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. [[alternative HTML version deleted]] _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
