I have posted here before to warn that three CRAN spatial infrastructure packages will be retired/archived in October 2023 [1]. It would be very helpful if Bioconductor 3.18 packages made no use at all of rgdal. rgeos or maptools, and that those using sp added sf as a suggested package if operations on coordinate reference systems are used. Is it possible to add blocks on the use of retiring packages to 3.18 checks? Roger [1] https://stat.ethz.ch/pipermail/bioc-devel/2023-June/019727.html -- Roger Bivand Emeritus Professor Norwegian School of Economics Postboks 3490 Ytre Sandviken, 5045 Bergen, Norway Roger.Bivand at nhh.no
[Bioc-devel] Package submission deadline Bioconductor 3.18
3 messages · Shepherd, Lori, Roger Bivand
We don't have a way to preemptively block use of those packages. It should happen naturally as when they are removed from CRAN the packages will start Erroring on the Bioconductor build system and they will receive warnings to fix or be at risk for deprecation. On my quick search over my local checkout, there seems to be no packages that use rgdal, one that uses rgeos (flowDensity) , and two that uses maptools (GEOexplorer, GateFinder) as listed in the DESCRIPTION/NAMESPACE file. I will reach out to these three packages individually as well to notify them of the impending changes. As far as use of sp, I could find five packages that currently list sp in the DESCRIPTION that I can also send an email too: synergyfinder, structToolbox, stJoincount, SPIAT, and flowDensity. Thank you for your diligence and advance notices of affected packages. Hopefully they can make changes early to avoid any disruption or potential deprecation. Cheers, Lori Shepherd - Kern Bioconductor Core Team Roswell Park Comprehensive Cancer Center Department of Biostatistics & Bioinformatics Elm & Carlton Streets Buffalo, New York 14263
From: Roger Bivand <Roger.Bivand at nhh.no>
Sent: Wednesday, August 23, 2023 7:52 AM
To: bioc-devel at r-project.org <bioc-devel at r-project.org>
Cc: Kern, Lori <Lori.Shepherd at RoswellPark.org>
Subject: Re: [Bioc-devel] Package submission deadline Bioconductor 3.18
Sent: Wednesday, August 23, 2023 7:52 AM
To: bioc-devel at r-project.org <bioc-devel at r-project.org>
Cc: Kern, Lori <Lori.Shepherd at RoswellPark.org>
Subject: Re: [Bioc-devel] Package submission deadline Bioconductor 3.18
I have posted here before to warn that three CRAN spatial infrastructure packages will be retired/archived in October 2023 [1]. It would be very helpful if Bioconductor 3.18 packages made no use at all of rgdal. rgeos or maptools, and that those using sp added sf as a suggested package if operations on coordinate reference systems are used. Is it possible to add blocks on the use of retiring packages to 3.18 checks? Roger [1] https://secure-web.cisco.com/1BdIiYTzLiDJv_Bo9hWJ13DAuVsySUqDi_KrkN50aUGHOr2oqpHECLIWaUfxxd6lEiLucW7WH46bjWhXOLcL-Vg-YsDLK_y08IlZm7uJ9rknoKr8H2zBk557Icb-8X-LjiLVwsuk6tjKIXbJPrFvG2g-fZ6c4r8rmvm8ZOMi9F37oYXyjYDA77I54pRwys5Zhkr-W9PQN-oR2Xku68F5zmo0K_GZqobvBp4aGXvfSqVFOqCAjM2fm9FaW_tYJ2OfLpk3TKwshfhTvixeoENUgtwGfA9x_5mVB46_69LEN3cPlvjQ0l9xmHaJmvPMrSwOj/https%3A%2F%2Fstat.ethz.ch%2Fpipermail%2Fbioc-devel%2F2023-June%2F019727.html -- Roger Bivand Emeritus Professor Norwegian School of Economics Postboks 3490 Ytre Sandviken, 5045 Bergen, Norway Roger.Bivand at nhh.no 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.
Thanks, that is helpful. As of now I have opened issues with https://github.com/guypwhunt/GEOexplorer/issues/44 and written to the maintainer of flowDensity (cc-ed here). I don't think splancs, used by GateFinder, is a problem. Those using sp but not retiring packages seem to be OK in my reverse dependency checks. So the exposure is limited, but other Bioconductor packages may depend on the exposed packages, so I hope that they will update while still on 3.17, and certainly before 3.18. Best wishes, Roger -- Roger Bivand Emeritus Professor Norwegian School of Economics Postboks 3490 Ytre Sandviken, 5045 Bergen, Norway Roger.Bivand at nhh.no
From: Kern, Lori <Lori.Shepherd at RoswellPark.org>
Sent: 23 August 2023 15:05
To: Roger Bivand; bioc-devel at r-project.org
Subject: Re: [Bioc-devel] Package submission deadline Bioconductor 3.18
Sent: 23 August 2023 15:05
To: Roger Bivand; bioc-devel at r-project.org
Subject: Re: [Bioc-devel] Package submission deadline Bioconductor 3.18
We don't have a way to preemptively block use of those packages. It should happen naturally as when they are removed from CRAN the packages will start Erroring on the Bioconductor build system and they will receive warnings to fix or be at risk for deprecation. On my quick search over my local checkout, there seems to be no packages that use rgdal, one that uses rgeos (flowDensity) , and two that uses maptools (GEOexplorer, GateFinder) as listed in the DESCRIPTION/NAMESPACE file. I will reach out to these three packages individually as well to notify them of the impending changes. As far as use of sp, I could find five packages that currently list sp in the DESCRIPTION that I can also send an email too: synergyfinder, structToolbox, stJoincount, SPIAT, and flowDensity. Thank you for your diligence and advance notices of affected packages. Hopefully they can make changes early to avoid any disruption or potential deprecation. Cheers, Lori Shepherd - Kern Bioconductor Core Team Roswell Park Comprehensive Cancer Center Department of Biostatistics & Bioinformatics Elm & Carlton Streets Buffalo, New York 14263 ________________________________ From: Roger Bivand <Roger.Bivand at nhh.no> Sent: Wednesday, August 23, 2023 7:52 AM To: bioc-devel at r-project.org <bioc-devel at r-project.org> Cc: Kern, Lori <Lori.Shepherd at RoswellPark.org> Subject: Re: [Bioc-devel] Package submission deadline Bioconductor 3.18 I have posted here before to warn that three CRAN spatial infrastructure packages will be retired/archived in October 2023 [1]. It would be very helpful if Bioconductor 3.18 packages made no use at all of rgdal. rgeos or maptools, and that those using sp added sf as a suggested package if operations on coordinate reference systems are used. Is it possible to add blocks on the use of retiring packages to 3.18 checks? Roger [1] https://secure-web.cisco.com/1BdIiYTzLiDJv_Bo9hWJ13DAuVsySUqDi_KrkN50aUGHOr2oqpHECLIWaUfxxd6lEiLucW7WH46bjWhXOLcL-Vg-YsDLK_y08IlZm7uJ9rknoKr8H2zBk557Icb-8X-LjiLVwsuk6tjKIXbJPrFvG2g-fZ6c4r8rmvm8ZOMi9F37oYXyjYDA77I54pRwys5Zhkr-W9PQN-oR2Xku68F5zmo0K_GZqobvBp4aGXvfSqVFOqCAjM2fm9FaW_tYJ2OfLpk3TKwshfhTvixeoENUgtwGfA9x_5mVB46_69LEN3cPlvjQ0l9xmHaJmvPMrSwOj/https%3A%2F%2Fstat.ethz.ch%2Fpipermail%2Fbioc-devel%2F2023-June%2F019727.html<https://eur02.safelinks.protection.outlook.com/?url=https%3A%2F%2Fsecure-web.cisco.com%2F1BdIiYTzLiDJv_Bo9hWJ13DAuVsySUqDi_KrkN50aUGHOr2oqpHECLIWaUfxxd6lEiLucW7WH46bjWhXOLcL-Vg-YsDLK_y08IlZm7uJ9rknoKr8H2zBk557Icb-8X-LjiLVwsuk6tjKIXbJPrFvG2g-fZ6c4r8rmvm8ZOMi9F37oYXyjYDA77I54pRwys5Zhkr-W9PQN-oR2Xku68F5zmo0K_GZqobvBp4aGXvfSqVFOqCAjM2fm9FaW_tYJ2OfLpk3TKwshfhTvixeoENUgtwGfA9x_5mVB46_69LEN3cPlvjQ0l9xmHaJmvPMrSwOj%2Fhttps%253A%252F%252Fstat.ethz.ch%252Fpipermail%252Fbioc-devel%252F2023-June%252F019727.html&data=05%7C01%7CRoger.Bivand%40nhh.no%7C80a858c9864346fc9d8e08dba3d9ad2d%7C33a15b2f849941998d56f20b5aa91af2%7C0%7C0%7C638283927537706944%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=FzG5VkoLhzXwRqOmmHPtZisc1J4eNFJzho1bAlLUAEw%3D&reserved=0> -- Roger Bivand Emeritus Professor Norwegian School of Economics Postboks 3490 Ytre Sandviken, 5045 Bergen, Norway Roger.Bivand at nhh.no 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.