gnu: trealla: Update to 2.94.5.

* gnu/packages/prolog.scm (trealla): Update to 2.94.5. Change-Id: I73249407b4653a14cdafc8ac139b2a6136bd1937
teams: javascript: Adopt gnu/packages/javascript.scm.
2026-04-28 14:43:51 +00:00 · 2026-04-28 10:38:20 -04:00 · 2026-04-28 12:30:51 +02:00 · 2026-04-28 10:14:36 +01:00 · 2026-04-28 10:14:36 +01:00 · 2026-04-28 10:14:36 +01:00
35 changed files with 3749 additions and 1133 deletions
--- a/1
+++ b/1
@@ -274,6 +274,7 @@ guix/build-system/ant\.scm                         @guix/java
 guix/build-system/clojure\.scm                     @guix/java
 guix/build-system/maven\.scm                       @guix/java

+gnu/packages/javascript\.scm                       @guix/javascript
 gnu/packages/node-xyz\.scm                         @guix/javascript
 gnu/packages/node\.scm                             @guix/javascript
 guix/build-system/node\.scm                        @guix/javascript
--- a/doc/guix.texi
+++ b/doc/guix.texi
@@ -45251,6 +45251,12 @@ Extra command line options for @code{guix-data-service}.
@item @code{extra-process-jobs-options} (default: @var{'()})
 Extra command line options for @code{guix-data-service-process-jobs}.

+@item @code{extra-environment-variables} (default: @var{'()})
+Extra environment variables for @code{guix-data-service}.
+
+@item @code{extra-process-jobs-environment-variables} (default: @var{'()})
+Extra environment variables for @code{guix-data-service-process-jobs}.
+
@item @code{git-repositories} (default: @var{#f})
 List of git-repository information to insert into the database.

--- a/etc/teams.scm
+++ b/etc/teams.scm
@@ -844,7 +844,8 @@ and the maven-build-system."
        #:name "JavaScript team"
        #:description
        "JavaScript/Node.js packages, the node build system."
-        #:scope (list "gnu/packages/node-xyz.scm"
+        #:scope (list "gnu/packages/javascript.scm"
+                      "gnu/packages/node-xyz.scm"
                      "gnu/packages/node.scm"
                      "guix/build-system/node.scm"
                      "guix/build/node-build-system.scm"
--- a/gnu/local.mk
+++ b/gnu/local.mk
@@ -2349,8 +2349,16 @@ 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	\
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -913,7 +913,7 @@ suite native in R.")
 (define-public r-bpcells
  (package
    (name "r-bpcells")
-    (version "0.3.0")
+    (version "0.3.1")
    (source
     (origin
       (method git-fetch)
@@ -922,7 +922,7 @@ suite native in R.")
             (commit (string-append "v" version))))
       (file-name (git-file-name name version))
       (sha256
-        (base32 "12h1di45fg06nhsliii7v0h1z567pkpis1xm4ar1qr8ns1n8iljw"))
+        (base32 "0yqgcajq83g25mznwcngaw7pi6vcqxqdnynpgb95yci57k3wrp6j"))
       (modules '((guix build utils)))
       (snippet
        '(delete-file-recursively "r/src/vendor/highway"))))
@@ -931,13 +931,15 @@ suite native in R.")
    (arguments
     (list
      #:phases
-      '(modify-phases %standard-phases
+      `(modify-phases %standard-phases
         (add-after 'unpack 'chdir
-           (lambda _
-             (substitute* "r/configure"
-               (("tools/hwy-test.cpp" m)
-                (string-append m " $HWY_LIBS $HWY_CFLAGS")))
-             (chdir "r"))))))
+           (lambda _ (chdir "r")))
+         ,@(if (target-x86-32?)
+               '((add-after 'chdir 'require-sse2
+                   ;; This avoids falling back to the scalar backend in
+                   ;; highway, which fails to build.
+                   (lambda _ (setenv "CFLAGS" "-msse2"))))
+               '()))))
    (propagated-inputs
     (list r-dplyr
           r-ggplot2
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
--- a/gnu/packages/duckdb.scm
+++ b/gnu/packages/duckdb.scm
@@ -148,13 +148,13 @@ system.")
 (define-public r-duckdb
  (package
    (name "r-duckdb")
-    (version "1.5.1")
+    (version "1.5.2")
    (source
     (origin
       (method url-fetch)
       (uri (cran-uri "duckdb" version))
       (sha256
-        (base32 "177621m08whqqk4yhj3zrr08l3d9hhlqh3gm9jzhi5cplg47cksq"))
+        (base32 "1dldlfwvc33czvlxfmwaj4p9y6sjjj5iqy98yda47a8kclrqmyam"))
       ;; This package bundles the duckdb sources and builds a custom variant
       ;; of duckdb.  I'd be happy to link it with our duckdb library instead,
       ;; but it does not seem possible to do that.
--- a/gnu/packages/electronics.scm
+++ b/gnu/packages/electronics.scm
@@ -2331,7 +2331,7 @@ Automation}, portable and vendor neutral FPGA place and route tool.")
 (define-public nvc
  (package
    (name "nvc")
-    (version "1.19.3")
+    (version "1.20.1")
    (source (origin
              (method git-fetch)
              (uri (git-reference
@@ -2340,7 +2340,7 @@ Automation}, portable and vendor neutral FPGA place and route tool.")
              (file-name (git-file-name name version))
              (sha256
               (base32
-                "1zizz2dafm53lzpjayy6vig5pz5ri9cszdivg0jzzh8s3ggkpy1i"))))
+                "1b38x2ch468s4p6mrq6c8s0d95vb84p6w4v8in79l4w7sfy8jnr0"))))
    (build-system gnu-build-system)
    (arguments
     (list #:out-of-source? #t
@@ -3461,7 +3461,7 @@ form of AXI, AXI lite, and AXI stream modules.")
 (define-public python-edalize
  (package
    (name "python-edalize")
-    (version "0.6.6")
+    (version "0.6.8")
    (source
     (origin
       (method git-fetch)
@@ -3470,7 +3470,7 @@ form of AXI, AXI lite, and AXI stream modules.")
             (commit (string-append "v" version))))
       (file-name (git-file-name name version))
       (sha256
-        (base32 "115nc15n2cx4x9irjim07zkg0287418djqd6ja7rm8jrnyldvln9"))))
+        (base32 "04m2lhkclw9fj92k43c06j003qnq9i1yhy2131fvcnkkr0d9438m"))))
    (build-system pyproject-build-system)
    (arguments
     (list
@@ -4516,7 +4516,7 @@ unique design feature of Trilinos is its focus on packages.")
 (define-public verilator
  (package
    (name "verilator")
-    (version "5.046")
+    (version "5.048")
    (source
     (origin
       (method git-fetch)
@@ -4525,7 +4525,7 @@ unique design feature of Trilinos is its focus on packages.")
              (commit (string-append "v" version))))
       (file-name (git-file-name name version))
       (sha256
-        (base32 "1gr1qhxvl4856hnmnx46dqd2qp0jhdh959zm2qfmxzzh19np7xkm"))))
+        (base32 "16c1x66kqmc5ldqjij81kypj471fibfihcqn6kz4wbxvnn0smyn6"))))
    (native-inputs
     (list autoconf
           automake
--- a/gnu/packages/freedesktop.scm
+++ b/gnu/packages/freedesktop.scm
@@ -3418,49 +3418,49 @@ interfaces.")
  (package
    (name "xdg-desktop-portal-wlr")
    (version "0.8.2")
-    (source (origin
-              (method git-fetch)
-              (uri (git-reference
-                     (url "https://github.com/emersion/xdg-desktop-portal-wlr")
-                     (commit (string-append "v" version))))
-              (file-name (git-file-name name version))
-              (sha256
-               (base32
-                "1jj0a9s3h3i04qsxkhcpxjzbb17hs9ngdy7wkypja09233zdz10w"))
-              (patches (search-patches "xdg-desktop-portal-wlr-harcoded-length.patch"))))
+    (source
+     (origin
+       (method git-fetch)
+       (uri (git-reference
+             (url "https://github.com/emersion/xdg-desktop-portal-wlr")
+             (commit (string-append "v" version))))
+       (file-name (git-file-name name version))
+       (sha256
+        (base32 "1jj0a9s3h3i04qsxkhcpxjzbb17hs9ngdy7wkypja09233zdz10w"))
+       (patches (search-patches "xdg-desktop-portal-wlr-harcoded-length.patch"))))
    (build-system meson-build-system)
    (arguments
-     `(#:configure-flags
-       '("-Dsystemd=disabled"
-         "-Dsd-bus-provider=libelogind")
-       #:phases
-       (modify-phases %standard-phases
-         (add-after 'unpack 'hardcode-binaries
-           (lambda* (#:key inputs #:allow-other-keys)
-             (let ((sh (search-input-file inputs "/bin/sh"))
-                   (grim (search-input-file inputs "/bin/grim"))
-                   (slurp (search-input-file inputs "/bin/slurp")))
-               (substitute* "src/screenshot/screenshot.c"
-                 (("grim") grim)
-                 (("slurp") slurp)
-                 (("execl\\(\"/bin/sh\", \"/bin/sh\"")
-                  (string-append "execl(\"" sh "\", \"" sh "\"")))
-               (substitute* "src/screencast/screencast.c"
-                 (("execvp\\(\"sh")
-                  (string-append "execvp(\"" sh))))))
-         (add-after 'install 'install-documentation
-           (lambda* (#:key outputs #:allow-other-keys)
-             (install-file "../source/README.md"
-                           (string-append (assoc-ref outputs "out")
-                                          "/share/doc/" ,name)))))))
-    (native-inputs
-     (list cmake-minimal pkg-config scdoc))
-    (inputs (list elogind
-                  bash-minimal
+     (list
+      #:configure-flags
+      #~(list "-Dsystemd=disabled"
+              "-Dsd-bus-provider=libelogind")
+      #:phases
+      #~(modify-phases %standard-phases
+          (add-after 'unpack 'hardcode-binaries
+            (lambda* (#:key inputs #:allow-other-keys)
+              (let ((sh (search-input-file inputs "/bin/sh"))
+                    (grim (search-input-file inputs "/bin/grim"))
+                    (slurp (search-input-file inputs "/bin/slurp")))
+                (substitute* '("src/screencast/chooser.c"
+                               "src/screenshot/screenshot.c")
+                  (("grim") grim)
+                  (("slurp") slurp)
+                  (("/bin/sh") sh))
+                (substitute* "src/screencast/screencast.c"
+                  (("execvp\\(\"sh")
+                   (format #f "execvp(\"~a" sh))))))
+          (add-after 'install 'install-documentation
+            (lambda _
+              (install-file "../source/README.md"
+                            (string-append #$output "/share/doc/"
+                                           #$name)))))))
+    (native-inputs (list cmake-minimal pkg-config scdoc))
+    (inputs (list bash-minimal
+                  elogind
                  grim
                  iniparser
-                  mesa
                  libinih
+                  mesa
                  pipewire
                  slurp
                  wayland
--- a/gnu/packages/geo.scm
+++ b/gnu/packages/geo.scm
@@ -425,14 +425,29 @@ hierarchical hexagonal geospatial indexing system")
               (base32
                "00qdk9a4048pzfj2rhzkfw3lvm642znf6kr4x29i3d94494pxsnn"))))
    (build-system cmake-build-system)
-    (arguments `(#:phases
-                 (modify-phases %standard-phases
-                   (add-after
-                    'unpack 'patch-test-shebangs
-                    (lambda _
-                      (substitute* '("tests/xmltester/testrunner.sh"
-                                     "tests/xmltester/safe_to_xml.sh")
-                        (("/bin/sh") (which "sh"))))))))
+    (arguments
+     `(#:phases
+       (modify-phases %standard-phases
+         ,@(if (or (target-x86-32?) (target-arm32?))
+               '((add-after 'unpack 'disable-broken-tests
+                   (lambda _
+                     ;; This test fails due to limited accuracy.
+                     (delete-file "tests/xmltester/tests/general/TestCentroid.xml")
+                     (with-directory-excursion "tests/unit"
+                       ;; These also fail due to limited accuracy.
+                       (delete-file "algorithm/MinimumAreaRectangleTest.cpp")
+                       (delete-file "capi/GEOSMinimumRotatedRectangleTest.cpp")
+                       ;; It is unclear why these fail, but I'm guessing:
+                       ;; limited accuracy.
+                       (delete-file "linearref/LengthIndexedLineTest.cpp")
+                       (delete-file "math/DDTest.cpp")))))
+               '())
+         (add-after
+             'unpack 'patch-test-shebangs
+           (lambda _
+             (substitute* '("tests/xmltester/testrunner.sh"
+                            "tests/xmltester/safe_to_xml.sh")
+               (("/bin/sh") (which "sh"))))))))
    (inputs
     (list glib))
    (home-page "https://libgeos.org/")
@@ -955,6 +970,29 @@ hydrology and waste deposition.")
        (base32
         "03r6mspfv22fs4x4jcgv25v9gsj5k6zy8incvyf94qf50g47s2bc"))))
    (build-system cmake-build-system)
+    (arguments
+     (if (target-32bit?)
+         (list
+          #:phases
+          '(modify-phases %standard-phases
+             (add-after 'unpack 'patch-tests
+               (lambda _
+                 ;; These regression tests fail due to accuracy problems.
+                 (substitute* "test/unit/test_factory.cpp"
+                   (("^TEST\\(factory, AuthorityFactory_createUnitOfMeasure_linear_us_survey_foot\\) \\{" m)
+                    (string-append m "\nGTEST_SKIP();\n")))
+                 (substitute* "test/unit/test_grids.cpp"
+                   (("^TEST_F\\(GridTest, VerticalShiftGridSet_gtx\\) \\{" m)
+                    (string-append m "\nGTEST_SKIP();\n")))
+                 (substitute* "test/unit/test_defmodel.cpp"
+                   (("^TEST\\(defmodel, evaluator_horizontal_unit_metre\\) \\{" m)
+                    (string-append m "\nGTEST_SKIP();\n")))
+                 ;; These regression tests fail due to accuracy problems.
+                 (substitute* "test/CMakeLists.txt"
+                   (("proj_add_gie_test\\(\"4D-API-cs2cs-style\".+") "")
+                   (("proj_add_gie_test\\(\"Builtins\".+") "")
+                   (("proj_add_gie_test\\(\"peirce_q\".+") ""))))))
+         '()))
    (native-inputs (list googletest pkg-config))
    (propagated-inputs (list curl libtiff sqlite)) ;required by proj.pc
    (home-page "https://proj.org/")
@@ -984,7 +1022,34 @@ lets developers use the functionality of Proj in their own software.")
                           version ".tar.gz"))
       (sha256
        (base32
-         "1g0hkpiablvhsmw0kn5frwgdir3q7avc45p6lc1zhhhzkv5ikydh"))))))
+         "1g0hkpiablvhsmw0kn5frwgdir3q7avc45p6lc1zhhhzkv5ikydh"))))
+    (arguments
+     (if (target-32bit?)
+         (list
+          #:phases
+          '(modify-phases %standard-phases
+             (add-after 'unpack 'patch-tests
+               (lambda _
+                 ;; These regression tests fail due to accuracy problems.
+                 (substitute* "test/unit/test_factory.cpp"
+                   (("^TEST\\(factory, AuthorityFactory_createUnitOfMeasure_linear_us_survey_foot\\) \\{" m)
+                    (string-append m "\nGTEST_SKIP();\n")))
+                 (substitute* "test/unit/test_grids.cpp"
+                   (("^TEST_F\\(GridTest, VerticalShiftGridSet_gtx\\) \\{" m)
+                    (string-append m "\nGTEST_SKIP();\n")))
+                 (substitute* "test/unit/test_defmodel.cpp"
+                   (("^TEST\\(defmodel, evaluator_horizontal_unit_metre\\) \\{" m)
+                    (string-append m "\nGTEST_SKIP();\n")))
+                 ;; These regression tests fail due to accuracy problems.
+                 (substitute* "test/CMakeLists.txt"
+                   (("proj_add_gie_test\\(\"4D-API-cs2cs-style\".+") "")
+                   (("proj_add_gie_test\\(\"Builtins\".+") "")
+                   (("proj_add_gie_test\\(\"peirce_q\".+") "")
+                   (("proj_add_gie_test\\(\"adams_ws2\".+") ""))
+                 (substitute* "test/cli/CMakeLists.txt"
+                   (("proj_add_test_script_sh\\(\"testvarious\" CS2CS_BIN\\)") ""))))))
+         '()))))
+

 (define-public python-obspy
  (package
--- a/gnu/packages/guile-xyz.scm
+++ b/gnu/packages/guile-xyz.scm
@@ -7764,8 +7764,8 @@ is an attempt to combine both into something useful.")
      (license license:asl2.0))))

 (define-public guile-knots
-  (let ((commit "f767eca066495e6582e89ba1b91907c0c5657878")
-        (revision "34"))
+  (let ((commit "49996c432a4616e03ecaf01cb42afc5fd78eafd5")
+        (revision "35"))
    (package
    (name "guile-knots")
    (version (git-version "0.1" revision commit))
@@ -7776,7 +7776,7 @@ is an attempt to combine both into something useful.")
                    (commit commit)))
              (sha256
               (base32
-                "18fqmpyrrxy8phxxm5b7d1qhhvc3rsrs243xiinkj2hn2ca1cqi8"))
+                "0i6vk432shy7qmsq1hli71a9kmgf8yy9hx3bck0r9qzsldv1m3m9"))
              (file-name (git-file-name name version))))
    (build-system gnu-build-system)
    (arguments
--- a/gnu/packages/java-bootstrap.scm
+++ b/gnu/packages/java-bootstrap.scm
@@ -1,5 +1,5 @@
 ;;; GNU Guix --- Functional package management for GNU
-;;; Copyright © 2014, 2015, 2016, 2017, 2018, 2019, 2021 Ricardo Wurmus <rekado@elephly.net>
+;;; Copyright © 2014-2019, 2021, 2026 Ricardo Wurmus <rekado@elephly.net>
 ;;; Copyright © 2021, 2026 Ludovic Courtès <ludo@gnu.org>
 ;;; Copyright © 2017 Leo Famulari <leo@famulari.name>
 ;;; Copyright © 2017, 2022 Marius Bakke <marius@gnu.org>
@@ -226,6 +226,18 @@ JNI.")
             (setenv "JAVACMD" (search-input-file inputs "/bin/jamvm"))
             (setenv "JAVAC" (search-input-file inputs "/bin/jikes"))
             (setenv "CLASSPATH" (search-input-file inputs "/lib/rt.jar"))))
+         ,@(if (target-x86-32?)
+               ;; XXX: On i686 isFile() always seems to return true.  Patching
+               ;; this here is very ugly, but the effects are limited.  None
+               ;; of these changes remain by the time we've built Icedtea and
+               ;; the other JDKs.
+               '((add-after 'unpack 'disable-isFile-checks
+                   (lambda _
+                     (substitute* "src/main/org/apache/tools/ant/util/ResourceUtils.java"
+                       (("destFile = \\(\\(FileProvider\\).*") ""))
+                     (substitute* "src/main/org/apache/tools/ant/taskdefs/Mkdir.java"
+                       (("dir.isFile\\(\\)") "false")))))
+               '())
         (replace 'build
           (lambda* (#:key inputs outputs #:allow-other-keys)
             ;; Ant complains if this file doesn't exist.
--- a/gnu/packages/java.scm
+++ b/gnu/packages/java.scm
@@ -1285,7 +1285,13 @@ new Date();"))))
                ;; It looks like the "--disable-warnings-as-errors" option of
                ;; the 'configure' phase is not working.
                (substitute* "make/autoconf/generated-configure.sh"
-                  (("-Werror") ""))))))
+                  (("-Werror") ""))))
+            #$@(if (target-x86-32?)
+                   ;; On i686 the C2 compiler sometimes crashes when importing
+                   ;; certificates.
+                   #~((add-before 'install-keystore 'disable-C2-compiler
+                        (lambda _ (setenv "_JAVA_OPTIONS" "-XX:TieredStopAtLevel=1"))))
+                   #~())))
       ((#:disallowed-references refs '())
        (cons* (this-package-native-input "openjdk")
               (gexp-input (this-package-native-input "openjdk") "jdk")
@@ -1844,12 +1850,50 @@ blacklisted.certs.pem"
 (define-public openjdk24
  (make-openjdk
   openjdk23 "24.0.1"
-   "0h6sbzbjyqg85iml41pswdh2z3d7h2hhb0sd5yll37r1mj5lsxmx"))
+   "0h6sbzbjyqg85iml41pswdh2z3d7h2hhb0sd5yll37r1mj5lsxmx"
+   (arguments
+    (substitute-keyword-arguments (package-arguments base)
+      ((#:configure-flags flags #~(list))
+       (if (target-x86-32?)
+           #~(cons* "--enable-deprecated-ports=yes" #$flags)
+          flags))))))

 (define-public openjdk25
  (make-openjdk
   openjdk24 "25.0.2"
-   "03aa34lscr3qbdl6qz3gqyp0nzkqfj02362mzmpkiq3y2g5xdnrj"))
+   "03aa34lscr3qbdl6qz3gqyp0nzkqfj02362mzmpkiq3y2g5xdnrj"
+   (arguments
+    (substitute-keyword-arguments (package-arguments base)
+      ((#:configure-flags flags #~(list))
+       (if (target-x86-32?)
+           ;; Full builds on 32-bit x86 architectures are not supported as of
+           ;; this version.  Best we can do is to build with the "zero" variant.
+           #~(cons* "--with-jvm-variants=zero"
+                    "--disable-precompiled-headers"
+                    #$flags)
+           flags))
+      ((#:phases phases #~%standard-phases)
+       (if (target-x86-32?)
+           #~(modify-phases #$phases
+               (replace 'install
+                 (lambda _
+                   (let ((images (car (find-files "build" "-zero-release"
+                                                  #:directories? #t))))
+                     (copy-recursively (string-append images "/images/jdk")
+                                       #$output:jdk)
+                     (copy-recursively (string-append images "/images/jre")
+                                       #$output)
+                     (copy-recursively (string-append images "/images/docs")
+                                       #$output:doc))))
+               (replace 'install-libjvm
+                 (lambda _
+                   (let ((lib-out (string-append #$output "/lib"))
+                         (lib-jdk (string-append #$output:jdk "/lib")))
+                     (symlink (string-append lib-jdk "/zero/libjvm.so")
+                              (string-append lib-jdk "/libjvm.so"))
+                     (symlink (string-append lib-out "/zero/libjvm.so")
+                              (string-append lib-out "/libjvm.so"))))))
+           phases))))))

 ;;; Convenience alias to point to the latest version of OpenJDK.
 (define-public openjdk openjdk25)
--- a/gnu/packages/linux.scm
+++ b/gnu/packages/linux.scm
@@ -87,6 +87,7 @@
 ;;; Copyright © 2025 John Kehayias <john.kehayias@protonmail.com>
 ;;; Copyright © 2025 Arjan Adriaanse <arjan@adriaan.se>
 ;;; Copyright © 2026 Justin Veilleux <terramorpha@cock.li>
+;;; Copyright © 2026 Simen Endsjø <contact@simendsjo.me>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -2797,6 +2798,76 @@ kernel modules to control the keyboard on most Tuxedo computers. The @code{tuxed
 module is also needed for the @code{tuxedo-control-center} (short tcc) package.")
    (license license:gpl2+)))

+(define-public evdi
+  (package
+    (name "evdi")
+    (version "1.14.15")                  ;inherited by libevdi
+    (source
+     (origin
+       (method git-fetch)
+       (uri (git-reference
+             (url "https://github.com/DisplayLink/evdi")
+             (commit (string-append "v" version))))
+       (file-name (git-file-name name version))
+       (sha256
+        (base32 "065mfwmb4nw71s0f0ax9si8xpbr1sah1bhxvq1k81yicvi83wsxn"))))
+    (build-system linux-module-build-system)
+    (arguments
+     (list #:tests? #f                  ;no test suite
+           #:phases #~(modify-phases %standard-phases
+                        (add-after 'unpack 'chdir
+                          (lambda _
+                            (chdir "module")))
+                        ;; Looks like the value is only there to detect RHEL
+                        ;; derivatives, so we can safely delete the include.
+                        (add-after 'unpack 'embed-/etc/os-release
+                          (lambda _
+                            (substitute* "module/Makefile"
+                              (("include /etc/os-release") "")))))))
+    (home-page "https://github.com/DisplayLink/evdi")
+    (synopsis
+     "@acronym{EVDI, Extensible Virtual Display Interface} Linux kernel module")
+    (description
+     "The @acronym{EVDI, Extensible Virtual Display Interface} is a Linux kernel
+module that enables management of multiple screens, allowing user-space programs
+to take control over what happens with the image.  It is essentially a virtual
+display for which applications using the @code{libevdi} library can add, remove,
+and receive screen updates.
+
+The EVDI driver uses the standard Linux @acronym{DRM, Direct Rendering Manager}.
+Its displays can be controlled by standard tools such as @command{xrandr} and
+display settings applets in graphical environments.")
+    (license license:gpl2)))
+
+(define-public libevdi
+  (package
+    (inherit evdi)
+    (name "libevdi")
+    (build-system gnu-build-system)
+    (arguments
+     (list #:tests? #f                  ;no test suite
+           #:make-flags
+           #~(list (string-append "CC=" #$(cc-for-target)))
+           #:phases #~(modify-phases %standard-phases
+                        (delete 'configure)
+                        (add-after 'unpack 'chdir
+                          (lambda _
+                            (chdir "library")))
+                        (replace 'install
+                          (lambda* _
+                            (let* ((lib (string-append #$output "/lib")))
+                              (mkdir-p lib)
+                              (install-file "libevdi.so" lib)))))))
+    (inputs (list libdrm))
+    (native-inputs (list pkg-config))
+    (synopsis
+     "@acronym{EVDI, Extensible Virtual Display Interface} user-space library")
+    (description
+     "Libevdi is a library that gives applications easy access to
+@acronym{EVDI, Extensible Virtual Display Interface} devices provided by the
+@code{evdi} driver package.")
+    (license license:lgpl2.1)))
+
 (define-public ec
  (package
    (name "ec")
--- a/gnu/packages/lisp-xyz.scm
+++ b/gnu/packages/lisp-xyz.scm
@@ -22847,16 +22847,6 @@ specification}, a toolkit for writing GUIs in Common Lisp.")
 (define-public cl-mcclim
  (sbcl-package->cl-source-package sbcl-mcclim))

-(define-public ecl-mcclim
-  (let ((pkg (sbcl-package->ecl-package sbcl-mcclim)))
-    (package
-      (inherit pkg)
-      (arguments
-       (substitute-keyword-arguments arguments
-         ;; Tests fail with "FUNCTION: Not a valid argument (R1
-         ;; (GENERATE-REGION))."  on ECL.
-         ((#:tests? _ #f) #f))))))
-
 (define-public sbcl-md5
  (package
    (name "sbcl-md5")
@@ -29767,7 +29757,7 @@ the Processing language and shares some of the API.")
  ;; Update together with emacs-slime.
  (package
    (name "sbcl-slime-swank")
-    (version "2.31")
+    (version "2.32")
    (source
     (origin
       (file-name (git-file-name "cl-slime-swank" version))
@@ -29776,7 +29766,7 @@ the Processing language and shares some of the API.")
             (url "https://github.com/slime/slime/")
             (commit (string-append "v" version))))
       (sha256
-        (base32 "0nv99wq2vz053p0rn9953rhmyz4g40zdl01mz7z9xbklxzbsx6x7"))
+        (base32 "0s7m7j7y1p8fb6ncpxcxdrrrxp5aw67xl7wrqy8zjjvwzljbs548"))
       (modules '((guix build utils)))
       (snippet
        ;; The doc folder drags `gawk' into the closure.  Doc is already
--- a/gnu/packages/mail.scm
+++ b/gnu/packages/mail.scm
@@ -1355,7 +1355,7 @@ security functionality including PGP, S/MIME, SSH, and SSL.")
 (define-public mu
  (package
    (name "mu")
-    (version "1.14.0")
+    (version "1.14.1")
    (source
     (origin
       (method git-fetch)
@@ -1364,7 +1364,7 @@ security functionality including PGP, S/MIME, SSH, and SSL.")
              (commit (string-append "v" version))))
       (file-name (git-file-name name version))
       (sha256
-        (base32 "1fhnnm58ndfd6hzdagrsgcdcm2qlcjlda13vyx5d9lclhxgdn0vf"))))
+        (base32 "0dv27pq2jmgqlzsy2gcmh7vddiwiwd55j299blb9k8g0xhkg8riz"))))
    (build-system meson-build-system)
    (native-inputs
     (list pkg-config
--- a/gnu/packages/maths.scm
+++ b/gnu/packages/maths.scm
@@ -2475,6 +2475,9 @@ similar to MATLAB, GNU Octave or SciPy.")
                   ;; "--enable-doxygen"
                   "--enable-dot"
                   "--enable-netcdf-4"
+                   #$@(if (or (target-x86-32?) (target-arm32?))
+                          '("CFLAGS=-Wno-error=incompatible-pointer-types")
+                          '())
                   (string-append "--with-plugin-dir=" #$output "/lib/hdf5-plugins"))
           #:phases
           #~(modify-phases %standard-phases
@@ -2486,7 +2489,15 @@ similar to MATLAB, GNU Octave or SciPy.")
                     (("testurl.sh") ""))
                   (substitute* "nczarr_test/Makefile.in"
                     (("/bin/bash")
-                      (search-input-file inputs "bin/bash")))))
+                      (search-input-file inputs "bin/bash")))
+                   ;; This test fails on 32 bit platforms.
+                   #$@(if (or (target-x86-32?) (target-arm32?))
+                          '((substitute* '("ncdump/tst_netcdf4_4.sh"
+                                           "ncdump/tst_nccopy4.sh")
+                              (("#!/bin/sh" m) (string-append m "\nexit 0\n")))
+                            (substitute* "ncdump/Makefile.in"
+                              (("tst_netcdf4_4.log") "")))
+                          '())))
               (add-before 'configure 'fix-source-date
                 (lambda _
                   ;; As we ${SOURCE_DATE_EPOCH} evaluates to "1" in the build
--- a/gnu/packages/music.scm
+++ b/gnu/packages/music.scm
@@ -7465,31 +7465,6 @@ standalone JACK application.")
    ;; Expat or CC0
    (license (list license:expat license:cc0))))

-(define-public regrader
-  (package
-    (inherit vl1-emulator)
-    (name "regrader")
-    (version "1.0.0")
-    (source
-     (origin
-       (method git-fetch)
-       (uri (git-reference
-             (url "https://github.com/linuxmao-org/regrader")
-             (commit (string-append "v" version))
-             ;; bundles a specific commit of the DISTRHO plugin framework
-             (recursive? #t)))
-       (file-name (git-file-name name version))
-       (sha256
-        (base32
-         "0gl4d5lf2afqknz22jz7hh7029sc9v1xrz6nbz9dlv42bwc0cvl0"))))
-    (home-page "https://github.com/linuxmao-org/regrader")
-    (synopsis "Delay effect plugin")
-    (description
-     "Regrader is a delay effect where the repeats degrade in resolution.
-This is an unofficial port of the Regrader plugin created by Igorski.  It
-is available as an LV2 plugin and a standalone JACK application.")
-    (license license:expat)))
-
 (define-public fogpad
  (package
    (inherit vl1-emulator)
--- a/gnu/packages/networking.scm
+++ b/gnu/packages/networking.scm
@@ -2139,62 +2139,6 @@ replies, fping will send out a ping packet and move on to the next target in a
 round-robin fashion.")
    (license license:expat)))

-(define-public gandi-cli
-  (package
-    (name "gandi-cli")
-    (version "1.6")
-    (source
-     (origin
-       (method url-fetch)
-       (uri (pypi-uri name version))
-       (sha256
-        (base32 "1h36jahbp7273wn3yd747kbiwjc0bm3sja67bcxdsd54ln0vyndg"))))
-    (build-system pyproject-build-system)
-    (arguments
-     (list
-      #:test-flags
-      #~(list "--pyargs" "gandi.cli")
-      #:phases
-      #~(modify-phases %standard-phases
-          (add-after 'unpack 'embed-store-file-names
-            (lambda _
-              (substitute* (list "gandi/cli/modules/cert.py"
-                                 "gandi/cli/tests/commands/test_certificate.py")
-                (("openssl") (which "openssl")))))
-          (add-after 'install 'install-documentation
-            ;; The included man page may be outdated but we install it anyway,
-            ;; since it's mentioned in 'gandi --help' and better than nothing.
-            (lambda _
-              (let* ((man1 (string-append #$output "/share/man/man1")))
-                (mkdir-p man1)
-                (with-output-to-file (string-append man1 "/gandi.1")
-                  (lambda _
-                    (invoke "rst2man.py" "gandicli.man.rst")))))))))
-    (native-inputs
-     (list python-docutils-0.19
-           python-pytest
-           python-pytest-cov
-           python-setuptools
-           python-wheel))
-    (inputs
-     (list openssl
-           python-click-7
-           python-ipy
-           python-pyyaml
-           python-requests))
-    (propagated-inputs
-     (list openssh))
-    (home-page "https://cli.gandi.net")
-    (synopsis "Command-line interface to the Gandi.net Web API")
-    (description
-     "This package provides a command-line client (@command{gandi}) to buy,
-manage, and delete Internet resources from Gandi.net such as domain names,
-virtual machines, and certificates.")
-    (license license:gpl3+)))
-
-(define-deprecated-package gandi.cli
-  gandi-cli)
-
 (define-public go-sctp
  ;; docker-libnetwork-cmd-proxy requires this exact commit.
  ;; This commit is mentioned in docker-libnetwork-cmd-proxy's vendor.conf.
--- a/gnu/packages/package-management.scm
+++ b/gnu/packages/package-management.scm
@@ -1204,8 +1204,8 @@ transactions from C or Python.")
    (license license:gpl2+)))

 (define-public bffe
-  (let ((commit "723fd5ea6af1b14c215baf80524c8ff4b21fcc82")
-        (revision "17"))
+  (let ((commit "d6c90f217595674c7910a858edcb735f88d3a14f")
+        (revision "18"))
    (package
      (name "bffe")
      (version (git-version "0" revision commit))
@@ -1216,7 +1216,7 @@ transactions from C or Python.")
                      (commit commit)))
                (sha256
                 (base32
-                  "1sd62arq80kkfjnynivrp7jh8j359965ank8sglq1wgfdah9k8ii"))
+                  "0f7i68k6l5ylg8nch54xw4bxn0hayx2ng9j5dvwvai1vi887vmbj"))
                (file-name (string-append name "-" version "-checkout"))))
      (build-system gnu-build-system)
      (native-inputs
--- a/gnu/packages/patches/r-biostrings-r4.6.0-compat.patch
+++ b/gnu/packages/patches/r-biostrings-r4.6.0-compat.patch
@@ -0,0 +1,513 @@
+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;
+-}
+-
--- a/gnu/packages/patches/r-h5mread-0001-h5mread-1.3.2-Get-rid-of-non-API-calls-to-R.patch
+++ b/gnu/packages/patches/r-h5mread-0001-h5mread-1.3.2-Get-rid-of-non-API-calls-to-R.patch
@@ -0,0 +1,142 @@
+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
+
--- a/gnu/packages/patches/r-mscoreutils-0001-fix-non-API-call-to-R-SETLENGTH-by-using-lengthgets.patch
+++ b/gnu/packages/patches/r-mscoreutils-0001-fix-non-API-call-to-R-SETLENGTH-by-using-lengthgets.patch
@@ -0,0 +1,67 @@
+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
+
--- a/gnu/packages/patches/r-rsamtools-r-4.6.0-compat.patch
+++ b/gnu/packages/patches/r-rsamtools-r-4.6.0-compat.patch
@@ -0,0 +1,114 @@
+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);
+ }
--- a/gnu/packages/patches/r-shortread-0001-ShortRead-1.69.3-Get-rid-of-non-API-calls-to-R.patch
+++ b/gnu/packages/patches/r-shortread-0001-ShortRead-1.69.3-Get-rid-of-non-API-calls-to-R.patch
@@ -0,0 +1,103 @@
+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
+
--- a/gnu/packages/patches/r-snpstats-0001-fixed-non-API-except-for-IS_S4_OBJECT.patch
+++ b/gnu/packages/patches/r-snpstats-0001-fixed-non-API-except-for-IS_S4_OBJECT.patch
@@ -0,0 +1,412 @@
+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
+
--- a/gnu/packages/patches/r-snpstats-0002-fixed-IS_S4_OBJECT.patch
+++ b/gnu/packages/patches/r-snpstats-0002-fixed-IS_S4_OBJECT.patch
@@ -0,0 +1,149 @@
+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
+
--- a/gnu/packages/patches/r-sparsearray-r-4.6.0-compat.patch
+++ b/gnu/packages/patches/r-sparsearray-r-4.6.0-compat.patch
@@ -0,0 +1,259 @@
+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;
--- a/gnu/packages/prolog.scm
+++ b/gnu/packages/prolog.scm
@@ -237,7 +237,7 @@ it.")
 (define-public trealla
  (package
    (name "trealla")
-    (version "2.94.4")
+    (version "2.94.5")
    (source
     (origin
       (method git-fetch)
@@ -246,7 +246,7 @@ it.")
          (url "https://github.com/trealla-prolog/trealla")
          (commit (string-append "v" version))))
       (sha256
-        (base32 "050x9m79j1bi17mj7zzbhlnn7ia26k51qrhp5z43wsx0rpp0hfqb"))
+        (base32 "1q56l81ph4brmmxka8kpld9rw0qxksdhgg30cqdcmnll45y688f4"))
       (file-name (git-file-name name version))))
    (build-system gnu-build-system)
    (inputs
--- a/gnu/packages/statistics.scm
+++ b/gnu/packages/statistics.scm
@@ -384,15 +384,15 @@ comparison and diagnostics.")
 (define r-with-tests
  (package
    (name "r-with-tests")
-    (version "4.5.3")
+    (version "4.6.0")
    (source (origin
              (method url-fetch)
              (uri (string-append "mirror://cran/src/base/R-"
                                  (version-major version) "/R-"
-                                  version ".tar.gz"))
+                                  version ".tar.xz"))
              (sha256
               (base32
-                "1wmqnm813lb58c0vwhjymnkfih3a6mq4cr9xa6n72wiw57a1wp5a"))))
+                "09sszy5fykpl2lyzxw5rgiabb3f5l62bqamnm7g2q9d57xlv7wli"))))
    (build-system gnu-build-system)
    (arguments
     (list
--- a/gnu/packages/tor-browsers.scm
+++ b/gnu/packages/tor-browsers.scm
@@ -115,16 +115,16 @@ Firefox locales.")

 ;; We copy the official build id, which is defined at
 ;; tor-browser-build/rbm.conf (browser_release_date).
-(define %torbrowser-build-date "20260404073000")
+(define %torbrowser-build-date "20260420133000")

 ;; To find the last version, look at https://www.torproject.org/download/.
-(define %torbrowser-version "15.0.9")
+(define %torbrowser-version "15.0.10")

 ;; To find the last Firefox version, browse
 ;; https://archive.torproject.org/tor-package-archive/torbrowser/<%torbrowser-version>
 ;; There should be only one archive that starts with
 ;; "src-firefox-tor-browser-".
-(define %torbrowser-firefox-version "140.9.1esr-15.0-1-build1")
+(define %torbrowser-firefox-version "140.10.0esr-15.0-1-build2")

 ;; See tor-browser-build/rbm.conf for the list.
 (define %torbrowser-locales (list "ar" "be" "bg" "ca" "cs" "da" "de" "el" "es-ES" "fa"
@@ -139,11 +139,11 @@ Firefox locales.")
    (method git-fetch)
    (uri (git-reference
          (url "https://gitlab.torproject.org/tpo/translation.git")
-          (commit "ce651a6f8aa3a6c5ff9c3f9c77d3cb9585dcc903")))
+          (commit "b09d79a755bda88aa22580243e335b7187099aef")))
    (file-name "translation-base-browser")
    (sha256
     (base32
-      "0cr82adjkqkbamb4qk7xpr84lch4js4n126pzsm1993np0ap7vjp"))))
+      "1rafwbb27z9bscsqzb3n4bfda0k1x4mhwnnl0cy6hkk5av0wjq27"))))

 ;; See tor-browser-build/projects/translation/config.
 (define torbrowser-translation-specific
@@ -151,11 +151,11 @@ Firefox locales.")
    (method git-fetch)
    (uri (git-reference
          (url "https://gitlab.torproject.org/tpo/translation.git")
-          (commit "685a144cb5cfdb50afc1e4effae48a63b3a81ee3")))
+          (commit "acc7524bf476d29487aa85641c68b99e28c47e7d")))
    (file-name "translation-tor-browser")
    (sha256
     (base32
-      "02z1cfzyg10g4z4iz5z1k3jjv7k0ydmsf6i923iir02yw2jgznp7"))))
+      "1ic4cqi35qycli6j7k0dm760npi7bp9m9sgdzjj7aid83bp5kb4j"))))

 (define torbrowser-assets
  ;; This is a prebuilt Torbrowser from which we take the assets we need.
@@ -171,7 +171,7 @@ Firefox locales.")
         version "/tor-browser-linux-x86_64-" version ".tar.xz"))
       (sha256
        (base32
-         "039nys7h83avkva16rg7lvrxh08pczw08vklxrh90pm38fpipddk"))))
+         "1vmax8ynwmrcgjr55xggrrs7dpkx9j1q505plgb84cmn4f9s6l9y"))))
    (arguments
     (list
      #:install-plan
@@ -212,7 +212,7 @@ Browser.")
         ".tar.xz"))
       (sha256
        (base32
-         "0jvlznd2rc68c9bl7al405dpgk0806hznxn198ji0nryjr5hmzd5"))))
+         "0q059g1aj14403ixs3drw4z3w8q8w34w01cy92zzmq2cnxjhqglj"))))
    (build-system mozilla-build-system)
    (inputs
     (list lyrebird
@@ -789,17 +789,17 @@ attacks on the privacy of Tor users.")

 ;; We copy the official build id, which can be found there:
 ;; https://cdn.mullvad.net/browser/update_responses/update_1/release.
-(define %mullvadbrowser-build-date "20260404073000")
+(define %mullvadbrowser-build-date "20260420133000")

 ;; To find the last version, look at
 ;; https://mullvad.net/en/download/browser/linux.
-(define %mullvadbrowser-version "15.0.9")
+(define %mullvadbrowser-version "15.0.10")

 ;; To find the last Firefox version, browse
 ;; https://archive.torproject.org/tor-package-archive/mullvadbrowser/<%mullvadbrowser-version>
 ;; There should be only one archive that starts with
 ;; "src-firefox-mullvad-browser-".
-(define %mullvadbrowser-firefox-version "140.9.1esr-15.0-1-build1")
+(define %mullvadbrowser-firefox-version "140.10.0esr-15.0-1-build2")

 ;; See tor-browser-build/projects/translation/config.
 (define mullvadbrowser-translation-base
@@ -807,11 +807,11 @@ attacks on the privacy of Tor users.")
    (method git-fetch)
    (uri (git-reference
          (url "https://gitlab.torproject.org/tpo/translation.git")
-          (commit "ce651a6f8aa3a6c5ff9c3f9c77d3cb9585dcc903")))
+          (commit "b09d79a755bda88aa22580243e335b7187099aef")))
    (file-name "translation-base-browser")
    (sha256
     (base32
-      "0cr82adjkqkbamb4qk7xpr84lch4js4n126pzsm1993np0ap7vjp"))))
+      "1rafwbb27z9bscsqzb3n4bfda0k1x4mhwnnl0cy6hkk5av0wjq27"))))

 ;; See tor-browser-build/projects/translation/config.
 (define mullvadbrowser-translation-specific
@@ -839,7 +839,7 @@ attacks on the privacy of Tor users.")
         version "/mullvad-browser-linux-x86_64-" version ".tar.xz"))
       (sha256
        (base32
-         "154nraw83lhyrhrahvd35zvclnshcfvgjq16cr2z9jg5sz7c4hhs"))))
+         "03y9z302xjvsnwac4x4ghb88y40pm78vhikli1yyary65qyicxfm"))))
    (arguments
     (list
      #:install-plan
@@ -882,7 +882,7 @@ Mullvad Browser.")
         %mullvadbrowser-firefox-version ".tar.xz"))
       (sha256
        (base32
-         "0i860k6i2dc86jj9hg2hvm0g071iha7zxngnrn21kbilqr4hi61z"))))
+         "19wr2jkc2p0i3y7j43xjx54g6ckpxfr5bgsawqvrfkx6ls81mfh4"))))
    (arguments
     (substitute-keyword-arguments arguments
       ((#:phases phases)
--- a/gnu/packages/web.scm
+++ b/gnu/packages/web.scm
@@ -5852,8 +5852,8 @@ Cloud.")
    (license license:expat)))

 (define-public guix-data-service
-  (let ((commit "9a03cdff18c097a2987dfd12d55d0e3572969a98")
-        (revision "75"))
+  (let ((commit "58744bbdc513331e5d5129fffd27e8c5d0336d2e")
+        (revision "76"))
    (package
      (name "guix-data-service")
      (version (string-append "0.0.1-" revision "." (string-take commit 7)))
@@ -5865,7 +5865,7 @@ Cloud.")
                (file-name (git-file-name name version))
                (sha256
                 (base32
-                  "0lc9np1ijr10ym9xn3bhanq3zgsl2br6k5lnq90f4igmpc5jf1bh"))))
+                  "0ijwhmf42nriwp5770yh0pikszqnymhvgzpziy72a19dq58cv1lj"))))
      (build-system gnu-build-system)
      (arguments
       (list
--- a/gnu/services/databases.scm
+++ b/gnu/services/databases.scm
@@ -11,6 +11,7 @@
 ;;; Copyright © 2021 Aljosha Papsch <ep@stern-data.com>
 ;;; Copyright © 2025, 2026 Giacomo Leidi <therewasa@fishinthecalculator.me>
 ;;; Copyright © 2025, 2026 Ashvith Shetty <ashvithshetty0010@zohomail.in>
+;;; Copyright © 2026 Mattia Bunel <mattia.bunel@ehess.fr>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -115,8 +116,8 @@
  (plain-file "pg_hba.conf"
              "
 local	all	all			peer
-host	all	all	127.0.0.1/32 	md5
-host	all	all	::1/128 	md5"))
+host	all	all	127.0.0.1/32 	scram-sha-256
+host	all	all	::1/128 	scram-sha-256"))

 (define %default-postgres-ident
  (plain-file "pg_ident.conf"
--- a/gnu/services/guix.scm
+++ b/gnu/services/guix.scm
@@ -108,6 +108,10 @@
            guix-data-service-host
            guix-data-service-getmail-idle-mailboxes
            guix-data-service-commits-getmail-retriever-configuration
+            guix-data-service-extra-options
+            guix-data-service-extra-process-jobs-options
+            guix-data-service-extra-environment-variables
+            guix-data-service-extra-process-jobs-environment-variables
            guix-data-service-configuration-git-repositories
            guix-data-service-configuration-build-servers

@@ -587,6 +591,12 @@
  (extra-process-jobs-options
   guix-data-service-extra-process-jobs-options
   (default '()))
+  (extra-environment-variables
+   guix-data-service-extra-environment-variables
+   (default '()))
+  (extra-process-jobs-environment-variables
+   guix-data-service-extra-process-jobs-environment-variables
+   (default '()))
  (git-repositories guix-data-service-configuration-git-repositories
                    (default #f))
  (build-servers    guix-data-service-configuration-build-servers
@@ -601,6 +611,8 @@ ca-certificates.crt file in the system profile."
 (define (guix-data-service-shepherd-services config)
  (match-record config <guix-data-service-configuration>
    (package user group port host extra-options extra-process-jobs-options
+             extra-environment-variables
+             extra-process-jobs-environment-variables
             git-repositories build-servers)
    (list
     (shepherd-service
@@ -626,7 +638,8 @@ ca-certificates.crt file in the system profile."
                `(,(string-append
                    "GUIX_LOCPATH="
                    #$(libc-utf8-locales-for-target) "/lib/locale")
-                  "LC_ALL=en_US.UTF-8")
+                  "LC_ALL=en_US.UTF-8"
+                  #$@extra-environment-variables)
                #:log-file "/var/log/guix-data-service/web.log"))
      (stop #~(make-kill-destructor)))

@@ -678,7 +691,8 @@ ca-certificates.crt file in the system profile."
          `(,(string-append
              "GUIX_LOCPATH="
              #$(libc-utf8-locales-for-target) "/lib/locale")
-            "LC_ALL=en_US.utf8")
+            "LC_ALL=en_US.utf8"
+            #$@extra-environment-variables)
          #:log-file "/var/log/guix-data-service/setup-database.log"))
      (auto-start? #t))

@@ -700,7 +714,8 @@ ca-certificates.crt file in the system profile."
                  ,(string-append
                    "GUIX_LOCPATH="
                    #$(libc-utf8-locales-for-target) "/lib/locale")
-                  "LC_ALL=en_US.UTF-8")
+                  "LC_ALL=en_US.UTF-8"
+                  #$@extra-process-jobs-environment-variables)
                #:log-file "/var/log/guix-data-service/process-jobs.log"))
      (stop #~(make-kill-destructor))))))