gnu: r-metaneighbor: Update to 1.20.0.

* gnu/packages/bioconductor.scm (r-metaneighbor): Update to 1.20.0.
author: Ricardo Wurmus <rekado@elephly.net> 2023-04-28 17:59:56 +0200
committer: Ricardo Wurmus <rekado@elephly.net> 2023-04-29 20:27:57 +0200
commit: 15efeebe536949b4f2fd6f74c54989c16b17dca7 (patch)
tree: a12e59328cb2460893544ded642f1e62bcd14dfd /.gitignore
parent: 0ee6b4203d2b13e268f67fcb8ac0e18bea3e3cb2 (diff)
download: guix-15efeebe536949b4f2fd6f74c54989c16b17dca7.tar.gz
guix-15efeebe536949b4f2fd6f74c54989c16b17dca7.zip
0 files changed, 0 insertions, 0 deletions
diff --git a/gnu/packages/batik.scm b/gnu/packages/batik.scm
index cd77c9a12b..c8f4a34c72 100644
--- a/gnu/packages/batik.scm
+++ b/gnu/packages/batik.scm
@@ -1,5 +1,6 @@
 ;;; GNU Guix --- Functional package management for GNU
 ;;; Copyright © 2018 Danny Milosavljevic <dannym@scratchpost.org>
+;;; Copyright © 2020 Tobias Geerinckx-Rice <me@tobias.gr>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -198,7 +199,7 @@ SAC is an interface for CSS parsers.")
 (define-public java-xmlgraphics-commons
   (package
     (name "java-xmlgraphics-commons")
-    (version "2.3")
+    (version "2.4")
     (source
       (origin
         (method url-fetch)
@@ -206,8 +207,7 @@ SAC is an interface for CSS parsers.")
               "mirror://apache/xmlgraphics/commons/source/xmlgraphics-commons-"
               version "-src.tar.gz"))
         (sha256
-         (base32
-          "0a432a4ca3vgnbada5cy9mlmfzmq6hi4i176drfxrp17q2d43w23"))
+         (base32 "0zdkngb896cr35jq1v859j2kpqyn6a87k6a893h394hgvnz7yi3v"))
         (modules '((guix build utils)))
         (snippet
          `(begin
diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 2fbfdba2d8..3ada92085e 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -3501,8 +3501,8 @@ phenotype of interest.")
     (synopsis "Fast gene set enrichment analysis")
     (description
      "The package implements an algorithm for fast gene set enrichment
-analysis.  Using the fast algorithm allows to make more permutations and get
-more fine grained p-values, which allows to use accurate stantard approaches
+analysis.  Using the fast algorithm makes more permutations and gets
+more fine grained p-values, which allows using accurate standard approaches
 to multiple hypothesis correction.")
     (license license:expat)))
 
@@ -4271,7 +4271,7 @@ investigation using RNA-seq data.")
     (home-page "https://bioconductor.org/packages/AUCell/")
     (synopsis "Analysis of gene set activity in single-cell RNA-seq data")
     (description
-     "AUCell allows to identify cells with active gene sets (e.g. signatures,
+     "AUCell identifies cells with active gene sets (e.g. signatures,
 gene modules, etc) in single-cell RNA-seq data.  AUCell uses the @dfn{Area
 Under the Curve} (AUC) to calculate whether a critical subset of the input
 gene set is enriched within the expressed genes for each cell.  The
@@ -6426,7 +6426,7 @@ parametric mixture model.  The protein binding sites (clusters) are then
 resolved at high resolution and cluster statistics are estimated using a
 rigorous Bayesian framework.  Post-processing of the results, data export for
 UCSC genome browser visualization and motif search analysis are provided.  In
-addition, the package allows to integrate RNA-Seq data to estimate the False
+addition, the package integrates RNA-Seq data to estimate the False
 Discovery Rate of cluster detection.  Key functions support parallel multicore
 computing.  While wavClusteR was designed for PAR-CLIP data analysis, it can
 be applied to the analysis of other NGS data obtained from experimental
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 4c3d2b793b..cd01027bce 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -8401,7 +8401,7 @@ system.  It is used to analyze experimental crosses for identifying
 genes contributing to variation in quantitative traits (so-called
 quantitative trait loci, QTLs).
 
-Using a hidden Markov model, R/qtl allows to estimate genetic maps, to
+Using a hidden Markov model, R/qtl estimates genetic maps, to
 identify genotyping errors, and to perform single-QTL and two-QTL,
 two-dimensional genome scans.")
   (license license:gpl3)))
@@ -8532,7 +8532,7 @@ of other R packages who wish to make use of HTSlib.")
     (home-page "https://bioconductor.org/packages/bamsignals")
     (synopsis "Extract read count signals from bam files")
     (description
-     "This package allows to efficiently obtain count vectors from indexed bam
+     "This package efficiently obtains count vectors from indexed bam
 files.  It counts the number of nucleotide sequence reads in given genomic
 ranges and it computes reads profiles and coverage profiles.  It also handles
 paired-end data.")
diff --git a/gnu/packages/build-tools.scm b/gnu/packages/build-tools.scm
index d7e4fd946b..a8ffa56bc6 100644
--- a/gnu/packages/build-tools.scm
+++ b/gnu/packages/build-tools.scm
@@ -4,7 +4,7 @@
 ;;; Copyright © 2017, 2018, 2019, 2020 Tobias Geerinckx-Rice <me@tobias.gr>
 ;;; Copyright © 2018 Fis Trivial <ybbs.daans@hotmail.com>
 ;;; Copyright © 2018 Tomáš Čech <sleep_walker@gnu.org>
-;;; Copyright © 2018 Marius Bakke <mbakke@fastmail.com>
+;;; Copyright © 2018, 2020 Marius Bakke <mbakke@fastmail.com>
 ;;; Copyright © 2018 Alex Vong <alexvong1995@gmail.com>
 ;;; Copyright © 2019 Brett Gilio <brettg@gnu.org>
 ;;; Copyright © 2019 Jonathan Brielmaier <jonathan.brielmaier@web.de>
@@ -103,8 +103,8 @@ generate such a compilation database.")
     (license license:gpl3+)))
 
 (define-public gn
-  (let ((commit "6e5ba2e7210823cf7ccce3eb2a23336a4e7f1349")
-        (revision "1666"))          ;as returned by `git describe`, used below
+  (let ((commit "ec938ddaa276646eb8f1ab33e160c156011d8217")
+        (revision "1736"))            ;as returned by `git describe`, used below
     (package
       (name "gn")
       (version (git-version "0.0" revision commit))
@@ -114,7 +114,7 @@ generate such a compilation database.")
                 (uri (git-reference (url home-page) (commit commit)))
                 (sha256
                  (base32
-                  "157ax65sixjm0i1j89wvny48v1mbsl4pbvv5vqinjc6r0fryaf2r"))
+                  "0j1qjwp2biw12s6npzpx4z8nvih7pyn68q6cz2k4700bk9y0d574"))
                 (file-name (git-file-name name version))))
       (build-system gnu-build-system)
       (arguments
@@ -135,8 +135,10 @@ generate such a compilation database.")
                         (call-with-output-file "out/last_commit_position.h"
                           (lambda (port)
                             (format port
-                                    "#define LAST_COMMIT_POSITION \"~a (~a)\"\n"
-                                    ,revision ,(string-take commit 8))
+                                    (string-append
+                                     "#define LAST_COMMIT_POSITION_NUM ~a\n"
+                                     "#define LAST_COMMIT_POSITION \"~a (~a)\"\n")
+                                    ,revision ,revision ,(string-take commit 8))
                             #t))))
                     (replace 'build
                       (lambda _
diff --git a/gnu/packages/check.scm b/gnu/packages/check.scm
index b7267e14ec..7bca0468cf 100644
--- a/gnu/packages/check.scm
+++ b/gnu/packages/check.scm
@@ -582,14 +582,14 @@ but it works for any C/C++ project.")
 (define-public python-parameterized
   (package
     (name "python-parameterized")
-    (version "0.7.1")
+    (version "0.7.3")
     (source
      (origin
        (method url-fetch)
        (uri (pypi-uri "parameterized" version))
        (sha256
         (base32
-         "1vapry9lyfb2mlpgk2wh9079hzxzq5120bsczncxxay663mdp53a"))))
+         "0g1q6n7fkanjv7i1djzw62f46xf573jvza7afabh3baqjqxy7rpd"))))
     (build-system python-build-system)
     (arguments
      '(#:phases (modify-phases %standard-phases
@@ -1952,8 +1952,8 @@ possible to write plugins to add your own checks.")
     (synopsis
      "Simple extension to have parametrized unit tests")
     (description
-     "This package allows to create parametrized unit-tests that work with the standard
-unittest package.  A parametrized test case is automatically converted to multiple test
+     "This package creates parameterized unit-tests that work with the standard
+unittest package.  A parameterized test case is automatically converted to multiple test
 cases.  Since they are TestCase subclasses, they work with other test suites that
 recognize TestCases.")
     (license license:bsd-2)))
diff --git a/gnu/packages/chromium.scm b/gnu/packages/chromium.scm
index fb8a813b7a..3625eb7964 100644
--- a/gnu/packages/chromium.scm
+++ b/gnu/packages/chromium.scm
@@ -135,8 +135,11 @@
     "third_party/dawn" ;ASL2.0
     "third_party/depot_tools/owners.py" ;BSD-3
     "third_party/devtools-frontend" ;BSD-3
+    "third_party/devtools-frontend/src/front_end/third_party/fabricjs" ;Expat
+    "third_party/devtools-frontend/src/front_end/third_party/wasmparser" ;ASL2.0
     "third_party/devtools-frontend/src/third_party/axe-core" ;MPL2.0
     "third_party/devtools-frontend/src/third_party/pyjson5" ;ASL2.0
+    "third_party/devtools-frontend/src/third_party/typescript" ;ASL2.0
     "third_party/dom_distiller_js" ;BSD-3
     "third_party/emoji-segmenter" ;ASL2.0
     "third_party/flatbuffers" ;ASL2.0
@@ -196,7 +199,6 @@
     "third_party/qcms" ;Expat
     "third_party/rnnoise" ;BSD-3
     "third_party/s2cellid" ;ASL2.0
-    "third_party/sfntly" ;ASL2.0
     "third_party/skia" ;BSD-3
     "third_party/skia/include/third_party/skcms" ;BSD-3
     "third_party/skia/third_party/skcms" ;BSD-3
@@ -206,7 +208,6 @@
     "third_party/spirv-headers" ;ASL2.0
     "third_party/SPIRV-Tools" ;ASL2.0
     "third_party/sqlite" ;Public domain
-    "third_party/ungoogled" ;BSD-3
     "third_party/usb_ids" ;BSD-3
     "third_party/usrsctp" ;BSD-2
     "third_party/wayland/wayland_scanner_wrapper.py" ;BSD-3
@@ -247,9 +248,9 @@ from forcing GEXP-PROMISE."
                       #:system system
                       #:guile-for-build guile)))
 
-(define %chromium-version "80.0.3987.163")
-(define %ungoogled-revision "516e2d990a50a4bbeb8c583e56333c2935e2af95")
-(define %debian-revision "debian/80.0.3987.116-1")
+(define %chromium-version "81.0.4044.92")
+(define %ungoogled-revision "b484ad4c0bdb696c86d941798ae6b0e2bd0db35d")
+(define %debian-revision "debian/81.0.4044.92-1")
 (define package-revision "0")
 (define %package-version (string-append %chromium-version "-"
                                         package-revision "."
@@ -263,7 +264,7 @@ from forcing GEXP-PROMISE."
                         %chromium-version ".tar.xz"))
     (sha256
      (base32
-      "0ikk4cgz3jgjhyncsvlqvlc03y7jywjpa6v34fwsjxs88flyzpdn"))))
+      "0i0szd749ihb08rxnsmsbxq75b6x952wpk94jwc0ncv6gb83zkx2"))))
 
 (define %ungoogled-origin
   (origin
@@ -274,7 +275,7 @@ from forcing GEXP-PROMISE."
                               (string-take %ungoogled-revision 7)))
     (sha256
      (base32
-      "0nm55qq4ahw9haf5g7hmzic4mr2xjgpay7lxps7xjp7s1pda4g0q"))))
+      "071a33idn2zcix6z8skn7y85mhb9w5s0bh0fvrjm269y7cmjrh3l"))))
 
 (define %debian-origin
   (origin
@@ -288,7 +289,7 @@ from forcing GEXP-PROMISE."
                                 (_ (string-take %debian-revision 7)))))
     (sha256
      (base32
-      "1cc5sp566dd8f2grgr770xwbxgxf58dk1w7q3s8pmv4js5h3pwq8"))))
+      "0srgbcqga3l75bfkv3bnmjk416189nazsximvzdx2k5n8v5k4p3m"))))
 
 ;; This is a "computed" origin that does the following:
 ;; *) Runs the Ungoogled scripts on a pristine Chromium tarball.
@@ -319,8 +320,7 @@ from forcing GEXP-PROMISE."
                   (list #+(canonical-package patch)
                         #+(canonical-package xz)
                         #+(canonical-package tar)
-                        #+python-2
-                        #+python))
+                        #+python-wrapper))
 
                  (copy-recursively #+ungoogled-source "/tmp/ungoogled")
 
@@ -338,11 +338,11 @@ from forcing GEXP-PROMISE."
 
                    (format #t "Ungooglifying...~%")
                    (force-output)
-                   (invoke "python3" "utils/prune_binaries.py" chromium-dir
+                   (invoke "python" "utils/prune_binaries.py" chromium-dir
                            "pruning.list")
-                   (invoke "python3" "utils/patches.py" "apply"
+                   (invoke "python" "utils/patches.py" "apply"
                            chromium-dir "patches")
-                   (invoke "python3" "utils/domain_substitution.py" "apply" "-r"
+                   (invoke "python" "utils/domain_substitution.py" "apply" "-r"
                            "domain_regex.list" "-f" "domain_substitution.list"
                            "-c" "/tmp/domainscache.tar.gz" chromium-dir)
 
@@ -390,13 +390,13 @@ from forcing GEXP-PROMISE."
 
                      (format #t "Pruning third party files...~%")
                      (force-output)
-                     (apply invoke "python"
+                     (apply invoke (string-append #+python-2 "/bin/python")
                             "build/linux/unbundle/remove_bundled_libraries.py"
                             "--do-remove" preserved-files)
 
                      (format #t "Replacing GN files...~%")
                      (force-output)
-                     (invoke "python3" "build/linux/unbundle/replace_gn_files.py"
+                     (invoke "python" "build/linux/unbundle/replace_gn_files.py"
                              "--system-libraries" "ffmpeg" "flac" "fontconfig"
                              "freetype" "harfbuzz-ng" "icu" "libdrm" "libevent"
                              "libjpeg" "libpng" "libvpx" "libwebp" "libxml"
@@ -450,7 +450,6 @@ from forcing GEXP-PROMISE."
        ;; directory for an exhaustive list of supported flags.
        ;; (Note: The 'configure' phase will do that for you.)
        (list "is_debug=false"
-             "is_cfi=false"
              "use_gold=false"
              "use_lld=false"
              "clang_use_chrome_plugins=false"
@@ -636,8 +635,13 @@ from forcing GEXP-PROMISE."
              (setenv "AR" "ar") (setenv "NM" "nm")
              (setenv "CC" "clang") (setenv "CXX" "clang++")
 
-             ;; Do not optimize away null pointer safety checks.
-             (setenv "CXXFLAGS" "-fno-delete-null-pointer-checks")
+             (setenv "CXXFLAGS"
+                     (string-join
+                      '(;; Do not optimize away null pointer safety checks.
+                        "-fno-delete-null-pointer-checks"
+                        ;; Disable warnings about unknown warnings that require
+                        ;; Clang plugins or newer versions.
+                        "-Wno-unknown-warning-option")))
 
              ;; TODO: pre-compile instead. Avoids a race condition.
              (setenv "PYTHONDONTWRITEBYTECODE" "1")
@@ -782,7 +786,7 @@ from forcing GEXP-PROMISE."
        ("glib" ,glib)
        ("gtk+" ,gtk+)
        ("harfbuzz" ,harfbuzz)
-       ("icu4c" ,icu4c)
+       ("icu4c" ,icu4c-66.1)
        ("jsoncpp" ,jsoncpp)
        ("lcms" ,lcms)
        ("libevent" ,libevent)
diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index 59bfd8833a..ecfc053017 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
author	Ricardo Wurmus <rekado@elephly.net>	2023-04-28 17:59:56 +0200
committer	Ricardo Wurmus <rekado@elephly.net>	2023-04-29 20:27:57 +0200
commit	15efeebe536949b4f2fd6f74c54989c16b17dca7 (patch)
tree	a12e59328cb2460893544ded642f1e62bcd14dfd /.gitignore
parent	0ee6b4203d2b13e268f67fcb8ac0e18bea3e3cb2 (diff)
download	guix-15efeebe536949b4f2fd6f74c54989c16b17dca7.tar.gz guix-15efeebe536949b4f2fd6f74c54989c16b17dca7.zip