WIP: Binary distributions via GitHub Releases. by zivy · Pull Request #98 · SimpleITK/SimpleITKRInstaller

zivy · 2026-05-19T16:40:45Z

When a tag that matches the SITK_TARGET is pushed
to the repository, binary R packages for all tested platforms and that specific tag are created and uploaded to a draft release on GitHub.

Binary packages built and uploaded by CircleCI
use the GitHub CLI tool and requiere a GitHub
personal access token (PAT) with full repo control. In CircleCI project settings, under
Environment Variables add a variable:
GITHUB_TOKEN = PAT_value.

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blowekamp · 2026-05-20T20:21:01Z

+    name: Create GitHub Draft Release
+    # Only run this job for tag pushes after the R-build job completes
+    # successfully (also means the pushed tag matches SITK_TARGET since
+    # R-build validates that at the beginning).


Keep it simple. Just run when there is a tag starting with be. The whole comparison is really not needed.

The tag matching is now only performed for the draft release creation job. That step should only happen when the intention is to create a release and then the pushed tag should match the one in the DESCRIPTION file so that the installer and the SimpleITK versions are kept in sync.

Artur-man · 2026-05-22T18:51:15Z

Hey guys,

It is amazing that you guys are officially releasing binaries. I think I saw that the Python binary releases of new SimpleITK versions now will come with Elastix installed too.

Can we also do the same with R binaries here? Would be a nice addition since most of R wrappers of registration software out there cannot handle large images.

Best,
Artür

zivy · 2026-05-22T21:00:09Z

Hi @Artur-man,

This is still experimental, but we are thinking of turning SimpleElastix on by default, so that will apply to all languages. Note that the two developments, SimpleElastix and R binary distribution, are independent of each other.

Currently it looks like the workflow for R binary distribution is working. Would appreciate it if you could try some of the artifacts on your side. The PR testing is still running but some of the artifacts have already been uploaded here. Let us know if you test some of them and if you encounter problems.

Note that the macos-ARM are not there as those are built on CircleCI and we're a bit cautious in terms of security and setting it up to allow CircleCI to automatically upload artifacts to the GitHub release. With SimpleITK 3.0 we hope that the required build resources on GitHub will be sufficient and we'll add the ARM builds here. Otherwise, we'll need to think of another solution.

Artur-man · 2026-05-26T06:36:59Z

Thanks so much @zivy, will do. Is there anything in particular do you want me to try ? I can scan ...

zivy · 2026-05-27T00:50:08Z

Hi @Artur-man,

Would appreciate it if you tested the windows packages.

Also, just an FYI, the effort to provide binary packages just exposed an issue with the configure script. The generated binary for linux is overly large. The CMake code in the configure script was missing some settings that greatly reduce the binary size.

You've set us on a path of improvement.

Artur-man · 2026-05-27T07:30:22Z

You've set us on a path of improvement.

Always a pleasure XD ok I will bring out the windows machine tonight.

Artur-man · 2026-05-30T21:16:26Z

Trying to find the binaries ... shall make my own or can I get it somewhere, probably from your other repo @zivy ?

Artur-man · 2026-05-30T21:18:39Z

ah ok ok found it, some reason could not scroll down in the action page earlier.

Artur-man · 2026-05-30T21:56:54Z

For now I am getting this error, I have tried dplyr binary to compare and it works ... but below does not:

> install.packages("SimpleITK_2.5.5_R4.6_windows-x86_64.zip", repos = NULL, type = "binary")
Installing package into ‘C:/Users/asus/AppData/Local/R/win-library/4.6’
(as ‘lib’ is unspecified)
Error in read.dcf(file.path(pkgname, "DESCRIPTION"), c("Package", "Type")) : 
  bağlantı açılamadı
Ek olarak: Uyarı mesajları:
In read.dcf(file.path(pkgname, "DESCRIPTION"), c("Package", "Type")) :
  sıkıştırılmış dosya SimpleITK_2.5.5_R4.6_windows-x86/DESCRIPTION' açılamadı, muhtemel sebep: No such file or directory

I will try more tomorrow, sorry about the turkish messages it basically says the file is not found. This dplyr for comparison

> install.packages("dplyr_1.2.1.zip")
Installing package into ‘C:/Users/asus/AppData/Local/R/win-library/4.6’
(as ‘lib’ is unspecified)
inferring 'repos = NULL' from 'pkgs'
package ‘dplyr’ successfully unpacked and MD5 sums checked

zivy · 2026-06-04T16:59:55Z

Hi @Artur-man,

Thanks for testing. Took me a while to figure out the issues.

When downloading an artifact it is zipped before download, so an artifact named a.zip will be downloaded to a.zip and not a.zip.zip. Consequentially, when you try to install a.zip it will fail because the contents inside are another zip file. Also, the install.packages expects the file name to have a specific format <package_name>_<version>.zip.

Bottom line, after you unzip and rename the downloaded file you should be able to do:

install.packages("SimpleITK_2.5.5.zip", repos = NULL, type = "binary")

Latest artifacts are here.

For all triggering events, the workflow builds SimpleITK using the installer, creates binary packages from the results and uploads the artifacts to GitHub. When the triggering event is a tag push that matches the SITK_TARGET (DESCRIPTION file) a draft release is created and the packages are uploaded to it.

Refer to actions using the hash and not the tag that can be moved. Also limit permissions to read-only.

Stripped debug symbols from the binaries to reduce package size. Hides symbols by default in shared libraries and hide inline C++ functions to reduce binary size and prevent symbol conflicts with other packages.

Use a gh-pages branch for GitHub pages hosting of a CRAN-like repository. When a release is created, there is a workflow that automatically updates the CRAN-like repository using the information from the release assets. Note that the CRAN-like repository does not include the binary packages themselves, it forwards to the URLs of the release assets on GitHub.

zivy · 2026-06-16T13:03:20Z

Hello @Artur-man, @blowekamp, @richardbeare

I believe this PR is finally working and will enable us to build and distribute binary packages via GitHub using the standard R install.packages method, though requiring the foyer package two step approach (the R community's solution for large packages that cannot go on CRAN - at least I couldn't find another recommended solution).

As I did not want to corrupt the official repository with my trials and I couldn't test this without merging, I have a development repository under my personal account in which I (1) merged the PR (2) tagged a "release" and pushed the tag to the repo which automatically builds the binaries and creates a draft release (3) changed from draft release to an official release which automatically updates the foyer package and the gh-pages branch of the repository (the usage of a gh-pages branch is so that the updates are automatic, the bot can directly push to the branch which we block on the main branch where we require PRs and review).

All this functionality can be found on https://github.com/zivy/sitk_r_installer_dev . Please go to the release page and check that the instructions are clear. Try it out and tell me if you encountered problems.

Hopefully this is in a good enough spot that we can merge this long running branch. After merging I will work on adding the missing macos-arm releases and writing a short document describing the release process.

blowekamp · 2026-06-16T13:14:53Z

Is there a blocker for Mac ARM binaries?

zivy · 2026-06-16T13:19:51Z

No real blocker I'm aware of. I got things running and tested on the platforms I have access to (linux, macos-intel and windows) so just wanted to finish this PR and then find out if macos-arm is a trivial addition or I encounter a problem.

Previous CRAN-like structure was not working with standard R install tools. The File specification in the PACKAGES file is appended to the CRAN-like's URL which works if the actual package is on the website but specifying a URL as the File value results in an invalid URL structure (https://cran_likehttps://file_location). Moving to a foyer package approach supports download from arbitrary location. The user installs the SimpleITK foyer package using standard R tools (mimicing a SimpleITK install). Then calls the library(SimpleITK); install_simpleitk() which downloads and installs SimpleITK itself, overwritting the foyer package. Next call to library(SimpleITK) loads the actual SimpleITK package.

Artur-man · 2026-06-17T18:53:56Z

Thanks @zivy, I will try to try installing this again tomorrow morning, and apologies for the silence on my side ... multiple projects and grants (I have a few that I am leading), are ruining my life :D ....

one question though, cant we put the foyer package to r-universe ?

You can even make your r-universe setup to target a subfolder of a repo ... which is the foyer subfolder under simpleitk_installer ... let me show you an example.

Here in our r-universe page ... we target the r subfolder of bpcells ... which builds the R package directly from that subfolder, without checking the entire repo.
https://github.com/BIMSBbioinfo/bimsbbioinfo.r-universe.dev/blob/ad8deb32aca1459c4b28125f4420119d54a9806b/packages.json#L22-L26

I can explain more if needed.

zivy requested a review from blowekamp May 19, 2026 16:41

blowekamp requested a review from Copilot May 20, 2026 20:16

Copilot AI reviewed May 20, 2026

blowekamp requested changes May 20, 2026

View reviewed changes

zivy force-pushed the releaseAndBinaryPackages branch 6 times, most recently from 95a05ca to cc5585f Compare May 22, 2026 17:55

zivy force-pushed the releaseAndBinaryPackages branch from cc5585f to 62362b2 Compare May 26, 2026 13:53

zivy force-pushed the releaseAndBinaryPackages branch 2 times, most recently from 2f479a8 to 5ece5d7 Compare May 30, 2026 13:55

zivy force-pushed the releaseAndBinaryPackages branch 8 times, most recently from 679f14f to cb9b2da Compare June 4, 2026 16:52

zivy force-pushed the releaseAndBinaryPackages branch from cb9b2da to f055bf1 Compare June 9, 2026 17:26

zivy added 5 commits June 12, 2026 13:41

Security improvements to workflow.

ac19b80

Refer to actions using the hash and not the tag that can be moved. Also limit permissions to read-only.

Improve binary packaging.

1c370c3

Stripped debug symbols from the binaries to reduce package size. Hides symbols by default in shared libraries and hide inline C++ functions to reduce binary size and prevent symbol conflicts with other packages.

Use formal language in the DESCRIPTION file.

415f992

zivy force-pushed the releaseAndBinaryPackages branch 2 times, most recently from 3ccb4f5 to b9ba0af Compare June 15, 2026 17:51

zivy force-pushed the releaseAndBinaryPackages branch from b9ba0af to 01ed642 Compare June 16, 2026 14:52

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