Begin forwarded message:
From: Ludwig Geistlinger <Ludwig.Geistlinger at 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.bioc at gmail.com>
Cc: "Shepherd, Lori" <Lori.Shepherd at 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.bioc at 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.Geistlinger at sph.cuny.edu <mailto:Ludwig.Geistlinger at sph.cuny.edu>> wrote:
Many thanks, Lori + Nitesh for swift action!
From: Shepherd, Lori <Lori.Shepherd at RoswellPark.org <mailto:Lori.Shepherd at 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.Geistlinger at sph.cuny.edu <mailto:Ludwig.Geistlinger at sph.cuny.edu>>
Sent: Tuesday, June 9, 2020 9:33 AM
To: Shepherd, Lori <Lori.Shepherd at RoswellPark.org <mailto:Lori.Shepherd at 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.Shepherd at RoswellPark.org <mailto:Lori.Shepherd at 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_Barry at rhoworld.com <mailto:Bill_Barry at rhoworld.com>>
Sent: Tuesday, June 9, 2020 9:03 AM
To: Shepherd, Lori <Lori.Shepherd at RoswellPark.org <mailto:Lori.Shepherd at RoswellPark.org>>; Ludwig Geistlinger <Ludwig.Geistlinger at sph.cuny.edu <mailto:Ludwig.Geistlinger at 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.Shepherd at RoswellPark.org <mailto:Lori.Shepherd at RoswellPark.org>>
Sent: Tuesday, June 09, 2020 8:40 AM
To: Ludwig Geistlinger <Ludwig.Geistlinger at sph.cuny.edu <mailto:Ludwig.Geistlinger at sph.cuny.edu>>; Bill Barry <Bill_Barry at rhoworld.com <mailto:Bill_Barry at 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.Geistlinger at sph.cuny.edu <mailto:Ludwig.Geistlinger at sph.cuny.edu>>
Sent: Monday, June 8, 2020 1:12 PM
To: bill_barry at rhoworld.com <mailto:bill_barry at rhoworld.com> <bill_barry at rhoworld.com <mailto:bill_barry at rhoworld.com>>
Cc: Shepherd, Lori <Lori.Shepherd at RoswellPark.org <mailto:Lori.Shepherd at 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
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