* guix-science/packages/bioinformatics.scm (igor): New variable.
* patches/igor-fix-missing-return.patch: Add patch for igor.

Python 3.12 removed distutils.  This commit moves all substitutions of
WORKSPACE into a patch file and patches out the CI dependency
buildkite, which relied on distutils.

* guix-science/packages/machine-learning.scm (python-ray/wheel)[arguments]:
Move substitutions for WORKSPACE into a patch file.
[source]: Reference that patch file here.
* patches/python-ray.patch: New file.

* patches/rstudio-server-install.patch: Update file.
* patches/rstudio-server-multi-version/0001-handleClientInit-Store-R-versions-in-sessionInfo.patch,
  patches/rstudio-server-multi-version/0002-launchAndTrackSession-Configure-R-version-from-activ.patch,
  patches/rstudio-server-multi-version/0003-NewProjectWizard-Unhide-version-selector-widget.patch,
  patches/rstudio-server-multi-version/0004-handleConnection-Switch-R-version-when-switching-pro.patch,
  patches/rstudio-server-multi-version/0005-Add-version-switcher-widget-to-toolbar.patch,
  patches/rstudio-server-multi-version/0006-Look-at-.local-share-rstudio-r-versions-for-custom-R.patch,
  patches/rstudio-server-multi-version/0007-detectRLocationsUsingR-Restore-R_HOME-at-the-end.patch:
  Update to latest version.
* guix-science/packages/rstudio.scm (dtl-for-rstudio,
utfcpp-for-rstudio): New variables.
(rstudio-server): Update to 2026.04.0+526.
[arguments]: Do not use #:OUT-OF-SOURCE?, add extra configure flags;
update generated cmake files; rename phase 'unpack-dictionary to
'unpack-extras and unpack GWT sources; update patching in
'patch-paths; update location of script in 'generate-server-options.
[native-inputs]: Replace openjdk11:jdk with openjdk:jdk; add
googletest and r-here; add origin for gwt sources.
[inputs]: Replace boost-1.88 with boost; add dtl-for-rstudio, libgit2,
and utfcpp-for-rstudio.

* patches/rstudio-server-panmirror.patch: Delete file.
* patches/rstudio-server-install.patch: Update to changes in 2025.05.1+513.
* guix-science/packages/rstudio-node.scm: Replace file with newly
generated contents.
* guix-science/packages/rstudio.scm
(js-panmirror): Update to 0.1.0.
(gsl-lite-for-rstudio, rapidjson-for-rstudio, hunspell-for-rstudio,
yaml-cpp-for-rstudio): New variables.
(rstudio-server): Update to 2025.05.1+513.
[source]: Remove rstudio-server-panmirror.patch.
[arguments]: Disable copilot support; add phase
'find-hunspell-and-rapidjson; update phase 'patch-paths to patch
search for system libraries; add phase 'patch-rapidjson.
[native-inputs]: Add libexpected and pkg-config.
[inputs]: Replace boost-1.83 with boost-1.88; replace yaml-cpp with
yaml-cpp-for-rstudio; add fmt-11, gsl-lite-for-rstudio,
hunspell-for-rstudio, rapidjson-for-rstudio, and websocketpp-next.

Fixes #566.

* guix-science/packages/jasp.scm: Remove file.
* patches/jasp-0.14.0.0-includes.patch: Remove file.
* patches/jasp-0.14.0.0-noupdate.patch: Remove file.

Newer versions require Electron.

* patches/rstudio-desktop-install.patch: New file.
* guix-science/packages/rstudio.scm (rstudio): Do not inherit from
rstudio-server; use sources at version 2023.12.1.

* guix-science/packages/rstudio.scm (rstudio-server): Update to
2024.12.1+563.
[arguments]: Adjust patches.
* patches/rstudio-server-install.patch: New file.
* patches/rstudio-server-panmirror.patch: New file.
* patches/rstudio-server-multi-version/0001-handleClientInit-Store-R-versions-in-sessionInfo.patch,
patches/rstudio-server-multi-version/0002-launchAndTrackSession-Configure-R-version-from-activ.patch,
patches/rstudio-server-multi-version/0003-NewProjectWizard-Unhide-version-selector-widget.patch,
patches/rstudio-server-multi-version/0004-handleConnection-Switch-R-version-when-switching-pro.patch,
patches/rstudio-server-multi-version/0005-Add-version-switcher-widget-to-toolbar.patch,
patches/rstudio-server-multi-version/0006-Look-at-.local-share-rstudio-r-versions-for-custom-R.patch,
patches/rstudio-server-multi-version/0007-detectRLocationsUsingR-Restore-R_HOME-at-the-end.patch:
Port to latest version.

* guix-science/packages/algebra.scm (composyx)
  [source]: Update to 1.5.0.
* patches/composyx-chameleon-1.4.patch: Remove.

Signed-off-by: Ghislain Vaillant <ghislain.vaillant@inria.fr>

Chameleon upgrade caused an API breakage in Composyx.

* guix-science/packages/algebra.scm (composyx): Fix API breakage from
Chameleon.
* patches/composyx-chameleon-1.4.patch: New file.

* patches/rstudio-server-install.patch: New file.
* guix-science/packages/rstudio.scm (rstudio-server)
[source]: Fetch from upstream repository; add patch.
[arguments]: Drop unnecessary configure flag; set
RSTUDIO_NODE_VERSION; add phase 'create-os-release; update phase
'patch-paths to address node locations; use THIS-PACKAGE-INPUT where
possible.
[native-inputs]: Drop labels.
[inputs]: Drop labels; add node.