Hi Luigi,
I'll add Claudio to these packages. To make that happen, I'll create a new
BiocCredentials account for Claudio and email him privately with information
regarding his account username and password.
Claudio would have to add his SSH keys once he activates his account and he'll
have access to the following packages,
- RTopper
- switchBox
- matchBox
- mammaPrintData
- seventyGeneData
Best,
Nitesh
On 1/29/21, 6:49 AM, "Bioc-devel on behalf of Luigi Marchionni"
<bioc-devel-boun...@r-project.org on behalf of lum4...@med.cornell.edu> wrote:
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.sheph...@roswellpark.org<mailto:lori.sheph...@roswellpark.org>>
Subject: Re: Bioconductor package RTopper
Date: January 28, 2021 at 1:32:52 PM EST
To: Claudio Zanettini
<claudio.zanett...@gmail.com<mailto:claudio.zanett...@gmail.com>>
Cc: Luigi Marchionni <march...@jhu.edu<mailto:march...@jhu.edu>>
External Email - Use Caution
Could you please have Luigi request you have access at
bioc-devel@r-project.org<mailto:bioc-devel@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.zanett...@gmail.com<mailto:claudio.zanett...@gmail.com>>
Sent: Thursday, January 28, 2021 1:26 PM
To: Kern, Lori
<lori.sheph...@roswellpark.org<mailto:lori.sheph...@roswellpark.org>>
Cc: Luigi Marchionni <march...@jhu.edu<mailto:march...@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.sheph...@roswellpark.org<mailto:lori.sheph...@roswellpark.org>>
Subject: Re: Bioconductor package RTopper
Date: January 25, 2021 at 2:14:12 PM EST
To: "march...@jhu.edu<mailto:march...@jhu.edu>"
<march...@jhu.edu<mailto:march...@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: march...@jhu.edu<mailto:march...@jhu.edu>
<march...@jhu.edu<mailto:march...@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.sheph...@roswellpark.org<mailto:lori.sheph...@roswellpark.org>>
Subject: Bioconductor package RTopper
Date: January 12, 2021 at 10:55:25 AM EST
To: "march...@jhu.edu<mailto:march...@jhu.edu>"
<march...@jhu.edu<mailto:march...@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.
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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