Hi, This is just following up that this issue has been resolved.
Best, Nitesh > Begin forwarded message: > > From: Ludwig Geistlinger <ludwig.geistlin...@sph.cuny.edu> > Subject: Re: safe: Bioc build error in release and devel > Date: June 10, 2020 at 5:30:45 PM EDT > To: Nitesh Turaga <nturaga.b...@gmail.com> > Cc: "Shepherd, Lori" <lori.sheph...@roswellpark.org> > > Thanks, Nitesh, that worked. > > Lori, the I fixed the issue and the build is clean now: > > http://bioconductor.org/checkResults/release/bioc-LATEST/safe/ > <http://bioconductor.org/checkResults/release/bioc-LATEST/safe/> > http://bioconductor.org/checkResults/devel/bioc-LATEST/safe/ > <http://bioconductor.org/checkResults/devel/bioc-LATEST/safe/> > > except for the deprecation warning in devel. > > Best, > Ludwig > > -- > Dr. Ludwig Geistlinger > Department of Epidemiology and Biostatistics > CUNY School of Public Health > New York, NY 10027 > From: Nitesh Turaga <nturaga.b...@gmail.com> > Sent: Tuesday, June 9, 2020 12:57 PM > To: Ludwig Geistlinger > Cc: Shepherd, Lori > Subject: Re: safe: Bioc build error in release and devel > > Hi Ludwig, > > You should have access now. > > Nitesh > >> On Jun 9, 2020, at 10:40 AM, Ludwig Geistlinger >> <ludwig.geistlin...@sph.cuny.edu <mailto:ludwig.geistlin...@sph.cuny.edu>> >> wrote: >> >> Many thanks, Lori + Nitesh for swift action! >> >> From: Shepherd, Lori <lori.sheph...@roswellpark.org >> <mailto:lori.sheph...@roswellpark.org>> >> Sent: Tuesday, June 9, 2020 9:37:16 AM >> To: Ludwig Geistlinger; Turaga, Nitesh; Nitesh Turaga >> Subject: Re: safe: Bioc build error in release and devel >> >> Great! I am putting you in touch with Nitesh who can handle giving you push >> access to our bioconductor git repository for safe. Don't forget to >> update the maintainer field in the DESCRIPTION of the package as well. When >> it is building cleanly on our builders, please email me so I know to >> undeprecate it (we won't undeprecate until it is fixed) >> >> >> Nitesh, the original maintain has already given permission for Ludwig to >> take over as maintainer. Documented in the email thread below. Could you >> please make sure he can push changes to safe. >> >> >> >> Lori Shepherd >> Bioconductor Core Team >> Roswell Park Comprehensive Cancer Center >> Department of Biostatistics & Bioinformatics >> Elm & Carlton Streets >> Buffalo, New York 14263 >> >> >> From: Ludwig Geistlinger <ludwig.geistlin...@sph.cuny.edu >> <mailto:ludwig.geistlin...@sph.cuny.edu>> >> Sent: Tuesday, June 9, 2020 9:33 AM >> To: Shepherd, Lori <lori.sheph...@roswellpark.org >> <mailto:lori.sheph...@roswellpark.org>> >> Subject: Re: safe: Bioc build error in release and devel >> >> Yes I would be interested in taking over the responsibilities for >> maintenance of the safe package. Ludwig >> >> From: Shepherd, Lori <lori.sheph...@roswellpark.org >> <mailto:lori.sheph...@roswellpark.org>> >> Sent: Tuesday, June 9, 2020 9:30 AM >> To: Ludwig Geistlinger >> Subject: Re: safe: Bioc build error in release and devel >> >> ***ATTENTION: This email came from an external source. Do not open >> attachments or click on links from unknown senders or unexpected emails.*** >> >> >> Based on Bill's response, did you have any interest or know of anyone that >> would be interested in taking over as a permanent maintainer of the safe >> package? >> >> >> Cheers, >> >> Lori Shepherd >> Bioconductor Core Team >> Roswell Park Comprehensive Cancer Center >> Department of Biostatistics & Bioinformatics >> Elm & Carlton Streets >> Buffalo, New York 14263 >> >> From: Bill Barry <bill_ba...@rhoworld.com <mailto:bill_ba...@rhoworld.com>> >> Sent: Tuesday, June 9, 2020 9:03 AM >> To: Shepherd, Lori <lori.sheph...@roswellpark.org >> <mailto:lori.sheph...@roswellpark.org>>; Ludwig Geistlinger >> <ludwig.geistlin...@sph.cuny.edu <mailto:ludwig.geistlin...@sph.cuny.edu>> >> Subject: RE: safe: Bioc build error in release and devel >> >> Dear Lori and Ludwig, >> >> Thank you both for reaching out, and I am very glad to hear the safe >> package remains of value to the community. I apologize that my contact >> information was out of date, and glad you all found me. >> >> I do not have capacity to do the programming and maintenance of the package >> now that I am no longer at an academic institution. I would be grateful if >> it were opened up to the community such that changes including the ones >> Ludwig indicated could be made. Please let me know if more is needed from me >> to do that. >> >> I am happy to be consulted on the original theory and methodology, or engage >> in other discussions. I have always held high regard for what Bioconductor >> has achieved in biostatistics and data science, and been proud of my past >> participation in the community. >> >> My best to you both, >> >> William (Bill) Barry, PhD >> Senior Research Scientist >> Rho Federal Systems Division, Inc. >> 2635 E. NC Hwy 54 • Durham, NC 27713 >> Phone: 919.595.6867 • Fax: 919.408.0999 >> >> >> >> From: Shepherd, Lori <lori.sheph...@roswellpark.org >> <mailto:lori.sheph...@roswellpark.org>> >> Sent: Tuesday, June 09, 2020 8:40 AM >> To: Ludwig Geistlinger <ludwig.geistlin...@sph.cuny.edu >> <mailto:ludwig.geistlin...@sph.cuny.edu>>; Bill Barry >> <bill_ba...@rhoworld.com <mailto:bill_ba...@rhoworld.com>> >> Subject: Re: safe: Bioc build error in release and devel >> >> The safe package is currently deprecated as we tried to reach out multiple >> times since January but apparently to an invalid email. We were notified >> that this might be a better email to reach you at. >> >> If this is a good email and you wish to keep maintaining the safe package, >> please don't forget to update the email in the DESCRIPTION of the package >> and try to make the changes as soon as possible. >> >> If you no longer wish to maintain the safe package, do we have your >> permission to open it up to members of the Bioconductor community to take >> over maintenance of the package? >> >> Please let us know your intentions. Thank you. >> >> Cheers, >> >> Lori Shepherd >> Bioconductor Core Team >> Roswell Park Comprehensive Cancer Center >> Department of Biostatistics & Bioinformatics >> Elm & Carlton Streets >> Buffalo, New York 14263 >> From: Ludwig Geistlinger <ludwig.geistlin...@sph.cuny.edu >> <mailto:ludwig.geistlin...@sph.cuny.edu>> >> Sent: Monday, June 8, 2020 1:12 PM >> To: bill_ba...@rhoworld.com <mailto:bill_ba...@rhoworld.com> >> <bill_ba...@rhoworld.com <mailto:bill_ba...@rhoworld.com>> >> Cc: Shepherd, Lori <lori.sheph...@roswellpark.org >> <mailto:lori.sheph...@roswellpark.org>> >> Subject: safe: Bioc build error in release and devel >> >> Dear Dr. Barry, >> >> I am big fan of the your safe package which implements a number of very >> useful functions for gene set enrichment analysis. >> >> Given this useful functionality, I am actually depending on your package in >> my EnrichmentBrowser package: >> >> https://bioconductor.org/packages/EnrichmentBrowser >> <https://secure-web.cisco.com/11FlNj83QPeNeN-YcJa8fbYCifHgb-ebbPC7JOB0KcNPgSchIq0dN4pS_9qbXp40YAtQ9g3JsBvU9ClBilsknCKbh2pobzSaCWISPhqS9Z2JPD0IBvvC995cUjEFLoURvCAUbjLpChi8QC8EqwiNr5CdlNtSo2tEvhWJCWYFumUNYYus4REvqGELOz5el97NmQX8L_9zfEti3UVWbE86ymg5uUtS-9wg5ghf3FMxfKuH616JEi6SnKlO-tGC8yYrzL6gBRN8i1auMRurJQB1VWsMY7BWQnyxfa3ntSpvbNsl3qffhxGsvwXUsqhqOxDI-14IQWeZNq9J_VVn_BCUGzg/https%3A%2F%2Furldefense.com%2Fv3%2F__https%3A%2Fsecure-web.cisco.com%2F1NpG9ODhY3C_WyWt7IqPaOkBKxnjRqG_Q1ZQ13SBWCkdqgMGXJjLOvtJ3SlDm_TSt_Yo8I-8b3H7AsOpFIet25Z0yXMK1NkQnw7sr8XxTzR-Iuq_fvF3BdiWmCG4BAf77nS7WrI8am9MpiUq2Jxneik8cjGaWswzHzsw78SxIRoveqa8fwhTTmBrJC4D_GvsldysSTcFZGGAm_ZLjc48E5ZiIol799XKI5YAqweIjrIDptNYBs3oGiAj-rXxNU8tJ3UudlzwUhGDHMlWoYb7y5JsHhsu0zfAuFft6pCyDSpLXBDXvoGxBPBTvSHlfvQ2Ytppm7e_KqOS3uZAEB-UiK5ZeC-GhTqw6xgfBTxb5hDs%2Fhttps%2A3A%2A2F%2A2Fbioconductor.org%2A2Fpackages%2A2FEnrichmentBrowser__%3BJSUlJSU%21%21JzPv%218pU_GBFkyzAC9Qp9gxzOXHtXdVV4T49EpQxO8hiT_lWY8TGL5Pym9nfvATpY7Il7J6U%24> >> >> With the recent release of R-4.0.0, safe starts to error on the Bioc-Builder: >> >> http://bioconductor.org/checkResults/devel/bioc-LATEST/safe/ >> <https://secure-web.cisco.com/1gRnCbvxspWmd8Rp5QJtaKWqcKWFLPb9q6aiEG3tcIAUdHs_Zb9iS7YagN_8noOTMhCsr8gxy0ZA18x2oey4IjmAycXNzhgJR3JHm9MY8QvgtPsDEm-yX4w9TKkAIFkqJxTeu9QLLo2xSL7AStKMvkZhay4xGcjwof-mXy5C0TYUS1eELSl5raoiiSwlWQQI_Ld42qcvWXQ2r8C6VwhsIiZxzOwRL2cNvQ3fYFz1livqF6_QQP_FnQwapYCP4gqfNgLLwJ_81ekkjxhpGwWLpl05f2Jhq3Y4Ek6AWebUSMjANYmaFT1-qmbf2INoR2rfvHILTwK5-ENeq1z4RhxaCow/https%3A%2F%2Furldefense.com%2Fv3%2F__http%3A%2Fsecure-web.cisco.com%2F1IN32bzlZz964uyh1eXmm2QBCb2e6vgIQ6K2olqNS1Go1H5D_KTT6ErU_hdDGBZ1Y7hrVndhtlCE_6eafymUsqL_L4lQDSvzWe3iRlU88BLKECot4wwcIzMgr-2qwVKrxKlb0siJmDqDIj1vX0-DNJYLj1vLg97NdHGjWrzG9Q4M5OkbD94z4dwfsV6l2jevBm_pjETmYSfaUq23VRt9T5nKe4y2t6GIYUJ4QDHIH_kcoWO3I2bECA2XBAKH7eEQbESChgElLpfK44ZKJ7h7jjDEq8yZEa_tqMdfPmmr4q0OqKo4Hsu29vO78u_Vu-80gVHSBsA4h3S9A5nOiN9lCu-F4Eo53Y61IuT0tvC4O7WQ%2Fhttp%2A3A%2A2F%2A2Fbioconductor.org%2A2FcheckResults%2A2Fdevel%2A2Fbioc-LATEST%2A2Fsafe%2A2F__%3BJSUlJSUlJSU%21%21JzPv%218pU_GBFkyzAC9Qp9gxzOXHtXdVV4T49EpQxO8hiT_lWY8TGL5Pym9nfvATpYft7xlQc%24> >> http://bioconductor.org/checkResults/release/bioc-LATEST/safe/ >> <https://secure-web.cisco.com/1Gqi-Bxbowu9mBEH3s0onl-e8-yKO_gKdPeRHLzKU7rl_I3Zt6hVf6Y4nRK-y27uJjgF90jPc0JW_4Emamt8k1dEUyHtG33GCqKFxVoo6N3A-cS6korzfeycg3bMwatALDiD-aqEDgMHaW7DSOrKIvnPC1hvN19-1AclHSdPDkk-f0gbknuYYavCgem6XwaZ5jwOjDMfgcmNcu1hzbOvqqudFmIuAUEybTmcZatc8He-e0iWaLQdVThkf_lC3s1i5Men3ARvpFbYG-TRmCYeee5ka-tZ9YCzY5MvqcrpcAQ8dpPMWv5f1r3mISK-qkiCLe9ruu5Fv3oCH9py__aCEMg/https%3A%2F%2Furldefense.com%2Fv3%2F__http%3A%2Fsecure-web.cisco.com%2F1Y48ZRqarvBf0zkvleZF5k5T6Ou4X-3uYL7MKRHg2HQKhnVuJmmHF2pkV08zaLQZgErES2oGmRwTEX7EcNbKKfJP4owD6pmFYc0w1hOGyVrLgmMRxJ76DIQICSOrmtZWyGwdHEE9xJM28Meek0KmW8EFtbIuNKzE_lhOJwEGQO0LqUdRfEuISbZsHe67lG7bO24D1OnME2kHmuQuXkgKuqZGKQSpIac1R6wgdFwaJ2AkwqJGz-Fx8bq_ZFvk4RlwxV35JDXw7uTDx313XLs7gTx4R0njGY0_sMNVZ1LRvteWckHsdwKjG-3D7Z7XaSb_uklby3bnkUoKEJqgqYl4Iqk2JFCWTYUYGxX2alPD5iq8%2Fhttp%2A3A%2A2F%2A2Fbioconductor.org%2A2FcheckResults%2A2Frelease%2A2Fbioc-LATEST%2A2Fsafe%2A2F__%3BJSUlJSUlJSU%21%21JzPv%218pU_GBFkyzAC9Qp9gxzOXHtXdVV4T49EpQxO8hiT_lWY8TGL5Pym9nfvATpYNJiSFoQ%24> >> >> This is due to a quite disruptive update in R-4.0.0 >> (https://cran.r-project.org/doc/manuals/r-release/NEWS.pdf >> <https://secure-web.cisco.com/1KCrYh9_jMwfZQdpkx4aZySc7imFIvwOrLTq3rnzs2CpF2bt_DP9pe6vWVc2dJdaEx0qOywFqJGtAyU1lXo6sSBpYQBaUGlZdEXWi07_s42hHW9PhnEZToKVn-7TgWDvo02kKZu_C-3fimXmYF_uSnYEwUI-52l6vvGIkSbQp3WIeo_B2v_elIjLaMZPrgz_A6gHHT3aByxMYcZWeX5A2g5TIf9kKxvWFOe7RXxBp9Z3vPFJ_5qLqNcwGlqRlAlLdiPrfjbKaPIoN4cu8Yhs-qDRO4-NQNdUoaIJ0kf7Tko5iWYPXusnd-2j0JOZjXkYERYB5q4hgYWoSGI9YrTqc-A/https%3A%2F%2Furldefense.com%2Fv3%2F__https%3A%2Fsecure-web.cisco.com%2F1kauJrRLUErC-FEFHx7pySMOwtXhBv_Kcr5zYCBXoOtm3va8KlSXwMxDdYtlvIag9o29o37dl8-47nr30H4JUidloRjHjHbQ8Yu4hcOI07hA8APiZF4NP4PnY95If2w9yjE8fJclXEgS0mjSI6L4oRBd1KYYjtKs3FlKnnikh_9O_Pj8SIEEBF3cUG4Pcz8p06iyzm2eaK0qTuwiBh5LBZ3iY2FTMyaKS1-ezQphpch4KyF2gpVcfa3l_IdQ543CXveLuSx1iPyGJln2Ivzl3BRK0FwA6QzEq85qWx4-VhBWbesvSnGFaJg9pJUL7ZdGzVtSMGM_JVt1Hpy400CZ4lQ%2Fhttps%2A3A%2A2F%2A2Fcran.r-project.org%2A2Fdoc%2A2Fmanuals%2A2Fr-release%2A2FNEWS.pdf__%3BJSUlJSUlJQ%21%21JzPv%218pU_GBFkyzAC9Qp9gxzOXHtXdVV4T49EpQxO8hiT_lWY8TGL5Pym9nfvATpYhbQWZQ8%24>): >> >> "matrix objects now also inherit from class"array", so >> e.g.,class(diag(1))isc("matrix","array"). >> This invalidates code incorrectly assuming thatclass(matrix_obj))has length >> one" >> >> and breaks code of the form >> >> class(obj) == "matrix" >> >> which are best updated to >> >> is.matrix(obj) >> >> Would it be possible to update safe's codebase accordingly? >> I can provide a pull request if that is helpful. >> >> Thank you for your support, >> Ludwig Geistlinger >> >> -- >> Dr. Ludwig Geistlinger >> Department of Epidemiology and Biostatistics >> CUNY School of Public Health >> New York, NY 10027 >> >> 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. 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