[Bioc-devel] Fwd: Bioconductor package RTopper

Fri Jan 29 17:32:36 CET 2021

To whom it may concern:

In response to a request from Lori Shepherd we have updated the RTopper package fixing its dependency from the KEGG.db package.
All necessary changes were made by Claudio Zanettini in my group, we need now to push these changes to the bioC gitHub repository.
To this end, I would like to add Claudio Zanettini credentials and enable him to push changes to the RTopper repository.

Since he will be possibly;y involved in updating and maintaining additional packages contributed by my lab, would it be possible to do the same for the following packages:

- switchBox
- matchBox
- mammaPrintData
- seventyGeneData

I thank you in advance for your help and assistance.

Please let me know if you need further information.

Luigi

Begin forwarded message:

From: "Kern, Lori" <Lori.Shepherd using RoswellPark.org<mailto:Lori.Shepherd using RoswellPark.org>>
Subject: Re: Bioconductor package RTopper
Date: January 28, 2021 at 1:32:52 PM EST
To: Claudio Zanettini <claudio.zanettini using gmail.com<mailto:claudio.zanettini using gmail.com>>
Cc: Luigi Marchionni <marchion using jhu.edu<mailto:marchion using jhu.edu>>

      External Email - Use Caution

Could you please have Luigi request you have access at bioc-devel using r-project.org<mailto:bioc-devel using r-project.org>.  We have dedicated members of the team that access with git / git credential related issues.

Thank you for looking into this! We appreciate your contribution to Bioconductor.

Lori Shepherd
Bioconductor Core Team
Roswell Park Comprehensive Cancer Center
Department of Biostatistics & Bioinformatics
Elm & Carlton Streets
Buffalo, New York 14263
________________________________
From: Claudio Zanettini <claudio.zanettini using gmail.com<mailto:claudio.zanettini using gmail.com>>
Sent: Thursday, January 28, 2021 1:26 PM
To: Kern, Lori <Lori.Shepherd using RoswellPark.org<mailto:Lori.Shepherd using RoswellPark.org>>
Cc: Luigi Marchionni <marchion using jhu.edu<mailto:marchion using jhu.edu>>
Subject: Bioconductor package RTopper

Hello Lori,
we fixed the problem related to KEGG and update our  repo on https://github.com/marchion/RTopper<https://secure-web.cisco.com/1X0OQn4o5zRaaAVQ_7vuID_-kiMb6rCSd123WJi11oyO90Vnu8PxmNTF9jyYfDh7en2GpHsuP2QiOxu8wQuV2hz21dyInTzDpvhxQHRyXP27SLi-47ymwbriDmXkcf5iYkXOkL6bw_CZxhKyX2KSoxpOtXk8zTPeTCJdj5g6iIVC5FSTeKuALHYq3X0ZKBbgNxtL1hzPtduJnCWL88j2_7etvbJHUZCD2WcYtGize_pNsLCQIDV2SUbNiUO8c67wWuxO7gw9uzPg55nOU-dpJ2Do5kljs3G8d6rkRpoU4oObhRBxkErqa6oh_WjGm1mQu/https%3A%2F%2Fgithub.com%2Fmarchion%2FRTopper>

I understand that the workflow is that I push it to the bioconductor rep.  I don't think that my SSH is listed among the contributors that have access to the bioconductor repo.
Would it be possible to add me so that I can proceed?

Thanks
Claudio

Begin forwarded message:

From: "Kern, Lori" <Lori.Shepherd using RoswellPark.org<mailto:Lori.Shepherd using RoswellPark.org>>
Subject: Re: Bioconductor package RTopper
Date: January 25, 2021 at 2:14:12 PM EST
To: "marchion using jhu.edu<mailto:marchion using jhu.edu>" <marchion using jhu.edu<mailto:marchion using jhu.edu>>

      External Email - Use Caution

This is your second warning. Please fix your package 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: Kern, Lori
Sent: Tuesday, January 12, 2021 10:55 AM
To: marchion using jhu.edu<mailto:marchion using jhu.edu> <marchion using jhu.edu<mailto:marchion using jhu.edu>>
Subject: Bioconductor package RTopper

Hello

The package you maintain if failing in the devel version of Bioconductor and needs your immediate attention. The reason for failure is your package imports  KEGG.db which was removed in Bioconductor 3.12 and not available for Bioconductor 3.13.  The KEGG.db package was deprecated for two releases prior and should have been producing warnings when utilized.   The replacement package in KEGGREST.

See the link below for KEGGREST
https://www.bioconductor.org/packages/devel/bioc/html/KEGGREST.html<https://secure-web.cisco.com/1mCGWqti1LSbi3MLUrm36khesE_Ab6ugz6ElrPazK3446O7LfFvP6XgX_D1nDwi4cWMWXui3csaXb9540Hd_-mJcE-BVDl1Lnbp2LTBkax65_2_kqOnuUeRjlizq63M7enZYhoiOF1DqbhWymr-14yUeTf-XK7s0f3CEuv6bKClbyDC1Q7LFpfedJ_gXUZgvjWt5iipOpkJjCNdfWbCYu_og46MWB72sN8nd1b380PaAoKj2T0qhsuVtCPfu9dMWA58YEBggNAws0UtAPzuJlp-FgTca5ejDV18993cQxNxKPCblNQHBgj9LWfpsMIkFt/https%3A%2F%2Fwww.bioconductor.org%2Fpackages%2Fdevel%2Fbioc%2Fhtml%2FKEGGREST.html>

Please update your package immediately
The package in question is RTopper

Thank you.

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.
Begin forwarded message:

From: "Kern, Lori" <Lori.Shepherd using RoswellPark.org<mailto:Lori.Shepherd using RoswellPark.org>>
Subject: Bioconductor package RTopper
Date: January 12, 2021 at 10:55:25 AM EST
To: "marchion using jhu.edu<mailto:marchion using jhu.edu>" <marchion using jhu.edu<mailto:marchion using jhu.edu>>

      External Email - Use Caution

Hello

The package you maintain if failing in the devel version of Bioconductor and needs your immediate attention. The reason for failure is your package imports  KEGG.db which was removed in Bioconductor 3.12 and not available for Bioconductor 3.13.  The KEGG.db package was deprecated for two releases prior and should have been producing warnings when utilized.   The replacement package in KEGGREST.

See the link below for KEGGREST
https://www.bioconductor.org/packages/devel/bioc/html/KEGGREST.html<https://secure-web.cisco.com/1mCGWqti1LSbi3MLUrm36khesE_Ab6ugz6ElrPazK3446O7LfFvP6XgX_D1nDwi4cWMWXui3csaXb9540Hd_-mJcE-BVDl1Lnbp2LTBkax65_2_kqOnuUeRjlizq63M7enZYhoiOF1DqbhWymr-14yUeTf-XK7s0f3CEuv6bKClbyDC1Q7LFpfedJ_gXUZgvjWt5iipOpkJjCNdfWbCYu_og46MWB72sN8nd1b380PaAoKj2T0qhsuVtCPfu9dMWA58YEBggNAws0UtAPzuJlp-FgTca5ejDV18993cQxNxKPCblNQHBgj9LWfpsMIkFt/https%3A%2F%2Fwww.bioconductor.org%2Fpackages%2Fdevel%2Fbioc%2Fhtml%2FKEGGREST.html>

Please update your package immediately
The package in question is RTopper

Thank you.

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.

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