Dear Bioconductor Team, A package that SurfR depended on was recently removed from CRAN. I noticed that the authors have been active on its GitHub repo lately, so I am hopeful that it will become available again soon. In the meantime, I have addressed the issue by rewriting the affected SurfR-related functions and removing that package from SurfR's dependencies. Currently, I recommend users who encounter installation issues due to this dependency to install the development version of SurfR directly from my GitHub repository. Would it be possible for you to sync the released version of SurfR on Bioconductor to reflect these changes? This would ensure that users can continue to install and use SurfR without encountering dependency issues. Thank you for your time and assistance. Please let me know if there are any additional steps I need to take to facilitate this process. Best wishes, Aurora
[Bioc-devel] Fix dependency issues in devel and release
3 messages · Aurora Maurizio, Shepherd, Lori, Marcel Ramos
You should update the package yourself by pushing to the RELEASE_3_20 and devel branches on git.bioconductor.org 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 at r-project.org> on behalf of Aurora Maurizio <auroramaurizio1 at gmail.com>
Sent: Monday, December 30, 2024 4:14 AM
To: bioc-devel at r-project.org <bioc-devel at r-project.org>
Subject: [Bioc-devel] Fix dependency issues in devel and release
Sent: Monday, December 30, 2024 4:14 AM
To: bioc-devel at r-project.org <bioc-devel at r-project.org>
Subject: [Bioc-devel] Fix dependency issues in devel and release
Dear Bioconductor Team,
A package that SurfR depended on was recently removed from CRAN. I noticed
that the authors have been active on its GitHub repo lately, so I am
hopeful that it will become available again soon.
In the meantime, I have addressed the issue by rewriting the affected
SurfR-related functions and removing that package from SurfR's
dependencies. Currently, I recommend users who encounter installation
issues due to this dependency to install the development version of SurfR
directly from my GitHub repository.
Would it be possible for you to sync the released version of SurfR on
Bioconductor to reflect these changes? This would ensure that users can
continue to install and use SurfR without encountering dependency issues.
Thank you for your time and assistance. Please let me know if there are any
additional steps I need to take to facilitate this process.
Best wishes,
Aurora
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Hi Aurora, It looks like you were able to sync your package updates to Bioconductor. I think the question is more about when will those changes be reflected in the landing page. Please note that Bioconductor 3.20 builds every Monday and Thursday [1]. Your fixes should be reflected on today's report (~3 PM EST). Best regards, Marcel PS. You can checked for sync'ed changes at https://code.bioconductor.org/browse/SurfR/. [1]: https://bioconductor.org/checkResults/
On 12/30/24 10:03 AM, Kern, Lori via Bioc-devel wrote:
* This email originates from a sender outside of CUNY. Verify the sender before replying or clicking on links and attachments. * You should update the package yourself by pushing to the RELEASE_3_20 and devel branches on git.bioconductor.org 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 at r-project.org> on behalf of Aurora Maurizio<auroramaurizio1 at gmail.com>
Sent: Monday, December 30, 2024 4:14 AM
To:bioc-devel at r-project.org <bioc-devel at r-project.org>
Subject: [Bioc-devel] Fix dependency issues in devel and release
Dear Bioconductor Team,
A package that SurfR depended on was recently removed from CRAN. I noticed
that the authors have been active on its GitHub repo lately, so I am
hopeful that it will become available again soon.
In the meantime, I have addressed the issue by rewriting the affected
SurfR-related functions and removing that package from SurfR's
dependencies. Currently, I recommend users who encounter installation
issues due to this dependency to install the development version of SurfR
directly from my GitHub repository.
Would it be possible for you to sync the released version of SurfR on
Bioconductor to reflect these changes? This would ensure that users can
continue to install and use SurfR without encountering dependency issues.
Thank you for your time and assistance. Please let me know if there are any
additional steps I need to take to facilitate this process.
Best wishes,
Aurora
[[alternative HTML version deleted]]
_______________________________________________
Bioc-devel at r-project.org mailing list
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____ *Marcel Ramos, MPH* Sr. Data Scientist CUNY Graduate School of Public Health & Health Policy 55 W. 125th Street, 6th Fl.| New York, NY 10027 marcel.ramos at sph.cuny.edu <mailto:marcel.ramos at sph.cuny.edu> | (646) 364-9585 sph.cuny.edu <https://sph.cuny.edu>