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>gnu: rclone: Update to 1.49.3....Tobias Geerinckx-Rice 2019-09-10gnu: rclone: Update to 1.49.2....Tobias Geerinckx-Rice 2019-09-02gnu: rclone: Update to 1.49.1....Nicolas Goaziou m?id=7fde16671523f3fc3bda0c07a47a1fa33f8675b1&id2=241772d5c068fb7c4fa69d4673174254742eb410'>gnu/packages/assembly.scm6
-rw-r--r--gnu/packages/astronomy.scm54
-rw-r--r--gnu/packages/audio.scm2
-rw-r--r--gnu/packages/backup.scm4
-rw-r--r--gnu/packages/bioconductor.scm89
-rw-r--r--gnu/packages/bioinformatics.scm242
-rw-r--r--gnu/packages/bootloaders.scm817
-rw-r--r--gnu/packages/build-tools.scm89
-rw-r--r--gnu/packages/cdrom.scm2
-rw-r--r--gnu/packages/chromium.scm42
-rw-r--r--gnu/packages/code.scm4
-rw-r--r--gnu/packages/compression.scm8
-rw-r--r--gnu/packages/cook.scm4
-rw-r--r--gnu/packages/cran.scm672
-rw-r--r--gnu/packages/crates-graphics.scm54
-rw-r--r--gnu/packages/crates-gtk.scm25
-rw-r--r--gnu/packages/crates-io.scm3235
-rw-r--r--gnu/packages/cups.scm10
-rw-r--r--gnu/packages/curl.scm5
-rw-r--r--gnu/packages/debug.scm29
-rw-r--r--gnu/packages/digest.scm12
-rw-r--r--gnu/packages/disk.scm7
-rw-r--r--gnu/packages/dns.scm4
-rw-r--r--gnu/packages/emacs-xyz.scm12
-rw-r--r--gnu/packages/embedded.scm35
-rw-r--r--gnu/packages/engineering.scm45
-rw-r--r--gnu/packages/finance.scm4
-rw-r--r--gnu/packages/freedesktop.scm4
-rw-r--r--gnu/packages/ftp.scm2
-rw-r--r--gnu/packages/game-development.scm28
-rw-r--r--gnu/packages/games.scm24
-rw-r--r--gnu/packages/geo.scm2
-rw-r--r--gnu/packages/gnome.scm2
-rw-r--r--gnu/packages/gnupg.scm4
-rw-r--r--gnu/packages/gnuzilla.scm149
-rw-r--r--gnu/packages/golang.scm15
-rw-r--r--gnu/packages/gstreamer.scm2
-rw-r--r--gnu/packages/gtk.scm14
-rw-r--r--gnu/packages/hardware.scm23
-rw-r--r--gnu/packages/jami.scm2
-rw-r--r--gnu/packages/libreoffice.scm22
-rw-r--r--gnu/packages/linux.scm171
-rw-r--r--gnu/packages/lisp-xyz.scm75
-rw-r--r--gnu/packages/lisp.scm7
-rw-r--r--gnu/packages/loko.scm75
-rw-r--r--gnu/packages/mail.scm17
-rw-r--r--gnu/packages/music.scm62
-rw-r--r--gnu/packages/networking.scm34
-rw-r--r--gnu/packages/patches/jami-sip-contacts.patch38
-rw-r--r--gnu/packages/patches/jami-sipaccount-segfault.patch30
-rw-r--r--gnu/packages/patches/rust-1.64-fix-riscv64-bootstrap.patch565
-rw-r--r--gnu/packages/patches/sbcl-fix-build-on-arm64-with-clisp-as-host.patch27
-rw-r--r--gnu/packages/patches/sssd-optional-systemd.patch45
-rw-r--r--gnu/packages/protobuf.scm13
-rw-r--r--gnu/packages/python-check.scm29
-rw-r--r--gnu/packages/python-science.scm4
-rw-r--r--gnu/packages/python-xyz.scm115
-rw-r--r--gnu/packages/qt.scm285
-rw-r--r--gnu/packages/raspberry-pi.scm136
-rw-r--r--gnu/packages/rust-apps.scm303
-rw-r--r--gnu/packages/rust.scm17
-rw-r--r--gnu/packages/sssd.scm9
-rw-r--r--gnu/packages/statistics.scm844
-rw-r--r--gnu/packages/telephony.scm104
-rw-r--r--gnu/packages/texinfo.scm6
-rw-r--r--gnu/packages/text-editors.scm6
-rw-r--r--gnu/packages/video.scm33
-rw-r--r--gnu/packages/web.scm63
-rw-r--r--gnu/packages/wm.scm82
-rw-r--r--gnu/packages/wxwidgets.scm232
72 files changed, 6318 insertions, 3120 deletions
diff --git a/gnu/packages/admin.scm b/gnu/packages/admin.scm
index 99231a710e..b1f928014e 100644
--- a/gnu/packages/admin.scm
+++ b/gnu/packages/admin.scm
@@ -1175,7 +1175,7 @@ would need and has several interesting built-in capabilities.")
(define-public netcat-openbsd
(package
(name "netcat-openbsd")
- (version "1.218-5")
+ (version "1.219-1")
(source (origin
(method git-fetch)
(uri (git-reference
@@ -1184,7 +1184,7 @@ would need and has several interesting built-in capabilities.")
(file-name (git-file-name name version))
(sha256
(base32
- "0hpbmz9m2q22a6qgbn9590z2x96xgffim8g0m1v47mariz3pqhlc"))))
+ "1fhrmnbdl6bgsjk02vi78zy9i486mmniymbbbhdkzl8zfjbjkpxc"))))
(build-system gnu-build-system)
(arguments
`(#:tests? #f ; no test suite
diff --git a/gnu/packages/apparmor.scm b/gnu/packages/apparmor.scm
new file mode 100644
index 0000000000..ddbd9eb7a9
--- /dev/null
+++ b/gnu/packages/apparmor.scm
@@ -0,0 +1,202 @@
+;;; GNU Guix --- Functional package management for GNU
+;;; Copyright © 2022 Hilton Chain <hako@ultrarare.space>
+;;;
+;;; This file is part of GNU Guix.
+;;;
+;;; GNU Guix is free software; you can redistribute it and/or modify it
+;;; under the terms of the GNU General Public License as published by
+;;; the Free Software Foundation; either version 3 of the License, or (at
+;;; your option) any later version.
+;;;
+;;; GNU Guix is distributed in the hope that it will be useful, but
+;;; WITHOUT ANY WARRANTY; without even the implied warranty of
+;;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+;;; GNU General Public License for more details.
+;;;
+;;; You should have received a copy of the GNU General Public License
+;;; along with GNU Guix. If not, see <http://www.gnu.org/licenses/>.
+
+(define-module (gnu packages apparmor)
+ #:use-module ((guix licenses) #:prefix license:)
+ #:use-module (gnu packages autotools)
+ #:use-module (gnu packages base)
+ #:use-module (gnu packages bison)
+ #:use-module (gnu packages dejagnu)
+ #:use-module (gnu packages flex)
+ #:use-module (gnu packages gawk)
+ #:use-module (gnu packages gettext)
+ #:use-module (gnu packages linux)
+ #:use-module (gnu packages perl)
+ #:use-module (gnu packages pkg-config)
+ #:use-module (gnu packages python)
+ #:use-module (gnu packages python-xyz)
+ #:use-module (gnu packages ruby)
+ #:use-module (gnu packages swig)
+ #:use-module (guix build-system gnu)
+ #:use-module (guix gexp)
+ #:use-module (guix git-download)
+ #:use-module (guix packages)
+ #:use-module (guix utils))
+
+(define-public libapparmor
+ (package
+ (name "libapparmor")
+ (version "3.1.2")
+ (source (origin
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://gitlab.com/apparmor/apparmor")
+ (commit (string-append "v" version))))
+ (file-name (git-file-name name version))
+ (sha256
+ (base32
+ "1h77a7ww0rxfv5nsi1iy4fffklxdr2vq6r7kdsqm15yysglhbjyi"))))
+ (build-system gnu-build-system)
+ (arguments
+ (list #:configure-flags
+ #~(list (string-append "LDFLAGS=-Wl,-rpath=" #$output "/lib")
+ "--with-perl" "--with-python" "--with-ruby")
+ #:phases
+ #~(modify-phases %standard-phases
+ (add-after 'unpack 'fix-paths
+ (lambda* (#:key inputs #:allow-other-keys)
+ (for-each patch-shebang
+ '("common/list_af_names.sh"
+ "common/list_capabilities.sh"))
+ (for-each (lambda (file)
+ (substitute* file
+ (("/usr") "")
+ (("/bin/\\<(pod2man|pod2html|podchecker|prove)\\>" path)
+ (search-input-file inputs path))
+ (("/include/linux/capability.h" path)
+ (search-input-file inputs path))))
+ '("common/Make-po.rules"
+ "common/Make.rules"
+ "binutils/Makefile"
+ "parser/Makefile"
+ "parser/tst/Makefile"
+ "profiles/Makefile"
+ "utils/Makefile"
+ "utils/python-tools-setup.py"
+ "utils/vim/Makefile"))))
+ (add-after 'fix-paths 'change-directory
+ (lambda _
+ (chdir "libraries/libapparmor"))))))
+ (native-inputs
+ (list autoconf
+ automake
+ bison
+ dejagnu
+ flex
+ libtool
+ perl
+ python-minimal
+ ruby
+ swig
+ which))
+ (home-page "https://apparmor.net")
+ (synopsis "Linux kernel security module")
+ (description
+ "AppArmor is an effective and easy-to-use Linux application security
+system.
+
+AppArmor proactively protects the operating system and applications from
+external or internal threats, even zero-day attacks, by enforcing good
+behavior and preventing both known and unknown application flaws from being
+exploited.
+
+AppArmor supplements the traditional Unix discretionary access control (DAC)
+model by providing mandatory access control (MAC). It has been included in
+the mainline Linux kernel since version 2.6.36 and its development has been
+supported by Canonical since 2009.")
+ (license license:lgpl2.1)
+ (supported-systems (filter (lambda (system)
+ (string-suffix? "-linux" system))
+ %supported-systems))))
+
+(define-public apparmor
+ (let ((base libapparmor))
+ (package
+ (inherit base)
+ (name "apparmor")
+ (arguments
+ (append
+ (list #:make-flags
+ #~(list (string-append "CC=" #$(cc-for-target))
+ (string-append "DESTDIR=" #$output)
+ "USE_SYSTEM=1"
+ ;; No need to run the linter
+ "PYFLAKES=true"))
+ (substitute-keyword-arguments (package-arguments base)
+ ((#:phases phases)
+ #~(modify-phases #$phases
+ (delete 'configure)
+ ;; apparmor-binutils
+ (replace 'change-directory
+ (lambda _
+ (chdir "binutils")))
+
+ ;; apparmor-parser
+ (add-after 'install 'chdir-parser
+ (lambda _
+ (chdir "../parser")))
+ (add-after 'chdir-parser 'patch-source-shebangs-parser
+ (assoc-ref %standard-phases 'patch-source-shebangs))
+ (add-after 'patch-source-shebangs-parser 'build-parser
+ (assoc-ref %standard-phases 'build))
+ (add-after 'build-parser 'check-parser
+ (assoc-ref %standard-phases 'check))
+ (add-after 'check-parser 'install-parser
+ (assoc-ref %standard-phases 'install))
+
+ ;; apparmor-utils
+ ;; FIXME: Tests required Python library from this package
+ ;; (itself).
+ (add-after 'install-parser 'chdir-utils
+ (lambda _
+ (chdir "../utils")
+ ;; Fix paths to installed policygroups and templates for
+ ;; easyprof.
+ (substitute* "easyprof/easyprof.conf"
+ (("/usr") #$output))))
+ (add-after 'chdir-utils 'build-utils
+ (assoc-ref %standard-phases 'build))
+ (add-after 'build-utils 'install-utils
+ (assoc-ref %standard-phases 'install))
+
+ ;; apparmor-profiles
+ ;; FIXME: Tests need an AppArmor-enabled system.
+ (add-after 'install-utils 'chdir-profiles
+ (lambda _
+ (chdir "../profiles")))
+ (add-after 'chdir-profiles 'build-profiles
+ (assoc-ref %standard-phases 'build))
+ (add-after 'check-build 'install-profiles
+ (assoc-ref %standard-phases 'install)))))))
+ (propagated-inputs
+ (list libapparmor))
+ ;; Python module `readline' needed
+ (native-inputs
+ (list bison flex gettext-minimal perl python which))
+ (license license:gpl2))))
+
+(define-public pam-apparmor
+ (let ((base apparmor))
+ (package
+ (inherit base)
+ (name "pam-apparmor")
+ (arguments
+ (append
+ (list #:tests? #f) ;no tests
+ (substitute-keyword-arguments (package-arguments base)
+ ((#:phases phases)
+ #~(modify-phases #$phases
+ (delete 'chdir-parser)
+ (delete 'chdir-utils)
+ (delete 'chdir-profiles)
+ (replace 'change-directory
+ (lambda _
+ (chdir "changehat/pam_apparmor"))))))))
+ (native-inputs (list pkg-config perl which))
+ (inputs (list libapparmor linux-pam))
+ (license license:bsd-3))))
diff --git a/gnu/packages/assembly.scm b/gnu/packages/assembly.scm
index 8a899f0020..7e36bbcc71 100644
--- a/gnu/packages/assembly.scm
+++ b/gnu/packages/assembly.scm
@@ -144,8 +144,10 @@ debugging information in STABS, DWARF 2, and CodeView 8 formats.")
(build-system gnu-build-system)
(native-inputs (list zlib))
(arguments
- ;; Some tests fail when run in parallel.
- `(#:parallel-tests? #f))
+ `(#:configure-flags
+ (list "--disable-static")
+ ;; Some tests fail when run in parallel.
+ #:parallel-tests? #f))
(synopsis "Library for generating assembly code at runtime")
(description
"GNU Lightning is a library that generates assembly language code at
diff --git a/gnu/packages/astronomy.scm b/gnu/packages/astronomy.scm
index 439fdf72a8..759ccbec9e 100644
--- a/gnu/packages/astronomy.scm
+++ b/gnu/packages/astronomy.scm
@@ -89,6 +89,58 @@
#:use-module (ice-9 match)
#:use-module (srfi srfi-1))
+(define-public alfa
+ (package
+ (name "alfa")
+ (version "2.2")
+ (source (origin
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/rwesson/ALFA")
+ (commit (string-append "v" version))))
+ (sha256
+ (base32
+ "0aqxqar36822mh373awsl79j7zn8vik4yddyydsxv0c76gn4i2k3"))
+ (file-name (git-file-name name version))))
+ (build-system gnu-build-system)
+ (arguments
+ (list #:parallel-build? #f
+ #:make-flags #~(list (string-append "PREFIX="
+ #$output)
+ (string-append "VERSION="
+ #$version))
+ #:phases #~(modify-phases %standard-phases
+ (delete 'configure)
+ (delete 'check)
+ (add-after 'install 'post-install-check
+ (lambda* (#:key tests? #:allow-other-keys)
+ (when tests?
+ (invoke "make" "fittest")))))))
+ (inputs (list cfitsio gfortran))
+ (home-page "https://nebulousresearch.org/codes/alfa/")
+ (synopsis "Automated line fitting algorithm")
+ (description
+ "This package provides @acronym{ALFA, Automatic line fitting algorithm},
+which can identify and fit hundreds of lines in emission line spectra in just a
+few seconds with following features:
+@itemize
+
+@item A population of synthetic spectra is generated using a reference line
+catalogue.
+
+@item The goodness of fit for each synthetic spectrum is calculated. The best
+sets of parameters are retained and the rest discarded.
+
+@item A new population of synthetic spectra is obtained by averaging pairs of
+the best performers.
+
+@item A small fraction of the parameters of the lines in the new generation are
+randomly altered.
+
+@item The process repeats until a good fit is obtained.
+@end itemize")
+ (license license:gpl3)))
+
(define-public aocommon
(let ((commit "7329a075271edab8f6264db649e81e62b2b6ae5e")
(revision "1"))
@@ -1873,7 +1925,7 @@ It can be used to calculate the trajectory of satellites.")
(native-inputs
(list boost pkg-config))
(inputs
- (list cfitsio freeimage glew wxwidgets))
+ (list cfitsio freeimage glew wxwidgets-3.0))
(home-page "https://github.com/GreatAttractor/imppg")
(synopsis "Astronomical Image Post-Proccessor (ImPPG)")
(description
diff --git a/gnu/packages/audio.scm b/gnu/packages/audio.scm
index ead5ce5963..2f9cb9526e 100644
--- a/gnu/packages/audio.scm
+++ b/gnu/packages/audio.scm
@@ -892,7 +892,7 @@ engineers, musicians, soundtrack editors and composers.")
#t))))
(build-system cmake-build-system)
(inputs
- (list wxwidgets-3.1
+ (list wxwidgets
gtk+
alsa-lib
jack-1
diff --git a/gnu/packages/backup.scm b/gnu/packages/backup.scm
index 67708138a6..00d95e7b3d 100644
--- a/gnu/packages/backup.scm
+++ b/gnu/packages/backup.scm
@@ -1088,14 +1088,14 @@ interactive mode.")
(define-public btrbk
(package
(name "btrbk")
- (version "0.32.4")
+ (version "0.32.5")
(source (origin
(method url-fetch)
(uri (string-append "https://digint.ch/download/btrbk/releases/"
"btrbk-" version ".tar.xz"))
(sha256
(base32
- "1nl6cbzqkc2srwi1428vijq69rp5cdx7484zcx61ph0rnhg9srfc"))))
+ "1d4zqf5klad55gdzzldipsjrhpprixzjmn03g66df5h2d28l1zpi"))))
(build-system gnu-build-system)
(arguments
(list
diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index bb319a13e5..c62c5970b8 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -2454,13 +2454,13 @@ plants. The method has been specifically designed to:
(define-public r-alpine
(package
(name "r-alpine")
- (version "1.22.0")
+ (version "1.24.0")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "alpine" version))
(sha256
(base32
- "1nl1hxwakh5m9rqm3ksn2jzknsj9xnwl51bmc30knknm4q35wdv9"))))
+ "0rjnwljh4c2f7ml0m14pllns4pvyjwwf23qsn6zjygm5x04bapf0"))))
(properties `((upstream-name . "alpine")))
(build-system r-build-system)
(propagated-inputs
@@ -4216,18 +4216,19 @@ mapping.")
(define-public r-nmf
(package
(name "r-nmf")
- (version "0.24.0")
+ (version "0.25")
(source
(origin
(method url-fetch)
(uri (cran-uri "NMF" version))
(sha256
(base32
- "14yxra6in5c1md5nr75y8cdmh9pg0lxqabqflvlhgg1vbg9i2628"))))
+ "0kdl7yz4v7pms6y2lff4x5w7pwkx54488qx0v539qmvcbxv1if98"))))
(properties `((upstream-name . "NMF")))
(build-system r-build-system)
(propagated-inputs
(list r-cluster
+ r-codetools
r-biobase
r-biocmanager
r-bigmemory ; suggested
@@ -4238,7 +4239,6 @@ mapping.")
r-foreach
r-ggplot2
r-gridbase
- r-pkgmaker
r-rcolorbrewer
r-registry
r-reshape2
@@ -4787,13 +4787,13 @@ only one command.")
(define-public r-biocparallel
(package
(name "r-biocparallel")
- (version "1.32.1")
+ (version "1.32.3")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "BiocParallel" version))
(sha256
(base32
- "1fkfbs0n0sdssli7ibrswkfag080kgv8n1zf6ssxx729g1fz3m3h"))))
+ "0z2g3p6ip4g865na9bmqaa7w2s52769pmjr3hpiv6x8bhifh3nm5"))))
(properties
`((upstream-name . "BiocParallel")))
(build-system r-build-system)
@@ -6010,6 +6010,42 @@ reduction (between group analysis) and joint dimension reduction of two
datasets (coinertia analysis).")
(license license:artistic2.0)))
+(define-public r-metaneighbor
+ (package
+ (name "r-metaneighbor")
+ (version "1.18.0")
+ (source (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "MetaNeighbor" version))
+ (sha256
+ (base32
+ "1gjjp5qlmv26sd3fvrd8cgv3invckxr8ldjpizpqm4mxjzifxwpm"))))
+ (properties `((upstream-name . "MetaNeighbor")))
+ (build-system r-build-system)
+ (propagated-inputs
+ (list r-beanplot
+ r-dplyr
+ r-ggplot2
+ r-gplots
+ r-igraph
+ r-matrix
+ r-matrixstats
+ r-rcolorbrewer
+ r-singlecellexperiment
+ r-summarizedexperiment
+ r-tibble
+ r-tidyr))
+ (native-inputs (list r-knitr))
+ (home-page "https://bioconductor.org/packages/MetaNeighbor")
+ (synopsis "Single cell replicability analysis")
+ (description
+ "This package implements a method to rapidly assess cell type identity using
+both functional and random gene sets and it allows users to quantify cell type
+replicability across datasets using neighbor voting. @code{MetaNeighbor} works
+on the basis that cells of the same type should have more similar gene expression
+profiles than cells of different types.")
+ (license license:expat)))
+
(define-public r-methylkit
(package
(name "r-methylkit")
@@ -8765,6 +8801,41 @@ representations of analysis results in order to provide additional
information.")
(license license:lgpl3)))
+(define-public r-glmgampoi
+ (package
+ (name "r-glmgampoi")
+ (version "1.10.0")
+ (source (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "glmGamPoi" version))
+ (sha256
+ (base32
+ "12jbqigg4k2ngrk2anbrrxrwkp57bbzdz492lg8lc6w1gygp5yip"))))
+ (properties `((upstream-name . "glmGamPoi")))
+ (build-system r-build-system)
+ (propagated-inputs
+ (list r-beachmat
+ r-biocgenerics
+ r-delayedarray
+ r-delayedmatrixstats
+ r-hdf5array
+ r-matrixgenerics
+ r-matrixstats
+ r-rcpp
+ r-rcpparmadillo
+ r-rlang
+ r-singlecellexperiment
+ r-summarizedexperiment))
+ (native-inputs (list r-knitr))
+ (home-page "https://github.com/const-ae/glmGamPoi")
+ (synopsis "Fit a Gamma-Poisson Generalized Linear Model")
+ (description
+ "Fit linear models to overdispersed count data. The package can estimate
+the overdispersion and fit repeated models for matrix input. It is designed
+to handle large input datasets as they typically occur in single cell RNA-seq
+experiments.")
+ (license license:gpl3)))
+
(define-public r-rots
(package
(name "r-rots")
@@ -17820,14 +17891,14 @@ the Bioconductor project.")
(define-public r-biodb
(package
(name "r-biodb")
- (version "1.6.0")
+ (version "1.6.1")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "biodb" version))
(sha256
(base32
- "08ahz3v2xbhwfh89dbnhhcdm0x5qv4hibi8wknlqf5x8gqm5j5w6"))))
+ "0mbqsias2ajw29d1wgl10y2cjqv3slrsgifccz0kh9l5r6bk28vz"))))
(properties `((upstream-name . "biodb")))
(build-system r-build-system)
(propagated-inputs
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 6c6ff3e25a..3a7dc1a1b7 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -57,6 +57,7 @@
#:use-module (guix build-system meson)
#:use-module (guix build-system ocaml)
#:use-module (guix build-system perl)
+ #:use-module (guix build-system pyproject)
#:use-module (guix build-system python)
#:use-module (guix build-system qt)
#:use-module (guix build-system r)
@@ -846,7 +847,7 @@ intended to behave exactly the same as the original BWK awk.")
(define-public python-cellbender
(package
(name "python-cellbender")
- (version "0.2.1")
+ (version "0.2.2")
(source
(origin
(method git-fetch)
@@ -856,8 +857,8 @@ intended to behave exactly the same as the original BWK awk.")
(file-name (git-file-name name version))
(sha256
(base32
- "1zav2q8nnss80i25y06fccagkvrqsy7lpylsl4dxv4qkj8p4fnv3"))))
- (build-system python-build-system)
+ "12q22va7rbc3sx9ygc6p6hh6xw9wbqjmhba5h5gb836p5xplj5fa"))))
+ (build-system pyproject-build-system)
(arguments
(list #:tests? #false)) ;there are none
(propagated-inputs
@@ -884,14 +885,14 @@ from high-throughput single-cell RNA sequencing (scRNA-seq) data.")
(define-public python-htsget
(package
(name "python-htsget")
- (version "0.2.5")
+ (version "0.2.6")
(source (origin
(method url-fetch)
(uri (pypi-uri "htsget" version))
(sha256
(base32
- "0ic07q85vhw9djf23k57b21my7i5xp400m8gfqgr5gcryqvdr0yk"))))
- (build-system python-build-system)
+ "111q4pzkav26aa3hkgh948wqlyrq7dq6sjml9z63n3blw8s6b0c4"))))
+ (build-system pyproject-build-system)
(native-inputs
(list python-setuptools-scm))
(propagated-inputs
@@ -913,11 +914,12 @@ servers supporting the protocol.")
(sha256
(base32
"18rhzk08d3rpxhi5xh6pqg64x6v5q3daw6y3v54k85v4swncjrwj"))))
- (build-system python-build-system)
+ (build-system pyproject-build-system)
(arguments
`(#:modules ((srfi srfi-26)
(guix build utils)
- (guix build python-build-system))
+ (guix build python-build-system)
+ (guix build pyproject-build-system))
;; See https://github.com/daler/pybedtools/issues/192
#:phases
(modify-phases %standard-phases
@@ -977,7 +979,7 @@ which are widely used for genomic interval manipulation or \"genome algebra\".
pybedtools extends BEDTools by offering feature-level manipulations from with
Python.")
;; pypi lists GPLv2 in the PKG-INFO and website, but was relicensed in
- ;; version 0.9.0 and the LICENSE.txt is consistant with the source code.
+ ;; version 0.9.0 and the LICENSE.txt is consistent with the source code.
;;
;; pybedtools/include/gzstream.cpp and pybedtools/include/gzstream.h are
;; licensed lgpl2.1+
@@ -1031,7 +1033,7 @@ use-case, we encourage users to compose functions to achieve their goals.")
(define-public python-biom-format
(package
(name "python-biom-format")
- (version "2.1.10")
+ (version "2.1.12")
(source
(origin
(method git-fetch)
@@ -1043,25 +1045,22 @@ use-case, we encourage users to compose functions to achieve their goals.")
(file-name (git-file-name name version))
(sha256
(base32
- "0i62j6ksmp78ap2dnl969gq6vprc3q87zc8ksj9if8g2603iq6i8"))
+ "06x2d8fv80jp86kd66fm3ragmxrpa2j0lzsbm337ziqjnpsdwc0f"))
(modules '((guix build utils)))
;; Delete generated C files.
(snippet
'(for-each delete-file (find-files "." "\\.c")))))
(build-system python-build-system)
(arguments
- `(#:phases
- (modify-phases %standard-phases
+ (list
+ #:phases
+ '(modify-phases %standard-phases
(add-after 'unpack 'use-cython
(lambda _ (setenv "USE_CYTHON" "1")))
- (add-after 'unpack 'relax
- (lambda _
- (substitute* "setup.py"
- (("pytest < 5.3.4") "pytest"))))
(add-after 'unpack 'disable-broken-tests
(lambda _
- (substitute* "biom/tests/test_cli/test_validate_table.py"
- (("^(.+)def test_invalid_hdf5" m indent)
+ (substitute* "biom/tests/test_util.py"
+ (("^(.+)def test_biom_open_hdf5_no_h5py" m indent)
(string-append indent
"@npt.dec.skipif(True, msg='Guix')\n"
m)))
@@ -1072,13 +1071,14 @@ use-case, we encourage users to compose functions to achieve their goals.")
m))))))))
(propagated-inputs
(list python-anndata
- python-numpy
- python-scipy
+ python-click
python-flake8
python-future
- python-click
python-h5py
- python-pandas))
+ python-numpy
+ python-pandas
+ python-scikit-bio
+ python-scipy))
(native-inputs
(list python-cython python-pytest python-pytest-cov python-nose))
(home-page "http://www.biom-format.org")
@@ -1093,42 +1093,45 @@ e.g. microbiome samples, genomes, metagenomes.")
(define-public python-pairtools
(package
(name "python-pairtools")
- (version "0.3.0")
+ (version "1.0.2")
(source (origin
(method git-fetch)
(uri (git-reference
- (url "https://github.com/mirnylab/pairtools")
+ (url "https://github.com/open2c/pairtools")
(commit (string-append "v" version))))
(file-name (git-file-name name version))
(sha256
(base32
- "0gr8y13q7sd6yai6df4aavl2470n1f9s3cib6r473z4hr8hcbwmc"))))
+ "0xn4cg4jq3rfn42h8rfwg0k6xkvihjrv32gwldb9y0jp05lzw9cs"))))
(build-system python-build-system)
(arguments
`(#:phases
(modify-phases %standard-phases
(add-after 'unpack 'fix-references
(lambda _
- (substitute* '("pairtools/pairtools_merge.py"
- "pairtools/pairtools_sort.py")
- (("/bin/bash") (which "bash")))
- #t))
+ (substitute* '("pairtools/cli/header.py"
+ "pairtools/cli/merge.py"
+ "pairtools/cli/sort.py")
+ (("/bin/bash") (which "bash")))))
(replace 'check
- (lambda* (#:key inputs outputs #:allow-other-keys)
- (add-installed-pythonpath inputs outputs)
- (with-directory-excursion "/tmp"
- (invoke "pytest" "-v")))))))
+ (lambda* (#:key tests? #:allow-other-keys)
+ (when tests?
+ (with-directory-excursion "/tmp"
+ (invoke "pytest" "-v"))))))))
(native-inputs
- (list python-cython python-nose python-pytest))
- (inputs
- `(("python" ,python-wrapper)))
+ (list python-cython python-pytest))
(propagated-inputs
(list htslib ; for bgzip, looked up in PATH
samtools ; looked up in PATH
lz4 ; for lz4c
+ python-bioframe
python-click
- python-numpy))
- (home-page "https://github.com/mirnylab/pairtools")
+ python-numpy
+ python-pandas
+ python-pysam
+ python-pyyaml
+ python-scipy))
+ (home-page "https://github.com/open2c/pairtools")
(synopsis "Process mapped Hi-C data")
(description "Pairtools is a simple and fast command-line framework to
process sequencing data from a Hi-C experiment. Process pair-end sequence
@@ -2973,6 +2976,71 @@ generation, and transformation to RDF. Salad provides a bridge between document
and record oriented data modeling and the Semantic Web.")
(license license:asl2.0)))
+(define-public python-scikit-bio
+ (package
+ (name "python-scikit-bio")
+ (version "0.5.7")
+ (source (origin
+ (method url-fetch)
+ (uri (pypi-uri "scikit-bio" version))
+ (sha256
+ (base32
+ "1a8xbp3vrw8wfpm3pa2nb4rcar0643iqnb043ifwqbqyc86clhv3"))))
+ (build-system pyproject-build-system)
+ (arguments
+ (list
+ #:phases
+ '(modify-phases %standard-phases
+ ;; See https://github.com/biocore/scikit-bio/pull/1826
+ (add-after 'unpack 'compatibility
+ (lambda _
+ (substitute* "skbio/sequence/tests/test_sequence.py"
+ (("def test_concat_strict_many")
+ "def _do_not_test_concat_strict_many"))
+ (substitute* "skbio/stats/distance/_mantel.py"
+ (("from scipy.stats import PearsonRConstantInputWarning")
+ "from scipy.stats import ConstantInputWarning")
+ (("from scipy.stats import PearsonRNearConstantInputWarning")
+ "from scipy.stats import NearConstantInputWarning")
+ (("from scipy.stats import SpearmanRConstantInputWarning") "")
+ (("warnings.warn\\(PearsonRConstantInputWarning\\(\\)\\)")
+ "warnings.warn(ConstantInputWarning())")
+ (("warnings.warn\\(PearsonRNearConstantInputWarning\\(\\)\\)")
+ "warnings.warn(NearConstantInputWarning())")
+ (("warnings.warn\\(SpearmanRConstantInputWarning\\(\\)\\)")
+ "warnings.warn(ConstantInputWarning())"))
+ (substitute* "skbio/diversity/alpha/tests/test_base.py"
+ (("self.assertEqual\\(pielou_e")
+ "self.assertAlmostEqual(pielou_e"))))
+ (add-before 'check 'build-extensions
+ (lambda _
+ ;; Cython extensions have to be built before running the tests.
+ (invoke "python3" "setup.py" "build_ext" "--inplace")))
+ (replace 'check
+ (lambda* (#:key tests? #:allow-other-keys)
+ (when tests? (invoke "python3" "-m" "skbio.test")))))))
+ (propagated-inputs
+ (list python-cachecontrol
+ python-decorator
+ python-h5py
+ python-hdmedians
+ python-ipython
+ python-lockfile
+ python-matplotlib
+ python-natsort
+ python-numpy
+ python-pandas
+ python-scikit-learn
+ python-scipy))
+ (native-inputs
+ (list python-coverage python-pytest))
+ (home-page "https://scikit-bio.org")
+ (synopsis "Data structures, algorithms and educational resources for bioinformatics")
+ (description
+ "This package provides data structures, algorithms and educational
+resources for bioinformatics.")
+ (license license:bsd-3)))
+
(define-public cwltool
(package
(name "cwltool")
@@ -10601,6 +10669,102 @@ traditional read alignments) and massively-parallel stochastic collapsed
variational inference.")
(license license:gpl3+)))
+(define-public python-fanc
+ (package
+ (name "python-fanc")
+ (version "0.9.25")
+ (source (origin
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/vaquerizaslab/fanc")
+ ;; There are no tags. This commit corresponds to
+ ;; version 0.9.25.
+ (commit "e2205346c13ea5349681dff21adeb271d4ea5261")))
+ (file-name (git-file-name name version))
+ (sha256
+ (base32
+ "0rxq24p852iiayi0083fyigvc30as695rha71q6xd4s2ij1k9mqi"))))
+ (build-system pyproject-build-system)
+ (arguments
+ (list
+ #:phases
+ '(modify-phases %standard-phases
+ (replace 'check
+ (lambda* (#:key tests? #:allow-other-keys)
+ (when tests?
+ (invoke "pytest" "-vv"
+ "-k"
+ ;; XXX: These all fail because they fail to read
+ ;; the included test_{cooler,juicer}.hic files.
+ (string-append "not test_edges_iter"
+ " and not test_get_edges_uncorrected"
+ " and not test_get_edges"))))))))
+ (propagated-inputs
+ (list python-biopython
+ python-cooler
+ python-deprecated
+ python-future
+ python-genomic-regions
+ python-gridmap
+ python-h5py
+ python-intervaltree
+ python-matplotlib
+ python-msgpack
+ python-msgpack-numpy
+ python-numpy
+ python-pandas
+ python-pillow
+ python-progressbar2
+ python-pybedtools
+ python-pybigwig
+ python-pysam
+ python-pytest
+ python-pyyaml
+ python-scikit-image
+ python-scikit-learn
+ python-scipy
+ python-seaborn
+ python-tables))
+ (native-inputs
+ (list python-cython))
+ (home-page "https://github.com/vaquerizaslab/fanc")
+ (synopsis "Framework for the analysis of C-data")
+ (description
+ "FAN-C provides a pipeline for analysing Hi-C data starting at
+mapped paired-end sequencing reads.")
+ (license license:gpl3+)))
+
+(define-public python-genomic-regions
+ (package
+ (name "python-genomic-regions")
+ (version "0.0.10")
+ (source (origin
+ (method url-fetch)
+ (uri (pypi-uri "genomic_regions" version))
+ (sha256
+ (base32
+ "0hz811iyd1prml1r90qyzimmwyjwycwkjqw4vnl12bxy61rfzjz5"))))
+ (build-system pyproject-build-system)
+ (propagated-inputs
+ (list python-future
+ python-intervaltree
+ python-numpy
+ python-pandas
+ python-pybedtools
+ python-pybigwig
+ python-pytest
+ python-msgpack-numpy
+ python-cython
+ python-msgpack
+ python-pysam))
+ (home-page "https://pypi.org/project/genomic-regions/")
+ (synopsis "Consistently handle genomic regions")
+ (description "This package aims to simplify working with genomic region /
+interval data by providing a common interface that lets you access a wide
+selection of file types and formats for handling genomic region data---all
+using the same syntax.")
+ (license license:expat)))
+
(define-public python-loompy
(package
(name "python-loompy")
diff --git a/gnu/packages/bootloaders.scm b/gnu/packages/bootloaders.scm
index 210bc30536..8888c51736 100644
--- a/gnu/packages/bootloaders.scm
+++ b/gnu/packages/bootloaders.scm
@@ -16,6 +16,7 @@
;;; Copyright © 2021 Vincent Legoll <vincent.legoll@gmail.com>
;;; Copyright © 2021 Brice Waegeneire <brice@waegenei.re>
;;; Copyright © 2022 Denis 'GNUtoo' Carikli <GNUtoo@cyberdimension.org>
+;;; Copyright © 2021 Stefan <stefan-guix@vodafonemail.de>
;;;
;;; This file is part of GNU Guix.
;;;
@@ -67,13 +68,17 @@
#:use-module (gnu packages virtualization)
#:use-module (gnu packages xorg)
#:use-module (guix build-system gnu)
+ #:use-module (guix build-system trivial)
#:use-module (guix download)
+ #:use-module (guix gexp)
#:use-module (guix git-download)
#:use-module ((guix licenses) #:prefix license:)
#:use-module (guix packages)
#:use-module (guix utils)
#:use-module (srfi srfi-1)
#:use-module (srfi srfi-26)
+ #:use-module (ice-9 optargs)
+ #:use-module (ice-9 match)
#:use-module (ice-9 regex))
(define unifont
@@ -92,22 +97,22 @@
(name "grub")
(version "2.06")
(source (origin
- (method url-fetch)
- (uri (string-append "mirror://gnu/grub/grub-" version ".tar.xz"))
- (sha256
- (base32
- "1qbycnxkx07arj9f2nlsi9kp0dyldspbv07ysdyd34qvz55a97mp"))
- (patches (search-patches
- "grub-efi-fat-serial-number.patch"
- "grub-setup-root.patch"))
- (modules '((guix build utils)))
- (snippet
- '(begin
- ;; Adjust QEMU invocation to not use a deprecated device
- ;; name that was removed in QEMU 6.0. Remove for >2.06.
- (substitute* "tests/ahci_test.in"
- (("ide-drive")
- "ide-hd"))))))
+ (method url-fetch)
+ (uri (string-append "mirror://gnu/grub/grub-" version ".tar.xz"))
+ (sha256
+ (base32
+ "1qbycnxkx07arj9f2nlsi9kp0dyldspbv07ysdyd34qvz55a97mp"))
+ (patches (search-patches
+ "grub-efi-fat-serial-number.patch"
+ "grub-setup-root.patch"))
+ (modules '((guix build utils)))
+ (snippet
+ '(begin
+ ;; Adjust QEMU invocation to not use a deprecated device
+ ;; name that was removed in QEMU 6.0. Remove for >2.06.
+ (substitute* "tests/ahci_test.in"
+ (("ide-drive")
+ "ide-hd"))))))
(build-system gnu-build-system)
(arguments
`(#:configure-flags
@@ -117,65 +122,62 @@
(list "PYTHON=true")
;; Grub fails to load modules stripped with --strip-unneeded.
#:strip-flags '("--strip-debug" "--enable-deterministic-archives")
- #:phases (modify-phases %standard-phases
- (add-after 'unpack 'patch-stuff
- (lambda* (#:key native-inputs inputs #:allow-other-keys)
- (substitute* "grub-core/Makefile.in"
- (("/bin/sh") (which "sh")))
-
- ;; Give the absolute file name of 'mdadm', used to
- ;; determine the root file system when it's a RAID
- ;; device. Failing to do that, 'grub-probe' silently
- ;; fails if 'mdadm' is not in $PATH.
- (when (assoc-ref inputs "mdadm")
- (substitute* "grub-core/osdep/linux/getroot.c"
- (("argv\\[0\\] = \"mdadm\"")
- (string-append "argv[0] = \""
- (assoc-ref inputs "mdadm")
- "/sbin/mdadm\""))))
-
- ;; Make the font visible.
- (copy-file (assoc-ref (or native-inputs inputs)
- "unifont")
- "unifont.bdf.gz")
- (system* "gunzip" "unifont.bdf.gz")
-
- ;; Give the absolute file name of 'ckbcomp'.
- (substitute* "util/grub-kbdcomp.in"
- (("^ckbcomp ")
- (string-append
- (search-input-file inputs "/bin/ckbcomp")
- " ")))))
- (add-after 'unpack 'set-freetype-variables
- ;; These variables need to be set to the native versions
- ;; of the dependencies because they are used to build
- ;; programs which are executed during build time.
- (lambda* (#:key native-inputs #:allow-other-keys)
- (when (assoc-ref native-inputs "freetype")
- (let ((freetype (assoc-ref native-inputs "freetype")))
- (setenv "BUILD_FREETYPE_LIBS"
- (string-append "-L" freetype
- "/lib -lfreetype"))
- (setenv "BUILD_FREETYPE_CFLAGS"
- (string-append "-I" freetype
- "/include/freetype2"))))
- #t))
- (add-before 'check 'disable-flaky-test
- (lambda _
- ;; This test is unreliable. For more information, see:
- ;; <https://bugs.gnu.org/26936>.
- (substitute* "Makefile.in"
- (("grub_cmd_date grub_cmd_set_date grub_cmd_sleep")
- "grub_cmd_date grub_cmd_sleep"))
- #t))
- (add-before 'check 'disable-pixel-perfect-test
- (lambda _
- ;; This test compares many screenshots rendered with an
- ;; older Unifont (9.0.06) than that packaged in Guix.
- (substitute* "Makefile.in"
- (("test_unset grub_func_test")
- "test_unset"))
- #t)))
+ #:phases
+ (modify-phases %standard-phases
+ (add-after 'unpack 'patch-stuff
+ (lambda* (#:key native-inputs inputs #:allow-other-keys)
+ (substitute* "grub-core/Makefile.in"
+ (("/bin/sh") (which "sh")))
+
+ ;; Give the absolute file name of 'mdadm', used to determine the
+ ;; root file system when it's a RAID device. Failing to do that,
+ ;; 'grub-probe' silently fails if 'mdadm' is not in $PATH.
+ (when (assoc-ref inputs "mdadm")
+ (substitute* "grub-core/osdep/linux/getroot.c"
+ (("argv\\[0\\] = \"mdadm\"")
+ (string-append "argv[0] = \""
+ (assoc-ref inputs "mdadm")
+ "/sbin/mdadm\""))))
+
+ ;; Make the font visible.
+ (copy-file (assoc-ref (or native-inputs inputs)
+ "unifont")
+ "unifont.bdf.gz")
+ (system* "gunzip" "unifont.bdf.gz")
+
+ ;; Give the absolute file name of 'ckbcomp'.
+ (substitute* "util/grub-kbdcomp.in"
+ (("^ckbcomp ")
+ (string-append
+ (search-input-file inputs "/bin/ckbcomp")
+ " ")))))
+ (add-after 'unpack 'set-freetype-variables
+ ;; These variables need to be set to the native versions of the
+ ;; dependencies because they are used to build programs which are
+ ;; executed during build time.
+ (lambda* (#:key native-inputs #:allow-other-keys)
+ (when (assoc-ref native-inputs "freetype")
+ (let ((freetype (assoc-ref native-inputs "freetype")))
+ (setenv "BUILD_FREETYPE_LIBS"
+ (string-append "-L" freetype
+ "/lib -lfreetype"))
+ (setenv "BUILD_FREETYPE_CFLAGS"
+ (string-append "-I" freetype
+ "/include/freetype2"))))))
+ (add-before 'check 'disable-flaky-test
+ (lambda _
+ ;; This test is unreliable. For more information, see:
+ ;; <https://bugs.gnu.org/26936>.
+ (substitute* "Makefile.in"
+ (("grub_cmd_date grub_cmd_set_date grub_cmd_sleep")
+ "grub_cmd_date grub_cmd_sleep"))))
+ (add-before 'check 'disable-pixel-perfect-test
+ (lambda _
+ ;; This test compares many screenshots rendered with an older
+ ;; Unifont (9.0.06) than that packaged in Guix.
+ (substitute* "Makefile.in"
+ (("test_unset grub_func_test")
+ "test_unset")))))
;; Disable tests on ARM and AARCH64 platforms or when cross-compiling.
#:tests? ,(not (or (any (cute string-prefix? <> (or (%current-target-system)
(%current-system)))
@@ -222,19 +224,19 @@
("flex" ,flex)
("texinfo" ,texinfo)
("help2man" ,help2man)
- ("freetype" ,freetype) ; native version needed for build-grub-mkfont
+ ("freetype" ,freetype) ;native version needed for build-grub-mkfont
;; XXX: When building GRUB 2.02 on 32-bit x86, we need a binutils
;; capable of assembling 64-bit instructions. However, our default
;; binutils on 32-bit x86 is not 64-bit capable.
,@(if (string-match "^i[3456]86-" (%current-system))
(let ((binutils (package/inherit
- binutils
- (name "binutils-i386")
- (arguments
- (substitute-keyword-arguments (package-arguments binutils)
- ((#:configure-flags flags ''())
- `(cons "--enable-64-bit-bfd" ,flags)))))))
+ binutils
+ (name "binutils-i386")
+ (arguments
+ (substitute-keyword-arguments (package-arguments binutils)
+ ((#:configure-flags flags ''())
+ `(cons "--enable-64-bit-bfd" ,flags)))))))
`(("ld-wrapper" ,(make-ld-wrapper "ld-wrapper-i386"
#:binutils binutils))
("binutils" ,binutils)))
@@ -342,21 +344,21 @@ menu to select one of the installed operating systems.")
`(,@(substitute-keyword-arguments (package-arguments grub-efi)
((#:configure-flags flags ''())
`(cons*
- ,@(cond ((target-x86?) '("--target=i386"))
- ((target-aarch64?)
- (list "--target=arm"
- (string-append "TARGET_CC="
- (cc-for-target "arm-linux-gnueabihf"))))
- ((target-arm?) '("--target=arm"))
- (else '()))
- ,flags)))))
+ ,@(cond ((target-x86?) '("--target=i386"))
+ ((target-aarch64?)
+ (list "--target=arm"
+ (string-append "TARGET_CC="
+ (cc-for-target "arm-linux-gnueabihf"))))
+ ((target-arm?) '("--target=arm"))
+ (else '()))
+ ,flags)))))
(native-inputs
(if (target-aarch64?)
- (modify-inputs (package-native-inputs grub-efi)
- (prepend
- (cross-gcc "arm-linux-gnueabihf")
- (cross-binutils "arm-linux-gnueabihf")))
- (package-native-inputs grub-efi)))))
+ (modify-inputs (package-native-inputs grub-efi)
+ (prepend
+ (cross-gcc "arm-linux-gnueabihf")
+ (cross-binutils "arm-linux-gnueabihf")))
+ (package-native-inputs grub-efi)))))
;; Because grub searches hardcoded paths it's easiest to just build grub
;; again to make it find both grub-pc and grub-efi. There is a command
@@ -392,6 +394,92 @@ menu to select one of the installed operating systems.")
(scandir input-dir))
#t)))))))))
+(define-public (make-grub-efi-netboot name subdir)
+ "Make a grub-efi-netboot package named NAME, which will be able to boot over
+network via TFTP by accessing its files in the SUBDIR of a TFTP root directory.
+This package is also able to boot from local storage devices.
+
+A bootloader-installer basically needs to copy the package content into the
+bootloader-target directory, which will usually be the TFTP root, as
+'grub-mknetdir' will be invoked already during the package creation.
+
+Alternatively the bootloader-target directory can be a mounted EFI System
+Partition (ESP), or a similar partition with a FAT file system, for booting
+from local storage devices.
+
+The name of the GRUB EFI binary will conform to the UEFI specification for
+removable media. Depending on the system it will be e.g. bootx64.efi or
+bootaa64.efi below SUBDIR.
+
+The SUBDIR argument needs to be set to \"efi/boot\" to create a package which
+conforms to the UEFI specification for removable media.
+
+The SUBDIR argument defaults to \"efi/Guix\", as it is also the case for
+'grub-efi-bootloader'."
+ (package
+ (name name)
+ (version (package-version grub-efi))
+ ;; Source is not needed, but it cannot be omitted.
+ (source #f)
+ (build-system trivial-build-system)
+ (arguments
+ (let* ((system (string-split (nix-system->gnu-triplet
+ (or (%current-target-system)
+ (%current-system)))
+ #\-))
+ (arch (first system))
+ (boot-efi
+ (match system
+ ;; These are the supportend systems and the names defined by
+ ;; the UEFI standard for removable media.
+ (("i686" _ ...) "/bootia32.efi")
+ (("x86_64" _ ...) "/bootx64.efi")
+ (("arm" _ ...) "/bootarm.efi")
+ (("aarch64" _ ...) "/bootaa64.efi")
+ (("riscv" _ ...) "/bootriscv32.efi")
+ (("riscv64" _ ...) "/bootriscv64.efi")
+ ;; Other systems are not supported, although defined.
+ ;; (("riscv128" _ ...) "/bootriscv128.efi")
+ ;; (("ia64" _ ...) "/bootia64.efi")
+ ((_ ...) #f)))
+ (core-efi (string-append
+ ;; This is the arch dependent file name of GRUB, e.g.
+ ;; i368-efi/core.efi or arm64-efi/core.efi.
+ (match arch
+ ("i686" "i386")
+ ("aarch64" "arm64")
+ ("riscv" "riscv32")
+ (_ arch))
+ "-efi/core.efi")))
+ (list
+ #:modules '((guix build utils))
+ #:builder
+ #~(begin
+ (use-modules (guix build utils))
+ (let* ((bootloader #$(this-package-input "grub-efi"))
+ (net-dir #$output)
+ (sub-dir (string-append net-dir "/" #$subdir "/"))
+ (boot-efi (string-append sub-dir #$boot-efi))
+ (core-efi (string-append sub-dir #$core-efi)))
+ ;; Install GRUB, which refers to the grub.cfg, with support for
+ ;; encrypted partitions,
+ (setenv "GRUB_ENABLE_CRYPTODISK" "y")
+ (invoke/quiet (string-append bootloader "/bin/grub-mknetdir")
+ (string-append "--net-directory=" net-dir)
+ (string-append "--subdir=" #$subdir)
+ ;; These modules must be pre-loaded to allow booting
+ ;; from an ESP or a similar partition with a FAT
+ ;; file system.
+ (string-append "--modules=part_msdos part_gpt fat"))
+ ;; Move GRUB's core.efi to the removable media name.
+ (false-if-exception (delete-file boot-efi))
+ (rename-file core-efi boot-efi))))))
+ (inputs (list grub-efi))
+ (synopsis (package-synopsis grub-efi))
+ (description (package-description grub-efi))
+ (home-page (package-home-page grub-efi))
+ (license (package-license grub-efi))))
+
(define-public syslinux
(let ((commit "bb41e935cc83c6242de24d2271e067d76af3585c"))
(package
@@ -481,14 +569,14 @@ menu to select one of the installed operating systems.")
(build-system gnu-build-system)
(native-inputs
(append
- (list bison
- flex
- libyaml
- pkg-config
- swig)
- (if (member (%current-system) (package-supported-systems valgrind))
- (list valgrind)
- '())))
+ (list bison
+ flex
+ libyaml
+ pkg-config
+ swig)
+ (if (member (%current-system) (package-supported-systems valgrind))
+ (list valgrind)
+ '())))
(inputs
(list python))
(arguments
@@ -545,7 +633,7 @@ tree binary files. These are board description files used by Linux and BSD.")
(name "u-boot")
(version "2022.04")
(source (origin
- (patches
+ (patches
(list %u-boot-rockchip-inno-usb-patch
%u-boot-allow-disabling-openssl-patch
%u-boot-sifive-prevent-relocating-initrd-fdt
@@ -594,12 +682,12 @@ also initializes the boards (RAM etc).")
(add-after 'unpack 'patch
(lambda* (#:key inputs #:allow-other-keys)
(substitute* "Makefile"
- (("/bin/pwd") (which "pwd"))
- (("/bin/false") (which "false")))
+ (("/bin/pwd") (which "pwd"))
+ (("/bin/false") (which "false")))
(substitute* "tools/dtoc/fdt_util.py"
- (("'cc'") "'gcc'"))
+ (("'cc'") "'gcc'"))
(substitute* "tools/patman/test_util.py"
- ;; python3-coverage is simply called coverage in guix.
+ ;; python3-coverage is simply called coverage in guix.
(("python3-coverage") "coverage")
;; Don't require 100% coverage since it's brittle and can
@@ -607,40 +695,40 @@ also initializes the boards (RAM etc).")
(("raise ValueError\\('Test coverage failure'\\)")
"print('Continuing anyway since Guix does not care :O')"))
(substitute* "test/run"
- ;; Make it easier to find test failures.
- (("#!/bin/bash") "#!/bin/bash -x")
- ;; This test would require git.
- (("\\./tools/patman/patman") (which "true"))
- ;; FIXME: test fails, needs further investiation
- (("run_test \"binman\"") "# run_test \"binman\"")
- ;; FIXME: test_spl fails, needs further investiation
- (("test_ofplatdata or test_handoff or test_spl")
+ ;; Make it easier to find test failures.
+ (("#!/bin/bash") "#!/bin/bash -x")
+ ;; This test would require git.
+ (("\\./tools/patman/patman") (which "true"))
+ ;; FIXME: test fails, needs further investiation
+ (("run_test \"binman\"") "# run_test \"binman\"")
+ ;; FIXME: test_spl fails, needs further investiation
+ (("test_ofplatdata or test_handoff or test_spl")
"test_ofplatdata or test_handoff")
- ;; FIXME: code coverage not working
- (("run_test \"binman code coverage\"")
- "# run_test \"binman code coverage\"")
- ;; This test would require internet access.
- (("\\./tools/buildman/buildman") (which "true")))
+ ;; FIXME: code coverage not working
+ (("run_test \"binman code coverage\"")
+ "# run_test \"binman code coverage\"")
+ ;; This test would require internet access.
+ (("\\./tools/buildman/buildman") (which "true")))
(substitute* "test/py/tests/test_sandbox_exit.py"
- (("def test_ctrl_c")
- "@pytest.mark.skip(reason='Guix has problems with SIGINT')
+ (("def test_ctrl_c")
+ "@pytest.mark.skip(reason='Guix has problems with SIGINT')
def test_ctrl_c"))
;; Test against the tools being installed rather than tools built
;; for "sandbox" target.
(substitute* "test/image/test-imagetools.sh"
(("BASEDIR=sandbox") "BASEDIR=."))
(for-each (lambda (file)
- (substitute* file
- ;; Disable features that require OpenSSL due
- ;; to GPL/Openssl license incompatibilities.
- ;; See https://bugs.gnu.org/34717 for
- ;; details.
- (("CONFIG_FIT_SIGNATURE=y")
- "CONFIG_FIT_SIGNATURE=n\nCONFIG_UT_LIB_ASN1=n\nCONFIG_TOOLS_LIBCRYPTO=n")
- ;; This test requires a sound system, which is un-used
- ;; in u-boot-tools.
- (("CONFIG_SOUND=y") "CONFIG_SOUND=n")))
- (find-files "configs" "sandbox_.*defconfig$|tools-only_defconfig"))
+ (substitute* file
+ ;; Disable features that require OpenSSL due
+ ;; to GPL/Openssl license incompatibilities.
+ ;; See https://bugs.gnu.org/34717 for
+ ;; details.
+ (("CONFIG_FIT_SIGNATURE=y")
+ "CONFIG_FIT_SIGNATURE=n\nCONFIG_UT_LIB_ASN1=n\nCONFIG_TOOLS_LIBCRYPTO=n")
+ ;; This test requires a sound system, which is un-used
+ ;; in u-boot-tools.
+ (("CONFIG_SOUND=y") "CONFIG_SOUND=n")))
+ (find-files "configs" "sandbox_.*defconfig$|tools-only_defconfig"))
#t))
(replace 'configure
(lambda* (#:key make-flags #:allow-other-keys)
@@ -668,28 +756,37 @@ def test_ctrl_c"))
"tools/env/fw_printenv"
"tools/sunxi-spl-image-builder"))
#t)))
- (delete 'check)
- (add-after 'install 'check
- (lambda* (#:key make-flags test-target #:allow-other-keys)
- (invoke "test/image/test-imagetools.sh")))
- ;; Only run full test suite on x86_64 systems, as many tests
- ;; assume x86_64.
- ,@(if (string-match "^x86_64-linux"
- (or (%current-target-system)
- (%current-system)))
- '((add-after 'check 'check-x86
- (lambda* (#:key make-flags test-target #:allow-other-keys)
- (apply invoke "make" "mrproper" make-flags)
- (setenv "SDL_VIDEODRIVER" "dummy")
- (setenv "PAGER" "cat")
- (apply invoke "make" test-target make-flags))))
- '()))))
- (description "U-Boot is a bootloader used mostly for ARM boards. It
-also initializes the boards (RAM etc). This package provides its
-board-independent tools.")))
-
-(define-public (make-u-boot-package board triplet)
- "Returns a u-boot package for BOARD cross-compiled for TRIPLET."
+ (delete 'check)
+ (add-after 'install 'check
+ (lambda* (#:key make-flags test-target #:allow-other-keys)
+ (invoke "test/image/test-imagetools.sh")))
+ ;; Only run full test suite on x86_64 systems, as many tests
+ ;; assume x86_64.
+ ,@(if (string-match "^x86_64-linux"
+ (or (%current-target-system)
+ (%current-system)))
+ '((add-after 'check 'check-x86
+ (lambda* (#:key make-flags test-target #:allow-other-keys)
+ (apply invoke "make" "mrproper" make-flags)
+ (setenv "SDL_VIDEODRIVER" "dummy")
+ (setenv "PAGER" "cat")
+ (apply invoke "make" test-target make-flags))))
+ '()))))
+ (description (string-append
+ (package-description u-boot)
+ " This package provides board-independent tools "
+ "of U-Boot."))))
+
+(define*-public (make-u-boot-package board triplet
+ #:key
+ defconfig
+ configs
+ name-suffix
+ append-description)
+ "Return a U-Boot package for BOARD cross-compiled for TRIPLET with the
+optional DEFCONFIG file and optional configuration changes from CONFIGS.
+NAME-SUFFIX is appended to the package name, while APPEND-DESCRIPTION is
+appended to the package description."
(let ((same-arch? (lambda ()
(string=? (%current-system)
(gnu-triplet->nix-system triplet)))))
@@ -697,33 +794,51 @@ board-independent tools.")))
(inherit u-boot)
(name (string-append "u-boot-"
(string-replace-substring (string-downcase board)
- "_" "-")))
+ "_" "-")
+ (or name-suffix "")))
+ (description (if append-description
+ (string-append (package-description u-boot)
+ "\n\n" append-description)
+ (package-description u-boot)))
(native-inputs
`(,@(if (not (same-arch?))
- `(("cross-gcc" ,(cross-gcc triplet))
- ("cross-binutils" ,(cross-binutils triplet)))
- `())
+ `(("cross-gcc" ,(cross-gcc triplet))
+ ("cross-binutils" ,(cross-binutils triplet)))
+ `())
,@(package-native-inputs u-boot)))
(arguments
`(#:modules ((ice-9 ftw)
(srfi srfi-1)
- (guix build utils)
- (guix build gnu-build-system))
+ (guix build gnu-build-system)
+ (guix build kconfig)
+ (guix build utils))
+ #:imported-modules (,@%gnu-build-system-modules
+ (guix build kconfig))
#:test-target "test"
#:make-flags
(list "HOSTCC=gcc"
,@(if (not (same-arch?))
- `((string-append "CROSS_COMPILE=" ,triplet "-"))
- '()))
+ `((string-append "CROSS_COMPILE=" ,triplet "-"))
+ '()))
#:phases
(modify-phases %standard-phases
(replace 'configure
(lambda* (#:key outputs make-flags #:allow-other-keys)
- (let ((config-name (string-append ,board "_defconfig")))
- (if (file-exists? (string-append "configs/" config-name))
- (apply invoke "make" `(,@make-flags ,config-name))
+ (let* ((config-name (string-append ,board "_defconfig"))
+ (config-file (string-append "configs/" config-name))
+ (defconfig ,defconfig)
+ (configs ',configs))
+ (when defconfig
+ ;; Replace the board-specific defconfig with the given one.
+ (copy-file defconfig config-file))
+ (if (file-exists? config-file)
+ (begin
+ (when configs
+ (modify-defconfig config-file configs))
+ (apply invoke "make" `(,@make-flags ,config-name))
+ (verify-config ".config" config-file))
(begin
- (display "Invalid board name. Valid board names are:"
+ (display "invalid board name; valid board names are:"
(current-error-port))
(let ((suffix-len (string-length "_defconfig"))
(entries (scandir "configs")))
@@ -734,7 +849,7 @@ board-independent tools.")))
(string-drop-right file-name
suffix-len))))
(sort entries string-ci<)))
- (error "Invalid boardname ~s." ,board))))))
+ (error "invalid boardname ~s" ,board))))))
(add-after 'configure 'disable-tools-libcrypto
;; Disable libcrypto due to GPL and OpenSSL license
;; incompatibilities
@@ -775,52 +890,37 @@ board-independent tools.")))
(make-u-boot-package "malta" "mips64el-linux-gnuabi64"))
(define-public u-boot-am335x-boneblack
- (let ((base (make-u-boot-package "am335x_evm" "arm-linux-gnueabihf")))
- (package
- (inherit base)
- (name "u-boot-am335x-boneblack")
- (description "U-Boot is a bootloader used mostly for ARM boards. It
-also initializes the boards (RAM etc).
-
-This U-Boot is built for the BeagleBone Black, which was removed upstream,
-adjusted from the am335x_evm build with several device trees removed so that
-it fits within common partitioning schemes.")
- (arguments
- (substitute-keyword-arguments (package-arguments base)
- ((#:phases phases)
- `(modify-phases ,phases
- (add-after 'unpack 'patch-defconfig
- ;; Patch out other devicetrees to build image small enough to
- ;; fit within typical partitioning schemes where the first
- ;; partition begins at sector 2048.
- (lambda _
- (substitute* "configs/am335x_evm_defconfig"
- (("CONFIG_OF_LIST=.*$") "CONFIG_OF_LIST=\"am335x-evm am335x-boneblack\"\n"))
- #t)))))))))
+ (make-u-boot-package
+ "am335x_evm" "arm-linux-gnueabihf"
+ ;; Patch out other device trees to build an image small enough to fit
+ ;; within typical partitioning schemes where the first partition begins at
+ ;; sector 2048.
+ #:configs '("CONFIG_OF_LIST=\"am335x-evm am335x-boneblack\"")
+ #:name-suffix "-boneblack"
+ #:append-description "This U-Boot is built for the BeagleBone Black, which
+was removed upstream, adjusted from the am335x_evm build with several device
+trees removed so that it fits within common partitioning schemes."))
(define-public u-boot-am335x-evm
(make-u-boot-package "am335x_evm" "arm-linux-gnueabihf"))
-(define-public (make-u-boot-sunxi64-package board triplet)
- (let ((base (make-u-boot-package board triplet)))
+(define*-public (make-u-boot-sunxi64-package board triplet
+ #:key defconfig configs)
+ (let ((base (make-u-boot-package
+ board triplet #:defconfig defconfig #:configs configs)))
(package
(inherit base)
(arguments
- (substitute-keyword-arguments (package-arguments base)
- ((#:phases phases)
- `(modify-phases ,phases
- (add-after 'unpack 'set-environment
- (lambda* (#:key native-inputs inputs #:allow-other-keys)
- (let ((bl31
- (string-append
- (assoc-ref (or native-inputs inputs) "firmware")
- "/bl31.bin")))
- (setenv "BL31" bl31)
- ;; This is necessary when we're using the bundled dtc.
- ;(setenv "PATH" (string-append (getenv "PATH") ":"
- ; "scripts/dtc"))
- )
- #t))))))
+ (substitute-keyword-arguments (package-arguments base)
+ ((#:phases phases)
+ `(modify-phases ,phases
+ (add-after 'unpack 'set-environment
+ (lambda* (#:key native-inputs inputs #:allow-other-keys)
+ (let ((bl31
+ (string-append
+ (assoc-ref (or native-inputs inputs) "firmware")
+ "/bl31.bin")))
+ (setenv "BL31" bl31))))))))
(native-inputs
`(("firmware" ,arm-trusted-firmware-sun50i-a64)
,@(package-native-inputs base))))))
@@ -832,20 +932,11 @@ it fits within common partitioning schemes.")
(make-u-boot-sunxi64-package "pine64-lts" "aarch64-linux-gnu"))
(define-public u-boot-pinebook
- (let ((base (make-u-boot-sunxi64-package "pinebook" "aarch64-linux-gnu")))
- (package
- (inherit base)
- (arguments
- (substitute-keyword-arguments (package-arguments base)
- ((#:phases phases)
- `(modify-phases ,phases
- (add-after 'unpack 'patch-pinebook-config
- ;; Fix regression with LCD video output introduced in 2020.01
- ;; https://patchwork.ozlabs.org/patch/1225130/
- (lambda _
- (substitute* "configs/pinebook_defconfig"
- (("CONFIG_VIDEO_BRIDGE_ANALOGIX_ANX6345=y") "CONFIG_VIDEO_BRIDGE_ANALOGIX_ANX6345=y\nCONFIG_VIDEO_BPP32=y"))
- #t)))))))))
+ (make-u-boot-sunxi64-package
+ "pinebook" "aarch64-linux-gnu"
+ ;; Fix regression with LCD video output introduced in 2020.01
+ ;; https://patchwork.ozlabs.org/patch/1225130/
+ #:configs '("CONFIG_VIDEO_BPP32=y")))
(define-public u-boot-bananapi-m2-ultra
(make-u-boot-package "Bananapi_M2_Ultra" "arm-linux-gnueabihf"))
@@ -861,7 +952,14 @@ it fits within common partitioning schemes.")
(define-public u-boot-nintendo-nes-classic-edition
(let ((base (make-u-boot-package "Nintendo_NES_Classic_Edition"
- "arm-linux-gnueabihf")))
+ "arm-linux-gnueabihf"
+ #:append-description "This version is for
+the Nintendo NES Classic Edition. It is assumed that you have added a serial
+port to pins PB0 and PB1 as described on
+@url{https://linux-sunxi.org/Nintendo_NES_Classic_Edition}.
+
+In order to use FEL mode on the device, hold the Reset button on the
+device while it's being turned on (and a while longer).")))
(package
(inherit base)
;; Starting with 2019.01, FEL doesn't work anymore on A33.
@@ -875,16 +973,7 @@ it fits within common partitioning schemes.")
(base32
"0znkwljfwwn4y7j20pzz4ilqw8znphrfxns0x1lwdzh3xbr96z3k"))
(patches (search-patches
- "u-boot-nintendo-nes-serial.patch"))))
- (description "U-Boot is a bootloader used mostly for ARM boards. It
-also initializes the boards (RAM etc).
-
-This version is for the Nintendo NES Classic Edition. It is assumed that
-you have added a serial port to pins PB0 and PB1 as described on
-@url{https://linux-sunxi.org/Nintendo_NES_Classic_Edition}.
-
-In order to use FEL mode on the device, hold the Reset button on the
-device while it's being turned on (and a while longer).")
+ "u-boot-nintendo-nes-serial.patch"))))
(native-inputs
`(("python" ,python-2)
,@(package-native-inputs base))))))
@@ -896,25 +985,14 @@ device while it's being turned on (and a while longer).")
(make-u-boot-package "mx6cuboxi" "arm-linux-gnueabihf"))
(define-public u-boot-novena
- (let ((base (make-u-boot-package "novena" "arm-linux-gnueabihf")))
- (package
- (inherit base)
- (description "U-Boot is a bootloader used mostly for ARM boards. It
-also initializes the boards (RAM etc).
-
-This U-Boot is built for Novena. Be advised that this version, contrary
-to Novena upstream, does not load u-boot.img from the first partition.")
- (arguments
- (substitute-keyword-arguments (package-arguments base)
- ((#:phases phases)
- `(modify-phases ,phases
- (add-after 'unpack 'patch-novena-defconfig
- ;; Patch configuration to disable loading u-boot.img from FAT partition,
- ;; allowing it to be installed at a device offset.
- (lambda _
- (substitute* "configs/novena_defconfig"
- (("CONFIG_SPL_FS_FAT=y") "# CONFIG_SPL_FS_FAT is not set"))
- #t)))))))))
+ (make-u-boot-package
+ "novena" "arm-linux-gnueabihf"
+ ;; Patch configuration to disable loading u-boot.img from FAT partition,
+ ;; allowing it to be installed at a device offset.
+ #:configs '("# CONFIG_SPL_FS_FAT is not set")
+ #:append-description "This U-Boot is built for Novena. Be advised that this
+version, contrary to Novena upstream, does not load u-boot.img from the first
+partition."))
(define-public u-boot-cubieboard
(make-u-boot-package "Cubieboard" "arm-linux-gnueabihf"))
@@ -927,16 +1005,16 @@ to Novena upstream, does not load u-boot.img from the first partition.")
(package
(inherit base)
(arguments
- (substitute-keyword-arguments (package-arguments base)
- ((#:phases phases)
- `(modify-phases ,phases
- (add-after 'unpack 'set-environment
- (lambda* (#:key inputs #:allow-other-keys)
- (setenv "BL31"
- (search-input-file inputs "/bl31.elf"))))
- ;; Phases do not succeed on the bl31 ELF.
- (delete 'strip)
- (delete 'validate-runpath)))))
+ (substitute-keyword-arguments (package-arguments base)
+ ((#:phases phases)
+ `(modify-phases ,phases
+ (add-after 'unpack 'set-environment
+ (lambda* (#:key inputs #:allow-other-keys)
+ (setenv "BL31"
+ (search-input-file inputs "/bl31.elf"))))
+ ;; Phases do not succeed on the bl31 ELF.
+ (delete 'strip)
+ (delete 'validate-runpath)))))
(native-inputs
`(("firmware" ,arm-trusted-firmware-rk3399)
,@(package-native-inputs base))))))
@@ -988,65 +1066,62 @@ to Novena upstream, does not load u-boot.img from the first partition.")
(package
(inherit base)
(arguments
- (substitute-keyword-arguments (package-arguments base)
- ((#:phases phases)
- `(modify-phases ,phases
- (add-after 'unpack 'set-environment
- (lambda* (#:key inputs #:allow-other-keys)
- (setenv "BL31" (search-input-file inputs "/bl31.elf"))))
- ;; Phases do not succeed on the bl31 ELF.
- (delete 'strip)
- (delete 'validate-runpath)))))
+ (substitute-keyword-arguments (package-arguments base)
+ ((#:phases phases)
+ `(modify-phases ,phases
+ (add-after 'unpack 'set-environment
+ (lambda* (#:key inputs #:allow-other-keys)
+ (setenv "BL31" (search-input-file inputs "/bl31.elf"))))
+ ;; Phases do not succeed on the bl31 ELF.
+ (delete 'strip)
+ (delete 'validate-runpath)))))
(native-inputs
`(("firmware" ,arm-trusted-firmware-rk3399)
,@(package-native-inputs base))))))
(define-public u-boot-rockpro64-rk3399
- (let ((base (make-u-boot-package "rockpro64-rk3399" "aarch64-linux-gnu")))
+ (let ((base (make-u-boot-package "rockpro64-rk3399" "aarch64-linux-gnu"
+ #:configs '("CONFIG_USB=y"
+ "CONFIG_AHCI=y"
+ "CONFIG_AHCI_PCI=y"
+ "CONFIG_SATA=y"
+ "CONFIG_SATA_SIL=y"
+ "CONFIG_SCSI=y"
+ "CONFIG_SCSI_AHCI=y"
+ "CONFIG_DM_SCSI=y"))))
(package
(inherit base)
(arguments
- (substitute-keyword-arguments (package-arguments base)
- ((#:phases phases)
- `(modify-phases ,phases
- (add-after 'unpack 'set-environment
- (lambda* (#:key inputs #:allow-other-keys)
- (setenv "BL31"
- (search-input-file inputs "/bl31.elf"))))
- (add-after 'unpack 'patch-config
- (lambda _
- (substitute* "configs/rockpro64-rk3399_defconfig"
- (("CONFIG_USB=y") "\
-CONFIG_USB=y
-CONFIG_AHCI=y
-CONFIG_AHCI_PCI=y
-CONFIG_SATA=y
-CONFIG_SATA_SIL=y
-CONFIG_SCSI=y
-CONFIG_SCSI_AHCI=y
-CONFIG_DM_SCSI=y
-"))
- (substitute* "include/config_distro_bootcmd.h"
- (("\"scsi_need_init=false")
- "\"setenv scsi_need_init false")
- (("#define BOOTENV_SET_SCSI_NEED_INIT \"scsi_need_init=;")
- "#define BOOTENV_SET_SCSI_NEED_INIT \"setenv scsi_need_init;"))
- (substitute* "include/configs/rockchip-common.h"
- (("#define BOOT_TARGET_DEVICES\\(func\\)")
- "
+ (substitute-keyword-arguments (package-arguments base)
+ ((#:phases phases)
+ `(modify-phases ,phases
+ (add-after 'unpack 'set-environment
+ (lambda* (#:key inputs #:allow-other-keys)
+ (setenv "BL31"
+ (search-input-file inputs "/bl31.elf"))))
+ (add-after 'unpack 'patch-header
+ (lambda _
+ (substitute* "include/config_distro_bootcmd.h"
+ (("\"scsi_need_init=false")
+ "\"setenv scsi_need_init false")
+ (("#define BOOTENV_SET_SCSI_NEED_INIT \"scsi_need_init=;")
+ "#define BOOTENV_SET_SCSI_NEED_INIT \"setenv scsi_need_init;"))
+ (substitute* "include/configs/rockchip-common.h"
+ (("#define BOOT_TARGET_DEVICES\\(func\\)")
+ "
#if CONFIG_IS_ENABLED(CMD_SCSI)
#define BOOT_TARGET_SCSI(func) func(SCSI, scsi, 0)
#else
#define BOOT_TARGET_SCSI(func)
#endif
#define BOOT_TARGET_DEVICES(func)")
- (("BOOT_TARGET_NVME\\(func\\) \\\\")
- "\
+ (("BOOT_TARGET_NVME\\(func\\) \\\\")
+ "\
BOOT_TARGET_NVME(func) \\
BOOT_TARGET_SCSI(func) \\"))))
- ;; Phases do not succeed on the bl31 ELF.
- (delete 'strip)
- (delete 'validate-runpath)))))
+ ;; Phases do not succeed on the bl31 ELF.
+ (delete 'strip)
+ (delete 'validate-runpath)))))
(native-inputs
`(("firmware" ,arm-trusted-firmware-rk3399)
,@(package-native-inputs base))))))
@@ -1056,20 +1131,132 @@ BOOT_TARGET_NVME(func) \\
(package
(inherit base)
(arguments
- (substitute-keyword-arguments (package-arguments base)
- ((#:phases phases)
- `(modify-phases ,phases
- (add-after 'unpack 'set-environment
- (lambda* (#:key inputs #:allow-other-keys)
- (setenv "BL31"
- (search-input-file inputs "/bl31.elf"))))
- ;; Phases do not succeed on the bl31 ELF.
- (delete 'strip)
- (delete 'validate-runpath)))))
+ (substitute-keyword-arguments (package-arguments base)
+ ((#:phases phases)
+ `(modify-phases ,phases
+ (add-after 'unpack 'set-environment
+ (lambda* (#:key inputs #:allow-other-keys)
+ (setenv "BL31"
+ (search-input-file inputs "/bl31.elf"))))
+ ;; Phases do not succeed on the bl31 ELF.
+ (delete 'strip)
+ (delete 'validate-runpath)))))
(native-inputs
`(("firmware" ,arm-trusted-firmware-rk3399)
,@(package-native-inputs base))))))
+(define*-public (make-u-boot-bin-package u-boot-package
+ #:key
+ (u-boot-bin "u-boot.bin"))
+ "Return a package with a single U-BOOT-BIN file from the U-BOOT-PACKAGE.
+The package name will be that of the U-BOOT package suffixed with \"-bin\"."
+ (package
+ (name (string-append (package-name u-boot-package) "-bin"))
+ (version (package-version u-boot-package))
+ (source #f)
+ (build-system trivial-build-system)
+ (arguments
+ (list
+ #:builder
+ (with-imported-modules '((guix build utils))
+ #~(begin
+ (use-modules (guix build utils))
+ (mkdir #$output)
+ (symlink (search-input-file %build-inputs
+ (string-append "libexec/" #$u-boot-bin))
+ (string-append #$output "/" #$u-boot-bin))))))
+ (inputs (list u-boot-package))
+ (home-page (package-home-page u-boot-package))
+ (synopsis (package-synopsis u-boot-package))
+ (description (string-append
+ (package-description u-boot-package)
+ "\n\n"
+ (format #f
+ "This package only contains the file ~a."
+ u-boot-bin)))
+ (license (package-license u-boot-package))))
+
+(define-public %u-boot-rpi-efi-configs
+ '("CONFIG_OF_EMBED"
+ "CONFIG_OF_BOARD=y"))
+
+(define %u-boot-rpi-description-32-bit
+ "This is a 32-bit build of U-Boot.")
+
+(define %u-boot-rpi-description-64-bit
+ "This is a common 64-bit build of U-Boot for all 64-bit capable Raspberry Pi
+variants.")
+
+(define %u-boot-rpi-efi-description
+ "It allows network booting and uses the device-tree from the firmware,
+allowing the usage of overlays. It can act as an EFI firmware for the
+grub-efi-netboot-removable-bootloader.")
+
+(define %u-boot-rpi-efi-description-32-bit
+ (string-append %u-boot-rpi-efi-description " "
+ %u-boot-rpi-description-32-bit))
+
+(define-public u-boot-rpi-2
+ (make-u-boot-package "rpi_2" "arm-linux-gnueabihf"
+ #:append-description %u-boot-rpi-description-32-bit))
+
+(define-public u-boot-rpi-3-32b
+ (make-u-boot-package "rpi_3_32b" "arm-linux-gnueabihf"
+ #:append-description %u-boot-rpi-description-32-bit))
+
+(define-public u-boot-rpi-4-32b
+ (make-u-boot-package "rpi_4_32b" "arm-linux-gnueabihf"
+ #:append-description %u-boot-rpi-description-32-bit))
+
+(define-public u-boot-rpi-arm64
+ (make-u-boot-package "rpi_arm64" "aarch64-linux-gnu"
+ #:append-description %u-boot-rpi-description-64-bit))
+
+(define-public u-boot-rpi-2-efi
+ (make-u-boot-package "rpi_2" "arm-linux-gnueabihf"
+ #:name-suffix "-efi"
+ #:configs %u-boot-rpi-efi-configs
+ #:append-description %u-boot-rpi-efi-description-32-bit))
+
+(define-public u-boot-rpi-3-32b-efi
+ (make-u-boot-package "rpi_3_32b" "arm-linux-gnueabihf"
+ #:name-suffix "-efi"
+ #:configs %u-boot-rpi-efi-configs
+ #:append-description %u-boot-rpi-efi-description-32-bit))
+
+(define-public u-boot-rpi-4-32b-efi
+ (make-u-boot-package "rpi_4_32b" "arm-linux-gnueabihf"
+ #:name-suffix "-efi"
+ #:configs %u-boot-rpi-efi-configs
+ #:append-description %u-boot-rpi-efi-description-32-bit))
+
+(define-public u-boot-rpi-arm64-efi
+ (make-u-boot-package "rpi_arm64""aarch64-linux-gnu"
+ #:name-suffix "-efi"
+ #:configs %u-boot-rpi-efi-configs
+ #:append-description (string-append
+ %u-boot-rpi-efi-description " "
+ %u-boot-rpi-description-64-bit)))
+
+(define-public u-boot-rpi-2-bin (make-u-boot-bin-package u-boot-rpi-2))
+
+(define-public u-boot-rpi-3_32b-bin (make-u-boot-bin-package u-boot-rpi-3-32b))
+
+(define-public u-boot-rpi-4_32b-bin (make-u-boot-bin-package u-boot-rpi-4-32b))
+
+(define-public u-boot-rpi-arm64-bin (make-u-boot-bin-package u-boot-rpi-arm64))
+
+(define-public u-boot-rpi-2-efi-bin (make-u-boot-bin-package u-boot-rpi-2-efi))
+
+(define-public u-boot-rpi-3-32b-efi-bin
+ (make-u-boot-bin-package u-boot-rpi-3-32b-efi))
+
+(define-public u-boot-rpi-4-32b-efi-bin
+ (make-u-boot-bin-package u-boot-rpi-4-32b-efi))
+
+(define-public u-boot-rpi-arm64-efi-bin
+ (make-u-boot-bin-package u-boot-rpi-arm64-efi))
+
(define-public vboot-utils
(package
(name "vboot-utils")
diff --git a/gnu/packages/build-tools.scm b/gnu/packages/build-tools.scm
index 8627f699a1..6c1350c44f 100644
--- a/gnu/packages/build-tools.scm
+++ b/gnu/packages/build-tools.scm
@@ -204,8 +204,8 @@ programs and other files depend.")
(license license:bsd-3)))
(define-public gn
- (let ((commit "e327ffdc503815916db2543ec000226a8df45163")
- (revision "1819")) ;as returned by `git describe`, used below
+ (let ((commit "1c4151ff5c1d6fbf7fa800b8d4bb34d3abc03a41")
+ (revision "2072")) ;as returned by `git describe`, used below
(package
(name "gn")
(version (git-version "0.0" revision commit))
@@ -215,49 +215,56 @@ programs and other files depend.")
(uri (git-reference (url home-page) (commit commit)))
(sha256
(base32
- "0kvlfj3www84zp1vmxh76x8fdjm9hyk8lkh2vdsidafpmm75fphr"))
+ "02621c9nqpr4pwcapy31x36l5kbyd0vdgd0wdaxj5p8hrxk67d6b"))
(file-name (git-file-name name version))))
(build-system gnu-build-system)
(arguments
- `(#:phases (modify-phases %standard-phases
- (add-before 'configure 'set-build-environment
- (lambda _
- (setenv "CC" "gcc") (setenv "CXX" "g++")
- (setenv "AR" "ar")))
- (replace 'configure
- (lambda _
- (invoke "python" "build/gen.py"
- "--no-last-commit-position")))
- (add-after 'configure 'create-last-commit-position
- (lambda _
- ;; Create "last_commit_position.h" to avoid a dependency
- ;; on 'git' (and the checkout..).
- (call-with-output-file "out/last_commit_position.h"
- (lambda (port)
- (format port
- (string-append
- "#define LAST_COMMIT_POSITION_NUM ~a\n"
- "#define LAST_COMMIT_POSITION \"~a (~a)\"\n")
- ,revision ,revision ,(string-take commit 8))))))
- (replace 'build
- (lambda _
- (invoke "ninja" "-C" "out" "gn"
- "-j" (number->string (parallel-job-count)))))
- (replace 'check
- (lambda* (#:key tests? #:allow-other-keys)
- (if tests?
- (begin
- (invoke "ninja" "-C" "out" "gn_unittests"
- "-j" (number->string (parallel-job-count)))
- (invoke "./out/gn_unittests"))
- (format #t "test suite not run~%"))))
- (replace 'install
- (lambda* (#:key outputs #:allow-other-keys)
- (let ((out (assoc-ref outputs "out")))
- (install-file "out/gn" (string-append out "/bin"))))))))
+ (list #:phases
+ #~(modify-phases %standard-phases
+ (add-before 'configure 'set-build-environment
+ (lambda _
+ (setenv "CC" "gcc")
+ (setenv "CXX" "g++")
+ (setenv "AR" "ar")))
+ (replace 'configure
+ (lambda _
+ (invoke "python" "build/gen.py"
+ "--no-last-commit-position")))
+ (add-after 'configure 'create-last-commit-position
+ (lambda _
+ ;; Mimic GenerateLastCommitPosition from gen.py.
+ (call-with-output-file "out/last_commit_position.h"
+ (lambda (port)
+ (format port
+ "// Generated by Guix.
+
+#ifndef OUT_LAST_COMMIT_POSITION_H_
+#define OUT_LAST_COMMIT_POSITION_H_
+
+#define LAST_COMMIT_POSITION_NUM ~a
+#define LAST_COMMIT_POSITION \"~a (~a)\"
+
+#endif // OUT_LAST_COMMIT_POSITION_H_
+"
+ #$revision #$revision
+ #$(string-take commit 12))))))
+ (replace 'build
+ (lambda _
+ (invoke "ninja" "-C" "out" "gn"
+ "-j" (number->string (parallel-job-count)))))
+ (replace 'check
+ (lambda* (#:key tests? #:allow-other-keys)
+ (if tests?
+ (begin
+ (invoke "ninja" "-C" "out" "gn_unittests"
+ "-j" (number->string (parallel-job-count)))
+ (invoke "./out/gn_unittests"))
+ (format #t "test suite not run~%"))))
+ (replace 'install
+ (lambda _
+ (install-file "out/gn" (string-append #$output "/bin")))))))
(native-inputs
- `(("ninja" ,ninja)
- ("python" ,python-wrapper)))
+ (list ninja python-wrapper))
(synopsis "Generate Ninja build files")
(description
"GN is a tool that collects information about a project from @file{.gn}
diff --git a/gnu/packages/cdrom.scm b/gnu/packages/cdrom.scm
index 8cf106b5e4..b544f0e59d 100644
--- a/gnu/packages/cdrom.scm
+++ b/gnu/packages/cdrom.scm
@@ -515,7 +515,7 @@ capacity is user-selectable.")
#t)))
#:tests? #f)) ; No tests.
(inputs ; TODO package bundled wxvillalib
- `(("wxwidgets" ,wxwidgets-3.1)
+ `(("wxwidgets" ,wxwidgets)
("wssvg" ,wxsvg)
("dbus" ,dbus)
("cdrtools" ,cdrtools)
diff --git a/gnu/packages/chromium.scm b/gnu/packages/chromium.scm
index e0a9f5fbad..7ef5104006 100644
--- a/gnu/packages/chromium.scm
+++ b/gnu/packages/chromium.scm
@@ -183,11 +183,11 @@
"third_party/libaddressinput" ;ASL2.0
"third_party/libaom" ;BSD-2 or "Alliance for Open Media Patent License 1.0"
"third_party/libaom/source/libaom/third_party/fastfeat" ;BSD-3
+ "third_party/libaom/source/libaom/third_party/SVT-AV1" ;BSD-3
"third_party/libaom/source/libaom/third_party/vector" ;Expat
"third_party/libaom/source/libaom/third_party/x86inc" ;ISC
"third_party/libjxl" ;ASL2.0
"third_party/libgav1" ;ASL2.0
- "third_party/libgifcodec" ;MPL1.1/GPL2+/LGPL2.1+, BSD-3, BSD-2
"third_party/libjingle_xmpp" ;BSD-3
"third_party/libphonenumber" ;ASL2.0
"third_party/libsecret" ;LGPL2.1+
@@ -273,7 +273,7 @@
"third_party/utf" ;Expat
"third_party/vulkan-deps" ;ASL2.0, BSD-3, Expat
"third_party/vulkan_memory_allocator" ;Expat
- "third_party/wayland/protocol" ;Expat
+ "third_party/wayland/src/protocol" ;Expat
"third_party/wayland/stubs" ;BSD-3, Expat
"third_party/wayland/wayland_scanner_wrapper.py" ;BSD-3
"third_party/wayland-protocols" ;Expat
@@ -317,10 +317,10 @@
;; run the Blink performance tests, just remove everything to save ~70MiB.
'("third_party/blink/perf_tests"))
-(define %chromium-version "107.0.5304.121")
+(define %chromium-version "108.0.5359.94")
(define %ungoogled-revision (string-append %chromium-version "-1"))
(define %debian-revision "debian/102.0.5005.61-1")
-(define %arch-revision "6afedb08139b97089ce8ef720ece5cd14c83948c")
+(define %arch-revision "4de5019014aeb77187a517c5ca6db8723d622a40")
(define %ungoogled-origin
(origin
@@ -330,7 +330,7 @@
(file-name (git-file-name "ungoogled-chromium" %ungoogled-revision))
(sha256
(base32
- "1ns664y7qx0ry8hg8r704z64jmx8j6rpxn2lkliv0xjfwlrbbfx3"))))
+ "0hlrcp34cf6m8c7100m8xr99s02ch0vmkgwl9pqkrinaghh29kgn"))))
(define %debian-origin
(origin
@@ -360,9 +360,6 @@
"system/zlib.patch"
"system/openjpeg.patch")))
-(define %gcc-patches
- '())
-
(define (arch-patch revision name hash)
(origin
(method url-fetch)
@@ -376,10 +373,12 @@
(arch-patch %arch-revision "REVERT-roll-src-third_party-ffmpeg-m102.patch"
"0i7crn6fcwq09kd6a4smqnffaldyv61lmv2p0drcnpfrwalmkprh")
(arch-patch %arch-revision "REVERT-roll-src-third_party-ffmpeg-m106.patch"
- "0li10cvxnppmmmsc7w77b1s7z02s5bzd39zsal9x768708fx64jc")
- ;; Fix crash when using Global Media Controls.
- (arch-patch %arch-revision "REVERT-enable-GlobalMediaControlsCastStartStop.patch"
- "1ilsw421lylkjnq3lvc607bdx7cvwlish8qzgwx9s84l4hzv37vp")))
+ "0li10cvxnppmmmsc7w77b1s7z02s5bzd39zsal9x768708fx64jc")))
+
+(define %arch-patches
+ (list
+ (arch-patch %arch-revision "disable-GlobalMediaControlsCastStartStop.patch"
+ "00m361ka38d60zpbss7qnfw80vcwnip2pjcz3wf46wd2sqi1nfvz")))
(define %guix-patches
(list (local-file
@@ -398,6 +397,9 @@
(assume-valid-file-name
(search-patch "ungoogled-chromium-system-nspr.patch")))))
+(define %patches
+ (append %debian-patches %arch-patches %guix-patches))
+
;; This is a source 'snippet' that does the following:
;; *) Applies various patches for unbundling purposes and libstdc++ compatibility.
;; *) Runs the ungoogled patch-, domain substitution-, and scrubbing scripts.
@@ -419,8 +421,7 @@
(for-each (lambda (patch)
(invoke "patch" "-p1" "--force" "--input"
patch "--no-backup-if-mismatch"))
- (append '#+%debian-patches '#+%guix-patches
- '#+%gcc-patches))
+ '#+%patches)
;; These patches are "reversed", i.e. their changes should be undone.
(for-each (lambda (patch)
@@ -495,7 +496,7 @@
%chromium-version ".tar.xz"))
(sha256
(base32
- "12z0fhgxcsdkf6shnsg9maj3v901226cjcy8y2x8m88maw2apc0j"))
+ "1zmndi4q9x8fyixwl1mp5qyf883x9xafq7ipzf9vk9d8h62521q6"))
(modules '((guix build utils)))
(snippet (force ungoogled-chromium-snippet))))
(build-system gnu-build-system)
@@ -561,7 +562,7 @@
"use_system_libjpeg=true"
"use_system_libopenjpeg2=true"
"use_system_libpng=true"
- "use_system_libwayland_server=true"
+ "use_system_libwayland=true"
"use_system_wayland_scanner=true"
(string-append "system_wayland_scanner_path=\""
(search-input-file %build-inputs
@@ -613,11 +614,12 @@
#~(modify-phases %standard-phases
(add-after 'unpack 'patch-stuff
(lambda* (#:key inputs #:allow-other-keys)
- (let ((openjpeg (search-input-directory
- inputs "include/openjpeg-2.4")))
+ (let* ((libopenjp2 (search-input-file inputs "lib/libopenjp2.so"))
+ (openjpeg (dirname (dirname libopenjp2))))
(substitute* "third_party/pdfium/BUILD.gn"
;; This include path is added by Debians openjpeg patch.
- (("/usr/include/openjpeg-2.4") openjpeg))
+ (("/usr/include/openjpeg-")
+ (string-append openjpeg "/include/openjpeg-")))
;; Adjust minizip header inclusions.
(substitute* (find-files "third_party/tflite_support\
@@ -910,7 +912,7 @@
gdk-pixbuf
glib
gtk+
- harfbuzz-3
+ harfbuzz-5
icu4c-71
jsoncpp
lcms
diff --git a/gnu/packages/code.scm b/gnu/packages/code.scm
index 1bbbb1e2fe..0ed978a768 100644
--- a/gnu/packages/code.scm
+++ b/gnu/packages/code.scm
@@ -391,7 +391,7 @@ features that are not supported by the standard @code{stdio} implementation.")
(define-public universal-ctags
(package
(name "universal-ctags")
- (version "5.9.20220807.0")
+ (version "5.9.20221127.0")
(source
(origin
(method git-fetch)
@@ -401,7 +401,7 @@ features that are not supported by the standard @code{stdio} implementation.")
(file-name (git-file-name name version))
(sha256
(base32
- "1wjj6hlda7xyjm8yrl2zz74ks7azymm9yyrpz36zxxpx2scf6lsk"))
+ "0nvkx5j2vyzjf935a2s5w56gamlr6f12jy1x38bkqz78p5l0d3ja"))
(modules '((guix build utils)))
(snippet
'(begin
diff --git a/gnu/packages/compression.scm b/gnu/packages/compression.scm
index f60ed4f597..d2a1ed36f7 100644
--- a/gnu/packages/compression.scm
+++ b/gnu/packages/compression.scm
@@ -1127,7 +1127,7 @@ tarballs.")
(define-public libjcat
(package
(name "libjcat")
- (version "0.1.11")
+ (version "0.1.12")
(source
(origin
(method git-fetch)
@@ -1137,7 +1137,7 @@ tarballs.")
(commit version)))
(file-name (git-file-name name version))
(sha256
- (base32 "08zywwhm9q8m8v17w2mp23w3w93p40ir1w4x18zrlbhs10xnhiys"))))
+ (base32 "0fbcmnpc0y7s2ls3q829dv3ardhv0m5gxqqmbn0dnkzgkh42vv7p"))))
(build-system meson-build-system)
(native-inputs
(list gobject-introspection help2man pkg-config))
@@ -2695,7 +2695,7 @@ to their original, binary CD format.")
(define-public libdeflate
(package
(name "libdeflate")
- (version "1.12")
+ (version "1.14")
(source (origin
(method git-fetch)
(uri (git-reference
@@ -2704,7 +2704,7 @@ to their original, binary CD format.")
(file-name (git-file-name name version))
(sha256
(base32
- "16n9232zjavcp5wp17cx0gh2v7gipxpncsha05j3ybajfs7g88jv"))))
+ "09y69mnbv3mprgjp53zvin5zqznqajginrk5b25xmi9y0b83bns8"))))
(build-system gnu-build-system)
(arguments
(list #:make-flags
diff --git a/gnu/packages/cook.scm b/gnu/packages/cook.scm
index 7a064480d4..584f561ceb 100644
--- a/gnu/packages/cook.scm
+++ b/gnu/packages/cook.scm
@@ -24,8 +24,8 @@
#:use-module (guix download)
#:use-module (gnu packages ed)
#:use-module (gnu packages bison)
- #:use-module (gnu packages groff)
#:use-module (gnu packages compression)
+ #:use-module (gnu packages groff)
#:use-module (guix build-system gnu))
(define-public cook
@@ -70,7 +70,7 @@
(setenv "SH" (which "sh"))
#t)))))
- (native-inputs (list bison
+ (native-inputs (list bison-3.0
;; For building the documentation:
groff
;; For the tests:
diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index ad0657ef3b..5c5258d6e0 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm