Re: [Rd] FYI: daily R source tarballs from ETH: *.xz instead of *.bz2)
On 9/11/23 22:39, Prof Brian Ripley wrote: > On 09/09/2023 01:56, Hervé Pagès wrote: >> Hi Martin, >> >> Sounds good. Are there any plans to support the xz compression for >> package source tarballs? > > What makes you think it is not supported? I guess because I've never seen source tarballs distributed as .xz files but it's good to know that 'R CMD build' and 'R CMD INSTALL' support that. So let me reformulate my question: do CRAN have any plans to switch from .tar.gz to .xz for the distribution of source tarballs? Is this something that tools like write_PACKAGES(), available.packages(), and install.packages() would be able to handle? Would they be able to handle a mix of .tar.gz and .xz packages? (Which would be important for a smooth transition from .tar.gz to .xz across CRAN/Bioconductor.) I'm just trying to get a sense if the effort to reduce bandwidth will go beyond the distribution of R source snapshots. Thanks, H. -- Hervé Pagès Bioconductor Core Team hpages.on.git...@gmail.com [[alternative HTML version deleted]] __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
[R-pkg-devel] published packages not showing updated macOS results
Hi. It looks like macOS package publishing may have stalled. One of my packages, rsconnect 1.1.0, arrived on CRAN about a week ago. It is built almost everywhere, but r-release-macos* and r-release-macos-arm64 are still showing results from the previous release. Recent releases did see check failures on the r-release-macos-x86_64 host (because its Pandoc installation was older than supported by one of our dependencies). The rsconnect 1.1.0 release should address these failures, but I am still waiting to see builds flow through. https://cran.r-project.org/web/packages/rsconnect/index.html https://cran.r-project.org/web/checks/check_results_rsconnect.html Is someone able to look into this or otherwise offer advice? Thanks, Aron -- email: aron.atk...@gmail.com home: http://gweep.net/~aron/ [[alternative HTML version deleted]] __ R-package-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-package-devel
Re: [Bioc-devel] Omada package failing due to removed dependency
It would be great if you were able to also update the current release RELEASE_3_17 branch so that the current users can use the package and so that a broken version of the package is not saved for the Bioc 3.17 version of packages. But the package will be ok for the new release as long as it is fixed in devel and will progate the fixed package at the end of October to the new release. Lori Shepherd - Kern Bioconductor Core Team Roswell Park Comprehensive Cancer Center On Mon, Sep 11, 2023 at 10:05 PM Sokratis Kariotis < sokratiskario...@gmail.com> wrote: > Hey, > > Will the package be ok for the new release even though I still get the same > error? > > Cheers, > Sokratis > > On Thu, Aug 17, 2023 at 3:38 PM Mike Smith wrote: > > > Hi Sokratis, > > > > You've address the problems successfully in the devel branch (3.18) but > > they remain in the release (3.17), so you're probably still getting the > > messages relating to these builds ( > > https://bioconductor.org/checkResults/3.17/bioc-LATEST/omada/). > > > > To fix this you'll need to checkout the RELEASE_3_17 branch, and then > make > > the same changes you've already applied. You can either do that via git > > cherry-pick and select the appropriate commits from devel branch, or > > perhaps more straightforward is to just copy/paste the relevant sections. > > Then bump the RELEASE_3_17 version number to 1.2.1 and push that branch. > > Hopefully this will fix the issues there too. > > > > Best, > > Mike > > > > On Thu, 17 Aug 2023 at 03:47, Sokratis Kariotis < > > sokratiskario...@gmail.com> wrote: > > > >> Hey all, > >> > >> I can see all is green but I still get messages about failing builds and > >> on > >> the website shows build error. Do I still have to do something? Thanks > in > >> advance. > >> > >> Regards, > >> Sokratis > >> > >> On Thu, Aug 10, 2023 at 2:53 PM Martin Grigorov < > >> martin.grigo...@gmail.com> > >> wrote: > >> > >> > Hi, > >> > > >> > All is green at > >> > https://bioconductor.org/checkResults/3.18/bioc-LATEST/omada/ > >> > > >> > Regards, > >> > Martin > >> > > >> > On Thu, Aug 10, 2023 at 9:44 AM Sokratis Kariotis < > >> > sokratiskario...@gmail.com> wrote: > >> > > >> >> Hey all, > >> >> > >> >> Is this fixed now? I think I can see all pass, but on the actual > >> website > >> >> its still on error. Thanks! > >> >> > >> >> Cheers, > >> >> Sokratis > >> >> > >> >> On Tue, Aug 1, 2023 at 4:25 PM Sokratis Kariotis < > >> >> sokratiskario...@gmail.com> wrote: > >> >> > >> >>> Hey, > >> >>> > >> >>> I believe I have resolved the conflicts and now can run: *git push > >> >>> upstream main:devel* > >> >>> with Everything up-to-date as a result. However, *git push origin > >> main* > >> >>> does not yield > >> >>> anything and it keeps hanging without a message. I checked > >> https://bioconductor.org/checkResults/3.18/bioc-LATEST/omada/ > >> >>> and the last commit is April. > >> >>> > >> >>> > >> >>> On Mon, Jul 31, 2023 at 10:01 PM Kern, Lori < > >> >>> lori.sheph...@roswellpark.org> wrote: > >> >>> > >> You'll need to find the merge conflicts and resolve them. Recommit > >> those files and then it should go. > >> > >> 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 on behalf of > >> Sokratis Kariotis > >> *Sent:* Monday, July 31, 2023 7:27 AM > >> *To:* Martin Grigorov > >> *Cc:* bioc-devel@r-project.org > >> *Subject:* Re: [Bioc-devel] Omada package failing due to removed > >> dependency > >> > >> Tried but its Already up to date. > >> > >> On Mon, 31 Jul 2023, 7:22 pm Martin Grigorov, < > >> martin.grigo...@gmail.com> > >> wrote: > >> > >> > Hi Sokratis, > >> > > >> > You need to do "git pull --rebase" before trying to push. > >> > Most probably the version has been bumped upstream. > >> > > >> > Regards, > >> > Martin > >> > > >> > On Mon, Jul 31, 2023 at 2:16 PM Sokratis Kariotis < > >> > sokratiskario...@gmail.com> wrote: > >> > > >> >> Hey all, > >> >> > >> >> I created a new key and now I can commit etc but there is a > >> conflict > >> that > >> >> is not allowing me to go ahead. > >> >> > >> >> My commands: > >> >> git add . > >> >> git commit -m "Update metrics" > >> >> git push upstream main:devel > >> >> > >> >> *The above results in the following error:* > >> >> > >> >> > >> >> > >> >> > >> >> > >> >> > >> >> > >> >> > >> >> > >> >> > >> >> > >> >> > >> >> > >> >> *Enumerating objects: 19, done.Counting objects: 100% (17/17), > >>
[Bioc-devel] Single Package Builder Maintenance
We will be performing maintenance on the single package builder for new submissions today. There may be short intervals where the on-demand/build on version bump capabilities will not be accessible. We appreciate your understanding. Cheers, Lori Shepherd - Kern Bioconductor Core Team Roswell Park Comprehensive Cancer Center Department of Biostatistics & Bioinformatics Elm & Carlton Streets Buffalo, New York 14263 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. [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
Re: [R-pkg-devel] How to fix Archived Package Rpdb?
On 09.09.2023 20:15, Leonard Mada via R-package-devel wrote:
Thank you very much for this help.
1.) I am a little bit unsure about the LICENSE file - see below (in-text).
2.) There is a new error in the meantime:
- the check works on Windows, but fails everywhere else with:
Warning: Found the following significant warnings:
Warning: 'rgl.init' failed, running with 'rgl.useNULL = TRUE'.
On non Windows systems, You cannot use rgl if you do not have any X11
available.
Support for Unix alikes is optional, so in packages X11() should be used
conditionally after checking capabilities("X11").
Googling the web was not very informative either: it mentions something
about quartz device - but I am uncertain what to do.
>
On 9/8/2023 6:59 PM, Hadley Wickham wrote:
On Fri, Sep 8, 2023 at 6:02 AM Leonard Mada via R-package-devel
wrote:
Dear Members,
I would like to reanimate the archived package Rpdb:
https://cran.r-project.org/web/packages/Rpdb/index.html
[...]
2.b.) Description file
- I left the original author as the author (with the provided e-mail
address): should I delete this email?
It probably doesn't matter than much either way, but since the author
doesn't appear to respond to emails to that address, I personally
would lean towards deleting it.
Do *not* delete any authours/copyright holders.
- I have added myself as maintainer; [...]
- updated the licence to GPL v3: the original does not specify any
version number;
Is there anything else that needs to be done?
There are at least three 3 R CMD check failures you need to address:
* [...]
* You need to add LICENSE to .Rbuildignore, or and IMO better, delete
that file and use usethis::use_gpl3_license() to the license in
markdown form, and correctly ignored for CRAN submission
If I understand correctly:
- delete the "LICENSE" file and use usethis::use_gpl3_license(), which
adds the "LICENSE.md" file;
- should I also add some code to the DESCRIPTION file?
LICENSE: GPL-3
in the DESCRIPTION should be fine, and no license file unless you want
to add additional restrictions that are permitted by GPL-3 such as
attribution requirements.
No idea what usethis::use_gpl3_license() does.
Best,
Uwe Ligges
* Many examples use `\%in\%` instead of `%in%.
Hopefully, this is fixed now. But it was quit a hassle to find out which
files were affected. [I could have used gawk, but the error-reporting
could be improved as well!]
Sincerely,
Leonard
To make these sorts of problems easier to spot in the future I'd
suggest setting up a GitHub action to automatically run R CMD check
every time you push to GitHub. One easy way to do that is to run
usethis::use_github_action("check-standard").
Hadley
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