gnu: linux-libre: Update default version to 7.0.

* gnu/packages/linux.scm (linux-libre-version, linux-libre-gnu-revision,
linux-libre-pristine-source, linux-libre-source, linux-libre,
linux-libre-arm64-mnt-reform): Update to 7.0.

gnu/local.mk

@@ -1452,7 +1452,6 @@ dist_patch_DATA =						\
   %D%/packages/patches/ghc-aeson-encodeDouble.patch		\
   %D%/packages/patches/ghc-basement-fix-32bit.patch		\
   %D%/packages/patches/ghc-bytestring-handle-ghc9.patch	\
-  %D%/packages/patches/ghc-chell-quickcheck-enable-qc-2.15.patch	\
   %D%/packages/patches/ghc-clock-realfrag.patch	\
   %D%/packages/patches/ghc-language-haskell-extract-ghc-8.10.patch	\
   %D%/packages/patches/ghc-memory-fix-32bit.patch		\
@@ -2369,8 +2368,16 @@ 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	\
@@ -2455,7 +2462,6 @@ dist_patch_DATA =						\
   %D%/packages/patches/shared-mime-info-xdgmime-path.patch	\
   %D%/packages/patches/sharutils-CVE-2018-1000097.patch		\
   %D%/packages/patches/showtime-python-3.11-compat.patch        \
-  %D%/packages/patches/simpleitk-r-4.6.0.patch			\
   %D%/packages/patches/sipwitch-fix-build-with-exosip5.patch	\
   %D%/packages/patches/slim-config.patch			\
   %D%/packages/patches/slim-gcc-14.patch			\
@@ -2490,7 +2496,6 @@ dist_patch_DATA =						\
   %D%/packages/patches/swift-corelibs-libdispatch-5.7.3-modulemap.patch	\
   %D%/packages/patches/swift-llvm-5.7.3-linux.patch	\
   %D%/packages/patches/swig-support-gcc-12.patch		\
-  %D%/packages/patches/swig-support-r-4.6.0.patch		\
   %D%/packages/patches/swish-e-search.patch			\
   %D%/packages/patches/swish-e-format-security.patch		\
   %D%/packages/patches/t1lib-CVE-2010-2642.patch		\

gnu/packages/audio.scm

@@ -2135,17 +2135,7 @@ envelope follower, distortion effects, tape effects and more.")
 	        (base32
                  "01hnx4hhbz3ap3bw15s42q4q1mw1mhdjwygq4550wvjfg6k4ga8w"))))
       (build-system waf-build-system)
-      (arguments
-       (list
-        #:tests? #false ;There are no tests.
-        #:phases
-        '(modify-phases %standard-phases
-           (add-after 'unpack 'python3.12-compatibility
-             (lambda _
-               (substitute* "waflib/Context.py"
-                 (("imp.new_module") "types.ModuleType")
-                 (("import os, re, imp, sys")
-                  "import os, re, types, sys")))))))
+      (arguments (list #:tests? #false)) ;There are no tests.
       (inputs (list lv2))
       (native-inputs (list pkg-config))
       (home-page "https://git.drobilla.net/cgit.cgi/omins.lv2.git/")

gnu/packages/bioinformatics.scm

@@ -1430,86 +1430,33 @@ within this package are the 3000 bone marrow cells used for vignettes.")
       (license license:gpl3))))
 
 (define-public r-pizzarr
-  (package
-    (name "r-pizzarr")
-    (version "0.2.0")
-    (source
-     (origin
-       (method git-fetch)
-       (uri (git-reference
-              (url "https://github.com/keller-mark/pizzarr")
-              (commit (string-append "v" version))))
-       (file-name (git-file-name name version))
-       (sha256
-        (base32 "1m38c57pfliycxkhb3mwgh01cl2q76r1jhd3vnk07dbfhqdbqai6"))))
-    (properties `((upstream-name . "pizzarr")))
-    (build-system cargo-build-system)
-    (arguments
-     (list
-      #:imported-modules
-      (append %cargo-build-system-modules
-              %r-build-system-modules)
-      #:modules
-      '((guix build cargo-build-system)
-        ((guix build r-build-system) #:prefix r:)
-        (guix build utils))
-      #:cargo-build-flags
-      '(list "--target-dir=./target" "--release")
-      #:phases
-      #~(append (modify-phases %standard-phases
-                  (add-after 'unpack 'patch-Makevars
-                    (lambda _
-                      ;; At this point we've already built the Rust parts.
-                      (substitute* "src/Makevars.in"
-                        (("^all:.*") "all:")
-                        (("^\\$\\(STATLIB\\):") "NOBODYCARES:")
-                        (("@PKG_LIBS_EXTRA@") "@PKG_LIBS_EXTRA@ -lzstd -lz"))))
-                  (add-after 'patch-Makevars 'chdir
-                    (lambda _ (chdir "src/rust")))
-                  (add-after 'chdir 'patch-rust-dependency
-                    (lambda _
-                      (setenv "RUSTFLAGS" "--print=native-static-libs")
-                      (substitute* "Cargo.toml"
-                        (("extendr-api = \\{ git.* \\}") "extendr-api = \"0.8.1\""))))
-                  (add-after 'package 'chdir-back
-                    (lambda _ (chdir "../..")))
-                  (delete 'install)
-                  (delete 'check))
-                (modify-phases (@ (guix build r-build-system) %standard-phases)
-                  (delete 'unpack)
-                  (replace 'patch-tests
-                    (lambda* (#:key inputs outputs tests? #:allow-other-keys)
-                      ((assoc-ref (@ (guix build r-build-system) %standard-phases)
-                                  'patch-tests)
-                       #:skipped-tests
-                       ;; These files contain tests that require Internet access.
-                       '("test-compat.R" "test-get.R"
-                         ;; HttpStore requires the crul package
-                         ("test-zarrs-dispatch.R" "can_use_zarrs_create returns FALSE for HttpStore")
-                         ("test-zarrs-store-cache.R" "HttpStore get_store_identifier returns URL")))))
-                  (replace 'check
-                    (lambda* (#:key inputs outputs tests? #:allow-other-keys)
-                      ((assoc-ref (@ (guix build r-build-system) %standard-phases)
-                                  'check)
-                       #:test-target "tests"
-                       #:test-types #false
-                       #:inputs inputs
-                       #:outputs outputs
-                       #:tests? tests?)))))))
-    (propagated-inputs (list r-jsonlite r-memoise r-qs2 r-r6 r-stringr))
-    (inputs
-     (cons* openssl zlib `(,zstd "lib")
-            (cargo-inputs 'r-pizzarr)))
-    (native-inputs
-     (list pkg-config
-           r-minimal r-pbapply r-testthat r-vcr))
-    (home-page "https://github.com/keller-mark/pizzarr")
-    (synopsis "Slice into Zarr arrays in R")
-    (description
-     "This package provides an implementation of chunked, compressed,
+  (let ((commit "5f4705789ba29344dcb97023f290a26a7f7abd0c")
+        (revision "2"))
+    (package
+      (name "r-pizzarr")
+      (version (git-version "0.1.0" revision commit))
+      (source
+       (origin
+         (method git-fetch)
+         (uri (git-reference
+               (url "https://github.com/keller-mark/pizzarr")
+               (commit commit)))
+         (file-name (git-file-name name version))
+         (sha256
+          (base32 "17pd6bk8kvnrvvyfqvm8q47kzghlfyfjdd9b7cwiazc5xr4vz6f0"))))
+      (properties `((upstream-name . "pizzarr")))
+      (build-system r-build-system)
+      ;; Some tests require Internet access.
+      (arguments (list #:tests? #false))
+      (propagated-inputs (list r-jsonlite r-memoise r-qs r-r6 r-stringr))
+      (native-inputs (list r-pbapply r-testthat r-vcr))
+      (home-page "https://github.com/keller-mark/pizzarr")
+      (synopsis "Slice into Zarr arrays in R")
+      (description
+       "This package provides an implementation of chunked, compressed,
 N-dimensional arrays for R, Zarr specification version 2 (2024)
 <doi:10.5281/zenodo.11320255>.")
-    (license license:expat)))
+      (license license:expat))))
 
 (define-public r-rhtslib12
   (let ((commit "ee186daf04876969c7f31c16a0e0fda8e7c16a30")
@@ -4625,11 +4572,8 @@ into separate processes; and more.")
      (list
       #:phases
       #~(modify-phases %standard-phases
-          (add-after 'unpack 'python3.12-compatibility
+          (add-after 'unpack 'python3.11-compatibility
             (lambda _
-              ;; This was removed in Python 3.12
-              (substitute* "Bio/Align/_aligners.c"
-                (("case PyUnicode_WCHAR_KIND:") ""))
               ;; Py_TYPE was changed to an inline static function in Python
               ;; 3.11, so it cannot be used on the left-hand side.
               (substitute* "Bio/triemodule.c"
@@ -14046,20 +13990,33 @@ of scRNA-seq data.")
 (define-public r-misha
   (package
     (name "r-misha")
-    (version "5.6.23")
+    (version "4.1.0")
     (source
      (origin
        (method git-fetch)
        (uri (git-reference
              (url "https://github.com/tanaylab/misha")
-             (commit (string-append "v" version))))
+             (commit version)))
        (file-name (git-file-name name version))
        (sha256
         (base32
-         "1k973j04iq02dy4f7qgi3cmp3rcx5yinyx0m7vyag54rqanird8x"))))
+         "0bgivx3lzjh3173jsfrhb5kvhjsn53br0n4hmyx7i3dwy2cnnp2p"))
+       ;; Delete bundled executable.
+       (snippet
+        '(delete-file "exec/bigWigToWig"))))
     (build-system r-build-system)
-    (propagated-inputs (list r-curl r-digest r-magrittr r-ps r-yaml))
-    (native-inputs (list r-knitr r-testthat))
+    (arguments
+     `(#:phases
+       (modify-phases %standard-phases
+         (add-after 'unpack 'do-not-use-bundled-bigWigToWig
+           (lambda* (#:key inputs #:allow-other-keys)
+             (substitute* "R/misha.R"
+               (("get\\(\".GLIBDIR\"\\), \"/exec/bigWigToWig")
+                (string-append "\""
+                               (assoc-ref inputs "kentutils")
+                               "/bin/bigWigToWig"))))))))
+    (inputs
+     (list kentutils))
     (home-page "https://github.com/tanaylab/misha")
     (synopsis "Toolkit for analysis of genomic data")
     (description "This package is intended to help users to efficiently
@@ -18859,28 +18816,26 @@ activity prediction from transcriptomics data, and its R implementation
       (build-system r-build-system)
       (arguments
        (list
-        #:skipped-tests
-        ;; These tests attempt to connect to the Internet.
-        '(("test-liana_utils.R" "Test liana pipe")
-          ("test-liana_tensor.R"
-           ".*Test tensor wrapper.*"
-           ".*Test decompose_tensor.*")
-          ;; XXX: This test returns a data.frame instead of an error.
-          ("test-liana_cytotalk.R" ".*Test Cytotalk Wrap.*"))
         #:phases
         '(modify-phases %standard-phases
            ;; This is needed to find ~/.config/OmnipathR/omnipathr.yml
            (add-after 'unpack 'set-HOME
              (lambda _ (setenv "HOME" "/tmp")))
-           (add-after 'unpack 'seurat-compatibility
+           (add-after 'unpack 'disable-bad-tests
              (lambda _
-               ;; The `slot` argument of `GetAssayData()` was deprecated in
-               ;; SeuratObject 5.0.0.
-               (substitute* '("R/cellchat_pipe.R"
-                              "R/sca_pipe.R"
-                              "R/liana_prep.R"
-                              "R/natmi_pipe.R")
-                 (("slot =") "layer =")))))))
+               ;; These tests attempt to connect to the Internet.
+               (substitute* "tests/testthat/test-liana_utils.R"
+                 ((".*Test liana pipe.*" m)
+                  (string-append m "skip('guix')\n")))
+               (substitute* "tests/testthat/test-liana_tensor.R"
+                 ((".*Test tensor wrapper.*" m)
+                  (string-append m "skip('guix')\n"))
+                 ((".*Test decompose_tensor.*" m)
+                  (string-append m "skip('guix')\n")))
+               ;; XXX: This test returns a data.frame instead of an error.
+               (substitute* "tests/testthat/test-liana_cytotalk.R"
+                 ((".*Test Cytotalk Wrap.*" m)
+                  (string-append m "skip('guix')\n"))))))))
       (propagated-inputs
        (list r-basilisk
              r-basilisk-utils
@@ -21745,6 +21700,70 @@ want to explore e.g.: the function of a set of differentially expressed
 genes.")
       (license license:gpl3))))
 
+(define-public r-seurat-utils
+  (let ((commit "c0374cc9e25ce391ba8013fda0f8c7babbb9201d")
+        (revision "1"))
+    (package
+      (name "r-seurat-utils")
+      (version (git-version "2.5.0" revision commit))
+      (source (origin
+                (method git-fetch)
+                (uri (git-reference
+                      (url "https://github.com/vertesy/Seurat.utils")
+                      (commit commit)))
+                (file-name (git-file-name name version))
+                (sha256
+                 (base32
+                  "15l86b43q245gzz7gsr5rhs4sir74lc14d64yqxfqcb0zrb2bzzd"))))
+      (properties `((upstream-name . "Seurat.utils")))
+      (build-system r-build-system)
+      (propagated-inputs (list r-codeandroll2
+                               r-cowplot
+                               r-databaselinke-r
+                               r-dplyr
+                               r-enhancedvolcano
+                               r-foreach
+                               r-ggcorrplot
+                               r-ggexpress
+                               r-ggplot2
+                               r-ggpubr
+                               r-ggrepel
+                               r-hgnchelper
+                               r-htmlwidgets
+                               r-job
+                               r-magrittr
+                               r-markdownhelpers
+                               r-markdownreports
+                               r-matrix
+                               r-matrixstats
+                               r-pheatmap
+                               r-plotly
+                               r-princurve
+                               r-qs
+                               r-r-utils
+                               r-readr
+                               r-readwriter
+                               r-reshape2
+                               r-rstudioapi
+                               r-scales
+                               r-seurat
+                               r-soupx
+                               r-sparsematrixstats
+                               r-stringendo
+                               r-stringr
+                               r-tibble
+                               r-tictoc
+                               r-tidyverse
+                               r-vroom))
+      (home-page "https://github.com/vertesy/Seurat.utils")
+      (synopsis "Collection of utility functions for Seurat")
+      (description
+       "This is a collection of utility functions for Seurat.  These functions
+allow the automation and multiplexing of plotting, 3D plotting, visualization
+of statistics & QC, interaction with the Seurat object.  Some functionalities
+require functions from CodeAndRoll and MarkdownReports libraries.")
+      (license license:gpl3))))
+
 (define-public r-seuratextend
   (let ((commit "5dacd7c1e1da3bc0e78ab81d60056f6d7da3d386")
         (revision "1"))
@@ -22459,39 +22478,38 @@ frames with arbitrary sets of columns.")
       (license license:expat))))
 
 (define-public r-imagearray
-  (package
-    (name "r-imagearray")
-    (version "1.0.0")
-    (source
-     (origin
-       (method url-fetch)
-       (uri (bioconductor-uri "ImageArray" version))
-       (sha256
-        (base32 "07zq5fcw2dsvm4qaksaj4gy9gj5lxcgq82l497c5kgvl4wba049c"))))
-    (properties `((upstream-name . "ImageArray")))
-    (build-system r-build-system)
-    (arguments
-     (list
-      #:skipped-tests
-      ;; RBiomFormats is not installed.
-      '(("test-array.R" "check indexing \\(BFArray\\)"))))
-    (propagated-inputs (list r-delayedarray
-                             r-ebimage
-                             r-hdf5array
-                             r-magick
-                             r-rarr
-                             r-rhdf5
-                             r-s4arrays
-                             r-s4vectors
-                             r-zarrarray))
-    (native-inputs (list r-ggplot2 r-knitr r-testthat))
-    (home-page "https://github.com/BIMSBbioinfo/ImageArray")
-    (synopsis "Framework for on-disk and in-memory image arrays")
-    (description
-     "@code{ImageArray} provides a framework for on-disk and in-memory image
-arrays, specifically for pyramidal images stored in HDF5, Zarr and life
-sciences image file formats (OME Bio-Formats).")
-    (license license:expat)))
+  (let ((commit "2f90694fa33ed8320a6a2f7e0ad5c8a1796cbfc6")
+        (revision "1"))
+    (package
+      (name "r-imagearray")
+      (version (git-version "0.99.6" revision commit))
+      (source
+       (origin
+         (method git-fetch)
+         (uri (git-reference
+               (url "https://github.com/BIMSBbioinfo/ImageArray")
+               (commit commit)))
+         (file-name (git-file-name name version))
+         (sha256
+          (base32 "1mf68b007dc5wdzdva4vkjgkavgagjk45qv05f7vahbpi24yjj4n"))))
+      (properties `((upstream-name . "ImageArray")))
+      (build-system r-build-system)
+      (propagated-inputs (list r-delayedarray
+                               r-ebimage
+                               r-hdf5array
+                               r-magick
+                               r-rarr
+                               r-rhdf5
+                               r-s4arrays
+                               r-s4vectors))
+      (native-inputs (list r-knitr r-testthat))
+      (home-page "https://github.com/BIMSBbioinfo/ImageArray")
+      (synopsis "Framework for on-disk and in-memory image arrays")
+      (description
+       "@code{ImageArray} provides a framework for on-disk and in-memory image
+arrays, specifically for pyramidal images stored in either HDF5 files or Zarr
+stores.")
+      (license license:expat))))
 
 (define-public r-velocyto
   (let ((commit "d7790346cb99f49ab9c2b23ba70dcf9d2c9fc350")
@@ -22575,7 +22593,7 @@ dependencies of @code{VoltRon} package.")
 (define-public r-voltron
   (package
     (name "r-voltron")
-    (version "0.2.6")
+    (version "0.2.5")
     (source
      (origin
        (method git-fetch)
@@ -22584,7 +22602,7 @@ dependencies of @code{VoltRon} package.")
               (commit (string-append "v" version))))
        (file-name (git-file-name name version))
        (sha256
-        (base32 "00fl5dmyd9ad4hd0cblgi0415sf6q4q67wh04r7fws828vs5vaj1"))))
+        (base32 "057n4yipkq3gnlyrb63l2ryi78nlmaas02avargm352g5ra1xl9s"))))
     (properties `((upstream-name . "VoltRon")))
     (build-system r-build-system)
     (arguments
@@ -22648,15 +22666,18 @@ guix_python <- \"~a\";"
                              r-irlba
                              r-magick
                              r-matrix
+                             r-pizzarr
                              r-rann
                              r-rcdt
                              r-rcpp
                              r-rcppannoy
                              r-rcpparmadillo
+                             r-reshape2
+                             r-reticulate
+                             r-rhdf5
                              r-rjson
                              r-rlang
                              r-s4arrays
-                             r-s4vectors
                              r-shiny
                              r-shinyjs
                              r-sp
@@ -22709,8 +22730,8 @@ spots, cells and even molecules.")
     (license license:expat)))
 
 (define-public r-zarrdataframe
-  (let ((commit "f5f671521934b2afc3c511f8c09181bc7bb789a4")
-        (revision "3"))
+  (let ((commit "84c7db2f6f5f84b4a4308f8eb72bedc131fb68bc")
+        (revision "2"))
     (package
       (name "r-zarrdataframe")
       (version (git-version "0.0.0" revision commit))
@@ -22722,13 +22743,13 @@ spots, cells and even molecules.")
                (commit commit)))
          (file-name (git-file-name name version))
          (sha256
-          (base32 "0klp2njn6qsa8n6c01v1z2dfaa93lhbzhwhbyhl23h8gg7d28yc1"))))
+          (base32 "1idrvdlzbwyixlg830sn19vfdn3n3irmlyr4ncf7dpk72r08g3hw"))))
       (properties
        '((upstream-name . "ZarrDataFrame")
          (updater-extra-native-inputs . ("r-testthat"))))
       (build-system r-build-system)
       (propagated-inputs (list r-biocgenerics r-delayedarray r-rarr
-                               r-s4vectors r-zarrarray))
+                               r-s4vectors))
       (native-inputs (list r-knitr r-testthat))
       (home-page "https://github.com/BIMSBbioinfo/ZarrDataFrame")
       (synopsis "Bioconductor-friendly Bindings for Zarr")
@@ -22740,35 +22761,39 @@ frames with arbitrary sets of columns.")
       (license license:expat))))
 
 (define-public r-zarrarray
-  (package
-    (name "r-zarrarray")
-    (version "1.0.0")
-    (source
-     (origin
-       (method url-fetch)
-       (uri (bioconductor-uri "ZarrArray" version))
-       (sha256
-        (base32 "1ny91qg257kgb1hz2h4jvb0rna9cwyw7fqyj5axv52r3b98xn040"))))
-    (properties `((upstream-name . "ZarrArray")))
-    (build-system r-build-system)
-    (propagated-inputs (list r-biocgenerics
-                             r-delayedarray
-                             r-iranges
-                             r-rarr
-                             r-s4arrays
-                             r-s4vectors
-                             r-sparsearray))
-    (native-inputs (list r-knitr r-testthat))
-    (home-page "https://bioconductor.org/packages/ZarrArray")
-    (synopsis "Bring Zarr datasets in R as DelayedArray objects")
-    (description
-     "The @code{ZarrArray} package leverages the Rarr package to bring Zarr
-datasets in R as @code{DelayedArray} objects.  The main class in the package
-is the @code{ZarrArray} class.  A @code{ZarrArray} object is an array-like
-object that represents a Zarr dataset in R. @code{ZarrArray} objects are
-@code{DelayedArray} derivatives and therefore support all operations (delayed
-or block-processed) supported by @code{DelayedArray} objects.")
-    (license license:artistic2.0)))
+  (let ((commit "3cc3e6acf986074dfaece2ad23f9b56962054625")
+        (revision "2"))
+    (package
+      (name "r-zarrarray")
+      (version (git-version "1.0" revision commit))
+      (source
+       (origin
+         (method git-fetch)
+         (uri (git-reference
+               (url "https://github.com/BIMSBbioinfo/ZarrArray")
+               (commit commit)))
+         (file-name (git-file-name name version))
+         (sha256
+          (base32 "1qjj92cpxpm3zh05vf60h5gmcn1qady0s38hibb0l57iwdhlhrb3"))))
+      (properties
+       '((upstream-name . "ZarrArray")
+         (updater-extra-native-inputs . ("r-testthat"))))
+      (build-system r-build-system)
+      ;; The tests seem to be outdated.
+      (arguments (list #:tests? #false))
+      (propagated-inputs (list r-biocgenerics
+                               r-delayedarray
+                               r-iranges
+                               r-matrix
+                               r-rarr
+                               r-s4arrays
+                               r-s4vectors
+                               r-sparsearray))
+      (native-inputs (list r-testthat))
+      (home-page "https://github.com/BIMSBbioinfo/ZarrArray")
+      (synopsis "Zarr backend for DelayedArray objects")
+      (description "Zarr backend for @code{DelayedArray} objects.")
+      (license license:expat))))
 
 (define-public methyldackel
   (package
@@ -24406,77 +24431,79 @@ It also handles cell type-specific differential expression.")
       (license license:gpl3))))
 
 (define-public r-spectre
-  (package
-    (name "r-spectre")
-    (version "1.3.0")
-    (source
-     (origin
-       (method git-fetch)
-       (uri (git-reference
-              (url "https://github.com/ImmuneDynamics/Spectre")
-              (commit (string-append "v" version))))
-       (file-name (git-file-name name version))
-       (sha256
-        (base32
-         "15g9w08x0pz2ia9qfalhcg3z5z2zx2085mfbr8gx9w5yxnw475ld"))))
-    (properties `((upstream-name . "Spectre")))
-    (build-system r-build-system)
-    (propagated-inputs
-     (list r-biobase
-           r-biocmanager
-           r-caret
-           r-class
-           r-colorramps
-           r-data-table
-           r-dendsort
-           r-devtools
-           r-dplyr
-           r-exactextractr
-           r-factoextra
-           r-flowcore
-           r-flowsom
-           r-flowviz
-           r-fnn
-           r-ggplot2
-           r-ggpointdensity
-           r-ggpubr
-           r-ggraph
-           r-ggthemes
-           r-gridextra
-           r-gridextra
-           r-gtools
-           r-hdf5array
-           r-irlba
-           r-patchwork
-           r-pheatmap
-           r-plyr
-           r-qs2
-           r-raster
-           r-rcolorbrewer
-           r-rhdf5
-           r-rstudioapi
-           r-rsvd
-           r-rtsne
-           r-s2
-           r-scales
-           r-scattermore
-           r-sf
-           r-sp
-           r-stars
-           r-stringr
-           r-tidygraph
-           r-tidyr
-           r-tidyr
-           r-tiff
-           r-umap
-           r-uwot))
-    (home-page "https://github.com/ImmuneDynamics/Spectre")
-    (synopsis "High-dimensional cytometry and imaging analysis")
-    (description
-     "This package provides a computational toolkit in R for the
+  (let ((commit "ff5314fd5b3f29121e52f948d91e222a19dd4d25")
+        (revision "1"))
+    (package
+      (name "r-spectre")
+      (version "1.2.0")
+      (source
+       (origin
+         (method git-fetch)
+         (uri (git-reference
+               (url "https://github.com/ImmuneDynamics/Spectre")
+               (commit commit)))
+         (file-name (git-file-name name version))
+         (sha256
+          (base32
+           "0hziqlaq6mnkxi4bwp5xilxy90yh1vz1j1n117d38vmchvclx9yq"))))
+      (properties `((upstream-name . "Spectre")))
+      (build-system r-build-system)
+      (propagated-inputs
+       (list r-biobase
+             r-biocmanager
+             r-caret
+             r-class
+             r-colorramps
+             r-data-table
+             r-dendsort
+             r-devtools
+             r-dplyr
+             r-exactextractr
+             r-factoextra
+             r-flowcore
+             r-flowsom
+             r-flowviz
+             r-fnn
+             r-ggplot2
+             r-ggpointdensity
+             r-ggpubr
+             r-ggraph
+             r-ggthemes
+             r-gridextra
+             r-gridextra
+             r-gtools
+             r-hdf5array
+             r-irlba
+             r-patchwork
+             r-pheatmap
+             r-plyr
+             r-qs
+             r-raster
+             r-rcolorbrewer
+             r-rhdf5
+             r-rstudioapi
+             r-rsvd
+             r-rtsne
+             r-s2
+             r-scales
+             r-scattermore
+             r-sf
+             r-sp
+             r-stars
+             r-stringr
+             r-tidygraph
+             r-tidyr
+             r-tidyr
+             r-tiff
+             r-umap
+             r-uwot))
+      (home-page "https://github.com/ImmuneDynamics/Spectre")
+      (synopsis "High-dimensional cytometry and imaging analysis")
+      (description
+       "This package provides a computational toolkit in R for the
 integration, exploration, and analysis of high-dimensional single-cell
 cytometry and imaging data.")
-    (license license:expat)))
+      (license license:expat))))
 
 (define-public r-compgenomrdata
   (let ((commit "24484cb77631e1123ead6c329b9d62c160e600c6")

gnu/packages/chez.scm

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

gnu/packages/databases.scm

@@ -5645,7 +5645,7 @@ with integrated support for finding required rows quickly.")
 (define-public apache-arrow
   (package
     (name "apache-arrow")
-    (version "24.0.0")
+    (version "23.0.1")
     (source
      (origin
        (method git-fetch)
@@ -5655,7 +5655,7 @@ with integrated support for finding required rows quickly.")
        (file-name (git-file-name name version))
        (sha256
         (base32
-         "1j3gs5ffa9gx2y2nggmi2zn5rj0bsnjnxrzfnipx6050jz6n8dx9"))))
+         "1qn7wgavi3kiz4d6w1naqj5631bg87fnj6gbhaxmpmynm5hi9wm7"))))
     (build-system cmake-build-system)
     (arguments
      (list
@@ -5823,8 +5823,6 @@ __version_tuple__ = version_tuple = (~a)~%" version version-tuple))))))
            pkg-config
            python-cython
            python-pytest
-           python-pytest-runner
-           python-scikit-build-core
            python-setuptools-scm
            python-setuptools))
     (outputs '("out"))

gnu/packages/dhall.scm

@@ -31,13 +31,13 @@
 (define-public dhall
   (package
     (name "dhall")
-    (version "1.42.2")
-    (source
-     (origin
-       (method url-fetch)
-       (uri (hackage-uri "dhall" version))
-       (sha256
-        (base32 "0fvvqvh6diqi55dmncfs06rvcw8k0a1hs2gq228yxvsfbzcpv44s"))))
+    (version "1.41.2")
+    (source (origin
+              (method url-fetch)
+              (uri (hackage-uri "dhall" version))
+              (sha256
+               (base32
+                "14m5rrvkid76qnvg0l14xw1mnqclhip3gjrz20g1lp4fd5p056ka"))))
     (build-system haskell-build-system)
     (properties '((upstream-name . "dhall")))
     (inputs (list ghc-aeson
@@ -73,8 +73,8 @@
                   ghc-text-manipulate
                   ghc-text-short
                   ghc-th-lift-instances
-                  ghc-unix-compat
                   ghc-unordered-containers
+                  ghc-uri-encode
                   ghc-vector
                   ghc-cryptohash-sha256
                   ghc-http-types
@@ -86,6 +86,7 @@
                          ghc-quickcheck-instances
                          ghc-special-values
                          ghc-spoon
+                         ghc-system-filepath
                          ghc-tasty
                          ghc-tasty-expected-failure
                          ghc-tasty-hunit
@@ -96,8 +97,9 @@
                          ghc-mockery
                          ghc-doctest))
     (arguments
-     `(#:cabal-revision ("2"
-                         "1h9kxpn3kzwmxj07mqc0cxjj2ak3dyxnifb78z5vn34xn747j5bk")))
+     `(#:tests? #f ; Tries to access httpbin.org
+       #:cabal-revision ("4"
+                         "0innb3cn98ynb8bd83jdyrm64ij7wcvajg5qcwzdwbyzpr62anfx")))
     (home-page "http://hackage.haskell.org/package/dhall")
     (synopsis "Configuration language guaranteed to terminate")
     (description

gnu/packages/electronics.scm

@@ -1314,7 +1314,7 @@ package.")
        #:tests? #f)) ;no test suite
     (native-inputs (list asciidoc
                          gettext-minimal
-                         git-minimal/pinned
+                         git-minimal
                          perl
                          perl-unicode-linebreak
                          perl-yaml-tiny

gnu/packages/emacs-xyz.scm

@@ -23831,8 +23831,8 @@ actually changing the buffer's text.")
 
 (define-public emacs-diff-hl
   ;; No new tags or releases since 2024.
-  (let ((commit "7d873b2f58908de1ea2f499da9bf993e088953d7")
-        (revision "1"))
+  (let ((commit "e79aa49ad3cbbe85379cf6646db3aaacd3b04708")
+        (revision "0"))
     (package
       (name "emacs-diff-hl")
       (version (git-version "1.10.0" revision commit))
@@ -23844,7 +23844,7 @@ actually changing the buffer's text.")
                 (commit commit)))
          (file-name (git-file-name name version))
          (sha256
-          (base32 "15a9cjlpjsfcb2hxqbb123389qhiqs06mn01pas2l0jqhc2p86v9"))))
+          (base32 "0fvxngcbx36vqj72fllfp5iqwihcqd1dfhmqr3m1284191q83na3"))))
       (build-system emacs-build-system)
       (arguments
        (list
@@ -23867,7 +23867,7 @@ actually changing the buffer's text.")
                 (invoke "git" "init")
                 (invoke "git" "add" ".")
                 (invoke "git" "commit" "-m" "Commit all."))))))
-      (native-inputs (list git-minimal/pinned))
+      (native-inputs (list git-minimal))
       (home-page "https://github.com/dgutov/diff-hl")
       (synopsis "Highlight uncommitted changes using VC")
       (description

gnu/packages/finance.scm

@@ -321,41 +321,37 @@ based on Qt.")
 (define-public ghc-hledger
   (package
     (name "ghc-hledger")
-    (version "1.43.2")
-    (source
-     (origin
-       (method url-fetch)
-       (uri (hackage-uri "hledger" version))
-       (sha256
-        (base32 "043gw3amc29fbjxlzyc4m97bw5i5462352lmk61adlxcd12l47i1"))))
+    (version "1.27.1")
+    (source (origin
+              (method url-fetch)
+              (uri (hackage-uri "hledger" version))
+              (sha256
+               (base32
+                "0qdg87m7ys2ykqqq32p7h7aw827w4f5bcqx4dspxxq6zqlvzddqb"))))
     (build-system haskell-build-system)
     (properties '((upstream-name . "hledger")))
     (inputs (list ghc-decimal
                   ghc-diff
                   ghc-aeson
                   ghc-ansi-terminal
+                  ghc-breakpoint
                   ghc-cmdargs
                   ghc-data-default
                   ghc-extra
                   ghc-githash
                   ghc-hashable
                   ghc-hledger-lib
-                  ghc-http-client
-                  ghc-http-types
                   ghc-lucid
                   ghc-math-functions
                   ghc-megaparsec
                   ghc-microlens
-                  ghc-modern-uri
                   ghc-regex-tdfa
-                  ghc-req
                   ghc-safe
                   ghc-shakespeare
                   ghc-split
                   ghc-tabular
                   ghc-tasty
                   ghc-temporary
-                  ghc-text-ansi
                   ghc-timeit
                   ghc-unordered-containers
                   ghc-utf8-string
@@ -386,8 +382,8 @@ Accounting.")
       #~(modify-phases %standard-phases
           (add-after 'install 'install-doc
             (lambda _
-              (install-file "embeddedfiles/hledger.info" (string-append #$output "/share/info"))
-              (install-file "embeddedfiles/hledger.1" (string-append #$output "/man/man1"))))
+              (install-file "hledger.info" (string-append #$output "/share/info"))
+              (install-file "hledger.1" (string-append #$output "/man/man1"))))
            (add-after 'register 'remove-libraries
              (lambda* (#:key outputs #:allow-other-keys)
                (delete-file-recursively (string-append (assoc-ref outputs "out") "/lib")))))))))
@@ -2284,13 +2280,13 @@ textual ledgers to Beancount files.")
 (define-public hledger-web
   (package
     (name "hledger-web")
-    (version "1.43.2")
-    (source
-     (origin
-       (method url-fetch)
-       (uri (hackage-uri "hledger-web" version))
-       (sha256
-        (base32 "0d4sv9k3m7s0764lbq2l8w9p2p47cby177l0avl5w3fa9y8d0gyd"))))
+    (version "1.27.1")
+    (source (origin
+              (method url-fetch)
+              (uri (hackage-uri "hledger-web" version))
+              (sha256
+               (base32
+                "151dxci7dld8626dzw823sr3d9iaac92wfzbfcbdz4jh9f7n07wa"))))
     (build-system haskell-build-system)
     (properties '((upstream-name . "hledger-web")))
     (inputs (list ghc-decimal
@@ -2298,6 +2294,7 @@ textual ledgers to Beancount files.")
                   ghc-base64
                   ghc-blaze-html
                   ghc-blaze-markup
+                  ghc-breakpoint
                   ghc-case-insensitive
                   ghc-clientsession
                   ghc-cmdargs
@@ -2305,8 +2302,6 @@ textual ledgers to Beancount files.")
                   ghc-conduit-extra
                   ghc-data-default
                   ghc-extra
-                  ghc-file-embed
-                  ghc-githash
                   ghc-hjsmin
                   ghc-hledger
                   ghc-hledger-lib
@@ -2316,7 +2311,6 @@ textual ledgers to Beancount files.")
                   ghc-http-types
                   ghc-megaparsec
                   ghc-network
-                  ghc-safe
                   ghc-shakespeare
                   ghc-unix-compat
                   ghc-unordered-containers

gnu/packages/graph.scm

@@ -1,5 +1,5 @@
 ;;; GNU Guix --- Functional package management for GNU
-;;; Copyright © 2017-2026 Ricardo Wurmus <rekado@elephly.net>
+;;; Copyright © 2017-2025 Ricardo Wurmus <rekado@elephly.net>
 ;;; Copyright © 2018 Joshua Sierles, Nextjournal <joshua@nextjournal.com>
 ;;; Copyright © 2018, 2020, 2022 Tobias Geerinckx-Rice <me@tobias.gr>
 ;;; Copyright © 2019, 2021, 2022, 2024 Efraim Flashner <efraim@flashner.co.il>
@@ -227,7 +227,7 @@ more.")
    (package
      (inherit igraph)
      (name "igraph")
-     (version "1.0.1")
+     (version "0.10.15")
      (source
       (origin
         (inherit (package-source igraph))
@@ -239,39 +239,7 @@ more.")
         (file-name (git-file-name name version))
         (sha256
          (base32
-          "01mynhbl2ph0gkc0zr5klwqvczwcimfs2kdn6didwg4k8gsrcxlr"))
-        (modules '((guix build utils)
-                   (ice-9 ftw)
-                   (srfi srfi-26)))
-        ;; We need the vendored versions of qhull and cxsparse.
-        (snippet '(begin
-                    (delete-file-recursively "src/isomorphism/bliss")
-                    (substitute* '("src/CMakeLists.txt"
-                                   "etc/cmake/benchmark_helpers.cmake")
-                      ;; Remove extraneous bundling related variables.
-                      ((".*_IS_VENDORED.*") "")
-                      ((".*add_sub.*isomorphism/bliss.*") "")
-                      (("(.*TARGETS.*)bliss(.*)pcg(.*)"
-                        _ part1 part2 part3)
-                       (string-append part1 part2 part3))
-                      ((" pcg ") " pcg_random "))))))
-     (arguments
-      (substitute-keyword-arguments (package-arguments igraph)
-        ((#:phases phases '%standard-phases)
-         #~(modify-phases #$phases
-             ;; We have to use the bundled version because it has been
-             ;; modified from upstream.
-             (delete 'patch-suitesparse)))
-        ((#:configure-flags flags)
-         #~(list "-DBUILD_SHARED_LIBS=ON"
-                 "-DIGRAPH_INFOMAP_SUPPORT=OFF"
-                 "-DCMAKE_C_FLAGS=-Wno-error=incompatible-pointer-types"
-                 ;; Use the same integer width as suitesparse-cxsparse, which
-                 ;; uses int64_t in SuiteSparse v6.0.0 and later.
-                 "-DIGRAPH_INTEGER_SIZE=64"))))
-     (inputs
-      (modify-inputs (package-inputs igraph)
-        (delete "suitesparse-cxsparse"))))))
+          "0z9jqvl65j4z6brrjlfyykba2bs10az6dx6m8g41snlfnx21a82d")))))))
 
 (define-public python-igraph
   (package

gnu/packages/haskell-apps.scm

@@ -64,17 +64,16 @@
 (define-public apply-refact
   (package
     (name "apply-refact")
-    (version "0.15.0.0")
+    (version "0.10.0.0")
     (source (origin
               (method url-fetch)
               (uri (hackage-uri "apply-refact" version))
               (sha256
                (base32
-                "0iny8ynxx46afbzjp14rvpd4sqk8c1p5883mbln53gmlxcm8zq53"))))
+                "129bf8n66kpwh5420rxprngg43bqr2agyd8q8d7l49k2rxsjl1fb"))))
     (build-system haskell-build-system)
     (properties '((upstream-name . "apply-refact")))
     (inputs (list ghc-refact
-                  ghc-data-default
                   ghc-exactprint
                   ghc-paths
                   ghc-extra
@@ -97,13 +96,13 @@ library.  It is primarily used with HLint's @code{--refactor} flag.")
 (define-public cabal-install
  (package
    (name "cabal-install")
-   (version "3.12.1.0")
-   (source
-    (origin
-      (method url-fetch)
-      (uri (hackage-uri "cabal-install" version))
-      (sha256
-       (base32 "1cmifq189i4x0r0yha3dl8nrzzfh92bnd2saak7dqvvjkkysqj38"))))
+   (version "3.6.2.0")
+   (source (origin
+             (method url-fetch)
+             (uri (hackage-uri "cabal-install" version))
+             (sha256
+              (base32
+               "0dihpm4h3xh13vnpvwflnb7v614qdvljycc6ffg5cvhwbwfrxyfw"))))
    (build-system haskell-build-system)
    (properties '((upstream-name . "cabal-install")))
    (inputs (list ghc-async
@@ -118,35 +117,13 @@ library.  It is primarily used with HLint's @code{--refactor} flag.")
                  ghc-tar
                  ghc-zlib
                  ghc-hackage-security
-                 ghc-open-browser
                  ghc-regex-base
                  ghc-regex-posix
-                 ghc-safe-exceptions
-                 ghc-semaphore-compat
                  ghc-resolv
                  ghc-lukko))
-   (native-inputs (list ghc-tasty
-                        ghc-tasty-golden
-                        ghc-tasty-quickcheck
-                        ghc-tasty-expected-failure
-                        ghc-tasty-hunit
-                        ghc-tree-diff
-                        ghc-quickcheck
-                        ghc-tasty
-                        ghc-tasty-hunit
-                        ghc-tasty
-                        ghc-tasty-hunit
-                        ghc-tagged
-                        ghc-tagged
-                        ghc-tasty
-                        ghc-tasty-expected-failure
-                        ghc-tasty-hunit
-                        ghc-tasty-quickcheck
-                        ghc-quickcheck
-                        ghc-pretty-show))
    (arguments
     `(#:cabal-revision ("2"
-                        "0fdzqdkg2vbyg0lnbk9bdskr2d23hwjpmnc7jnvpzkcmxmcvl99n")))
+                        "1kpgyfl5njxp4c8ax5ziag1bhqvph3h0pn660v3vpxalz8d1j6xv")))
    (home-page "https://www.haskell.org/cabal/")
    (synopsis "Command-line interface for Cabal and Hackage")
    (description
@@ -168,10 +145,11 @@ installation of Haskell libraries and programs.")
          "17wi7fma2qaqdm1hwgaam3fd140v9bpa8ky0wg708h1pqc5v2nbz"))))
     (build-system haskell-build-system)
     (properties '((upstream-name . "cpphs")))
-    (inputs (list ghc-polyparse))
+    (inputs
+     (list ghc-polyparse ghc-old-locale ghc-old-time))
     (arguments
-     `(#:cabal-revision ("2"
-                         "0vxav36p0kplp4dpd17i4cfzrsl3r437d840xwv83lf1bqp7mrxc")))
+     `(#:cabal-revision ("1"
+                         "1f8jzs8zdh4wwbcq8fy6qqxkv75ypnvsm4yzw49wpr3b9vpnzlha")))
     (home-page "https://projects.haskell.org/cpphs/")
     (synopsis "Liberalised re-implementation of cpp, the C pre-processor")
     (description "Cpphs is a re-implementation of the C pre-processor that is
@@ -291,18 +269,20 @@ unique algebra of patches called @url{http://darcs.net/Theory,Patchtheory}.
 (define-public ghcid
   (package
     (name "ghcid")
-    (version "0.8.9")
+    (version "0.8.7")
     (source
      (origin
        (method url-fetch)
        (uri (hackage-uri "ghcid" version))
        (sha256
-        (base32 "1dq8lc0dwzib8y21279q4j54cmm7lvx64b3hw2yiym1kzi9rrhj4"))))
+        (base32 "0yqc1pkfajnr56gnh43sbj50r7c3r41b2jfz07ivgl6phi4frjbq"))))
     (build-system haskell-build-system)
     (properties '((upstream-name . "ghcid")))
-    (inputs (list ghc-extra ghc-ansi-terminal ghc-cmdargs ghc-fsnotify
-                  ghc-terminal-size))
-    (native-inputs (list ghc-tasty ghc-tasty-hunit))
+    (inputs
+     (list ghc-extra ghc-ansi-terminal ghc-cmdargs ghc-fsnotify
+           ghc-terminal-size))
+    (native-inputs
+     (list ghc-tasty ghc-tasty-hunit))
     (home-page "https://github.com/ndmitchell/ghcid#readme")
     (synopsis "GHCi based bare bones IDE")
     (description
@@ -424,97 +404,95 @@ to @code{cabal repl}).")
                         (string-append bin "/git-remote-annex"))
                (symlink (string-append bin "/git-annex")
                         (string-append bin "/git-remote-tor-annex"))))))))
-    (inputs (list ghc-network-uri
-                  ghc-optparse-applicative
-                  ghc-uuid
-                  ghc-data-default
-                  ghc-case-insensitive
-                  ghc-random
-                  ghc-dlist
-                  ghc-unix-compat
-                  ghc-safesemaphore
-                  ghc-async
-                  ghc-disk-free-space
-                  ghc-ifelse
-                  ghc-monad-logger
-                  ghc-free
-                  ghc-utf8-string
-                  ghc-sandi
-                  ghc-monad-control
-                  ghc-bloomfilter
-                  ghc-edit-distance
-                  ghc-resourcet
-                  ghc-http-client
-                  ghc-http-client-tls
-                  ghc-http-types
-                  ghc-http-conduit
-                  ghc-http-client-restricted
-                  ghc-conduit
-                  ghc-old-locale
-                  ghc-persistent-sqlite
-                  ghc-persistent
-                  ghc-persistent-template
-                  ghc-unliftio-core
-                  ghc-microlens
-                  ghc-aeson
-                  ghc-vector
-                  ghc-tagsoup
-                  ghc-unordered-containers
-                  ghc-feed
-                  ghc-regex-tdfa
-                  ghc-socks
-                  ghc-byteable
-                  ghc-stm-chans
-                  ghc-securemem
-                  ghc-crypto-api
-                  ghc-memory
-                  ghc-split
-                  ghc-attoparsec
-                  ghc-concurrent-output
-                  ghc-unbounded-delays
-                  ghc-quickcheck
-                  ghc-tasty
-                  ghc-tasty-hunit
-                  ghc-tasty-quickcheck
-                  ghc-tasty-rerun
-                  ghc-ansi-terminal
-                  ghc-aws
-                  ghc-dav
-                  ghc-network
-                  ghc-network-bsd
-                  ghc-git-lfs
-                  ghc-clock
-                  ghc-crypton
-                  ghc-servant
-                  ghc-servant-server
-                  ghc-servant-client
-                  ghc-servant-client-core
-                  ghc-warp
-                  ghc-warp-tls
-                  ghc-os-string
-                  ghc-file-io
-                  ghc-mountpoints
-                  ghc-yesod
-                  ghc-yesod-static
-                  ghc-yesod-form
-                  ghc-yesod-core
-                  ghc-path-pieces
-                  ghc-wai
-                  ghc-wai-extra
-                  ghc-blaze-builder
-                  ghc-clientsession
-                  ghc-shakespeare
-                  ghc-hinotify
-                  ghc-dbus
-                  ghc-fdo-notify
-                  ghc-network-multicast
-                  ghc-network-info
-                  ghc-torrent
-                  ghc-magic
-                  ghc-criterion))
+    (inputs
+     (list curl
+           ghc-aeson
+           ghc-ansi-terminal
+           ghc-async
+           ghc-attoparsec
+           ghc-aws
+           ghc-bloomfilter
+           ghc-byteable
+           ghc-case-insensitive
+           ghc-clientsession
+           ghc-concurrent-output
+           ghc-conduit
+           ghc-connection
+           ghc-crypto-api
+           ghc-cryptonite
+           ghc-data-default
+           ghc-dav
+           ghc-dbus
+           ghc-disk-free-space
+           ghc-dlist
+           ghc-edit-distance
+           ghc-exceptions
+           ghc-fdo-notify
+           ghc-feed
+           ghc-filepath-bytestring
+           ghc-free
+           ghc-git-lfs
+           ghc-hinotify
+           ghc-http-client
+           ghc-http-client-tls
+           ghc-http-client-restricted
+           ghc-http-conduit
+           ghc-http-types
+           ghc-ifelse
+           ghc-magic
+           ghc-memory
+           ghc-microlens
+           ghc-monad-control
+           ghc-monad-logger
+           ghc-mountpoints
+           ghc-network
+           ghc-network-bsd
+           ghc-network-info
+           ghc-network-multicast
+           ghc-network-uri
+           ghc-old-locale
+           ghc-optparse-applicative
+           ghc-persistent
+           ghc-persistent-sqlite
+           ghc-persistent-template
+           ghc-quickcheck
+           ghc-random
+           ghc-regex-tdfa
+           ghc-resourcet
+           ghc-safesemaphore
+           ghc-sandi
+           ghc-securemem
+           ghc-servant-client
+           ghc-servant-server
+           ghc-socks
+           ghc-split
+           ghc-stm-chans
+           ghc-tagsoup
+           ghc-torrent
+           ghc-transformers
+           ghc-unbounded-delays
+           ghc-unix-compat
+           ghc-unliftio-core
+           ghc-unordered-containers
+           ghc-utf8-string
+           ghc-uuid
+           ghc-vector
+           ghc-wai
+           ghc-wai-extra
+           ghc-warp
+           ghc-warp-tls
+           ghc-yesod
+           ghc-yesod-core
+           ghc-yesod-form
+           ghc-yesod-static
+           lsof
+           rsync
+           xdg-utils))
     (propagated-inputs
      (list git))
-    (native-inputs (list ghc-filepath-bytestring))
+    (native-inputs
+     (list ghc-tasty ghc-tasty-hunit ghc-tasty-quickcheck ghc-tasty-rerun
+           perl))
     (home-page "https://git-annex.branchable.com/")
     (synopsis "Manage files with Git, without checking in their contents")
     (description "This package allows managing files with Git, without
@@ -535,13 +513,13 @@ used to keep a folder in sync between computers.")
 (define-public hlint
   (package
     (name "hlint")
-    (version "3.10")
-    (source
-     (origin
-       (method url-fetch)
-       (uri (hackage-uri "hlint" version))
-       (sha256
-        (base32 "0dzy7spc45v88yplczhd3la464bhcbaihi619a45bd06ghrp55nr"))))
+    (version "3.4.1")
+    (source (origin
+              (method url-fetch)
+              (uri (hackage-uri "hlint" version))
+              (sha256
+               (base32
+                "0bkk03c9hacvfd73dk89g4r81b50g7pjgw5pavldali4qwss34cz"))))
     (build-system haskell-build-system)
     (properties '((upstream-name . "hlint")))
     (inputs (list ghc-unordered-containers
@@ -558,10 +536,12 @@ used to keep a folder in sync between computers.")
                   ghc-aeson
                   ghc-deriving-aeson
                   ghc-filepattern
-                  ghc-lib-parser
                   ghc-lib-parser-ex
                   hscolour
                   ghc-yaml))
+    (arguments
+     `(#:cabal-revision ("1"
+                         "1rdaffg5n179yfcn5zjwjb0bki09qy13gz2ijky455y9pbaz8yz9")))
     (home-page "https://github.com/ndmitchell/hlint#readme")
     (synopsis "Suggest improvements for Haskell source code")
     (description
@@ -573,13 +553,13 @@ unwanted suggestions, and to add your own custom suggestions.")
 (define-public hoogle
   (package
     (name "hoogle")
-    (version "5.0.18.4")
-    (source
-     (origin
-       (method url-fetch)
-       (uri (hackage-uri "hoogle" version))
-       (sha256
-        (base32 "08z32d87vqzhapb2vw21h25jb2g74csxlpvd8f54xl91k3ijs3wx"))))
+    (version "5.0.18.3")
+    (source (origin
+              (method url-fetch)
+              (uri (hackage-uri "hoogle" version))
+              (sha256
+               (base32
+                "0v6k75w0an9pqgb7a6cicnpf9rz77xd2lmxfbafc5l4f99jg83bn"))))
     (build-system haskell-build-system)
     (properties '((upstream-name . "hoogle")))
     (inputs (list ghc-quickcheck
@@ -589,7 +569,7 @@ unwanted suggestions, and to add your own custom suggestions.")
                   ghc-cmdargs
                   ghc-conduit
                   ghc-conduit-extra
-                  ghc-crypton-connection
+                  ghc-connection
                   ghc-extra
                   ghc-foundation
                   ghc-old-locale
@@ -602,7 +582,6 @@ unwanted suggestions, and to add your own custom suggestions.")
                   ghc-mmap
                   ghc-process-extras
                   ghc-resourcet
-                  ghc-safe
                   ghc-storable-tuple
                   ghc-tar
                   ghc-uniplate
@@ -614,9 +593,6 @@ unwanted suggestions, and to add your own custom suggestions.")
                   ghc-warp-tls
                   ghc-zlib
                   ghc-semigroups))
-    (arguments
-     `(#:cabal-revision ("1"
-                         "1129flhhb1992rijw46dclvmpqlylmbrzl4swsnk2knylx6jgw5a")))
     (home-page "https://hoogle.haskell.org/")
     (synopsis "Haskell API Search")
     (description
@@ -628,13 +604,14 @@ or by approximate type signature.")
 (define-public hscolour
   (package
     (name "hscolour")
-    (version "1.25")
+    (version "1.24.4")
     (source
      (origin
        (method url-fetch)
        (uri (hackage-uri "hscolour" version))
        (sha256
-        (base32 "0z679khnmb6as1zcdb44n9qjk7in32jpm4ldscpqg7jrapd31kjl"))))
+        (base32
+         "079jwph4bwllfp03yfr26s5zc6m6kw3nhb1cggrifh99haq34cr4"))))
     (build-system haskell-build-system)
     (properties '((upstream-name . "hscolour")))
     (home-page "https://hackage.haskell.org/package/hscolour")
@@ -783,12 +760,12 @@ Wayland, and Linux console environments alike.")
                   ghc-text-zipper
                   ghc-timezone-olson
                   ghc-timezone-series
-                  ghc-unix-compat
+                  ghc-unix-compat-7
                   ghc-unordered-containers
                   ghc-utf8-string
                   ghc-uuid
                   ghc-vector
-                  ghc-vty
+                  ghc-vty-6
                   ghc-vty-crossplatform
                   ghc-word-wrap
                   ghc-xdg-basedir))
@@ -834,31 +811,20 @@ Wayland, and Linux console environments alike.")
 (define-public nixfmt
   (package
     (name "nixfmt")
-    (version "1.1.0")
+    (version "0.5.0")
     (source
      (origin
-       (method git-fetch)
-       (uri
-        (git-reference
-          (url "https://github.com/NixOS/nixfmt")
-          (commit (string-append "v" version))))
+       (method url-fetch)
+       (uri (hackage-uri "nixfmt" version))
        (sha256
-        (base32 "19sydkdw1579qmvzx0zq06s23bm6m6l9wp1kvsfhxawk8pkz2pc2"))
-       (snippet
-        #~(substitute* "nixfmt.cabal"
-            (("(megaparsec|filepath)  *[0-9<>=^&|. ]*" _ package)
-             package)))
-       (modules '((guix build utils)))))
+        (base32 "0rxi8zrd2xr72w673nvgnhb0g3r7rssc1ahlhz8rmdpc6c1a82wl"))))
     (build-system haskell-build-system)
-    (inputs (list ghc-megaparsec
-                  ghc-parser-combinators
-                  ghc-scientific
-                  ghc-pretty-simple
-                  ghc-cmdargs
-                  ghc-file-embed
-                  ghc-safe-exceptions))
-    (home-page "https://github.com/NixOS/nixfmt")
-    (synopsis "Official formatter for Nix code")
+    (properties '((upstream-name . "nixfmt")))
+    (inputs
+     (list ghc-megaparsec ghc-parser-combinators ghc-cmdargs
+           ghc-safe-exceptions))
+    (home-page "https://github.com/serokell/nixfmt")
+    (synopsis "Opinionated formatter for Nix")
     (description
      "Nixfmt is a formatter for Nix that ensures consistent and clear
 formatting by forgetting all existing formatting during parsing.")
@@ -988,7 +954,6 @@ too slow and you'll get wound up in the scroll and crushed.")
     (build-system haskell-build-system)
     (arguments
      (list #:haddock? #f ; TODO: Fails to build.
-           #:cabal-revision '("1" "1935jrzy1r3g9cc74b330fmxnz2i1j8hsdk9jnl557qgk6xjqzs7")
            #:phases
            #~(modify-phases %standard-phases
                (add-after 'build 'build-man-page
@@ -1028,13 +993,13 @@ advanced user's otherwise working script to fail under future circumstances.
 (define-public shelltestrunner
   (package
     (name "shelltestrunner")
-    (version "1.10")
-    (source
-     (origin
-       (method url-fetch)
-       (uri (hackage-uri "shelltestrunner" version))
-       (sha256
-        (base32 "1c6bjyxqa4mgnh3w4pqp6sbr5cf160n7jf9i1b4b9sdxzdjk7g87"))))
+    (version "1.9")
+    (source (origin
+              (method url-fetch)
+              (uri (hackage-uri "shelltestrunner" version))
+              (sha256
+               (base32
+                "1a5kzqbwg6990249ypw0cx6cqj6663as1kbj8nzblcky8j6kbi6b"))))
     (build-system haskell-build-system)
     (properties '((upstream-name . "shelltestrunner")))
     (arguments
@@ -1057,19 +1022,17 @@ advanced user's otherwise working script to fail under future circumstances.
                            "tests/examples")
                    (format #t "test suite not run~%"))
                #t))))))
-    (inputs (list ghc-diff
-                  ghc-filemanip
-                  ghc-hunit
-                  ghc-cmdargs
-                  ghc-pretty-show
-                  ghc-regex-tdfa
-                  ghc-safe
-                  ghc-test-framework
-                  ghc-test-framework-hunit
-                  ghc-utf8-string
-                  ghc-hspec
-                  ghc-hspec-core
-                  ghc-hspec-contrib))
+    (inputs
+     (list ghc-diff
+           ghc-cmdargs
+           ghc-filemanip
+           ghc-hunit
+           ghc-pretty-show
+           ghc-regex-tdfa
+           ghc-safe
+           ghc-utf8-string
+           ghc-test-framework
+           ghc-test-framework-hunit))
     (home-page "https://github.com/simonmichael/shelltestrunner")
     (synopsis "Test CLI programs")
     (description
@@ -1082,13 +1045,13 @@ output, stderr, and exit status.")
 (define-public stylish-haskell
   (package
     (name "stylish-haskell")
-    (version "0.15.1.0")
-    (source
-     (origin
-       (method url-fetch)
-       (uri (hackage-uri "stylish-haskell" version))
-       (sha256
-        (base32 "06y6f7bv5j5k7q81194v9jqcbmmqcv7h8ii3lq1783bpfnyd6h19"))))
+    (version "0.14.3.0")
+    (source (origin
+              (method url-fetch)
+              (uri (hackage-uri "stylish-haskell" version))
+              (sha256
+               (base32
+                "17w92v0qnwj7m6yqdq5cxbr04xiz0yfnnyx5q54218wdl7n5lf6d"))))
     (build-system haskell-build-system)
     (properties '((upstream-name . "stylish-haskell")))
     (inputs (list ghc-aeson
@@ -1098,7 +1061,6 @@ output, stderr, and exit status.")
                   ghc-hsyaml-aeson
                   ghc-hsyaml
                   ghc-semigroups
-                  ghc-lib-parser
                   ghc-lib-parser-ex
                   ghc-strict
                   ghc-optparse-applicative))

gnu/packages/haskell-check.scm

@@ -45,18 +45,22 @@
 (define-public ghc-tasty-ant-xml
   (package
     (name "ghc-tasty-ant-xml")
-    (version "1.1.9")
+    (version "1.1.8")
     (source
      (origin
        (method url-fetch)
        (uri (hackage-uri "tasty-ant-xml" version))
        (sha256
-        (base32 "00zgsd6jjfwasr69d0y781vhjr7d8p1jbaaz4pn75ljf33akd92l"))))
+        (base32
+         "0h9mllhw9cd0rn34xhj8grwmbny7z7hpd8qmp9lfcdj0s4qx9vx8"))))
     (build-system haskell-build-system)
     (properties '((upstream-name . "tasty-ant-xml")))
-    (inputs (list ghc-generic-deriving ghc-tagged ghc-tasty ghc-xml))
-    (home-page "http://github.com/ocharles/tasty-ant-xml")
-    (synopsis "Render tasty output to XML for Jenkins")
+    (inputs
+     (list ghc-generic-deriving ghc-xml ghc-tagged ghc-tasty))
+    (home-page
+     "https://github.com/ocharles/tasty-ant-xml")
+    (synopsis
+     "Render tasty output to XML for Jenkins")
     (description
      "A tasty ingredient to output test results in XML, using the Ant
 schema.  This XML can be consumed by the Jenkins continuous integration
@@ -72,37 +76,33 @@ framework.")
        (method url-fetch)
        (uri (hackage-uri "tasty-smallcheck" version))
        (sha256
-        (base32 "0csgwn3vch0jnpqyyfnrfjq4z0dpl67imh5a7byll3hhlyidgjym"))))
+        (base32
+         "0csgwn3vch0jnpqyyfnrfjq4z0dpl67imh5a7byll3hhlyidgjym"))))
     (build-system haskell-build-system)
     (properties '((upstream-name . "tasty-smallcheck")))
-    (inputs (list ghc-tasty ghc-smallcheck ghc-tagged ghc-optparse-applicative))
-    (arguments
-     `(#:cabal-revision ("1"
-                         "0033ha2w9rzc1rxpzh1dkfdrn256i5lvb41pqbdh2i6kli0v5vmh")))
-    (home-page "https://github.com/feuerbach/tasty")
+    (inputs
+     (list ghc-tasty ghc-smallcheck ghc-async ghc-tagged))
+    (home-page "https://documentup.com/feuerbach/tasty")
     (synopsis "SmallCheck support for the Tasty test framework")
     (description "This package provides SmallCheck support for the Tasty
 Haskell test framework.")
-    (license license:expat)))
+    (license license:bsd-3)))
 
 (define-public ghc-tasty-quickcheck
   (package
     (name "ghc-tasty-quickcheck")
-    (version "0.11.1")
-    (source
-     (origin
-       (method url-fetch)
-       (uri (hackage-uri "tasty-quickcheck" version))
-       (sha256
-        (base32 "0si4ccgqlv8h33d6310rrqba7f4pz3g8cinqfj42yd7damsdxm73"))))
+    (version "0.10.2")
+    (source (origin
+              (method url-fetch)
+              (uri (hackage-uri "tasty-quickcheck" version))
+              (sha256
+               (base32
+                "1qnc6rdvjvlw08q6sln2n98rvj0s0pp689h6w4z58smjbn0lr25l"))))
     (build-system haskell-build-system)
     (properties '((upstream-name . "tasty-quickcheck")))
     (inputs (list ghc-tagged ghc-tasty ghc-random ghc-quickcheck
                   ghc-optparse-applicative))
-    (native-inputs (list ghc-regex-tdfa ghc-tasty-hunit))
-    (arguments
-     `(#:cabal-revision ("3"
-                         "1wzvha4xam8npx5mk33c056grmrqnjd6m38nnm6d7y99w2mn1a7w")))
+    (native-inputs (list ghc-tasty-hunit ghc-pcre-light))
     (home-page "https://github.com/UnkindPartition/tasty")
     (synopsis "QuickCheck support for the Tasty test framework")
     (description "This package provides QuickCheck support for the Tasty
@@ -140,23 +140,22 @@ contains the correct result for the test.")
 (define-public ghc-tasty
   (package
     (name "ghc-tasty")
-    (version "1.5.3")
-    (source
-     (origin
-       (method url-fetch)
-       (uri (hackage-uri "tasty" version))
-       (sha256
-        (base32 "10076vlklbcyiz7plakrihava5sy3dvwhskjldqzhfl18jvcg82l"))))
+    (version "1.4.3")
+    (source (origin
+              (method url-fetch)
+              (uri (hackage-uri "tasty" version))
+              (sha256
+               (base32
+                "006bf4gyc30i2gvb17hj1mzrh1kwnwf7l050x3f72wi6c2axl87l"))))
     (build-system haskell-build-system)
     (properties '((upstream-name . "tasty")))
     (inputs
-      (list ghc-tagged
-            ghc-optparse-applicative
-            ghc-ansi-terminal
-            ghc-unbounded-delays)) ; needed on 32-bit architectures
-    (arguments
-     `(#:cabal-revision ("2"
-                         "04llcf1i3gawdik0bjhxdgls2wkiqlx0gi76nfh784nv2qzxlpbb")))
+      (append
+        (list ghc-tagged ghc-optparse-applicative ghc-ansi-terminal)
+        ;; TODO: Add ghc-unbounded-delays unconditionally on next rebuild cycle.
+        (if (member (%current-system) '("i686-linux"))
+            (list ghc-unbounded-delays)
+            '())))
     (home-page "https://github.com/UnkindPartition/tasty")
     (synopsis "Modern and extensible testing framework")
     (description
@@ -168,20 +167,17 @@ and any other types of tests into a single test suite.")
 (define-public ghc-tasty-hedgehog
   (package
     (name "ghc-tasty-hedgehog")
-    (version "1.4.0.2")
-    (source
-     (origin
-       (method url-fetch)
-       (uri (hackage-uri "tasty-hedgehog" version))
-       (sha256
-        (base32 "0lki03z0p38x0dkqx5cqga30zy5m31gxn1saqylja9bi6bbq8d25"))))
+    (version "1.3.1.0")
+    (source (origin
+              (method url-fetch)
+              (uri (hackage-uri "tasty-hedgehog" version))
+              (sha256
+               (base32
+                "1iq452mvd9wc9pfmjsmm848jwp3cvsk1faf2mlr21vcs0yaxvq3m"))))
     (build-system haskell-build-system)
     (properties '((upstream-name . "tasty-hedgehog")))
     (inputs (list ghc-tagged ghc-tasty ghc-hedgehog))
     (native-inputs (list ghc-tasty-expected-failure))
-    (arguments
-     `(#:cabal-revision ("6"
-                         "1rb8ncp6xyy7jr6v0hyls9m529ba0djndsxgxmkgr52rk3qq8lrc")))
     (home-page "https://github.com/qfpl/tasty-hedgehog")
     (synopsis "Integration for tasty and hedgehog")
     (description
@@ -194,25 +190,22 @@ framework}.")
 (define-public ghc-tasty-hspec
   (package
     (name "ghc-tasty-hspec")
-    (version "1.2.0.4")
+    (version "1.2.0.2")
     (source
      (origin
        (method url-fetch)
        (uri (hackage-uri "tasty-hspec" version))
        (sha256
-        (base32 "1hk1nkjvhp89xxgzj6dhbgw0fknnghpng6afq4i39hjkwv5p78ni"))))
+        (base32 "0cfcpi25jmnmzfzsx364qsj68q6gyph5z112kl8ja222hnhhr2n2"))))
     (build-system haskell-build-system)
     (properties '((upstream-name . "tasty-hspec")))
     (inputs (list ghc-hspec
-                  ghc-hspec-api
                   ghc-hspec-core
                   ghc-quickcheck
                   ghc-tasty
                   ghc-tasty-smallcheck
-                  ghc-tasty-quickcheck))
-    (arguments
-     `(#:cabal-revision ("7"
-                         "0s1y34i8g7fva0z10ws3ipcy2jmlvqk0v4hdbx8rqnby5n0l5kay")))
+                  ghc-tasty-quickcheck
+                  ghc-tagged))
     (home-page "https://github.com/mitchellwrosen/tasty-hspec")
     (synopsis "Hspec support for the Tasty test framework")
     (description
@@ -222,17 +215,19 @@ framework}.")
 (define-public ghc-tasty-hunit
   (package
     (name "ghc-tasty-hunit")
-    (version "0.10.2")
+    (version "0.10.0.3")
     (source
      (origin
        (method url-fetch)
        (uri (hackage-uri "tasty-hunit" version))
        (sha256
-        (base32 "1xh33ss7dncm7zanzkzh7ywb3a46k7vkcbh6v8jb767gq6kizw2s"))))
+        (base32
+         "0gz6zz3w7s44pymw33xcxnawryl27zk33766sab96nz2xh91kvxp"))))
     (build-system haskell-build-system)
     (properties '((upstream-name . "tasty-hunit")))
-    (inputs (list ghc-tasty ghc-call-stack-boot))
-    (home-page "https://github.com/UnkindPartition/tasty")
+    (inputs
+     (list ghc-call-stack-boot ghc-tasty))
+    (home-page "http://documentup.com/feuerbach/tasty")
     (synopsis "HUnit support for the Tasty test framework")
     (description "This package provides HUnit support for the Tasty Haskell
 test framework.")
@@ -262,13 +257,13 @@ tasty.")
 (define-public ghc-tasty-lua
   (package
     (name "ghc-tasty-lua")
-    (version "1.1.1.1")
-    (source
-     (origin
-       (method url-fetch)
-       (uri (hackage-uri "tasty-lua" version))
-       (sha256
-        (base32 "03b2n3gw2w70cnl57w3sh3cv5ka270sf07jlxpb4zs0z5gh83p1r"))))
+    (version "1.0.2")
+    (source (origin
+              (method url-fetch)
+              (uri (hackage-uri "tasty-lua" version))
+              (sha256
+               (base32
+                "1vnyvgcjsvqhwwyqkbgqksr9ppj5whiihpwcqkg33sl7jj3ysdwv"))))
     (build-system haskell-build-system)
     (properties '((upstream-name . "tasty-lua")))
     (inputs (list ghc-hslua-core
@@ -293,15 +288,16 @@ from Lua.")
        (method url-fetch)
        (uri (hackage-uri "tasty-th" version))
        (sha256
-        (base32 "0b2ivrw2257m4cy4rjnkwqlarh83j1y3zywnmaqqqbvy667sqnj3"))))
+        (base32
+         "0b2ivrw2257m4cy4rjnkwqlarh83j1y3zywnmaqqqbvy667sqnj3"))))
     (build-system haskell-build-system)
     (properties '((upstream-name . "tasty-th")))
-    (inputs (list ghc-haskell-src-exts ghc-tasty))
-    (native-inputs (list ghc-tasty-hunit))
+    (inputs
+     (list ghc-haskell-src-exts ghc-tasty ghc-tasty-hunit))
     (home-page "https://github.com/bennofs/tasty-th")
     (synopsis "Automatically generate tasty TestTrees")
     (description
-     "Tasty-th automatically generates tasty TestTrees from functions of the
+      "Tasty-th automatically generates tasty TestTrees from functions of the
 current module, using TemplateHaskell.  This is a fork the original
 test-framework-th package, modified to work with tasty instead of
 test-framework.")
@@ -310,27 +306,28 @@ test-framework.")
 (define-public ghc-tasty-rerun
   (package
     (name "ghc-tasty-rerun")
-    (version "1.1.20")
-    (source
-     (origin
-       (method url-fetch)
-       (uri (hackage-uri "tasty-rerun" version))
-       (sha256
-        (base32 "0px58jm1yqbg32qf2s0yk09d2qdjxkkz9df89f31q3nzw85jv2ky"))))
+    (version "1.1.18")
+    (source (origin
+              (method url-fetch)
+              (uri (hackage-uri "tasty-rerun" version))
+              (sha256
+               (base32
+                "0sccp5zx9v2rx741nbmgd8mzjhy5m4v74hk26d23xz93ph8aqx7s"))))
     (build-system haskell-build-system)
     (properties '((upstream-name . "tasty-rerun")))
-    (inputs (list ghc-optparse-applicative ghc-split ghc-tagged ghc-tasty))
+    (inputs
+     (list ghc-optparse-applicative ghc-reducers ghc-split ghc-tagged
+           ghc-tasty))
     (arguments
-     `(#:cabal-revision ("1"
-                         "13xmx91hp7i0qzrhada9ckliqkynwlwa8x6pjbvxjcy1y0qsd7hk")))
+     `(#:cabal-revision ("3"
+                         "0091arn90cx5rzn5n2bpb9alzybwraf9yj7hb0bwdfyamzpf3pkb")))
     (home-page "https://github.com/ocharles/tasty-rerun")
     (synopsis "Run tests by filtering the test tree")
-    (description
-     "This package adds the ability to run tests by filtering the
+    (description "This package adds the ability to run tests by filtering the
 test tree based on the result of a previous test run.  You can use this to run
 only those tests that failed in the last run, or to only run the tests that have
 been added since previous test run.")
-    (license license:bsd-3)))
+  (license license:bsd-3)))
 
 (define-public ghc-tasty-expected-failure
   (package
@@ -365,17 +362,17 @@ development.")
 (define-public ghc-quickcheck-instances
   (package
     (name "ghc-quickcheck-instances")
-    (version "0.3.33")
+    (version "0.3.29.1")
     (source
      (origin
        (method url-fetch)
        (uri (hackage-uri "quickcheck-instances" version))
        (sha256
-        (base32 "0rl8y3rb4fm4nqz122bp5f2aya4f8bc9m9i9n2vwlyq2gdacs0v8"))))
+        (base32 "0jx2wfy7y5dr14s9i457g2aah4isjxry4mlbqhj7vlav6ib84gdj"))))
     (build-system haskell-build-system)
     (properties '((upstream-name . "quickcheck-instances")))
     (inputs (list ghc-quickcheck
-                  ghc-splitmix-bootstrap
+                  ghc-splitmix
                   ghc-case-insensitive
                   ghc-data-fix
                   ghc-hashable
@@ -386,15 +383,17 @@ development.")
                   ghc-scientific
                   ghc-strict
                   ghc-tagged
-                  ghc-text-short
                   ghc-these
                   ghc-time-compat
+                  ghc-transformers-compat
                   ghc-unordered-containers
                   ghc-uuid-types
-                  ghc-vector))
+                  ghc-vector
+                  ghc-data-array-byte
+                  ghc-text-short))
     (arguments
-     `(#:cabal-revision ("1"
-                         "1xkc7rsfgya4rwiizh0yfincws3knpdnh08m280v1dgik4kv37vh")))
+     `(#:cabal-revision ("2"
+                         "118xy4z4dy4bpkzsp98daiv3l4n5j7ph9my0saca7cqjybqwkcip")))
     (home-page "https://github.com/haskellari/qc-instances")
     (synopsis "Common quickcheck instances")
     (description "This package provides QuickCheck instances for types
@@ -410,38 +409,17 @@ provided by the Haskell Platform.")
        (method url-fetch)
        (uri (hackage-uri "quickcheck-unicode" version))
        (sha256
-        (base32 "0s43s1bzbg3gwsjgm7fpyksd1339f0m26dlw2famxwyzgvm0a80k"))))
+        (base32
+         "0s43s1bzbg3gwsjgm7fpyksd1339f0m26dlw2famxwyzgvm0a80k"))))
     (build-system haskell-build-system)
     (properties '((upstream-name . "quickcheck-unicode")))
     (inputs (list ghc-quickcheck))
-    (home-page "https://github.com/bos/quickcheck-unicode")
+    (home-page
+     "https://github.com/bos/quickcheck-unicode")
     (synopsis "Generator functions Unicode-related tests")
     (description "This package provides generator and shrink functions for
 testing Unicode-related software.")
-    (license license:bsd-2)))
-
-(define-public ghc-quickcheck-text
-  (package
-    (name "ghc-quickcheck-text")
-    (version "0.1.2.1")
-    (source
-     (origin
-       (method url-fetch)
-       (uri (hackage-uri "quickcheck-text" version))
-       (sha256
-        (base32 "02dbs0k6igmsa1hcw8yfvp09v7038vp4zlsp9706km3cmswgshj4"))))
-    (build-system haskell-build-system)
-    (properties '((upstream-name . "quickcheck-text")))
-    (inputs (list ghc-quickcheck))
-    (home-page "https://github.com/olorin/quickcheck-text")
-    (synopsis "Alternative arbitrary instance for Text")
-    (description
-     "The usual Arbitrary instance for Text (in
-<https://hackage.haskell.org/package/quickcheck-instances quickcheck-instances>)
-only has single-byte instances and so isn't an ideal representation of a valid
-UTF-8 character.  This package has generators for one-, two- and three-byte
-UTF-8 characters (all that are currently in use).")
-    (license license:expat)))
+    (license license:bsd-3)))
 
 (define-public ghc-quickcheck-io
   (package
@@ -468,19 +446,17 @@ use HUnit assertions as QuickCheck properties.")
 (define-public ghc-quickcheck
   (package
     (name "ghc-quickcheck")
-    (version "2.15.0.1")
+    (version "2.14.3")
     (source
      (origin
        (method url-fetch)
        (uri (hackage-uri "QuickCheck" version))
        (sha256
-        (base32 "0zvfydg44ibs1br522rzvdlxj9mpz0h62js1hay1sj5gvdnj3cm3"))))
+        (base32 "0085lwy14r7hk7ibmv8d7d54ja9zin0ijf0b27xai898dfrj43sw"))))
     (build-system haskell-build-system)
     (properties '((upstream-name . "QuickCheck")))
-    (inputs (list ghc-random-bootstrap ghc-splitmix-bootstrap))
-    (arguments
-     `(#:cabal-revision ("1"
-                         "0cgfp4s51cjphsn9cls6rndisvqmi94vn95xan9g1yz6p5xk7z8c")))
+    (inputs
+     (list ghc-random ghc-splitmix-bootstrap))
     (home-page "https://github.com/nick8325/quickcheck")
     (synopsis "Automatic testing of Haskell programs")
     (description
@@ -503,8 +479,10 @@ expressed in Haskell, using combinators defined in the QuickCheck library.")
         (base32 "1kyam4cy7qmnizjwjm8jamq43w7f0fs6ljfplwj0ib6wi2kjh0wv"))))
     (build-system haskell-build-system)
     (properties '((upstream-name . "quickcheck-assertions")))
-    (inputs (list ghc-quickcheck ghc-ieee754 ghc-pretty-show))
-    (native-inputs (list ghc-hspec))
+    (native-inputs
+     (list ghc-hspec))
+    (inputs
+     (list ghc-ieee754 ghc-pretty-show ghc-quickcheck))
     (home-page "https://github.com/s9gf4ult/quickcheck-assertions")
     (synopsis "HUnit-like assertions for QuickCheck")
     (description
@@ -516,27 +494,33 @@ HUnit.")
 (define-public ghc-test-framework
   (package
     (name "ghc-test-framework")
-    (version "0.8.2.2")
+    (version "0.8.2.0")
     (source
      (origin
        (method url-fetch)
        (uri (hackage-uri "test-framework" version))
        (sha256
-        (base32 "04ijf5x6xx8i5lqv9ir33zs1rfzc4qkwwz8c1fdycnzvydcv4dnp"))))
+        (base32
+         "1hhacrzam6b8f10hyldmjw8pb7frdxh04rfg3farxcxwbnhwgbpm"))))
     (build-system haskell-build-system)
     (properties '((upstream-name . "test-framework")))
-    (inputs (list ghc-ansi-terminal
-                  ghc-ansi-wl-pprint
-                  ghc-random
-                  ghc-regex-posix
-                  ghc-old-locale
-                  ghc-xml
-                  ghc-hostname))
-    (native-inputs (list ghc-hunit ghc-quickcheck ghc-semigroups-bootstrap))
     (arguments
-     `(#:cabal-revision ("1"
-                         "1yv1qsr6bxphxk9430id9bqhfmkffdqmfg0k017dp9pnn4pqj0zh")))
-    (home-page "https://github.com/haskell/test-framework#readme")
+     `(#:tests? #f  ; FIXME: Tests do not build.
+       #:cabal-revision
+       ("6" "0wbq9wiaag69nsqxwijzhs5y1hb9kbpkp1x65dvx158cxp8i9w9r")))
+    ;(native-inputs
+    ; (list ghc-hunit ghc-quickcheck))
+    (inputs
+     `(("ghc-ansi-terminal" ,ghc-ansi-terminal)
+       ("ghc-ansi-wl-pprint" ,ghc-ansi-wl-pprint)
+       ("ghc-hostname" ,ghc-hostname)
+       ("ghc-old-locale" ,ghc-old-locale)
+       ("ghc-random" ,ghc-random)
+       ("ghc-regex-posix" ,ghc-regex-posix)
+       ("ghc-xml" ,ghc-xml)
+       ("ghc-libxml" ,ghc-libxml)
+       ("ghc-semigroups" ,ghc-semigroups-bootstrap)))
+    (home-page "https://batterseapower.github.io/test-framework/")
     (synopsis "Framework for running and organising tests")
     (description
      "This package allows tests such as QuickCheck properties and HUnit test
@@ -573,21 +557,23 @@ reporting and test statistics output.")
 (define-public ghc-test-framework-quickcheck2
   (package
     (name "ghc-test-framework-quickcheck2")
-    (version "0.3.0.6")
+    (version "0.3.0.5")
     (source
      (origin
        (method url-fetch)
        (uri (hackage-uri "test-framework-quickcheck2" version))
        (sha256
-        (base32 "1d0w2q9sm8aayk0aj1zr2irpnqwpzixn6pdfq1i904vs1kkb2xin"))))
+        (base32
+         "0ngf9vvby4nrdf1i7dxf5m9jn0g2pkq32w48xdr92n9hxka7ixn9"))))
     (build-system haskell-build-system)
     (properties '((upstream-name . "test-framework-quickcheck2")))
-    (inputs (list ghc-test-framework ghc-quickcheck ghc-extensible-exceptions
-                  ghc-random))
     (arguments
-     `(#:cabal-revision ("1"
-                         "1af2gw9gvq143jdqmsnxj23cgss9ffdyr67951a5x151aps04y7z")))
-    (home-page "https://github.com/haskell/test-framework")
+     `(#:cabal-revision
+       ("3" "0mglqfimla4vvv80mg08aj76zf4993wmngqlirh05h8i9nmgv6lh")))
+    (inputs
+     (list ghc-extensible-exceptions ghc-quickcheck ghc-random
+           ghc-test-framework))
+    (home-page "https://batterseapower.github.io/test-framework/")
     (synopsis "QuickCheck2 support for test-framework")
     (description
      "This package provides QuickCheck2 support for the test-framework
@@ -606,8 +592,9 @@ package.")
         (base32 "1xpgpk1gp4w7w46b4rhj80fa0bcyz8asj2dcjb5x1c37b7rw90b0"))))
     (build-system haskell-build-system)
     (properties '((upstream-name . "test-framework-smallcheck")))
-    (inputs (list ghc-test-framework ghc-smallcheck))
-    (home-page "https://github.com/feuerbach/smallcheck")
+    (inputs
+     (list ghc-smallcheck ghc-test-framework))
+    (home-page "https://github.com/Bodigrim/smallcheck")
     (synopsis "SmallCheck support for test-framework")
     (description
      "This package lets programmers use SmallCheck properties in Haskell's
@@ -673,17 +660,17 @@ JUnit tool for Java.")
 (define-public hspec-discover
   (package
     (name "hspec-discover")
-    (version "2.11.12")
-    (source
-     (origin
-       (method url-fetch)
-       (uri (hackage-uri "hspec-discover" version))
-       (sha256
-        (base32 "044vgsy45ff00h9z2k3jgn2m37npcjiacc4cifahrjlmwa7a7ylp"))))
+    (version "2.9.7")
+    (source (origin
+              (method url-fetch)
+              (uri (hackage-uri "hspec-discover" version))
+              (sha256
+               (base32
+                "0536kdxjw6p8b6gcwvmr22jbmb6cgzbddi0fkd01b2m847z37sb5"))))
     (build-system haskell-build-system)
     (properties '((upstream-name . "hspec-discover")))
     (native-inputs (list ghc-quickcheck ghc-hspec-meta ghc-mockery-bootstrap))
-    (home-page "https://hspec.github.io/")
+    (home-page "http://hspec.github.io/")
     (synopsis "Automatically discover and run Hspec tests")
     (description "hspec-discover is a tool which automatically discovers and
 runs Hspec tests.")
@@ -692,30 +679,28 @@ runs Hspec tests.")
 (define-public ghc-hspec-core
   (package
     (name "ghc-hspec-core")
-    (version "2.11.12")
-    (source
-     (origin
-       (method url-fetch)
-       (uri (hackage-uri "hspec-core" version))
-       (sha256
-        (base32 "030400w95775jrivbi7n1nnx6j5z717rqd3986ggklb8h9hjalfc"))))
+    (version "2.9.7")
+    (source (origin
+              (method url-fetch)
+              (uri (hackage-uri "hspec-core" version))
+              (sha256
+               (base32
+                "040rzqiqwkp373jjpij8lkmv08pp2ya92zzcf95bw8px215rp08n"))))
     (build-system haskell-build-system)
     (properties '((upstream-name . "hspec-core")))
     (inputs (list ghc-hunit
                   ghc-quickcheck
                   ghc-ansi-terminal
                   ghc-call-stack
-                  ghc-haskell-lexer
+                  ghc-clock
                   ghc-hspec-expectations
                   ghc-quickcheck-io
                   ghc-random
+                  ghc-setenv
                   ghc-tf-random))
     (native-inputs (list ghc-base-orphans-bootstrap ghc-hspec-meta
-                         ghc-silently-bootstrap ghc-temporary-bootstrap))
-    (arguments
-     `(#:cabal-revision ("1"
-                         "0yq9nnawcgbgxiz4ymfa8k66jrvgrhmv8j7g880x8k6q8q4ncqlq")))
-    (home-page "https://hspec.github.io/")
+                         ghc-silently-bootstrap ghc-temporary))
+    (home-page "http://hspec.github.io/")
     (synopsis "Testing framework for Haskell")
     (description "This library exposes internal types and functions that can
 be used to extend Hspec's functionality.")
@@ -724,28 +709,23 @@ be used to extend Hspec's functionality.")
 (define-public ghc-hspec-meta
   (package
     (name "ghc-hspec-meta")
-    (version "2.11.12")
-    (source
-     (origin
-       (method url-fetch)
-       (uri (hackage-uri "hspec-meta" version))
-       (sha256
-        (base32 "1612pg5gihqjxrzqqvbbgckaqiwq3rmz3rg07lrjhzklg975nj69"))))
+    (version "2.9.3")
+    (source (origin
+              (method url-fetch)
+              (uri (hackage-uri "hspec-meta" version))
+              (sha256
+               (base32
+                "1raxwpsmcijl3x2h5naw6aydhbiknxvhj3x7v384bi1rqi51ainm"))))
     (build-system haskell-build-system)
     (properties '((upstream-name . "hspec-meta")))
-    (inputs (list ghc-hunit
-                  ghc-quickcheck
+    (inputs (list ghc-quickcheck
                   ghc-ansi-terminal
                   ghc-call-stack-boot
-                  ghc-haskell-lexer
-                  ghc-hspec-expectations
+                  ghc-clock
                   ghc-quickcheck-io
                   ghc-random
-                  ghc-tf-random))
-    (arguments
-     `(#:cabal-revision ("2"
-                         "1jrk14s51psb0zjici56220iyb98i3q06sd3rsyx594s3cddgn5d")))
-    (home-page "https://hspec.github.io/")
+                  ghc-setenv))
+    (home-page "http://hspec.github.io/")
     (synopsis "Version of Hspec to test Hspec itself")
     (description "This library provides a stable version of Hspec which is
 used to test the in-development version of Hspec.")
@@ -754,58 +734,38 @@ used to test the in-development version of Hspec.")
 (define-public ghc-hspec
   (package
     (name "ghc-hspec")
-    (version "2.11.12")
-    (source
-     (origin
-       (method url-fetch)
-       (uri (hackage-uri "hspec" version))
-       (sha256
-        (base32 "1zdgkn0gkcphcsfqcqwcfqiqvkz12ljks46v3czpaysndz8icfip"))))
+    (version "2.9.7")
+    (source (origin
+              (method url-fetch)
+              (uri (hackage-uri "hspec" version))
+              (sha256
+               (base32
+                "092sfqjkargxxszp9jjqa8ldjz0xv34jwn6k21q59ys5ckvsrpc1"))))
     (build-system haskell-build-system)
     (properties '((upstream-name . "hspec")))
     (inputs (list ghc-quickcheck ghc-hspec-core hspec-discover
                   ghc-hspec-expectations))
-    (home-page "https://hspec.github.io/")
+    (home-page "http://hspec.github.io/")
     (synopsis "Testing Framework for Haskell")
     (description "This library provides the Hspec testing framework for
 Haskell, inspired by the Ruby library RSpec.")
     (license license:expat)))
 
-(define-public ghc-hspec-api
-  (package
-    (name "ghc-hspec-api")
-    (version "2.11.12")
-    (source
-     (origin
-       (method url-fetch)
-       (uri (hackage-uri "hspec-api" version))
-       (sha256
-        (base32 "1xn2b2hafyq6qm3zaia9nw27ir4cg8v2qn499bz2zwnp2vkjra07"))))
-    (build-system haskell-build-system)
-    (properties '((upstream-name . "hspec-api")))
-    (inputs (list ghc-hspec-core))
-    (native-inputs (list ghc-hspec))
-    (home-page "https://hspec.github.io/")
-    (synopsis "A Testing Framework for Haskell")
-    (description
-     "This package provides a stable API that can be used to extend Hspec's
-functionality.")
-    (license license:expat)))
-
 (define-public ghc-hspec-contrib
   (package
     (name "ghc-hspec-contrib")
-    (version "0.5.2")
+    (version "0.5.1.1")
     (source
      (origin
        (method url-fetch)
        (uri (hackage-uri "hspec-contrib" version))
        (sha256
-        (base32 "0002xzvyh790iwf1y33d4nflrbp5sxvpsp010srcfryf1n3qx2b0"))))
+        (base32 "1nyb5n2jiq920yyf3flzyxrs5xpfyppl3jn18zhviyysjjk5drpx"))))
     (build-system haskell-build-system)
     (properties '((upstream-name . "hspec-contrib")))
     (inputs (list ghc-hunit ghc-call-stack ghc-hspec-core))
     (native-inputs (list ghc-quickcheck ghc-hspec hspec-discover))
+    (arguments (list #:tests? #f)) ; Fail to build.
     (home-page "https://hspec.github.io/")
     (synopsis "Contributed functionality for Hspec")
     (description "This package provides contributed Hspec extensions.")
@@ -814,25 +774,22 @@ functionality.")
 (define-public ghc-hspec-expectations
   (package
     (name "ghc-hspec-expectations")
-    (version "0.8.4")
+    (version "0.8.2")
     (source
      (origin
        (method url-fetch)
        (uri (hackage-uri "hspec-expectations" version))
        (sha256
-        (base32 "1zr1pqchcwglfr5dvcrgc1l5x924n9w09n2zr68dmkqf4dzdx3bv"))))
+        (base32
+         "1vxl9zazbaapijr6zmcj72j9wf7ka1pirrjbwddwwddg3zm0g5l1"))))
     (build-system haskell-build-system)
     (properties '((upstream-name . "hspec-expectations")))
-    (inputs (list ghc-hunit ghc-call-stack))
-    (arguments
     ;; Tests depend on ghc-nanospec.
-     `(#:tests? #f
-       #:cabal-revision ("2"
-                         "14zzsjqcz1zbnvi50i82lx84nc8b5da7ar5cazzh44lklyag0ds2")))
-    (home-page "https://github.com/hspec/hspec-expectations#readme")
+    (arguments '(#:tests? #f))
+    (inputs (list ghc-hunit))
+    (home-page "https://github.com/sol/hspec-expectations")
     (synopsis "Catchy combinators for HUnit")
-    (description
-     "This library provides catchy combinators for HUnit, see
+    (description "This library provides catchy combinators for HUnit, see
 @uref{https://github.com/sol/hspec-expectations#readme, the README}.")
     (license license:expat)))
 
@@ -897,13 +854,13 @@ implementations of cryptographic ciphers.")
 (define-public ghc-hedgehog
   (package
     (name "ghc-hedgehog")
-    (version "1.5")
-    (source
-     (origin
-       (method url-fetch)
-       (uri (hackage-uri "hedgehog" version))
-       (sha256
-        (base32 "0sl6x9q9kyrpv73565w9na9dm10wzxdl0qgiraqarffynfgn0hg9"))))
+    (version "1.1.2")
+    (source (origin
+              (method url-fetch)
+              (uri (hackage-uri "hedgehog" version))
+              (sha256
+               (base32
+                "0dbk75hk6hqpzkjdlpw3s63qhm42kqigij33p321by6xndb59jg1"))))
     (build-system haskell-build-system)
     (properties '((upstream-name . "hedgehog")))
     (inputs (list ghc-ansi-terminal
@@ -918,12 +875,8 @@ implementations of cryptographic ciphers.")
                   ghc-primitive
                   ghc-random
                   ghc-resourcet
-                  ghc-safe-exceptions
                   ghc-transformers-base
                   ghc-wl-pprint-annotated))
-    (arguments
-     `(#:cabal-revision ("2"
-                         "1m0b9m8dw5nw4b3w1jbp5fd0b0kqlyvvy3qsfxc7md77iafxq169")))
     (home-page "https://hedgehog.qa")
     (synopsis "Property-based testing in the spirt of QuickCheck")
     (description
@@ -939,16 +892,26 @@ To get started quickly, see the examples:
 (define-public cabal-doctest
   (package
     (name "cabal-doctest")
-    (version "1.0.11")
-    (source
-     (origin
-       (method url-fetch)
-       (uri (hackage-uri "cabal-doctest" version))
-       (sha256
-        (base32 "0gwjpwv2v7c7gs2dvf7ixsxx6likmgw5yi0fy4bqc0i7nkqg4bfw"))))
+    (version "1.0.9")
+    (source (origin
+              (method url-fetch)
+              (uri (hackage-uri "cabal-doctest" version))
+              (sha256
+               (base32
+                "0wxs0xkspc80h0g8ks792lrzldxvcnhc9rja1j0k678ijs20hmjm"))))
     (build-system haskell-build-system)
     (properties '((upstream-name . "cabal-doctest")))
-    (home-page "https://github.com/ulidtko/cabal-doctest")
+    (arguments
+     `(#:cabal-revision ("2"
+                         "0868js0qgfhvmyw4hjzrvmlzyqsm8dfsbmqhybxb90x44xi3r0i1")
+       #:phases
+       (modify-phases %standard-phases
+         (add-before 'configure 'update-constraints
+           (lambda _
+             (substitute* "cabal-doctest.cabal"
+               (("\\b(Cabal|base)\\s+[^,]+" all dep)
+                dep)))))))
+    (home-page "https://github.com/haskellari/cabal-doctest")
     (synopsis "Setup.hs helper for running doctests")
     (description
      "To properly work, the @code{doctest} package needs plenty of
@@ -1008,13 +971,13 @@ random testing, and hybrids of the two.")
 (define-public ghc-inspection-testing
   (package
     (name "ghc-inspection-testing")
-    (version "0.6.2")
-    (source
-     (origin
-       (method url-fetch)
-       (uri (hackage-uri "inspection-testing" version))
-       (sha256
-        (base32 "0zi1q86sd9jy5dpqfs2j71acdl7kvik0ps78xirpdhyldhwwyqws"))))
+    (version "0.4.6.1")
+    (source (origin
+              (method url-fetch)
+              (uri (hackage-uri "inspection-testing" version))
+              (sha256
+               (base32
+                "0mxff0v3ciccbk4b8kxnh4752fzbwn7213qd8xji0csv6gi2w83y"))))
     (build-system haskell-build-system)
     (properties '((upstream-name . "inspection-testing")))
     (home-page "https://github.com/nomeata/inspection-testing")
@@ -1047,33 +1010,33 @@ examples and more information.")
     (name "ghc-quickcheck-classes")
     (version "0.6.5.0")
     (source
-     (origin
-       (method url-fetch)
-       (uri (hackage-uri "quickcheck-classes" version))
-       (sha256
-        (base32 "19iw15mvb7gws3ljdxqwsbb4pmfc0sfflf8szgmrhiqr3k82mqv2"))))
+      (origin
+        (method url-fetch)
+        (uri (hackage-uri "quickcheck-classes" version))
+        (sha256
+          (base32 "19iw15mvb7gws3ljdxqwsbb4pmfc0sfflf8szgmrhiqr3k82mqv2"))))
     (build-system haskell-build-system)
     (properties '((upstream-name . "quickcheck-classes")))
-    (inputs (list ghc-quickcheck
-                  ghc-primitive
-                  ghc-primitive-addr
-                  ghc-quickcheck-classes-base
-                  ghc-semigroups-bootstrap
-                  ghc-fail
-                  ghc-tagged
-                  ghc-aeson
-                  ghc-semigroupoids
-                  ghc-semirings
-                  ghc-vector))
-    (native-inputs (list ghc-base-orphans ghc-base-orphans ghc-tasty
-                         ghc-tasty-quickcheck))
-    (arguments
-     `(#:cabal-revision ("3"
-                         "1pawam5rsdcdv21fqc87khzqjm0ixwzklfxd6gk3b2qrr5q66bn5")))
+    (inputs
+      (list ghc-quickcheck
+            ghc-primitive
+            ghc-primitive-addr
+            ghc-quickcheck-classes-base
+            ghc-aeson
+            ghc-semigroupoids
+            ghc-semirings
+            ghc-vector))
+    (native-inputs
+      (list ghc-base-orphans
+            ghc-tagged
+            ghc-base-orphans
+            ghc-tagged
+            ghc-tasty
+            ghc-tasty-quickcheck))
     (home-page "https://github.com/andrewthad/quickcheck-classes#readme")
     (synopsis "QuickCheck common typeclasses")
     (description
-     "This library provides QuickCheck properties to ensure that typeclass
+      "This library provides QuickCheck properties to ensure that typeclass
 instances adhere to the set of laws that they are supposed to.  There are
 other libraries that do similar things, such as @code{genvalidity-hspec} and
 @code{checkers}.  This library differs from other solutions by not introducing
@@ -1089,26 +1052,24 @@ constraints more cleanly.")
     (name "ghc-quickcheck-classes-base")
     (version "0.6.2.0")
     (source
-     (origin
-       (method url-fetch)
-       (uri (hackage-uri "quickcheck-classes-base" version))
-       (sha256
-        (base32 "16c6gq4cqpkwnq1pzkhm6r7mrwk4an50ha5w77bmiia2qkhla6ch"))))
+      (origin
+        (method url-fetch)
+        (uri (hackage-uri "quickcheck-classes-base" version))
+        (sha256
+          (base32 "16c6gq4cqpkwnq1pzkhm6r7mrwk4an50ha5w77bmiia2qkhla6ch"))))
     (build-system haskell-build-system)
     (properties '((upstream-name . "quickcheck-classes-base")))
-    (inputs (list ghc-quickcheck
-                  ghc-contravariant
-                  ghc-bifunctors
-                  ghc-semigroups-bootstrap
-                  ghc-fail
-                  ghc-tagged))
-    (arguments
-     `(#:cabal-revision ("1"
-                         "1p3v38jhpx0r6rnvaspkkivl8xyq2mq4xnmycgmkj1gr77vplkdr")))
+    (inputs
+      (list ghc-quickcheck
+            ghc-contravariant
+            ghc-bifunctors
+            ghc-semigroups
+            ghc-fail
+            ghc-tagged))
     (home-page "https://github.com/andrewthad/quickcheck-classes#readme")
     (synopsis "QuickCheck common typeclasses from `base`")
     (description
-     "This library is a minimal variant of `quickcheck-classes` that only
+      "This library is a minimal variant of `quickcheck-classes` that only
 provides laws for typeclasses from `base`.  The main purpose of splitting this
 out is so that `primitive` can depend on `quickcheck-classes-base` in its test
 suite, avoiding the circular dependency that arises if `quickcheck-classes` is
@@ -1126,61 +1087,67 @@ this library uses the higher-kinded typeclasses
 (define-public ghc-doctest-lib
   (package
     (name "ghc-doctest-lib")
-    (version "0.1.1.1")
+    (version "0.1")
     (source
-     (origin
-       (method url-fetch)
-       (uri (hackage-uri "doctest-lib" version))
-       (sha256
-        (base32 "1hb3zx1xzib3v41blnwcbhc2v0rzwdzq7gm4sajqndimwjkkxc67"))))
+      (origin
+        (method url-fetch)
+        (uri (hackage-uri "doctest-lib" version))
+        (sha256
+          (base32 "1vswam0dhw52dihgnzirh18gqs8rj8h6jd7pl6y1mg2f9f9zmih2"))))
     (build-system haskell-build-system)
     (properties '((upstream-name . "doctest-lib")))
     (home-page "https://hub.darcs.net/thielema/doctest-lib/")
     (synopsis "Parts of doctest exposed as library")
     (description
-     "Parts of doctest exposed as library.  For use with the doctest-extract utility.")
+      "Parts of doctest exposed as library.  For use with the doctest-extract utility.")
     (license license:expat)))
 
 (define-public ghc-doctest-exitcode-stdio
   (package
     (name "ghc-doctest-exitcode-stdio")
-    (version "0.0.0.1")
+    (version "0.0")
     (source
-     (origin
-       (method url-fetch)
-       (uri (hackage-uri "doctest-exitcode-stdio" version))
-       (sha256
-        (base32 "0kg5xiw4giyvqpcj6cxqqnysvixhxlwm0pbg3qks8dzwb5w79dvk"))))
+      (origin
+        (method url-fetch)
+        (uri (hackage-uri "doctest-exitcode-stdio" version))
+        (sha256
+          (base32 "1g3c7yrqq2mwqbmvs8vkx1a3cf0p0x74b7fnn344dsk7bsfpgv0x"))))
     (build-system haskell-build-system)
     (properties '((upstream-name . "doctest-exitcode-stdio")))
-    (inputs (list ghc-doctest-lib ghc-quickcheck ghc-semigroups))
+    (inputs
+      (list ghc-doctest-lib ghc-quickcheck ghc-semigroups))
+    (arguments
+     `(#:cabal-revision ("1"
+                         "1065s8bch6zhl6mc8nhvfpwd1irmjd04z7xgycbpihc14x4ijim3")))
     (home-page "https://hub.darcs.net/thielema/doctest-exitcode-stdio/")
     (synopsis "Run Doctests in a @code{Cabal.Test.exitcode-stdio} environment")
     (description
-     "This package allows on to run Doctests in a Cabal.Test.exitcode-stdio
+      "This package allows on to run Doctests in a Cabal.Test.exitcode-stdio
 environment.")
     (license license:bsd-3)))
 
 (define-public ghc-tasty-silver
   (package
     (name "ghc-tasty-silver")
-    (version "3.3.2.1")
-    (source
-     (origin
-       (method url-fetch)
-       (uri (hackage-uri "tasty-silver" version))
-       (sha256
-        (base32 "01w3576kymglcddinh10m1wgy71dia49k2pnw5y1c97jjrhanf17"))))
+    (version "3.3.1.1")
+    (source (origin
+              (method url-fetch)
+              (uri (hackage-uri "tasty-silver" version))
+              (sha256
+               (base32
+                "13j0zs0ciijv9q2nncna1gbgsgw2g7xc228hzmqic1750n3ybz9m"))))
     (build-system haskell-build-system)
     (properties '((upstream-name . "tasty-silver")))
     (inputs (list ghc-ansi-terminal
+                  ghc-async
                   ghc-optparse-applicative
                   ghc-process-extras
                   ghc-regex-tdfa
                   ghc-silently
                   ghc-tagged
                   ghc-tasty
-                  ghc-temporary))
+                  ghc-temporary
+                  ghc-semigroups))
     (native-inputs (list ghc-tasty-hunit))
     (home-page "https://github.com/phile314/tasty-silver")
     (synopsis "Fancy test runner, including support for golden tests")
@@ -1196,19 +1163,16 @@ result of golden tests.")
 (define-public ghc-tasty-inspection-testing
   (package
     (name "ghc-tasty-inspection-testing")
-    (version "0.2.1")
-    (source
-     (origin
-       (method url-fetch)
-       (uri (hackage-uri "tasty-inspection-testing" version))
-       (sha256
-        (base32 "0wl2xlnbmqdkwhi4ic6a4q4lxf9qg433lidi8d0hlp3ykrjpbcay"))))
+    (version "0.1.0.1")
+    (source (origin
+              (method url-fetch)
+              (uri (hackage-uri "tasty-inspection-testing" version))
+              (sha256
+               (base32
+                "0p46w44f19w7lvdzyg3vq6qzix0rjp8p23ilxz82dviq38lgmifp"))))
     (build-system haskell-build-system)
     (properties '((upstream-name . "tasty-inspection-testing")))
     (inputs (list ghc-inspection-testing ghc-tasty))
-    (arguments
-     `(#:cabal-revision ("2"
-                         "0z9al0hyq381fw146agbpz7rf24rwms1w91m7s0k1w3xbfw16l9n")))
     (home-page "https://github.com/Bodigrim/tasty-inspection-testing")
     (synopsis "Inspection testing support for tasty")
     (description
@@ -1218,13 +1182,13 @@ result of golden tests.")
 (define-public ghc-proctest
   (package
     (name "ghc-proctest")
-    (version "0.1.3.1")
+    (version "0.1.3.0")
     (source (origin
               (method url-fetch)
               (uri (hackage-uri "proctest" version))
               (sha256
                (base32
-                "0yvhc0l5aj170ymhjx4ig0im0yd7wfa150m5lqhabr8j7cf16l7y"))))
+                "02iz323arx9zwclvspgaaqz81bp6jdnj89pjm08n2gamg39zsbdn"))))
     (build-system haskell-build-system)
     (properties '((upstream-name . "proctest")))
     (inputs (list ghc-hunit ghc-hspec ghc-quickcheck))

gnu/packages/haskell-crypto.scm

@@ -62,19 +62,18 @@ format.")
   (package
     (name "ghc-asn1-encoding")
     (version "0.9.6")
-    (source
-     (origin
-       (method url-fetch)
-       (uri (hackage-uri "asn1-encoding" version))
-       (sha256
-        (base32 "02nsr30h5yic1mk7znf0q4z3n560ip017n60hg7ya25rsfmxxy6r"))))
+    (source (origin
+              (method url-fetch)
+              (uri (hackage-uri "asn1-encoding" version))
+              (sha256
+               (base32
+                "02nsr30h5yic1mk7znf0q4z3n560ip017n60hg7ya25rsfmxxy6r"))))
     (build-system haskell-build-system)
     (properties '((upstream-name . "asn1-encoding")))
-    (inputs (list ghc-hourglass ghc-asn1-types))
-    (native-inputs (list ghc-tasty ghc-tasty-quickcheck))
-    (arguments
-     `(#:cabal-revision ("2"
-                         "16503ryhq15f2rfdav2qnkq11dg2r3vk3f9v64q9dmxf8dh8zv97")))
+    (inputs
+     (list ghc-hourglass ghc-asn1-types))
+    (native-inputs
+     (list ghc-tasty ghc-tasty-quickcheck))
     (home-page "https://github.com/vincenthz/hs-asn1")
     (synopsis "ASN1 data reader and writer in RAW, BER and DER forms")
     (description
@@ -112,18 +111,15 @@ when ASN1 pattern matching is not convenient.")
        (method url-fetch)
        (uri (hackage-uri "crypto-api" version))
        (sha256
-        (base32 "19bsmkqkpnvh01b77pmyarx00fic15j4hvg4pzscrj4prskrx2i9"))))
+        (base32
+         "19bsmkqkpnvh01b77pmyarx00fic15j4hvg4pzscrj4prskrx2i9"))))
     (build-system haskell-build-system)
     (properties '((upstream-name . "crypto-api")))
     (inputs (list ghc-cereal ghc-tagged ghc-entropy))
-    (arguments
-     `(#:cabal-revision ("1"
-                         "1z6n1sa5pn3iqvqjrd8hv4bc2pxzsrhm5sh0l8z7g9lbqp6w0wp5")))
     (home-page "https://github.com/TomMD/crypto-api")
     (synopsis "Provides generic interface for cryptographic operations
 for Haskell")
-    (description
-     "This Haskell package provides a generic interface for
+    (description "This Haskell package provides a generic interface for
 cryptographic operations (hashes, ciphers, randomness).
 
 Maintainers of hash and cipher implementations are encouraged to add instances
@@ -201,15 +197,13 @@ that hides the C implementation.")
        (method url-fetch)
        (uri (hackage-uri "cryptohash-md5" version))
        (sha256
-        (base32 "018g13hkmq5782i24b4518hcd926fl6x6fh5hd7b9wlxwc5dn21v"))))
+        (base32
+         "018g13hkmq5782i24b4518hcd926fl6x6fh5hd7b9wlxwc5dn21v"))))
     (build-system haskell-build-system)
     (properties '((upstream-name . "cryptohash-md5")))
     (native-inputs (list ghc-base16-bytestring ghc-puremd5 ghc-tasty
-                         ghc-tasty-quickcheck ghc-tasty-hunit))
-    (arguments
-     `(#:cabal-revision ("6"
-                         "0m7f9mgw4w9vcch37ja9zgbn0knq8rjppqr9x2ylkcdxfdnmhhif")))
-    (home-page "https://github.com/haskell-hvr/cryptohash-md5")
+                         ghc-tasty-hunit ghc-tasty-quickcheck))
+    (home-page "https://github.com/hvr/cryptohash-md5")
     (synopsis "MD5 implementation for Haskell")
     (description "This Haskell package provides implementation of MD5.")
     (license license:bsd-3)))
@@ -218,20 +212,20 @@ that hides the C implementation.")
   (package
     (name "ghc-cryptohash-sha1")
     (version "0.11.101.0")
-    (source
-     (origin
-       (method url-fetch)
-       (uri (hackage-uri "cryptohash-sha1" version))
-       (sha256
-        (base32 "0h9jl9v38gj0vnscqx7xdklk634p05fa6z2pcvknisq2mnbjq154"))))
+    (source (origin
+              (method url-fetch)
+              (uri (hackage-uri "cryptohash-sha1" version))
+              (sha256
+               (base32
+                "0h9jl9v38gj0vnscqx7xdklk634p05fa6z2pcvknisq2mnbjq154"))))
     (build-system haskell-build-system)
     (properties '((upstream-name . "cryptohash-sha1")))
     (native-inputs (list ghc-base16-bytestring ghc-sha ghc-tasty
                          ghc-tasty-quickcheck ghc-tasty-hunit))
     (arguments
-     `(#:cabal-revision ("6"
-                         "1cxdw2y10z4v0mz91wki7f233jziipx85j4qy5msig4nv3djkprb")))
-    (home-page "https://github.com/haskell-hvr/cryptohash-sha1")
+     `(#:cabal-revision ("1"
+                         "0bz9rfl7b2iwn45m0lxcmsyi5rrv3xdgzx2lzr79bds91dw6i25b")))
+    (home-page "https://github.com/hvr/cryptohash-sha1")
     (synopsis "SHA-1 implementation for Haskell")
     (description
      "This Haskell package provides an incremental and one-pass,
@@ -252,18 +246,20 @@ the C implementation.")
        (method url-fetch)
        (uri (hackage-uri "cryptohash-sha256" version))
        (sha256
-        (base32 "1xkb7iqplbw4fy1122p79xf1zcb7k44rl0wmfj1q06l7cdqxr9vk"))))
+        (base32
+         "1xkb7iqplbw4fy1122p79xf1zcb7k44rl0wmfj1q06l7cdqxr9vk"))))
     (build-system haskell-build-system)
     (properties '((upstream-name . "cryptohash-sha256")))
-    (native-inputs (list ghc-base16-bytestring ghc-sha ghc-tasty
-                         ghc-tasty-quickcheck ghc-tasty-hunit))
     (arguments
-     `(#:cabal-revision ("6"
-                         "01s12sl5mxvraj5fj3cs0pkb03pm8xpjz13y09dpl7i6rv6f578f")))
-    (home-page "https://github.com/haskell-hvr/cryptohash-sha256")
+     `(#:cabal-revision
+       ("1" "1hyzqv30rpj920ddnr0zypyjjlh52vyp2d140pn2byayj820rkgs")
+       #:tests? #f)) ; TODO: tasty ==1.1.*
+    (native-inputs
+     (list ghc-base16-bytestring ghc-sha ghc-tasty ghc-tasty-hunit
+           ghc-tasty-quickcheck))
+    (home-page "https://github.com/hvr/cryptohash-sha1")
     (synopsis "SHA-256 implementation for Haskell")
-    (description
-     "This Haskell package provides an incremental and
+    (description "This Haskell package provides an incremental and
 one-pass, pure API to the @uref{https://en.wikipedia.org/wiki/SHA-2,
 SHA-256 cryptographic hash algorithm}, with performance close to the
 fastest implementations available in other languages.
@@ -276,12 +272,12 @@ the C implementation.")
   (package
     (name "ghc-cryptonite")
     (version "0.30")
-    (source
-     (origin
-       (method url-fetch)
-       (uri (hackage-uri "cryptonite" version))
-       (sha256
-        (base32 "07bb97iszhnrfddh5ql6p3dqd0c13xycjw5n2kljw7d0ia59q2an"))))
+    (source (origin
+              (method url-fetch)
+              (uri (hackage-uri "cryptonite" version))
+              (sha256
+               (base32
+                "07bb97iszhnrfddh5ql6p3dqd0c13xycjw5n2kljw7d0ia59q2an"))))
     (build-system haskell-build-system)
     (properties '((upstream-name . "cryptonite")))
     (inputs (list ghc-memory ghc-basement))
@@ -299,13 +295,13 @@ generators, and more.")
 (define-public ghc-curve25519
   (package
   (name "ghc-curve25519")
-  (version "0.2.8.1")
+  (version "0.2.7")
   (source
    (origin
      (method url-fetch)
      (uri (hackage-uri "curve25519" version))
      (sha256
-      (base32 "0p2rxad477cxbpxryvp78v8nrrf5gm35106jbqrj5cjgksappkdj"))))
+      (base32 "1p8b1lppkvc19974hr43lcqdi4nj55j2nf7gsnp8dn7gyf23aayq"))))
   (build-system haskell-build-system)
   (native-inputs
    (list ghc-hunit
@@ -330,17 +326,19 @@ elsewhere.")
 (define-public ghc-digest
   (package
     (name "ghc-digest")
-    (version "0.0.2.1")
+    (version "0.0.1.7")
     (source
      (origin
        (method url-fetch)
        (uri (hackage-uri "digest" version))
        (sha256
-        (base32 "163418p50bqdxn8ajzj6x3455xbch9jq1w6psbkdz5qzw017py6b"))))
+        (base32 "02jzw0bsng87y1n2kgpy7vb30lvqsnpbfd8dpg4hmvbg9s06qgdj"))))
     (build-system haskell-build-system)
     (properties '((upstream-name . "digest")))
     (arguments
-     `(#:extra-directories ("zlib")))
+     `(#:extra-directories ("zlib")
+       #:cabal-revision ("1"
+                         "0wh34kyag2vhwvsdwv8qmvm13gy32nc94yfyqfdnl67nyc2sx8wl")))
     (inputs (list zlib))
     (native-inputs (list pkg-config))
     (home-page "http://hackage.haskell.org/package/digest")
@@ -354,13 +352,13 @@ are implemented as FFI bindings to efficient code from zlib.")
 (define-public ghc-entropy
   (package
     (name "ghc-entropy")
-    (version "0.4.1.11")
-    (source
-     (origin
-       (method url-fetch)
-       (uri (hackage-uri "entropy" version))
-       (sha256
-        (base32 "1slj5n783k2amsx2hqs5qwvcw4rgfhdhgmiyg7cii0wg4w0mmpgm"))))
+    (version "0.4.1.10")
+    (source (origin
+              (method url-fetch)
+              (uri (hackage-uri "entropy" version))
+              (sha256
+               (base32
+                "1rbx4ydabrjs8kkdg9laznkh9nisiq6b5z93vnp9bh6iy59ivb45"))))
     (build-system haskell-build-system)
     (properties '((upstream-name . "entropy")))
     (home-page "https://github.com/TomMD/entropy")
@@ -417,35 +415,6 @@ the MD5 digest (hash) algorithm.  This now supports the @code{crypto-api} class
 interface.")
     (license license:bsd-3)))
 
-(define-public ghc-rsa
-  (package
-    (name "ghc-rsa")
-    (version "2.4.1")
-    (source
-     (origin
-       (method url-fetch)
-       (uri (hackage-uri "RSA" version))
-       (sha256
-        (base32 "0hchsqrxpfw7mqrqwscfy8ig1w2di6w3nxpzi873w0gibv2diibj"))))
-    (build-system haskell-build-system)
-    (properties '((upstream-name . "RSA")))
-    (inputs (list ghc-crypto-api ghc-crypto-pubkey-types ghc-sha))
-    (native-inputs (list ghc-quickcheck ghc-tagged ghc-test-framework
-                         ghc-test-framework-quickcheck2))
-    (arguments
-     `(#:cabal-revision ("2"
-                         "090yzm99fmh7c6z4m9hbkasqhc3xlw104g2b6wnk77n1abd13ryj")))
-    (home-page "http://hackage.haskell.org/package/RSA")
-    (synopsis
-     "Implementation of RSA, using the padding schemes of PKCS#1 v2.1.")
-    (description
-     "This library implements the RSA encryption and signature algorithms for
-arbitrarily-sized @code{ByteStrings}.  While the implementations work, they are
-not necessarily the fastest ones on the planet.  Particularly key generation.
-The algorithms included are based of RFC 3447, or the Public-Key Cryptography
-Standard for RSA, version 2.1 (a.k.a, PKCS#1 v2.1).")
-    (license license:bsd-3)))
-
 (define-public ghc-sha
   (package
     (name "ghc-sha")
@@ -625,24 +594,6 @@ implementation.  If it matters for your case, you should make sure you have
 AES-NI available, or you'll need to use a different implementation.")
     (license license:bsd-3)))
 
-(define-public ghc-crypto-pubkey-types
-  (package
-    (name "ghc-crypto-pubkey-types")
-    (version "0.4.3")
-    (source
-     (origin
-       (method url-fetch)
-       (uri (hackage-uri "crypto-pubkey-types" version))
-       (sha256
-        (base32 "0q0wlzjmpx536h1zcdzrpxjkvqw8abj8z0ci38138kpch4igbnby"))))
-    (build-system haskell-build-system)
-    (properties '((upstream-name . "crypto-pubkey-types")))
-    (inputs (list ghc-asn1-types ghc-asn1-encoding))
-    (home-page "http://github.com/vincenthz/hs-crypto-pubkey-types")
-    (synopsis "Generic cryptography Public keys algorithm types")
-    (description "Generic cryptography public keys algorithm types.")
-    (license license:bsd-3)))
-
 (define-public ghc-crypto-random
   (package
     (name "ghc-crypto-random")
@@ -666,13 +617,13 @@ abstraction for CPRNGs.")
 (define-public ghc-crypton
   (package
     (name "ghc-crypton")
-    (version "1.0.4")
+    (version "0.34")
     (source
      (origin
        (method url-fetch)
        (uri (hackage-uri "crypton" version))
        (sha256
-        (base32 "06h1qjvqd8gmiyzvh31sc061vcgns101l0774c44a8k44015925l"))))
+        (base32 "1mhypjhzn95in853bp7ary0a2xc6lsji6j8hrrgn2mfa4ilq8i24"))))
     (build-system haskell-build-system)
     (properties '((upstream-name . "crypton")))
     (inputs (list ghc-memory ghc-basement))
@@ -702,13 +653,13 @@ abstraction for CPRNGs.")
 (define-public ghc-crypton-x509
   (package
     (name "ghc-crypton-x509")
-    (version "1.7.7")
+    (version "1.7.6")
     (source
      (origin
        (method url-fetch)
        (uri (hackage-uri "crypton-x509" version))
        (sha256
-        (base32 "10pkva9wvm6ih48bprxlnyhnn3nr6xq9dhkrk4hfxpsaij6f9v7g"))))
+        (base32 "1zyaz0krf08g36g30zr5wn8f2x51l4dj2zcjnhpiw9h05p54mdzb"))))
     (build-system haskell-build-system)
     (properties '((upstream-name . "crypton-x509")))
     (inputs (list ghc-memory
@@ -718,7 +669,13 @@ abstraction for CPRNGs.")
                   ghc-asn1-encoding
                   ghc-asn1-parse
                   ghc-crypton))
-    (native-inputs (list ghc-tasty ghc-tasty-quickcheck))
+    (native-inputs (list ghc-tasty ghc-tasty-quickcheck ghc-x509))
+    (arguments
+     `(#:cabal-revision ("1"
+                         "10a2x47znhbayyfr6fqgq27623akpycyjbfxz4hnavavf1x6ary5")
+       ;; build phase fails when tests are activated.
+       ;; See https://github.com/kazu-yamamoto/crypton-certificate/pull/7
+       #:tests? #f))
     (home-page "https://github.com/kazu-yamamoto/crypton-certificate")
     (synopsis "X509 reader and writer")
     (description "This package provides generic X509 support for Haskell.")
@@ -727,13 +684,13 @@ abstraction for CPRNGs.")
 (define-public ghc-crypton-x509-store
   (package
     (name "ghc-crypton-x509-store")
-    (version "1.6.11")
+    (version "1.6.9")
     (source
      (origin
        (method url-fetch)
        (uri (hackage-uri "crypton-x509-store" version))
        (sha256
-        (base32 "07vq7f883cm5krqz2kc0qkh9ks54jknrwdqvfqsk91s12b693a83"))))
+        (base32 "0vr5b9cyf9x016wn1g0bryslf5nz8jq2sy8r3llwqfg02apihqiy"))))
     (build-system haskell-build-system)
     (properties '((upstream-name . "crypton-x509-store")))
     (inputs (list ghc-pem ghc-asn1-types ghc-asn1-encoding ghc-crypton
@@ -770,25 +727,24 @@ storage methods, and accessors.")
 (define-public ghc-crypton-x509-validation
   (package
     (name "ghc-crypton-x509-validation")
-    (version "1.6.14")
+    (version "1.6.12")
     (source
      (origin
        (method url-fetch)
        (uri (hackage-uri "crypton-x509-validation" version))
        (sha256
-        (base32 "07b09kgrd3m5ahxpj458r5ycd30bz8ldwjwf19mdcnfv4x0kj3pd"))))
+        (base32 "1xjhwvmkcy47a6xiqxb3xy944ca7g660203jdrz5xzd46zibfq0f"))))
     (build-system haskell-build-system)
     (properties '((upstream-name . "crypton-x509-validation")))
     (inputs (list ghc-memory
                   ghc-hourglass
-                  ghc-data-default
+                  ghc-data-default-class
                   ghc-pem
                   ghc-asn1-types
                   ghc-asn1-encoding
                   ghc-crypton-x509
                   ghc-crypton-x509-store
-                  ghc-crypton
-                  ghc-iproute))
+                  ghc-crypton))
     (native-inputs (list ghc-tasty ghc-tasty-hunit))
     (home-page "https://github.com/kazu-yamamoto/crypton-certificate")
     (synopsis "X.509 Certificate and CRL validation")
@@ -796,44 +752,6 @@ storage methods, and accessors.")
 and @dfn{Certificates revocation list} (CRL) validation.")
     (license license:bsd-3)))
 
-(define-public ghc-crypton-socks
-  (package
-    (name "ghc-crypton-socks")
-    (version "0.6.2")
-    (source
-     (origin
-       (method url-fetch)
-       (uri (hackage-uri "crypton-socks" version))
-       (sha256
-        (base32 "0fwzlvndyxjwhxambxdjzzm63yvb6jzsg53dkv3i6x17biz0hdm8"))))
-    (build-system haskell-build-system)
-    (properties '((upstream-name . "crypton-socks")))
-    (inputs (list ghc-cereal ghc-network ghc-network-bsd))
-    (home-page "http://github.com/mpilgrem/crypton-socks")
-    (synopsis "SOCKS Protocol Version 5")
-    (description
-     "This package provides a library implementing SOCKS Protocol Version 5.")
-    (license license:bsd-3)))
-
-(define-public ghc-crypto-token
-  (package
-    (name "ghc-crypto-token")
-    (version "0.1.2")
-    (source
-     (origin
-       (method url-fetch)
-       (uri (hackage-uri "crypto-token" version))
-       (sha256
-        (base32 "18xphlvn6wzyi6lqrvm5vic97pkcbiph1938p5l1mb22rj5215zm"))))
-    (build-system haskell-build-system)
-    (properties '((upstream-name . "crypto-token")))
-    (inputs (list ghc-crypton ghc-memory ghc-network-byte-order))
-    (native-inputs (list ghc-hspec hspec-discover))
-    (home-page "http://hackage.haskell.org/package/crypto-token")
-    (synopsis "crypto tokens")
-    (description "Encrypted tokens/tickets to keep state in the client side.")
-    (license license:bsd-3)))
-
 (define-public ghc-cprng-aes
   (package
     (name "ghc-cprng-aes")
@@ -886,19 +804,20 @@ percent.
        (method url-fetch)
        (uri (hackage-uri "ed25519" version))
        (sha256
-        (base32 "0v8msqvgzimhs7p5ri25hrb1ni2wvisl5rmdxy89fc59py79b9fq"))))
+        (base32
+         "0v8msqvgzimhs7p5ri25hrb1ni2wvisl5rmdxy89fc59py79b9fq"))))
     (build-system haskell-build-system)
     (properties '((upstream-name . "ed25519")))
-    (native-inputs (list ghc-quickcheck ghc-doctest))
     (arguments
-     `(#:cabal-revision ("9"
-                         "0y5vfdcys18waa5k5zxiq9n8jq0l05j76riml23i0gxmwgdhsmgi")
-       ;; the tests don't work with current versions of the test frameworks
-       #:tests? #f))
-    (home-page "https://github.com/thoughtpolice/hs-ed25519/")
+     `(#:cabal-revision
+       ("6" "0qyx6cl52fnll8lp6v9133wfvv3zhvq7v2crn441mng520j9wp48")
+       ;; We omit these test suites because they require old versions of
+       ;; packages and packages we do not have.
+       #:configure-flags
+       '("--flags=-test-hlint -test-doctests -test-properties")))
+    (home-page "http://thoughtpolice.github.com/hs-ed25519")
     (synopsis "Ed25519 cryptographic signatures")
-    (description
-     "This package provides a simple, fast, self-contained
+    (description "This package provides a simple, fast, self-contained
 copy of the Ed25519 public-key signature system with a clean interface.
 It also includes support for detached signatures, and thorough
 documentation on the design and implementation, including usage
@@ -908,41 +827,29 @@ guidelines.")
 (define-public ghc-tls
   (package
     (name "ghc-tls")
-    (version "2.1.8")
+    (version "1.5.8")
     (source (origin
               (method url-fetch)
               (uri (hackage-uri "tls" version))
               (sha256
                (base32
-                "1csdy3426lva1a5f7gh9qm96vzfraqj91jbxlm79wbf1jsdzfhsq"))))
+                "0rxdv8ab98kd4nqql7djmmi51k4vayq21s38s43sx3rzn0iyla3b"))))
     (build-system haskell-build-system)
     (properties '((upstream-name . "tls")))
-    (inputs (list ghc-asn1-types
-                  ghc-asn1-encoding
-                  ghc-base16-bytestring
-                  ghc-cereal
-                  ghc-crypton
-                  ghc-crypton-x509
-                  ghc-crypton-x509-store
-                  ghc-crypton-x509-validation
-                  ghc-data-default
+    (inputs (list ghc-cereal
+                  ghc-data-default-class
                   ghc-memory
-                  ghc-network
-                  ghc-serialise
-                  ghc-transformers
-                  ghc-unix-time
-                  ghc-zlib))
-    (native-inputs (list ghc-quickcheck
-                         ghc-asn1-types
-                         ghc-async
-                         ghc-crypton
-                         ghc-crypton-x509
-                         ghc-crypton-x509-validation
-                         ghc-hourglass
-                         ghc-hspec
-                         ghc-serialise
-                         hspec-discover))
-    (home-page "http://github.com/haskell-tls/hs-tls")
+                  ghc-cryptonite
+                  ghc-asn1-types
+                  ghc-asn1-encoding
+                  ghc-x509
+                  ghc-x509-store
+                  ghc-x509-validation
+                  ghc-async
+                  ghc-hourglass
+                  ghc-network))
+    (native-inputs (list ghc-tasty ghc-tasty-quickcheck ghc-quickcheck))
+    (home-page "http://github.com/vincenthz/hs-tls")
     (synopsis "TLS/SSL protocol native implementation (Server and Client)")
     (description
      "Native Haskell TLS and SSL protocol implementation for server and client.
@@ -954,6 +861,43 @@ Ephemeral (Elliptic curve and regular) Diffie Hellman key exchanges, and many
 extensions.")
     (license license:bsd-3)))
 
+(define-public ghc-tls-1.9
+  (package
+    (name "ghc-tls")
+    (version "1.9.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (hackage-uri "tls" version))
+       (sha256
+        (base32 "0gj3af9sqd0bw7dpcqfyvbslpxsk2ij00a77kl710fwhw35vj1an"))))
+    (build-system haskell-build-system)
+    (properties '((upstream-name . "tls")))
+    (inputs (list ghc-cereal
+                  ghc-data-default-class
+                  ghc-memory
+                  ghc-crypton
+                  ghc-asn1-types
+                  ghc-asn1-encoding
+                  ghc-crypton-x509
+                  ghc-crypton-x509-store
+                  ghc-crypton-x509-validation
+                  ghc-async
+                  ghc-unix-time
+                  ghc-network))
+    (native-inputs (list ghc-tasty ghc-tasty-quickcheck ghc-quickcheck))
+    (home-page "https://github.com/haskell-tls/hs-tls")
+    (synopsis "TLS/SSL protocol native implementation (server and client)")
+    (description
+     "This package provides a native Haskell TLS and SSL protocol
+implementation for server and client.  It provides a high-level implementation
+of a sensitive security protocol, eliminating a common set of security issues
+through the use of the advanced type system, high level constructions and
+common Haskell features.  It currently implements the SSL3.0, TLS1.0, TLS1.1
+and TLS1.2 protocol, and supports RSA and Ephemeral (Elliptic curve and
+regular) Diffie Hellman key exchanges, and many extensions.")
+    (license license:bsd-3)))
+
 (define-public ghc-hsopenssl
   (package
     (name "ghc-hsopenssl")
@@ -1016,14 +960,17 @@ the tls package, and borrows some ideas from x509-system.")
        (method url-fetch)
        (uri (hackage-uri "openssl-streams" version))
        (sha256
-        (base32 "10pnnpzgb5xr811kc9qdk7h2cgn6hk2yiyhnzz8f8p0fjzc0pwjm"))))
+        (base32
+         "10pnnpzgb5xr811kc9qdk7h2cgn6hk2yiyhnzz8f8p0fjzc0pwjm"))))
     (build-system haskell-build-system)
     (properties '((upstream-name . "openssl-streams")))
-    (inputs (list ghc-hsopenssl ghc-io-streams ghc-network))
-    (native-inputs (list ghc-hunit ghc-test-framework ghc-test-framework-hunit))
+    (inputs
+     (list ghc-hsopenssl ghc-io-streams ghc-network))
+    (native-inputs
+     (list ghc-hunit ghc-test-framework ghc-test-framework-hunit))
     (arguments
-     `(#:cabal-revision ("3"
-                         "1vizl9yajkbd59rrnfb38xwq7hfj36avbv6vwqnkhbvz3qaj3dwg")))
+     `(#:cabal-revision ("1"
+                         "0vfawnfcjrw29qg1n7k6z6bk4bmnk869gjlr9mxw4mzxgl80b2vp")))
     (home-page "https://hackage.haskell.org/package/openssl-streams")
     (synopsis "OpenSSL network support for io-streams")
     (description "This library contains io-streams routines for secure

gnu/packages/haskell.scm

@@ -1686,6 +1686,12 @@ SRC_HC_OPTS += -optc-mno-outline-atomics
               (file-pattern ".*\\.conf\\.d$")
               (file-type 'directory)))))))
 
+;; Versions newer than ghc defined below (i.e. the compiler
+;; haskell-build-system uses) should use ghc-next as their name to
+;; ensure ghc (without version specification) and ghc-* packages are
+;; always compatible. See https://issues.guix.gnu.org/issue/47335.
+(define-public ghc ghc-9.2)
+
 ;; 9.4 is the last version to support the make-based build system,
 ;; but it boot with 9.2, only 9.0 is supported.
 (define ghc-bootstrap-for-9.4 ghc-9.0)
@@ -1749,24 +1755,22 @@ SRC_HC_OPTS += -optc-mno-outline-atomics
   (let ((base ghc-9.2))
     (package
       (inherit base)
-      (name "ghc")
-      (version "9.4.3")
+      (name "ghc-next")
+      (version "9.4.4")
       (source (origin
                 (method url-fetch)
                 (uri (string-append "https://www.haskell.org/ghc/dist/" version
                                     "/ghc-" version "-src.tar.xz"))
                 (sha256
                  (base32
-                  "0nlhx2cbq1jh2yr6zk475lavjkh9sncj57qp77p51pkfad4kkxpa"))
+                  "1qk7rlqf02s3b6m6sqqngmjq1mxnrz88h159lz6k25gddmdg5kp8"))
                 (patches (search-patches "ghc-9-StgCRunAsm-only-when-needed.patch"))))
       (arguments
        (substitute-keyword-arguments arguments
          ((#:phases phases '%standard-phases)
           #~(modify-phases #$phases
              ;; Files don’t exist any more.
-             (delete 'skip-tests)))
-         ((#:tests? _ #f)
-          #f)))
+             (delete 'skip-tests)))))
       (native-inputs
        `(;; GHC 9.4 must be built with GHC >= 9.0.
          ("ghc-bootstrap" ,ghc-bootstrap-for-9.4)
@@ -1778,7 +1782,8 @@ SRC_HC_OPTS += -optc-mno-outline-atomics
                     version "/ghc-" version "-testsuite.tar.xz"))
              (sha256
               (base32
-               "1xbps33pq6mg2bwp5gvmc4qhgdq52yng5993if99b9s3fylqk86l"))))
+               "04p2lawxxg3nyv6frzhyjyh3arhqqyh5ka3alxa2pxhcd2hdcja3"))
+             (patches (search-patches "ghc-testsuite-recomp015-execstack.patch"))))
          ("ghc-alex" ,ghc-alex-bootstrap-for-9.4)
          ("ghc-happy" ,ghc-happy-bootstrap-for-9.4)
          ,@(filter (match-lambda
@@ -1793,326 +1798,4 @@ SRC_HC_OPTS += -optc-mno-outline-atomics
               (file-pattern ".*\\.conf\\.d$")
               (file-type 'directory)))))))
 
-;;; GHC >= 9.6 must be built using it's new haskell-written Hadrian build
-;;; system. Use this opportunity to cut the inheritance chain to simplify
-;;; understanding what building ghc requires with the new build system.
-
-(define-public ghc-9.8
-  (let ((ghc-bootstrap ghc-9.4))
-    (package
-      (name "ghc")
-      (version "9.8.1")
-      (source (origin
-                (method url-fetch)
-                (uri (string-append "https://downloads.haskell.org/~ghc/" version
-                                    "/ghc-" version "-src.tar.xz"))
-                (sha256
-                 (base32
-                  "0l87yb8hmd350klrp6lw2h9hjlla11pgzx1n4jlrfdvkgxmyvy5j"))))
-      (outputs (list "out" "doc"))
-      (arguments
-       (list
-        #:make-flags #~(list "-V" "--docs=no-sphinx")
-       #:configure-flags
-       #~(list
-           (string-append "--with-gmp-libraries="
-                          (assoc-ref %build-inputs "gmp") "/lib")
-           (string-append "--with-gmp-includes="
-                          (assoc-ref %build-inputs "gmp") "/include")
-           "--with-system-libffi"
-           (string-append "--with-ffi-libraries="
-                          (assoc-ref %build-inputs "libffi") "/lib")
-           (string-append "--with-ffi-includes="
-                          (assoc-ref %build-inputs "libffi") "/include")
-           (string-append "--with-curses-libraries="
-                          (assoc-ref %build-inputs "ncurses") "/lib")
-           (string-append "--with-curses-includes="
-                          (assoc-ref %build-inputs "ncurses") "/include"))
-        #:phases
-        #~(modify-phases %standard-phases
-            (add-before 'build 'fix-iserv-rpath
-              (lambda _
-                (mkdir-p "_build")
-                (call-with-output-file
-                 "_build/hadrian.settings"
-                 (lambda (port)
-                   (display
-                    (string-append
-                     "*.iserv.ghc.link.opts += -optl-Wl,-rpath,"
-                     #$output "/lib/ghc-" #$(package-version this-package)
-                     "/lib/" #$(or (%current-target-system)
-                                   (%current-system))
-                     "-ghc-" #$(package-version this-package) "/")
-                    port)))))
-            ;; This phase patches the 'ghc-pkg' command so that it sorts the list
-            ;; of packages in the binary cache it generates.
-            (add-before 'build 'fix-ghc-pkg-nondeterminism
-              (lambda _
-                (substitute* "utils/ghc-pkg/Main.hs"
-                  (("confs = map \\(path </>\\) \\$ filter \\(\".conf\" `isSuffixOf`\\) fs")
-                   "confs = map (path </>) $ filter (\".conf\" `isSuffixOf`) (sort fs)"))))
-            (add-after 'unpack 'unpack-testsuite
-              (lambda* (#:key inputs #:allow-other-keys)
-                (with-directory-excursion ".."
-                  (invoke "tar" "xvf" (assoc-ref inputs "ghc-testsuite")))))
-            (add-after 'unpack-testsuite 'fix-/bin/sh-references
-              (lambda* (#:key inputs #:allow-other-keys)
-                (substitute*
-                 (list "hadrian/src/Rules/BinaryDist.hs"
-                       "hadrian/src/Rules/Test.hs"
-                       "libraries/process/System/Process/Posix.hs"
-                       "libraries/process/jsbits/process.js"
-                       "libraries/unix/cbits/execvpe.c"
-                       "testsuite/tests/driver/T8602/T8602.script"
-                       "testsuite/timeout/timeout.py")
-                 (("/bin/sh") (search-input-file inputs "/bin/sh")))))
-            (add-after 'unpack-testsuite 'fix-cc-reference
-              (lambda* (#:key inputs #:allow-other-keys)
-                (substitute*
-                 (list "utils/hsc2hs/src/Common.hs")
-                 (("\"cc\"") "\"gcc\""))))
-            ;; XXX: something causes ld-wrapper to see test\ \ \ spaces/... and
-            ;; look for the files "test\", "\", "\" and "spaces/...", which obviously
-            ;; don't exist
-            (add-after 'unpack-testsuite 'fix-testsuite
-              (lambda _
-                (substitute*
-                  (list "testsuite/driver/runtests.py")
-                  (("'test   spaces'") "'dont-test-spaces'"))))
-            (add-before 'configure 'set-target-programs
-              (lambda* (#:key inputs #:allow-other-keys)
-                (let ((binutils (assoc-ref inputs "binutils"))
-                      (gcc (assoc-ref inputs "gcc"))
-                      (ld-wrapper (assoc-ref inputs "ld-wrapper")))
-                  (setenv "CC" (string-append gcc "/bin/gcc"))
-                  (setenv "CXX" (string-append gcc "/bin/g++"))
-                  (setenv "LD" (string-append ld-wrapper "/bin/ld"))
-                  (setenv "NM" (string-append binutils "/bin/nm"))
-                  (setenv "RANLIB" (string-append binutils "/bin/ranlib"))
-                  (setenv "STRIP" (string-append binutils "/bin/strip"))
-                  ;; The 'ar' command does not follow the same pattern.
-                  (setenv "fp_prog_ar" (string-append binutils "/bin/ar")))))
-            (add-before 'build 'build-hadrian
-              (lambda* (#:key (inputs '()) #:allow-other-keys)
-                (invoke "./hadrian/bootstrap/bootstrap.py"
-                        "-s" (assoc-ref inputs "hadrian-bootstrap")
-                        "-w" (which "ghc"))))
-            (add-before 'build-hadrian 'fix-environment
-              (lambda _
-                (unsetenv "GHC_PACKAGE_PATH")
-                (setenv "CONFIG_SHELL" (which "bash"))))
-            (replace 'build
-              (lambda* (#:key (parallel-build? #f) (make-flags '())
-                       #:allow-other-keys)
-                (apply invoke "_build/bin/hadrian"
-                       `("binary-dist-dir"
-                         ,@(if parallel-build?
-                             (list (string-append
-                                    "-j" (number->string
-                                          (parallel-job-count)))))
-                         ,@make-flags))))
-            (replace 'check
-              (lambda* (#:key (tests? #t) (parallel-tests? #f) (make-flags '())
-                        #:allow-other-keys)
-                (if tests?
-                  (apply invoke "_build/bin/hadrian"
-                         `(,@(if parallel-tests?
-                               (list (string-append
-                                      "-j"
-                                      (number->string (parallel-job-count))))
-                               '())
-                           ,@make-flags
-                           "test"
-                           ,(string-append
-                             "--broken-test="
-                             (string-join
-                              (list  "T15904" ; ld-wrapper, apparently
-                                     "T16521" ; no idea
-                                     ;; These fail due to gcc
-                                     ;; -Wincompatible-pointer-types, which
-                                     ;; apparently is not used in GHC's CI
-                                     ;; https://gitlab.haskell.org/ghc/ghc/-/issues/22263
-                                     "hs_try_putmvar001"
-                                     "list_threads_and_misc_roots"
-                                     "testwsdeque")))
-                           "--skip-perf"))
-                  (format #t "test suite not run~%"))))
-            (replace 'install
-              (lambda* (#:key (make-flags '()) #:allow-other-keys)
-                (apply invoke "_build/bin/hadrian"
-                       `("install"
-                         ,@make-flags
-                         ,(string-append "--prefix=" #$output)))))
-           (add-after 'install 'remove-unnecessary-references
-             (lambda* (#:key outputs #:allow-other-keys)
-               (substitute* (find-files (string-append (assoc-ref outputs "out") "/lib/")
-                                        "settings")
-                 (("/gnu/store/.*/bin/(.*)" m program) program))
-
-               ;; Remove references to "doc" output from "out" by rewriting
-               ;; the "haddock-interfaces" fields and removing the optional
-               ;; "haddock-html" field in the generated .conf files.
-               (let ((doc (assoc-ref outputs "doc"))
-                     (out (assoc-ref outputs "out")))
-                 (with-fluids ((%default-port-encoding #f))
-                   (for-each (lambda (config-file)
-                               (substitute* config-file
-                                 (("^haddock-html: .*") "\n")
-                                 (((format #f "^haddock-interfaces: ~a" doc))
-                                  (string-append "haddock-interfaces: " out))))
-                             (find-files (string-append out "/lib") ".conf")))
-                 ;; Move the referenced files to the "out" output.
-                 (for-each (lambda (haddock-file)
-                             (let* ((subdir (string-drop haddock-file (string-length doc)))
-                                    (new    (string-append out subdir)))
-                               (mkdir-p (dirname new))
-                               (rename-file haddock-file new)))
-                           (find-files doc "\\.haddock$")))))
-            (add-after 'install 'replace-$pkgroot
-              (lambda* (#:key outputs #:allow-other-keys)
-                ((@ (srfi srfi-11) let*-values)
-                  (((out) (assoc-ref outputs "out"))
-                   ((_ version) (package-name->name+version
-                                    (strip-store-file-name out))))
-                 ;; We split out the version because we want this to also work
-                 ;; with packages named "ghc-next" instead of "ghc"
-                 (substitute*
-                   (find-files
-                    (string-append (assoc-ref outputs "out") "/lib/ghc-"
-                                   version "/lib/package.conf.d/")
-                    "^.*\\.conf$")
-                   (("\\$\\{pkgroot\\}/")
-                    (string-append (assoc-ref outputs "out") "/lib/ghc-"
-                                   version "/lib/")))))))))
-      (build-system gnu-build-system)
-      (inputs (list bash-minimal gmp ncurses libffi))
-      (native-inputs
-       `(("perl" ,perl)
-         ("python" ,python)
-         ("git" ,git-minimal/pinned)
-         ("which" ,which)
-         ("ghostscript" ,ghostscript)
-         ("autoconf" ,autoconf)
-         ("automake" ,automake)
-
-         ("ghc-bootstrap" ,ghc-bootstrap)
-         ("ghc-alex" ,ghc-alex-bootstrap-for-9.4)
-         ("ghc-happy" ,ghc-happy-bootstrap-for-9.4)
-         ("ghc-testsuite"
-          ,(origin
-             (method url-fetch)
-             (uri (string-append
-                   "https://www.haskell.org/ghc/dist/"
-                   version "/ghc-" version "-testsuite.tar.xz"))
-             (sha256
-              (base32
-               "1hxylm3nhxzl7yidarlavvcg1240w4bk0hy5jnvwna24jyxz69i6"))
-             (patches (search-patches "ghc-testsuite-recomp015-execstack.patch"))))
-         ("hadrian-bootstrap"
-          ,(origin
-             (method url-fetch)
-             (uri (string-append "https://downloads.haskell.org/~ghc/"
-                                 version "/hadrian-bootstrap-sources/"
-                                 "hadrian-bootstrap-sources-"
-                                 (package-version ghc-bootstrap) ".tar.gz"))
-             (sha256
-               (base32
-                 "14dkxif9x4hy85phcj3j0glf95k04g4ab6hfchpw9vxgvk97syi1"))))))
-      (native-search-paths
-       (list (search-path-specification
-              (variable "GHC_PACKAGE_PATH")
-              (files (list (string-append "lib/ghc-" version)))
-              (file-pattern ".*\\.conf\\.d$")
-              (file-type 'directory))))
-      (home-page "https://www.haskell.org/ghc")
-      (synopsis "The Glasgow Haskell Compiler")
-      (description
-        "The Glasgow Haskell Compiler (GHC) is a state-of-the-art compiler and
-interactive environment for the functional language Haskell.")
-      (license license:bsd-3))))
-
-(define-public ghc-9.10
-  (let ((base ghc-9.8))
-    (package
-      (inherit base)
-      (name "ghc")
-      (version "9.10.2")
-      (source
-        (origin
-          (method url-fetch)
-          (uri (string-append "https://downloads.haskell.org/~ghc/" version
-                              "/ghc-" version "-src.tar.xz"))
-          (sha256
-            (base32
-             "1pm84cgr3yg99r3srdjllgz6zig8h7dbwa597srwcnjp0nh41zam"))))
-      (arguments
-        (substitute-keyword-arguments (package-arguments base)
-          ((#:phases phases #~%standard-phases)
-           #~(modify-phases #$phases
-               (replace 'check
-                 (lambda* (#:key (tests? #t) (parallel-tests? #f) (make-flags '())
-                           #:allow-other-keys)
-                   (if tests?
-                     (apply invoke "_build/bin/hadrian"
-                            `(,@(if parallel-tests?
-                                  (list (string-append
-                                         "-j"
-                                         (number->string (parallel-job-count))))
-                                  '())
-                              ,@make-flags
-                              "test"
-                              ,(string-append
-                                "--broken-test="
-                                (string-join
-                                 (list  "T15904" ; ld-wrapper, apparently
-                                        "T16521" ; no idea
-                                        ;; These fail due to gcc
-                                        ;; -Wincompatible-pointer-types, which
-                                        ;; apparently is not used in GHC's CI
-                                        ;; https://gitlab.haskell.org/ghc/ghc/-/issues/22263
-                                        "list_threads_and_misc_roots"
-                                        "stack_misc_closures")))
-                              "--skip-perf"))
-                     (format #t "test suite not run~%"))))))))
-      (native-inputs
-       `(("ghc-bootstrap" ,base)
-         ("ghc-testsuite"
-          ,(origin
-             (method url-fetch)
-             (uri (string-append
-                    "https://downloads.haskell.org/~ghc/"
-                    version "/ghc-" version "-testsuite.tar.xz"))
-             (sha256
-              (base32
-               "143ifc4g3jc6s9hcry5qha913rzwg4hpsvk6pqvxk5r0qigfxjwx"))
-             (patches (search-patches "ghc-testsuite-recomp015-execstack.patch"))))
-         ("hadrian-bootstrap"
-          ,(origin
-             (method url-fetch)
-             (uri (string-append "https://downloads.haskell.org/~ghc/" version
-                                 "/hadrian-bootstrap-sources/"
-                                 "hadrian-bootstrap-sources-"
-                                 (package-version base) ".tar.gz"))
-             (sha256
-               (base32
-                 "162lbafvdamfhx1jldax3shgk8jbbqn4an97ny363lxbdjgdn708"))))
-         ,@(filter (match-lambda
-                     (("ghc-bootstrap" . _) #f)
-                     (("ghc-testsuite" . _) #f)
-                     (("hadrian-bootstrap" . _) #f)
-                     (_ #t))
-                   (package-native-inputs base))))
-      (native-search-paths
-       (list (search-path-specification
-              (variable "GHC_PACKAGE_PATH")
-              (files (list (string-append "lib/ghc-" version)))
-              (file-pattern ".*\\.conf\\.d$")
-              (file-type 'directory)))))))
-
-;; Versions newer than ghc defined below (i.e. the compiler
-;; haskell-build-system uses) should use ghc-next as their name to
-;; ensure ghc (without version specification) and ghc-* packages are
-;; always compatible. See https://issues.guix.gnu.org/issue/47335.
-(define-public ghc ghc-9.10)
-
 ;;; haskell.scm ends here

gnu/packages/image-processing.scm

@@ -1923,7 +1923,7 @@ and Scan Tailor Enhanced versions as well as including many more bug fixes.")
 (define-public simpleitk
   (package
     (name "simpleitk")
-    (version "2.5.4")
+    (version "2.5.3")
     (source
      (origin
        (method git-fetch)
@@ -1932,9 +1932,7 @@ and Scan Tailor Enhanced versions as well as including many more bug fixes.")
              (commit (string-append "v" version))))
        (file-name (git-file-name name version))
        (sha256
-        (base32 "1bzj5naqbgv2b31iqgz7qqk9rixsvjqycjz6l7w3gm7v1aj14jpb"))
-       (patches
-        (search-patches "simpleitk-r-4.6.0.patch"))))
+        (base32 "0fvacjfq0p8v7r2cmzwwh7bxb6ayavznhj0m81dah463x472qkd2"))))
     (build-system cmake-build-system)
     (outputs '("out" "python" "r"))
     (arguments
@@ -2034,7 +2032,7 @@ and Scan Tailor Enhanced versions as well as including many more bug fixes.")
                    version "/SimpleITKData-" version ".tar.gz"))
              (sha256
               (base32
-               "0hryvi9fgqac00ng1bfhw3lm0al1dh0ka6jglba2q368nls428nx")))))
+               "0i4f87g1rh6xxisw06gwwyi8f216qqs6ih3gghi3k49vsl0h4g5d")))))
     (synopsis "Simplified interface to @acronym{ITK, Insight Toolkit}")
     (description
      "SimpleITK is an image analysis toolkit built on top of @acronym{ITK,

gnu/packages/linux.scm

@@ -1218,6 +1218,12 @@ Linux kernel.  It has been modified to remove all non-free binary blobs.")
                        "aarch64-linux" "powerpc64le-linux" "riscv64-linux")
                      #:configuration-file kernel-config))
 
+(define-public linux-libre-version         linux-libre-7.0-version)
+(define-public linux-libre-gnu-revision    linux-libre-7.0-gnu-revision)
+(define-public linux-libre-pristine-source linux-libre-7.0-pristine-source)
+(define-public linux-libre-source          linux-libre-7.0-source)
+(define-public linux-libre                 linux-libre-7.0)
+
 (define-public linux-libre-6.19
   (make-linux-libre* linux-libre-6.19-version
                      linux-libre-6.19-gnu-revision
@@ -1234,12 +1240,6 @@ Linux kernel.  It has been modified to remove all non-free binary blobs.")
                        "aarch64-linux" "powerpc64le-linux" "riscv64-linux")
                      #:configuration-file kernel-config))
 
-(define-public linux-libre-version         linux-libre-6.18-version)
-(define-public linux-libre-gnu-revision    linux-libre-6.18-gnu-revision)
-(define-public linux-libre-pristine-source linux-libre-6.18-pristine-source)
-(define-public linux-libre-source          linux-libre-6.18-source)
-(define-public linux-libre                 linux-libre-6.18)
-
 (define-public linux-libre-6.12
   (make-linux-libre* linux-libre-6.12-version
                      linux-libre-6.12-gnu-revision
@@ -1979,6 +1979,8 @@ dtb-$(CONFIG_ARCH_ROCKCHIP) += rk3588-mnt-reform2-dsi.dtb
 dtb-$(CONFIG_ARCH_ROCKCHIP) += rk3588-mnt-reform-next.dtb
 dtb-$(CONFIG_ARCH_ROCKCHIP) += rk3588-mnt-pocket-reform.dtb")))))))))))
 
+(define-public linux-libre-arm64-mnt-reform linux-libre-arm64-mnt-reform-7.0)
+
 (define-public linux-libre-arm64-mnt-reform-6.19
   ;; Kernel for use on the MNT/Reform systems
   ;; https://mntre.com/reform.html
@@ -2315,8 +2317,6 @@ dtb-$(CONFIG_ARCH_ROCKCHIP) += rk3588-mnt-reform2-dsi.dtb
 dtb-$(CONFIG_ARCH_ROCKCHIP) += rk3588-mnt-reform-next.dtb
 dtb-$(CONFIG_ARCH_ROCKCHIP) += rk3588-mnt-pocket-reform.dtb")))))))))))
 
-(define-public linux-libre-arm64-mnt-reform linux-libre-arm64-mnt-reform-6.18)
-
 (define-public linux-libre-arm64-mnt-reform-6.12
   ;; Kernel for use on the MNT/Reform systems
   ;; https://mntre.com/reform.html

gnu/packages/music.scm

@@ -3857,15 +3857,11 @@ follows a traditional multi-track tape recorder control paradigm.")
      (list
       #:phases
       '(modify-phases %standard-phases
-         (add-after 'unpack 'python3.12-compatibility
+         (add-after 'unpack 'python3.11-compatibility
            (lambda _
              (substitute* '("waflib/Context.py"
                             "waflib/ConfigSet.py")
-               (("'rU'") "'r'"))
-             (substitute* "waflib/Context.py"
-               (("imp.new_module") "types.ModuleType")
-               (("import os, re, imp, sys")
-                "import os, re, types, sys"))))
+               (("'rU'") "'r'"))))
          (add-after 'unpack 'remove-sse-flags
            (lambda* (#:key system #:allow-other-keys)
              (unless (or (string-prefix? "x86_64" system)

gnu/packages/networking.scm

@@ -1006,11 +1006,11 @@ publish/subscribe, RPC-style request/reply, or service discovery.")
     (home-page "https://nng.nanomsg.org/")
     (license license:expat)))
 
-(define-public nng-1.11
+(define-public nng-1.10
   (package
     (inherit nng)
     (name "nng")
-    (version "1.11")
+    (version "1.10.1")
     (source
      (origin
        (method git-fetch)
@@ -1019,12 +1019,9 @@ publish/subscribe, RPC-style request/reply, or service discovery.")
              (commit (string-append "v" version))))
        (file-name (git-file-name name version))
        (sha256
-        (base32 "1l4rxwnc9knndwmy7xg53adyrm17ld7c5gxwm7vgfmgfy0my4zy8"))))
+        (base32 "13nmz1p8qd12gyj7wm8fz1ccap47qh41sxz4jqdhj8gnd0kiy5h4"))))
     (arguments
      (list
-      ;; At least on aarch64-linux, running tests in parallel leads to ports
-      ;; being unavailable in later tests, which then fail.
-      #:parallel-tests? #false
       #:configure-flags
       '(list "-DNNG_ENABLE_COVERAGE=ON"
              "-DNNG_ENABLE_TLS=ON"
@@ -1038,7 +1035,6 @@ publish/subscribe, RPC-style request/reply, or service discovery.")
                (("add_nng_test1\\(httpclient 60 NNG_SUPP_HTTP\\)") "")
                (("add_nng_test\\(tls 60\\)") ""))
              (substitute* "src/platform/CMakeLists.txt"
-               ;; This test only seems to fail on aarch64-linux
                (("nng_test\\(platform_test\\)") "")
                (("nng_test\\(resolver_test\\)") ""))
              (substitute* "src/sp/transport/tcp/CMakeLists.txt"

gnu/packages/patches/ghc-chell-quickcheck-enable-qc-2.15.patch

@@ -1,58 +0,0 @@
-From 4617d2682738aeaece613ea61390dd47447c2d9f Mon Sep 17 00:00:00 2001
-From: Potato Hatsue <1793913507@qq.com>
-Date: Fri, 12 Sep 2025 06:07:02 -0700
-Subject: [PATCH] Allow QuickCheck 2.15.0
-
----
- Test/Chell/QuickCheck.hs | 8 ++++++++
- chell-quickcheck.cabal   | 2 +-
- 2 files changed, 9 insertions(+), 1 deletion(-)
-
-diff --git a/Test/Chell/QuickCheck.hs b/Test/Chell/QuickCheck.hs
-index ea1c488..3227b8e 100644
---- a/Test/Chell/QuickCheck.hs
-+++ b/Test/Chell/QuickCheck.hs
-@@ -1,3 +1,4 @@
-+{-# LANGUAGE CPP #-}
- module Test.Chell.QuickCheck (property) where
- 
- import Test.Chell qualified as Chell
-@@ -30,7 +31,12 @@ property name prop = Chell.test name $ \opts -> Text.withNullTerminal $ \term ->
-             { State.terminal = term,
-               State.maxSuccessTests = QuickCheck.maxSuccess args,
-               State.maxDiscardedRatio = QuickCheck.maxDiscardRatio args,
-+#if MIN_VERSION_QuickCheck(2,15,0)
-+              State.replayStartSize = Nothing,
-+              State.maxTestSize = QuickCheck.maxSize args,
-+#else
-               State.computeSize = computeSize (QuickCheck.maxSize args) (QuickCheck.maxSuccess args),
-+#endif
-               State.numSuccessTests = 0,
-               State.numDiscardedTests = 0,
-               State.classes = mempty,
-@@ -59,6 +65,7 @@ property name prop = Chell.test name $ \opts -> Text.withNullTerminal $ \term ->
-         Test.GaveUp {} -> Chell.TestAborted notes output
-         Test.NoExpectedFailure {} -> Chell.TestFailed notes [failure]
- 
-+#if !MIN_VERSION_QuickCheck(2,15,0)
- -- copied from quickcheck-2.4.1.1/src/Test/QuickCheck/Test.hs
- computeSize :: Int -> Int -> Int -> Int -> Int
- computeSize maxSize maxSuccess n d
-@@ -79,3 +86,4 @@ computeSize maxSize maxSuccess n d
- 
- roundTo :: Int -> Int -> Int
- roundTo n m = (n `div` m) * m
-+#endif
-diff --git a/chell-quickcheck.cabal b/chell-quickcheck.cabal
-index e854412..1f3a1d9 100644
---- a/chell-quickcheck.cabal
-+++ b/chell-quickcheck.cabal
-@@ -34,7 +34,7 @@ library
-     build-depends:
-       , base ^>= 4.16 || ^>= 4.17 || ^>= 4.18 || ^>= 4.19 || ^>= 4.20 || ^>= 4.21
-       , chell ^>= 0.5
--      , QuickCheck ^>= 2.14.2
-+      , QuickCheck ^>= 2.14.2 || ^>= 2.15.0
-       , random ^>= 1.2.1 || ^>= 1.3.0
- 
-     exposed-modules:

gnu/packages/patches/ghc-testsuite-recomp015-execstack.patch

@@ -4,7 +4,7 @@
  	# number of sections)
  	'$(TEST_HC)' $(TEST_HC_OPTS) Generate.hs
  	./Generate > ManySections.s
-+	echo '.section .note.GNU-stack,"",@progbits' >> ManySections.s
++	echo '.section .note.GNU-stack,"",@progbits' > ManySections.s
  	echo 'main = putStrLn "Running main..."' > Main.hs
  	'$(TEST_HC)' $(TEST_HC_OPTS) -c ManySections.s
  	'$(TEST_HC)' $(TEST_HC_OPTS) --make -O Main.hs ManySections.o

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;
+-}
+-

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
+

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
+

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);
+ }

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
+

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
+

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
+

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;

gnu/packages/patches/simpleitk-r-4.6.0.patch

@@ -1,46 +0,0 @@
-From 1654599ea228efdd7b378ff44ed4e19d547641e0 Mon Sep 17 00:00:00 2001
-From: Bradley Lowekamp <blowekamp@mail.nih.gov>
-Date: Wed, 29 Apr 2026 16:22:49 +0000
-Subject: [PATCH 1/8] BUG: Replace removed CLOENV with R_ClosureEnv for R 4.6.0
- compatibility
-
-R 4.6.0 removed the non-API macro CLOENV from its public headers.
-The replacement R_ClosureEnv() was added in R 4.5.0. Add a version-
-guarded backport so that builds against older R versions (< 4.5.0)
-continue to work.
-
-Fixes #2574
----
- Wrapping/R/sitkRCommand.cxx | 7 ++++++-
- 1 file changed, 6 insertions(+), 1 deletion(-)
-
-diff --git a/Wrapping/R/sitkRCommand.cxx b/Wrapping/R/sitkRCommand.cxx
-index 216a9327b8..c3a62bead9 100644
---- a/Wrapping/R/sitkRCommand.cxx
-+++ b/Wrapping/R/sitkRCommand.cxx
-@@ -19,10 +19,15 @@
- // The python header defines _POSIX_C_SOURCE without a preceding #undef
- #include <iostream>
- #include <Rinternals.h>
-+#include <Rversion.h>
- 
- #include "sitkRCommand.h"
- #include "sitkExceptionObject.h"
- 
-+// R_ClosureEnv was added in R 4.5.0, CLOENV was removed in R 4.6.0
-+#if R_VERSION < R_Version(4, 5, 0)
-+#  define R_ClosureEnv(x) CLOENV(x)
-+#endif
- 
- namespace itk
- {
-@@ -86,7 +91,7 @@ RCommand::SetFunctionClosure(SEXP FN)
-     // element
-     R_fcall = PROTECT(Rf_lang1(this->m_FunctionClosure));
-     this->SetCallbackRCallable(R_fcall);
--    this->SetCallbackREnviron(CLOENV(this->m_FunctionClosure));
-+    this->SetCallbackREnviron(R_ClosureEnv(this->m_FunctionClosure));
-     UNPROTECT(1);
-   }
- }
-

gnu/packages/patches/swig-support-r-4.6.0.patch

@@ -1,171 +0,0 @@
-From 494259f19b3ca4ad0b11c858bc3ba9b587fa2ed5 Mon Sep 17 00:00:00 2001
-From: Bradley Lowekamp <blowekamp@mail.nih.gov>
-Date: Thu, 30 Apr 2026 16:09:54 +0000
-Subject: [PATCH 1/2] [R] Fix compilation with R 4.6.0 which removed non-API
- macros #3407
-
-R 4.6.0 (April 2025) removed the non-API macro SET_S4_OBJECT and made
-CHARACTER_POINTER return a const pointer, breaking compilation of SWIG
-generated R code.
-
-Replace with proper R API equivalents:
-- SET_S4_OBJECT(x) -> x = Rf_asS4(x, TRUE, 0)  (3 sites in rrun.swg)
-- CHARACTER_POINTER(v)[i] = ... -> SET_STRING_ELT(v, i, ...)  (2 sites in std_vector.i)
-- CHARACTER_POINTER() via pstr -> STRING_ELT(, i) directly  (argcargv.i)
-
-All replacement APIs have been available since R 2.x so no version
-guards are required.
----
- CHANGES.current    | 6 ++++++
- Lib/r/argcargv.i   | 4 +---
- Lib/r/rrun.swg     | 6 +++---
- Lib/r/std_vector.i | 4 ++--
- 4 files changed, 12 insertions(+), 8 deletions(-)
-
-diff --git a/Lib/r/argcargv.i b/Lib/r/argcargv.i
-index 73380f4e2c9..af7aa14d66c 100644
---- a/Lib/r/argcargv.i
-+++ b/Lib/r/argcargv.i
-@@ -14,7 +14,6 @@
- %}
- %typemap(in) (int ARGC, char **ARGV) {
-   $1_ltype i;
--  SEXP *pstr;
-   if ($input == R_NilValue) {
-     /* Empty array */
-     $1 = 0;
-@@ -22,14 +21,13 @@
-     SWIG_exception_fail(SWIG_RuntimeError, "Wrong array type.");
-   } else {
-     $1 = Rf_length($input);
--    pstr = CHARACTER_POINTER($input);
-   }
-   $2 = ($2_ltype) malloc(($1+1)*sizeof($*2_ltype));
-   if ($2 == NULL) {
-     SWIG_exception_fail(SWIG_MemoryError, "Memory allocation failed.");
-   }
-   for (i = 0; i < $1; i++) {
--    $2[i] = ($*2_ltype)STRING_VALUE(pstr[i]);
-+    $2[i] = ($*2_ltype)STRING_VALUE(STRING_ELT($input, i));
-   }
-   $2[i] = NULL;
- }
-diff --git a/Lib/r/rrun.swg b/Lib/r/rrun.swg
-index 4c03d5884d7..5dee391f32f 100644
---- a/Lib/r/rrun.swg
-+++ b/Lib/r/rrun.swg
-@@ -267,7 +267,7 @@ SWIG_MakePtr(void *ptr, const char *typeName, int flags)
-     R_RegisterCFinalizer(external, R_SWIG_ReferenceFinalizer);
- 
-   r_obj = SET_SLOT(r_obj, Rf_mkString((char *) "ref"), external);
--  SET_S4_OBJECT(r_obj);
-+  r_obj = Rf_asS4(r_obj, TRUE, 0);
-   Rf_unprotect(2);
- 
-   return(r_obj);
-@@ -285,7 +285,7 @@ R_SWIG_create_SWIG_R_Array(const char *typeName, SEXP ref, int len)
-    Rf_protect(arr = R_do_slot_assign(arr, Rf_mkString("dims"), Rf_ScalarInteger(len)));
- 
-    Rf_unprotect(3); 			   
--   SET_S4_OBJECT(arr);	
-+   arr = Rf_asS4(arr, TRUE, 0);
-    return arr;
- }
- 
-@@ -308,7 +308,7 @@ SWIG_R_NewPointerObj(void *ptr, swig_type_info *type, int flags) {
-   }
-   rptr = R_MakeExternalPtr(ptr, 
-   R_MakeExternalPtr(type, R_NilValue, R_NilValue), R_NilValue); 
--  SET_S4_OBJECT(rptr);
-+  rptr = Rf_asS4(rptr, TRUE, 0);
-   return rptr;
- }
- 
-diff --git a/Lib/r/std_vector.i b/Lib/r/std_vector.i
-index 6b32c9f6fc2..7db6d3814ac 100644
---- a/Lib/r/std_vector.i
-+++ b/Lib/r/std_vector.i
-@@ -203,7 +203,7 @@
-          PROTECT(result = Rf_allocVector(STRSXP, val->size()));
-          for (unsigned pos = 0; pos < val->size(); pos++)
-            {
--             CHARACTER_POINTER(result)[pos] = Rf_mkChar(((*val)[pos]).c_str());
-+             SET_STRING_ELT(result, pos, Rf_mkChar(((*val)[pos]).c_str()));
-            }
-         UNPROTECT(1);
-         return(result);
-@@ -669,7 +669,7 @@
-             // Fill the R vector
-             for (unsigned vpos = 0; vpos < val->at(pos).size(); ++vpos)
-               {
--                CHARACTER_POINTER(VECTOR_ELT(result, pos))[vpos] = Rf_mkChar(val->at(pos).at(vpos).c_str());
-+                SET_STRING_ELT(VECTOR_ELT(result, pos), vpos, Rf_mkChar(val->at(pos).at(vpos).c_str()));
-               }
-           }
-         UNPROTECT(1);
-
-From 77d8826b46a967af158e982d56008aea2c8f6cb1 Mon Sep 17 00:00:00 2001
-From: Erez Geva <ErezGeva2@gmail.com>
-Date: Fri, 1 May 2026 18:47:42 +0200
-Subject: [PATCH 2/2] Add versioned `R` testing
-
-Signed-off-by: Erez Geva <ErezGeva2@gmail.com>
----
- .github/workflows/linux.yml |  7 +++++++
- Tools/CI-linux-install.sh   | 20 +++++++++++++++++++-
- configure.ac                | 11 +++++++++++
- 3 files changed, 37 insertions(+), 1 deletion(-)
-
-diff --git a/Tools/CI-linux-install.sh b/Tools/CI-linux-install.sh
-index ad74ad3f21f..8f459899906 100644
---- a/Tools/CI-linux-install.sh
-+++ b/Tools/CI-linux-install.sh
-@@ -181,7 +181,25 @@ case "$SWIGLANG" in
- 		fi
- 		;;
- 	"r")
--		$RETRY sudo apt-get -qq install r-base
-+		if [[ -n "$VER" ]]; then
-+			# Should helps with old version, but do not work
-+			#$RETRY sudo apt-get -qq remove r-base r-base-core r-base-dev r-base-html r-doc-html r-recommended
-+			sudo sed -i 's%^# deb-src %deb-src %' /etc/apt/sources.list
-+			sudo sed -i 's%^Types: deb$%Types: deb deb-src%' /etc/apt/sources.list.d/*
-+			$RETRY sudo apt-get -qq update
-+			$RETRY sudo apt-get -qq build-dep r-base
-+			r_build=`mktemp -d`
-+			r_tarball=R-$VER.tar.gz
-+			URL=https://cran.r-project.org/src/base/R-${VER:0:1}
-+			$RETRY wget $URL/$r_tarball
-+			tar -xf "$r_tarball" --strip-components=1 -C "$r_build"
-+			cd "$r_build"
-+			./configure
-+			make
-+			sudo make install
-+		else
-+			$RETRY sudo apt-get -qq install r-base
-+		fi
- 		;;
- 	"ruby")
- 		if [[ "$VER" ]]; then
-diff --git a/configure.ac b/configure.ac
-index e113f4b877c..e309b36ff45 100644
---- a/configure.ac
-+++ b/configure.ac
-@@ -2292,6 +2292,17 @@ else
- if test "x$RBIN" = xyes; then
-    AC_PATH_PROG(RBIN, R)
- fi
-+if test -n "$RBIN" && test -x "$RBIN"; then
-+   r_min_version=2.4.0
-+   AC_MSG_CHECKING([for R version])
-+   r_version=`R --version | grep 'R version' | sed 's%^R version %%;s% (.*%%'`
-+   AS_VERSION_COMPARE(["$r_version"], ["$r_min_version"],
-+                  [AC_MSG_RESULT([older then $r_min_version])
-+                   AS_UNSET([RBIN])],        dnl bellow r_min_version
-+                  [AC_MSG_RESULT([$r_version])],   dnl equal r_min_version
-+                  [AC_MSG_RESULT([$r_version])])   dnl above r_min_version
-+fi
-+
- fi
- 
- AC_SUBST(RBIN)

gnu/packages/prolog.scm

@@ -237,7 +237,7 @@ it.")
 (define-public trealla
   (package
     (name "trealla")
-    (version "2.100.15")
+    (version "2.100.10")
     (source
      (origin
        (method git-fetch)
@@ -246,7 +246,7 @@ it.")
           (url "https://github.com/trealla-prolog/trealla")
           (commit (string-append "v" version))))
        (sha256
-        (base32 "1fr3h0hqk5bbzr8n415pd24n2nvxhyaxi03hn5s78q1yklynw13f"))
+        (base32 "09aqszk3kwjb8qznaywzvhir3nxkf6mkib68mkyn4f7siswb3apg"))
        (file-name (git-file-name name version))))
     (build-system gnu-build-system)
     (inputs

gnu/packages/python-xyz.scm

@@ -18311,21 +18311,9 @@ is binding LibSass.")
        (sha256
         (base32 "1fj4zkcnx3mk7kbnf4d6pjgv331n17wzpphpwdnmr498ghbsph9k"))))
     (build-system pyproject-build-system)
-    (arguments
-     (list
-      #:tests? #f  ;circular dependency with python-aiohttp
-      #:phases
-      '(modify-phases %standard-phases
-         (add-after 'unpack 'python3.12-compatibility
-           (lambda _
-             (substitute* '("idna_ssl.py"
-                            "tests/test_base.py")
-               (("import ssl")
-                "import ssl\nimport urllib3")
-               (("ssl.match_hostname")
-                "urllib3.util.ssl_match_hostname")))))))
+    (arguments (list #:tests? #f))  ;circular dependency with python-aiohttp
     (native-inputs (list python-setuptools))
-    (propagated-inputs (list python-idna python-urllib3))
+    (propagated-inputs (list python-idna))
     (home-page "https://github.com/aio-libs/idna-ssl")
     (synopsis "Support Unicode(idna) domains for Python's @code{ssl} module")
     (description

gnu/packages/python.scm

@@ -1255,7 +1255,7 @@ base, via the @file{pythoncapi_compat.h} header file.")
 (define-public micropython
   (package
     (name "micropython")
-    (version "1.28.0")
+    (version "1.26.1")
     (source
       (origin
         (method url-fetch)
@@ -1263,7 +1263,7 @@ base, via the @file{pythoncapi_compat.h} header file.")
                             "releases/download/v" version
                             "/micropython-" version ".tar.xz"))
         (sha256
-         (base32 "05d2gd3g8v3paxf4fin4cv5scgnc4yl0jdahpjs37nmqaybcahsf"))
+         (base32 "165c8g60f5zf82gw2d94snyjmcgn999jn4i8ngyc0wk2vwa6bghj"))
       (modules '((guix build utils)))
       (snippet
        '(begin

gnu/packages/racket.scm

@@ -202,7 +202,7 @@
 ;;
 ;; CODE:
 
-(define %racket-version "9.1") ; Remember to update chez-scheme-for-racket!
+(define %racket-version "8.18") ; Remember to update chez-scheme-for-racket!
 (define %racket-commit
   (string-append "v" %racket-version))
 (define %racket-origin
@@ -212,7 +212,7 @@
           (url "https://github.com/racket/racket")
           (commit %racket-commit)))
     (sha256
-     (base32 "1yc6lkydg32998ajnqws83zakksmbp3hb21spq0sfaq4v7wg2ng6"))
+     (base32 "0m38im7a3b3w7sdl15vpsrx7dxw5iz22f1zzffy1bkbbqz45pm87"))
     (file-name (git-file-name "racket" %racket-version))
     (patches (search-patches "racket-chez-scheme-bin-sh.patch"
                              "racket-launcher-config-dir.patch"
@@ -695,7 +695,6 @@ DrRacket IDE, are not included.")
          ("net-lib" "pkgs/net-lib")
          ("racket-doc" "pkgs/racket-doc")
          ("racket-index" "pkgs/racket-index")
-         ("racket-index-exe" "pkgs/racket-index-exe")
          ("scheme-doc" "pkgs/scheme-doc")
          ("sandbox-lib" "pkgs/sandbox-lib")
          ("sequence-tools-lib" "pkgs/sequence-tools-lib")
@@ -707,10 +706,10 @@ DrRacket IDE, are not included.")
        "class-iop" (base32 "08z57q83cr7wnh6g8ah3hdhmsmf9zp1jfs7yvxv188l3hzvygy5l")
        '("class-iop-lib"))
       (simple-racket-origin
-       "compatibility" (base32 "0q5k4p44sf2y4gl69js11qvicyzqwy16ry74bvj1vrn8i8xws55b")
+       "compatibility" (base32 "1d1py9wizi4jnzak7b6d0p9filxv1x9mlx5gsp3yhcjajigq182p")
        '("compatibility" "compatibility-doc" "compatibility-lib"))
       (simple-racket-origin
-       "contract-profile" (base32 "068z8flwcznqg0bjk227i2qapqbciyrckgqf8mvk57gxmr6zh3d3")
+       "contract-profile" (base32 "1xm2z8g0dpv5d9h2sg680vx1a8ix9gbsdpxxb8qv1w7akp73paj3")
        '(("contract-profile" ".")))
       (simple-racket-origin
        "data" (base32 "11ai6c9h0brbblc6xn045ajj4gyrvbjpk1pqcqm1m0dy9q2rzd4a")
@@ -719,7 +718,7 @@ DrRacket IDE, are not included.")
        "datalog" (base32 "0nf6cy4djpyhfvgpa6yn72apbz9s83gp0qg95pzjd0az4v6qwq1s")
        '(("datalog" ".")))
       (simple-racket-origin
-       "db" (base32 "09f2wysqmgs46nbzmwrhbn6jqnkpj6bsabm6s6kw8qmp6azca9q2")
+       "db" (base32 "0qwl8gyd71sm56kcs021g99cpw5bibaycvk1x7ng69jhkylg6q6f")
        '("db" "db-doc" "db-lib"))
       (simple-racket-origin
        "deinprogramm" (base32 "1zkasf94gzp97q0fhrd065d56zv10h0j0ncmaghzglkmjj8c3vvx")
@@ -732,10 +731,10 @@ DrRacket IDE, are not included.")
        "distributed-places" (base32 "1dajpkj9balqcpv6cdk9hwjz592h1vq8rrx5vncariiac4vbdpa0")
        '("distributed-places" "distributed-places-doc" "distributed-places-lib"))
       (simple-racket-origin
-       "draw" (base32 "157r861rx2avbjpqhrrxwdqxwf5ksvw38km3pw7rxiwvwh9nys8k")
+       "draw" (base32 "1nny22h0hnd40qs3ndkhfrgg793y6f4gl9jpdz1g2k0cpr3818rg")
        '("draw" "draw-doc" "draw-lib"))
       (simple-racket-origin
-       "drracket" (base32 "17sszhx5nd549w7kj6pd3c3cyjps2swbp7rmg36yaxm71pli5gs5")
+       "drracket" (base32 "07qh9dzgd2xhd0375z78vcsf32za08cacj4s2mcrhilcvcgw9s0j")
        '("drracket"
          "drracket-core"
          "drracket-core-lib"
@@ -754,7 +753,7 @@ DrRacket IDE, are not included.")
        "eopl" (base32 "0qihajdpwf2q7hbs6fsw6mmmzy57kgzgry3vyp9z8w7ay8df3w15")
        '(("eopl" ".")))
       (simple-racket-origin
-       "errortrace" (base32 "02z80khr4kqhcpq1k3djz7jgkwa31vnacid4qx8naab9dkbcp5x8")
+       "errortrace" (base32 "0l9k2rx6z4jkid7kxhbs763s66pxbzvfrgxajykbrmqkv77lhb3w")
        '("errortrace" "errortrace-doc" "errortrace-lib"))
       (simple-racket-origin
        "expeditor" (base32 "1nk88jq0blzcw45fr8nwp024cysplayi3paaay4z824lkn1smzaa")
@@ -771,13 +770,13 @@ DrRacket IDE, are not included.")
        "games" (base32 "13z7fnbr48s98lmfxc0nbfhbqkd4hphymy2r63hqm783xzn6ylzi")
        '(("games" ".")))
       (simple-racket-origin
-       "gui" (base32 "1c47622y5cf1p7nnbycaf53m8vakf55lqzv8byqzj7zcvcsh8s16")
+       "gui" (base32 "0qkxa8cq0cblriamd7x502g918kjvq4348l6c8qmqdpn9cw9mg2h")
        '("gui" "gui-doc" "gui-lib" "tex-table"))
       (simple-racket-origin
-       "gui-pkg-manager" (base32 "1f0ssg37kdk3xn9js616ns345565q39j9h51wzd99753iqd45m92")
+       "gui-pkg-manager" (base32 "024880k3wmvkqhjc954prrkavwv3bgafcw00ajz7h2llygh0aqpl")
        '("gui-pkg-manager-lib"))
       (simple-racket-origin
-       "htdp" (base32 "02a5zny1njys40jfsi2spw82ar0kkbfddpk10al822ajs1manhak")
+       "htdp" (base32 "14bdv86zxs87rvvvbwvq3x0sqpg1hj16whjcv20r96c26b1xxj36")
        '("htdp" "htdp-doc" "htdp-lib"))
       (simple-racket-origin
        "html" (base32 "18n1jnjgzfknc8nv8dppi85nb8q08gqdwkg6hfjk08x0p00anx2x")
@@ -792,16 +791,16 @@ DrRacket IDE, are not included.")
        "lazy" (base32 "0rn8kd0ih7aw6fj1g7jdvi5978a6q4hyd6gbh89nb6j5ijvlgn43")
        '(("lazy" ".")))
       (simple-racket-origin
-       "macro-debugger" (base32 "08qmkrvm3qvac4829izmlwl9qrlsc1f6y8yqiradibhm05k7rwg7")
+       "macro-debugger" (base32 "133b74pxavbafcsmp34kgvwmx1l6xx4bykzvgwwjg3kg2fa5bg1g")
        '("macro-debugger" "macro-debugger-text-lib"))
       (simple-racket-origin
-       "main-distribution" (base32 "0gk7wrwy0r1yllk827h8awfswngl1lhlq765d6s42y841v33jn0i")
+       "main-distribution" (base32 "0m2n9s32s8a4a2gn4ywrm9l8jycdm5ayi5w9kh5wchhrrw7qzq7y")
        '(("main-distribution" ".")))
       (simple-racket-origin
        "make" (base32 "10852fj30bz5r46c3d99s37fkgy5yh44gb01j29sf3kxnhi0g2sa")
        '(("make" ".")))
       (simple-racket-origin
-       "math" (base32 "1mgqxx9lbwhd8if3mxz7ji2wryvihjmq5imn2316skkvr16yy8mx")
+       "math" (base32 "1399mynmcrybipjsy2ikzs600jjxda0lah653w3vx2lfspsn31if")
        '("math" "math-doc" "math-lib"))
       (simple-racket-origin
        "mysterx" (base32 "11p9jzrafw0hizhl0cs4sxx7rv281185q8hryic2rpk0kzjdyr48")
@@ -810,7 +809,7 @@ DrRacket IDE, are not included.")
        "mzcom" (base32 "0rc9pfj7gwm5azghqvcibz6si1x5s2v8mr2yngk7ssq9gzfbi6a4")
        '(("mzcom" ".")))
       (simple-racket-origin
-       "mzscheme" (base32 "0p7bp8rmzw7k12sjxdqlxf31d8ama4wv9qz6ryvnmjn2qyhrr3d1")
+       "mzscheme" (base32 "04kyrhznq46mklacf7pms4fv47zsimqqk3948r3w2ym9n04fhjsx")
        '("mzscheme" "mzscheme-doc" "mzscheme-lib"))
       (racket-packages-origin
        "net-cookies" (origin
@@ -819,7 +818,7 @@ DrRacket IDE, are not included.")
                              (url "https://github.com/RenaissanceBug/racket-cookies")
                              (commit %racket-commit)))
                        (sha256 (base32
-                                "0v6lbpv8ly4jwpjr3rk0q6izpsnfp45ysgrhngpw7jshkjc5wgyd"))
+                                "1fbl717w5801bydx3nzwxddd1rh1cc0gxwpjc7ka9zh5ak09sb0w"))
                        (file-name
                         (git-file-name "RenaissanceBug-racket-cookies" %racket-version)))
        '("net-cookies" "net-cookies-doc" "net-cookies-lib"))
@@ -839,16 +838,16 @@ DrRacket IDE, are not included.")
        "option-contract" (base32 "1914dcxy6qzpg3cpnzdm9lj0kwyw8xdb85mwiamqfkbg0xlyyhpa")
        '("option-contract" "option-contract-doc" "option-contract-lib"))
       (simple-racket-origin
-       "parser-tools" (base32 "0dp99d1a47kqyg2iqdijm5781qnd571iwvg85dvrjc76ab4pccgd")
+       "parser-tools" (base32 "0i822p7ik6q03l7mrlf0qb63xdxvx06yl5lg1g1qri5wmi5xj0pb")
        '("parser-tools" "parser-tools-doc" "parser-tools-lib"))
       (simple-racket-origin
        "pconvert" (base32 "0xw9f9692v2qp16fwmwmwmrb118kpz259vmx8cq6s9vsw0112zpq")
        '("pconvert-lib" "pconvert-doc"))
       (simple-racket-origin
-       "pict" (base32 "1xs1k98nr052p5v30abn7kl8pm1rdwj8xqvrghw8b62bvhhb072a")
+       "pict" (base32 "17pldgiifmwi968dwlk23c1wnrlks0x7aj5jdmdfsf9xgq31wkb5")
        '("pict" "pict-doc" "pict-lib"))
       (simple-racket-origin
-       "pict-snip" (base32 "1qrqbigw6arhccqgqzblfqqcpsdy15dwb0y22axwxgpw1ax0ki6f")
+       "pict-snip" (base32 "081nwiy4a0n4f7xws16hqbhf0j3kz5alizndi3nnyr3chm4kng6x")
        '("pict-snip" "pict-snip-doc" "pict-snip-lib"))
       (simple-racket-origin
        "picturing-programs" (base32 "1a3d6nw9n827b4711nvgrnw7w47k4fxvk8c2a8br6a1l748kxkwy")
@@ -866,7 +865,7 @@ DrRacket IDE, are not included.")
        "preprocessor" (base32 "1p5aid58ifnjy4xl0ysh85cq39k25661v975jrpk182z3k5621mg")
        '(("preprocessor" ".")))
       (simple-racket-origin
-       "profile" (base32 "1n6jlhkq0zs2sd132k92nvw08qscadjz3d6p2r5pjlcdawkmkik0")
+       "profile" (base32 "10lv3iz58hqk043llnbqrkmjnm1pbvr4j1j188g85zg798rqyjzs")
        '("profile" "profile-doc" "profile-lib"))
       (racket-packages-origin
        "quickscript" (origin
@@ -896,7 +895,7 @@ DrRacket IDE, are not included.")
                          (git-file-name "jeapostrophe-racket-cheat" %racket-version)))
        '(("racket-cheat" ".")))
       (simple-racket-origin
-       "racklog" (base32 "0i2jnghb5vqmk2f0cppgggyp73zy1q0dlhpvxrzdxw39skmhmgkc")
+       "racklog" (base32 "0fr8xij0sssfnmwn6dfdi4jj3l62f2yj3jrjljv13kaycrfls032")
        '(("racklog" ".")))
       (simple-racket-origin
        "rackunit" (base32 "191x4lgxg1bbkimdndg6j562zyxq48l0g21f9j2ln2hmh9s1v065")
@@ -915,7 +914,7 @@ DrRacket IDE, are not included.")
        "realm" (base32 "0rlvwyd6rpyl0zda4a5p8dp346fvqzc8555dgfnrhliymkxb6x4g")
        '(("realm" ".")))
       (simple-racket-origin
-       "redex" (base32 "1gg36wpd5kw01dwz353j5xvd2c673aws5l3jn2h2rzqlslk49dw7")
+       "redex" (base32 "1h60mhaaiiwqcnmskqfrl6jhg4d97xjdcxnhw9krm4aysa9b9bwf")
        '("redex"
          "redex-benchmark"
          "redex-doc"
@@ -930,7 +929,7 @@ DrRacket IDE, are not included.")
        "scheme-lib" (base32 "0pcf0y8rp4qyjhaz5ww5sr5diq0wpcdfrrnask7zapyklzx1jx8x")
        '(("scheme-lib" ".")))
       (simple-racket-origin
-       "scribble" (base32 "1h6rkkbvxa6fwcpv6y5n14y984z4bxlhn04hhv8r7398a6jsldg6")
+       "scribble" (base32 "0pg8brgyyziw3y8fp6ls6ii7i02cmm5168i4zmqfxjzywswljf17")
        '("scribble"
          "scribble-doc"
          "scribble-html-lib"
@@ -956,13 +955,13 @@ DrRacket IDE, are not included.")
        "slatex" (base32 "0pkm2isbbdk63slrbsxcql7rr0wdrw5kapw1xq4ps5k8dhlzv8x0")
        '(("slatex" ".")))
       (simple-racket-origin
-       "slideshow" (base32 "1aprcapyj0362lfh2pbcyxf4r2k01zmp6yy9ppag0xbz0jw437im")
+       "slideshow" (base32 "0dyg20qs40s2d6ha28zb9h5x4v7phkddinqm446b4jishyrg7dqc")
        '("slideshow" "slideshow-doc" "slideshow-exe" "slideshow-lib" "slideshow-plugin"))
       (simple-racket-origin
-       "snip" (base32 "10727bi2ybn2ahlkpikdknwfzfsppaw5wkvjmzd380jp1fw91q67")
+       "snip" (base32 "1jpy5728w9bszgsjczlzrjjxsvqlcn4ah6gd3rp0plp8zzk9mq0s")
        '("snip" "snip-lib"))
       (simple-racket-origin
-       "typed-racket" (base32 "1cmp3065fp9lm6rsfml7x5bvnilh1fs9k0511l11qdismz2sndpy")
+       "typed-racket" (base32 "00d5pb5h34066q4prb9v5s5m9ggbby31f3anshd9vfsrzhd38p4n")
        '("source-syntax"
          "typed-racket"
          "typed-racket-compatibility"
@@ -973,7 +972,7 @@ DrRacket IDE, are not included.")
        "srfi" (base32 "07q7wdgnf88z1rq0bfpn4b41abhfswa38c0s2hkn325blk53k4a6")
        '("srfi" "srfi-doc" "srfi-lib" "srfi-lite-lib"))
       (simple-racket-origin
-       "string-constants" (base32 "085anm6s5ghg5bfggavknpr52py1a72qwjihvp0rnxpkf181sn8c")
+       "string-constants" (base32 "0llalgdncn18ix5xnx82yyms221g47xh7s3w6inch53ip3yc6ksr")
        '("string-constants" "string-constants-doc" "string-constants-lib"))
       (simple-racket-origin
        "swindle" (base32 "1q8vdxpzczzwdw2mys2caab45yvadmqkixsr29k8pl03n8dsg8j9")
@@ -985,16 +984,16 @@ DrRacket IDE, are not included.")
        "trace" (base32 "1zx0kfbacidg5rllbvx842x949ra22n004irs3vm1hqmwmixy3is")
        '(("trace" ".")))
       (simple-racket-origin
-       "unix-socket" (base32 "039r2aqc6xc4b3x95ggjg4ab1pfiff6pavi4d40662zgwbi61pwk")
+       "unix-socket" (base32 "02dfwas5ynbpyz74w9kwb4wgb37y5wys7svrlmir8k0n9ph9vq0y")
        '("unix-socket" "unix-socket-doc" "unix-socket-lib"))
       (simple-racket-origin
-       "web-server" (base32 "0v66z9dklf02lc0g357h4rnfq5pnk87d1qz59sfrlzz24phxg9g6")
+       "web-server" (base32 "0ry5vwjd06ml9hmspgrwci8c99syx7zhp9sgldmhwwfvf5m1g29d")
        '("web-server" "web-server-doc" "web-server-lib"))
       (simple-racket-origin
        "wxme" (base32 "1qp5gr9gqsakiq3alw6m4yyv5vw4i3hp4y4nhq8vl2nkjmirvn0b")
        '("wxme" "wxme-lib"))
       (simple-racket-origin
-       "xrepl" (base32 "1kkcm68qyck2d6mp56h1j5fnfbx938a15dnyn1cf5yqpj9cc637m")
+       "xrepl" (base32 "0sw531zvd8xqckmrh5da4fiq0sfjyg1nj5d508l7bl3azn35khil")
        '("xrepl" "xrepl-doc" "xrepl-lib"))))
     (build-system gnu-build-system)
     (arguments

gnu/packages/ruby-xyz.scm

@@ -31,7 +31,7 @@
 ;;; Copyright © 2022-2025 Remco van 't Veer <remco@remworks.net>
 ;;; Copyright © 2022 Taiju HIGASHI <higashi@taiju.info>
 ;;; Copyright © 2023 Yovan Naumovski <yovan@gorski.stream>
-;;; Copyright © 2023, 2024, 2025, 2026 gemmaro <gemmaro.dev@gmail.com>
+;;; Copyright © 2023, 2024, 2025 gemmaro <gemmaro.dev@gmail.com>
 ;;; Copyright © 2023, 2024 Janneke Nieuwenhuizen <janneke@gnu.org>
 ;;; Copyright © 2023, 2024 Zheng Junjie <873216071@qq.com>
 ;;; Copyright © 2023-2025 Hartmut Goebel <h.goebel@crazy-compilers.com>
@@ -8201,27 +8201,19 @@ differences (added or removed nodes) between two XML/HTML documents.")
 (define-public ruby-racc
   (package
     (name "ruby-racc")
-    (version "1.8.1")
+    (version "1.5.2")
     (source
      (origin
-       (method git-fetch) ;for tests
-       (uri (git-reference
-             (url "https://github.com/ruby/racc")
-             (commit (string-append "v" version))))
-       (file-name (git-file-name name version))
+       (method url-fetch)
+       (uri (rubygems-uri "racc" version))
        (sha256
         (base32
-         "1sg2mqp6yxdxrn9kbbsxkd6930fxvm4yjl8knsc0wq6fkipnhm8q"))))
+         "178k7r0xn689spviqzhvazzvxfq6fyjldxb3ywjbgipbfi4s8j1g"))))
     (build-system ruby-build-system)
     (arguments
-     (list
-      #:phases
-      #~(modify-phases %standard-phases
-          (add-before 'build 'compile
-            (lambda _
-              (invoke "rake" "compile"))))))
+     `(#:tests? #f))            ; Fails while parsing test instructions.
     (native-inputs
-     (list ruby-rake-compiler ruby-test-unit-ruby-core))
+     (list ruby-hoe ruby-rake-compiler))
     (synopsis "LALR(1) parser generator for Ruby")
     (description
      "Racc is a LALR(1) parser generator.  It is written in Ruby itself, and

gnu/packages/rust-sources.scm

@@ -37,8 +37,6 @@
   #:use-module (gnu packages perl)
   #:use-module (gnu packages pkg-config)
   #:use-module (gnu packages python)
-  #:use-module (gnu packages rust)
-  #:use-module (gnu packages statistics)
   #:use-module (gnu packages textutils)
   #:use-module (gnu packages virtualization))
 
@@ -248,48 +246,6 @@ transliterating them.  It supports Emoji and Chinese.")
        ;; checkout and does not need a cargo input.
        (inputs (cargo-inputs 'rust-deunicode-1.6.2.cfb8552))))))
 
-;; Workspace dependency of r-pizzarr.
-(define-public rust-extendr-0.8.1.93d7244
-  (let ((commit "93d7244e3145d94186bc2f35258ad0ef25a28908")
-        (revision "1"))
-    (hidden-package
-     (package
-       (name "rust-extendr")
-       (version (git-version "0.8.1" revision commit))
-       (source (origin
-                 (method git-fetch)
-                 (uri (git-reference
-                        (url "https://github.com/extendr/extendr")
-                        (commit commit)))
-                 (file-name (git-file-name name version))
-                 (sha256
-                  (base32
-                   "03d16y7f1r0y1s8gwzw7wzn5yhcqr1wn0vga9dvdjxpbga372vx7"))))
-       (build-system cargo-build-system)
-       (arguments
-        (list
-         #:cargo-package-crates
-         ;; Note that the order matters!
-         '(list "extendr-ffi"
-                "extendr-macros"
-                "extendr-api"
-                "extendr-engine")
-         #:phases
-         #~(modify-phases %standard-phases
-             (add-after 'unpack 'set-R_HOME
-               (lambda _
-                 (delete-file-recursively ".cargo")
-                 (setenv "R_HOME"
-                         (string-append
-                          #$(this-package-input "r-minimal")
-                          "/lib/R")))))))
-       (inputs (cons r-minimal (cargo-inputs 'extendr)))
-       (home-page "https://extendr.rs/")
-       (synopsis "R extension library for Rust")
-       (description "This library allows you to extend R with Rust.  It can be
-used to write R packages that link with Rust libraries.")
-       (license license:expat)))))
-
 ;; Workspace dependency of zed.
 ;;
 ;; Cargo side: Cargo unifies dependency versions across zed's

gnu/packages/sequoia.scm

@@ -244,21 +244,26 @@ This Guix package is built to use the nettle cryptographic library.")
 (define-public sequoia-wot-tools
   (package
     (name "sequoia-wot-tools")
-    (version "0.15.2")
+    (version "0.15.0")
     (source
      (origin
        (method git-fetch)
        (uri (git-reference
-              (url "https://gitlab.com/sequoia-pgp/sequoia-wot.git/")
-              (commit (string-append "sequoia-wot/v" version))))
+              (url "https://gitlab.com/sequoia-pgp/sequoia-wot")
+              (commit (string-append "v" version))))
        (file-name (git-file-name name version))
        (sha256
-        (base32 "18v713n36sq5pvd1pbs34v7dly1bi614kwra09qxpsxk0ffp225z"))))
+        (base32 "03wa4l582hx0qq28pkhrf0pagckyx6df01pb4chyngadk49q1xn7"))))
     (build-system cargo-build-system)
     (arguments
      (list
        #:features '(list "sequoia-openpgp/crypto-nettle")
        #:cargo-package-crates ''("tools")
+       #:cargo-test-flags
+       '(list "--"
+              "--skip=gpg_trust_roots"
+              "--skip=backward_propagation::tests::cliques"
+              "--skip=tests::cliques")
        #:install-source? #f
        #:cargo-install-paths ''("tools")
        #:phases
@@ -271,12 +276,11 @@ This Guix package is built to use the nettle cryptographic library.")
                  (for-each (lambda (file)
                              (install-file file man1))
                            (find-files "target/release" "\\.1$"))
-                 (mkdir-p (string-append out "/share/bash-completion/completions"))
+                 (mkdir-p (string-append out "/etc/bash_completion.d"))
                  (mkdir-p (string-append share "/fish/vendor_completions.d"))
                  (mkdir-p (string-append share "/elvish/lib"))
                  (copy-file (car (find-files "target/release" "sq-wot.bash"))
-                            (string-append
-                              out "/share/bash-completion/completions/sq-wot"))
+                            (string-append out "/etc/bash_completion.d/sq-wot"))
                  (copy-file (car (find-files "target/release" "sq-wot.fish"))
                             (string-append
                               share "/fish/vendor_completions.d/sq-wot.fish"))
@@ -288,7 +292,7 @@ This Guix package is built to use the nettle cryptographic library.")
     (inputs
      (cons* nettle openssl sqlite (cargo-inputs 'sequoia-wot-tools)))
     (native-inputs
-     (list clang gnupg pkg-config))
+     (list clang pkg-config))
     (home-page "https://sequoia-pgp.org/")
     (synopsis "Implementation of OpenPGP's web of trust")
     (description

gnu/packages/swig.scm

@@ -88,9 +88,7 @@ you tailor the wrapping process to suit your application.")
                                  name "-" version ".tar.gz"))
               (sha256
                (base32
-                "1kqz533599d00rrz0g2ryf8w2ynb25ayylpx10nmkxsndiq2l5j0"))
-              (patches
-               (search-patches "swig-support-r-4.6.0.patch"))))
+                "1kqz533599d00rrz0g2ryf8w2ynb25ayylpx10nmkxsndiq2l5j0"))))
     (native-inputs (list boost
                          pcre2 ; for pcre2-config
                          ;; The following are for tests and examples:

gnu/packages/wm.scm

@@ -1677,13 +1677,13 @@ tiled on several screens.")
 (define-public ghc-xmobar
   (package
     (name "ghc-xmobar")
-    (version "0.50")
+    (version "0.48.1")
     (source (origin
               (method url-fetch)
               (uri (hackage-uri "xmobar" version))
               (sha256
                (base32
-                "026s0q718z89vzjgva19vg58dm1l016i67mzi0wbj7kgai89w909"))))
+                "1infcisv7l00a4z4byjwjisg4yndk0cymibfii1c7yzyzrlvavhl"))))
     (build-system haskell-build-system)
     (properties '((upstream-name . "xmobar")))
     (native-inputs
@@ -2804,7 +2804,7 @@ XDG-Output for wlclock to work.")
 (define-public wlroots
   (package
     (name "wlroots")
-    (version "0.20.1")
+    (version "0.20.0")
     (source
      (origin
        (method git-fetch)
@@ -2813,7 +2813,7 @@ XDG-Output for wlclock to work.")
              (commit version)))
        (file-name (git-file-name name version))
        (sha256
-        (base32 "0n9wkmqnja5fnwn8an36jqn6nzlb1vjdzi0v932pn5bpgmv3brxs"))))
+        (base32 "1gdmy4mpi7x23g81cdmcr9aakk3g6csl69h9j98yzssa48k6all5"))))
     (build-system meson-build-system)
     (arguments
      (list #:phases
@@ -4717,7 +4717,7 @@ read and write, and compatible with JSON.")
 (define-public labwc
   (package
     (name "labwc")
-    (version "0.20.0")
+    (version "0.9.7")
     (source (origin
               (method git-fetch)
               (uri (git-reference
@@ -4726,7 +4726,7 @@ read and write, and compatible with JSON.")
               (file-name (git-file-name name version))
               (sha256
                (base32
-                "0hq88p8ij1zd595rrfr6pxxkzbflgnafdvqjdw7p1y9l5dgkaar5"))))
+                "12mm4w9djgh7q30lswhl1q1cxf6h0pf8xr744jkcyjcqqsavynpf"))))
     (build-system meson-build-system)
     (native-inputs
      (list pkg-config gettext-minimal scdoc))
@@ -4739,7 +4739,7 @@ read and write, and compatible with JSON.")
            libxcb
            libxml2
            pango
-           wlroots-0.20))
+           wlroots-0.19))
     (home-page "https://labwc.github.io")
     (synopsis "Window-stacking compositor for Wayland")
     (description

guix/build/haskell-build-system.scm

@@ -84,6 +84,7 @@ and parameters ~s~%"
          (lib (assoc-ref outputs "lib"))
          (name-version (strip-store-file-name out))
          (extra-dirs (filter-map (cut assoc-ref inputs <>) extra-directories))
+         (ghc-path (getenv "GHC_PACKAGE_PATH"))
          (params `(,(string-append "--prefix=" out)
                    ,(string-append "--libdir=" (or lib out) "/lib")
                    ,(string-append "--docdir=" (or doc out)
@@ -119,7 +120,9 @@ and parameters ~s~%"
     ;; <https://www.haskell.org/cabal/users-guide/developing-packages.html>.
     (when (file-exists? "configure")
       (setenv "CONFIG_SHELL" "sh"))
-    (run-setuphs "configure" params)))
+    (run-setuphs "configure" params)
+
+    (setenv "GHC_PACKAGE_PATH" ghc-path)))
 
 (define* (build #:key parallel-build? #:allow-other-keys)
   "Build a given Haskell package."

guix/import/cran.scm

@@ -202,9 +202,9 @@ package definition."
 (define %cran-canonical-url "https://cran.r-project.org/package=")
 (define %bioconductor-url "https://bioconductor.org/packages/")
 
-;; The latest Bioconductor release is 3.23.  Bioconductor packages should be
+;; The latest Bioconductor release is 3.22.  Bioconductor packages should be
 ;; updated together.
-(define %bioconductor-version "3.23")
+(define %bioconductor-version "3.22")
 
 (define* (bioconductor-packages-list-url #:optional type)
   (string-append "https://bioconductor.org/packages/"

guix/import/stackage.scm

@@ -50,7 +50,7 @@
   (make-parameter "https://www.stackage.org/api/v1/snapshot"))
 
 ;; Latest LTS version compatible with current GHC.
-(define %default-lts-version "24.9")
+(define %default-lts-version "20.26")
 
 (define-json-mapping <stackage-lts> make-stackage-lts
   stackage-lts?