[Bioc-devel] Final Reminder: Submit Your Abstract for GBCC2025 by April 8th!

Tue Apr 8 13:58:31 CEST 2025

The R 4.5 release is this Friday April 11.

More over,   it will not be available via BiocManager in devel because it needs to build on our builders.  It is failing across all
https://bioconductor.org/checkResults/devel/bioc-LATEST/RbowtieCuda/

 but that is expected because of the Nvidia GPU/cuda requirement as you experienced in the review process as we had to set up an entirely different environment/builder for testing.

This should have been conveyed on the issue and I'm sorry it was not.  We have a plan that should not take very long to implement to add propagation from the GPU builders used in the review process.  However given that is a week before our semi-annual release we are at capacity to add this new integration until after the release next week.

Finally,
In seems this thread was linked by responding to a different thread regarding the conference abstracts.  Please do not reply to other threads to post new comments unless it is relevant to that thread.  Please send a new email to bioc-devel using r-projects so we can keep threads distinct and organized.

Lori Shepherd - Kern

Bioconductor Core Team

Roswell Park Comprehensive Cancer Center

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263

________________________________
From: Bioc-devel <bioc-devel-bounces using r-project.org> on behalf of Sean Davis <seandavi using gmail.com>
Sent: Monday, April 7, 2025 3:39 PM
To: Franck RICHARD <franck.richard using winstars.net>; bioc-devel using r-project.org <bioc-devel using r-project.org>
Subject: Re: [Bioc-devel] Final Reminder: Submit Your Abstract for GBCC2025 by April 8th!

Hi, Franck.

See here:

https://secure-web.cisco.com/1oyH73R6N9dMunhn_6hCTTbZ7tOMGxfU9MaVZ06P1rTbHI0zkE8rYXvv4JFAnmNi8qO3AJ4BvlDJGBzzyy9b-kr0L_vJT6vtpcLjY3cpmVa6QEhux2YCA113ehkIrHePxsXs-qr1YxxigG32f6x8i4xBnDofCDGsETHghL8PdoWDZCMNZnF8l3TJPteaoGE_B4fh7tTmC1u2HfK2M56yLwwJ6cs6WFHHQJ_ggHem6A-Nchu2rap7zV4cyCOldocB8WgTp-BF10sUSVd9TsgZKyREot9gdCPzI5UcLnUS-S8DERVafmIyFJyg11gr_U8Hc/https%3A%2F%2Fcontributions.bioconductor.org%2Fuse-devel.html

In short, you’ll need to use R-devel (which will become R 4.5) for a little longer.

Sean

From: Bioc-devel <bioc-devel-bounces using r-project.org> on behalf of Franck RICHARD <franck.richard using winstars.net>
Date: Monday, April 7, 2025 at 3:32 PM
To: bioc-devel using r-project.org <bioc-devel using r-project.org>
Subject: Re: [Bioc-devel] Final Reminder: Submit Your Abstract for GBCC2025 by April 8th!
Hello everyone !

I would like to test the installation of my RbowtieCuda package, but at
the moment it can only be installed from the devel version of bioconductor.

But when I switch Biocmanager to devel mode, I get the error message:

BiocManager::install(version='devel')
Error: Bioconductor version '3.21' requires R version '4.5'; use
`version = '3.20'` with R version 4.4; see https://secure-web.cisco.com/1IYm0ztbB5cLZMnzrtaWZuRTihgjp-zBHWIw2xL3XeX_jYKJvWgTEMCRxPVuFZHnA9prLFWxgZawIM7KMcwtIP3Ruzn6E2OQJ-GSrpMJpgtJHzl4F2HuXFe2hANqJNciEiNM2Q-KwPeJ5UMyr-47prFKy0QSmXTQ3PrqIfWCrpBezhX8Plq5lxtASZwbaDUuuWRgDGoBtdEt-hk0cW5_bXeQHhqrLKRndCndrralpkgWTHGjM-FGv9IRC4xvoZ6GuTPRfvf38USt8OOyQfqP83eu9Sq_F17VkQBPdmfS0sMuaxS_XTcBT5CI3Px2vDbYP/https%3A%2F%2Fbioconductor.org%2Finstall

R version 4.5 is still not available under Ubuntu 24.10 (Oracular),
which I'm using. And installing the repository
deb https://secure-web.cisco.com/1-d102RqsYaia6t8BSGz-R630iu2tA4f48oePHfesoVRPr63o-xqN9PO8GtRe8Uso8o0hDeP0f18koBjL7fVocu-QwZNtLBlSFy_hhhAhkuZdlzC0U3xGaFQ2kRsankRlfFDD3jeuAZrR8kjG6cvACKrDGOS_exjpUcvR404OwxcpOd1itIeIhI_q70FCBh2KjELagq2koNWclCtkhXlpKzIfxKSzCsxFSyzx3gdVeD_ybymp8GqjwKDyQ5NBAtPOdQ0NzAHQYrdODN9ZmxeHkuSgRJJhWcHHoxD71XAOX313v-V_Nd2VTgpCKthFIg_8/https%3A%2F%2Fcloud.r-project.org%2Fbin%2Flinux%2Fubuntu oracular-cran40/
doesn't work either.

Should I wait for the official release of Ubuntu 25.04 on April 17 to
install the package?

Thanks a lot!

Franck

Le 7/4/25 à 17:44, Maria.Doyle a écrit :
> Dear Bioconductor Community,
> This is your final reminder that the abstract submission deadline for GBCC2025 is tomorrow, April 8th, 2025! Don't miss your chance to be part of the first-ever joint Galaxy and Bioconductor Community Conference.
> Key Details:
>
>    *   Abstract Submission Deadline: April 8, 2025
>
>    *   Conference Dates: June 23-26, 2025, at Cold Spring Harbor Laboratory, New York
> Whether you're presenting groundbreaking research or sharing innovative approaches in genomics, data science, or bioinformatics, this is an opportunity you won't want to miss. Join us for a week of learning, collaboration, and networking with leaders in the field.
> To submit your abstract, please visit the GBCC2025 website<https://secure-web.cisco.com/1_cMdenSd4jlh0fE36jSsy01c6cyNzAb5ELgit2I5SiEwOtwJwKzxcz1SbNeDtekwd1ALxquXZoWdemWtg-LL8hEuo218XyTPGmW2nnd2GdBUbgT6hSYzBIrEQzuj357__0WKpiP2xT04bR_vuA_GgTFbxo3pGFvwSAoMmHTjFECvp4GzoYPLW8Q-JII1dK9JgjC4mn57nWtauimXkcRcd1dpsb3fDE1wSm71g6FTm9V1k_XgnG-eN57hwvsQ6Ino9d4GnlTX_VCx00CGAV8PhlNOAQNUNTmzub20yU92UBCYdZG6yV-z8Oq7Sbz_SWgj/https%3A%2F%2Fgbcc2025.bioconductor.org%2F>.
> We look forward to your submission and hope to see you at GBCC2025!
> Best regards,
> The GBCC2025 Organizing Committee
>
>
> Maria Doyle, PhD
> Bioconductor Community Manager
>
> School of Medicine,
> University of Limerick, Limerick, V94 T9PX
> Ireland
> Email: maria.doyle using ul.ie<mailto:maria.doyle using ul.ie>
> Phone (office): +353 61 234 768
> Connect with the Bioconductor community at our conferences:
>
>    *   GBCC 2025 (June 23-26, New York, USA)<https://secure-web.cisco.com/19rlO5kXLnWb6WIEo6zXDLgt8o3VZOwbKoMSiNPdfDRKhGyS1c63nCiKb93D2DMp-gyQmUJwc0UfXwtI1vxaKDIi5F0aNSCx_N9ZmaBpiL0CiArhaPMKhZogMFunkZvRoFZuMsj0HCV4Ea8XjE7w4_Yzniq8TpdRLSfv8bbnIleVpxmbTleIbTIgmPpzHT4WpXWEG5jg77jrFAWghfKsUDx55ADVItXzfpid5wxpKgxZxtVXgeMMnJwjihUvFqhfTp66qwg8YeW2tpTau1Cnz4X5kZRqv5XrrMPkgL2ZLfm5Ijr6OUsfM7TSLTWDRp6D0/https%3A%2F%2Fgbcc2025.org%2F>
>    *   EuroBioC 2025 (September 17-19, Barcelona, Spain)<https://secure-web.cisco.com/1NeyjmjxjTpJ26OU6el9qMXkyl5D8RakvbzhSRhTJYtVYumRMYVSYLI6eVf3CflVDOeyIzs-3XwqbFhkjL6dr7L5LRN69nsa5sE13JcNv7PjQn3H29WJSGsa8EEjmC2t7lhxAo4Yxmhgli8BGBIxUcPTd_J0NWypm1W4pQCumXLgfa41eClamHgeHHiWPCBu8-AoKLL7kFu3PtEZExbYIQoTHJscCkh4a9YO6AAxyfIf8XH1TwqFqb3c6nf78R-RPI0JjnwSE_bJ8xciAqaD3uBb5YTOTASK-uWbjlqV8RLCaANJ1kyy0OdQ8FoxXbJtI/https%3A%2F%2Feurobioc2025.bioconductor.org%2F>
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