[Bioc-devel] Fwd: safe: Bioc build error in release and devel

Thu Jun 11 15:10:37 CEST 2020

Hi,

This is just following up that this issue has been resolved.

Best,

Nitesh

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