Re: [R-pkg-devel] re-exporting plot method?

Kevin, welcome to the S4 world! ;) There is really no good solution since S4 only works at all if you attach the package since it relies on replacing the base S3 generic with its own - so the question remains what are your options to do it. The most obvious is to simply add Depends: Rgraphviz

[R-pkg-devel] re-exporting plot method?

Hi, I am working on a new package that primarily makes use of "igraph" representations of certain mathematical graphs, in order to apply lots of the comp sci algorithms already implemented in that package. For display purposes, my "igraph" objects already include information that defines

[Bioc-devel] Bioconductor Mirrors - Important Updates During Release Time

For anyone that is maintaining a Bioconductor mirror/rsync please make any necessary updates within the next two weeks regarding location / legacy Bioconductor releases. Starting last year, Bioconductor has moved archived versions of Bioconductor off the AWS cloudfront instance. Syncing to

[Bioc-devel] RELEASE_3_19 branch is now available and push access is re-enabled

Dear Maintainers, You are now able to push your commits to the Bioconductor git server. The RELEASE_3_19 branch is now available on Bioconductor. Please sync your GitHub repositories with the latest updates to your package on Bioconductor for a RELEASE_3_19 branch as well as the devel branch.

Re: [Rd] [External] Re: Patches for CVE-2024-27322

That should do it Sent from my iPad On Apr 30, 2024, at 9:57 AM, Iñaki Ucar wrote:  Many thanks both. I'll wait for Luke's confirmation to trigger the update with the backported fix. Iñaki On Tue, 30 Apr 2024 at 12:42, Dirk Eddelbuettel mailto:e...@debian.org>> wrote: On 30 April 2024 at

Re: [Bioc-devel] Adding git write access for newly accepted package when a key already exists

There was a configuration issue on our end. This should now be corrected. Please also see this announcement from this morning. https://stat.ethz.ch/pipermail/bioc-devel/2024-April/020416.html Commits are blocked for the release. We will announce when commits will resume (normally in a few

[Bioc-devel] Adding git write access for newly accepted package when a key already exists

Hi, my new rBLAST package was accepted and added to Bioc devel (https://bioconductor.org/packages/rBLAST). I got a message stating: "To use the git.bioconductor.org repository, we need an 'ssh' key to associate with your github user name. If your GitHub account already has ssh public keys

Re: [Rd] Patches for CVE-2024-27322

Many thanks both. I'll wait for Luke's confirmation to trigger the update with the backported fix. Iñaki On Tue, 30 Apr 2024 at 12:42, Dirk Eddelbuettel wrote: > > On 30 April 2024 at 11:59, peter dalgaard wrote: > | svn diff -c 86235 ~/r-devel/R > > Which is also available as > >

Re: [Bioc-devel] problem with git push to bioconductor ‘DENIED by fallthru’

Thanks, bad timing. I missed this time. Sorry for the noise. Lorena Pantano, PhD https://lpantano.github.io On April 30, 2024 at 10:43:48 AM, Kern, Lori (lori.sheph...@roswellpark.org) wrote: Please see this announcement from this morning.

Re: [Bioc-devel] problem with git push to bioconductor ‘DENIED by fallthru’

Please see this announcement from this morning. https://stat.ethz.ch/pipermail/bioc-devel/2024-April/020416.html Commits are blocked for the release. We will announce when commits will resume (normally in a few hours) Cheers, Lori Shepherd - Kern Bioconductor Core Team Roswell Park

[Bioc-devel] problem with git push to bioconductor ‘DENIED by fallthru’

Hi all, It is the first time I have issues, but I don’t know what else to check. I am the maintainer of isomiRs. I have modified this package before from the same computer I am having issues. I have a new key from last year but I have no problems pushing to GitHub and I checked Bioconductor is

[Bioc-devel] BioC2024 deadlines approaching

Hi everyone, Just a heads up that some deadlines for BioC2024 are approaching! Take note: * In-person Scholarships: Apply by May 15: Scholarship Application * BioC Award Nominations: Nominate by May 15: More details and

Re: [Bioc-devel] Error on macOS (merida1)

How can that be changed? How far as I understood the package will not be reviewed again when there is an error in the build report. Thanks in advance, Carlotta Meyring Carlotta Meyring Methods of Modelling and Bioinformatics in Systems Biomedicine (MSB) Institute of Medical Biometry and

Re: [Bioc-devel] Error on macOS (merida1)

The reviewers should be aware already but I can leave a message on the issue. Lori Shepherd - Kern Bioconductor Core Team Roswell Park Comprehensive Cancer Center Department of Biostatistics & Bioinformatics Elm & Carlton Streets Buffalo, New York 14263

[Bioc-devel] All commits to Bioconductor stopped from 8:00 am ET for release

Dear Maintainers, Please keep in mind that we are on schedule for our release as given in https://bioconductor.org/developers/release-schedule/ Today (April 30 th 2024) at 8:00 am ET, We will freeze the commits to all the branches and all packages in Bioconductor. We will notify here once we

Re: [Rd] Patches for CVE-2024-27322

On 30 April 2024 at 11:59, peter dalgaard wrote: | svn diff -c 86235 ~/r-devel/R Which is also available as https://github.com/r-devel/r-svn/commit/f7c46500f455eb4edfc3656c3fa20af61b16abb7 Dirk | (or 86238 for the port to the release branch) should be easily backported. | | (CC Luke in

Re: [Rd] Patches for CVE-2024-27322

svn diff -c 86235 ~/r-devel/R (or 86238 for the port to the release branch) should be easily backported. (CC Luke in case there is more to it) - pd > On 30 Apr 2024, at 11:28 , Iñaki Ucar wrote: > > Dear R-core, > > I just received notification of CVE-2024-27322 [1] in RedHat's Bugzilla. We

[Rd] Patches for CVE-2024-27322

Dear R-core, I just received notification of CVE-2024-27322 [1] in RedHat's Bugzilla. We updated R to v4.4.0 in Fedora rawhide, F40, EPEL9 and EPEL8, so no problem there. However, F38 and F39 will stay at v4.3.3, and I was wondering if there's a specific patch available, or if you could point me