben 
Date: Tuesday, May 11, 2021 at 8:02 AM
To: Nitesh Turaga , bioc-devel@r-project.org 

Subject: Re: BFG clean-up and reset for compartmap
Hi Nitesh,

It would be https://github.com/biobenkj/compartmap. Thanks!

Best,
Ben K Johnson

Postdoctoral Fellow
Department of Epigenetics
Van Andel Institute
333 Bostwick Ave. NE
Grand Rapids, MI 49503


From: Nitesh Turaga 
Date: Tuesday, May 11, 2021 at 2:01 PM
To: Johnson, Ben , bioc-devel@r-project.org 

Subject: [External] Re: BFG clean-up and reset for compartmap
Hi,

What exactly is the github repo we have to pull from?

Nitesh

From: Bioc-devel  on behalf of Johnson, Ben 

Date: Monday, May 10, 2021 at 3:11 AM
To: bioc-devel@r-project.org 
Subject: [Bioc-devel] BFG clean-up and reset for compartmap
Hi all,

We had a couple manifest files that were needing to be cleaned out to pass 
BiocCheck and were removed using the BFG. I�d like to request a reset/force 
pull upstream into the BioC devel git server repo 
(g...@git.bioconductor.org:packages/compartmap<mailto:g...@git.bioconductor.org:packages/compartmap>)
 to commit various bugfixes and API changes for compartmap.

Thanks so much!

Best,
Ben K Johnson

Postdoctoral Fellow
Department of Epigenetics
Van Andel Institute
333 Bostwick Ave. NE
Grand Rapids, MI 49503


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Re: [Bioc-devel] BFG clean-up and reset for compartmap

[Nitesh Turaga]

Hi,

What exactly is the github repo we have to pull from?

Nitesh

From: Bioc-devel  on behalf of Johnson, Ben 

Date: Monday, May 10, 2021 at 3:11 AM
To: bioc-devel@r-project.org 
Subject: [Bioc-devel] BFG clean-up and reset for compartmap
Hi all,

We had a couple manifest files that were needing to be cleaned out to pass 
BiocCheck and were removed using the BFG. I�d like to request a reset/force 
pull upstream into the BioC devel git server repo 
(g...@git.bioconductor.org:packages/compartmap)
 to commit various bugfixes and API changes for compartmap.

Thanks so much!

Best,
Ben K Johnson

Postdoctoral Fellow
Department of Epigenetics
Van Andel Institute
333 Bostwick Ave. NE
Grand Rapids, MI 49503


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Re: [Bioc-devel] Maintainer change Bioconductor packages

[Nitesh Turaga]

Hi,

I think this might be possible to try.

So the maintainer email again has to be changed from your end on the 
DESCRIPTION file.

As far as access goes, I can add 
gene-express...@ebi.ac.uk<mailto:gene-express...@ebi.ac.uk>, on the 
BiocCredentials system. You’ll have to activate the account and add SSH keys.

gene-express...@ebi.ac.uk<mailto:gene-express...@ebi.ac.uk> will also have to 
follow all the protocols of a maintainer, so someone will have to actively 
monitor it and subscribe to 
bioc-devel@r-project.org<mailto:bioc-devel@r-project.org> mailing list.

Best,

Nitesh


From: Pablo Moreno 
Date: Sunday, May 9, 2021 at 10:32 PM
To: Nitesh Turaga 
Cc: Suhaib Mohammed , maintai...@bioconductor.org 
, bioc-devel@r-project.org 
, gene-express...@ebi.ac.uk 

Subject: Re: Maintainer change Bioconductor packages
Dear Nitesh,

I think that in the rush of Suhaib leaving, we didn’t finalise this process.

Is it acceptable to have a group email/account as maintainer? We would have 
gene-express...@ebi.ac.uk, which email gets to all the Expression Atlas team 
members. Then we wouldn’t need to repeat the process if any of us leaves.

Thanks,
Pablo

> On 28 Jan 2021, at 18:27, Nitesh Turaga  wrote:
>
> Hi Suhaib,
>
> You are correct, the maintainer needs to be changed if you are unable to 
> maintain the package further. You need to nominate another maintainer for the 
> packages you listed.
>
> Once the new maintainer steps in,
>
> 1. Change the Maintainer or Authors@R field in the DESCRIPTION file of the 
> package to reflect the change.
>
> 2. Maintainer has to have a BiocCredentials account.
>
> 3. Maintainer has to be subscripted to bioc-devel@r-project.org mailing list.
>
> Best,
>
> Nitesh
>
>
> On 1/28/21, 7:00 AM, "Suhaib Mohammed"  wrote:
>
>To whom ever it may concern,
>
>I have been maintaining the Bioconductor R packages (ExpressionAtlas and
>ArrayExpress) of Gene Expression Atlas team at the EMBL-EBI. As I will
>be leaving EBI, I understand the maintainer needs to be changed. Could
>you point to the procedure for changing the maintainer ?
>
>Expression Atlas -
>https://bioconductor.org/packages/release/bioc/html/ExpressionAtlas.html
>Array Express -
>https://bioconductor.org/packages/release/bioc/html/ArrayExpress.html
>
>Many thanks,
>Suhaib
>
>--
>Suhaib Mohammed, Ph.D.
>Senior Bioinformatician
>European Bioinformatics Institute (EMBL-EBI)
>European Molecular Biology Laboratory
>Wellcome Trust Genome Campus
>Hinxton, Cambridge CB10 1SD
>United Kingdom
>tel : +44-1223494296
>email: suh...@ebi.ac.uk
>

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Re: [Bioc-devel] Transfer Maintainership of the Package NetSAM

[Nitesh Turaga]

Hi,

This is now done.

Please try to activate your account on BiocCredentials. 
https://git.bioconductor.org/BiocCredentials/account_activation and add SSH 
keys.

You will gain access to the package then.

Best,

Nitesh

From: Zhang, Bing 
Date: Sunday, May 9, 2021 at 5:07 PM
To: maintai...@bioconductor.org , 
bioc-devel@r-project.org 
Cc: zhiao@gmail.com 
Subject: Re: Transfer Maintainership of the Package NetSAM
Sorry, I used the wrong email address for the new maintainer. Here is the 
correct information:
First Name: Zhiao
Last Name: Shi
Email: zhiao@gmail.com

Bing

From: "Zhang, Bing" 
Date: Sunday, May 9, 2021 at 10:04 PM
To: "maintai...@bioconductor.org" , 
"bioc-devel@r-project.org" 
Cc: "justin@gmail.com" 
Subject: Transfer Maintainership of the Package NetSAM

Dear Sir or Madam,

I am the maintainer of the Bioconductor package NetSAM 
(https://bioconductor.org/packages/release/bioc/html/NetSAM.html ). My lab 
moved from the Vanderbilt University to the Baylor College of Medicine a few 
years ago, and my email address used for NetSAM was my Vanderbilt email account.

I would like to transfer the maintainership of NetSAM to a Lead Programer in my 
lab (cc�ed), please find below his contact information:
First Name: Zhiao
Last Name: Shi
Email: justin@gmail.com

Please let us know if you need additional information to make the transfer. 
Thanks!

Best regards,

Bing


Bing Zhang, Ph.D.
Professor of Molecular and Human Genetics
Breast Center
McNair Medical Institute Scholar
Cancer Prevention Research Institute of Texas (CPRIT) Scholar
Baylor College of Medicine
Houston, Texas 77030
Tel: 713-798-1443
Email: bing.zh...@bcm.edu
URL: http://www.zhang-lab.org

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Re: [Bioc-devel] Force Package Update after Removing Large Files from .git History

[Nitesh Turaga]

Hi Gabriel,

Thanks for taking the time to fix the package size to < 5MB.

I�ve synced your package repo on git.bioconductor.org. You should be good to go 
now.

If you have any further questions on this, please feel free to reply to this 
thread.

Best,

Nitesh

From: Bioc-devel  on behalf of Gabriel Odom 

Date: Thursday, May 6, 2021 at 9:47 AM
To: bioc-devel@r-project.org 
Cc: Fernanda Veitzman , Chedraoui Silva, Tiago 

Subject: [Bioc-devel] Force Package Update after Removing Large Files from .git 
History
Dear Bioconductor Team,

We are submitting the package coMethDMR 
(https://github.com/Bioconductor/Contributions/issues/2064) and we have fixed 
all errors and warnings listed in the multi-system build report.
One error was that the package was too large. We followed the steps to use BFG 
here (https://bioconductor.org/developers/how-to/git/remove-large-data/), and 
we have successfully reduced the package size to <5Mb in our GitHub repository. 
However, according to those instructions, force pushes are not allowed to the 
upstream branch, and we are to contact you for help.
Please advise.

Thanks in advance,
Gabriel

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Re: [Bioc-devel] Maintainer for preciseTAD

[Nitesh Turaga]

Hi Mikhail,

I�ve added you to have access to the package preciseTAD. You should be able to 
use your registered SSH keys with Bioconductor to access the package now.

I cannot make you the maintainer directly. This is a discussion you should have 
with Spiro and make the change in the package DESCRIPTION file yourself.

Best regards,

Nitesh

From: Bioc-devel  on behalf of Mikhail 
Dozmorov 
Date: Tuesday, May 4, 2021 at 9:45 PM
To: bioc-devel 
Subject: [Bioc-devel] Maintainer for preciseTAD
Hi,
I noted our package https://bioconductor.org/packages/preciseTAD/ shows
build error. This is because https://CRAN.R-project.org/package=DMwR was
removed. Please, add me as a maintainer to the preciseTAD repo. Spiro
should remain a maintainer, but he is getting harder to reach after
graduation.

Thanks,
Mikhail

---
Mikhail Dozmorov, Ph.D.
Department of Biostatistics, VCU
E-mail:  mdozmo...@vcu.edu
Phone: 804-827-2055

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Re: [Bioc-devel] Log in to the BiocCredentials app

[Nitesh Turaga]

Hi Mauro,

I just checked and you�ve never activated your account. You should try to 
activate it before you do anything else.

Best,

Nitesh

From: mauro castro 
Date: Tuesday, May 4, 2021 at 1:31 PM
To: Nitesh Turaga 
Cc: Bioc-devel 
Subject: Re: [Bioc-devel] Log in to the BiocCredentials app
Hi Nitesh,

Thank you for your email. I tried to do the password reset again, but
still haven't received an email from maintai...@bioconductor.org (and
also not in the spam box).

I tried the BiocCredentials app as in the attached print screen, using
the same email from my r-project.org mailing list membership, and
informed in my packages.

I don't know if this problem is some "shadow" from a time before the
git transition, so I revised my emails and found my very 1st
credential, the subversion user ID was "m.castro"; not sure if this
information would help to identify the problem. Sorry to bother you
with this apparent simple problem, but I dont know why this is
happening.

Many thanks,

Mauro

On Tue, 4 May 2021 at 10:02, Nitesh Turaga  wrote:
>
> Hi
>
>
>
> Have you checked your Spam or junk mail?
>
>
>
> You should have received an email from maintai...@bioconductor.org -  
> Bioconductor git credentials administrator.
>
>
>
> If it�s being filtered or something, could you please try to do the password 
> reset again? I checked our end, and everything seems to be in place.
>
>
>
> Best,
>
>
>
> Nitesh
>
>
>
> From: Bioc-devel  on behalf of mauro castro 
> 
> Date: Tuesday, May 4, 2021 at 8:48 AM
> To: Bioc-devel 
> Subject: [Bioc-devel] Log in to the BiocCredentials app
>
> Hi All,
>
> I�m a Bioconductor package maintainer, but I could not log in to the
> BiocCredentials app to submit a new SSH public key. A already tried to
> reset the password, but I didn't receive any email with instructions
> for setting a password.
>
> https://git.bioconductor.org/BiocCredentials/password_reset/
>
> The email I entered is the same associated with all my packages
> (mauro.a.cas...@gmail.com). Here a list of packages for which I am
> maintainer:
> - RedeR, RTN, RTNduals, RTNsurvival, geneplast, Fletcher2013a, Fletcher2013b
>
> Please, let me know if I am missing any steps.
>
> Many thanks,
>
> Mauro
>
> ___
> Bioc-devel@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel

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Re: [Bioc-devel] Log in to the BiocCredentials app

[Nitesh Turaga]

Hi

Have you checked your Spam or junk mail?

You should have received an email from 
maintai...@bioconductor.org -  Bioconductor 
git credentials administrator.

If it�s being filtered or something, could you please try to do the password 
reset again? I checked our end, and everything seems to be in place.

Best,

Nitesh

From: Bioc-devel  on behalf of mauro castro 

Date: Tuesday, May 4, 2021 at 8:48 AM
To: Bioc-devel 
Subject: [Bioc-devel] Log in to the BiocCredentials app
Hi All,

I�m a Bioconductor package maintainer, but I could not log in to the
BiocCredentials app to submit a new SSH public key. A already tried to
reset the password, but I didn't receive any email with instructions
for setting a password.

https://git.bioconductor.org/BiocCredentials/password_reset/

The email I entered is the same associated with all my packages
(mauro.a.cas...@gmail.com). Here a list of packages for which I am
maintainer:
- RedeR, RTN, RTNduals, RTNsurvival, geneplast, Fletcher2013a, Fletcher2013b

Please, let me know if I am missing any steps.

Many thanks,

Mauro

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Re: [Bioc-devel] Bioconductor Release Announcement: RELEASE_3_12 branch freeze

[Nitesh Turaga]

Hi,

The branch your linked is going to be the upcoming RELEASE_3_13 branch and 
currently �devel� (master branch).

I�m not sure how to help you as far as debugging the error goes, the best way 
is first try to be able to reproduce it on your local machine. You can also add 
a statement to avoid running the example if the OS is recognized as a mac 
(https://stat.ethz.ch/R-manual/R-patched/library/base/html/Platform.html)

```
if (.Platform$OS.type == �darwin�) ## maybe it�s just �unix� now
```

But this should be directed in a separate thread as question, it seems it has 
nothing to do with the RELEASE_3_12 branch freeze and discussion on this thread 
will lead to confusion.

Best,

Nitesh


From: Waldir Leoncio Netto 
Date: Tuesday, May 4, 2021 at 1:20 AM
To: bioc-devel@r-project.org , nturaga.b...@gmail.com 

Subject: Re: [Bioc-devel] Bioconductor Release Announcement: RELEASE_3_12 
branch freeze
Dear Nitesh,

What happens to packages presenting a check error (e.g. 
cellmigRation<http://bioconductor.org/checkResults/devel/bioc-LATEST/cellmigRation/>
 installs and builds on all supported OSs, but fails on macOS while checking a 
function example)? I've been working on solving that, but there can only be so 
much progress when using daily builds as a gauge.

Best regards,
Waldir

ma., 03.05.2021 kl. 17.07 +, skrev Nitesh Turaga:
Today - May 3, 2021.

My apologies.

Nitesh

From: Nitesh Turaga mailto:nturaga.b...@gmail.com>>
Date: Monday, May 3, 2021 at 1:04 PM
To: bioc-devel@r-project.org<mailto:bioc-devel@r-project.org> 
mailto:bioc-devel@r-project.org>>
Subject: Bioconductor Release Announcement: RELEASE_3_12 branch freeze
Dear Maintainers,

Please keep in mind that we are on schedule for our release as given in 
http://bioconductor.org/developers/release-schedule/.

Today (April 14th 2020) at 2pm EDT, I will freeze the commits to the 
RELEASE_3_12 branch in Bioconductor. This is for all packages (software, 
data-experiment and workflow).

After 2pm today, you will not be able to push to the RELEASE_3_12 branch.

Best regards,

Nitesh Turaga


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Re: [Bioc-devel] Bioconductor Release Announcement: RELEASE_3_12 branch freeze

[Nitesh Turaga]

Dear Maintainers,

The RELEASE_3_12 branch is now frozen.

Best,

Nitesh

From: Nitesh Turaga 
Date: Monday, May 3, 2021 at 1:08 PM
To: bioc-devel@r-project.org 
Subject: Re: Bioconductor Release Announcement: RELEASE_3_12 branch freeze
Today - May 3, 2021.

My apologies.

Nitesh

From: Nitesh Turaga 
Date: Monday, May 3, 2021 at 1:04 PM
To: bioc-devel@r-project.org 
Subject: Bioconductor Release Announcement: RELEASE_3_12 branch freeze
Dear Maintainers,

Please keep in mind that we are on schedule for our release as given in 
http://bioconductor.org/developers/release-schedule/.

Today (April 14th 2020) at 2pm EDT, I will freeze the commits to the 
RELEASE_3_12 branch in Bioconductor. This is for all packages (software, 
data-experiment and workflow).

After 2pm today, you will not be able to push to the RELEASE_3_12 branch.

Best regards,

Nitesh Turaga


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Re: [Bioc-devel] Bioconductor Release Announcement: RELEASE_3_12 branch freeze

[Nitesh Turaga]

Today - May 3, 2021.

My apologies.

Nitesh

From: Nitesh Turaga 
Date: Monday, May 3, 2021 at 1:04 PM
To: bioc-devel@r-project.org 
Subject: Bioconductor Release Announcement: RELEASE_3_12 branch freeze
Dear Maintainers,

Please keep in mind that we are on schedule for our release as given in 
http://bioconductor.org/developers/release-schedule/.

Today (April 14th 2020) at 2pm EDT, I will freeze the commits to the 
RELEASE_3_12 branch in Bioconductor. This is for all packages (software, 
data-experiment and workflow).

After 2pm today, you will not be able to push to the RELEASE_3_12 branch.

Best regards,

Nitesh Turaga


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[Bioc-devel] Bioconductor Release Announcement: RELEASE_3_12 branch freeze

[Nitesh Turaga]

Dear Maintainers,

Please keep in mind that we are on schedule for our release as given in 
http://bioconductor.org/developers/release-schedule/.

Today (April 14th 2020) at 2pm EDT, I will freeze the commits to the 
RELEASE_3_12 branch in Bioconductor. This is for all packages (software, 
data-experiment and workflow).

After 2pm today, you will not be able to push to the RELEASE_3_12 branch.

Best regards,

Nitesh Turaga


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Re: [Bioc-devel] Bioc Git credentials

[Nitesh Turaga]

Hi Leonard,

I�ve changed your email now, you should be able to activate your account.

The email listed was to a gene.com email address.

Add new SSH keys if you don�t have the old key pairs.

Best,

Nitesh

From: Bioc-devel  on behalf of Leonard 
Goldstein 
Date: Sunday, May 2, 2021 at 10:06 PM
To: bioc-devel@r-project.org 
Subject: [Bioc-devel] Bioc Git credentials
Hi,

I'm maintaining the SGSeq Bioc package and recently changed the maintainer
email address. I'm trying to activate a new account for Git credentials here
, but get
the following error message:

ldgoldst...@gmail.com is not associated with a maintainer of a Bioconductor
package. Please check the spelling or contact bioc-devel@r-project.org for
help.

Thanks for your help.

Leonard

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Re: [Bioc-devel] issue with ssh public key

[Nitesh Turaga]

Hi,

I�ve made the change in your account. You�ll need to activate your 
BioCredentials account now,

https://git.bioconductor.org/BiocCredentials/account_activation

Add new SSH keys and you should be good to go.

You cannot make the change on your end, if you change your email address again. 
This is a fail safe, we don�t want package maintainers to disappear and give us 
emails that aren�t valid.

Best,

Nitesh

From: Martin, Tiphaine 
Date: Monday, May 3, 2021 at 9:39 AM
To: Nitesh Turaga , bioc-devel@r-project.org 

Subject: RE: issue with ssh public key
Hi,
This was my previous email.
Please could you put my new email 
tiphaine.mar...@mssm.edu<mailto:tiphaine.mar...@mssm.edu>
Could you remind me how I can change later if need it.
Thanks,
Tiphaine

From: Nitesh Turaga 
Sent: Monday, May 3, 2021 9:07 AM
To: Martin, Tiphaine ; bioc-devel@r-project.org
Subject: Re: issue with ssh public key

USE CAUTION: External Message.
The email registered is 
tiphaine.mar...@kcl.ac.uk<mailto:tiphaine.mar...@kcl.ac.uk> .

If this is not correct, I will have to change it on my end.

Best,

Nitesh

From: Bioc-devel 
mailto:bioc-devel-boun...@r-project.org>> on 
behalf of Martin, Tiphaine 
mailto:tiphaine.mar...@mssm.edu>>
Date: Saturday, May 1, 2021 at 11:47 PM
To: bioc-devel@r-project.org<mailto:bioc-devel@r-project.org> 
mailto:bioc-devel@r-project.org>>
Subject: [Bioc-devel] issue with ssh public key
Hi,

I try to submit update of my package comet
I do not remember about my ssh public key
I have this error message and I request it
tiphaine.mar...@mssm.edu<mailto:tiphaine.mar...@mssm.edu> is not associated 
with a maintainer of a Bioconductor package.


Could you help me please?

Thanks,
Tiphaine


Tiphaine Martin
Postdoc Fellow
Parsons lab
Department of Oncological Sciences
The Tisch Cancer Institute at Mount Sinai
Icahn School of Medicine at Mount Sinai
Hess Center for Science and Medicine
1470 Madison Ave, 6th Floor
New York, NY 10029
tel: 1- 212-824-9253
Email: 
tiphaine.mar...@mssm.edu<mailto:tiphaine.mar...@mssm.edu%3E<mailto:tiphaine.mar...@mssm.edu%3cmailto:tiphaine.mar...@mssm.edu%3E>


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Re: [Bioc-devel] issue with ssh public key

[Nitesh Turaga]

The email registered is 
tiphaine.mar...@kcl.ac.uk .

If this is not correct, I will have to change it on my end.

Best,

Nitesh

From: Bioc-devel  on behalf of Martin, 
Tiphaine 
Date: Saturday, May 1, 2021 at 11:47 PM
To: bioc-devel@r-project.org 
Subject: [Bioc-devel] issue with ssh public key
Hi,

I try to submit update of my package comet
I do not remember about my ssh public key
I have this error message and I request it
tiphaine.mar...@mssm.edu is not associated with a maintainer of a Bioconductor 
package.


Could you help me please?

Thanks,
Tiphaine


Tiphaine Martin
Postdoc Fellow
Parsons lab
Department of Oncological Sciences
The Tisch Cancer Institute at Mount Sinai
Icahn School of Medicine at Mount Sinai
Hess Center for Science and Medicine
1470 Madison Ave, 6th Floor
New York, NY 10029
tel: 1- 212-824-9253
Email: tiphaine.mar...@mssm.edu


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Re: [Bioc-devel] upstream push error

[Nitesh Turaga]

Hi,

Have you followed http://bioconductor.org/developers/how-to/git/faq/ points 
14,15 ,16 ?

It�s more likely your keys aren�t set up properly on your end. If it persists, 
just add a new SSH key.

Best,

Nitesh

From: Bioc-devel  on behalf of Lieven Clement 

Date: Wednesday, April 28, 2021 at 7:17 AM
To: bioc-devel@r-project.org 
Subject: [Bioc-devel] upstream push error
Dear All,


We recently migrated my lab git account from user to organisation which is 
linked to my email lieven.clem...@ugent.be.
My user account is lievenclement is linked to my gmail account 
lieven.clem...@gmail.com

I have submitted the msqrob2 package to bioconductor. The maintainer email 
address is lieven.clement@ugent,be, which is also linked to my GitHub 
organisation account.

I would like to push a new commit to the bioconductor remote but get the error 
attached below  (I included all steps to setup the remote).

I noticed that the error refers to my organisation account.

It would be great if you could help me out.

Best,

Lieven

$ git remote add upstream 
g...@git.bioconductor.org:packages/msqrob2.git

$ git remote -v
origin g...@github.com:statOmics/msqrob2.git (fetch)
origin g...@github.com:statOmics/msqrob2.git (push)
upstream 
g...@git.bioconductor.org:packages/msqrob2.git
 (fetch)
upstream 
g...@git.bioconductor.org:packages/msqrob2.git
 (push)

$ git fetch --all
Fetching origin
Enter passphrase for key '/Users/lclement/.ssh/id_rsa':
Fetching upstream
Enter passphrase for key '/Users/lclement/.ssh/id_rsa�:

$ git merge origin/master
Already up to date.

$ git add .
$ git commit -m "DESCRIPTION R version and added NEWS file�

$ git push upstream master
Enter passphrase for key '/Users/lclement/.ssh/id_rsa':
FATAL: W any packages/msqrob2 statOmics 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.



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Re: [Bioc-devel] Error pushing upstream

[Nitesh Turaga]

Hi Pedro,

There is no �main� branch on the Bioconductor repository. There is only the 
master branch.

Try

git push upstream master

From: Bioc-devel  on behalf of Pedro Baldoni 

Date: Wednesday, April 28, 2021 at 7:27 AM
To: bioc-devel@r-project.org 
Subject: [Bioc-devel] Error pushing upstream
Hi all,

I am also having issues to push changes to g...@git.bioconductor.org. Any
ideas on what could be causing this error?

Any help would be much appreciated.

Thanks,
Pedro

(base) baldoni@MacBook-Pro epigraHMM %  git push upstream main


Enumerating objects: 145, done.

Counting objects: 100% (145/145), done.

Delta compression using up to 8 threads

Compressing objects: 100% (126/126), done.

Writing objects: 100% (126/126), 21.15 KiB | 2.35 MiB/s, done.

Total 126 (delta 74), reused 0 (delta 0)

remote: Resolving deltas: 100% (74/74), completed with 15 local objects.

remote: FATAL: W refs/heads/main packages/epigraHMM plbaldoni DENIED by
fallthru

remote: *error*: hook declined to update refs/heads/main

To git.bioconductor.org:packages/epigraHMM.git

 ! [remote rejected] main -> main (hook declined)

error: failed to push some refs to 'g...@git.bioconductor.org:
packages/epigraHMM.git'


(base) baldoni@MacBook-Pro epigraHMM % git remote -v


origin g...@github.com:plbaldoni/epigraHMM.git (fetch)

origin g...@github.com:plbaldoni/epigraHMM.git (push)

upstream g...@git.bioconductor.org:packages/epigraHMM.git (fetch)

upstream g...@git.bioconductor.org:packages/epigraHMM.git (push)


(base) baldoni@MacBook-Pro epigraHMM % ssh -T g...@git.bioconductor.org |
grep 'epigraHMM'

 R W packages/epigraHMM

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Re: [Bioc-devel] unable to push to new package

[Nitesh Turaga]

Hi,

If you think the warnings are transient, I suggest you issue a new build by 
bumping the version number on your package.

Try that and then go ahead with further debugging. Make sure you are using the 
correct version of R and Bioconductor.


Nitesh

From: Gross Fridolin 
Date: Tuesday, April 27, 2021 at 3:56 AM
To: Nitesh Turaga 
Cc: bioc-devel@r-project.org , Germain Pierre-Luc 

Subject: Re: unable to push to new package
Dear Nitesh,

Thanks so much! After we did as you suggested, pushing upstream worked fine.

There is still a warning in the build 
report<http://bioconductor.org/spb_reports/scanMiR_buildreport_20210426195015.html>,
 but it seems that this is not under our control:
* checking whether package 'scanMiR' can be installed ... WARNING
Found the following significant warnings:
  Warning: no function found corresponding to methods exports from 'S4Vectors' 
for: 'combineRows'
See 
'C:/Users/pkgbuild/packagebuilder/workers/jobs/2067/scanMiR_20210426194208/scanMiR.Rcheck/00install.out'
 for details.

Do you have any suggestions on how to proceed?

Thanks again.

Best,
Fridolin


On 23 Apr 2021, at 14:49, Nitesh Turaga 
mailto:nturaga.b...@gmail.com>> wrote:

Another problem is you SSH key available on your github accout is compromised. 
It�s available on another account already. (This usually happens when you share 
the same key around and it gets added to user accounts who that want to 
maintain the same package).

Please create a new SSH key and add it to your account after you activate 
ithttps://git.bioconductor.org/BiocCredentials/account_activation .

I would also recommend deleting your Github SSH key, because it matches 
Pierre�s. This is the wrong way to do it. Both of you should delete that key.

Best,

Nitesh

From: Nitesh Turaga mailto:nturaga.b...@gmail.com>>
Date: Friday, April 23, 2021 at 8:41 AM
To: Gross Fridolin 
mailto:fridolin.gr...@hest.ethz.ch>>, 
bioc-devel@r-project.org<mailto:bioc-devel@r-project.org> 
mailto:bioc-devel@r-project.org>>
Subject: Re: unable to push to new package
Hi,

You do not have write privileges to the package because only the maintainer 
(cre) is given write access.

The submission is a little messy here, because


  1.  It�s submitted from a lab account (this is ok in general)
  2.  You are not listed as maintainer, but want to maintain the package.
  3.  You are the one corresponding with us, when ideally,  ("Pierre-Luc", 
"Germain", 
email=pierre-luc.germ...@hest.ethz.ch<mailto:pierre-luc.germ...@hest.ethz.ch>) 
should be the one.

I will manually make an account for you. Please add your SSH keys to your 
BiocCredentials account (https://git.bioconductor.org/BiocCredentials/) after 
activating it. Then change the Maintainer field in the description file.

Best,

Nitesh

From: Bioc-devel 
mailto:bioc-devel-boun...@r-project.org>> on 
behalf of Gross Fridolin 
mailto:fridolin.gr...@hest.ethz.ch>>
Date: Friday, April 23, 2021 at 4:14 AM
To: bioc-devel@r-project.org<mailto:bioc-devel@r-project.org> 
mailto:bioc-devel@r-project.org>>
Subject: [Bioc-devel] unable to push to new package
Hi all,

I have submitted our package �scanMiR� yesterday, which is now in the 'review 
in progress� phase (https://github.com/Bioconductor/Contributions/issues/2067).

When trying to push changes upstream, I get the error:

> $ git push upstream master
> Enter passphrase for key '/home/fgross/.ssh/id_ed25519':
> FATAL: W any packages/scanMiR plger 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.


The remotes seem to be set up correctly:

> $ git remote -v
> originhttps://github.com/ETHZ-INS/scanMiR/ (fetch)
> originhttps://github.com/ETHZ-INS/scanMiR/ (push)
> upstream  
> g...@git.bioconductor.org<mailto:g...@git.bioconductor.org>:packages/scanMiR 
> (fetch)
> upstream  
> g...@git.bioconductor.org<mailto:g...@git.bioconductor.org>:packages/scanMiR 
> (push)


However, I do not have write permission to the package (as shown by  ssh -T 
g...@git.bioconductor.org<mailto:g...@git.bioconductor.org>).

Could this be related to the fact that the original repo was located not on my 
account but at an organization? Or that I am listed as �author� in the package 
description, and not as �creator�?

I�d be grateful for any kind of help to understand and resolve this problem.

Best,
Fridolin




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Re: [Bioc-devel] CGEN package maintainer change request

[Nitesh Turaga]

Hi,

Please check http://bioconductor.org/developers/how-to/git/



From: Nilotpal Sanyal 
Date: Friday, April 23, 2021 at 12:04 PM
To: Nitesh Turaga , Wheeler, Bill (IMS) 
, maintai...@bioconductor.org 
, bioc-devel@r-project.org 

Cc: Summer S Han , nilan...@jhu.edu 
Subject: Re: CGEN package maintainer change request
Hi Nitesh,

Thank you. I have activated my account and added a SSH key. But I am trying to 
figure out where to access the package and update the files.

Thanks,
Nilotpal




From: Nitesh Turaga 
Sent: Friday, April 23, 2021 6:19 AM
To: Wheeler, Bill (IMS) ; maintai...@bioconductor.org 
; bioc-devel@r-project.org 

Cc: Summer S Han ; nilan...@jhu.edu ; 
Nilotpal Sanyal 
Subject: Re: CGEN package maintainer change request


Hi,



I�ve created a new account for Nilotpal in the BiocCredentials platform. 
Nilotpal would have to activate the account first, and then add SSH keys to 
gain access to the package.



Once access is gained, please change the maintainer field in the DESCRIPTION 
file of the package.



Best,



Nitesh



From: Wheeler, Bill (IMS) 
Date: Friday, April 23, 2021 at 8:41 AM
To: maintai...@bioconductor.org , 
bioc-devel@r-project.org 
Cc: Summer S Han , nilan...@jhu.edu , 
Nilotpal Sanyal 
Subject: RE: CGEN package maintainer change request

Dear Bioconductor,



Please let Nilotpal Sanyal be the new maintainer of the CGEN package.



Sincerely,



Bill



From: Nilotpal Sanyal 
Sent: Thursday, April 22, 2021 7:24 PM
To: maintai...@bioconductor.org; bioc-devel@r-project.org
Cc: Wheeler, Bill (IMS) ; Summer S Han 
; nilan...@jhu.edu
Subject: CGEN package maintainer change request



Hi,



Regarding the package CGEN, I am going to be the new maintainer and planning to 
submit an updated version of the package by tomorrow's deadline. This is in 
agreement with the previous maintainer Bill Wheeler (copied in this email). Can 
you please make the necessary changes on your side so that I can submit the 
updated package in due time?



Thank you,

Nilotpal Sanyal





--

Nilotpal Sanyal, PhD

Postdoctoral Research Fellow, Quantitative Sciences Unit

Stanford Center for Biomedical Informatics Research (BMIR)

School of Medicine, Stanford University

1701 Page Mill Rd, Palo Alto, CA 94304

Mobile: +1(650)334-8718; Email: 
nsan...@stanford.edu<mailto:nsan...@stanford.edu>

Web: https://med.stanford.edu/profiles/nilotpal-sanyal



-- "The vanity of the sciences.�Physical science will not console me for the 
ignorance of morality in the time of affliction. But the science of ethics will 
always console me for the ignorance of the physical sciences."

~ Blaise Pascal (Pens�es, 1670) [Section II, 67, trans. by W.F. Trotter]

 --







Information in this e-mail may be confidential. It is intended only for the 
addressee(s) identified above. If you are not the addressee(s), or an employee 
or agent of the addressee(s), please note that any dissemination, distribution, 
or copying of this communication is strictly prohibited. If you have received 
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Re: [Bioc-devel] CGEN package maintainer change request

[Nitesh Turaga]

Hi,

I�ve created a new account for Nilotpal in the BiocCredentials platform. 
Nilotpal would have to activate the account first, and then add SSH keys to 
gain access to the package.

Once access is gained, please change the maintainer field in the DESCRIPTION 
file of the package.

Best,

Nitesh

From: Wheeler, Bill (IMS) 
Date: Friday, April 23, 2021 at 8:41 AM
To: maintai...@bioconductor.org , 
bioc-devel@r-project.org 
Cc: Summer S Han , nilan...@jhu.edu , 
Nilotpal Sanyal 
Subject: RE: CGEN package maintainer change request
Dear Bioconductor,

Please let Nilotpal Sanyal be the new maintainer of the CGEN package.

Sincerely,

Bill

From: Nilotpal Sanyal 
Sent: Thursday, April 22, 2021 7:24 PM
To: maintai...@bioconductor.org; bioc-devel@r-project.org
Cc: Wheeler, Bill (IMS) ; Summer S Han 
; nilan...@jhu.edu
Subject: CGEN package maintainer change request

Hi,

Regarding the package CGEN, I am going to be the new maintainer and planning to 
submit an updated version of the package by tomorrow's deadline. This is in 
agreement with the previous maintainer Bill Wheeler (copied in this email). Can 
you please make the necessary changes on your side so that I can submit the 
updated package in due time?

Thank you,
Nilotpal Sanyal



--

Nilotpal Sanyal, PhD

Postdoctoral Research Fellow, Quantitative Sciences Unit

Stanford Center for Biomedical Informatics Research (BMIR)

School of Medicine, Stanford University

1701 Page Mill Rd, Palo Alto, CA 94304

Mobile: +1(650)334-8718; Email: 
nsan...@stanford.edu

Web: https://med.stanford.edu/profiles/nilotpal-sanyal



-- "The vanity of the sciences.�Physical science will not console me for the 
ignorance of morality in the time of affliction. But the science of ethics will 
always console me for the ignorance of the physical sciences."
~ Blaise Pascal (Pens�es, 1670) [Section II, 67, trans. by W.F. Trotter]
 --




Information in this e-mail may be confidential. It is intended only for the 
addressee(s) identified above. If you are not the addressee(s), or an employee 
or agent of the addressee(s), please note that any dissemination, distribution, 
or copying of this communication is strictly prohibited. If you have received 
this e-mail in error, please notify the sender of the error.

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Re: [Bioc-devel] Bioconductor Package Version

[Nitesh Turaga]

Hi AJ,

This issue has been resolved.  You should be able to push versions from 1.23.2 
and onwards.

Going forward, please make sure to check your version numbers for both release 
and devel.

Check if your files have git merge conflicts.

Most importantly, if you have questions please ask either on the slack channel 
or on the bioc-devel@r-project.org<mailto:bioc-devel@r-project.org> mailing 
list.

Best,

Nitesh

From: AJ Kinstlick 
Date: Thursday, April 22, 2021 at 6:37 PM
To: Nitesh Turaga 
Cc: Kern, Lori 
Subject: Re: [Bioc-devel] Bioconductor Package Version
Hi Nitesh and Lori,
I wanted to check in and see if there was anything else I could do at this time 
to try and fix these version numbers. Will you guys be able to update it 
manually if nothing else works?
Thanks,
AJ

On Tue, Apr 20, 2021 at 2:39 PM Nitesh Turaga 
mailto:nturaga.b...@gmail.com>> wrote:
Hi,

Thanks for looping me in.

I�ll take a look at this and keep you posted.

Best,

Nitesh

From: Kern, Lori 
Date: Tuesday, April 20, 2021 at 3:36 PM
To: AJ Kinstlick mailto:akinstl...@uchicago.edu>>, 
Nitesh Turaga mailto:nturaga.b...@gmail.com>>
Subject: Re: [Bioc-devel] Bioconductor Package Version
Hey Nitesh,

I think we might have to force push a version up to straighten this out?  Can 
you please assist.


Cheers,



Lori Shepherd

Bioconductor Core Team

Roswell Park Comprehensive Cancer Center

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263


From: AJ Kinstlick mailto:akinstl...@uchicago.edu>>
Sent: Tuesday, April 20, 2021 3:34 PM
To: Kern, Lori 
Subject: Re: [Bioc-devel] Bioconductor Package Version

Hi Lori,
I tried to push the package with version 1.23.1 and got the error "Illegal 
version bump from '1.18.0' to '1.23.1'.
Do you know if there's anything I can do?
Thanks,
Arjun

On Mon, Apr 19, 2021 at 2:03 PM Kern, Lori 
mailto:lori.sheph...@roswellpark.org>> wrote:
At Bioconductor releases, the core team increases the version numbers of all 
packages.   It is important to remember to git pull upstream master  after each 
Bioconductor release before making any further changes to package and to 
resolve all DESCRIPTION file merge conflicts appropriately using the 
Bioconductor version number or higher.

At release we bumped the release 3.12 version of the package to 1.22.0 and 
devel version of the package to 1.23.0 which is reflected in the landing page 
and the built version of the package.

Somewhere along the way you had a merge conflict and changed the version back 
down to 1.18.0 in devel.  This is not supposed to be possible but managed to 
slip through our checks.

Version numbers should NEVER go down!

Please try and change the version number to 1.23.1 and try to push to the 
master branch again. If you continue to have issues, please reach back out.

Cheers,


Lori Shepherd

Bioconductor Core Team

Roswell Park Comprehensive Cancer Center

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263


From: Bioc-devel 
mailto:bioc-devel-boun...@r-project.org>> on 
behalf of AJ Kinstlick mailto:akinstl...@uchicago.edu>>
Sent: Monday, April 19, 2021 2:28 PM
To: bioc-devel@r-project.org<mailto:bioc-devel@r-project.org> 
mailto:bioc-devel@r-project.org>>
Subject: [Bioc-devel] Bioconductor Package Version

Hello,
I am trying to update the package seq2pathway.data, and I'm getting a
message that says "built version is LOWER than in internal repository".
Does anyone know how I can correct this error with my version numbers?

Trying to commit having directly bumped the version number fails.
It appears that the release version (
https://secure-web.cisco.com/1LH1a9lQCskb-SIBRlxp8f9spU0u2LNHud5_T6RYShbRqpMlBTwliMU78f7NlHz79tyzG2n6EWTNid7Lqy5fzQJGv81OhraorQ0DD-LsvscJaix2k19oDjQmvfi9bjcWp7nTl3QGFIfqsQbr0Ahk0xLjYmM6NtRJ1tXPa_Y0MbSE7XUBPCPVQShfnNYm16q0jiVuGjBXdO9iICW5t2TwrBXU4AYB2aaozpemovsNZpHsQ1ZhBWwJuI4H5galFMNzpVbmnrwRlEopQ8AcVtVGjJGIP_5selfIXdAYJtJEvu06MthoNbQ2xTI4yNS0MLbwCqiHh-W0Oc6k4E5ST0T8QRA/https%3A%2F%2Fbioconductor.org%2Fpackages%2F3.13%2Fdata%2Fexperiment%2Fhtml%2Fseq2pathway.data.html<https://urldefense.com/v3/__https:/secure-web.cisco.com/1WUkdyaZv0BnyI_3kaNdttR3xK_jy3xnmg0kUb6CRtZespvTPlexJFvrk3QpYavvM-wVnAioZ0kJCS9PxFTXJHBN-SEwpVL-Y3OJA3uG4zFxbG6-FY2naW_fX_BuKFAck-AnRvYUcftprLvS3_frkXiKTRoj56p9Ui1WOeFoChRC4GQwBmOafhXZBcu3joijIjp44iY578_QiALw_ZYQ7KkNSqG2TpumPe7AVd7jtlOk29XfZqIaNTscU-Wd0xyBLYbY6ytuOr677PUGkmM9s0aiVroWO-IDvmGjwxDERaEqVp3jj_UlpPSiAoRQqZnyN/https*3A*2F*2Furldefense.com*2Fv3*2F__https*3A*2F*2Fsecure-web.cisco.com*2F1LH1a9lQCskb-SIBRlxp8f9spU0u2LNHud5_T6RYShbRqpMlBTwliMU78f7NlHz79tyzG2n6EWTNid7Lqy5fzQJGv81OhraorQ0DD-LsvscJaix2k19oDjQmvfi9bjcWp7nTl3QGFIfqsQbr0Ahk0xLjYmM6NtRJ1tXPa_Y0MbSE7XUBPCPVQShfnNYm16q0jiVuGjBXdO9iICW5t2TwrBXU4AYB2aaozpemovsNZpHsQ1ZhBWwJuI4H5galFMNzpVbmnrwRlEo

Re: [Bioc-devel] unable to push to new package

[Nitesh Turaga]

Hi,

You do not have write privileges to the package because only the maintainer 
(cre) is given write access.

The submission is a little messy here, because


  1.  It�s submitted from a lab account (this is ok in general)
  2.  You are not listed as maintainer, but want to maintain the package.
  3.  You are the one corresponding with us, when ideally,  ("Pierre-Luc", 
"Germain", 
email=pierre-luc.germ...@hest.ethz.ch) 
should be the one.

I will manually make an account for you. Please add your SSH keys to your 
BiocCredentials account (https://git.bioconductor.org/BiocCredentials/) after 
activating it. Then change the Maintainer field in the description file.

Best,

Nitesh

From: Bioc-devel  on behalf of Gross Fridolin 

Date: Friday, April 23, 2021 at 4:14 AM
To: bioc-devel@r-project.org 
Subject: [Bioc-devel] unable to push to new package
Hi all,

I have submitted our package �scanMiR� yesterday, which is now in the 'review 
in progress� phase (https://github.com/Bioconductor/Contributions/issues/2067).

When trying to push changes upstream, I get the error:

> $ git push upstream master
> Enter passphrase for key '/home/fgross/.ssh/id_ed25519':
> FATAL: W any packages/scanMiR plger 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.


The remotes seem to be set up correctly:

> $ git remote -v
> originhttps://github.com/ETHZ-INS/scanMiR/ (fetch)
> originhttps://github.com/ETHZ-INS/scanMiR/ (push)
> upstream  g...@git.bioconductor.org:packages/scanMiR (fetch)
> upstream  g...@git.bioconductor.org:packages/scanMiR (push)


However, I do not have write permission to the package (as shown by  ssh -T 
g...@git.bioconductor.org).

Could this be related to the fact that the original repo was located not on my 
account but at an organization? Or that I am listed as �author� in the package 
description, and not as �creator�?

I�d be grateful for any kind of help to understand and resolve this problem.

Best,
Fridolin




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Re: [Bioc-devel] unable to push to new package

[Nitesh Turaga]

Another problem is you SSH key available on your github accout is compromised. 
It�s available on another account already. (This usually happens when you share 
the same key around and it gets added to user accounts who that want to 
maintain the same package).

Please create a new SSH key and add it to your account after you activate it 
https://git.bioconductor.org/BiocCredentials/account_activation .

I would also recommend deleting your Github SSH key, because it matches 
Pierre�s. This is the wrong way to do it. Both of you should delete that key.

Best,

Nitesh

From: Nitesh Turaga 
Date: Friday, April 23, 2021 at 8:41 AM
To: Gross Fridolin , bioc-devel@r-project.org 

Subject: Re: unable to push to new package
Hi,

You do not have write privileges to the package because only the maintainer 
(cre) is given write access.

The submission is a little messy here, because


  1.  It�s submitted from a lab account (this is ok in general)
  2.  You are not listed as maintainer, but want to maintain the package.
  3.  You are the one corresponding with us, when ideally,  ("Pierre-Luc", 
"Germain", 
email=pierre-luc.germ...@hest.ethz.ch<mailto:pierre-luc.germ...@hest.ethz.ch>) 
should be the one.

I will manually make an account for you. Please add your SSH keys to your 
BiocCredentials account (https://git.bioconductor.org/BiocCredentials/) after 
activating it. Then change the Maintainer field in the description file.

Best,

Nitesh

From: Bioc-devel  on behalf of Gross Fridolin 

Date: Friday, April 23, 2021 at 4:14 AM
To: bioc-devel@r-project.org 
Subject: [Bioc-devel] unable to push to new package
Hi all,

I have submitted our package �scanMiR� yesterday, which is now in the 'review 
in progress� phase (https://github.com/Bioconductor/Contributions/issues/2067).

When trying to push changes upstream, I get the error:

> $ git push upstream master
> Enter passphrase for key '/home/fgross/.ssh/id_ed25519':
> FATAL: W any packages/scanMiR plger 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.


The remotes seem to be set up correctly:

> $ git remote -v
> originhttps://github.com/ETHZ-INS/scanMiR/ (fetch)
> originhttps://github.com/ETHZ-INS/scanMiR/ (push)
> upstream  g...@git.bioconductor.org:packages/scanMiR (fetch)
> upstream  g...@git.bioconductor.org:packages/scanMiR (push)


However, I do not have write permission to the package (as shown by  ssh -T 
g...@git.bioconductor.org).

Could this be related to the fact that the original repo was located not on my 
account but at an organization? Or that I am listed as �author� in the package 
description, and not as �creator�?

I�d be grateful for any kind of help to understand and resolve this problem.

Best,
Fridolin




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Re: [Bioc-devel] New maintainer for BASiCS

[Nitesh Turaga]

Hi,

I've added Allan to have access to the package BASiCS. It is up to you to 
update the maintainer record on the DESCRIPTION file of the package, this is 
not something Bioconductor does for you.

Remember there can only be 1 active maintainer of the package listed in the 
DESCRIPTION file, but there can be multiple authors. 

Best,

Nitesh 

On 4/16/21, 6:31 AM, "Bioc-devel on behalf of VALLEJOS Catalina" 
 
wrote:

Dear all,

Could you please update your records for BASiCS to have Alan O’Callaghan 
(alan.ocallag...@outlook.com) as the 
maintainer?

Many thanks in advance.

Best wishes,

Cata

_
Catalina Vallejos PhD
Chancellor’s Fellow and Group Leader
MRC Human Genetics Unit
University of Edinburgh
Fellow, The Alan Turing Institute

Website: vallejosgroup.github.io
_
MRC Human Genetics Unit
Institute of Genetics & Molecular Medicine
University of Edinburgh
EH4 2XU Edinburgh
ed.ac.uk/mrc-human-genetics-unit





The University of Edinburgh is a charitable body, registered in Scotland, 
with registration number SC005336. Is e buidheann carthannais a th’ ann an 
Oilthigh Dhùn Èideann, clàraichte an Alba, àireamh clàraidh SC005336.

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Re: [Bioc-devel] Update maintainer of nucleR package

[Nitesh Turaga]

Hi Diego,

We have added the new maintainer for the package as requested.

Hi Alba,

You have to activate your BiocCredentials account at 
https://git.bioconductor.org/BiocCredentials/account_activation with the email 
you gave us.

Once you activate, please add SSH keys and you�ll gain access to the package.

You will also need to change the maintainer information on the DESCRIPTION file 
of the package

Best,

Nitesh

From: Diego Gallego 
Date: Friday, April 16, 2021 at 5:28 AM
To: "bioc-devel@r-project.org" , 
"maintai...@bioconductor.org" , Alba Sala 

Subject: Update maintainer of nucleR package

Hello,

I am Diego and I am the current maintainer of the nucleR package [1].
As per [2], we would like to change the current maintainer to be Alba, (with 
email alba.s...@irbbarcelona.org), CCed here.

Please, let me know if you need anything else to do the change.

Thanks

[1] https://bioconductor.org/packages/release/bioc/html/nucleR.html
[2] https://bioconductor.org/developers/how-to/git/change-maintainer/

--
Diego Gallego P�rez, PhD Student

Molecular Modeling and Bioinformatics Group
Institute for Research in Biomedicine (IRB Barcelona)
Barcelona Institute of Science and Technology (BIST)

Dept. Biochemistry and Molecular Biomedicine
University of Barcelona

The information contained in this e-mail is confidential...{{dropped:8}}

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Re: [Bioc-devel] Bioconductor package InterMineR

[Nitesh Turaga]

Hi,

Going back in time like this will cause major breaks in the way Bioconductor 
does releases and also just in general for users of the InterMineR package.

I think a better way is to just copy the changes from your earlier version 
during �Release 3.10� and apply them to your �devel� branch as a simple commit.

Also, I�d like you to think if making such a drastic change is needed for a 
�release� version. �Release 3.12� or any release is meant to fix high priority 
bugs only, and with Release 3.13 coming in about one month, is it worth it? 
Please think about this.

Best,

Nitesh

From: Kern, Lori 
Date: Thursday, April 15, 2021 at 8:27 AM
To: rac...@intermine.org , Nitesh Turaga 

Subject: Re: Bioconductor package InterMineR
Looping one of our better git experts in for an opinion on this.

Nitesh, advise on reverting to previous version that won't cause conflicting 
issues?




Lori Shepherd

Bioconductor Core Team

Roswell Park Comprehensive Cancer Center

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263


From: rac...@intermine.org 
Sent: Thursday, April 15, 2021 6:40 AM
To: Kern, Lori 
Subject: Re: Bioconductor package InterMineR

Hi Lori,

Apologies for this.  I thought I had fixed a minor issue only to
introduce some more major errors.  I think I will need to go back to our
release 3.10 version so that we can then work on the errors now in the
3_12 version.  We had student work on this package but it seems we need
to fix a few things before we can submit their updates.

I have a question though - if I submit our 3.10 version to the
Bioconductor 3.12 release, should I sync with Bioconductor first? Or
would this re-introduce our current errors into our 3_10 version?

Many thanks,

Rachel.



On 2021-04-12 15:47, Kern, Lori wrote:
> The package has been failing since January. The package continues to
> fail.  This needs to be resolved to avoid deprecation.
>
> Lori Shepherd
>
> Bioconductor Core Team
>
> Roswell Park Comprehensive Cancer Center
>
> Department of Biostatistics & Bioinformatics
>
> Elm & Carlton Streets
>
> Buffalo, New York 14263
>
> -
>
> FROM: rac...@intermine.org 
> SENT: Friday, February 26, 2021 7:20 AM
> TO: Kern, Lori 
> SUBJECT: Re: Bioconductor package InterMineR
>
> Hi Lori,
>
> Apologies, this is taking a little longer than I anticipated to sort
> out
> - but please be assured that we are working towards fixing the problem
>
> and hope to have it resolved by the end of next week,
>
> Best wishes,
>
> Rachel.
>
> On 2021-02-08 16:16, Kern, Lori wrote:
>> We would like to bring to your attention that your package is
> failing
>> to build
>> or check on our release and devel build machines:
>>
>> Devel:
>> bioconductor.org/checkResults/devel/bioc-LATEST/InterMineR
>>
>> Release:
>> bioconductor.org/checkResults/release/bioc-LATEST/InterMineR
>>
>> Would you mind taking a look at this? Don't hesitate to ask on the
>> bioc-devel mailing list if you have any question or need help.
>>
>>  This is very problematic.   If no action is taken over the next few
>> weeks we will begin the deprecation process for your package.  Thank
>> you for your time and effort
>>
>> 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.
>
> 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.

This email message may contain legally privileged and/or confidential 
information. If you are not the intended recipient(s), or the employee

Re: [Bioc-devel] BFG repo cleanup for package under review

[Nitesh Turaga]

Hi Spencer,

I�ve fixed the issue please try now.

Best,

Nitesh

From: Nitesh Turaga 
Date: Wednesday, April 7, 2021 at 1:31 PM
To: Spencer Nystrom , bioc-devel@r-project.org 

Subject: Re: [Bioc-devel] BFG repo cleanup for package under review
Hi Spencer,

I�ll take a look at this today and get back to you

Thanks for the reminder.

Best,

Nitesh

From: Bioc-devel  on behalf of Spencer 
Nystrom 
Date: Wednesday, April 7, 2021 at 1:24 PM
To: bioc-devel@r-project.org 
Subject: [Bioc-devel] BFG repo cleanup for package under review
Sorry to ping about this twice, but my guess is this got buried over the
long weekend.

I need some help getting a cleaned up repo force pushed to the bioconductor
repository ( g...@git.bioconductor.org:packages/memes ). This is for a
package under review here:
https://github.com/Bioconductor/Contributions/issues/1997.

Thanks,
   -Spencer

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Re: [Bioc-devel] BFG repo cleanup for package under review

[Nitesh Turaga]

Hi Spencer,

I�ll take a look at this today and get back to you

Thanks for the reminder.

Best,

Nitesh

From: Bioc-devel  on behalf of Spencer 
Nystrom 
Date: Wednesday, April 7, 2021 at 1:24 PM
To: bioc-devel@r-project.org 
Subject: [Bioc-devel] BFG repo cleanup for package under review
Sorry to ping about this twice, but my guess is this got buried over the
long weekend.

I need some help getting a cleaned up repo force pushed to the bioconductor
repository ( g...@git.bioconductor.org:packages/memes ). This is for a
package under review here:
https://github.com/Bioconductor/Contributions/issues/1997.

Thanks,
   -Spencer

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Re: [Bioc-devel] BFG cleanup on `spiky` repo (under submission)

[Nitesh Turaga]

Hi Tim,

This package should be fixed now. I've synced your github repo with the one on 
git.bioconductor.org.

Please check to make sure everything is as expected including the size. 

Best,

Nitesh 

On 4/1/21, 6:22 AM, "Bioc-devel on behalf of Triche, Tim" 
 wrote:

Hi all, 

We had a couple of chr22 BAMs in this package that kept sneaking in, so I 
nuked them with the BFG and would like to request a reset (force pull) upstream 
into the BioC git server repo (g...@git.bioconductor.org:packages/spiky).  This 
should allow for us to proceed with committing the various bugfixes and changes 
that have occurred downstream of BioC (about 46 last time I checked) and make 
sure we have cleaned up everything on the spb. 

I nuked everything larger than 10M (realistically I could have whacked 
everything larger than 3M but 10M was sufficient to catch the BAMs).

Thanks!

Timothy J. Triche, Jr., PhD
Assistant Professor of Bioinformatics, Van Andel Institute
330 Bostwick Avenue NE, Grand Rapids, MI, 49503
(616) 234-5316 (office)
(626) 375-9663 (mobile)
(616) 234-5252 (administrative, courtesy of Lauren Dunkelberg)
https://trichelab.vai.org/

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Re: [Bioc-devel] Bioconductor Git Credentials error

[Nitesh Turaga]

Hi Ashish,

I replied to your email yesterday, let�s stick to the same thread there.

From: Ashish Jain 
Date: Friday, April 2, 2021 at 1:02 PM
To: Nitesh Turaga 
Cc: raman sethi , Chen Jinmiao 
, "bioc-devel@r-project.org" 

Subject: Re: [Bioc-devel] Bioconductor Git Credentials error

Hi Nitesh,

I am Ashish Jain, author, and maintainer of the package "TissueEnrich".  I am 
also facing a similar issue as I am not able to login to the BiocCredentials 
website. I need to update my package with some fixes. Can you please also look 
into this?

Regards,
Ashish Jain

On Fri, Apr 2, 2021 at 8:48 AM Nitesh Turaga 
mailto:nturaga.b...@gmail.com>> wrote:
Hi Raman,

You should have access to the package. Please check again.

Best,

Nitesh

From: raman sethi mailto:ramanseth...@gmail.com>>
Date: Friday, April 2, 2021 at 1:38 AM
To: Nitesh Turaga mailto:nturaga.b...@gmail.com>>, Chen 
Jinmiao 
mailto:chen_jinm...@immunol.a-star.edu.sg>>
Subject: Re: [Bioc-devel] Bioconductor Git Credentials error

Hi Nitesh,

We have activated the account using the email ID : 
ramanseth...@gmail.com<mailto:ramanseth...@gmail.com><mailto:ramanseth...@gmail.com<mailto:ramanseth...@gmail.com>>
 and added SSH keys to the account.

We want to submit the code of the R package cytofkit2 
(https://github.com/raman91/cytofkit2) to Bioconductor which was modified from 
the package : https://github.com/JinmiaoChenLab/cytofkit2

The author of the Package cytofkit (Dr. Chen Jinmiao) is copied in this email 
as per your request.

Thank you

Best Regards
Raman



On Wed, Mar 31, 2021 at 10:46 PM Nitesh Turaga 
mailto:nturaga.b...@gmail.com><mailto:nturaga.b...@gmail.com<mailto:nturaga.b...@gmail.com>>>
 wrote:
Hi Raman,

I�ve created your own BiocCredentials account for you now.

Email: 
ramanseth...@gmail.com<mailto:ramanseth...@gmail.com><mailto:ramanseth...@gmail.com<mailto:ramanseth...@gmail.com>>

Please activate the account, add your Github username or SSH keys. 
(https://git.bioconductor.org/BiocCredentials/account_activation)

Once you know which packages you want access to, let me know and please copy on 
the email the authors of those packages.

You should be accessing these packages with your own SSH keys and Credentials 
account.

Best,

Nitesh



From: raman sethi 
mailto:ramanseth...@gmail.com><mailto:ramanseth...@gmail.com<mailto:ramanseth...@gmail.com>>>
Date: Wednesday, March 31, 2021 at 6:49 AM
To: Nitesh Turaga 
mailto:nturaga.b...@gmail.com><mailto:nturaga.b...@gmail.com<mailto:nturaga.b...@gmail.com>>>
Subject: Re: [Bioc-devel] Bioconductor Git Credentials error

Hi Nitesh,

Sorry for the late reply.
I am running gitch fetch --all but i am getting an error message:

g...@git.bioconductor.org<mailto:g...@git.bioconductor.org><mailto:g...@git.bioconductor.org<mailto:g...@git.bioconductor.org>>:
 Permission denied (publickey).
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

Can you please tell me how can i solve this problem?

Thank you

Best Regards
Raman

On Mon, Mar 22, 2021 at 8:23 PM Nitesh Turaga 
mailto:nturaga.b...@gmail.com><mailto:nturaga.b...@gmail.com<mailto:nturaga.b...@gmail.com>>>
 wrote:
Hi,

You cannot have two maintainers to a package. We operate under the assumption 
that there is a single maintainer per package. The user that has access to the 
package is �j.chen2�., there are no SSH keys with that username so there is no 
access. I�ve deleted the other account with username �raman..� under the same 
email as �j.chen2�.

The best way forward is to add keys under j.chen2 and get access to the package.

https://github.com/JinmiaoChenLab/cytofkit2/blob/master/DESCRIPTION#L10

Take a look at this link: 
http://bioconductor.org/developers/package-guidelines/#description


�Only one person should be listed as the Maintainer to ensure a single point of 
contact. This person by default will have commit access to the git repository 
on 
git.bioconductor.org<http://git.bioconductor.org><http://git.bioconductor.org>. 
Commit access can be given to other developers by request on the bioc-devel 
mailing list. Another option is to add collaborators to the github repository. 
This approach enables development by many but restricts push access to 
git.bioconductor.org.�


Best,

Nitesh



From: raman sethi 
mailto:ramanseth...@gmail.com><mailto:ramanseth...@gmail.com<mailto:ramanseth...@gmail.com>>>
Date: Monday, March 22, 2021 at 2:40 AM
To: Nitesh Turaga 
mailto:nturaga.b...@gmail.com><mailto:nturaga.b...@gmail.com<mailto:nturaga.b...@gmail.com>>>
Cc: Bioc-devel 
mailto:bioc-devel@r-project.org><mailto:bioc-devel@r-project.org<mailto:bioc-devel@r-project.org>>>
Subject: Re: