Merge branch 'master' into mesa-updates

Change-Id: I4b468bb3148d392c9ade30dfe0cfb68c574a8e27

Makefile.am

@@ -18,6 +18,7 @@
 # Copyright © 2021 Chris Marusich <cmmarusich@gmail.com>
 # Copyright © 2021 Andrew Tropin <andrew@trop.in>
 # Copyright © 2023 Clément Lassieur <clement@lassieur.org>
+# Copyright © 2023 Wilko Meyer <w@wmeyer.eu>
 #
 # This file is part of GNU Guix.
 #
@@ -415,6 +416,10 @@ AUX_FILES =						\
   gnu/packages/aux-files/chromium/master-preferences.json		\
   gnu/packages/aux-files/emacs/guix-emacs.el		\
   gnu/packages/aux-files/guix.vim			\
+  gnu/packages/aux-files/linux-libre/6.6-arm.conf	\
+  gnu/packages/aux-files/linux-libre/6.6-arm64.conf	\
+  gnu/packages/aux-files/linux-libre/6.6-i686.conf	\
+  gnu/packages/aux-files/linux-libre/6.6-x86_64.conf	\
   gnu/packages/aux-files/linux-libre/6.5-arm.conf	\
   gnu/packages/aux-files/linux-libre/6.5-arm64.conf	\
   gnu/packages/aux-files/linux-libre/6.5-i686.conf	\

etc/teams.scm

@@ -529,6 +529,15 @@ GLib/GIO, GTK, GStreamer and Webkit."
         #:description "Audio related packages."
         #:scope (list "gnu/packages/audio.scm")))
 
+(define-team zig
+  (team 'zig
+        #:name "Zig team"
+        #:description "Zig, Zig packages, and the zig-build system"
+        #:scope (list "gnu/packages/zig.scm"
+                      "gnu/packages/zig-xyz.scm"
+                      "guix/build/zig-build-system.scm"
+                      "guix/build-system/zig.scm")))
+
 
 (define-member (person "Eric Bavier"
                        "bavier@posteo.net")
@@ -662,6 +671,10 @@ GLib/GIO, GTK, GStreamer and Webkit."
                        "gabriel@erlikon.ch")
   audio)
 
+(define-member (person "Ekaitz Zarraga"
+                       "ekaitz@elenq.tech")
+  bootstrap zig)
+
 
 (define (find-team name)
   (or (hash-ref %teams (string->symbol name))

gnu/local.mk

@@ -899,7 +899,9 @@ dist_patch_DATA =						\
   %D%/packages/patches/aegisub-make43.patch			\
   %D%/packages/patches/agda-categories-remove-incompatible-flags.patch	\
   %D%/packages/patches/agda-categories-use-find.patch	\
+  %D%/packages/patches/agda-categories-use-stdlib-1.7.3.patch	\
   %D%/packages/patches/agda-libdirs-env-variable.patch	\
+  %D%/packages/patches/agda-use-sphinx-5.patch	\
   %D%/packages/patches/agda-stdlib-use-runhaskell.patch	\
   %D%/packages/patches/agg-am_c_prototype.patch			\
   %D%/packages/patches/agg-2.5-gcc8.patch			\
@@ -1016,6 +1018,8 @@ dist_patch_DATA =						\
   %D%/packages/patches/clang-13.0-libc-search-path.patch	\
   %D%/packages/patches/clang-14.0-libc-search-path.patch	\
   %D%/packages/patches/clang-15.0-libc-search-path.patch	\
+  %D%/packages/patches/clang-16.0-libc-search-path.patch	\
+  %D%/packages/patches/clang-17.0-libc-search-path.patch	\
   %D%/packages/patches/clang-runtime-asan-build-fixes.patch	\
   %D%/packages/patches/clang-runtime-esan-build-fixes.patch	\
   %D%/packages/patches/clang-runtime-9-libsanitizer-mode-field.patch	\

gnu/packages/agda.scm

@@ -44,7 +44,7 @@
 (define-public agda
   (package
     (name "agda")
-    (version "2.6.3")
+    (version "2.6.4")
     (source
      (origin
        (method git-fetch)
@@ -53,12 +53,14 @@
              (commit (string-append "v" version))))
        (file-name (git-file-name name version))
        (sha256
-        (base32 "1s7zd01i8pmvi90ywx497kc07z50nah7h0fc2dn6jzb132k5sh1q"))
+        (base32 "0n4avd58j45rdcmnwgrmz5s0ril0z4n2z711mwwbahl50f7359ky"))
-       (patches (search-patches "agda-libdirs-env-variable.patch"))))
+       (patches (search-patches "agda-libdirs-env-variable.patch"
+                                "agda-use-sphinx-5.patch"))))
     (build-system haskell-build-system)
     (inputs
      (list ghc-aeson
            ghc-alex
+           ghc-ansi-terminal
            ghc-async
            ghc-blaze-html
            ghc-boxes
@@ -73,9 +75,11 @@
            ghc-monad-control
            ghc-murmur-hash
            ghc-parallel
+           ghc-peano
            ghc-regex-tdfa
            ghc-split
            ghc-strict
+           ghc-text-icu
            ghc-unordered-containers
            ghc-uri-encode
            ghc-vector-hashtables
@@ -91,6 +95,7 @@
                        (guix build utils)
                        (srfi srfi-26)
                        (ice-9 match))
+           #:configure-flags #~(list "-foptimise-heavily" "-fenable-cluster-counting")
            #:phases
            #~(modify-phases %standard-phases
                ;; This allows us to call the 'agda' binary before installing.
@@ -194,7 +199,7 @@ come from Agda's standard library.")
 (define-public agda-stdlib
   (package
     (name "agda-stdlib")
-    (version "1.7.2")
+    (version "1.7.3")
     (source (origin
               (method git-fetch)
               (uri (git-reference
@@ -203,7 +208,7 @@ come from Agda's standard library.")
               (file-name (git-file-name name version))
               (sha256
                (base32
-                "065hf24xjpciwdrvk4isslgcgi01q0k93ql0y1sjqqvy5ryg5xmy"))))
+                "0y6rns64rrkh8hw7mamcf6797329pi4ravpak5zijpnkzdagmlmy"))))
     (build-system agda-build-system)
     (arguments
      (list
@@ -241,7 +246,8 @@ try agda-prelude instead.")
                (base32
                 "0xwgm2mfl2pxipsv31bin8p14y1yhd9n27lv3clvsxd4z9yc034m"))
               (patches (search-patches "agda-categories-remove-incompatible-flags.patch"
-                                       "agda-categories-use-find.patch"))))
+                                       "agda-categories-use-find.patch"
+                                       "agda-categories-use-stdlib-1.7.3.patch"))))
     (build-system agda-build-system)
     (arguments
      (list
@@ -259,12 +265,9 @@ try agda-prelude instead.")
     (license license:expat)))
 
 (define-public agda-cubical
-  ;; Upstream's HEAD follows the latest Agda release, but they don't release
-  ;; until a newer Agda release comes up, so their releases are always one
-  ;; version late.
   (package
     (name "agda-cubical")
-    (version "0.5")
+    (version "0.6")
     (source (origin
               (method git-fetch)
               (uri (git-reference
@@ -273,7 +276,7 @@ try agda-prelude instead.")
               (file-name (git-file-name name version))
               (sha256
                (base32
-                "0yfg7gr55n08ly1qgzpcp16s15k1abycppbcdi9lzg1hjryqxcg3"))))
+                "0zq0z328zcjmm43mrv2ks27i1dnbylcf8mhzja2hd4gvz1kq1ays"))))
     (build-system agda-build-system)
     (arguments
      (list
@@ -290,10 +293,10 @@ agda-stdlib but using cubical methods.")
     (license license:expat)))
 
 (define-public agda-1lab
-  ;; Upstream doesn't do releases (yet).  Use a commit that builds with 2.6.3,
+  ;; Upstream doesn't do releases (yet).  Use a commit that builds with 2.6.4,
   ;; since they use Agda HEAD.
-  (let* ((revision "1")
+  (let* ((revision "2")
-         (commit "47ca1d23640a6f49a3abe3c2fe27738bcc10c9c6"))
+         (commit "549fdb1c948a975e90e70f871993a4a4239aa280"))
     (package
       (name "agda-1lab")
       (version (git-version "0.0" revision commit))
@@ -306,10 +309,12 @@ agda-stdlib but using cubical methods.")
          (file-name (git-file-name name version))
          (sha256
           (base32
-           "0j7mp6c0xd0849skdxzncklkxynxnyfrbpcjv4qp5p1xfn0dnfqx"))))
+           "1k4zj8dibyplakpxaw4a8hpsaqhakynjb83dqxrva4h4ssj6gkqj"))))
       (build-system agda-build-system)
       (arguments
-       (list #:plan '(("src/index\\.lagda\\.md$"))))
+       ;; Check files individually first, to avoid running out of heap :(
+       (list #:plan '(("src/.+/.+\\.lagda\\.md$")
+                      ("src/index\\.lagda\\.md$"))))
       (synopsis "Reference resource for mathematics done in Homotopy Type Theory")
       (description "A formalised, cross-linked reference resource for
 mathematics done in Homotopy Type Theory.  Unlike the HoTT book, the 1lab is

gnu/packages/bioconductor.scm

@@ -543,6 +543,28 @@ Finder (TRF mask).  Only the AGAPS and AMB masks are \"active\" by default.")
 as provided by UCSC (danRer11, May 2017) and stored in Biostrings objects.")
     (license license:artistic2.0)))
 
+(define-public r-bsgenome-ecoli-ncbi-20080805
+  (package
+    (name "r-bsgenome-ecoli-ncbi-20080805")
+    (version "1.3.1000")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (bioconductor-uri "BSgenome.Ecoli.NCBI.20080805" version
+                              'annotation))
+       (sha256
+        (base32 "1l7mjyys1kaq4mbia9jamyw6sd0ij1wypwxvwy8aksan3gcfnh27"))))
+    (properties `((upstream-name . "BSgenome.Ecoli.NCBI.20080805")))
+    (build-system r-build-system)
+    (propagated-inputs (list r-bsgenome))
+    (home-page
+     "https://bioconductor.org/packages/BSgenome.Ecoli.NCBI.20080805")
+    (synopsis "Escherichia coli full genomes")
+    (description
+     "This package provides Escherichia coli full genomes for several strains
+as provided by NCBI on 2008/08/05 and stored in Biostrings objects.")
+    (license license:artistic2.0)))
+
 (define-public r-bsgenome-hsapiens-1000genomes-hs37d5
   (package
     (name "r-bsgenome-hsapiens-1000genomes-hs37d5")
@@ -1611,6 +1633,26 @@ biscuiteer.")
 demonstrate functionalities of the @code{breakpointR} package.")
     (license license:expat)))
 
+(define-public r-breastcancervdx
+  (package
+    (name "r-breastcancervdx")
+    (version "1.40.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (bioconductor-uri "breastCancerVDX" version
+                              'experiment))
+       (sha256
+        (base32 "12r8zql30ssr0cxy8v1qawwsky54321c737ny19n2yrl7sm08gf0"))))
+    (properties `((upstream-name . "breastCancerVDX")))
+    (build-system r-build-system)
+    (home-page "https://bioconductor.org/packages/breastCancerVDX")
+    (synopsis "Gene expression datasets")
+    (description
+     "This package is a collection of gene expression data from a breast
+cancer study published in Wang et al. 2005 and Minn et al 2007.")
+    (license license:artistic2.0)))
+
 (define-public r-celldex
   (package
     (name "r-celldex")
@@ -4201,6 +4243,27 @@ BaalChIP is able to account for copy number differences between the two
 alleles, a known phenotypical feature of cancer samples.")
     (license license:artistic2.0)))
 
+(define-public r-bags
+  (package
+    (name "r-bags")
+    (version "2.42.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (bioconductor-uri "BAGS" version))
+       (sha256
+        (base32 "0356ragpcldr48yycqj91sn3bcqvvfp5spv2z02r8g6hs0dndwdh"))))
+    (properties `((upstream-name . "BAGS")))
+    (build-system r-build-system)
+    (propagated-inputs (list r-biobase r-breastcancervdx))
+    (home-page "https://bioconductor.org/packages/BAGS")
+    (synopsis "Bayesian approach for geneset selection")
+    (description
+     "This R package is providing functions to perform geneset significance
+analysis over simple cross-sectional data between 2 and 5 phenotypes of
+interest.")
+    (license license:artistic2.0)))
+
 (define-public r-basespacer
   (package
     (name "r-basespacer")
@@ -22528,6 +22591,122 @@ within a certain time frame are deleted.  This aims to reduce disk usage by
 eliminating obsolete caches generated by old versions of packages.")
     (license license:gpl3)))
 
+(define-public r-basic4cseq
+  (package
+    (name "r-basic4cseq")
+    (version "1.38.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (bioconductor-uri "Basic4Cseq" version))
+       (sha256
+        (base32 "1vlrrkg885w77w34m2q8hngr95hhh5bkw9hrzyhnp39igjkcwqx4"))))
+    (properties `((upstream-name . "Basic4Cseq")))
+    (build-system r-build-system)
+    (propagated-inputs
+     (list r-biostrings
+           r-bsgenome-ecoli-ncbi-20080805
+           r-catools
+           r-genomicalignments
+           r-genomicranges
+           r-rcircos))
+    (home-page "https://bioconductor.org/packages/Basic4Cseq")
+    (synopsis "Analyzing 4C-seq data")
+    (description
+     "Basic4Cseq is an R package for basic filtering, analysis and subsequent
+visualization of @acronym{4C-seq, circular chromosome conformation capture
+sequencing} data.  Virtual fragment libraries can be created for any BSGenome
+package, and filter functions for both reads and fragments and basic quality
+controls are included.  Fragment data in the vicinity of the experiment's
+viewpoint can be visualized as a coverage plot based on a running median
+approach and a multi-scale contact profile.")
+    (license license:lgpl3)))
+
+(define-public r-basics
+  (package
+    (name "r-basics")
+    (version "2.14.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (bioconductor-uri "BASiCS" version))
+       (sha256
+        (base32 "0kf215n151sxphc5w9h4i2xsk7lmysi4abwcpyz4slbwhpki3ac8"))))
+    (properties `((upstream-name . "BASiCS")))
+    (build-system r-build-system)
+    (propagated-inputs
+     (list r-assertthat
+           r-biobase
+           r-biocgenerics
+           r-biocparallel
+           r-coda
+           r-cowplot
+           r-ggextra
+           r-ggplot2
+           r-hexbin
+           r-mass
+           r-matrix
+           r-matrixstats
+           r-posterior
+           r-rcpp
+           r-rcpparmadillo
+           r-reshape2
+           r-s4vectors
+           r-scran
+           r-scuttle
+           r-singlecellexperiment
+           r-summarizedexperiment
+           r-viridis))
+    (native-inputs (list r-knitr))
+    (home-page "https://github.com/catavallejos/BASiCS")
+    (synopsis "Bayesian analysis of single-cell sequencing data")
+    (description
+     "@acronym{BASiCS, Bayesian analysis of single-cell sequencing data} is an
+integrated Bayesian hierarchical model to perform statistical analyses of
+single-cell RNA sequencing datasets in the context of supervised experiments
+(where the groups of cells of interest are known a priori.  BASiCS performs
+built-in data normalisation (global scaling) and technical noise quantification
+(based on spike-in genes).  BASiCS provides an intuitive detection criterion
+for highly (or lowly) variable genes within a single group of cells.
+Additionally, BASiCS can compare gene expression patterns between two or more
+pre-specified groups of cells.")
+    (license license:gpl3)))
+
+(define-public r-basicstarrseq
+  (package
+    (name "r-basicstarrseq")
+    (version "1.30.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (bioconductor-uri "BasicSTARRseq" version))
+       (sha256
+        (base32 "1dw6bv1qk2bn0l3m458sqgvm3s1karh4n3431pl7r0jj2r3mr6xa"))))
+    (properties `((upstream-name . "BasicSTARRseq")))
+    (build-system r-build-system)
+    (propagated-inputs
+     (list r-genomeinfodb
+           r-genomicalignments
+           r-genomicranges
+           r-iranges
+           r-s4vectors))
+    (native-inputs (list r-knitr))
+    (home-page "https://bioconductor.org/packages/BasicSTARRseq")
+    (synopsis "Basic peak calling on STARR-seq data")
+    (description
+     "This package implements a method that aims to identify enhancers on
+large scale.  The STARR-seq data consists of two sequencing datasets of the
+same targets in a specifc genome.  The input sequences show which regions
+where tested for enhancers.  Significant enriched peaks i.e. a lot more
+sequences in one region than in the input where enhancers in the genomic DNA
+are, can be identified.  So the approach pursued is to call peak every region
+in which there is a lot more
+(significant in a binomial model) STARR-seq signal than input signal and
+propose an enhancer at that very same position.  Enhancers then are called
+weak or strong dependent of there degree of enrichment in comparison to
+input.")
+    (license license:lgpl3)))
+
 (define-public r-basilisk-utils
   (package
     (name "r-basilisk-utils")
@@ -22578,6 +22757,166 @@ Functions are also provided to enable smooth interoperability of multiple
 Python environments in a single R session.")
     (license license:gpl3)))
 
+(define-public r-bayesknockdown
+  (package
+    (name "r-bayesknockdown")
+    (version "1.28.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (bioconductor-uri "BayesKnockdown" version))
+       (sha256
+        (base32 "1argd4gfld2yb0vvpgb5k7m6agmi58712f6g5dj4gnb7kg4rp1l8"))))
+    (properties `((upstream-name . "BayesKnockdown")))
+    (build-system r-build-system)
+    (propagated-inputs (list r-biobase))
+    (home-page "https://bioconductor.org/packages/BayesKnockdown")
+    (synopsis "Posterior probabilities for edges from knockdown data")
+    (description
+     "This package provides a simple, fast Bayesian method for computing
+posterior probabilities for relationships between a single predictor variable
+and multiple potential outcome variables, incorporating prior probabilities of
+relationships.  In the context of knockdown experiments, the predictor
+variable is the knocked-down gene, while the other genes are potential
+targets.  It can also be used for differential expression/2-class data.")
+    (license license:gpl3)))
+
+(define-public r-bayesspace
+  (package
+    (name "r-bayesspace")
+    (version "1.12.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (bioconductor-uri "BayesSpace" version))
+       (sha256
+        (base32 "1mqgsylnrvf197cin5zzihjv31bm2q0m5a612ncbglys6n1jd105"))))
+    (properties `((upstream-name . "BayesSpace")))
+    (build-system r-build-system)
+    (propagated-inputs
+     (list r-assertthat
+           r-biocfilecache
+           r-biocsingular
+           r-coda
+           r-dirichletreg
+           r-ggplot2
+           r-matrix
+           r-mclust
+           r-purrr
+           r-rcpp
+           r-rcpparmadillo
+           r-rcppdist
+           r-rcppprogress
+           r-rcurl
+           r-rhdf5
+           r-s4vectors
+           r-scales
+           r-scater
+           r-scran
+           r-singlecellexperiment
+           r-summarizedexperiment
+           r-xgboost))
+    (native-inputs (list r-knitr))
+    (home-page "https://www.ezstatconsulting.com/BayesSpace/")
+    (synopsis "Clustering and resolution enhancement of spatial transcriptomes")
+    (description
+     "This package provides tools for clustering and enhancing the resolution
+of spatial gene expression experiments.  BayesSpace clusters a low-dimensional
+representation of the gene expression matrix, incorporating a spatial prior to
+encourage neighboring spots to cluster together.  The method can enhance the
+resolution of the low-dimensional representation into \"sub-spots\", for which
+features such as gene expression or cell type composition can be imputed.")
+    (license license:expat)))
+
+(define-public r-baynorm
+  (package
+    (name "r-baynorm")
+    (version "1.20.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (bioconductor-uri "bayNorm" version))
+       (sha256
+        (base32 "01lv4w1x43x3f9sdrqikhsr1gdvkgqzrgcd9wnjj76qsljn57ifq"))))
+    (properties `((upstream-name . "bayNorm")))
+    (build-system r-build-system)
+    (propagated-inputs
+     (list r-bb
+           r-biocparallel
+           r-dosnow
+           r-fitdistrplus
+           r-foreach
+           r-iterators
+           r-locfit
+           r-mass
+           r-matrix
+           r-rcpp
+           r-rcpparmadillo
+           r-rcppprogress
+           r-singlecellexperiment
+           r-summarizedexperiment))
+    (native-inputs (list r-knitr))
+    (home-page "https://github.com/WT215/bayNorm")
+    (synopsis "Single-cell RNA sequencing data normalization")
+    (description
+     "The bayNorm package is used for normalizing single-cell RNA-seq data.
+The main function is @code{bayNorm}, which is a wrapper function for gene
+specific prior parameter estimation and normalization.  The input is a matrix
+of scRNA-seq data with rows different genes and coloums different cells.  The
+output is either point estimates from posterior (2D array) or samples from
+posterior (3D array).")
+    (license license:gpl2+)))
+
+(define-public r-bbcanalyzer
+  (package
+    (name "r-bbcanalyzer")
+    (version "1.32.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (bioconductor-uri "BBCAnalyzer" version))
+       (sha256
+        (base32 "108jcgsf5hyj348y17hcw8m3zcfjgzpx8nz4n5jgxp2lgxjyizy1"))))
+    (properties `((upstream-name . "BBCAnalyzer")))
+    (build-system r-build-system)
+    (propagated-inputs
+     (list r-biostrings
+           r-genomicranges
+           r-iranges
+           r-rsamtools
+           r-summarizedexperiment
+           r-variantannotation))
+    (home-page "https://bioconductor.org/packages/BBCAnalyzer")
+    (synopsis "Visualizing base counts")
+    (description
+     "BBCAnalyzer is a package for visualizing the relative or absolute number
+of bases, deletions and insertions at defined positions in sequence alignment
+data available as bam files in comparison to the reference bases.  Markers for
+the relative base frequencies, the mean quality of the detected bases, known
+mutations or polymorphisms and variants called in the data may additionally be
+included in the plots.")
+    (license license:lgpl3)))
+
+(define-public r-bcrank
+  (package
+    (name "r-bcrank")
+    (version "1.64.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (bioconductor-uri "BCRANK" version))
+       (sha256
+        (base32 "1m1ccacryf8wjzp0d37n9n1kpa6734ddb8nvv1sy0sz5gplrars9"))))
+    (properties `((upstream-name . "BCRANK")))
+    (build-system r-build-system)
+    (propagated-inputs (list r-biostrings))
+    (home-page "https://bioconductor.org/packages/BCRANK")
+    (synopsis "Predicting binding site consensus from ranked DNA sequences")
+    (description
+     "This package provides functions and classes for de novo prediction of
+transcription factor binding consensus by heuristic search.")
+    (license license:gpl2)))
+
 (define-public r-biocthis
   (package
     (name "r-biocthis")

gnu/packages/bioinformatics.scm

@@ -15657,6 +15657,41 @@ analysing cytometry data in R.")
 spatial single-cell expression data.")
       (license license:expat))))
 
+;; Variant of r-illuminahumanmethylationepicmanifest in the
+;; (gnu packages bioconductor) module.
+(define-public r-illuminahumanmethylationepicmanifest-latest
+  (let ((commit "a9ffbad36f5e496ece6c4c37b80e2f4f7e02d0c3")
+        (revision "1"))
+    (package
+      (name "r-illuminahumanmethylationepicmanifest")
+      (version (git-version "1.0.0" revision commit))
+      (source
+       (origin
+         (method git-fetch)
+         (uri (git-reference
+               (url
+                "https://github.com/achilleasNP/IlluminaHumanMethylationEPICmanifest")
+               (commit commit)))
+         (file-name (git-file-name name version))
+         (sha256
+          (base32 "0v8f0hl0v8gwi61vgqw56rn5j09h95hj54rb8pzbn0znm162n4fc"))))
+      (properties `((upstream-name . "IlluminaHumanMethylationEPICmanifest")))
+      (build-system r-build-system)
+      (home-page
+       "https://github.com/achilleasNP/IlluminaHumanMethylationEPICmanifest")
+      (synopsis "Illumina Human Methylation Manifest 1.0 B5 for R and minfi")
+      (description
+       "This is a drop-in replacement for the
+@code{IlluminaHumanMethylationEPIC} package.  It utilizes a Manifest based on
+1.0B5 annotation.  As of version 0.3.0, the
+@code{IlluminaHumanMethylationEPIC} package still employs the 1.0B2 annotation
+manifest.  A corresponding annotation package,
+@code{IlluminaHumanMethylationEPICanno.ilm10b5.hg38}, is available to ensure
+proper annotation.  The decision to maintain the same name is due to
+complications in downstream processing caused by array name lookup in certain
+preprocessing options.")
+      (license license:artistic2.0))))
+
 (define-public r-illuminahumanmethylationepicanno-ilm10b5-hg38
   (let ((commit "3db06910e27f626e0cc8b335ff45cf9a4050a36a")
         (revision "1"))

gnu/packages/cran.scm

@@ -6206,6 +6206,30 @@ and Francois (2011, JSS), and the book by Eddelbuettel (2013, Springer); see
 performs global optimization by differential evolution.")
     (license license:gpl2+)))
 
+(define-public r-rcppdist
+  (package
+    (name "r-rcppdist")
+    (version "0.1.1")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "RcppDist" version))
+       (sha256
+        (base32 "02g57xwfipdcljv06krhm02dbqn9kfyj2km6rdg0a7vq9prwdz1x"))))
+    (properties `((upstream-name . "RcppDist")))
+    (build-system r-build-system)
+    (propagated-inputs (list r-rcpp r-rcpparmadillo))
+    (native-inputs (list r-knitr))
+    (home-page "https://github.com/duckmayr/RcppDist")
+    (synopsis "Integration of additional probability distributions")
+    (description
+     "RcppDist provides a header-only C++ library with functions for
+additional statistical distributions that can be called from C++ when writing
+code using Rcpp or RcppArmadillo.  Functions are available that return a
+@code{NumericVector} as well as doubles, and for multivariate or matrix
+distributions, Armadillo vectors and matrices.")
+    (license license:gpl2+)))
+
 (define-public r-rcppml
   (package
     (name "r-rcppml")
@@ -6316,6 +6340,27 @@ with Rcpp and retrieve an @code{XPtr} that can be passed to other C++
 components.")
     (license license:expat)))
 
+(define-public r-bb
+  (package
+    (name "r-bb")
+    (version "2019.10-1")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "BB" version))
+       (sha256
+        (base32 "0kf9sfsm3n036a8a8gjfpc9qdryvadb019kqjh80n1szdv7bdl04"))))
+    (properties `((upstream-name . "BB")))
+    (build-system r-build-system)
+    (propagated-inputs (list r-quadprog))
+    (home-page "https://publichealth.jhu.edu/")
+    (synopsis "Solving and optimizing large-scale nonlinear systems")
+    (description
+     "This package implements Barzilai-Borwein spectral methods for solving
+nonlinear system of equations, and for optimizing nonlinear objective
+functions subject to simple constraints.")
+    (license license:gpl3)))
+
 (define-public r-bindr
   (package
     (name "r-bindr")

gnu/packages/emacs-xyz.scm

@@ -8348,7 +8348,7 @@ for Flow files.")
 (define-public emacs-flycheck-grammalecte
   (package
     (name "emacs-flycheck-grammalecte")
-    (version "2.0")
+    (version "2.4")
     (source
      (origin
        (method git-fetch)
@@ -8357,39 +8357,39 @@ for Flow files.")
              (commit (string-append "v" version))))
        (file-name (git-file-name name version))
        (sha256
-        (base32 "040mb9djj4cxpjsjch9i30pi36a2z7grkhnsnfdi5qyh341p4pq0"))))
+        (base32 "0vsf0zsqqfaarwq1k34kg5sqgywzr6dklqv093imm9q6ys18p8c4"))))
     (build-system emacs-build-system)
     (arguments
-     `(#:include (cons "\\.py$" %default-include)
+     (list
-       #:exclude '("^test-profile.el$")
+      #:include #~(cons "\\.py$" %default-include)
-       #:emacs ,emacs                   ;need libxml support
+      #:emacs emacs-no-x                ;need libxml support
-       #:phases
+      #:phases
-       (modify-phases %standard-phases
+      #~(modify-phases %standard-phases
-         (add-after 'unpack 'specify-python-location
+          (add-after 'unpack 'specify-python-location
-           ;; Hard-code python3 executable location in the library.
+            ;; Hard-code python3 executable location in the library.
-           (lambda* (#:key inputs #:allow-other-keys)
+            (lambda* (#:key inputs #:allow-other-keys)
-             (let ((python3 (search-input-file inputs "/bin/python3")))
+              (let ((python3 (search-input-file inputs "/bin/python3")))
-               (substitute* '("flycheck-grammalecte.el" "grammalecte.el")
+                (substitute* '("flycheck-grammalecte.el" "grammalecte.el")
-                 (("\"python3") (string-append "\"" python3)))
+                  (("\"python3") (string-append "\"" python3)))
-               (substitute* '("conjugueur.py" "flycheck_grammalecte.py")
+                (substitute* '("conjugueur.py" "flycheck_grammalecte.py")
-                 (("/usr/bin/env python3?") python3)))))
+                  (("/usr/bin/env python3?") python3)))))
-         (add-after 'unpack 'specify-grammalecte-location
+          (add-after 'unpack 'specify-grammalecte-location
-           ;; Use our own Grammalecte.
+            ;; Use our own Grammalecte.
-           (lambda* (#:key inputs #:allow-other-keys)
+            (lambda* (#:key inputs #:allow-other-keys)
-             (make-file-writable "grammalecte.el")
+              (make-file-writable "grammalecte.el")
-             (emacs-substitute-variables "grammalecte.el"
+              (emacs-substitute-variables "grammalecte.el"
-               ("grammalecte-python-package-directory"
+                ("grammalecte-python-package-directory"
-                (search-input-directory
+                 (search-input-directory
-                 inputs
+                  inputs
-                 (string-append "lib/python"
+                  (string-append "lib/python"
-                                ,(version-major+minor (package-version python))
+                                 #$(version-major+minor (package-version python))
-                                "/site-packages/grammalecte"))))))
+                                 "/site-packages/grammalecte"))))))
-         (add-after 'unpack 'do-not-phone-home
+          (add-after 'unpack 'do-not-phone-home
-           ;; Do not check for Grammalecte updates, ever.
+            ;; Do not check for Grammalecte updates, ever.
-           (lambda _
+            (lambda _
-             (make-file-writable "grammalecte.el")
+              (make-file-writable "grammalecte.el")
-             (emacs-substitute-variables "grammalecte.el"
+              (emacs-substitute-variables "grammalecte.el"
-               ("grammalecte-check-upstream-version-delay" 0)))))))
+                ("grammalecte-check-upstream-version-delay" 0)))))))
     (inputs
      (list grammalecte python))
     (propagated-inputs
@@ -9017,14 +9017,14 @@ variables, and so on.  The mode also allows you to execute Tup commands.")
 (define-public emacs-compat
   (package
     (name "emacs-compat")
-    (version "29.1.4.3")
+    (version "29.1.4.4")
     (source (origin
               (method url-fetch)
               (uri (string-append "https://elpa.gnu.org/packages/"
                                   "compat-" version ".tar"))
               (sha256
                (base32
-                "08lg6jph1hqkamf1fhm5ajwy4klh2a2260llr1z7wlbbq52032k5"))))
+                "0710g552b1nznnfx2774gmg6yizs27s0bakqm95nsjrp6kgznbfr"))))
     (build-system emacs-build-system)
     (home-page "https://git.sr.ht/~pkal/compat")
     (synopsis "Emacs Lisp Compatibility Library")
@@ -16416,7 +16416,7 @@ passive voice.")
 (define-public emacs-org
   (package
     (name "emacs-org")
-    (version "9.6.11")
+    (version "9.6.12")
     (source
      (origin
        (method git-fetch)
@@ -16425,7 +16425,7 @@ passive voice.")
              (commit (string-append "release_" version))))
        (file-name (git-file-name name version))
        (sha256
-        (base32 "167cnc7iq5i278a7rph2rs9dhxb5anckzjz5d4anbkghzk48qa9x"))))
+        (base32 "1anzvsa7kj2rp419qc5rv8jz50h7np391lcgbxcin727njyc7wpr"))))
     (build-system emacs-build-system)
     (arguments
      (list
@@ -16756,11 +16756,10 @@ basic syntax highlighting and indentation.")
     (license license:gpl3+)))
 
 (define-public emacs-danneskjold-theme
-  (let* ((commit "e4d1f2c76245fe9d0d07133a841e789d139df28d")
+  (let ((commit "b3335e44f468c019c95a8210ce1ed9fe23c65735")) ;version bump
-         (revision "2"))
     (package
       (name "emacs-danneskjold-theme")
-      (version (git-version "0.0.0" revision commit))
+      (version "20231110.0")
       (source
        (origin
          (method git-fetch)
@@ -16769,14 +16768,15 @@ basic syntax highlighting and indentation.")
                (commit commit)))
          (file-name (git-file-name name version))
          (sha256
-          (base32 "1ii3cgf4hlclwaraisxksv98mmhajx517i60p1cgd7vapznn2b6v"))))
+          (base32 "19lncwxzxyi73cn7439rk8cvgcj6l4x1kj6fykmw3b18s7rj555f"))))
       (build-system emacs-build-system)
       (arguments
-       `(#:phases
+       (list
-         (modify-phases %standard-phases
+        #:phases
-           (add-after 'unpack 'delete-screenshots
+        #~(modify-phases %standard-phases
-             (lambda _
+            (add-after 'unpack 'delete-screenshots
-               (delete-file-recursively "screenshots"))))))
+              (lambda _
+                (delete-file-recursively "screenshots"))))))
       (home-page "https://github.com/rails-to-cosmos/danneskjold-theme")
       (synopsis "High-contrast Emacs theme")
       (description
@@ -16784,11 +16784,10 @@ basic syntax highlighting and indentation.")
       (license license:gpl3+))))
 
 (define-public emacs-dream-theme
-  (let* ((commit "107a11d74365046f28a1802a2bdb5e69e4a7488b")
+  (let ((commit "62caa37d5f1ddb1187ee0b9e7dd9833679cc5eb5")) ;version bump
-         (revision "1"))
     (package
       (name "emacs-dream-theme")
-      (version (string-append "0.0.0-" revision "." (string-take commit 7)))
+      (version "1.0")
       (source
        (origin
          (method git-fetch)
@@ -16798,7 +16797,7 @@ basic syntax highlighting and indentation.")
          (file-name (git-file-name name version))
          (sha256
           (base32
-           "0za18nfkq4xqm35k6006vsixcbmvmxqgma4iw5sw37h8vmcsdylk"))))
+           "13ziwd6cw8s8gyzbklxlvpvbx5dbchvvhlxq9pi8vn3zlzpprd6h"))))
       (build-system emacs-build-system)
       (home-page "https://github.com/djcb/dream-theme")
       (synopsis "High-contrast Emacs theme")
@@ -16810,7 +16809,7 @@ by zenburn, sinburn and similar themes, but slowly diverging from them.")
 (define-public emacs-dracula-theme
   (package
     (name "emacs-dracula-theme")
-    (version "1.8.1")
+    (version "1.8.2")
     (source
      (origin
        (method git-fetch)
@@ -16819,7 +16818,7 @@ by zenburn, sinburn and similar themes, but slowly diverging from them.")
              (commit (string-append "v" version))))
        (file-name (git-file-name name version))
        (sha256
-        (base32 "0mb7pix1wbmg4laba06fvcb8q822584iq0cw8mwf0nzaf1yh12l8"))))
+        (base32 "0hjimiv6a0kaszypndb5l0axhiv0zih728p8wffil6jff9k8pr38"))))
     (build-system emacs-build-system)
     (home-page "https://draculatheme.com/")
     (synopsis "Dark theme for Emacs")
@@ -17023,7 +17022,7 @@ you to deal with multiple log levels.")
 (define-public emacs-denote
   (package
     (name "emacs-denote")
-    (version "2.0.0")
+    (version "2.1.0")
     (source
      (origin
        (method git-fetch)
@@ -17032,7 +17031,7 @@ you to deal with multiple log levels.")
              (commit version)))
        (file-name (git-file-name name version))
        (sha256
-        (base32 "0nwqghh73lbw6v6yhkalcwwqjs1fyhxqi53d9y2dcfhfq58g1rb9"))))
+        (base32 "1gfjckqh170z8slhm0wdqf0570ywgni7b1wdnifxf5cb69h3izpr"))))
     (build-system emacs-build-system)
     (native-inputs (list texinfo))
     (home-page "https://protesilaos.com/emacs/denote/")
@@ -26830,7 +26829,7 @@ image, rotate it, save modified images, and more.")
 (define-public emacs-package-lint
   (package
     (name "emacs-package-lint")
-    (version "0.20")
+    (version "0.21")
     (source
      (origin
        (method git-fetch)
@@ -26840,7 +26839,7 @@ image, rotate it, save modified images, and more.")
        (file-name (git-file-name name version))
        (sha256
         (base32
-         "1v12l8mbsrgkq5rmgzypkiabhfrd5cq6nrnmsairnpw8rrz4w739"))))
+         "1y0h8rrmvi3j5maig6i69kxxr1igb96075vpzbycaqln3xn11g36"))))
     (arguments
      (list #:include #~(cons "^data/" %default-include)))
     (build-system emacs-build-system)

gnu/packages/gnuzilla.scm

@@ -1057,10 +1057,12 @@ variable defined below.  It requires guile-json to be installed."
             (lambda* (#:key (make-flags '()) (parallel-build? #t)
                       #:allow-other-keys)
               (apply invoke "./mach" "build"
-                     ;; mach will use parallel build if possible by default
+                     ;; mach will use a wide parallel build if possible by
-                     `(,@(if parallel-build?
+                     ;; default, so reign it in if requested.
-                             '()
+                     `(,(string-append
-                             '("-j1"))
+                         "-j" (number->string (if parallel-build?
+                                                  (parallel-job-count)
+                                                  1)))
                        ,@make-flags))))
           (add-after 'build 'neutralise-store-references
             (lambda _

gnu/packages/guile-xyz.scm

@@ -1284,8 +1284,8 @@ works with Guile 1.4.x to 2.0.x.")
     (license license:gpl3+)))
 
 (define-public guile-prometheus
-  (let ((commit "35dc26c0ea44c3d70f1819f240d84e2cbb4b7b4c")
+  (let ((commit "4aaf902eb45b3a4c1003f854bda56c516fdf4f5b")
-        (revision "5"))
+        (revision "6"))
     (package
     (name "guile-prometheus")
     (version (git-version "0" revision commit))
@@ -1296,7 +1296,7 @@ works with Guile 1.4.x to 2.0.x.")
                     (commit commit)))
               (sha256
                (base32
-                "07822jj4appw37lf444kc4xlgl7nm64mgldag56072l55kwashgb"))
+                "03sr7wgksi9ys6jyzsnwanl2qqa8csi8jzcgrc3wfzp17vcc16yi"))
               (file-name (string-append name "-" version "-checkout"))))
     (build-system gnu-build-system)
     (native-inputs

gnu/packages/hardware.scm

@@ -1089,11 +1089,17 @@ technology, such as head mounted displays with built in head tracking.")
                  (("dependencies/json")
                   (string-append #$(this-package-input "nlohmann-json")
                                  "/include/nlohmann")))))
+           (add-after 'unpack 'patch-chmod
+             (lambda* (#:key inputs #:allow-other-keys)
+               (substitute* "scripts/build-udev-rules.sh"
+                (("/bin/chmod") (string-append (assoc-ref inputs "coreutils")
+                                               "/bin/chmod")))))
            ;; Call qmake instead of configure to create a Makefile.
            (replace 'configure
              (lambda _ (invoke "qmake" "PREFIX=/" "OpenRGB.pro"))))))
     (inputs
-     (list hidapi
+     (list coreutils
+           hidapi
            hueplusplus
            nlohmann-json
            libusb

gnu/packages/haskell-xyz.scm

@@ -65,6 +65,7 @@
   #:use-module (gnu packages haskell-check)
   #:use-module (gnu packages haskell-crypto)
   #:use-module (gnu packages haskell-web)
+  #:use-module (gnu packages icu4c)
   #:use-module (gnu packages libffi)
   #:use-module (gnu packages linux)
   #:use-module (gnu packages llvm)
@@ -8352,6 +8353,46 @@ require aeson
     (description "Safe conversions between textual types")
     (license license:isc)))
 
+(define-public ghc-text-icu
+  (package
+    (name "ghc-text-icu")
+    (version "0.8.0.4")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (hackage-uri "text-icu" version))
+       (sha256
+        (base32 "1yj0jdjrsx12sy6lj1gizb2ys5likp9rcv8ryc6sjf2dw74097rd"))))
+    (build-system haskell-build-system)
+    (properties '((upstream-name . "text-icu")))
+    (inputs (list icu4c))
+    (native-inputs (list ghc-hunit
+                         ghc-quickcheck
+                         ghc-random
+                         ghc-test-framework
+                         ghc-test-framework-hunit
+                         ghc-test-framework-quickcheck2
+                         pkg-config))
+    (home-page "https://github.com/haskell/text-icu")
+    (synopsis "Bindings to the ICU library")
+    (description
+     "Haskell bindings to the International Components for Unicode (ICU) libraries.
+These libraries provide robust and full-featured Unicode services on a wide
+variety of platforms. .  Features include: . * Both pure and impure bindings, to
+allow for fine control over efficiency and ease of use. . * Breaking of strings
+on character, word, sentence, and line boundaries. . * Access to the Unicode
+Character Database (UCD) of character metadata. . * String collation functions,
+for locales where the conventions for lexicographic ordering differ from the
+simple numeric ordering of character codes. . * Character set conversion
+functions, allowing conversion between Unicode and over 220 character encodings.
+. * Unicode normalization. (When implementations keep strings in a normalized
+form, they can be assured that equivalent strings have a unique binary
+representation.) . * Regular expression search and replace. . * Security checks
+for visually confusable (spoofable) strings. . * Bidirectional Unicode algorithm
+. * Calendar objects holding dates and times. . * Number and calendar
+formatting.")
+    (license license:bsd-3)))
+
 (define-public ghc-text-short
   (package
     (name "ghc-text-short")

gnu/packages/image-processing.scm

@@ -1412,7 +1412,12 @@ combine the information contained in both.")
        (uri (string-append "mirror://sourceforge/itk/itk/4.12/"
                            "InsightToolkit-" version ".tar.xz"))
        (sha256
-        (base32 "1qw9mxbh083siljygahl4gdfv91xvfd8hfl7ghwii19f60xrvn2w"))))))
+        (base32 "1qw9mxbh083siljygahl4gdfv91xvfd8hfl7ghwii19f60xrvn2w"))))
+    (arguments
+     (substitute-keyword-arguments (package-arguments insight-toolkit-4)
+       ((#:configure-flags cf #~'())
+        ;; error: ISO C++17 does not allow dynamic exception specifications
+        #~(cons* "-DCMAKE_CXX_FLAGS=-std=c++14" #$cf))))))
 
 (define-public itk-snap
   (package

gnu/packages/linux.scm

@@ -493,7 +493,22 @@ corresponding UPSTREAM-SOURCE (an origin), using the given DEBLOB-SCRIPTS."
 ;; The current "stable" kernels. That is, the most recently released major
 ;; versions that are still supported upstream.
 
-(define-public linux-libre-6.5-version "6.5.10")
+(define-public linux-libre-6.6-version "6.6.1")
+(define-public linux-libre-6.6-gnu-revision "gnu")
+(define deblob-scripts-6.6
+  (linux-libre-deblob-scripts
+   linux-libre-6.6-version
+   linux-libre-6.6-gnu-revision
+   (base32 "0g8m0rb15b0231dv8ji456s75a67szsaim71may3yprplycz6pav")
+   (base32 "1hg3ck1j8288fhlhcvhgs1zzwh3i62nfvphw7x3vsaqr75kiwbjp")))
+(define-public linux-libre-6.6-pristine-source
+  (let ((version linux-libre-6.6-version)
+        (hash (base32 "0d42b1hbvv9w3y3q4wydr6il0g5a823n54a06p4p5vcpgkadf7ns")))
+   (make-linux-libre-source version
+                            (%upstream-linux-source version hash)
+                            deblob-scripts-6.6)))
+
+(define-public linux-libre-6.5-version "6.5.11")
 (define-public linux-libre-6.5-gnu-revision "gnu")
 (define deblob-scripts-6.5
   (linux-libre-deblob-scripts
@@ -503,7 +518,7 @@ corresponding UPSTREAM-SOURCE (an origin), using the given DEBLOB-SCRIPTS."
    (base32 "066z5lw5vrfayhv23hpfcm6fh6b7zmn2v13kfv1g3z3jl1wblhfh")))
 (define-public linux-libre-6.5-pristine-source
   (let ((version linux-libre-6.5-version)
-        (hash (base32 "12sswml8jvabv6bqx35lg3jj6gq8jjk365rghjngdy5d0j34jpx1")))
+        (hash (base32 "06dmb4hbwrms0lp4axphwgj8wbnzsym70sx55lxr501b53wlmqif")))
    (make-linux-libre-source version
                             (%upstream-linux-source version hash)
                             deblob-scripts-6.5)))
@@ -511,7 +526,7 @@ corresponding UPSTREAM-SOURCE (an origin), using the given DEBLOB-SCRIPTS."
 ;; The "longterm" kernels — the older releases with long-term upstream support.
 ;; Here are the support timelines:
 ;; <https://www.kernel.org/category/releases.html>
-(define-public linux-libre-6.1-version "6.1.61")
+(define-public linux-libre-6.1-version "6.1.62")
 (define-public linux-libre-6.1-gnu-revision "gnu")
 (define deblob-scripts-6.1
   (linux-libre-deblob-scripts
@@ -521,12 +536,12 @@ corresponding UPSTREAM-SOURCE (an origin), using the given DEBLOB-SCRIPTS."
    (base32 "1hdibv43xbn1lv83i6qjgfmf1bvqxvq17fryfsq4r4sjgs9212js")))
 (define-public linux-libre-6.1-pristine-source
   (let ((version linux-libre-6.1-version)
-        (hash (base32 "1kk4d7ph6pvgdrdmaklg15wf58nw9n7yqgkag7jdvqinzh99sb5d")))
+        (hash (base32 "1v453q4sf0j8708ivs1zmdf645hgimqvxfc8xz7czgnnmipn3zdr")))
    (make-linux-libre-source version
                             (%upstream-linux-source version hash)
                             deblob-scripts-6.1)))
 
-(define-public linux-libre-5.15-version "5.15.137")
+(define-public linux-libre-5.15-version "5.15.138")
 (define-public linux-libre-5.15-gnu-revision "gnu")
 (define deblob-scripts-5.15
   (linux-libre-deblob-scripts
@@ -536,12 +551,12 @@ corresponding UPSTREAM-SOURCE (an origin), using the given DEBLOB-SCRIPTS."
    (base32 "1idjrn2w8jrixj8ifkk1awxyyq5042nc4p2mld4rda96azlnp948")))
 (define-public linux-libre-5.15-pristine-source
   (let ((version linux-libre-5.15-version)
-        (hash (base32 "1xxjbxldrhmnh2q6rykpxyfbj8xqgl82q30n8sfavrzr14bb4jcp")))
+        (hash (base32 "1ajaxy97gx0c9cdxiyxa49ykfsykir22i9abfrcizh71ci0yb15g")))
    (make-linux-libre-source version
                             (%upstream-linux-source version hash)
                             deblob-scripts-5.15)))
 
-(define-public linux-libre-5.10-version "5.10.199")
+(define-public linux-libre-5.10-version "5.10.200")
 (define-public linux-libre-5.10-gnu-revision "gnu1")
 (define deblob-scripts-5.10
   (linux-libre-deblob-scripts
@@ -551,12 +566,12 @@ corresponding UPSTREAM-SOURCE (an origin), using the given DEBLOB-SCRIPTS."
    (base32 "0xrrnmb5kcc5r21bdm24aq0fnkk1imn367c1cxlj78b6l6gigx4b")))
 (define-public linux-libre-5.10-pristine-source
   (let ((version linux-libre-5.10-version)
-        (hash (base32 "1h944syk7n6c4j1djlx19n77alzwbxcdza77c9ykicgfynhpgsm0")))
+        (hash (base32 "012i41bj8rcqn0vhfxrwq3gg82nb6pp2cwq8n146wj47pwgrcbcx")))
    (make-linux-libre-source version
                             (%upstream-linux-source version hash)
                             deblob-scripts-5.10)))
 
-(define-public linux-libre-5.4-version "5.4.259")
+(define-public linux-libre-5.4-version "5.4.260")
 (define-public linux-libre-5.4-gnu-revision "gnu1")
 (define deblob-scripts-5.4
   (linux-libre-deblob-scripts
@@ -566,27 +581,27 @@ corresponding UPSTREAM-SOURCE (an origin), using the given DEBLOB-SCRIPTS."
    (base32 "0sw67b2pk3lng4y67diqqnhxaggnp3nbkx8dxc5fs27rinfxr4m1")))
 (define-public linux-libre-5.4-pristine-source
   (let ((version linux-libre-5.4-version)
-        (hash (base32 "195v4fidavzm637glj6580006mrcaygnbj4za874imb62bxf9rpz")))
+        (hash (base32 "1zpbaipd2j3idj8h9iznlj0ywcq5nkhwj707a1f9ixf82h3q4c4q")))
    (make-linux-libre-source version
                             (%upstream-linux-source version hash)
                             deblob-scripts-5.4)))
 
-(define-public linux-libre-4.19-version "4.19.297")
+(define-public linux-libre-4.19-version "4.19.298")
 (define-public linux-libre-4.19-gnu-revision "gnu1")
 (define deblob-scripts-4.19
   (linux-libre-deblob-scripts
    linux-libre-4.19-version
    linux-libre-4.19-gnu-revision
-   (base32 "0ghdizzs6969872rnjcv9p6sl9rcbs29v3ismk125yyvjaczd428")
+   (base32 "0pjal2cc2f99cvw8r4icb4l24j41k48jkj6bqk7pcahzcgx33ycb")
    (base32 "1425mhkfxn18vxn05bb4h3li7x1jl7l1hf1zi8xhnqv3wa31h9wl")))
 (define-public linux-libre-4.19-pristine-source
   (let ((version linux-libre-4.19-version)
-        (hash (base32 "0c9xxqgv2i36hrr06dwz7f3idc04xpv0a5pxg08xdh03cnyf12cx")))
+        (hash (base32 "0mhgq6hdcls1af7nj999x1mds5b37s7vwin8nsb4q0lnx2y1da4x")))
     (make-linux-libre-source version
                              (%upstream-linux-source version hash)
                              deblob-scripts-4.19)))
 
-(define-public linux-libre-4.14-version "4.14.328")
+(define-public linux-libre-4.14-version "4.14.329")
 (define-public linux-libre-4.14-gnu-revision "gnu1")
 (define deblob-scripts-4.14
   (linux-libre-deblob-scripts
@@ -596,7 +611,7 @@ corresponding UPSTREAM-SOURCE (an origin), using the given DEBLOB-SCRIPTS."
    (base32 "1faagsj4i31z2bp83hflx3q9vrddjnn37a3ah2b47iaplva7z1nd")))
 (define-public linux-libre-4.14-pristine-source
   (let ((version linux-libre-4.14-version)
-        (hash (base32 "1igcpvnhwwrczfdsafmszvi0456k7f6j4cgpfw6v6afw09p95d8x")))
+        (hash (base32 "1dvb4xf0b7snabznl7bg7gga7ffdmywy8vr8q65pzl9yf6fnhdny")))
     (make-linux-libre-source version
                              (%upstream-linux-source version hash)
                              deblob-scripts-4.14)))
@@ -629,6 +644,11 @@ corresponding UPSTREAM-SOURCE (an origin), using the given DEBLOB-SCRIPTS."
     (patches (append (origin-patches source)
                      patches))))
 
+(define-public linux-libre-6.6-source
+  (source-with-patches linux-libre-6.6-pristine-source
+                       (list %boot-logo-patch
+                             %linux-libre-arm-export-__sync_icache_dcache-patch)))
+
 (define-public linux-libre-6.5-source
   (source-with-patches linux-libre-6.5-pristine-source
                        (list %boot-logo-patch
@@ -748,6 +768,11 @@ corresponding UPSTREAM-SOURCE (an origin), using the given DEBLOB-SCRIPTS."
     (description "Headers of the Linux-Libre kernel.")
     (license license:gpl2)))
 
+(define-public linux-libre-headers-6.6
+  (make-linux-libre-headers* linux-libre-6.6-version
+                             linux-libre-6.6-gnu-revision
+                             linux-libre-6.6-source))
+
 (define-public linux-libre-headers-6.5
   (make-linux-libre-headers* linux-libre-6.5-version
                              linux-libre-6.5-gnu-revision
@@ -1092,6 +1117,14 @@ Linux kernel.  It has been modified to remove all non-free binary blobs.")
 ;;; Generic kernel packages.
 ;;;
 
+(define-public linux-libre-6.6
+  (make-linux-libre* linux-libre-6.6-version
+                     linux-libre-6.6-gnu-revision
+                     linux-libre-6.6-source
+                     '("x86_64-linux" "i686-linux" "armhf-linux"
+                       "aarch64-linux" "powerpc64le-linux" "riscv64-linux")
+                     #:configuration-file kernel-config))
+
 (define-public linux-libre-6.5
   (make-linux-libre* linux-libre-6.5-version
                      linux-libre-6.5-gnu-revision

gnu/packages/llvm.scm

@@ -26,6 +26,7 @@
 ;;; Copyright © 2022 John Kehayias <john.kehayias@protonmail.com>
 ;;; Copyright © 2022 Clément Lassieur <clement@lassieur.org>
 ;;; Copyright © 2022 Zhu Zihao <all_but_last@163.com>
+;;; Copyright © 2023 Hilton Chain <hako@ultrarare.space>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -139,9 +140,19 @@ as \"x86_64-linux\"."
            (patches (map search-patch patches)))
          (llvm-monorepo (package-version llvm))))
     (build-system cmake-build-system)
-    (native-inputs (package-native-inputs llvm))
+    (native-inputs
+     (if (version>=? version "15")
+         ;; TODO: Remove this when GCC 12 is the default.
+         ;; libfuzzer fails to build with GCC 11
+         (modify-inputs (package-native-inputs llvm)
+           (prepend gcc-12))
+         (package-native-inputs llvm)))
     (inputs
-     (list llvm))
+     (append
+      (list llvm)
+      (if (version>=? version "15")
+          (list libffi)
+          '())))
     (arguments
      `(;; Don't use '-g' during the build to save space.
        #:build-type "Release"
@@ -150,6 +161,11 @@ as \"x86_64-linux\"."
                   (ice-9 match)
                   ,@%cmake-build-system-modules)
        #:phases (modify-phases (@ (guix build cmake-build-system) %standard-phases)
+                  ,@(if hash
+                        '()
+                        '((add-after 'unpack 'change-directory
+                            (lambda _
+                              (chdir "compiler-rt")))))
                   (add-after 'set-paths 'hide-glibc
                     ;; Work around https://issues.guix.info/issue/36882.  We need to
                     ;; remove glibc from CPLUS_INCLUDE_PATH so that the one hardcoded
@@ -342,6 +358,15 @@ until LLVM/Clang 14."
                                 (("@GLIBC_LIBDIR@")
                                  (string-append libc "/lib"))))))
                         #t)))
+                  ,@(if (version>=? version "17")
+                        '((add-after 'unpack 'include-test-runner
+                            (lambda _
+                              (substitute* "CMakeLists.txt"
+                                ((".*llvm_gtest" line)
+                                 (string-append
+                                  "add_subdirectory(${LLVM_THIRD_PARTY_DIR}/uni\
+ttest third-party/unittest)\n" line))))))
+                        '())
                   ;; Awkwardly, multiple phases added after the same phase,
                   ;; e.g. unpack, get applied in the reverse order.  In other
                   ;; words, adding 'change-directory last means it occurs
@@ -574,11 +599,15 @@ output), and Binutils.")
 
 (define %llvm-monorepo-hashes
   '(("14.0.6" . "14f8nlvnmdkp9a9a79wv67jbmafvabczhah8rwnqrgd5g3hfxxxx")
-    ("15.0.7" . "12sggw15sxq1krh1mfk3c1f07h895jlxbcifpwk3pznh4m1rjfy2")))
+    ("15.0.7" . "12sggw15sxq1krh1mfk3c1f07h895jlxbcifpwk3pznh4m1rjfy2")
+    ("16.0.6" . "0jxmapg7shwkl88m4mqgfjv4ziqdmnppxhjz6vz51ycp2x4nmjky")
+    ("17.0.3" . "1fhrnsv87if7kbqmrsxy2r7ykx3gnr9lmbmvkhvycc91ii4ihybx")))
 
 (define %llvm-patches
   '(("14.0.6" . ("clang-14.0-libc-search-path.patch"))
-    ("15.0.7" . ("clang-15.0-libc-search-path.patch"))))
+    ("15.0.7" . ("clang-15.0-libc-search-path.patch"))
+    ("16.0.6" . ("clang-16.0-libc-search-path.patch"))
+    ("17.0.3" . ("clang-17.0-libc-search-path.patch"))))
 
 (define (llvm-monorepo version)
   (origin
@@ -703,34 +732,10 @@ of programming tools as well as libraries with equivalent functionality.")
        ("perl"   ,perl)))))
 
 (define-public clang-runtime-15
-  (let ((template (clang-runtime-from-llvm llvm-15)))
+  (clang-runtime-from-llvm llvm-15))
-    (package
-      (inherit template)
-      (arguments
-       (substitute-keyword-arguments (package-arguments template)
-         ((#:phases phases '(@ (guix build cmake-build-system) %standard-phases))
-          #~(modify-phases #$phases
-              (add-after 'unpack 'change-directory
-                (lambda _
-                  (chdir "compiler-rt")))))))
-      (native-inputs
-       (modify-inputs (package-native-inputs template)
-         (prepend gcc-12)))             ;libfuzzer fails to build with GCC 11
-      (inputs
-       (modify-inputs (package-inputs template)
-         (append libffi))))))
 
 (define-public clang-runtime-14
-  (let ((template (clang-runtime-from-llvm llvm-14)))
+  (clang-runtime-from-llvm llvm-14))
-    (package
-      (inherit template)
-      (arguments
-       (substitute-keyword-arguments (package-arguments template)
-         ((#:phases phases '(@ (guix build cmake-build-system) %standard-phases))
-          #~(modify-phases #$phases
-              (add-after 'unpack 'change-directory
-                (lambda _
-                  (chdir "compiler-rt"))))))))))
 
 (define-public clang-15
   (clang-from-llvm
@@ -1458,6 +1463,74 @@ Library.")
                    #:legacy-build-shared-libs? #t
                    #:patches '("clang-3.5-libc-search-path.patch")))
 
+(define-public llvm-16
+  (package
+    (inherit llvm-15)
+    (version "16.0.6")
+    (source (llvm-monorepo version))))
+
+(define-public clang-runtime-16
+  (clang-runtime-from-llvm llvm-16))
+
+(define-public clang-16
+  (clang-from-llvm
+   llvm-16 clang-runtime-16
+   #:tools-extra
+   (origin
+     (method url-fetch)
+     (uri (llvm-uri "clang-tools-extra"
+                    (package-version llvm-16)))
+     (sha256
+      (base32
+       "0cbgffciql06a1i0ybyyqbnkkr4g7x8cxaar5a5v3415vd27hk0p")))))
+
+(define-public libomp-16
+  (package
+    (inherit libomp-15)
+    (version (package-version llvm-16))
+    (source (llvm-monorepo version))
+    (native-inputs
+     (modify-inputs (package-native-inputs libomp-15)
+       (replace "clang" clang-16)
+       (replace "llvm" llvm-16)))))
+
+(define-public clang-toolchain-16
+  (make-clang-toolchain clang-16 libomp-16))
+
+(define-public llvm-17
+  (package
+    (inherit llvm-15)
+    (version "17.0.3")
+    (source (llvm-monorepo version))))
+
+(define-public clang-runtime-17
+  (clang-runtime-from-llvm llvm-17))
+
+(define-public clang-17
+  (clang-from-llvm
+   llvm-17 clang-runtime-17
+   #:tools-extra
+   (origin
+     (method url-fetch)
+     (uri (llvm-uri "clang-tools-extra"
+                    (package-version llvm-17)))
+     (sha256
+      (base32
+       "0an16xdc8rgrdf0dcq3sdg82ajyb00h4bff9n0gm7gqf48ds0da8")))))
+
+(define-public libomp-17
+  (package
+    (inherit libomp-15)
+    (version (package-version llvm-17))
+    (source (llvm-monorepo version))
+    (native-inputs
+     (modify-inputs (package-native-inputs libomp-15)
+       (replace "clang" clang-17)
+       (replace "llvm" llvm-17)))))
+
+(define-public clang-toolchain-17
+  (make-clang-toolchain clang-17 libomp-17))
+
 ;; Default LLVM and Clang version.
 (define-public libomp libomp-13)
 (define-public llvm llvm-13)
@@ -1602,6 +1675,20 @@ components which highly leverage existing libraries in the larger LLVM Project."
     (inputs (modify-inputs (package-inputs lld)
               (replace "llvm" llvm-11)))))
 
+(define-public lld-16
+  (package
+    (inherit lld-15)
+    (version (package-version llvm-16))
+    (source (llvm-monorepo version))
+    (inputs (list llvm-16))))
+
+(define-public lld-17
+  (package
+    (inherit lld-15)
+    (version (package-version llvm-17))
+    (source (llvm-monorepo version))
+    (inputs (list llvm-17))))
+
 (define-public lld lld-14)
 
 (define* (make-lld-wrapper lld #:key lld-as-ld?)

gnu/packages/networking.scm

@@ -4398,6 +4398,27 @@ client and server.  It allows you to use remote block devices over a TCP/IP
 network.")
     (license license:gpl2)))
 
+(define-public ngtcp2
+  (package
+    (name "ngtcp2")
+    (version "1.0.1")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (string-append "https://github.com/ngtcp2/ngtcp2/"
+                           "releases/download/v" version "/"
+                           "ngtcp2-" version ".tar.xz"))
+       (sha256
+        (base32 "0l84hnj9n4bfxjizgmqsqbz71jx7m00a7l1z43fg5ls3apx9ij11"))))
+    (build-system gnu-build-system)
+    (native-inputs (list cunit))
+    (home-page "https://nghttp2.org/ngtcp2/")
+    (synopsis "QUIC protocol implementation")
+    (description
+     "The ngtcp2 project is an effort to implement the RFC9000 (IETF)
+QUIC protocol.")
+    (license license:expat)))
+
 (define-public yggdrasil
   (package
     (name "yggdrasil")

gnu/packages/package-management.scm

@@ -1754,8 +1754,8 @@ in an isolated environment, in separate namespaces.")
     (license license:gpl3+)))
 
 (define-public nar-herder
-  (let ((commit "53682fac7e00cd2801406edbd014922c1720c347")
+  (let ((commit "bf539aa08edfe8010606a31c00e0296c3d400319")
-        (revision "21"))
+        (revision "22"))
     (package
       (name "nar-herder")
       (version (git-version "0" revision commit))
@@ -1766,7 +1766,7 @@ in an isolated environment, in separate namespaces.")
                       (commit commit)))
                 (sha256
                  (base32
-                  "18mzrpc5ni8d6xbp1bg0nzdj0brmnji4jm1gyiq77dm17c118zyz"))
+                  "1i9q7ys26r6y2xa4qqy21bcxlqiynxp3p1wl5gmyj33jnb9ryjby"))
                 (file-name (string-append name "-" version "-checkout"))))
       (build-system gnu-build-system)
       (arguments

gnu/packages/patches/agda-categories-use-stdlib-1.7.3.patch

@@ -0,0 +1,28 @@
+From 76d3863a5e6e7b9ee948f10a3faec3420a2020f1 Mon Sep 17 00:00:00 2001
+Message-ID: <76d3863a5e6e7b9ee948f10a3faec3420a2020f1.1698265016.git.dev@jpoiret.xyz>
+From: Josselin Poiret <dev@jpoiret.xyz>
+Date: Wed, 25 Oct 2023 22:15:43 +0200
+Subject: [PATCH] Bump stdlib to 1.7.3
+
+From: Josselin Poiret <dev@jpoiret.xyz>
+
+---
+ agda-categories.agda-lib | 2 +-
+ 1 file changed, 1 insertion(+), 1 deletion(-)
+
+diff --git a/agda-categories.agda-lib b/agda-categories.agda-lib
+index 5b19c405..4d63d415 100644
+--- a/agda-categories.agda-lib
++++ b/agda-categories.agda-lib
+@@ -1,3 +1,3 @@
+ name: agda-categories
+-depend: standard-library-1.7.2
++depend: standard-library-1.7.3
+ include: src/
+
+base-commit: 9d61106740147a67fa2cae0a89ac066897b24a51
+prerequisite-patch-id: 508dabd923ba9ac1ee4d8dab6697432b4bd8ba18
+prerequisite-patch-id: b5f39b4fc9e4c9993ab31300de041ed2c7eb696b
+-- 
+2.41.0
+

gnu/packages/patches/agda-use-sphinx-5.patch

@@ -0,0 +1,51 @@
+From 99ed1b59ef73fd35053810f6a09e034e1513caee Mon Sep 17 00:00:00 2001
+Message-ID: <99ed1b59ef73fd35053810f6a09e034e1513caee.1698243851.git.dev@jpoiret.xyz>
+From: Josselin Poiret <dev@jpoiret.xyz>
+Date: Wed, 25 Oct 2023 16:23:32 +0200
+Subject: [PATCH] Revert "Docs: bump Sphinx to 6.0.0"
+
+From: Josselin Poiret <dev@jpoiret.xyz>
+
+This reverts commit 40dd42eaa7c04e134fa38cb4f958414a76df27a7.
+---
+ doc/user-manual/conf.py          | 5 ++---
+ doc/user-manual/requirements.txt | 4 ++--
+ 2 files changed, 4 insertions(+), 5 deletions(-)
+
+diff --git a/doc/user-manual/conf.py b/doc/user-manual/conf.py
+index 127f6582dc..d737ede19b 100644
+--- a/doc/user-manual/conf.py
++++ b/doc/user-manual/conf.py
+@@ -35,7 +35,7 @@ release = version
+ #
+ # If your change the version here also change it in the
+ # `requirements.txt` file [Issue #1936].
+-needs_sphinx = '6.0.0'
++needs_sphinx = '5.0.0'
+ 
+ # Add any Sphinx extension module names here, as strings. They can be
+ # extensions coming with Sphinx (named 'sphinx.ext.*') or your custom
+@@ -43,8 +43,7 @@ needs_sphinx = '6.0.0'
+ extensions = [
+     'sphinx.ext.imgmath',
+     'sphinx.ext.ifconfig',
+-    'sphinx.ext.imgconverter',
+-    'sphinxcontrib.jquery'
++    'sphinx.ext.imgconverter'
+ ]
+ 
+ # Add any paths that contain templates here, relative to this directory.
+diff --git a/doc/user-manual/requirements.txt b/doc/user-manual/requirements.txt
+index 384b1466b4..656e6c9ac0 100644
+--- a/doc/user-manual/requirements.txt
++++ b/doc/user-manual/requirements.txt
+@@ -1,2 +1,2 @@
+-Sphinx           >= 7.2.5
+-sphinx_rtd_theme >= 1.3.0
++Sphinx           >= 5.0.0, != 5.2.0.post0
++sphinx_rtd_theme >= 1.0
+
+base-commit: 08b79a684d712ba3dc4b26e5052ec49f49f5ff6c
+-- 
+2.41.0
+

gnu/packages/patches/clang-16.0-libc-search-path.patch

@@ -0,0 +1,95 @@
+Clang attempts to guess file names based on the OS and distro (yes!),
+but unfortunately, that doesn't work for us.
+
+This patch makes it easy to insert libc's $libdir so that Clang passes the
+correct absolute file name of crt1.o etc. to 'ld'.  It also disables all
+the distro-specific stuff and removes the hard-coded FHS directory names
+to make sure Clang also works on foreign distros.
+
+diff --git a/clang/lib/Driver/Distro.cpp b/clang/lib/Driver/Distro.cpp
+index 87a0c5a58511..86ea82eda4b5 100644
+--- a/clang/lib/Driver/Distro.cpp
++++ b/clang/lib/Driver/Distro.cpp
+@@ -98,6 +98,10 @@ static Distro::DistroType DetectLsbRelease(llvm::vfs::FileSystem &VFS) {
+ }
+ 
+ static Distro::DistroType DetectDistro(llvm::vfs::FileSystem &VFS) {
++  // The compiler should always behave the same, even when used via Guix on a
++  // foreign distro.
++  return Distro::UnknownDistro;
++
+   Distro::DistroType Version = Distro::UnknownDistro;
+ 
+   // Newer freedesktop.org's compilant systemd-based systems
+diff --git a/clang/lib/Driver/ToolChains/Cuda.cpp b/clang/lib/Driver/ToolChains/Cuda.cpp
+index aa125bb308e8..8b86e144054c 100644
+--- a/clang/lib/Driver/ToolChains/Cuda.cpp
++++ b/clang/lib/Driver/ToolChains/Cuda.cpp
+@@ -124,6 +124,9 @@ CudaInstallationDetector::CudaInstallationDetector(
+     const Driver &D, const llvm::Triple &HostTriple,
+     const llvm::opt::ArgList &Args)
+     : D(D) {
++  // Don't look for CUDA in /usr.
++  return;
++
+   struct Candidate {
+     std::string Path;
+     bool StrictChecking;
+diff --git a/clang/lib/Driver/ToolChains/Linux.cpp b/clang/lib/Driver/ToolChains/Linux.cpp
+index c6fb290ffdb4..4736f4bb3392 100644
+--- a/clang/lib/Driver/ToolChains/Linux.cpp
++++ b/clang/lib/Driver/ToolChains/Linux.cpp
+@@ -189,6 +189,10 @@ Linux::Linux(const Driver &D, const llvm::Triple &Triple, const ArgList &Args)
+ 
+   Generic_GCC::PushPPaths(PPaths);
+ 
++  // Comment out the distro-specific tweaks so that they don't bite when
++  // using Guix on a foreign distro.
++#if 0
++
+   Distro Distro(D.getVFS(), Triple);
+ 
+   if (Distro.IsAlpineLinux() || Triple.isAndroid()) {
+@@ -249,6 +253,7 @@ Linux::Linux(const Driver &D, const llvm::Triple &Triple, const ArgList &Args)
+ 
+ #ifdef ENABLE_LINKER_BUILD_ID
+   ExtraOpts.push_back("--build-id");
++#endif
+ #endif
+ 
+   // The selection of paths to try here is designed to match the patterns which
+@@ -270,6 +275,7 @@ Linux::Linux(const Driver &D, const llvm::Triple &Triple, const ArgList &Args)
+   }
+   Generic_GCC::AddMultilibPaths(D, SysRoot, OSLibDir, MultiarchTriple, Paths);
+ 
++#if 0
+   addPathIfExists(D, concat(SysRoot, "/lib", MultiarchTriple), Paths);
+   addPathIfExists(D, concat(SysRoot, "/lib/..", OSLibDir), Paths);
+ 
+@@ -298,9 +304,11 @@ Linux::Linux(const Driver &D, const llvm::Triple &Triple, const ArgList &Args)
+     addPathIfExists(D, concat(SysRoot, "/", OSLibDir, ABIName), Paths);
+     addPathIfExists(D, concat(SysRoot, "/usr", OSLibDir, ABIName), Paths);
+   }
++#endif
+ 
+   Generic_GCC::AddMultiarchPaths(D, SysRoot, OSLibDir, Paths);
+ 
++#if 0
+   // The deprecated -DLLVM_ENABLE_PROJECTS=libcxx configuration installs
+   // libc++.so in D.Dir+"/../lib/". Detect this path.
+   // TODO Remove once LLVM_ENABLE_PROJECTS=libcxx is unsupported.
+@@ -310,6 +318,14 @@ Linux::Linux(const Driver &D, const llvm::Triple &Triple, const ArgList &Args)
+ 
+   addPathIfExists(D, concat(SysRoot, "/lib"), Paths);
+   addPathIfExists(D, concat(SysRoot, "/usr/lib"), Paths);
++#endif
++
++  // Add libc's lib/ directory to the search path, so that crt1.o, crti.o,
++  // and friends can be found.
++  addPathIfExists(D, "@GLIBC_LIBDIR@", Paths);
++
++  // Add GCC's lib/ directory so libstdc++.so can be found.
++  addPathIfExists(D, GCCInstallation.getParentLibPath(), Paths);
+ }
+ 
+ ToolChain::RuntimeLibType Linux::GetDefaultRuntimeLibType() const {

gnu/packages/patches/clang-17.0-libc-search-path.patch

@@ -0,0 +1,90 @@
+Clang attempts to guess file names based on the OS and distro (yes!),
+but unfortunately, that doesn't work for us.
+
+This patch makes it easy to insert libc's $libdir so that Clang passes the
+correct absolute file name of crt1.o etc. to 'ld'.  It also disables all
+the distro-specific stuff and removes the hard-coded FHS directory names
+to make sure Clang also works on foreign distros.
+
+diff --git a/clang/lib/Driver/Distro.cpp b/clang/lib/Driver/Distro.cpp
+index 6e0087565941..c0a3ba7d7702 100644
+--- a/clang/lib/Driver/Distro.cpp
++++ b/clang/lib/Driver/Distro.cpp
+@@ -99,6 +99,10 @@ static Distro::DistroType DetectLsbRelease(llvm::vfs::FileSystem &VFS) {
+ }
+ 
+ static Distro::DistroType DetectDistro(llvm::vfs::FileSystem &VFS) {
++  // The compiler should always behave the same, even when used via Guix on a
++  // foreign distro.
++  return Distro::UnknownDistro;
++
+   Distro::DistroType Version = Distro::UnknownDistro;
+ 
+   // Newer freedesktop.org's compilant systemd-based systems
+diff --git a/clang/lib/Driver/ToolChains/Cuda.cpp b/clang/lib/Driver/ToolChains/Cuda.cpp
+index 3a577650eb08..ca3373edc127 100644
+--- a/clang/lib/Driver/ToolChains/Cuda.cpp
++++ b/clang/lib/Driver/ToolChains/Cuda.cpp
+@@ -128,6 +128,9 @@ CudaInstallationDetector::CudaInstallationDetector(
+     const Driver &D, const llvm::Triple &HostTriple,
+     const llvm::opt::ArgList &Args)
+     : D(D) {
++  // Don't look for CUDA in /usr.
++  return;
++
+   struct Candidate {
+     std::string Path;
+     bool StrictChecking;
+diff --git a/clang/lib/Driver/ToolChains/Linux.cpp b/clang/lib/Driver/ToolChains/Linux.cpp
+index 1ba222bf83b1..28766c5ab792 100644
+--- a/clang/lib/Driver/ToolChains/Linux.cpp
++++ b/clang/lib/Driver/ToolChains/Linux.cpp
+@@ -220,6 +220,10 @@ Linux::Linux(const Driver &D, const llvm::Triple &Triple, const ArgList &Args)
+ 
+   Generic_GCC::PushPPaths(PPaths);
+ 
++  // Comment out the distro-specific tweaks so that they don't bite when
++  // using Guix on a foreign distro.
++#if 0
++
+   Distro Distro(D.getVFS(), Triple);
+ 
+   if (Distro.IsAlpineLinux() || Triple.isAndroid()) {
+@@ -280,6 +284,7 @@ Linux::Linux(const Driver &D, const llvm::Triple &Triple, const ArgList &Args)
+ 
+ #ifdef ENABLE_LINKER_BUILD_ID
+   ExtraOpts.push_back("--build-id");
++#endif
+ #endif
+ 
+   // The selection of paths to try here is designed to match the patterns which
+@@ -301,6 +306,7 @@ Linux::Linux(const Driver &D, const llvm::Triple &Triple, const ArgList &Args)
+   }
+   Generic_GCC::AddMultilibPaths(D, SysRoot, OSLibDir, MultiarchTriple, Paths);
+ 
++#if 0
+   addPathIfExists(D, concat(SysRoot, "/lib", MultiarchTriple), Paths);
+   addPathIfExists(D, concat(SysRoot, "/lib/..", OSLibDir), Paths);
+ 
+@@ -329,11 +335,21 @@ Linux::Linux(const Driver &D, const llvm::Triple &Triple, const ArgList &Args)
+     addPathIfExists(D, concat(SysRoot, "/", OSLibDir, ABIName), Paths);
+     addPathIfExists(D, concat(SysRoot, "/usr", OSLibDir, ABIName), Paths);
+   }
++#endif
+ 
+   Generic_GCC::AddMultiarchPaths(D, SysRoot, OSLibDir, Paths);
+ 
++#if 0
+   addPathIfExists(D, concat(SysRoot, "/lib"), Paths);
+   addPathIfExists(D, concat(SysRoot, "/usr/lib"), Paths);
++#endif
++
++  // Add libc's lib/ directory to the search path, so that crt1.o, crti.o,
++  // and friends can be found.
++  addPathIfExists(D, "@GLIBC_LIBDIR@", Paths);
++
++  // Add GCC's lib/ directory so libstdc++.so can be found.
++  addPathIfExists(D, GCCInstallation.getParentLibPath(), Paths);
+ }
+ 
+ ToolChain::RuntimeLibType Linux::GetDefaultRuntimeLibType() const {

gnu/packages/ruby.scm

@@ -34,6 +34,7 @@
 ;;; Copyright © 2023 Yovan Naumovski <yovan@gorski.stream>
 ;;; Copyright © 2023 gemmaro <gemmaro.dev@gmail.com>
 ;;; Copyright © 2023 Janneke Nieuwenhuizen <janneke@gnu.org>
+;;; Copyright © 2023 Zheng Junjie <873216071@qq.com>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -129,7 +130,13 @@
     (build-system gnu-build-system)
     (arguments
      `(#:test-target "test"
-       #:configure-flags '("--enable-shared") ; dynamic linking
+       #:configure-flags
+       ,(if (%current-target-system)
+            '(list (string-append
+                    "LDFLAGS=-Wl,-rpath="
+                    (assoc-ref %outputs "out") "/lib")
+                   "--enable-shared")
+            ''("--enable-shared")) ; dynamic linking
        #:phases
        (modify-phases %standard-phases
          (add-before 'configure 'replace-bin-sh-and-remove-libffi
@@ -147,6 +154,9 @@
                             "tool/rbinstall.rb")
                (("/bin/sh") (which "sh")))
              #t)))))
+    (native-inputs (if (%current-target-system)
+                       (list this-package)
+                       '()))
     (inputs
      (list readline openssl-1.1 libffi gdbm))
     (propagated-inputs
@@ -177,7 +187,13 @@ a focus on simplicity and productivity.")
          "042xrdk7hsv4072bayz3f8ffqh61i8zlhvck10nfshllq063n877"))))
     (arguments
      `(#:test-target "test"
-       #:configure-flags '("--enable-shared") ; dynamic linking
+       #:configure-flags
+       ,(if (%current-target-system)
+            '(list (string-append
+                    "LDFLAGS=-Wl,-rpath="
+                    (assoc-ref %outputs "out") "/lib")
+                   "--enable-shared")
+            ''("--enable-shared")) ; dynamic linking
        #:phases
        (modify-phases %standard-phases
          (add-before 'configure 'replace-bin-sh-and-remove-libffi
@@ -204,7 +220,10 @@ a focus on simplicity and productivity.")
                      (delete-file "test/ruby/test_io.rb"))))
                '()))))
     (native-inputs
-     (list autoconf))))
+     (append (if (%current-target-system)
+                 (list this-package)
+                 '())
+             (list autoconf)))))
 
 (define ruby-2.7-fixed
   (package

gnu/packages/video.scm

@@ -1783,14 +1783,14 @@ audio/video codec library.")
 (define-public ffmpeg-5
   (package
     (inherit ffmpeg)
-    (version "5.1.3")
+    (version "5.1.4")
     (source (origin
               (method url-fetch)
               (uri (string-append "https://ffmpeg.org/releases/ffmpeg-"
                                   version ".tar.xz"))
               (sha256
                (base32
-                "0biil32xnshg1b4lwzbdc5rxv1g7lpfsr5gdgaz96wlhzy9ka48v"))))))
+                "0qwhyhil805hns7yksdxagnrcc90h60al7lz1rc65kd1j2w3nf2l"))))))
 
 (define-public ffmpeg-4
   (package
@@ -1813,14 +1813,14 @@ audio/video codec library.")
 (define-public ffmpeg-3.4
   (package
     (inherit ffmpeg-4)
-    (version "3.4.11")
+    (version "3.4.13")
     (source (origin
              (method url-fetch)
              (uri (string-append "https://ffmpeg.org/releases/ffmpeg-"
                                  version ".tar.xz"))
              (sha256
               (base32
-               "1rijdvcx8xjqwh084qchwz91vcj8wsvb4diax0g8miywpir00ccw"))))
+               "0np0yalqdrm7rn7iykgfzz3ly4vbgigrajg48c1l6n7qrzqvfszv"))))
     (arguments
      (substitute-keyword-arguments (package-arguments ffmpeg-4)
        ((#:modules modules %gnu-build-system-modules)
@@ -1838,14 +1838,14 @@ audio/video codec library.")
 (define-public ffmpeg-2.8
   (package
     (inherit ffmpeg-3.4)
-    (version "2.8.20")
+    (version "2.8.22")
     (source (origin
               (method url-fetch)
               (uri (string-append "https://ffmpeg.org/releases/ffmpeg-"
                                   version ".tar.xz"))
               (sha256
                (base32
-                "1ivnfqmfnp3zmn1q2dxy4p85427y3r6d3jbnl5kprr7lqckf6rl5"))))
+                "0c8m4hhv2k5fybha908wzrpnf3wqkq52hayl658jq4bah0igdfqz"))))
     (arguments
      `(#:tests? #f               ; XXX: Enable them later, if required
        #:configure-flags

gnu/packages/web.scm

@@ -1004,7 +1004,7 @@ similar to live activity monitoring provided with NGINX plus.")
 (define-public lighttpd
   (package
     (name "lighttpd")
-    (version "1.4.72")
+    (version "1.4.73")
     (source (origin
               (method url-fetch)
               (uri (string-append "https://download.lighttpd.net/lighttpd/"
@@ -1012,7 +1012,7 @@ similar to live activity monitoring provided with NGINX plus.")
                                   "lighttpd-" version ".tar.xz"))
               (sha256
                (base32
-                "1v2m9vavrg3ibbl0kfq3rjlnqicbrlrkqih1iisa0m5pd56xxjpp"))))
+                "1a2cx3di07wf8qii7dpk4yr5wvaz8c9na1x7523smc0lng81d241"))))
     (build-system gnu-build-system)
     (arguments
      (list #:configure-flags
@@ -4955,8 +4955,8 @@ Cloud.")
     (license license:expat)))
 
 (define-public guix-data-service
-  (let ((commit "1c7539418743e0dfe3a9cad22c414fd732daef8f")
+  (let ((commit "37a07c2d6e8285877ad0440a7e4ae286b7b65177")
-        (revision "42"))
+        (revision "43"))
     (package
       (name "guix-data-service")
       (version (string-append "0.0.1-" revision "." (string-take commit 7)))
@@ -4968,7 +4968,7 @@ Cloud.")
                 (file-name (git-file-name name version))
                 (sha256
                  (base32
-                  "1gp4mhjssxky0jjjz916rfgz4w2f327wfd5ixb6lb00ydlfh5mws"))))
+                  "0h83j10bq7dyda2idbqh5y6dcvmbl3xgc147yq4pk6bkh10y29y6"))))
       (build-system gnu-build-system)
       (arguments
        (list