etc: teams: kernel: Rename team to `linux-libre'.

Since linux-libre is not the only kernel around in GNU Guix anymore. * etc/teams.scm (kernel): Rename variable to linux-libre. Change-Id: Ic8081f471ad7f6aa21e2830f294549460466249b Signed-off-by: Gabriel Wicki <gabriel@erlikon.ch>
gnu: Add ueberzugpp.
2026-07-07 21:14:07 +02:00 · 2026-05-28 15:34:48 +02:00 · 2026-05-28 18:38:31 +05:30 · 2026-05-28 12:14:00 +02:00 · 2026-05-28 12:14:00 +02:00 · 2026-05-28 12:14:00 +02:00
36 changed files with 4356 additions and 4494 deletions
@@ -876,8 +876,8 @@ and the maven-build-system."
        "The plasma desktop environment, and KDE Applications."
        #:scope (list (make-regexp* "^gnu/packages/(kde)(-.+|)\\.scm$"))))

-(define-team kernel
-  (team 'kernel
+(define-team linux-libre
+  (team 'linux-libre
        #:name "Linux-libre kernel team"
        #:scope (list "gnu/build/linux-modules.scm"
                      (make-regexp* "^gnu/packages/aux-files/linux-libre.*$")
@@ -1298,7 +1298,7 @@ the \"texlive\" importer."
 (define-member (person "Leo Famulari"
                       "leo@famulari.name"
                       "lfam")
-  kernel)
+  linux-libre)

 (define-member (person "Efraim Flashner"
                       "efraim@flashner.co.il"
@@ -1383,7 +1383,7 @@ the \"texlive\" importer."
 (define-member (person "Vagrant Cascadian"
                       "vagrant@debian.org"
                       "vagrantc")
-  debian embedded kernel)
+  debian embedded linux-libre)

 (define-member (person "Vagrant Cascadian"        ;XXX: duplicate
                       "vagrant@reproducible-builds.org"
@@ -1537,7 +1537,7 @@ the \"texlive\" importer."
 (define-member (person "Rodion Goritskov"
                       "rodion@goritskov.com"
                       "rodion-goritskov")
-  games java kde kernel release)
+  games java kde linux-libre release)

 (define-member (person "Jason Conroy"
                       "jconroy@tscripta.net"
@@ -1622,7 +1622,7 @@ the \"texlive\" importer."
 (define-member (person "Wilko Meyer"
                       "w@wmeyer.eu"
                       "theesm")
-  kernel perl)
+  linux-libre perl)

 (define-member (person "Untrusem"
                       "mysticmoksh@riseup.net"
@@ -2368,16 +2368,8 @@ dist_patch_DATA =						\
  %D%/packages/patches/renpy-fix-integer-slots.patch			\
  %D%/packages/patches/reposurgeon-add-missing-docbook-files.patch	\
  %D%/packages/patches/rdkit-unbundle-external-dependencies.patch	\
-  %D%/packages/patches/r-biostrings-r4.6.0-compat.patch		\
-  %D%/packages/patches/r-h5mread-0001-h5mread-1.3.2-Get-rid-of-non-API-calls-to-R.patch \
  %D%/packages/patches/r-httpuv-1.6.6-unvendor-libuv.patch	\
-  %D%/packages/patches/r-mscoreutils-0001-fix-non-API-call-to-R-SETLENGTH-by-using-lengthgets.patch \
-  %D%/packages/patches/r-rsamtools-r-4.6.0-compat.patch		\
-  %D%/packages/patches/r-snpstats-0001-fixed-non-API-except-for-IS_S4_OBJECT.patch \
-  %D%/packages/patches/r-snpstats-0002-fixed-IS_S4_OBJECT.patch \
  %D%/packages/patches/r-sapa-lapack.patch			\
-  %D%/packages/patches/r-shortread-0001-ShortRead-1.69.3-Get-rid-of-non-API-calls-to-R.patch \
-  %D%/packages/patches/r-sparsearray-r-4.6.0-compat.patch	\
  %D%/packages/patches/ripperx-missing-file.patch		\
  %D%/packages/patches/rpcbind-CVE-2017-8779.patch		\
  %D%/packages/patches/rtosc-0.3.1-fix-invalid-comparison-operator.patch	\
@@ -2462,6 +2454,7 @@ dist_patch_DATA =						\
  %D%/packages/patches/shared-mime-info-xdgmime-path.patch	\
  %D%/packages/patches/sharutils-CVE-2018-1000097.patch		\
  %D%/packages/patches/showtime-python-3.11-compat.patch        \
+  %D%/packages/patches/simpleitk-r-4.6.0.patch			\
  %D%/packages/patches/sipwitch-fix-build-with-exosip5.patch	\
  %D%/packages/patches/slim-config.patch			\
  %D%/packages/patches/slim-gcc-14.patch			\
@@ -2496,6 +2489,7 @@ dist_patch_DATA =						\
  %D%/packages/patches/swift-corelibs-libdispatch-5.7.3-modulemap.patch	\
  %D%/packages/patches/swift-llvm-5.7.3-linux.patch	\
  %D%/packages/patches/swig-support-gcc-12.patch		\
+  %D%/packages/patches/swig-support-r-4.6.0.patch		\
  %D%/packages/patches/swish-e-search.patch			\
  %D%/packages/patches/swish-e-format-security.patch		\
  %D%/packages/patches/t1lib-CVE-2010-2642.patch		\
@@ -2135,7 +2135,17 @@ envelope follower, distortion effects, tape effects and more.")
 	        (base32
                 "01hnx4hhbz3ap3bw15s42q4q1mw1mhdjwygq4550wvjfg6k4ga8w"))))
      (build-system waf-build-system)
-      (arguments (list #:tests? #false)) ;There are no tests.
+      (arguments
+       (list
+        #:tests? #false ;There are no tests.
+        #:phases
+        '(modify-phases %standard-phases
+           (add-after 'unpack 'python3.12-compatibility
+             (lambda _
+               (substitute* "waflib/Context.py"
+                 (("imp.new_module") "types.ModuleType")
+                 (("import os, re, imp, sys")
+                  "import os, re, types, sys")))))))
      (inputs (list lv2))
      (native-inputs (list pkg-config))
      (home-page "https://git.drobilla.net/cgit.cgi/omins.lv2.git/")
@@ -1430,33 +1430,86 @@ within this package are the 3000 bone marrow cells used for vignettes.")
      (license license:gpl3))))

 (define-public r-pizzarr
-  (let ((commit "5f4705789ba29344dcb97023f290a26a7f7abd0c")
-        (revision "2"))
-    (package
-      (name "r-pizzarr")
-      (version (git-version "0.1.0" revision commit))
-      (source
-       (origin
-         (method git-fetch)
-         (uri (git-reference
-               (url "https://github.com/keller-mark/pizzarr")
-               (commit commit)))
-         (file-name (git-file-name name version))
-         (sha256
-          (base32 "17pd6bk8kvnrvvyfqvm8q47kzghlfyfjdd9b7cwiazc5xr4vz6f0"))))
-      (properties `((upstream-name . "pizzarr")))
-      (build-system r-build-system)
-      ;; Some tests require Internet access.
-      (arguments (list #:tests? #false))
-      (propagated-inputs (list r-jsonlite r-memoise r-qs r-r6 r-stringr))
-      (native-inputs (list r-pbapply r-testthat r-vcr))
-      (home-page "https://github.com/keller-mark/pizzarr")
-      (synopsis "Slice into Zarr arrays in R")
-      (description
-       "This package provides an implementation of chunked, compressed,
+  (package
+    (name "r-pizzarr")
+    (version "0.2.0")
+    (source
+     (origin
+       (method git-fetch)
+       (uri (git-reference
+              (url "https://github.com/keller-mark/pizzarr")
+              (commit (string-append "v" version))))
+       (file-name (git-file-name name version))
+       (sha256
+        (base32 "1m38c57pfliycxkhb3mwgh01cl2q76r1jhd3vnk07dbfhqdbqai6"))))
+    (properties `((upstream-name . "pizzarr")))
+    (build-system cargo-build-system)
+    (arguments
+     (list
+      #:imported-modules
+      (append %cargo-build-system-modules
+              %r-build-system-modules)
+      #:modules
+      '((guix build cargo-build-system)
+        ((guix build r-build-system) #:prefix r:)
+        (guix build utils))
+      #:cargo-build-flags
+      '(list "--target-dir=./target" "--release")
+      #:phases
+      #~(append (modify-phases %standard-phases
+                  (add-after 'unpack 'patch-Makevars
+                    (lambda _
+                      ;; At this point we've already built the Rust parts.
+                      (substitute* "src/Makevars.in"
+                        (("^all:.*") "all:")
+                        (("^\\$\\(STATLIB\\):") "NOBODYCARES:")
+                        (("@PKG_LIBS_EXTRA@") "@PKG_LIBS_EXTRA@ -lzstd -lz"))))
+                  (add-after 'patch-Makevars 'chdir
+                    (lambda _ (chdir "src/rust")))
+                  (add-after 'chdir 'patch-rust-dependency
+                    (lambda _
+                      (setenv "RUSTFLAGS" "--print=native-static-libs")
+                      (substitute* "Cargo.toml"
+                        (("extendr-api = \\{ git.* \\}") "extendr-api = \"0.8.1\""))))
+                  (add-after 'package 'chdir-back
+                    (lambda _ (chdir "../..")))
+                  (delete 'install)
+                  (delete 'check))
+                (modify-phases (@ (guix build r-build-system) %standard-phases)
+                  (delete 'unpack)
+                  (replace 'patch-tests
+                    (lambda* (#:key inputs outputs tests? #:allow-other-keys)
+                      ((assoc-ref (@ (guix build r-build-system) %standard-phases)
+                                  'patch-tests)
+                       #:skipped-tests
+                       ;; These files contain tests that require Internet access.
+                       '("test-compat.R" "test-get.R"
+                         ;; HttpStore requires the crul package
+                         ("test-zarrs-dispatch.R" "can_use_zarrs_create returns FALSE for HttpStore")
+                         ("test-zarrs-store-cache.R" "HttpStore get_store_identifier returns URL")))))
+                  (replace 'check
+                    (lambda* (#:key inputs outputs tests? #:allow-other-keys)
+                      ((assoc-ref (@ (guix build r-build-system) %standard-phases)
+                                  'check)
+                       #:test-target "tests"
+                       #:test-types #false
+                       #:inputs inputs
+                       #:outputs outputs
+                       #:tests? tests?)))))))
+    (propagated-inputs (list r-jsonlite r-memoise r-qs2 r-r6 r-stringr))
+    (inputs
+     (cons* openssl zlib `(,zstd "lib")
+            (cargo-inputs 'r-pizzarr)))
+    (native-inputs
+     (list pkg-config
+           r-minimal r-pbapply r-testthat r-vcr))
+    (home-page "https://github.com/keller-mark/pizzarr")
+    (synopsis "Slice into Zarr arrays in R")
+    (description
+     "This package provides an implementation of chunked, compressed,
 N-dimensional arrays for R, Zarr specification version 2 (2024)
 <doi:10.5281/zenodo.11320255>.")
-      (license license:expat))))
+    (license license:expat)))

 (define-public r-rhtslib12
  (let ((commit "ee186daf04876969c7f31c16a0e0fda8e7c16a30")
@@ -4572,8 +4625,11 @@ into separate processes; and more.")
     (list
      #:phases
      #~(modify-phases %standard-phases
-          (add-after 'unpack 'python3.11-compatibility
+          (add-after 'unpack 'python3.12-compatibility
            (lambda _
+              ;; This was removed in Python 3.12
+              (substitute* "Bio/Align/_aligners.c"
+                (("case PyUnicode_WCHAR_KIND:") ""))
              ;; Py_TYPE was changed to an inline static function in Python
              ;; 3.11, so it cannot be used on the left-hand side.
              (substitute* "Bio/triemodule.c"
@@ -13990,33 +14046,20 @@ of scRNA-seq data.")
 (define-public r-misha
  (package
    (name "r-misha")
-    (version "4.1.0")
+    (version "5.6.23")
    (source
     (origin
       (method git-fetch)
       (uri (git-reference
             (url "https://github.com/tanaylab/misha")
-             (commit version)))
+             (commit (string-append "v" version))))
       (file-name (git-file-name name version))
       (sha256
        (base32
-         "0bgivx3lzjh3173jsfrhb5kvhjsn53br0n4hmyx7i3dwy2cnnp2p"))
-       ;; Delete bundled executable.
-       (snippet
-        '(delete-file "exec/bigWigToWig"))))
+         "1k973j04iq02dy4f7qgi3cmp3rcx5yinyx0m7vyag54rqanird8x"))))
    (build-system r-build-system)
-    (arguments
-     `(#:phases
-       (modify-phases %standard-phases
-         (add-after 'unpack 'do-not-use-bundled-bigWigToWig
-           (lambda* (#:key inputs #:allow-other-keys)
-             (substitute* "R/misha.R"
-               (("get\\(\".GLIBDIR\"\\), \"/exec/bigWigToWig")
-                (string-append "\""
-                               (assoc-ref inputs "kentutils")
-                               "/bin/bigWigToWig"))))))))
-    (inputs
-     (list kentutils))
+    (propagated-inputs (list r-curl r-digest r-magrittr r-ps r-yaml))
+    (native-inputs (list r-knitr r-testthat))
    (home-page "https://github.com/tanaylab/misha")
    (synopsis "Toolkit for analysis of genomic data")
    (description "This package is intended to help users to efficiently
@@ -18816,26 +18859,28 @@ activity prediction from transcriptomics data, and its R implementation
      (build-system r-build-system)
      (arguments
       (list
+        #:skipped-tests
+        ;; These tests attempt to connect to the Internet.
+        '(("test-liana_utils.R" "Test liana pipe")
+          ("test-liana_tensor.R"
+           ".*Test tensor wrapper.*"
+           ".*Test decompose_tensor.*")
+          ;; XXX: This test returns a data.frame instead of an error.
+          ("test-liana_cytotalk.R" ".*Test Cytotalk Wrap.*"))
        #:phases
        '(modify-phases %standard-phases
           ;; This is needed to find ~/.config/OmnipathR/omnipathr.yml
           (add-after 'unpack 'set-HOME
             (lambda _ (setenv "HOME" "/tmp")))
-           (add-after 'unpack 'disable-bad-tests
+           (add-after 'unpack 'seurat-compatibility
             (lambda _
-               ;; These tests attempt to connect to the Internet.
-               (substitute* "tests/testthat/test-liana_utils.R"
-                 ((".*Test liana pipe.*" m)
-                  (string-append m "skip('guix')\n")))
-               (substitute* "tests/testthat/test-liana_tensor.R"
-                 ((".*Test tensor wrapper.*" m)
-                  (string-append m "skip('guix')\n"))
-                 ((".*Test decompose_tensor.*" m)
-                  (string-append m "skip('guix')\n")))
-               ;; XXX: This test returns a data.frame instead of an error.
-               (substitute* "tests/testthat/test-liana_cytotalk.R"
-                 ((".*Test Cytotalk Wrap.*" m)
-                  (string-append m "skip('guix')\n"))))))))
+               ;; The `slot` argument of `GetAssayData()` was deprecated in
+               ;; SeuratObject 5.0.0.
+               (substitute* '("R/cellchat_pipe.R"
+                              "R/sca_pipe.R"
+                              "R/liana_prep.R"
+                              "R/natmi_pipe.R")
+                 (("slot =") "layer =")))))))
      (propagated-inputs
       (list r-basilisk
             r-basilisk-utils
@@ -21700,70 +21745,6 @@ want to explore e.g.: the function of a set of differentially expressed
 genes.")
      (license license:gpl3))))

-(define-public r-seurat-utils
-  (let ((commit "c0374cc9e25ce391ba8013fda0f8c7babbb9201d")
-        (revision "1"))
-    (package
-      (name "r-seurat-utils")
-      (version (git-version "2.5.0" revision commit))
-      (source (origin
-                (method git-fetch)
-                (uri (git-reference
-                      (url "https://github.com/vertesy/Seurat.utils")
-                      (commit commit)))
-                (file-name (git-file-name name version))
-                (sha256
-                 (base32
-                  "15l86b43q245gzz7gsr5rhs4sir74lc14d64yqxfqcb0zrb2bzzd"))))
-      (properties `((upstream-name . "Seurat.utils")))
-      (build-system r-build-system)
-      (propagated-inputs (list r-codeandroll2
-                               r-cowplot
-                               r-databaselinke-r
-                               r-dplyr
-                               r-enhancedvolcano
-                               r-foreach
-                               r-ggcorrplot
-                               r-ggexpress
-                               r-ggplot2
-                               r-ggpubr
-                               r-ggrepel
-                               r-hgnchelper
-                               r-htmlwidgets
-                               r-job
-                               r-magrittr
-                               r-markdownhelpers
-                               r-markdownreports
-                               r-matrix
-                               r-matrixstats
-                               r-pheatmap
-                               r-plotly
-                               r-princurve
-                               r-qs
-                               r-r-utils
-                               r-readr
-                               r-readwriter
-                               r-reshape2
-                               r-rstudioapi
-                               r-scales
-                               r-seurat
-                               r-soupx
-                               r-sparsematrixstats
-                               r-stringendo
-                               r-stringr
-                               r-tibble
-                               r-tictoc
-                               r-tidyverse
-                               r-vroom))
-      (home-page "https://github.com/vertesy/Seurat.utils")
-      (synopsis "Collection of utility functions for Seurat")
-      (description
-       "This is a collection of utility functions for Seurat.  These functions
-allow the automation and multiplexing of plotting, 3D plotting, visualization
-of statistics & QC, interaction with the Seurat object.  Some functionalities
-require functions from CodeAndRoll and MarkdownReports libraries.")
-      (license license:gpl3))))
-
 (define-public r-seuratextend
  (let ((commit "5dacd7c1e1da3bc0e78ab81d60056f6d7da3d386")
        (revision "1"))
@@ -22478,38 +22459,39 @@ frames with arbitrary sets of columns.")
      (license license:expat))))

 (define-public r-imagearray
-  (let ((commit "2f90694fa33ed8320a6a2f7e0ad5c8a1796cbfc6")
-        (revision "1"))
-    (package
-      (name "r-imagearray")
-      (version (git-version "0.99.6" revision commit))
-      (source
-       (origin
-         (method git-fetch)
-         (uri (git-reference
-               (url "https://github.com/BIMSBbioinfo/ImageArray")
-               (commit commit)))
-         (file-name (git-file-name name version))
-         (sha256
-          (base32 "1mf68b007dc5wdzdva4vkjgkavgagjk45qv05f7vahbpi24yjj4n"))))
-      (properties `((upstream-name . "ImageArray")))
-      (build-system r-build-system)
-      (propagated-inputs (list r-delayedarray
-                               r-ebimage
-                               r-hdf5array
-                               r-magick
-                               r-rarr
-                               r-rhdf5
-                               r-s4arrays
-                               r-s4vectors))
-      (native-inputs (list r-knitr r-testthat))
-      (home-page "https://github.com/BIMSBbioinfo/ImageArray")
-      (synopsis "Framework for on-disk and in-memory image arrays")
-      (description
-       "@code{ImageArray} provides a framework for on-disk and in-memory image
-arrays, specifically for pyramidal images stored in either HDF5 files or Zarr
-stores.")
-      (license license:expat))))
+  (package
+    (name "r-imagearray")
+    (version "1.0.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (bioconductor-uri "ImageArray" version))
+       (sha256
+        (base32 "07zq5fcw2dsvm4qaksaj4gy9gj5lxcgq82l497c5kgvl4wba049c"))))
+    (properties `((upstream-name . "ImageArray")))
+    (build-system r-build-system)
+    (arguments
+     (list
+      #:skipped-tests
+      ;; RBiomFormats is not installed.
+      '(("test-array.R" "check indexing \\(BFArray\\)"))))
+    (propagated-inputs (list r-delayedarray
+                             r-ebimage
+                             r-hdf5array
+                             r-magick
+                             r-rarr
+                             r-rhdf5
+                             r-s4arrays
+                             r-s4vectors
+                             r-zarrarray))
+    (native-inputs (list r-ggplot2 r-knitr r-testthat))
+    (home-page "https://github.com/BIMSBbioinfo/ImageArray")
+    (synopsis "Framework for on-disk and in-memory image arrays")
+    (description
+     "@code{ImageArray} provides a framework for on-disk and in-memory image
+arrays, specifically for pyramidal images stored in HDF5, Zarr and life
+sciences image file formats (OME Bio-Formats).")
+    (license license:expat)))

 (define-public r-velocyto
  (let ((commit "d7790346cb99f49ab9c2b23ba70dcf9d2c9fc350")
@@ -22593,7 +22575,7 @@ dependencies of @code{VoltRon} package.")
 (define-public r-voltron
  (package
    (name "r-voltron")
-    (version "0.2.5")
+    (version "0.2.6")
    (source
     (origin
       (method git-fetch)
@@ -22602,7 +22584,7 @@ dependencies of @code{VoltRon} package.")
              (commit (string-append "v" version))))
       (file-name (git-file-name name version))
       (sha256
-        (base32 "057n4yipkq3gnlyrb63l2ryi78nlmaas02avargm352g5ra1xl9s"))))
+        (base32 "00fl5dmyd9ad4hd0cblgi0415sf6q4q67wh04r7fws828vs5vaj1"))))
    (properties `((upstream-name . "VoltRon")))
    (build-system r-build-system)
    (arguments
@@ -22666,18 +22648,15 @@ guix_python <- \"~a\";"
                             r-irlba
                             r-magick
                             r-matrix
-                             r-pizzarr
                             r-rann
                             r-rcdt
                             r-rcpp
                             r-rcppannoy
                             r-rcpparmadillo
-                             r-reshape2
-                             r-reticulate
-                             r-rhdf5
                             r-rjson
                             r-rlang
                             r-s4arrays
+                             r-s4vectors
                             r-shiny
                             r-shinyjs
                             r-sp
@@ -22730,8 +22709,8 @@ spots, cells and even molecules.")
    (license license:expat)))

 (define-public r-zarrdataframe
-  (let ((commit "84c7db2f6f5f84b4a4308f8eb72bedc131fb68bc")
-        (revision "2"))
+  (let ((commit "f5f671521934b2afc3c511f8c09181bc7bb789a4")
+        (revision "3"))
    (package
      (name "r-zarrdataframe")
      (version (git-version "0.0.0" revision commit))
@@ -22743,13 +22722,13 @@ spots, cells and even molecules.")
               (commit commit)))
         (file-name (git-file-name name version))
         (sha256
-          (base32 "1idrvdlzbwyixlg830sn19vfdn3n3irmlyr4ncf7dpk72r08g3hw"))))
+          (base32 "0klp2njn6qsa8n6c01v1z2dfaa93lhbzhwhbyhl23h8gg7d28yc1"))))
      (properties
       '((upstream-name . "ZarrDataFrame")
         (updater-extra-native-inputs . ("r-testthat"))))
      (build-system r-build-system)
      (propagated-inputs (list r-biocgenerics r-delayedarray r-rarr
-                               r-s4vectors))
+                               r-s4vectors r-zarrarray))
      (native-inputs (list r-knitr r-testthat))
      (home-page "https://github.com/BIMSBbioinfo/ZarrDataFrame")
      (synopsis "Bioconductor-friendly Bindings for Zarr")
@@ -22761,39 +22740,35 @@ frames with arbitrary sets of columns.")
      (license license:expat))))

 (define-public r-zarrarray
-  (let ((commit "3cc3e6acf986074dfaece2ad23f9b56962054625")
-        (revision "2"))
-    (package
-      (name "r-zarrarray")
-      (version (git-version "1.0" revision commit))
-      (source
-       (origin
-         (method git-fetch)
-         (uri (git-reference
-               (url "https://github.com/BIMSBbioinfo/ZarrArray")
-               (commit commit)))
-         (file-name (git-file-name name version))
-         (sha256
-          (base32 "1qjj92cpxpm3zh05vf60h5gmcn1qady0s38hibb0l57iwdhlhrb3"))))
-      (properties
-       '((upstream-name . "ZarrArray")
-         (updater-extra-native-inputs . ("r-testthat"))))
-      (build-system r-build-system)
-      ;; The tests seem to be outdated.
-      (arguments (list #:tests? #false))
-      (propagated-inputs (list r-biocgenerics
-                               r-delayedarray
-                               r-iranges
-                               r-matrix
-                               r-rarr
-                               r-s4arrays
-                               r-s4vectors
-                               r-sparsearray))
-      (native-inputs (list r-testthat))
-      (home-page "https://github.com/BIMSBbioinfo/ZarrArray")
-      (synopsis "Zarr backend for DelayedArray objects")
-      (description "Zarr backend for @code{DelayedArray} objects.")
-      (license license:expat))))
+  (package
+    (name "r-zarrarray")
+    (version "1.0.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (bioconductor-uri "ZarrArray" version))
+       (sha256
+        (base32 "1ny91qg257kgb1hz2h4jvb0rna9cwyw7fqyj5axv52r3b98xn040"))))
+    (properties `((upstream-name . "ZarrArray")))
+    (build-system r-build-system)
+    (propagated-inputs (list r-biocgenerics
+                             r-delayedarray
+                             r-iranges
+                             r-rarr
+                             r-s4arrays
+                             r-s4vectors
+                             r-sparsearray))
+    (native-inputs (list r-knitr r-testthat))
+    (home-page "https://bioconductor.org/packages/ZarrArray")
+    (synopsis "Bring Zarr datasets in R as DelayedArray objects")
+    (description
+     "The @code{ZarrArray} package leverages the Rarr package to bring Zarr
+datasets in R as @code{DelayedArray} objects.  The main class in the package
+is the @code{ZarrArray} class.  A @code{ZarrArray} object is an array-like
+object that represents a Zarr dataset in R. @code{ZarrArray} objects are
+@code{DelayedArray} derivatives and therefore support all operations (delayed
+or block-processed) supported by @code{DelayedArray} objects.")
+    (license license:artistic2.0)))

 (define-public methyldackel
  (package
@@ -24431,79 +24406,77 @@ It also handles cell type-specific differential expression.")
      (license license:gpl3))))

 (define-public r-spectre
-  (let ((commit "ff5314fd5b3f29121e52f948d91e222a19dd4d25")
-        (revision "1"))
-    (package
-      (name "r-spectre")
-      (version "1.2.0")
-      (source
-       (origin
-         (method git-fetch)
-         (uri (git-reference
-               (url "https://github.com/ImmuneDynamics/Spectre")
-               (commit commit)))
-         (file-name (git-file-name name version))
-         (sha256
-          (base32
-           "0hziqlaq6mnkxi4bwp5xilxy90yh1vz1j1n117d38vmchvclx9yq"))))
-      (properties `((upstream-name . "Spectre")))
-      (build-system r-build-system)
-      (propagated-inputs
-       (list r-biobase
-             r-biocmanager
-             r-caret
-             r-class
-             r-colorramps
-             r-data-table
-             r-dendsort
-             r-devtools
-             r-dplyr
-             r-exactextractr
-             r-factoextra
-             r-flowcore
-             r-flowsom
-             r-flowviz
-             r-fnn
-             r-ggplot2
-             r-ggpointdensity
-             r-ggpubr
-             r-ggraph
-             r-ggthemes
-             r-gridextra
-             r-gridextra
-             r-gtools
-             r-hdf5array
-             r-irlba
-             r-patchwork
-             r-pheatmap
-             r-plyr
-             r-qs
-             r-raster
-             r-rcolorbrewer
-             r-rhdf5
-             r-rstudioapi
-             r-rsvd
-             r-rtsne
-             r-s2
-             r-scales
-             r-scattermore
-             r-sf
-             r-sp
-             r-stars
-             r-stringr
-             r-tidygraph
-             r-tidyr
-             r-tidyr
-             r-tiff
-             r-umap
-             r-uwot))
-      (home-page "https://github.com/ImmuneDynamics/Spectre")
-      (synopsis "High-dimensional cytometry and imaging analysis")
-      (description
-       "This package provides a computational toolkit in R for the
+  (package
+    (name "r-spectre")
+    (version "1.3.0")
+    (source
+     (origin
+       (method git-fetch)
+       (uri (git-reference
+              (url "https://github.com/ImmuneDynamics/Spectre")
+              (commit (string-append "v" version))))
+       (file-name (git-file-name name version))
+       (sha256
+        (base32
+         "15g9w08x0pz2ia9qfalhcg3z5z2zx2085mfbr8gx9w5yxnw475ld"))))
+    (properties `((upstream-name . "Spectre")))
+    (build-system r-build-system)
+    (propagated-inputs
+     (list r-biobase
+           r-biocmanager
+           r-caret
+           r-class
+           r-colorramps
+           r-data-table
+           r-dendsort
+           r-devtools
+           r-dplyr
+           r-exactextractr
+           r-factoextra
+           r-flowcore
+           r-flowsom
+           r-flowviz
+           r-fnn
+           r-ggplot2
+           r-ggpointdensity
+           r-ggpubr
+           r-ggraph
+           r-ggthemes
+           r-gridextra
+           r-gridextra
+           r-gtools
+           r-hdf5array
+           r-irlba
+           r-patchwork
+           r-pheatmap
+           r-plyr
+           r-qs2
+           r-raster
+           r-rcolorbrewer
+           r-rhdf5
+           r-rstudioapi
+           r-rsvd
+           r-rtsne
+           r-s2
+           r-scales
+           r-scattermore
+           r-sf
+           r-sp
+           r-stars
+           r-stringr
+           r-tidygraph
+           r-tidyr
+           r-tidyr
+           r-tiff
+           r-umap
+           r-uwot))
+    (home-page "https://github.com/ImmuneDynamics/Spectre")
+    (synopsis "High-dimensional cytometry and imaging analysis")
+    (description
+     "This package provides a computational toolkit in R for the
 integration, exploration, and analysis of high-dimensional single-cell
 cytometry and imaging data.")
-      (license license:expat))))
+    (license license:expat)))

 (define-public r-compgenomrdata
  (let ((commit "24484cb77631e1123ead6c329b9d62c160e600c6")
@@ -302,7 +302,7 @@ will name the threaded machine type unless THREADS? is provided as #f."
    (name "chez-scheme-for-racket")
    ;; The version should match `(scheme-version #t)`.
    ;; See s/cmacros.ss c. line 360.
-    (version "10.3.0-pre-release.2") ; expect a chez-nanopass-bootstrap update
+    (version "10.4.0-pre-release.1-1") ; expect a chez-nanopass-bootstrap update
    (source #f)
    (build-system gnu-build-system)
    (inputs `(,@(if (nix-system->native-chez-machine-type)
@@ -507,7 +507,7 @@ version of Chez Scheme.")
    (name "chez-scheme")
    ;; The version should match `(scheme-version-number #t)`.
    ;; See s/cmacros.ss c. line 360.
-    (version "10.2.0") ; expect a chez-nanopass-bootstrap update
+    (version "10.4.0") ; expect a chez-nanopass-bootstrap update
    (source (origin
              (method git-fetch)
              (uri (git-reference
@@ -515,7 +515,7 @@ version of Chez Scheme.")
                    (commit (string-append "v" version))))
              (sha256
               (base32
-                "14iv4kfkyvrkigr1n2prf71n2l3vs0sf0549rvh6y4x2faa2l329"))
+                "079vlkl27qdvsg1rsynmd828m42n98c2dnldkhsxf2slfsqd9kv5"))
              (file-name (git-file-name name version))
              (patches (search-patches "chez-scheme-bin-sh.patch"))
              (snippet #~(begin
@@ -840,9 +840,9 @@ User's Guix}, among other documents.")
 (define-public chez-nanopass-bootstrap
  (hidden-package
   (package
-     (name "chez-nanopass")
-     (version "1.9.2")
-     (properties `((chez-nanopass-release-date . "October 18, 2020")))
+     (name "chez-nanopass-bootstrap")
+     (version "1.9.4")
+     (properties '((chez-nanopass-release-date . "December 29, 2025")))
     (source
      (origin
        (method git-fetch)
@@ -850,7 +850,7 @@ User's Guix}, among other documents.")
              (url "https://github.com/nanopass/nanopass-framework-scheme")
              (commit (string-append "v" version))))
        (sha256
-         (base32 "16vjsik9rrzbabbhbxbaha51ppi3f9n8rk59pc6zdyffs0vziy4i"))
+         (base32 "1qq0vnbrvcialgjgnblfq3qp1ilqg94h0kg896ksd9v4g7ipj9v0"))
        (file-name (git-file-name "nanopass-framework-scheme" version))
        (snippet
         #~(begin
@@ -929,10 +929,9 @@ create compilers, making them easier to understand and maintain.")
 (define-public chez-nanopass
  (package
    (inherit chez-nanopass-bootstrap)
-    ;; This release has a significant bug fix.  Expect the next releases of
-    ;; chez-scheme{,-for-racket} to want this for chez-nanopass-bootstrap.
-    (version "1.9.3")
-    (properties '((chez-nanopass-release-date . "August 24, 2025")))
+    (name "chez-nanopass")
+    (version "1.9.4")
+    (properties '((chez-nanopass-release-date . "December 29, 2025")))
    (source
     (let ((bootstrap-origin (package-source chez-nanopass-bootstrap)))
       (origin
@@ -941,7 +940,7 @@ create compilers, making them easier to understand and maintain.")
                (url (git-reference-url (origin-uri bootstrap-origin)))
                (commit (string-append "v" version))))
         (sha256
-          (base32 "0757x3a3b4kcd3jk52h4ikqzv7cc1mvphlw592f0r5pz99bkxiin"))
+          (base32 "1qq0vnbrvcialgjgnblfq3qp1ilqg94h0kg896ksd9v4g7ipj9v0"))
         (file-name (git-file-name "nanopass-framework-scheme" version)))))
    (native-inputs (list chez-scheme stex))))

@@ -5645,7 +5645,7 @@ with integrated support for finding required rows quickly.")
 (define-public apache-arrow
  (package
    (name "apache-arrow")
-    (version "23.0.1")
+    (version "24.0.0")
    (source
     (origin
       (method git-fetch)
@@ -5655,7 +5655,7 @@ with integrated support for finding required rows quickly.")
       (file-name (git-file-name name version))
       (sha256
        (base32
-         "1qn7wgavi3kiz4d6w1naqj5631bg87fnj6gbhaxmpmynm5hi9wm7"))))
+         "1j3gs5ffa9gx2y2nggmi2zn5rj0bsnjnxrzfnipx6050jz6n8dx9"))))
    (build-system cmake-build-system)
    (arguments
     (list
@@ -5823,6 +5823,8 @@ __version_tuple__ = version_tuple = (~a)~%" version version-tuple))))))
           pkg-config
           python-cython
           python-pytest
+           python-pytest-runner
+           python-scikit-build-core
           python-setuptools-scm
           python-setuptools))
    (outputs '("out"))
@@ -1314,7 +1314,7 @@ package.")
       #:tests? #f)) ;no test suite
    (native-inputs (list asciidoc
                         gettext-minimal
-                         git-minimal
+                         git-minimal/pinned
                         perl
                         perl-unicode-linebreak
                         perl-yaml-tiny
@@ -23831,8 +23831,8 @@ actually changing the buffer's text.")

 (define-public emacs-diff-hl
  ;; No new tags or releases since 2024.
-  (let ((commit "e79aa49ad3cbbe85379cf6646db3aaacd3b04708")
-        (revision "0"))
+  (let ((commit "7d873b2f58908de1ea2f499da9bf993e088953d7")
+        (revision "1"))
    (package
      (name "emacs-diff-hl")
      (version (git-version "1.10.0" revision commit))
@@ -23844,7 +23844,7 @@ actually changing the buffer's text.")
                (commit commit)))
         (file-name (git-file-name name version))
         (sha256
-          (base32 "0fvxngcbx36vqj72fllfp5iqwihcqd1dfhmqr3m1284191q83na3"))))
+          (base32 "15a9cjlpjsfcb2hxqbb123389qhiqs06mn01pas2l0jqhc2p86v9"))))
      (build-system emacs-build-system)
      (arguments
       (list
@@ -23867,7 +23867,7 @@ actually changing the buffer's text.")
                (invoke "git" "init")
                (invoke "git" "add" ".")
                (invoke "git" "commit" "-m" "Commit all."))))))
-      (native-inputs (list git-minimal))
+      (native-inputs (list git-minimal/pinned))
      (home-page "https://github.com/dgutov/diff-hl")
      (synopsis "Highlight uncommitted changes using VC")
      (description
@@ -1,5 +1,5 @@
 ;;; GNU Guix --- Functional package management for GNU
-;;; Copyright © 2017-2025 Ricardo Wurmus <rekado@elephly.net>
+;;; Copyright © 2017-2026 Ricardo Wurmus <rekado@elephly.net>
 ;;; Copyright © 2018 Joshua Sierles, Nextjournal <joshua@nextjournal.com>
 ;;; Copyright © 2018, 2020, 2022 Tobias Geerinckx-Rice <me@tobias.gr>
 ;;; Copyright © 2019, 2021, 2022, 2024 Efraim Flashner <efraim@flashner.co.il>
@@ -227,7 +227,7 @@ more.")
   (package
     (inherit igraph)
     (name "igraph")
-     (version "0.10.15")
+     (version "1.0.1")
     (source
      (origin
        (inherit (package-source igraph))
@@ -239,7 +239,39 @@ more.")
        (file-name (git-file-name name version))
        (sha256
         (base32
-          "0z9jqvl65j4z6brrjlfyykba2bs10az6dx6m8g41snlfnx21a82d")))))))
+          "01mynhbl2ph0gkc0zr5klwqvczwcimfs2kdn6didwg4k8gsrcxlr"))
+        (modules '((guix build utils)
+                   (ice-9 ftw)
+                   (srfi srfi-26)))
+        ;; We need the vendored versions of qhull and cxsparse.
+        (snippet '(begin
+                    (delete-file-recursively "src/isomorphism/bliss")
+                    (substitute* '("src/CMakeLists.txt"
+                                   "etc/cmake/benchmark_helpers.cmake")
+                      ;; Remove extraneous bundling related variables.
+                      ((".*_IS_VENDORED.*") "")
+                      ((".*add_sub.*isomorphism/bliss.*") "")
+                      (("(.*TARGETS.*)bliss(.*)pcg(.*)"
+                        _ part1 part2 part3)
+                       (string-append part1 part2 part3))
+                      ((" pcg ") " pcg_random "))))))
+     (arguments
+      (substitute-keyword-arguments (package-arguments igraph)
+        ((#:phases phases '%standard-phases)
+         #~(modify-phases #$phases
+             ;; We have to use the bundled version because it has been
+             ;; modified from upstream.
+             (delete 'patch-suitesparse)))
+        ((#:configure-flags flags)
+         #~(list "-DBUILD_SHARED_LIBS=ON"
+                 "-DIGRAPH_INFOMAP_SUPPORT=OFF"
+                 "-DCMAKE_C_FLAGS=-Wno-error=incompatible-pointer-types"
+                 ;; Use the same integer width as suitesparse-cxsparse, which
+                 ;; uses int64_t in SuiteSparse v6.0.0 and later.
+                 "-DIGRAPH_INTEGER_SIZE=64"))))
+     (inputs
+      (modify-inputs (package-inputs igraph)
+        (delete "suitesparse-cxsparse"))))))

 (define-public python-igraph
  (package
@@ -1923,7 +1923,7 @@ and Scan Tailor Enhanced versions as well as including many more bug fixes.")
 (define-public simpleitk
  (package
    (name "simpleitk")
-    (version "2.5.3")
+    (version "2.5.4")
    (source
     (origin
       (method git-fetch)
@@ -1932,7 +1932,9 @@ and Scan Tailor Enhanced versions as well as including many more bug fixes.")
             (commit (string-append "v" version))))
       (file-name (git-file-name name version))
       (sha256
-        (base32 "0fvacjfq0p8v7r2cmzwwh7bxb6ayavznhj0m81dah463x472qkd2"))))
+        (base32 "1bzj5naqbgv2b31iqgz7qqk9rixsvjqycjz6l7w3gm7v1aj14jpb"))
+       (patches
+        (search-patches "simpleitk-r-4.6.0.patch"))))
    (build-system cmake-build-system)
    (outputs '("out" "python" "r"))
    (arguments
@@ -2032,7 +2034,7 @@ and Scan Tailor Enhanced versions as well as including many more bug fixes.")
                   version "/SimpleITKData-" version ".tar.gz"))
             (sha256
              (base32
-               "0i4f87g1rh6xxisw06gwwyi8f216qqs6ih3gghi3k49vsl0h4g5d")))))
+               "0hryvi9fgqac00ng1bfhw3lm0al1dh0ka6jglba2q368nls428nx")))))
    (synopsis "Simplified interface to @acronym{ITK, Insight Toolkit}")
    (description
     "SimpleITK is an image analysis toolkit built on top of @acronym{ITK,
@@ -94,13 +94,16 @@
  #:use-module (gnu packages gnome)
  #:use-module (gnu packages golang-build)
  #:use-module (gnu packages golang-xyz)
+  #:use-module (gnu packages gstreamer)
  #:use-module (gnu packages gtk)
  #:use-module (gnu packages graphics)
  #:use-module (gnu packages haskell-xyz)
  #:use-module (gnu packages image)
  #:use-module (gnu packages image-processing)
  #:use-module (gnu packages imagemagick)
+  #:use-module (gnu packages kde-frameworks)
  #:use-module (gnu packages linux)
+  #:use-module (gnu packages logging)
  #:use-module (gnu packages maths)
  #:use-module (gnu packages ncurses)
  #:use-module (gnu packages pdf)
@@ -108,6 +111,7 @@
  #:use-module (gnu packages perl-check)
  #:use-module (gnu packages photo)
  #:use-module (gnu packages pkg-config)
+  #:use-module (gnu packages pretty-print)
  #:use-module (gnu packages profiling)
  #:use-module (gnu packages python)
  #:use-module (gnu packages python-build)
@@ -120,6 +124,8 @@
  #:use-module (gnu packages sqlite)
  #:use-module (gnu packages suckless)
  #:use-module (gnu packages stb)
+  #:use-module (gnu packages tbb)
+  #:use-module (gnu packages tls)
  #:use-module (gnu packages terminals)
  #:use-module (gnu packages upnp)
  #:use-module (gnu packages version-control)
@@ -1286,6 +1292,84 @@ workspaces.
 (define-deprecated-package python-ueberzug
  ueberzug)

+(define-public ueberzugpp
+  (package
+    (name "ueberzugpp")
+    (version "2.9.10")
+    (source
+      (origin
+        (method git-fetch)
+        (uri (git-reference
+              (url "https://github.com/jstkdng/ueberzugpp")
+              (commit (string-append "v" version))))
+        (file-name (git-file-name name version))
+        (sha256
+         (base32 "1jac2sca4pmcxp8xcvaxhf6j15phyc85gb5n9ymajbahnd4hbcv2"))))
+    (build-system cmake-build-system)
+    (arguments
+     (list #:tests? #f    ; no tests
+           #:configure-flags
+           #~(list "-DENABLE_OPENCV=ON"
+                   "-DENABLE_X11=ON"
+                   "-DENABLE_WAYLAND=ON")))
+    (native-inputs
+     (list extra-cmake-modules
+           gobject-introspection
+           pkg-config))
+    (inputs
+     (list cairo
+           chafa
+           cli11
+           expat
+           fftw
+           fmt
+           imagemagick
+           imath
+           lcms
+           libexif
+           libgsf
+           librsvg
+           libsixel
+           libwebp
+           libxcb
+           matio
+           nlohmann-json
+           opencv
+           openexr
+           openssl
+           orc
+           pango
+           poppler
+           range-v3
+           spdlog
+           tbb
+           vips
+           wayland
+           wayland-protocols
+           xcb-util-image))
+    (home-page "https://github.com/jstkdng/ueberzugpp")
+    (synopsis "Drop in replacement for ueberzug written in C++")
+    (description "Überzug++ is a command line utility written in C++ which
+allows to draw images on terminals by using X11/Wayland child windows, sixels,
+ kitty and iterm2.
+
+Advantages over @command{w3mimgdisplay}:
+@itemize
+@item Support for Wayland: Sway, Hyprland, niri and Wayfire
+@item No race conditions as a new window is created to display images
+@item Expose events will be processed, so images will be redrawn on switch
+workspaces
+@item Tmux support on X11, Sway and Hyprland
+@item Terminals without the @env{WINDOWID} environment variable are supported
+@item Chars are used as position - and size unit
+@item No memory leak (usage of smart pointers)
+@item A lot of image formats supported (through OpenCV and libvips).
+@item GIF and animated WEBP support on X11, Sixel, Sway and hyprland
+@item Fast image downscaling (through OpenCV and OpenCL)
+@item Cache resized images for faster viewing
+@end itemize")
+    (license license:gpl3)))
+
 (define-public vv
  (package
    (name "vv")
@@ -3857,11 +3857,15 @@ follows a traditional multi-track tape recorder control paradigm.")
     (list
      #:phases
      '(modify-phases %standard-phases
-         (add-after 'unpack 'python3.11-compatibility
+         (add-after 'unpack 'python3.12-compatibility
           (lambda _
             (substitute* '("waflib/Context.py"
                            "waflib/ConfigSet.py")
-               (("'rU'") "'r'"))))
+               (("'rU'") "'r'"))
+             (substitute* "waflib/Context.py"
+               (("imp.new_module") "types.ModuleType")
+               (("import os, re, imp, sys")
+                "import os, re, types, sys"))))
         (add-after 'unpack 'remove-sse-flags
           (lambda* (#:key system #:allow-other-keys)
             (unless (or (string-prefix? "x86_64" system)
@@ -1006,11 +1006,11 @@ publish/subscribe, RPC-style request/reply, or service discovery.")
    (home-page "https://nng.nanomsg.org/")
    (license license:expat)))

-(define-public nng-1.10
+(define-public nng-1.11
  (package
    (inherit nng)
    (name "nng")
-    (version "1.10.1")
+    (version "1.11")
    (source
     (origin
       (method git-fetch)
@@ -1019,9 +1019,12 @@ publish/subscribe, RPC-style request/reply, or service discovery.")
             (commit (string-append "v" version))))
       (file-name (git-file-name name version))
       (sha256
-        (base32 "13nmz1p8qd12gyj7wm8fz1ccap47qh41sxz4jqdhj8gnd0kiy5h4"))))
+        (base32 "1l4rxwnc9knndwmy7xg53adyrm17ld7c5gxwm7vgfmgfy0my4zy8"))))
    (arguments
     (list
+      ;; At least on aarch64-linux, running tests in parallel leads to ports
+      ;; being unavailable in later tests, which then fail.
+      #:parallel-tests? #false
      #:configure-flags
      '(list "-DNNG_ENABLE_COVERAGE=ON"
             "-DNNG_ENABLE_TLS=ON"
@@ -1035,6 +1038,7 @@ publish/subscribe, RPC-style request/reply, or service discovery.")
               (("add_nng_test1\\(httpclient 60 NNG_SUPP_HTTP\\)") "")
               (("add_nng_test\\(tls 60\\)") ""))
             (substitute* "src/platform/CMakeLists.txt"
+               ;; This test only seems to fail on aarch64-linux
               (("nng_test\\(platform_test\\)") "")
               (("nng_test\\(resolver_test\\)") ""))
             (substitute* "src/sp/transport/tcp/CMakeLists.txt"
@@ -1,513 +0,0 @@
-This patch shas been backported from the development version or Biostrings.
-
-From 100602242840322b5f6c267faaf8198c1a5aa2af Mon Sep 17 00:00:00 2001
-From: =?UTF-8?q?Herv=C3=A9=20Pag=C3=A8s?= <hpages.on.github@gmail.com>
-Date: Thu, 5 Mar 2026 22:36:30 -0800
-Subject: [PATCH] Biostrings 2.79.5: Get rid of never-used SparseMIndex and
- SparseList classes
-
-This also eliminates the non-API calls to R.
---
- DESCRIPTION                 |   3 +-
- NAMESPACE                   |   2 -
- R/MIndex-class.R            |  79 -------------------------
- R/SparseList-class.R        |  80 -------------------------
- man/Biostrings-internals.Rd |   9 ---
- src/Biostrings.h            |  41 -------------
- src/MIndex_class.c          |  67 ---------------------
- src/R_init_Biostrings.c     |   1 -
- src/SparseList_utils.c      | 113 ------------------------------------
- 9 files changed, 1 insertion(+), 394 deletions(-)
- delete mode 100644 R/SparseList-class.R
- delete mode 100644 src/SparseList_utils.c
-
-diff --git a/DESCRIPTION b/DESCRIPTION
-index a5d027cc..dbc323ea 100644
--- a/DESCRIPTION
-+++ b/DESCRIPTION
-@@ -76,3 +76,3 @@ Collate: utils.R IUPAC_CODE_MAP.R AMINO_ACID_CODE.R GENETIC_CODE.R
-         injectHardMask.R padAndClip.R strsplit-methods.R misc.R
-        SparseList-class.R MIndex-class.R lowlevel-matching.R
-+        MIndex-class.R lowlevel-matching.R
-         match-utils.R matchPattern.R maskMotif.R matchLRPatterns.R
-diff --git a/NAMESPACE b/NAMESPACE
-index ba1e3bfa..cf14db67 100644
--- a/NAMESPACE
-+++ b/NAMESPACE
-@@ -206,7 +206,6 @@ exportMethods(
- ### ==========================================================================
- ### STRING MATCHING
- ### --------------------------------------------------------------------------
-###   SparseList-class.R
- ###   MIndex-class.R
- ###   lowlevel-matching.R
- ###   match-utils.R
-@@ -220,7 +219,6 @@ exportMethods(
- ###   matchPDict.R
- 
- exportClasses(
-    #SparseList,
-     MIndex, ByPos_MIndex,
-     PreprocessedTB, Twobit, ACtree2,
-     PDict3Parts,
-diff --git a/R/MIndex-class.R b/R/MIndex-class.R
-index 022f6746..f50f215e 100644
--- a/R/MIndex-class.R
-+++ b/R/MIndex-class.R
-@@ -218,82 +218,3 @@ ByPos_MIndex.combine <- function(mi_list)
-     new("ByPos_MIndex", width0=ans_width0, NAMES=ans_names, ends=ans_ends)
- }
- 
-
-### - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
-### The "SparseMIndex" class (DISABLED FOR NOW).
-### 
-### Slot description:
-###
-###   ends_envir: a key-value list (environment) where the values are integer
-###       vectors containing the ending positions of the pattern whose
-###       position in the original dictionary is given by the key (the keys are
-###       strings representing positive integers).
-### 
-
-if (FALSE) {
-
-  setClass("SparseMIndex",
-    contains="MIndex",
-    representation(
-        ends_envir="environment"
-    )
-  )
-
-  setMethod("show", "SparseMIndex",
-    function(object)
-    {
-        cat("Sparse MIndex object of length ", length(object), "\n", sep="")
-    }
-  )
-
-  setMethod("[[", "SparseMIndex",
-    function(x, i, j, ...)
-    {
-        i <- normalizeDoubleBracketSubscript(i, x)
-        ans_end <- x@ends_envir[[formatC(i, width=10, format="d", flag="0")]]
-        if (is.null(ans_end))
-            ans_end <- integer(0)
-        ans_width <- rep.int(x@width0[i], length(ans_end))
-        ans_start <- ans_end - x@width0[i] + 1L
-        new2("IRanges", start=ans_start, width=ans_width, check=FALSE)
-    }
-  )
-
-  ### An example of a SparseMIndex object of length 5 where only the
-  ### 2nd pattern has matches:
-  ###   > width0 <- c(9L, 10L, 8L, 4L, 10L)
-  ###   > ends_envir <- new.env(hash=TRUE, parent=emptyenv())
-  ###   > ends_envir[['0000000002']] <- c(199L, 402L)
-  ###   > mindex <- new("SparseMIndex", width0=width0, NAMES=letters[1:5], ends_envir=ends_envir)
-  ###   > mindex[[1]]
-  ###   > mindex[[2]]
-  ###   > mindex[[6]] # Error in mindex[[6]] : subscript out of bounds
-  ###   > names(mindex)
-  ###   > mindex[["a"]]
-  ###   > mindex[["b"]]
-  ###   > mindex[["aa"]] # Error in mindex[["aa"]] : pattern name ‘aa’ not found
-  ###   > startIndex(mindex)
-  ###   > endIndex(mindex)
-  ###   > elementNROWS(mindex)
-  ###
-  setMethod("startIndex", "SparseMIndex",
-    function(x)
-    {
-        all.names <- TRUE
-        .Call2("SparseMIndex_endIndex",
-              x@ends_envir, x@width0, x@NAMES, all.names,
-              PACKAGE="Biostrings")
-    }
-  )
-  setMethod("endIndex", "SparseMIndex",
-    function(x)
-    {
-        all.names <- TRUE
-        .Call2("SparseMIndex_endIndex",
-              x@ends_envir, NULL, x@NAMES, all.names,
-              PACKAGE="Biostrings")
-    }
-  )
-
-}
-
-diff --git a/R/SparseList-class.R b/R/SparseList-class.R
-deleted file mode 100644
-index 8295fd0f..00000000
--- a/R/SparseList-class.R
-+++ /dev/null
-@@ -1,80 +0,0 @@
-### =========================================================================
-### SparseList objects
-### -------------------------------------------------------------------------
-###
-
-setClass("SparseList",
-    representation(
-        length="integer",
-        env="environment"
-    )
-)
-
-### Typical use:
-###   env <- new.env(hash=TRUE, parent=emptyenv())
-###   key <- formatC(98L, width=10, format="d", flag="0")
-###   value <- 3:-2
-###   assign(key, value, envir=env)
-###   x <- new("SparseList", length=100L, env=env)
-###   length(x)
-###   ls(x)
-###   ls(x, all.names=TRUE)
-###   as.list(x)
-###   as.list(x, all.names=TRUE)
-###   x[[1]]
-###   x[[98]
-###   x[[101]]]
-###
-
-setMethod("length", "SparseList", function(x) x@length)
-
-### 'pos', 'envir' and 'pattern' args are ignored
-setMethod("ls", signature(name="SparseList"),
-    function(name, pos, envir, all.names=FALSE, pattern)
-    {
-        if (!all.names)
-            return(ls(name@env, all.names=TRUE))
-        seq_len(length(name))
-    }
-)
-
-setMethod("as.list", "SparseList",
-    function(x, all.names=FALSE, ...)
-    {
-        if (!all.names)
-            return(as.list(x@env, all.names=TRUE))
-        ans <- vector(mode="list", length=length(x))
-        symbols <- ls(x)
-        for (symb in symbols)
-            ans[[as.integer(symb)]] <- get(symb, envir=x@env)
-        ans
-    }
-)
-
-### Supported 'i' types: character or numeric vector of length 1.
-setMethod("[[", "SparseList",
-    function(x, i, j, ...)
-    {
-        if (!missing(j) || length(list(...)) > 0)
-            stop("invalid subsetting")
-        if (missing(i))
-            stop("subscript is missing")
-        if (!is.character(i) && !is.numeric(i))
-            stop("invalid subscript type")
-        if (length(i) < 1L)
-            stop("attempt to select less than one element")
-        if (length(i) > 1L)
-            stop("attempt to select more than one element")
-        if (is.na(i))
-            stop("subscript cannot be NA")
-        if (is.character(i))
-            return(get(i, envir=x@env))
-        if (!is.integer(i))
-            i <- as.integer(i)
-        if (i < 1L || i > length(x))
-            stop("subscript out of bounds")
-        i <- formatC(i, width=10, format="d", flag="0")
-        get(i, envir=x@env)
-    }
-)
-
-diff --git a/man/Biostrings-internals.Rd b/man/Biostrings-internals.Rd
-index 791b0870..609b7694 100644
--- a/man/Biostrings-internals.Rd
-+++ b/man/Biostrings-internals.Rd
-@@ -26,15 +26,6 @@
- \alias{make_XStringSet_from_strings}
- \alias{make_XStringSet_from_strings,XStringSet-method}
- 
-% SparseList class and methods:
-\alias{class:SparseList}
-\alias{SparseList-class}
-\alias{SparseList}
-
-\alias{length,SparseList-method}
-%\alias{ls,SparseList-method}
-\alias{as.list,SparseList-method}
-\alias{[[,SparseList-method}
- 
- \title{Biostrings internals}
- 
-diff --git a/src/Biostrings.h b/src/Biostrings.h
-index 6e725bd5..e86d0ff2 100644
--- a/src/Biostrings.h
-+++ b/src/Biostrings.h
-@@ -446,40 +446,6 @@ SEXP XStringSetList_unstrsplit(
- );
- 
- 
-/* SparseList_utils.c */
-
-SEXP _SparseList_int2symb(int symb_as_int);
-
-int _SparseList_symb2int(SEXP symbol);
-
-SEXP _get_val_from_env(
-	SEXP symbol,
-	SEXP env,
-	int error_on_unbound_value
-);
-
-SEXP _get_val_from_SparseList(
-	int symb_as_int,
-	SEXP env,
-	int error_on_unbound_value
-);
-
-int _get_int_from_SparseList(
-	int symb_as_int,
-	SEXP env
-);
-
-void _set_env_from_IntAE(
-	SEXP env,
-	const IntAE *int_ae
-);
-
-void _set_env_from_IntAEAE(
-	SEXP env,
-	const IntAEAE *int_aeae
-);
-
-
- /* match_reporting.c */
- 
- int _get_match_storing_code(const char *ms_mode);
-@@ -558,13 +524,6 @@ SEXP ByPos_MIndex_endIndex(
- 	SEXP x_width0
- );
- 
-SEXP SparseMIndex_endIndex(
-	SEXP x_ends_envir,
-	SEXP x_width0,
-	SEXP x_names,
-	SEXP all_names
-);
-
- SEXP ByPos_MIndex_combine(SEXP ends_listlist);
- 
- 
-diff --git a/src/MIndex_class.c b/src/MIndex_class.c
-index 00212fe9..dd6ad546 100644
--- a/src/MIndex_class.c
-+++ b/src/MIndex_class.c
-@@ -157,73 +157,6 @@ SEXP ByPos_MIndex_endIndex(SEXP x_high2low, SEXP x_ends, SEXP x_width0)
- 	return ans;
- }
- 
-/*
- * --- .Call ENTRY POINT ---
- * All the keys in 'x_ends_envir' must be representing integers left-padded with 0s
- * so they have the same length. This works properly:
-     library(Biostrings)
-     ends_envir <- new.env(parent=emptyenv())
-     ends_envir[['0000000010']] <- -2:1
-     ends_envir[['0000000004']] <- 9:6
-     .Call("SparseMIndex_endIndex",
-           ends_envir, NULL, letters[1:10], TRUE,
-           PACKAGE="Biostrings")
-     .Call("SparseMIndex_endIndex",
-           ends_envir, NULL, letters[1:10], FALSE,
-           PACKAGE="Biostrings")
- * but this doesn't:
-     ends_envir[['3']] <- 33L
-     .Call("SparseMIndex_endIndex",
-           ends_envir, NULL, letters[1:10], FALSE,
-           PACKAGE="Biostrings")
- */
-SEXP SparseMIndex_endIndex(SEXP x_ends_envir, SEXP x_width0, SEXP x_names, SEXP all_names)
-{
-	SEXP ans, ans_elt, ans_names, symbols, end;
-	int nelt, i, j;
-	IntAE *poffsets, *poffsets_order;
-
-	PROTECT(symbols = R_lsInternal(x_ends_envir, 1));
-	poffsets = new_IntAE_from_CHARACTER(symbols, -1);
-	nelt = IntAE_get_nelt(poffsets);
-	if (LOGICAL(all_names)[0]) {
-		PROTECT(ans = NEW_LIST(LENGTH(x_names)));
-		for (i = 0; i < nelt; i++) {
-			j = poffsets->elts[i];
-			end = _get_val_from_env(STRING_ELT(symbols, i), x_ends_envir, 1);
-			PROTECT(ans_elt = duplicate(end));
-			if (x_width0 != R_NilValue)
-				add_val_to_INTEGER(ans_elt, 1 - INTEGER(x_width0)[j]);
-			SET_ELEMENT(ans, j, ans_elt);
-			UNPROTECT(1);
-		}
-		SET_NAMES(ans, duplicate(x_names));
-		UNPROTECT(1);
-	} else {
-		//poffsets_order = new_IntAE(nelt, 0, 0);
-		//get_order_of_int_array(poffsets->elts, nelt, 0, 0,
-		//		       poffsets_order->elts, 0);
-		//IntAE_set_nelt(poffsets_order) = nelt; /* = poffsets_order->_buflength */
-		PROTECT(ans = NEW_LIST(nelt));
-		PROTECT(ans_names = NEW_CHARACTER(nelt));
-		for (i = 0; i < nelt; i++) {
-			//j = poffsets_order->elts[i];
-			j = i;
-			end = _get_val_from_env(STRING_ELT(symbols, j), x_ends_envir, 1);
-			PROTECT(ans_elt = duplicate(end));
-			if (x_width0 != R_NilValue)
-				add_val_to_INTEGER(ans_elt, 1 - INTEGER(x_width0)[i]);
-			SET_ELEMENT(ans, i, ans_elt);
-			UNPROTECT(1);
-			SET_STRING_ELT(ans_names, i, duplicate(STRING_ELT(x_names, poffsets->elts[j])));
-		}
-		SET_NAMES(ans, ans_names);
-		UNPROTECT(2);
-	}
-	UNPROTECT(1);
-	return ans;
-}
-
- /*
-  * --- .Call ENTRY POINT ---
-  */
-diff --git a/src/R_init_Biostrings.c b/src/R_init_Biostrings.c
-index 4d2943f8..c1410dbd 100644
--- a/src/R_init_Biostrings.c
-+++ b/src/R_init_Biostrings.c
-@@ -88,7 +88,6 @@ static const R_CallMethodDef callMethods[] = {
- 
- /* MIndex_class.c */
- 	CALLMETHOD_DEF(ByPos_MIndex_endIndex, 3),
-	CALLMETHOD_DEF(SparseMIndex_endIndex, 4),
- 	CALLMETHOD_DEF(ByPos_MIndex_combine, 1),
- 
- /* lowlevel_matching.c */
-diff --git a/src/SparseList_utils.c b/src/SparseList_utils.c
-deleted file mode 100644
-index 18597b55..00000000
--- a/src/SparseList_utils.c
-+++ /dev/null
-@@ -1,113 +0,0 @@
-/****************************************************************************
- *                        Fast SparseList utilities                         *
- *                            Author: H. Pag\`es                            *
- ****************************************************************************/
-#include "Biostrings.h"
-#include "S4Vectors_interface.h"
-
-
-SEXP _SparseList_int2symb(int symb_as_int)
-{
-	char symbbuf[11];
-
-	snprintf(symbbuf, sizeof(symbbuf), "%010d", symb_as_int);
-	return mkChar(symbbuf); /* UNPROTECTED! */
-}
-
-int _SparseList_symb2int(SEXP symbol)
-{
-	int symb_as_int;
-
-	sscanf(CHAR(symbol), "%d", &symb_as_int);
-	return symb_as_int;
-}
-
-/* 'symbol' must be a CHARSXP */
-SEXP _get_val_from_env(SEXP symbol, SEXP env, int error_on_unbound_value)
-{
-	SEXP ans;
-
-	/* The following code was inspired by R's do_get() code.
-	 * Note that do_get() doesn't use PROTECT at all and so do we...
-	 */
-	ans = findVar(install(translateChar(symbol)), env);
-	if (ans == R_UnboundValue) {
-		if (error_on_unbound_value)
-			error("Biostrings internal error in _get_val_from_env(): "
-			      "unbound value");
-		return R_UnboundValue;
-	}
-	if (TYPEOF(ans) == PROMSXP)
-		ans = eval(ans, env);
-	if (ans != R_NilValue && NAMED(ans) == 0)
-		SET_NAMED(ans, 1);
-	return ans;
-}
-
-SEXP _get_val_from_SparseList(int symb_as_int, SEXP env, int error_on_unbound_value)
-{
-	SEXP symbol, ans;
-
-	PROTECT(symbol = _SparseList_int2symb(symb_as_int));
-	ans = _get_val_from_env(symbol, env, error_on_unbound_value);
-	UNPROTECT(1);
-	return ans;
-}
-
-int _get_int_from_SparseList(int symb_as_int, SEXP env)
-{
-	SEXP value;
-	int val;
-
-	value = _get_val_from_SparseList(symb_as_int, env, 0);
-	if (value == R_UnboundValue)
-		return NA_INTEGER;
-	if (LENGTH(value) != 1)
-		error("Biostrings internal error in _get_int_from_SparseList(): "
-		      "value is not a single integer");
-	val = INTEGER(value)[0];
-	if (val == NA_INTEGER)
-		error("Biostrings internal error in _get_int_from_SparseList(): "
-		      "value is NA");
-	return val;
-}
-
-void _set_env_from_IntAE(SEXP env, const IntAE *int_ae)
-{
-	int nelt, symb_as_int, elt;
-	SEXP symbol, value;
-
-	nelt = IntAE_get_nelt(int_ae);
-	for (symb_as_int = 1; symb_as_int <= nelt; symb_as_int++)
-	{
-		elt = int_ae->elts[symb_as_int - 1];
-		if (elt == NA_INTEGER)
-			continue;
-		PROTECT(symbol = _SparseList_int2symb(symb_as_int));
-		PROTECT(value = ScalarInteger(elt));
-		defineVar(install(translateChar(symbol)), value, env);
-		UNPROTECT(2);
-	}
-	return;
-}
-
-void _set_env_from_IntAEAE(SEXP env, const IntAEAE *int_aeae)
-{
-	int nelt, symb_as_int;
-	IntAE *ae;
-	SEXP symbol, value;
-
-	nelt = IntAEAE_get_nelt(int_aeae);
-	for (symb_as_int = 1; symb_as_int <= nelt; symb_as_int++)
-	{
-		ae = int_aeae->elts[symb_as_int - 1];
-		if (IntAE_get_nelt(ae) == 0)
-			continue;
-		PROTECT(symbol = _SparseList_int2symb(symb_as_int));
-		PROTECT(value = new_INTEGER_from_IntAE(ae));
-		defineVar(install(translateChar(symbol)), value, env);
-		UNPROTECT(2);
-	}
-	return;
-}
-
@@ -1,142 +0,0 @@
-From 7fe34542bff0183c3a6a35a62df9035a71698eb2 Mon Sep 17 00:00:00 2001
-From: =?UTF-8?q?Herv=C3=A9=20Pag=C3=A8s?= <hpages.on.github@gmail.com>
-Date: Fri, 6 Mar 2026 15:54:23 -0800
-Subject: [PATCH] h5mread 1.3.2: Get rid of non-API calls to R
-
---
- DESCRIPTION                |  2 +-
- R/H5File-class.R           | 27 ++++++++++++++++-----------
- src/h5mread_index.c        |  5 +++--
- src/h5mread_startscounts.c |  3 ++-
- 4 files changed, 22 insertions(+), 15 deletions(-)
-
-diff --git a/R/H5File-class.R b/R/H5File-class.R
-index 2735166..6aeb80f 100644
--- a/R/H5File-class.R
-+++ b/R/H5File-class.R
-@@ -73,19 +73,23 @@
-     }
- }
- 
-.h5openfile <- function(filepath, s3=FALSE, s3credentials=NULL, use.rhdf5=FALSE)
-+.h5openfile <- function(filepath, readonly=TRUE,
-+                        s3=FALSE, s3credentials=NULL, use.rhdf5=FALSE)
- {
-     if (!isSingleString(filepath))
-         stop(wmsg("'filepath' must be a single string specifying ",
-                   "the path or URL to an HDF5 file"))
-+    if (!isTRUEorFALSE(readonly))
-+        stop(wmsg("'readonly' must be TRUE or FALSE"))
-     if (!isTRUEorFALSE(s3))
-         stop(wmsg("'s3' must be TRUE or FALSE"))
-
-+    if (s3 && !readonly)
-+        stop(wmsg("'readonly' must be set to TRUE when 's3' is TRUE"))
-     if (s3) {
-         ID <- .h5openS3file(filepath, s3credentials=s3credentials,
-                                       use.rhdf5=use.rhdf5)
-     } else {
-        ID <- .h5openlocalfile(filepath, readonly=TRUE, use.rhdf5=use.rhdf5)
-+        ID <- .h5openlocalfile(filepath, readonly=readonly, use.rhdf5=use.rhdf5)
-     }
-     ID
- }
-@@ -136,16 +140,16 @@
- 
- .ID_is_closed <- function(ID) { is.null(ID) || is.na(ID) }
- 
-.open_H5FileID_xp <- function(xp, filepath, s3=FALSE, s3credentials=NULL,
-                                            use.rhdf5=FALSE)
-+.open_H5FileID_xp <- function(xp, filepath, readonly=TRUE,
-+                              s3=FALSE, s3credentials=NULL, use.rhdf5=FALSE)
- {
-     ID <- .get_H5FileID_xp_ID(xp)
-     if (!.ID_is_closed(ID)) {
-         ## H5FileID object is already open.
-         return(FALSE)
-     }
-    ID <- .h5openfile(filepath, s3=s3, s3credentials=s3credentials,
-                                use.rhdf5=use.rhdf5)
-+    ID <- .h5openfile(filepath, readonly=readonly,
-+                      s3=s3, s3credentials=s3credentials, use.rhdf5=use.rhdf5)
-     .set_H5FileID_xp_ID(xp, ID)
-     TRUE
- }
-@@ -183,10 +187,11 @@ close.H5FileID <- function(con, ...)
-     .close_H5FileID_xp(con@xp, ..., use.rhdf5=con@from_rhdf5)
- }
- 
-H5FileID <- function(filepath, s3=FALSE, s3credentials=NULL, use.rhdf5=FALSE)
-+H5FileID <- function(filepath, readonly=TRUE,
-+                     s3=FALSE, s3credentials=NULL, use.rhdf5=FALSE)
- {
-    ID <- .h5openfile(filepath, s3=s3, s3credentials=s3credentials,
-                                use.rhdf5=use.rhdf5)
-+    ID <- .h5openfile(filepath, readonly=readonly,
-+                      s3=s3, s3credentials=s3credentials, use.rhdf5=use.rhdf5)
-     xp <- .new_H5FileID_xp(ID)
-     reg.finalizer(xp,
-                   function(e) .close_H5FileID_xp(e, use.rhdf5=use.rhdf5),
-@@ -272,7 +277,7 @@ H5File <- function(filepath, s3=FALSE, s3credentials=NULL, .no_rhdf5_h5id=FALSE)
-         rhdf5_h5id <- new("H5FileID")
-     } else {
-         rhdf5_h5id <- H5FileID(filepath, s3=s3, s3credentials=s3credentials,
-                                         use.rhdf5=TRUE)
-+                               use.rhdf5=TRUE)
-     }
-     if (!s3)
-         filepath <- file_path_as_absolute(filepath)
-diff --git a/src/h5mread_index.c b/src/h5mread_index.c
-index 7284815..ec93c25 100644
--- a/src/h5mread_index.c
-+++ b/src/h5mread_index.c
-@@ -9,6 +9,7 @@
- #include "h5mread_helpers.h"
- #include "TouchedChunks.h"
- 
-+#include <R_ext/Altrep.h>  /* only for DATAPTR_RW() */
- #include <stdlib.h>  /* for malloc, free */
- #include <string.h>  /* for memcmp */
- //#include <time.h>
-@@ -444,7 +445,7 @@ static int read_chunk_data_4_5(const H5DSetDescriptor *h5dset,
- 		const size_t *Rarray_dim, SEXP Rarray,
- 		int method, int use_H5Dread_chunk)
- {
-	void *out = DATAPTR(Rarray);
-+	void *out = DATAPTR_RW(Rarray);
- 	if (out == NULL)
- 		return -1;
- 
-@@ -874,7 +875,7 @@ static int read_data_6(const AllTChunks *all_tchunks,
- 	size_t *inner_nchip_buf = R_alloc0_size_t_array(ndim);
- 	LLongAEAE *inner_breakpoint_bufs = new_LLongAEAE(ndim, ndim);
- 
-	void *out = DATAPTR(Rarray);
-+	void *out = DATAPTR_RW(Rarray);
- 	if (out == NULL) {
- 		_destroy_TChunkIterator(&tchunk_iter);
- 		return -1;
-diff --git a/src/h5mread_startscounts.c b/src/h5mread_startscounts.c
-index de57fd5..959014f 100644
--- a/src/h5mread_startscounts.c
-+++ b/src/h5mread_startscounts.c
-@@ -8,6 +8,7 @@
- #include "uaselection.h"
- #include "h5mread_helpers.h"
- 
-+#include <R_ext/Altrep.h>  /* only for DATAPTR_RW() */
- #include <stdlib.h>  /* for malloc, free */
- //#include <time.h>
- 
-@@ -402,7 +403,7 @@ SEXP _h5mread_startscounts(const H5DSetDescriptor *h5dset,
- 	SEXP ans = PROTECT(allocVector(h5dset->h5type->Rtype, ans_len));
- 
- 	if (ans_len != 0) {
-		void *mem = DATAPTR(ans);
-+		void *mem = DATAPTR_RW(ans);
- 		if (mem == NULL)
- 			goto on_error;
- 
-- 
-2.52.0
-
@@ -1,67 +0,0 @@
-From a827c9fdeb77edefe6cca81bdb9e0344bc8d3742 Mon Sep 17 00:00:00 2001
-From: Sebastian Gibb <mail@sebastiangibb.de>
-Date: Sat, 13 Dec 2025 23:06:12 +0100
-Subject: [PATCH] fix: non-API call to R: SETLENGTH by using lengthgets
-
---
- DESCRIPTION  |  2 +-
- NEWS.md      |  6 ++++++
- src/join.c   | 12 ++++--------
- src/reduce.c |  6 ++----
- 4 files changed, 13 insertions(+), 13 deletions(-)
-
-diff --git a/src/join.c b/src/join.c
-index f13a703..3849fdf 100644
--- a/src/join.c
-+++ b/src/join.c
-@@ -111,12 +111,10 @@ SEXP C_join_inner(SEXP x, SEXP y, SEXP tolerance, SEXP nomatch) {
-             ++j;
-         }
-     }
-    SETLENGTH(rx, j);
-    SETLENGTH(ry, j);
-     SEXP out = PROTECT(allocVector(VECSXP, 2));
-     SEXP nms = PROTECT(allocVector(STRSXP, 2));
-    SET_VECTOR_ELT(out, 0, rx);
-    SET_VECTOR_ELT(out, 1, ry);
-+    SET_VECTOR_ELT(out, 0, lengthgets(rx, j));
-+    SET_VECTOR_ELT(out, 1, lengthgets(ry, j));
-     SET_STRING_ELT(nms, 0, mkChar("x"));
-     SET_STRING_ELT(nms, 1, mkChar("y"));
-     setAttrib(out, R_NamesSymbol, nms);
-@@ -201,12 +199,10 @@ SEXP C_join_outer(SEXP x, SEXP y, SEXP tolerance, SEXP nomatch) {
-         ++i;
-     }
- 
-    SETLENGTH(rx, i);
-    SETLENGTH(ry, i);
-     SEXP out = PROTECT(allocVector(VECSXP, 2));
-     SEXP nms = PROTECT(allocVector(STRSXP, 2));
-    SET_VECTOR_ELT(out, 0, rx);
-    SET_VECTOR_ELT(out, 1, ry);
-+    SET_VECTOR_ELT(out, 0, lengthgets(rx, i));
-+    SET_VECTOR_ELT(out, 1, lengthgets(ry, i));
-     SET_STRING_ELT(nms, 0, mkChar("x"));
-     SET_STRING_ELT(nms, 1, mkChar("y"));
-     setAttrib(out, R_NamesSymbol, nms);
-diff --git a/src/reduce.c b/src/reduce.c
-index 5f87966..8e48058 100644
--- a/src/reduce.c
-+++ b/src/reduce.c
-@@ -66,11 +66,9 @@ SEXP C_reduce(SEXP start, SEXP end, SEXP check) {
-         }
-     }
- 
-    SETLENGTH(rs, pos + 1);
-    SETLENGTH(re, pos + 1);
-     SEXP out = PROTECT(allocVector(VECSXP, 2));
-    SET_VECTOR_ELT(out, 0, rs);
-    SET_VECTOR_ELT(out, 1, re);
-+    SET_VECTOR_ELT(out, 0, lengthgets(rs, pos + 1));
-+    SET_VECTOR_ELT(out, 1, lengthgets(re, pos + 1));
- 
-     UNPROTECT(4);
- 
-- 
-2.52.0
-
@@ -1,114 +0,0 @@
-From 57dc6579d8b53af9e633016705fa9a1cbe58c8c8 Mon Sep 17 00:00:00 2001
-From: =?UTF-8?q?Herv=C3=A9=20Pag=C3=A8s?= <hpages.on.github@gmail.com>
-Date: Fri, 6 Mar 2026 16:48:20 -0800
-Subject: [PATCH] Rsamtools 2.27.1: Get rid of non-API calls to R
-
---
- DESCRIPTION     | 2 +-
- src/utilities.h | 3 +--
- 2 files changed, 2 insertions(+), 3 deletions(-)
-
-diff --git a/src/utilities.h b/src/utilities.h
-index bffb98f7..f9d5e09f 100644
--- a/src/utilities.h
-+++ b/src/utilities.h
-@@ -51,8 +51,7 @@ SEXP find_mate_within_groups(SEXP group_sizes,
- /* call-building macros */
- 
- #define NEW_CALL(S, T, NAME, ENV, N)            \
-    PROTECT(S = T = allocList(N));              \
-    SET_TYPEOF(T, LANGSXP);                     \
-+    PROTECT(S = T = LCONS(R_NilValue, allocList(N-1))); \
-     SETCAR(T, findFun(install(NAME), ENV));     \
-     T = CDR(T)
- #define CSET_CDR(T, NAME, VALUE)                \
-
-From 8cdec143023e8348a4f8bdc310acd609d14fe493 Mon Sep 17 00:00:00 2001
-From: =?UTF-8?q?Herv=C3=A9=20Pag=C3=A8s?= <hpages.on.github@gmail.com>
-Date: Fri, 6 Mar 2026 16:59:42 -0800
-Subject: [PATCH] oops, forgot to also get rid of non-API call to FORMALS()
-
---
- src/pileupbam.c | 2 +-
- 1 file changed, 1 insertion(+), 1 deletion(-)
-
-diff --git a/src/pileupbam.c b/src/pileupbam.c
-index f3256ba..7725628 100644
--- a/src/pileupbam.c
-+++ b/src/pileupbam.c
-@@ -655,7 +655,7 @@ SEXP apply_pileups(SEXP files, SEXP names, SEXP regions, SEXP param,
-     if (R_NilValue == regions)
-         Rf_error("'NULL' regions not (yet) supported");
-     _checkparams(regions, R_NilValue, R_NilValue);
-    if (!Rf_isFunction(callback) || 1L != Rf_length(FORMALS(callback)))
-+    if (!Rf_isFunction(callback) || 1L != Rf_length(R_ClosureFormals(callback)))
-         Rf_error("'callback' must be a function of 1 argument");
-     call = PROTECT(Rf_lang2(callback, R_NilValue));
- 
-
-From ee01a1f13f3b012b0717247d1f21580225b6f3a0 Mon Sep 17 00:00:00 2001
-From: vjcitn <stvjc@channing.harvard.edu>
-Date: Wed, 8 Apr 2026 14:04:26 -0400
-Subject: [PATCH] API solutions
-
---
- DESCRIPTION     |  2 +-
- src/tabixfile.c |  4 ++++
- src/utilities.c | 13 ++++++++++---
- 3 files changed, 15 insertions(+), 4 deletions(-)
-
-diff --git a/src/tabixfile.c b/src/tabixfile.c
-index 230a381..6f96568 100644
--- a/src/tabixfile.c
-+++ b/src/tabixfile.c
-@@ -187,8 +187,12 @@ SEXP index_tabix(SEXP filename, SEXP format, SEXP seq, SEXP begin, SEXP end,
-         LOGICAL(zeroBased)[0] == TRUE)
-         conf.preset |= TBX_UCSC;
- 
-+/* following is deprecated in HTSLIB with no precise replacement proposed */
-+/* seems unimportant */
-+/*
-     if (bgzf_is_bgzf(fn) != 1)
-         Rf_error("file does not appear to be bgzip'd");
-+*/
-     if (tbx_index_build(fn, 0, &conf) == -1)
-         Rf_error("index build failed");
- 
-diff --git a/src/utilities.c b/src/utilities.c
-index e224f91..d15c1d1 100644
--- a/src/utilities.c
-+++ b/src/utilities.c
-@@ -5,6 +5,13 @@
- #include "XVector_interface.h"
- #include <htslib/khash.h>
- 
-+#include <Rversion.h>
-+
-+#if R_VERSION < R_Version(4, 6, 0)
-+# define R_getVar(x,y,z) findVar(x,y)
-+#endif
-+
-+
- void *_Rs_Realloc_impl(void *p, size_t n, size_t t)
- {
-     /* R_Realloc(p, 0, *) fails inappropriately */
-@@ -30,7 +37,7 @@ SEXP _get_namespace(const char *pkg)
- void _as_strand(SEXP vec)
- {
-     SEXP nmspc = PROTECT(_get_namespace("Rsamtools"));
-    SEXP lvls = PROTECT(eval(findVar(install(".STRAND_LEVELS"), nmspc), nmspc));
-+    SEXP lvls = PROTECT(eval(R_getVar(install(".STRAND_LEVELS"), nmspc, TRUE), nmspc));
-     _as_factor_SEXP(vec, lvls);
-     UNPROTECT(2);
- }
-@@ -38,8 +45,8 @@ void _as_strand(SEXP vec)
- void _as_nucleotide(SEXP vec)
- {
-     SEXP nmspc = PROTECT(_get_namespace("Rsamtools"));
-    SEXP lvls = PROTECT(eval(findVar(install(".PILEUP_NUCLEOTIDE_LEVELS"),
-                                     nmspc), nmspc));
-+    SEXP lvls = PROTECT(eval(R_getVar(install(".PILEUP_NUCLEOTIDE_LEVELS"),
-+                                     nmspc, TRUE), nmspc));
-     _as_factor_SEXP(vec, lvls);
-     UNPROTECT(2);
- }
@@ -1,103 +0,0 @@
-From e39852a54312bbc6ba435848890cc2a7f612357c Mon Sep 17 00:00:00 2001
-From: =?UTF-8?q?Herv=C3=A9=20Pag=C3=A8s?= <hpages.on.github@gmail.com>
-Date: Fri, 6 Mar 2026 17:04:19 -0800
-Subject: [PATCH] ShortRead 1.69.3: Get rid of non-API calls to R
-
---
- DESCRIPTION |  2 +-
- src/call.h  |  3 +--
- src/io.c    | 10 +++++-----
- 3 files changed, 7 insertions(+), 8 deletions(-)
-
-diff --git a/src/call.h b/src/call.h
-index e15bb5e..e72bbd6 100644
--- a/src/call.h
-+++ b/src/call.h
-@@ -6,8 +6,7 @@ extern "C" {
- #endif
- 
- #define NEW_CALL(S, T, NAME, ENV, N)				\
-    PROTECT((S) = (T) = allocList((N)));			\
-    SET_TYPEOF((T), LANGSXP);                                   \
-+    PROTECT((S) = (T) = LCONS(R_NilValue, allocList((N)-1)));	\
-     SETCAR((T), findFun(install((NAME)), (ENV)));               \
-     (T) = CDR((T))
- #define CSET_CDR(T, NAME, VALUE)				\
-diff --git a/src/io.c b/src/io.c
-index 25a0111..9cf4bf8 100644
--- a/src/io.c
-+++ b/src/io.c
-@@ -46,9 +46,9 @@ SEXP write_fastq(SEXP id, SEXP sread, SEXP quality,
-                  SEXP fname, SEXP fmode, SEXP full, SEXP compress,
-                  SEXP max_width)
- {
-    if (!(IS_S4_OBJECT(id) && strcmp(get_classname(id), "BStringSet") == 0))
-+    if (!(Rf_isS4(id) && strcmp(get_classname(id), "BStringSet") == 0))
-         Rf_error("'%s' must be '%s'", "id", "BStringSet");
-    if (!(IS_S4_OBJECT(sread) &&
-+    if (!(Rf_isS4(sread) &&
-           strcmp(get_classname(sread), "DNAStringSet") == 0))
-         Rf_error("'%s' must be '%s'", "sread", "DNAStringSet");
-     /* check in R -- C-level R_check_super... is not adequate */
-@@ -693,14 +693,14 @@ int _solexa_export_make_id(SEXP result)
-         *x = INTEGER(VECTOR_ELT(result, SLX_X)),
-         *y = INTEGER(VECTOR_ELT(result, SLX_Y)), *pairedReadNumber = NULL;
-     const SEXP
-        * run = STRING_PTR(VECTOR_ELT(result, SLX_RUN)),
-+        * run = STRING_PTR_RO(VECTOR_ELT(result, SLX_RUN)),
-         *multiplexIndex = NULL,
-        *machine = STRING_PTR(VECTOR_ELT(result, SLX_MACHINE));
-+        *machine = STRING_PTR_RO(VECTOR_ELT(result, SLX_MACHINE));
-     const Rboolean
-         withMultiplexIndex = R_NilValue != VECTOR_ELT(result, SLX_MULTIPLEX),
-         withPairedReadNumber = R_NilValue != VECTOR_ELT(result, SLX_PAIRID);
-     if (withMultiplexIndex)
-        multiplexIndex = STRING_PTR(VECTOR_ELT(result, SLX_MULTIPLEX));
-+        multiplexIndex = STRING_PTR_RO(VECTOR_ELT(result, SLX_MULTIPLEX));
-     if (withPairedReadNumber)
-         pairedReadNumber = INTEGER(VECTOR_ELT(result, SLX_PAIRID));
- 
-- 
-2.52.0
-
-
-From 2e3368a35e3955a0a92b7f3e2c8dface6709d135 Mon Sep 17 00:00:00 2001
-From: vjcitn <stvjc@channing.harvard.edu>
-Date: Thu, 16 Apr 2026 16:54:15 +0000
-Subject: [PATCH] fixapi
-
---
- src/util.c | 10 +++++++++-
- 1 file changed, 9 insertions(+), 1 deletion(-)
-
-diff --git a/src/util.c b/src/util.c
-index 4a10a90..59c089b 100644
--- a/src/util.c
-+++ b/src/util.c
-@@ -6,6 +6,14 @@ unsigned char _bDecode(char);
- unsigned char _dnaDecode(char);
- unsigned char _rnaDecode(char);
- 
-+
-+#include <Rversion.h>
-+
-+#if R_VERSION < R_Version(4, 6, 0)
-+# define R_getVar(x,y,z) findVar(x,y)
-+#endif
-+
-+
- /*
-  * Encode / decode XString wrappers
-  */
-@@ -80,7 +88,7 @@ SEXP _get_namespace(const char *pkg)
- SEXP _get_strand_levels()
- {
-     SEXP nmspc = PROTECT(_get_namespace("ShortRead"));
-    SEXP ans = eval(findVar(install(".STRAND_LEVELS"), nmspc), nmspc);
-+    SEXP ans = eval(R_getVar(install(".STRAND_LEVELS"), nmspc, TRUE), nmspc);
-     UNPROTECT(1);
-     return ans;
- }
-- 
-2.52.0
-
@@ -1,412 +0,0 @@
-From 803cda41994a22890e0a6e379e6588084d4bc91b Mon Sep 17 00:00:00 2001
-From: vjcitn <stvjc@channing.harvard.edu>
-Date: Fri, 13 Mar 2026 04:04:59 -0400
-Subject: [PATCH 1/2] fixed non-API except for IS_S4_OBJECT
-
---
- src/bind.c             |  8 ++++----
- src/glm_test_R.c       | 20 ++++++++++----------
- src/imputation.c       |  8 ++++----
- src/input.c            |  2 +-
- src/plink.c            |  2 +-
- src/read_uncertain.c   |  4 ++--
- src/readped.c          |  2 +-
- src/single_snp_tests.c |  8 ++++----
- src/snp_summary.c      |  8 ++++----
- src/snpmpy.c           |  8 ++++----
- src/structure.c        |  4 ++--
- src/subset.c           |  2 +-
- src/switch.c           |  2 +-
- src/tdt.c              |  8 ++++----
- src/testBig.c          |  2 +-
- 15 files changed, 44 insertions(+), 44 deletions(-)
-
-diff --git a/src/bind.c b/src/bind.c
-index 44b1536..fa87e7c 100644
--- a/src/bind.c
-+++ b/src/bind.c
-@@ -19,7 +19,7 @@ SEXP snp_rbind(SEXP args) {
-     const SEXP This = CAR(args);
-     Class = getAttrib(This, R_ClassSymbol);
-     if (TYPEOF(Class) != STRSXP) {
-      Class = R_data_class(This, FALSE);
-+      Class = R_class(This);
-     }
-     const char *cli = CHAR(STRING_ELT(Class, 0));
-     if(!IS_S4_OBJECT(This)) {
-@@ -66,7 +66,7 @@ SEXP snp_rbind(SEXP args) {
-   SEXP Result, Rnames, Dnames, Diploid = R_NilValue;
-   PROTECT(Result = allocMatrix(RAWSXP, nr, nc));
-   classgets(Result, duplicate(Class));
-  SET_S4_OBJECT(Result);
-+  Rf_asS4(Result, TRUE, 0);
-   PROTECT(Rnames = allocVector(STRSXP, nr));
-   PROTECT(Dnames = allocVector(VECSXP, 2));
-   SET_VECTOR_ELT(Dnames, 0, Rnames);
-@@ -148,7 +148,7 @@ SEXP snp_cbind(SEXP args) {
-     SEXP This = CAR(args);
-     Class = getAttrib(This, R_ClassSymbol);
-     if (TYPEOF(Class) != STRSXP) {
-      Class = R_data_class(This, FALSE);
-+      Class = R_class(This);
-     }
-     const char *cli = CHAR(STRING_ELT(Class, 0));
-     if(!IS_S4_OBJECT(This)) {
-@@ -205,7 +205,7 @@ SEXP snp_cbind(SEXP args) {
-   SEXP Result, Cnames, Dnames;
-   PROTECT(Result = allocMatrix(RAWSXP, nr, nc));
-   classgets(Result, duplicate(Class));
-  SET_S4_OBJECT(Result);
-+  Rf_asS4(Result, TRUE, 0);
-   PROTECT(Dnames = allocVector(VECSXP, 2));
-   setAttrib(Result, R_DimNamesSymbol, Dnames);
-   PROTECT(Cnames = allocVector(STRSXP, nc));
-diff --git a/src/glm_test_R.c b/src/glm_test_R.c
-index d865182..dc8ebef 100644
--- a/src/glm_test_R.c
-+++ b/src/glm_test_R.c
-@@ -19,8 +19,8 @@ SEXP snp_lhs_score(const SEXP Y, const SEXP X, const SEXP Stratum,
- 
-   /* Y should be a SnpMatrix or an XSnpMatrix */
-   const char *classY = NULL;
-  if (TYPEOF(R_data_class(Y, FALSE)) == STRSXP) {
-    classY = CHAR(STRING_ELT(R_data_class(Y, FALSE), 0));
-+  if (TYPEOF(R_class(Y)) == STRSXP) {
-+    classY = CHAR(STRING_ELT(R_class(Y), 0));
-   } else {
-     classY = CHAR(STRING_ELT(getAttrib(Y, R_ClassSymbol), 0));
-   }
-@@ -431,8 +431,8 @@ SEXP snp_rhs_score(SEXP Y, SEXP family, SEXP link,
-   /* Z should be a SnpMatrix or an XSnpMatrix */
- 
-   const char *classZ = NULL;
-  if (TYPEOF(R_data_class(Z, FALSE)) == STRSXP) {
-    classZ = CHAR(STRING_ELT(R_data_class(Z, FALSE), 0));
-+  if (TYPEOF(R_class(Z)) == STRSXP) {
-+    classZ = CHAR(STRING_ELT(R_class(Z), 0));
-   } else {
-     classZ = CHAR(STRING_ELT(getAttrib(Z, R_ClassSymbol), 0));
-   }
-@@ -1003,8 +1003,8 @@ SEXP snp_lhs_estimate(const SEXP Y, const SEXP X, const SEXP Stratum,
- 
-   /* Y should be a SnpMatrix or an XSnpMatrix */
-   const char *classY = NULL;
-  if (TYPEOF(R_data_class(Y, FALSE)) == STRSXP) {
-    classY = CHAR(STRING_ELT(R_data_class(Y, FALSE), 0));
-+  if (TYPEOF(R_class(Y)) == STRSXP) {
-+    classY = CHAR(STRING_ELT(R_class(Y), 0));
-   } else {
-     classY = CHAR(STRING_ELT(getAttrib(Y, R_ClassSymbol), 0));
-   }
-@@ -1286,7 +1286,7 @@ SEXP snp_lhs_estimate(const SEXP Y, const SEXP X, const SEXP Stratum,
-   LOGICAL(Lhs)[0] = 1;
-   setAttrib(Estimates, install("snpLHS"), Lhs);
-   UNPROTECT(6);
-  SET_S4_OBJECT(Estimates);
-+  Rf_asS4(Estimates, TRUE, 0);
-   return(Estimates);
- }
- 
-@@ -1360,8 +1360,8 @@ SEXP snp_rhs_estimate(SEXP Y, SEXP family, SEXP link,
- /* Z should be a SnpMatrix or an XSnpMatrix */
- 
-   const char *classZ = NULL;
-  if (TYPEOF(R_data_class(Z, FALSE)) == STRSXP) {
-    classZ = CHAR(STRING_ELT(R_data_class(Z, FALSE), 0));
-+  if (TYPEOF(R_class(Z)) == STRSXP) {
-+    classZ = CHAR(STRING_ELT(R_class(Z), 0));
-   } else {
-     classZ = CHAR(STRING_ELT(getAttrib(Z, R_ClassSymbol), 0));
-   }
-@@ -1724,7 +1724,7 @@ SEXP snp_rhs_estimate(SEXP Y, SEXP family, SEXP link,
- 
-   UNPROTECT(gen_names? 7: 6);
- 
-  SET_S4_OBJECT(Estimates);
-+  Rf_asS4(Estimates, TRUE, 0);
-   return(Estimates);
-   
- }
-diff --git a/src/imputation.c b/src/imputation.c
-index ff9403b..d796c1b 100644
--- a/src/imputation.c
-+++ b/src/imputation.c
-@@ -77,7 +77,7 @@ SEXP snp_impute(const SEXP X, const SEXP Y, const SEXP Xord, const SEXP Yord,
-   int *diploid = NULL;
-   SEXP cl = GET_CLASS(X);
-   if (TYPEOF(cl) != STRSXP) {
-    cl = R_data_class(X, FALSE); /* S4 way of getting class attribute */
-+    cl = R_class(X); /* S4 way of getting class attribute */
-   }
-   if (!strcmp(CHAR(STRING_ELT(cl, 0)), "XSnpMatrix")) {
-     SEXP Diploid = R_do_slot(X, mkString("diploid"));
-@@ -395,7 +395,7 @@ SEXP snp_impute(const SEXP X, const SEXP Y, const SEXP Xord, const SEXP Yord,
-   PROTECT(Maxpred = allocVector(INTSXP, 1));
-   INTEGER(Maxpred)[0] = maxpred;
-   setAttrib(Result, install("Max.predictors"), Maxpred);
-  SET_S4_OBJECT(Result);
-+  Rf_asS4(Result, TRUE, 0);
- 
-   /* Tidy up */
- 
-@@ -701,7 +701,7 @@ SEXP impute_snps(const SEXP Rules, const SEXP Snps, const SEXP Subset,
-   int *diploid_in=NULL, *diploid=NULL;
-   SEXP cl = GET_CLASS(Snps);
-   if (TYPEOF(cl) != STRSXP) {
-    cl = R_data_class(Snps, FALSE); /* S4 way of getting class attribute */
-+    cl = R_class(Snps); /* S4 way of getting class attribute */
-   }
-   if (!strcmp(CHAR(STRING_ELT(cl, 0)), "XSnpMatrix")) {
-     SEXP Diploid = R_do_slot(Snps, mkString("diploid"));
-@@ -753,7 +753,7 @@ SEXP impute_snps(const SEXP Rules, const SEXP Snps, const SEXP Subset,
-     SET_STRING_ELT(Package, 0, mkChar("snpStats"));
-     setAttrib(Class, install("package"), Package);
-     classgets(Result, Class);
-    SET_S4_OBJECT(Result);
-+    Rf_asS4(Result, TRUE, 0);
-   }
-   PROTECT(Dimnames = allocVector(VECSXP, 2));
-   SET_VECTOR_ELT(Dimnames, 0, VECTOR_ELT(names, 0));
-diff --git a/src/input.c b/src/input.c
-index 1d2a95b..60cdad8 100644
--- a/src/input.c
-+++ b/src/input.c
-@@ -330,7 +330,7 @@ SEXP insnp_new(const SEXP Filenames, const SEXP Sample_id, const SEXP Snp_id,
-   SET_STRING_ELT(Package, 0, mkChar("snpStats"));
-   setAttrib(Class, install("package"), Package);
-   classgets(Result, Class);
-  SET_S4_OBJECT(Result);
-+  Rf_asS4(Result, TRUE, 0);
-   unsigned char *result = RAW(Result);
-   memset(result, 0x00, Nsample*Nsnp);
- 
-diff --git a/src/plink.c b/src/plink.c
-index a413440..9095c2d 100644
--- a/src/plink.c
-+++ b/src/plink.c
-@@ -59,7 +59,7 @@ SEXP readbed(SEXP Bed, SEXP Id, SEXP Snps, SEXP Rsel, SEXP Csel) {
-   SET_STRING_ELT(Package, 0, mkChar("snpStats"));
-   setAttrib(Class, install("package"), Package);
-   classgets(Result, Class);
-  SET_S4_OBJECT(Result);
-+  Rf_asS4(Result, TRUE, 0);
-   
-   unsigned char *result = RAW(Result); 
-   R_xlen_t ncell = (R_xlen_t)nrow*(R_xlen_t)ncol;
-diff --git a/src/read_uncertain.c b/src/read_uncertain.c
-index 2e3b901..fd82617 100644
--- a/src/read_uncertain.c
-+++ b/src/read_uncertain.c
-@@ -137,7 +137,7 @@ SEXP read_mach(const SEXP Filename, const SEXP Colnames, const SEXP Nsubject) {
-   SET_STRING_ELT(Package, 0, mkChar("snpStats"));
-   setAttrib(Class, install("package"), Package);
-   classgets(Result, Class);
-  SET_S4_OBJECT(Result);
-+  Rf_asS4(Result, TRUE, 0);
-   UNPROTECT(2);
-  
-   /* Read in data */
-@@ -278,7 +278,7 @@ SEXP read_impute(const SEXP Filename, const SEXP Rownames, const SEXP Nsnp,
-   SET_STRING_ELT(Package, 0, mkChar("snpStats"));
-   setAttrib(Class, install("package"), Package);
-   classgets(Result, Class);
-  SET_S4_OBJECT(Result);
-+  Rf_asS4(Result, TRUE, 0);
-   UNPROTECT(2);
- 
-   char buffer[BUFFERSIZE];
-diff --git a/src/readped.c b/src/readped.c
-index 4e8563e..020d05f 100644
--- a/src/readped.c
-+++ b/src/readped.c
-@@ -327,7 +327,7 @@ SEXP readped(SEXP filename, SEXP snp_names, SEXP missing, SEXP X, SEXP sep) {
-   else
-     SET_STRING_ELT(SMClass, 0, mkChar("SnpMatrix"));
-   classgets(Smat, SMClass);
-  SET_S4_OBJECT(Smat);
-+  Rf_asS4(Smat, TRUE, 0);
-   PROTECT(DimNames = allocVector(VECSXP, 2));
-   SET_VECTOR_ELT(DimNames, 0, duplicate(Rnames));
-   protected += 2;
-diff --git a/src/single_snp_tests.c b/src/single_snp_tests.c
-index a242e17..08bd098 100644
--- a/src/single_snp_tests.c
-+++ b/src/single_snp_tests.c
-@@ -53,8 +53,8 @@ SEXP score_single(const SEXP Phenotype, const SEXP Stratum, const SEXP Snps,
-   /* SNPs ---- should be a SnpMatrix or an XSnpMatrix */
- 
-   const char *classS = NULL;
-  if (TYPEOF(R_data_class(Snps, FALSE)) == STRSXP) {
-    classS = CHAR(STRING_ELT(R_data_class(Snps, FALSE), 0));
-+  if (TYPEOF(R_class(Snps)) == STRSXP) {
-+    classS = CHAR(STRING_ELT(R_class(Snps), 0));
-   } else {
-     classS = CHAR(STRING_ELT(getAttrib(Snps, R_ClassSymbol), 0));
-   }
-@@ -108,8 +108,8 @@ SEXP score_single(const SEXP Phenotype, const SEXP Stratum, const SEXP Snps,
-   index_db name_index;
-   if (!isNull(Rules)) {
-     const char *classR = NULL;
-    if (TYPEOF(R_data_class(Rules, FALSE)) == STRSXP) {
-      classR = CHAR(STRING_ELT(R_data_class(Rules, FALSE), 0));
-+    if (TYPEOF(R_class(Rules)) == STRSXP) {
-+      classR = CHAR(STRING_ELT(R_class(Rules), 0));
-     } else {
-       classR = CHAR(STRING_ELT(getAttrib(Rules, R_ClassSymbol), 0));
-     }
-diff --git a/src/snp_summary.c b/src/snp_summary.c
-index 9b53693..6f181c9 100644
--- a/src/snp_summary.c
-+++ b/src/snp_summary.c
-@@ -47,8 +47,8 @@ SEXP X_snp_summary(const SEXP Snps, const SEXP Rules, const SEXP Uncertain) {
-   SEXP ruleNames = R_NilValue;
-   if (!isNull(Rules)) {
-     const char *classR = NULL;
-    if (TYPEOF(R_data_class(Rules, FALSE)) == STRSXP) {
-      classR = CHAR(STRING_ELT(R_data_class(Rules, FALSE), 0));
-+    if (TYPEOF(R_class(Rules)) == STRSXP) {
-+      classR = CHAR(STRING_ELT(R_class(Rules), 0));
-     } else {
-       classR = CHAR(STRING_ELT(getAttrib(Rules, R_ClassSymbol), 0));
-     }
-@@ -321,8 +321,8 @@ SEXP snp_summary(const SEXP Snps, const SEXP Rules, const SEXP Uncertain) {
-   SEXP ruleNames = R_NilValue;
-   if (!isNull(Rules)) {
-     const char *classR = NULL;
-    if (TYPEOF(R_data_class(Rules, FALSE)) == STRSXP) {
-      classR = CHAR(STRING_ELT(R_data_class(Rules, FALSE), 0));
-+    if (TYPEOF(R_class(Rules)) == STRSXP) {
-+      classR = CHAR(STRING_ELT(R_class(Rules), 0));
-     } else {
-       classR = CHAR(STRING_ELT(getAttrib(Rules, R_ClassSymbol), 0));
-     }
-diff --git a/src/snpmpy.c b/src/snpmpy.c
-index 2447048..56b84d9 100644
--- a/src/snpmpy.c
-+++ b/src/snpmpy.c
-@@ -34,7 +34,7 @@ SEXP snp_pre(const SEXP Snps, const SEXP Mat, const SEXP Frequency,
-   int *ifdiploid = NULL;
-   SEXP cl = GET_CLASS(Snps);
-   if (TYPEOF(cl) != STRSXP) {
-    cl = R_data_class(Snps, FALSE); /* S4 way of getting class attribute */
-+    cl = R_class(Snps); /* S4 way of getting class attribute */
-   }
-   if (!strcmp(CHAR(STRING_ELT(cl, 0)), "XSnpMatrix")) {
-     SEXP diploid = R_do_slot(Snps, mkString("diploid"));
-@@ -55,7 +55,7 @@ SEXP snp_pre(const SEXP Snps, const SEXP Mat, const SEXP Frequency,
- 
-   cl = GET_CLASS(Mat);
-   if (TYPEOF(cl) != STRSXP) {
-    cl = R_data_class(Mat, FALSE); /* S4 way of getting class attribute */
-+    cl = R_class(Mat); /* S4 way of getting class attribute */
-   }
-   if (strcmp(CHAR(STRING_ELT(cl, 0)), "matrix"))
-     error("Argument error - Mat wrong type");
-@@ -161,7 +161,7 @@ SEXP snp_post(const SEXP Snps, const SEXP Mat, const SEXP Frequency,
-   int *ifdiploid = NULL;
-   SEXP cl = GET_CLASS(Snps);
-   if (TYPEOF(cl) != STRSXP) {
-    cl = R_data_class(Snps, FALSE); /* S4 way of getting class attribute */
-+    cl = R_class(Snps); /* S4 way of getting class attribute */
-   }
-   if (!strcmp(CHAR(STRING_ELT(cl, 0)), "XSnpMatrix")) {
-     SEXP diploid = R_do_slot(Snps, mkString("diploid"));
-@@ -182,7 +182,7 @@ SEXP snp_post(const SEXP Snps, const SEXP Mat, const SEXP Frequency,
- 
-   cl = GET_CLASS(Mat);
-   if (TYPEOF(cl) != STRSXP) {
-    cl = R_data_class(Mat, FALSE); /* S4 way of getting class attribute */
-+    cl = R_class(Mat); /* S4 way of getting class attribute */
-   }
-   if (strcmp(CHAR(STRING_ELT(cl, 0)), "matrix"))
-     error("Argument error - Mat wrong type");
-diff --git a/src/structure.c b/src/structure.c
-index 2a05635..1f9b62e 100644
--- a/src/structure.c
-+++ b/src/structure.c
-@@ -66,7 +66,7 @@ SEXP xxt(const SEXP Snps, const SEXP Strata, const SEXP Correct_for_missing,
-   int *ifDiploid = NULL;
-   SEXP cl = GET_CLASS(Snps);
-   if (TYPEOF(cl) != STRSXP) {
-    cl = R_data_class(Snps, FALSE); /* S4 way of getting class attribute */
-+    cl = R_class(Snps); /* S4 way of getting class attribute */
-   }
-   if (!strcmp(CHAR(STRING_ELT(cl, 0)), "XSnpMatrix")) {
-     SEXP Diploid = R_do_slot(Snps, mkString("diploid"));
-@@ -409,7 +409,7 @@ SEXP ibs_count(const SEXP Snps, const SEXP Uncertain) {
-   int *ifDiploid = NULL;
-   SEXP cl = GET_CLASS(Snps);
-   if (TYPEOF(cl) != STRSXP) {
-    cl = R_data_class(Snps, FALSE); /* S4 way of getting class attribute */
-+    cl = R_class(Snps); /* S4 way of getting class attribute */
-   }
-   if (!strcmp(CHAR(STRING_ELT(cl, 0)), "XSnpMatrix")) {
-     SEXP Diploid = R_do_slot(Snps, mkString("diploid"));
-diff --git a/src/subset.c b/src/subset.c
-index cc7992d..4c2e2c4 100644
--- a/src/subset.c
-+++ b/src/subset.c
-@@ -55,7 +55,7 @@ SEXP subset(SEXP X, SEXP Rows, SEXP Cols) {
-   SET_STRING_ELT(Package, 0, mkChar("snpStats"));
-   setAttrib(Rclass, install("package"), Package);
-   setAttrib(Result, R_ClassSymbol, Rclass);
-  SET_S4_OBJECT(Result);
-+  Rf_asS4(Result, TRUE, 0);
-   PROTECT(Rdim = allocVector(INTSXP, 2));
-   int *rdim = INTEGER(Rdim);
-   rdim[0] = nrows;
-diff --git a/src/switch.c b/src/switch.c
-index 60f7e6c..e2a3287 100644
--- a/src/switch.c
-+++ b/src/switch.c
-@@ -16,7 +16,7 @@ SEXP test_switch(const SEXP Snps, const SEXP Snps2, const SEXP Split,
-   int *female = NULL;
-   SEXP cl = GET_CLASS(Snps);
-   if (TYPEOF(cl) != STRSXP) {
-    cl = R_data_class(Snps, FALSE); /* S4 way of getting class attribute */
-+    cl = R_class(Snps); /* S4 way of getting class attribute */
-   }
-   SEXP diploid = NULL;
-   if (!strcmp(CHAR(STRING_ELT(cl, 0)), "XSnpMatrix")) {
-diff --git a/src/tdt.c b/src/tdt.c
-index cece0d9..000d1c7 100644
--- a/src/tdt.c
-+++ b/src/tdt.c
-@@ -43,8 +43,8 @@ SEXP score_tdt(const SEXP Proband, const SEXP Father, const SEXP Mother,
-   /* SNPs ---- should be a SnpMatrix or an XSnpMatrix */
- 
-   const char *classS = NULL;
-  if (TYPEOF(R_data_class(Snps, FALSE)) == STRSXP) {
-    classS = CHAR(STRING_ELT(R_data_class(Snps, FALSE), 0));
-+  if (TYPEOF(R_class(Snps)) == STRSXP) {
-+    classS = CHAR(STRING_ELT(R_class(Snps), 0));
-   } else {
-     classS = CHAR(STRING_ELT(getAttrib(Snps, R_ClassSymbol), 0));
-   }
-@@ -84,8 +84,8 @@ SEXP score_tdt(const SEXP Proband, const SEXP Father, const SEXP Mother,
-   GTYPE **gt2ht = NULL;
-   if (!isNull(Rules)) {
-     const char *classR = NULL;
-    if (TYPEOF(R_data_class(Rules, FALSE)) == STRSXP) {
-      classR = CHAR(STRING_ELT(R_data_class(Rules, FALSE), 0));
-+    if (TYPEOF(R_class(Rules)) == STRSXP) {
-+      classR = CHAR(STRING_ELT(R_class(Rules), 0));
-     } else {
-       classR = CHAR(STRING_ELT(getAttrib(Rules, R_ClassSymbol), 0));
-     }
-diff --git a/src/testBig.c b/src/testBig.c
-index a6eb76f..3dca1da 100644
--- a/src/testBig.c
-+++ b/src/testBig.c
-@@ -18,7 +18,7 @@ SEXP snp_big(SEXP nrow, SEXP ncol) {
-   SET_STRING_ELT(Package, 0, mkChar("snpStats"));
-   setAttrib(Class, install("package"), Package);
-   classgets(Result, Class);
-  SET_S4_OBJECT(Result);
-+  Rf_asS4(Result, TRUE, 0);
- 
-   PROTECT(Dnames = allocVector(VECSXP, 2));
-   setAttrib(Result, R_DimNamesSymbol, Dnames);
-- 
-2.52.0
-
@@ -1,149 +0,0 @@
-From a505297e347aa72510ecfc83e7009668693e1260 Mon Sep 17 00:00:00 2001
-From: vjcitn <stvjc@channing.harvard.edu>
-Date: Fri, 13 Mar 2026 04:06:37 -0400
-Subject: [PATCH 2/2] fixed IS_S4_OBJECT
-
---
- src/bind.c             | 4 ++--
- src/fst.c              | 2 +-
- src/glm_test_R.c       | 8 ++++----
- src/single_snp_tests.c | 2 +-
- src/snp_summary.c      | 6 +++---
- src/tdt.c              | 2 +-
- 6 files changed, 12 insertions(+), 12 deletions(-)
-
-diff --git a/src/bind.c b/src/bind.c
-index fa87e7c..b3ef928 100644
--- a/src/bind.c
-+++ b/src/bind.c
-@@ -22,7 +22,7 @@ SEXP snp_rbind(SEXP args) {
-       Class = R_class(This);
-     }
-     const char *cli = CHAR(STRING_ELT(Class, 0));
-    if(!IS_S4_OBJECT(This)) {
-+    if(!Rf_isS4(This)) {
-       warning("rbinding SnpMatrix object without S4 object bit");
-     }
-     int nci = ncols(This);
-@@ -151,7 +151,7 @@ SEXP snp_cbind(SEXP args) {
-       Class = R_class(This);
-     }
-     const char *cli = CHAR(STRING_ELT(Class, 0));
-    if(!IS_S4_OBJECT(This)) {
-+    if(!Rf_isS4(This)) {
-       warning("cbinding SnpMatrix object without S4 object bit");
-     }
-     SEXP Di = R_NilValue;
-diff --git a/src/fst.c b/src/fst.c
-index bbc39c0..5451a51 100644
--- a/src/fst.c
-+++ b/src/fst.c
-@@ -23,7 +23,7 @@ SEXP Fst(SEXP Snps, SEXP Group, SEXP HapMap) {
-     ifX = 0; /* to avoid warning message */
-     error("Argument error - class(Snps)");
-   }
-  if(!IS_S4_OBJECT(Snps)) {
-+  if(!Rf_isS4(Snps)) {
-     error("Argument error - Snps is not S4 object");
-   }
- 
-diff --git a/src/glm_test_R.c b/src/glm_test_R.c
-index dc8ebef..fe9d9c8 100644
--- a/src/glm_test_R.c
-+++ b/src/glm_test_R.c
-@@ -24,7 +24,7 @@ SEXP snp_lhs_score(const SEXP Y, const SEXP X, const SEXP Stratum,
-   } else {
-     classY = CHAR(STRING_ELT(getAttrib(Y, R_ClassSymbol), 0));
-   }
-  if(!IS_S4_OBJECT(Y)) {
-+  if(!Rf_isS4(Y)) {
-     error("Y in snp_lhs_score is missing S4 Object bit");
-   }
-   int ifX = 0;
-@@ -443,7 +443,7 @@ SEXP snp_rhs_score(SEXP Y, SEXP family, SEXP link,
-     ifX = 1;
-   else 
-     error("Argument error - class(Z)");
-  if (!IS_S4_OBJECT(Z)) {
-+  if (!Rf_isS4(Z)) {
-     error("Z in snp_rhs_score is missing S4 Object bit");
-   }
-  
-@@ -1008,7 +1008,7 @@ SEXP snp_lhs_estimate(const SEXP Y, const SEXP X, const SEXP Stratum,
-   } else {
-     classY = CHAR(STRING_ELT(getAttrib(Y, R_ClassSymbol), 0));
-   }
-  if(!IS_S4_OBJECT(Y)) {
-+  if(!Rf_isS4(Y)) {
-     error("Y in snp_lhs_score is missing S4 Object bit");
-   }
-   int ifX = 0;
-@@ -1365,7 +1365,7 @@ SEXP snp_rhs_estimate(SEXP Y, SEXP family, SEXP link,
-   } else {
-     classZ = CHAR(STRING_ELT(getAttrib(Z, R_ClassSymbol), 0));
-   }
-  if(!IS_S4_OBJECT(Z)) {
-+  if(!Rf_isS4(Z)) {
-     error("Z in snp_rhs_score is missing S4 Object bit");
-   }
-   int ifX = 0;
-diff --git a/src/single_snp_tests.c b/src/single_snp_tests.c
-index 08bd098..b577300 100644
--- a/src/single_snp_tests.c
-+++ b/src/single_snp_tests.c
-@@ -67,7 +67,7 @@ SEXP score_single(const SEXP Phenotype, const SEXP Stratum, const SEXP Snps,
-     ifX = 0; /* to avoid warning message */
-     error("Argument error - class(Snps)");
-   }
-  if(!IS_S4_OBJECT(Snps)) {
-+  if(!Rf_isS4(Snps)) {
-     error("Argument error - Snps is not S4 object");
-   }
- 
-diff --git a/src/snp_summary.c b/src/snp_summary.c
-index 6f181c9..c2f1c73 100644
--- a/src/snp_summary.c
-+++ b/src/snp_summary.c
-@@ -24,7 +24,7 @@ SEXP X_snp_summary(const SEXP Snps, const SEXP Rules, const SEXP Uncertain) {
-   if (Snps == R_NilValue) {
-     error("Argument error - Snps = NULL");
-   }
-  if(!IS_S4_OBJECT(Snps)) {
-+  if(!Rf_isS4(Snps)) {
-     error("Argument error - Snps is not S4 object");
-   }
-   const unsigned char *snps = RAW(Snps);
-@@ -298,7 +298,7 @@ SEXP snp_summary(const SEXP Snps, const SEXP Rules, const SEXP Uncertain) {
-   if (Snps == R_NilValue) {
-     error("Argument error - Snps = NULL");
-   }
-  if(!IS_S4_OBJECT(Snps)) {
-+  if(!Rf_isS4(Snps)) {
-     error("Argument error - Snps is not S4 object");
-   }
-   const unsigned char *snps = RAW(Snps);
-@@ -538,7 +538,7 @@ SEXP row_summary(const SEXP Snps) {
-   if (Snps == R_NilValue) {
-     error("Argument error - Snps = NULL");
-   }
-  if(!IS_S4_OBJECT(Snps)) {
-+  if(!Rf_isS4(Snps)) {
-     error("Argument error - Snps is not S4 object");
-   }
-   const unsigned char *snps = RAW(Snps);
-diff --git a/src/tdt.c b/src/tdt.c
-index 000d1c7..634e1b3 100644
--- a/src/tdt.c
-+++ b/src/tdt.c
-@@ -57,7 +57,7 @@ SEXP score_tdt(const SEXP Proband, const SEXP Father, const SEXP Mother,
-     ifX = 0; /* to avoid warning message */
-     error("Argument error - class(Snps)");
-   }
-  if(!IS_S4_OBJECT(Snps)) {
-+  if(!Rf_isS4(Snps)) {
-     error("Argument error - Snps is not S4 object");
-   }
- 
-- 
-2.52.0
-
@@ -1,259 +0,0 @@
-From 633aa6e3f671e9b58b3508b3944ff0dd45f34f8a Mon Sep 17 00:00:00 2001
-From: =?UTF-8?q?Herv=C3=A9=20Pag=C3=A8s?= <hpages.on.github@gmail.com>
-Date: Thu, 5 Mar 2026 14:58:23 -0800
-Subject: [PATCH] SparseArray 1.11.11: Get rid of non-API calls to R
-
-From 65383c02f986832b1416c6ad39da800d8ced05df Mon Sep 17 00:00:00 2001
-From: =?UTF-8?q?Herv=C3=A9=20Pag=C3=A8s?= <hpages.on.github@gmail.com>
-Date: Tue, 31 Mar 2026 11:38:20 -0700
-Subject: [PATCH] SparseArray 1.11.13: Use R_getVar() instead of findVar() when
- R >= 4.6.0
-
---
- DESCRIPTION                     |  2 +-
- src/Makevars                    |  1 +
- src/Rvector_utils.c             | 15 ++++++++-------
- src/SparseArray_aperm.c         |  2 +-
- src/SparseArray_matrixStats.c   |  5 +++--
- src/SparseArray_subassignment.c |  6 +++---
- src/SparseVec.h                 |  3 ++-
- src/leaf_utils.c                |  5 +++--
- src/test.c                      |  3 +++
- 9 files changed, 25 insertions(+), 17 deletions(-)
-
-diff --git a/src/Makevars b/src/Makevars
-index 0ee3615..1c5b86e 100644
--- a/src/Makevars
-+++ b/src/Makevars
-@@ -1,2 +1,3 @@
-+## See https://cran.r-project.org/doc/manuals/r-release/R-exts.html#OpenMP-support
- PKG_CFLAGS = $(SHLIB_OPENMP_CFLAGS)
- PKG_LIBS = $(SHLIB_OPENMP_CFLAGS)
-diff --git a/src/Rvector_utils.c b/src/Rvector_utils.c
-index ad80168..7e61ac1 100644
--- a/src/Rvector_utils.c
-+++ b/src/Rvector_utils.c
-@@ -4,6 +4,7 @@
-  ****************************************************************************/
- #include "Rvector_utils.h"
- 
-+#include <R_ext/Altrep.h>  /* only for DATAPTR_RW() */
- #include <string.h>  /* for memset() and memcpy() */
- 
- 
-@@ -242,7 +243,7 @@ void _fill_Rvector_block_with_val(SEXP Rvector,
- 				     (const SEXP) val);
- 		return;
- 	}
-	_set_elts_to_val(TYPEOF(Rvector), DATAPTR(Rvector),
-+	_set_elts_to_val(TYPEOF(Rvector), DATAPTR_RW(Rvector),
- 			 block_offset, block_len, val);
- }
- 
-@@ -260,7 +261,7 @@ void _fill_Rvector_block_with_zeros(SEXP Rvector,
- 				     R_NilValue);
- 		return;
- 	}
-	_set_elts_to_zero(Rtype, DATAPTR(Rvector), block_offset, block_len);
-+	_set_elts_to_zero(Rtype, DATAPTR_RW(Rvector), block_offset, block_len);
- 	return;
- }
- 
-@@ -268,7 +269,7 @@ void _fill_Rvector_block_with_zeros(SEXP Rvector,
- void _fill_Rvector_block_with_ones(SEXP Rvector,
- 		R_xlen_t block_offset, R_xlen_t block_len)
- {
-	_set_elts_to_one(TYPEOF(Rvector), DATAPTR(Rvector),
-+	_set_elts_to_one(TYPEOF(Rvector), DATAPTR_RW(Rvector),
- 			 block_offset, block_len);
- 	return;
- }
-@@ -277,7 +278,7 @@ void _fill_Rvector_block_with_ones(SEXP Rvector,
- void _fill_Rvector_block_with_minus_one(SEXP Rvector,
- 		R_xlen_t block_offset, R_xlen_t block_len)
- {
-	_set_elts_to_minus_one(TYPEOF(Rvector), DATAPTR(Rvector),
-+	_set_elts_to_minus_one(TYPEOF(Rvector), DATAPTR_RW(Rvector),
- 			 block_offset, block_len);
- 	return;
- }
-@@ -293,7 +294,7 @@ void _fill_Rvector_block_with_NA(SEXP Rvector,
- 					  NA_STRING);
- 		return;
- 	}
-	_set_elts_to_NA(Rtype, DATAPTR(Rvector), block_offset, block_len);
-+	_set_elts_to_NA(Rtype, DATAPTR_RW(Rvector), block_offset, block_len);
- 	return;
- }
- 
-@@ -460,7 +461,7 @@ void _fill_Rvector_subset_with_zeros(SEXP Rvector,
- 				R_NilValue);
- 		return;
- 	}
-	_set_selected_elts_to_zero(Rtype, DATAPTR(Rvector),
-+	_set_selected_elts_to_zero(Rtype, DATAPTR_RW(Rvector),
- 				selection, selection_len, selection_offset);
- 	return;
- }
-@@ -470,7 +471,7 @@ void _fill_Rvector_subset_with_ones(SEXP Rvector,
- 		const int *selection, int selection_len,
- 		R_xlen_t selection_offset)
- {
-	_set_selected_elts_to_one(TYPEOF(Rvector), DATAPTR(Rvector),
-+	_set_selected_elts_to_one(TYPEOF(Rvector), DATAPTR_RW(Rvector),
- 				  selection, selection_len, selection_offset);
- 	return;
- }
-diff --git a/src/SparseArray_aperm.c b/src/SparseArray_aperm.c
-index 0bd092e..bbeaf2c 100644
--- a/src/SparseArray_aperm.c
-+++ b/src/SparseArray_aperm.c
-@@ -721,7 +721,7 @@ static SEXP REC_grow_output_tree(const int *dim, int ndim,
- 	const type *nzvals_p = NULL;  /* -Wmaybe-uninitialized */	\
- 	type v;								\
- 	if (nzvals != R_NilValue) {  /* standard leaf */		\
-		nzvals_p = (const type *) DATAPTR(nzvals);		\
-+		nzvals_p = DATAPTR_RO(nzvals);				\
- 	} else {  /* lacunar leaf */					\
- 		v = type ## 1;						\
- 	}								\
-diff --git a/src/SparseArray_matrixStats.c b/src/SparseArray_matrixStats.c
-index b626553..debacf6 100644
--- a/src/SparseArray_matrixStats.c
-+++ b/src/SparseArray_matrixStats.c
-@@ -16,6 +16,7 @@
- #include "leaf_utils.h"
- #include "SparseArray_summarization.h"
- 
-+#include <R_ext/Altrep.h>  /* only for DATAPTR_RW() */
- #include <string.h>  /* for memcpy() and memset() */
- 
- 
-@@ -272,7 +273,7 @@ SEXP C_colStats_SVT(SEXP x_dim, SEXP x_dimnames, SEXP x_type,
- 	int warn = 0;
- 	REC_colStats_SVT(x_SVT, x_bg_is_na, INTEGER(x_dim), LENGTH(x_dim),
- 			 &summarize_op,
-			 DATAPTR(ans), ans_Rtype,
-+			 DATAPTR_RW(ans), ans_Rtype,
- 			 out_incs, ans_ndim, pardim,
- 			 &warn);
- 	if (warn)
-@@ -1175,7 +1176,7 @@ SEXP C_rowStats_SVT(SEXP x_dim, SEXP x_dimnames, SEXP x_type,
- 		SVT_rowMinsMaxs(x_SVT, x_Rtype, x_bg_is_na,
- 			INTEGER(x_dim), LENGTH(x_dim),
- 			opcode, narm,
-			DATAPTR(ans), LENGTH(ans), ans_Rtype,
-+			DATAPTR_RW(ans), LENGTH(ans), ans_Rtype,
- 			out_incs, ans_ndim, nstrata);
- 		break;
- 	    case SUM_OPCODE:
-diff --git a/src/SparseArray_subassignment.c b/src/SparseArray_subassignment.c
-index 4cf1c3d..c3b2d5e 100644
--- a/src/SparseArray_subassignment.c
-+++ b/src/SparseArray_subassignment.c
-@@ -966,13 +966,13 @@ static inline int next_coords0(NindexIterator *Nindex_iter)
- 		midx_p++;
- 		coords0_p++;
- 	}
-	printf("coords0: ");
-+	//printf("coords0: ");
- 	coords0_p = Nindex_iter->coords0_buf;
- 	for (along = Nindex_iter->margin; along < Nindex_iter->ndim; along++) {
-		printf(" %3d", *coords0_p);
-+		//printf(" %3d", *coords0_p);
- 		coords0_p++;
- 	}
-	printf("\n");
-+	//printf("\n");
- 	return 1;
- }
- 
-diff --git a/src/SparseVec.h b/src/SparseVec.h
-index 894709b..73cd841 100644
--- a/src/SparseVec.h
-+++ b/src/SparseVec.h
-@@ -5,6 +5,7 @@
- 
- #include "Rvector_utils.h"
- 
-+#include <R_ext/Altrep.h>  /* only for DATAPTR_RW() */
- #include <limits.h>  /* for INT_MAX */
- 
- 
-@@ -122,7 +123,7 @@ static inline SparseVec toSparseVec(SEXP nzvals, SEXP nzoffs,
- 		if (IS_STRSXP_OR_VECSXP(Rtype)) {
- 			sv.nzvals = nzvals;
- 		} else {
-			sv.nzvals = DATAPTR(nzvals);
-+			sv.nzvals = DATAPTR_RW(nzvals);
- 		}
- 	}
- 	sv.nzoffs = INTEGER(nzoffs);
-diff --git a/src/leaf_utils.c b/src/leaf_utils.c
-index e8066c3..c5ff3aa 100644
--- a/src/leaf_utils.c
-+++ b/src/leaf_utils.c
-@@ -10,6 +10,7 @@
- #include "SparseVec_subsetting.h"
- #include "SparseVec_subassignment.h"
- 
-+#include <R_ext/Altrep.h>  /* only for DATAPTR_RW() */
- #include <string.h>  /* for memcpy() */
- 
- 
-@@ -129,7 +130,7 @@ SEXP _make_leaf_from_two_arrays(SEXPTYPE Rtype,
- 			return ans;
- 		}
- 		ans_nzvals = PROTECT(allocVector(Rtype, nzcount));
-		memcpy(DATAPTR(ans_nzvals), nzvals_p, Rtype_size * nzcount);
-+		memcpy(DATAPTR_RW(ans_nzvals), nzvals_p, Rtype_size * nzcount);
- 	}
- 	SEXP ans = zip_leaf(ans_nzvals, ans_nzoffs, 0);
- 	UNPROTECT(2);
-@@ -156,7 +157,7 @@ static SEXP make_leaf_from_Rvector_subset(SEXP Rvector,
- 
- 	if (avoid_copy_if_all_selected &&
- 	    selection_offset == 0 && selection_len == XLENGTH(Rvector) &&
-	    ATTRIB(Rvector) == R_NilValue)
-+	    !ANY_ATTRIB(Rvector))
- 	{
- 		/* The full 'Rvector' is selected so can be reused as-is
- 		   with no need to copy the selected elements to a new SEXP. */
-diff --git a/src/test.c b/src/test.c
-index 493538f..2205fa2 100644
--- a/src/test.c
-+++ b/src/test.c
-@@ -111,6 +111,9 @@ SEXP C_simple_omp_parallel_for_loop(SEXP nloop)
- 	for (int i = 0; i < INTEGER(nloop)[0]; i++) {
- #ifdef _OPENMP
- 		int thread_num = omp_get_thread_num();
-+		/* Can't use Rprintf() here because it's not thread-safe (it
-+		   can trigger R's garbage collector which itself is not
-+		   thread-safe). */
- 		printf("thread_num = %d\n", thread_num);
- #endif
- 	}
-diff --git a/src/readSparseCSV.c b/src/readSparseCSV.c
-index a3d8da0..de1cb95 100644
--- a/src/readSparseCSV.c
-+++ b/src/readSparseCSV.c
-@@ -11,6 +11,7 @@
- #include "ExtendableJaggedArray.h"
- 
- #include <R_ext/Connections.h>
-+#include <Rversion.h>
- 
- #include <string.h>  /* for memcpy() */
- 
-@@ -111,7 +112,11 @@ static SEXP dump_env_as_list_or_R_NilValue(SEXP env, int ans_len)
- 	is_empty = 1;
- 	for (i = 0; i < ans_len; i++) {
- 		key = PROTECT(idx0_to_key(i));
-+#if R_VERSION < R_Version(4, 6, 0)
- 		ans_elt = findVar(install(translateChar(key)), env);
-+#else
-+		ans_elt = R_getVar(install(translateChar(key)), env, FALSE);
-+#endif
- 		UNPROTECT(1);
- 		if (ans_elt == R_UnboundValue)
- 			continue;
@@ -0,0 +1,46 @@
+From 1654599ea228efdd7b378ff44ed4e19d547641e0 Mon Sep 17 00:00:00 2001
+From: Bradley Lowekamp <blowekamp@mail.nih.gov>
+Date: Wed, 29 Apr 2026 16:22:49 +0000
+Subject: [PATCH 1/8] BUG: Replace removed CLOENV with R_ClosureEnv for R 4.6.0
+ compatibility
+
+R 4.6.0 removed the non-API macro CLOENV from its public headers.
+The replacement R_ClosureEnv() was added in R 4.5.0. Add a version-
+guarded backport so that builds against older R versions (< 4.5.0)
+continue to work.
+
+Fixes #2574
+---
+ Wrapping/R/sitkRCommand.cxx | 7 ++++++-
+ 1 file changed, 6 insertions(+), 1 deletion(-)
+
+diff --git a/Wrapping/R/sitkRCommand.cxx b/Wrapping/R/sitkRCommand.cxx
+index 216a9327b8..c3a62bead9 100644
+--- a/Wrapping/R/sitkRCommand.cxx
+++ b/Wrapping/R/sitkRCommand.cxx
+@@ -19,10 +19,15 @@
+ // The python header defines _POSIX_C_SOURCE without a preceding #undef
+ #include <iostream>
+ #include <Rinternals.h>
+#include <Rversion.h>
+ 
+ #include "sitkRCommand.h"
+ #include "sitkExceptionObject.h"
+ 
+// R_ClosureEnv was added in R 4.5.0, CLOENV was removed in R 4.6.0
+#if R_VERSION < R_Version(4, 5, 0)
+#  define R_ClosureEnv(x) CLOENV(x)
+#endif
+ 
+ namespace itk
+ {
+@@ -86,7 +91,7 @@ RCommand::SetFunctionClosure(SEXP FN)
+     // element
+     R_fcall = PROTECT(Rf_lang1(this->m_FunctionClosure));
+     this->SetCallbackRCallable(R_fcall);
+-    this->SetCallbackREnviron(CLOENV(this->m_FunctionClosure));
+    this->SetCallbackREnviron(R_ClosureEnv(this->m_FunctionClosure));
+     UNPROTECT(1);
+   }
+ }
+
@@ -0,0 +1,171 @@
+From 494259f19b3ca4ad0b11c858bc3ba9b587fa2ed5 Mon Sep 17 00:00:00 2001
+From: Bradley Lowekamp <blowekamp@mail.nih.gov>
+Date: Thu, 30 Apr 2026 16:09:54 +0000
+Subject: [PATCH 1/2] [R] Fix compilation with R 4.6.0 which removed non-API
+ macros #3407
+
+R 4.6.0 (April 2025) removed the non-API macro SET_S4_OBJECT and made
+CHARACTER_POINTER return a const pointer, breaking compilation of SWIG
+generated R code.
+
+Replace with proper R API equivalents:
+- SET_S4_OBJECT(x) -> x = Rf_asS4(x, TRUE, 0)  (3 sites in rrun.swg)
+- CHARACTER_POINTER(v)[i] = ... -> SET_STRING_ELT(v, i, ...)  (2 sites in std_vector.i)
+- CHARACTER_POINTER() via pstr -> STRING_ELT(, i) directly  (argcargv.i)
+
+All replacement APIs have been available since R 2.x so no version
+guards are required.
+---
+ CHANGES.current    | 6 ++++++
+ Lib/r/argcargv.i   | 4 +---
+ Lib/r/rrun.swg     | 6 +++---
+ Lib/r/std_vector.i | 4 ++--
+ 4 files changed, 12 insertions(+), 8 deletions(-)
+
+diff --git a/Lib/r/argcargv.i b/Lib/r/argcargv.i
+index 73380f4e2c9..af7aa14d66c 100644
+--- a/Lib/r/argcargv.i
+++ b/Lib/r/argcargv.i
+@@ -14,7 +14,6 @@
+ %}
+ %typemap(in) (int ARGC, char **ARGV) {
+   $1_ltype i;
+-  SEXP *pstr;
+   if ($input == R_NilValue) {
+     /* Empty array */
+     $1 = 0;
+@@ -22,14 +21,13 @@
+     SWIG_exception_fail(SWIG_RuntimeError, "Wrong array type.");
+   } else {
+     $1 = Rf_length($input);
+-    pstr = CHARACTER_POINTER($input);
+   }
+   $2 = ($2_ltype) malloc(($1+1)*sizeof($*2_ltype));
+   if ($2 == NULL) {
+     SWIG_exception_fail(SWIG_MemoryError, "Memory allocation failed.");
+   }
+   for (i = 0; i < $1; i++) {
+-    $2[i] = ($*2_ltype)STRING_VALUE(pstr[i]);
+    $2[i] = ($*2_ltype)STRING_VALUE(STRING_ELT($input, i));
+   }
+   $2[i] = NULL;
+ }
+diff --git a/Lib/r/rrun.swg b/Lib/r/rrun.swg
+index 4c03d5884d7..5dee391f32f 100644
+--- a/Lib/r/rrun.swg
+++ b/Lib/r/rrun.swg
+@@ -267,7 +267,7 @@ SWIG_MakePtr(void *ptr, const char *typeName, int flags)
+     R_RegisterCFinalizer(external, R_SWIG_ReferenceFinalizer);
+ 
+   r_obj = SET_SLOT(r_obj, Rf_mkString((char *) "ref"), external);
+-  SET_S4_OBJECT(r_obj);
+  r_obj = Rf_asS4(r_obj, TRUE, 0);
+   Rf_unprotect(2);
+ 
+   return(r_obj);
+@@ -285,7 +285,7 @@ R_SWIG_create_SWIG_R_Array(const char *typeName, SEXP ref, int len)
+    Rf_protect(arr = R_do_slot_assign(arr, Rf_mkString("dims"), Rf_ScalarInteger(len)));
+ 
+    Rf_unprotect(3); 			   
+-   SET_S4_OBJECT(arr);	
+   arr = Rf_asS4(arr, TRUE, 0);
+    return arr;
+ }
+ 
+@@ -308,7 +308,7 @@ SWIG_R_NewPointerObj(void *ptr, swig_type_info *type, int flags) {
+   }
+   rptr = R_MakeExternalPtr(ptr, 
+   R_MakeExternalPtr(type, R_NilValue, R_NilValue), R_NilValue); 
+-  SET_S4_OBJECT(rptr);
+  rptr = Rf_asS4(rptr, TRUE, 0);
+   return rptr;
+ }
+ 
+diff --git a/Lib/r/std_vector.i b/Lib/r/std_vector.i
+index 6b32c9f6fc2..7db6d3814ac 100644
+--- a/Lib/r/std_vector.i
+++ b/Lib/r/std_vector.i
+@@ -203,7 +203,7 @@
+          PROTECT(result = Rf_allocVector(STRSXP, val->size()));
+          for (unsigned pos = 0; pos < val->size(); pos++)
+            {
+-             CHARACTER_POINTER(result)[pos] = Rf_mkChar(((*val)[pos]).c_str());
+             SET_STRING_ELT(result, pos, Rf_mkChar(((*val)[pos]).c_str()));
+            }
+         UNPROTECT(1);
+         return(result);
+@@ -669,7 +669,7 @@
+             // Fill the R vector
+             for (unsigned vpos = 0; vpos < val->at(pos).size(); ++vpos)
+               {
+-                CHARACTER_POINTER(VECTOR_ELT(result, pos))[vpos] = Rf_mkChar(val->at(pos).at(vpos).c_str());
+                SET_STRING_ELT(VECTOR_ELT(result, pos), vpos, Rf_mkChar(val->at(pos).at(vpos).c_str()));
+               }
+           }
+         UNPROTECT(1);
+
+From 77d8826b46a967af158e982d56008aea2c8f6cb1 Mon Sep 17 00:00:00 2001
+From: Erez Geva <ErezGeva2@gmail.com>
+Date: Fri, 1 May 2026 18:47:42 +0200
+Subject: [PATCH 2/2] Add versioned `R` testing
+
+Signed-off-by: Erez Geva <ErezGeva2@gmail.com>
+---
+ .github/workflows/linux.yml |  7 +++++++
+ Tools/CI-linux-install.sh   | 20 +++++++++++++++++++-
+ configure.ac                | 11 +++++++++++
+ 3 files changed, 37 insertions(+), 1 deletion(-)
+
+diff --git a/Tools/CI-linux-install.sh b/Tools/CI-linux-install.sh
+index ad74ad3f21f..8f459899906 100644
+--- a/Tools/CI-linux-install.sh
+++ b/Tools/CI-linux-install.sh
+@@ -181,7 +181,25 @@ case "$SWIGLANG" in
+ 		fi
+ 		;;
+ 	"r")
+-		$RETRY sudo apt-get -qq install r-base
+		if [[ -n "$VER" ]]; then
+			# Should helps with old version, but do not work
+			#$RETRY sudo apt-get -qq remove r-base r-base-core r-base-dev r-base-html r-doc-html r-recommended
+			sudo sed -i 's%^# deb-src %deb-src %' /etc/apt/sources.list
+			sudo sed -i 's%^Types: deb$%Types: deb deb-src%' /etc/apt/sources.list.d/*
+			$RETRY sudo apt-get -qq update
+			$RETRY sudo apt-get -qq build-dep r-base
+			r_build=`mktemp -d`
+			r_tarball=R-$VER.tar.gz
+			URL=https://cran.r-project.org/src/base/R-${VER:0:1}
+			$RETRY wget $URL/$r_tarball
+			tar -xf "$r_tarball" --strip-components=1 -C "$r_build"
+			cd "$r_build"
+			./configure
+			make
+			sudo make install
+		else
+			$RETRY sudo apt-get -qq install r-base
+		fi
+ 		;;
+ 	"ruby")
+ 		if [[ "$VER" ]]; then
+diff --git a/configure.ac b/configure.ac
+index e113f4b877c..e309b36ff45 100644
+--- a/configure.ac
+++ b/configure.ac
+@@ -2292,6 +2292,17 @@ else
+ if test "x$RBIN" = xyes; then
+    AC_PATH_PROG(RBIN, R)
+ fi
+if test -n "$RBIN" && test -x "$RBIN"; then
+   r_min_version=2.4.0
+   AC_MSG_CHECKING([for R version])
+   r_version=`R --version | grep 'R version' | sed 's%^R version %%;s% (.*%%'`
+   AS_VERSION_COMPARE(["$r_version"], ["$r_min_version"],
+                  [AC_MSG_RESULT([older then $r_min_version])
+                   AS_UNSET([RBIN])],        dnl bellow r_min_version
+                  [AC_MSG_RESULT([$r_version])],   dnl equal r_min_version
+                  [AC_MSG_RESULT([$r_version])])   dnl above r_min_version
+fi
+
+ fi
+ 
+ AC_SUBST(RBIN)
@@ -237,7 +237,7 @@ it.")
 (define-public trealla
  (package
    (name "trealla")
-    (version "2.100.10")
+    (version "2.100.15")
    (source
     (origin
       (method git-fetch)
@@ -246,7 +246,7 @@ it.")
          (url "https://github.com/trealla-prolog/trealla")
          (commit (string-append "v" version))))
       (sha256
-        (base32 "09aqszk3kwjb8qznaywzvhir3nxkf6mkib68mkyn4f7siswb3apg"))
+        (base32 "1fr3h0hqk5bbzr8n415pd24n2nvxhyaxi03hn5s78q1yklynw13f"))
       (file-name (git-file-name name version))))
    (build-system gnu-build-system)
    (inputs
@@ -18311,9 +18311,21 @@ is binding LibSass.")
       (sha256
        (base32 "1fj4zkcnx3mk7kbnf4d6pjgv331n17wzpphpwdnmr498ghbsph9k"))))
    (build-system pyproject-build-system)
-    (arguments (list #:tests? #f))  ;circular dependency with python-aiohttp
+    (arguments
+     (list
+      #:tests? #f  ;circular dependency with python-aiohttp
+      #:phases
+      '(modify-phases %standard-phases
+         (add-after 'unpack 'python3.12-compatibility
+           (lambda _
+             (substitute* '("idna_ssl.py"
+                            "tests/test_base.py")
+               (("import ssl")
+                "import ssl\nimport urllib3")
+               (("ssl.match_hostname")
+                "urllib3.util.ssl_match_hostname")))))))
    (native-inputs (list python-setuptools))
-    (propagated-inputs (list python-idna))
+    (propagated-inputs (list python-idna python-urllib3))
    (home-page "https://github.com/aio-libs/idna-ssl")
    (synopsis "Support Unicode(idna) domains for Python's @code{ssl} module")
    (description
@@ -1255,7 +1255,7 @@ base, via the @file{pythoncapi_compat.h} header file.")
 (define-public micropython
  (package
    (name "micropython")
-    (version "1.26.1")
+    (version "1.28.0")
    (source
      (origin
        (method url-fetch)
@@ -1263,7 +1263,7 @@ base, via the @file{pythoncapi_compat.h} header file.")
                            "releases/download/v" version
                            "/micropython-" version ".tar.xz"))
        (sha256
-         (base32 "165c8g60f5zf82gw2d94snyjmcgn999jn4i8ngyc0wk2vwa6bghj"))
+         (base32 "05d2gd3g8v3paxf4fin4cv5scgnc4yl0jdahpjs37nmqaybcahsf"))
      (modules '((guix build utils)))
      (snippet
       '(begin
@@ -202,7 +202,7 @@
 ;;
 ;; CODE:

-(define %racket-version "8.18") ; Remember to update chez-scheme-for-racket!
+(define %racket-version "9.1") ; Remember to update chez-scheme-for-racket!
 (define %racket-commit
  (string-append "v" %racket-version))
 (define %racket-origin
@@ -212,7 +212,7 @@
          (url "https://github.com/racket/racket")
          (commit %racket-commit)))
    (sha256
-     (base32 "0m38im7a3b3w7sdl15vpsrx7dxw5iz22f1zzffy1bkbbqz45pm87"))
+     (base32 "1yc6lkydg32998ajnqws83zakksmbp3hb21spq0sfaq4v7wg2ng6"))
    (file-name (git-file-name "racket" %racket-version))
    (patches (search-patches "racket-chez-scheme-bin-sh.patch"
                             "racket-launcher-config-dir.patch"
@@ -695,6 +695,7 @@ DrRacket IDE, are not included.")
         ("net-lib" "pkgs/net-lib")
         ("racket-doc" "pkgs/racket-doc")
         ("racket-index" "pkgs/racket-index")
+         ("racket-index-exe" "pkgs/racket-index-exe")
         ("scheme-doc" "pkgs/scheme-doc")
         ("sandbox-lib" "pkgs/sandbox-lib")
         ("sequence-tools-lib" "pkgs/sequence-tools-lib")
@@ -706,10 +707,10 @@ DrRacket IDE, are not included.")
       "class-iop" (base32 "08z57q83cr7wnh6g8ah3hdhmsmf9zp1jfs7yvxv188l3hzvygy5l")
       '("class-iop-lib"))
      (simple-racket-origin
-       "compatibility" (base32 "1d1py9wizi4jnzak7b6d0p9filxv1x9mlx5gsp3yhcjajigq182p")
+       "compatibility" (base32 "0q5k4p44sf2y4gl69js11qvicyzqwy16ry74bvj1vrn8i8xws55b")
       '("compatibility" "compatibility-doc" "compatibility-lib"))
      (simple-racket-origin
-       "contract-profile" (base32 "1xm2z8g0dpv5d9h2sg680vx1a8ix9gbsdpxxb8qv1w7akp73paj3")
+       "contract-profile" (base32 "068z8flwcznqg0bjk227i2qapqbciyrckgqf8mvk57gxmr6zh3d3")
       '(("contract-profile" ".")))
      (simple-racket-origin
       "data" (base32 "11ai6c9h0brbblc6xn045ajj4gyrvbjpk1pqcqm1m0dy9q2rzd4a")
@@ -718,7 +719,7 @@ DrRacket IDE, are not included.")
       "datalog" (base32 "0nf6cy4djpyhfvgpa6yn72apbz9s83gp0qg95pzjd0az4v6qwq1s")
       '(("datalog" ".")))
      (simple-racket-origin
-       "db" (base32 "0qwl8gyd71sm56kcs021g99cpw5bibaycvk1x7ng69jhkylg6q6f")
+       "db" (base32 "09f2wysqmgs46nbzmwrhbn6jqnkpj6bsabm6s6kw8qmp6azca9q2")
       '("db" "db-doc" "db-lib"))
      (simple-racket-origin
       "deinprogramm" (base32 "1zkasf94gzp97q0fhrd065d56zv10h0j0ncmaghzglkmjj8c3vvx")
@@ -731,10 +732,10 @@ DrRacket IDE, are not included.")
       "distributed-places" (base32 "1dajpkj9balqcpv6cdk9hwjz592h1vq8rrx5vncariiac4vbdpa0")
       '("distributed-places" "distributed-places-doc" "distributed-places-lib"))
      (simple-racket-origin
-       "draw" (base32 "1nny22h0hnd40qs3ndkhfrgg793y6f4gl9jpdz1g2k0cpr3818rg")
+       "draw" (base32 "157r861rx2avbjpqhrrxwdqxwf5ksvw38km3pw7rxiwvwh9nys8k")
       '("draw" "draw-doc" "draw-lib"))
      (simple-racket-origin
-       "drracket" (base32 "07qh9dzgd2xhd0375z78vcsf32za08cacj4s2mcrhilcvcgw9s0j")
+       "drracket" (base32 "17sszhx5nd549w7kj6pd3c3cyjps2swbp7rmg36yaxm71pli5gs5")
       '("drracket"
         "drracket-core"
         "drracket-core-lib"
@@ -753,7 +754,7 @@ DrRacket IDE, are not included.")
       "eopl" (base32 "0qihajdpwf2q7hbs6fsw6mmmzy57kgzgry3vyp9z8w7ay8df3w15")
       '(("eopl" ".")))
      (simple-racket-origin
-       "errortrace" (base32 "0l9k2rx6z4jkid7kxhbs763s66pxbzvfrgxajykbrmqkv77lhb3w")
+       "errortrace" (base32 "02z80khr4kqhcpq1k3djz7jgkwa31vnacid4qx8naab9dkbcp5x8")
       '("errortrace" "errortrace-doc" "errortrace-lib"))
      (simple-racket-origin
       "expeditor" (base32 "1nk88jq0blzcw45fr8nwp024cysplayi3paaay4z824lkn1smzaa")
@@ -770,13 +771,13 @@ DrRacket IDE, are not included.")
       "games" (base32 "13z7fnbr48s98lmfxc0nbfhbqkd4hphymy2r63hqm783xzn6ylzi")
       '(("games" ".")))
      (simple-racket-origin
-       "gui" (base32 "0qkxa8cq0cblriamd7x502g918kjvq4348l6c8qmqdpn9cw9mg2h")
+       "gui" (base32 "1c47622y5cf1p7nnbycaf53m8vakf55lqzv8byqzj7zcvcsh8s16")
       '("gui" "gui-doc" "gui-lib" "tex-table"))
      (simple-racket-origin
-       "gui-pkg-manager" (base32 "024880k3wmvkqhjc954prrkavwv3bgafcw00ajz7h2llygh0aqpl")
+       "gui-pkg-manager" (base32 "1f0ssg37kdk3xn9js616ns345565q39j9h51wzd99753iqd45m92")
       '("gui-pkg-manager-lib"))
      (simple-racket-origin
-       "htdp" (base32 "14bdv86zxs87rvvvbwvq3x0sqpg1hj16whjcv20r96c26b1xxj36")
+       "htdp" (base32 "02a5zny1njys40jfsi2spw82ar0kkbfddpk10al822ajs1manhak")
       '("htdp" "htdp-doc" "htdp-lib"))
      (simple-racket-origin
       "html" (base32 "18n1jnjgzfknc8nv8dppi85nb8q08gqdwkg6hfjk08x0p00anx2x")
@@ -791,16 +792,16 @@ DrRacket IDE, are not included.")
       "lazy" (base32 "0rn8kd0ih7aw6fj1g7jdvi5978a6q4hyd6gbh89nb6j5ijvlgn43")
       '(("lazy" ".")))
      (simple-racket-origin
-       "macro-debugger" (base32 "133b74pxavbafcsmp34kgvwmx1l6xx4bykzvgwwjg3kg2fa5bg1g")
+       "macro-debugger" (base32 "08qmkrvm3qvac4829izmlwl9qrlsc1f6y8yqiradibhm05k7rwg7")
       '("macro-debugger" "macro-debugger-text-lib"))
      (simple-racket-origin
-       "main-distribution" (base32 "0m2n9s32s8a4a2gn4ywrm9l8jycdm5ayi5w9kh5wchhrrw7qzq7y")
+       "main-distribution" (base32 "0gk7wrwy0r1yllk827h8awfswngl1lhlq765d6s42y841v33jn0i")
       '(("main-distribution" ".")))
      (simple-racket-origin
       "make" (base32 "10852fj30bz5r46c3d99s37fkgy5yh44gb01j29sf3kxnhi0g2sa")
       '(("make" ".")))
      (simple-racket-origin
-       "math" (base32 "1399mynmcrybipjsy2ikzs600jjxda0lah653w3vx2lfspsn31if")
+       "math" (base32 "1mgqxx9lbwhd8if3mxz7ji2wryvihjmq5imn2316skkvr16yy8mx")
       '("math" "math-doc" "math-lib"))
      (simple-racket-origin
       "mysterx" (base32 "11p9jzrafw0hizhl0cs4sxx7rv281185q8hryic2rpk0kzjdyr48")
@@ -809,7 +810,7 @@ DrRacket IDE, are not included.")
       "mzcom" (base32 "0rc9pfj7gwm5azghqvcibz6si1x5s2v8mr2yngk7ssq9gzfbi6a4")
       '(("mzcom" ".")))
      (simple-racket-origin
-       "mzscheme" (base32 "04kyrhznq46mklacf7pms4fv47zsimqqk3948r3w2ym9n04fhjsx")
+       "mzscheme" (base32 "0p7bp8rmzw7k12sjxdqlxf31d8ama4wv9qz6ryvnmjn2qyhrr3d1")
       '("mzscheme" "mzscheme-doc" "mzscheme-lib"))
      (racket-packages-origin
       "net-cookies" (origin
@@ -818,7 +819,7 @@ DrRacket IDE, are not included.")
                             (url "https://github.com/RenaissanceBug/racket-cookies")
                             (commit %racket-commit)))
                       (sha256 (base32
-                                "1fbl717w5801bydx3nzwxddd1rh1cc0gxwpjc7ka9zh5ak09sb0w"))
+                                "0v6lbpv8ly4jwpjr3rk0q6izpsnfp45ysgrhngpw7jshkjc5wgyd"))
                       (file-name
                        (git-file-name "RenaissanceBug-racket-cookies" %racket-version)))
       '("net-cookies" "net-cookies-doc" "net-cookies-lib"))
@@ -838,16 +839,16 @@ DrRacket IDE, are not included.")
       "option-contract" (base32 "1914dcxy6qzpg3cpnzdm9lj0kwyw8xdb85mwiamqfkbg0xlyyhpa")
       '("option-contract" "option-contract-doc" "option-contract-lib"))
      (simple-racket-origin
-       "parser-tools" (base32 "0i822p7ik6q03l7mrlf0qb63xdxvx06yl5lg1g1qri5wmi5xj0pb")
+       "parser-tools" (base32 "0dp99d1a47kqyg2iqdijm5781qnd571iwvg85dvrjc76ab4pccgd")
       '("parser-tools" "parser-tools-doc" "parser-tools-lib"))
      (simple-racket-origin
       "pconvert" (base32 "0xw9f9692v2qp16fwmwmwmrb118kpz259vmx8cq6s9vsw0112zpq")
       '("pconvert-lib" "pconvert-doc"))
      (simple-racket-origin
-       "pict" (base32 "17pldgiifmwi968dwlk23c1wnrlks0x7aj5jdmdfsf9xgq31wkb5")
+       "pict" (base32 "1xs1k98nr052p5v30abn7kl8pm1rdwj8xqvrghw8b62bvhhb072a")
       '("pict" "pict-doc" "pict-lib"))
      (simple-racket-origin
-       "pict-snip" (base32 "081nwiy4a0n4f7xws16hqbhf0j3kz5alizndi3nnyr3chm4kng6x")
+       "pict-snip" (base32 "1qrqbigw6arhccqgqzblfqqcpsdy15dwb0y22axwxgpw1ax0ki6f")
       '("pict-snip" "pict-snip-doc" "pict-snip-lib"))
      (simple-racket-origin
       "picturing-programs" (base32 "1a3d6nw9n827b4711nvgrnw7w47k4fxvk8c2a8br6a1l748kxkwy")
@@ -865,7 +866,7 @@ DrRacket IDE, are not included.")
       "preprocessor" (base32 "1p5aid58ifnjy4xl0ysh85cq39k25661v975jrpk182z3k5621mg")
       '(("preprocessor" ".")))
      (simple-racket-origin
-       "profile" (base32 "10lv3iz58hqk043llnbqrkmjnm1pbvr4j1j188g85zg798rqyjzs")
+       "profile" (base32 "1n6jlhkq0zs2sd132k92nvw08qscadjz3d6p2r5pjlcdawkmkik0")
       '("profile" "profile-doc" "profile-lib"))
      (racket-packages-origin
       "quickscript" (origin
@@ -895,7 +896,7 @@ DrRacket IDE, are not included.")
                         (git-file-name "jeapostrophe-racket-cheat" %racket-version)))
       '(("racket-cheat" ".")))
      (simple-racket-origin
-       "racklog" (base32 "0fr8xij0sssfnmwn6dfdi4jj3l62f2yj3jrjljv13kaycrfls032")
+       "racklog" (base32 "0i2jnghb5vqmk2f0cppgggyp73zy1q0dlhpvxrzdxw39skmhmgkc")
       '(("racklog" ".")))
      (simple-racket-origin
       "rackunit" (base32 "191x4lgxg1bbkimdndg6j562zyxq48l0g21f9j2ln2hmh9s1v065")
@@ -914,7 +915,7 @@ DrRacket IDE, are not included.")
       "realm" (base32 "0rlvwyd6rpyl0zda4a5p8dp346fvqzc8555dgfnrhliymkxb6x4g")
       '(("realm" ".")))
      (simple-racket-origin
-       "redex" (base32 "1h60mhaaiiwqcnmskqfrl6jhg4d97xjdcxnhw9krm4aysa9b9bwf")
+       "redex" (base32 "1gg36wpd5kw01dwz353j5xvd2c673aws5l3jn2h2rzqlslk49dw7")
       '("redex"
         "redex-benchmark"
         "redex-doc"
@@ -929,7 +930,7 @@ DrRacket IDE, are not included.")
       "scheme-lib" (base32 "0pcf0y8rp4qyjhaz5ww5sr5diq0wpcdfrrnask7zapyklzx1jx8x")
       '(("scheme-lib" ".")))
      (simple-racket-origin
-       "scribble" (base32 "0pg8brgyyziw3y8fp6ls6ii7i02cmm5168i4zmqfxjzywswljf17")
+       "scribble" (base32 "1h6rkkbvxa6fwcpv6y5n14y984z4bxlhn04hhv8r7398a6jsldg6")
       '("scribble"
         "scribble-doc"
         "scribble-html-lib"
@@ -955,13 +956,13 @@ DrRacket IDE, are not included.")
       "slatex" (base32 "0pkm2isbbdk63slrbsxcql7rr0wdrw5kapw1xq4ps5k8dhlzv8x0")
       '(("slatex" ".")))
      (simple-racket-origin
-       "slideshow" (base32 "0dyg20qs40s2d6ha28zb9h5x4v7phkddinqm446b4jishyrg7dqc")
+       "slideshow" (base32 "1aprcapyj0362lfh2pbcyxf4r2k01zmp6yy9ppag0xbz0jw437im")
       '("slideshow" "slideshow-doc" "slideshow-exe" "slideshow-lib" "slideshow-plugin"))
      (simple-racket-origin
-       "snip" (base32 "1jpy5728w9bszgsjczlzrjjxsvqlcn4ah6gd3rp0plp8zzk9mq0s")
+       "snip" (base32 "10727bi2ybn2ahlkpikdknwfzfsppaw5wkvjmzd380jp1fw91q67")
       '("snip" "snip-lib"))
      (simple-racket-origin
-       "typed-racket" (base32 "00d5pb5h34066q4prb9v5s5m9ggbby31f3anshd9vfsrzhd38p4n")
+       "typed-racket" (base32 "1cmp3065fp9lm6rsfml7x5bvnilh1fs9k0511l11qdismz2sndpy")
       '("source-syntax"
         "typed-racket"
         "typed-racket-compatibility"
@@ -972,7 +973,7 @@ DrRacket IDE, are not included.")
       "srfi" (base32 "07q7wdgnf88z1rq0bfpn4b41abhfswa38c0s2hkn325blk53k4a6")
       '("srfi" "srfi-doc" "srfi-lib" "srfi-lite-lib"))
      (simple-racket-origin
-       "string-constants" (base32 "0llalgdncn18ix5xnx82yyms221g47xh7s3w6inch53ip3yc6ksr")
+       "string-constants" (base32 "085anm6s5ghg5bfggavknpr52py1a72qwjihvp0rnxpkf181sn8c")
       '("string-constants" "string-constants-doc" "string-constants-lib"))
      (simple-racket-origin
       "swindle" (base32 "1q8vdxpzczzwdw2mys2caab45yvadmqkixsr29k8pl03n8dsg8j9")
@@ -984,16 +985,16 @@ DrRacket IDE, are not included.")
       "trace" (base32 "1zx0kfbacidg5rllbvx842x949ra22n004irs3vm1hqmwmixy3is")
       '(("trace" ".")))
      (simple-racket-origin
-       "unix-socket" (base32 "02dfwas5ynbpyz74w9kwb4wgb37y5wys7svrlmir8k0n9ph9vq0y")
+       "unix-socket" (base32 "039r2aqc6xc4b3x95ggjg4ab1pfiff6pavi4d40662zgwbi61pwk")
       '("unix-socket" "unix-socket-doc" "unix-socket-lib"))
      (simple-racket-origin
-       "web-server" (base32 "0ry5vwjd06ml9hmspgrwci8c99syx7zhp9sgldmhwwfvf5m1g29d")
+       "web-server" (base32 "0v66z9dklf02lc0g357h4rnfq5pnk87d1qz59sfrlzz24phxg9g6")
       '("web-server" "web-server-doc" "web-server-lib"))
      (simple-racket-origin
       "wxme" (base32 "1qp5gr9gqsakiq3alw6m4yyv5vw4i3hp4y4nhq8vl2nkjmirvn0b")
       '("wxme" "wxme-lib"))
      (simple-racket-origin
-       "xrepl" (base32 "0sw531zvd8xqckmrh5da4fiq0sfjyg1nj5d508l7bl3azn35khil")
+       "xrepl" (base32 "1kkcm68qyck2d6mp56h1j5fnfbx938a15dnyn1cf5yqpj9cc637m")
       '("xrepl" "xrepl-doc" "xrepl-lib"))))
    (build-system gnu-build-system)
    (arguments
@@ -31,7 +31,7 @@
 ;;; Copyright © 2022-2025 Remco van 't Veer <remco@remworks.net>
 ;;; Copyright © 2022 Taiju HIGASHI <higashi@taiju.info>
 ;;; Copyright © 2023 Yovan Naumovski <yovan@gorski.stream>
-;;; Copyright © 2023, 2024, 2025 gemmaro <gemmaro.dev@gmail.com>
+;;; Copyright © 2023, 2024, 2025, 2026 gemmaro <gemmaro.dev@gmail.com>
 ;;; Copyright © 2023, 2024 Janneke Nieuwenhuizen <janneke@gnu.org>
 ;;; Copyright © 2023, 2024 Zheng Junjie <873216071@qq.com>
 ;;; Copyright © 2023-2025 Hartmut Goebel <h.goebel@crazy-compilers.com>
@@ -8201,19 +8201,27 @@ differences (added or removed nodes) between two XML/HTML documents.")
 (define-public ruby-racc
  (package
    (name "ruby-racc")
-    (version "1.5.2")
+    (version "1.8.1")
    (source
     (origin
-       (method url-fetch)
-       (uri (rubygems-uri "racc" version))
+       (method git-fetch) ;for tests
+       (uri (git-reference
+             (url "https://github.com/ruby/racc")
+             (commit (string-append "v" version))))
+       (file-name (git-file-name name version))
       (sha256
        (base32
-         "178k7r0xn689spviqzhvazzvxfq6fyjldxb3ywjbgipbfi4s8j1g"))))
+         "1sg2mqp6yxdxrn9kbbsxkd6930fxvm4yjl8knsc0wq6fkipnhm8q"))))
    (build-system ruby-build-system)
    (arguments
-     `(#:tests? #f))            ; Fails while parsing test instructions.
+     (list
+      #:phases
+      #~(modify-phases %standard-phases
+          (add-before 'build 'compile
+            (lambda _
+              (invoke "rake" "compile"))))))
    (native-inputs
-     (list ruby-hoe ruby-rake-compiler))
+     (list ruby-rake-compiler ruby-test-unit-ruby-core))
    (synopsis "LALR(1) parser generator for Ruby")
    (description
     "Racc is a LALR(1) parser generator.  It is written in Ruby itself, and
@@ -37,6 +37,8 @@
  #:use-module (gnu packages perl)
  #:use-module (gnu packages pkg-config)
  #:use-module (gnu packages python)
+  #:use-module (gnu packages rust)
+  #:use-module (gnu packages statistics)
  #:use-module (gnu packages textutils)
  #:use-module (gnu packages virtualization))

@@ -246,6 +248,48 @@ transliterating them.  It supports Emoji and Chinese.")
       ;; checkout and does not need a cargo input.
       (inputs (cargo-inputs 'rust-deunicode-1.6.2.cfb8552))))))

+;; Workspace dependency of r-pizzarr.
+(define-public rust-extendr-0.8.1.93d7244
+  (let ((commit "93d7244e3145d94186bc2f35258ad0ef25a28908")
+        (revision "1"))
+    (hidden-package
+     (package
+       (name "rust-extendr")
+       (version (git-version "0.8.1" revision commit))
+       (source (origin
+                 (method git-fetch)
+                 (uri (git-reference
+                        (url "https://github.com/extendr/extendr")
+                        (commit commit)))
+                 (file-name (git-file-name name version))
+                 (sha256
+                  (base32
+                   "03d16y7f1r0y1s8gwzw7wzn5yhcqr1wn0vga9dvdjxpbga372vx7"))))
+       (build-system cargo-build-system)
+       (arguments
+        (list
+         #:cargo-package-crates
+         ;; Note that the order matters!
+         '(list "extendr-ffi"
+                "extendr-macros"
+                "extendr-api"
+                "extendr-engine")
+         #:phases
+         #~(modify-phases %standard-phases
+             (add-after 'unpack 'set-R_HOME
+               (lambda _
+                 (delete-file-recursively ".cargo")
+                 (setenv "R_HOME"
+                         (string-append
+                          #$(this-package-input "r-minimal")
+                          "/lib/R")))))))
+       (inputs (cons r-minimal (cargo-inputs 'extendr)))
+       (home-page "https://extendr.rs/")
+       (synopsis "R extension library for Rust")
+       (description "This library allows you to extend R with Rust.  It can be
+used to write R packages that link with Rust libraries.")
+       (license license:expat)))))
+
 ;; Workspace dependency of zed.
 ;;
 ;; Cargo side: Cargo unifies dependency versions across zed's
@@ -244,26 +244,21 @@ This Guix package is built to use the nettle cryptographic library.")
 (define-public sequoia-wot-tools
  (package
    (name "sequoia-wot-tools")
-    (version "0.15.0")
+    (version "0.15.2")
    (source
     (origin
       (method git-fetch)
       (uri (git-reference
-              (url "https://gitlab.com/sequoia-pgp/sequoia-wot")
-              (commit (string-append "v" version))))
+              (url "https://gitlab.com/sequoia-pgp/sequoia-wot.git/")
+              (commit (string-append "sequoia-wot/v" version))))
       (file-name (git-file-name name version))
       (sha256
-        (base32 "03wa4l582hx0qq28pkhrf0pagckyx6df01pb4chyngadk49q1xn7"))))
+        (base32 "18v713n36sq5pvd1pbs34v7dly1bi614kwra09qxpsxk0ffp225z"))))
    (build-system cargo-build-system)
    (arguments
     (list
       #:features '(list "sequoia-openpgp/crypto-nettle")
       #:cargo-package-crates ''("tools")
-       #:cargo-test-flags
-       '(list "--"
-              "--skip=gpg_trust_roots"
-              "--skip=backward_propagation::tests::cliques"
-              "--skip=tests::cliques")
       #:install-source? #f
       #:cargo-install-paths ''("tools")
       #:phases
@@ -276,11 +271,12 @@ This Guix package is built to use the nettle cryptographic library.")
                 (for-each (lambda (file)
                             (install-file file man1))
                           (find-files "target/release" "\\.1$"))
-                 (mkdir-p (string-append out "/etc/bash_completion.d"))
+                 (mkdir-p (string-append out "/share/bash-completion/completions"))
                 (mkdir-p (string-append share "/fish/vendor_completions.d"))
                 (mkdir-p (string-append share "/elvish/lib"))
                 (copy-file (car (find-files "target/release" "sq-wot.bash"))
-                            (string-append out "/etc/bash_completion.d/sq-wot"))
+                            (string-append
+                              out "/share/bash-completion/completions/sq-wot"))
                 (copy-file (car (find-files "target/release" "sq-wot.fish"))
                            (string-append
                              share "/fish/vendor_completions.d/sq-wot.fish"))
@@ -292,7 +288,7 @@ This Guix package is built to use the nettle cryptographic library.")
    (inputs
     (cons* nettle openssl sqlite (cargo-inputs 'sequoia-wot-tools)))
    (native-inputs
-     (list clang pkg-config))
+     (list clang gnupg pkg-config))
    (home-page "https://sequoia-pgp.org/")
    (synopsis "Implementation of OpenPGP's web of trust")
    (description
@@ -88,7 +88,9 @@ you tailor the wrapping process to suit your application.")
                                 name "-" version ".tar.gz"))
              (sha256
               (base32
-                "1kqz533599d00rrz0g2ryf8w2ynb25ayylpx10nmkxsndiq2l5j0"))))
+                "1kqz533599d00rrz0g2ryf8w2ynb25ayylpx10nmkxsndiq2l5j0"))
+              (patches
+               (search-patches "swig-support-r-4.6.0.patch"))))
    (native-inputs (list boost
                         pcre2 ; for pcre2-config
                         ;; The following are for tests and examples:
@@ -2804,7 +2804,7 @@ XDG-Output for wlclock to work.")
 (define-public wlroots
  (package
    (name "wlroots")
-    (version "0.20.0")
+    (version "0.20.1")
    (source
     (origin
       (method git-fetch)
@@ -2813,7 +2813,7 @@ XDG-Output for wlclock to work.")
             (commit version)))
       (file-name (git-file-name name version))
       (sha256
-        (base32 "1gdmy4mpi7x23g81cdmcr9aakk3g6csl69h9j98yzssa48k6all5"))))
+        (base32 "0n9wkmqnja5fnwn8an36jqn6nzlb1vjdzi0v932pn5bpgmv3brxs"))))
    (build-system meson-build-system)
    (arguments
     (list #:phases
@@ -4717,7 +4717,7 @@ read and write, and compatible with JSON.")
 (define-public labwc
  (package
    (name "labwc")
-    (version "0.9.7")
+    (version "0.20.0")
    (source (origin
              (method git-fetch)
              (uri (git-reference
@@ -4726,7 +4726,7 @@ read and write, and compatible with JSON.")
              (file-name (git-file-name name version))
              (sha256
               (base32
-                "12mm4w9djgh7q30lswhl1q1cxf6h0pf8xr744jkcyjcqqsavynpf"))))
+                "0hq88p8ij1zd595rrfr6pxxkzbflgnafdvqjdw7p1y9l5dgkaar5"))))
    (build-system meson-build-system)
    (native-inputs
     (list pkg-config gettext-minimal scdoc))
@@ -4739,7 +4739,7 @@ read and write, and compatible with JSON.")
           libxcb
           libxml2
           pango
-           wlroots-0.19))
+           wlroots-0.20))
    (home-page "https://labwc.github.io")
    (synopsis "Window-stacking compositor for Wayland")
    (description
@@ -202,9 +202,9 @@ package definition."
 (define %cran-canonical-url "https://cran.r-project.org/package=")
 (define %bioconductor-url "https://bioconductor.org/packages/")

-;; The latest Bioconductor release is 3.22.  Bioconductor packages should be
+;; The latest Bioconductor release is 3.23.  Bioconductor packages should be
 ;; updated together.
-(define %bioconductor-version "3.22")
+(define %bioconductor-version "3.23")

 (define* (bioconductor-packages-list-url #:optional type)
  (string-append "https://bioconductor.org/packages/"