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Merge branch 'master' into mesa-updates

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Change-Id: I94c6874e5fdf916e3eb911f1a7df610cd3275474
This commit is contained in:
John Kehayias 2023-11-21 18:11:10 -05:00
commit 8d2a5a36af
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2
doc/contributing.texi
View file

@ -524,7 +524,7 @@ We also recommend that you run @code{:set autoindent} so that your code is
automatically indented as you type.
For the interaction with Git,
@uref{https://www.vim.org/scripts/script.php?script_id=2975
@uref{https://www.vim.org/scripts/script.php?script_id=2975,
@code{fugitive.vim}} is the most commonly used plugin:
@example

1
etc/teams.scm
View file

@ -300,6 +300,7 @@ (define-team go
(team 'go
#:name "Go team"
#:scope (list "gnu/packages/golang.scm"
"gnu/packages/golang-check.scm"
"guix/build/go-build-system.scm"
"guix/build-system/go.scm"
"guix/import/go.scm"

18
gnu/packages/admin.scm
View file

@ -4432,6 +4432,9 @@ (define-public launchmon
" *lmonpl = '\\0'"))
#t))))
(build-system gnu-build-system)
(arguments
;; GCC 11 defaults to c++17 but this package needs something older.
(list #:configure-flags #~'("CXXFLAGS=-std=c++14 -O2 -g")))
(inputs
(list openmpi
munge
@ -4439,7 +4442,7 @@ (define-public launchmon
libelf
libgcrypt
libgpg-error))
(synopsis "Infrastructue for large scale tool daemon launching")
(synopsis "Infrastructure for large-scale tool daemon launching")
(description
"LaunchMON is a software infrastructure that enables HPC run-time
tools to co-locate tool daemons with a parallel job. Its API allows a
@ -4452,7 +4455,7 @@ (define-public launchmon
(define-public spindle
(package
(name "spindle")
(version "0.10")
(version "0.13")
(source (origin
;; We use git checkout to avoid github auto-generated tarballs
(method git-fetch)
@ -4462,16 +4465,15 @@ (define-public spindle
(file-name (git-file-name name version))
(sha256
(base32
"15n3ay0qq81r5v7fif61q1vdjcq44pp2nynkh3fvbzc9fj3c39wd"))))
"1z594nhash1him9v00qmyqv9jvikzrs4wxqy1cvnfwqwnrrkp707"))))
(build-system gnu-build-system)
(arguments '(#:configure-flags '("--enable-sec-launchmon"
"--enable-sec-munge"
"--enable-sec-none")))
"--enable-sec-none"
;; Fails to build as c++17.
"CXXFLAGS=-std=c++14 -O2 -g")))
(inputs
`(("mpi" ,openmpi)
("munge" ,munge)
("launchmon" ,launchmon)
("libgcrypt" ,libgcrypt)))
(list openmpi munge launchmon libgcrypt))
(synopsis "Scalable library loading in HPC environments")
(description
"Spindle is a tool for improving the performance of dynamic library and

281
gnu/packages/astronomy.scm
View file

@ -589,13 +589,13 @@ (define-public python-astroml
(define-public python-fitsio
(package
(name "python-fitsio")
(version "1.2.0")
(version "1.2.1")
(source
(origin
(method url-fetch)
(uri (pypi-uri "fitsio" version))
(sha256
(base32 "04fbg1ffj7qrlzw50xzzkfnlk6qjjqq96j0im7phprmwb1rbvzzh"))
(base32 "19him5rcpjyz14ghkmifnd1xl3ivlyy84h45k6j2pyr5ixc60ky6"))
(modules '((guix build utils)))
(snippet
;; Remove the bundled cfitsio. When update the package check the
@ -1121,7 +1121,7 @@ (define-public siril
(define-public splash
(package
(name "splash")
(version "3.8.4")
(version "3.9.0")
(source (origin
(method git-fetch)
(uri (git-reference
@ -1129,7 +1129,7 @@ (define-public splash
(commit (string-append "v" version))))
(sha256
(base32
"1l18sqz5mpab9wb5hlbfy18wfwq6fpijc3p9wa5bv6lrcymvpirp"))
"19r5j4jrxhp3gf865ns59vvfnn5a303dqgmb8y2kgcsx26fci1hs"))
(file-name (git-file-name name version))))
(build-system gnu-build-system)
(arguments
@ -1385,7 +1385,7 @@ (define-public swarp
(define-public celestia
(package
(name "celestia")
(version "1.6.3")
(version "1.6.4")
(source
(origin
(method git-fetch)
@ -1394,7 +1394,7 @@ (define-public celestia
(commit version)))
(file-name (git-file-name name version))
(sha256
(base32 "0dzci5n7gcnm1vq916gsn9zddkhbzhbsakqxrpnmvzibsqznn6c8"))))
(base32 "0nz9k5nd2zmrbwj1qhsfwmvqymqk8c4yjxpybck44isrild2ah9j"))))
(build-system gnu-build-system)
(arguments
(list
@ -1614,19 +1614,27 @@ (define-public python-astroquery
(uri (pypi-uri "astroquery" version))
(sha256
(base32 "1vhkzsqlgn3ji5by2rdf2gwklhbyzvpzb1iglalhqjkkrdaaaz1h"))))
(build-system python-build-system)
(build-system pyproject-build-system)
(arguments
(list #:phases
#~(modify-phases %standard-phases
(add-before 'check 'writable-home
(lambda _ ; some tests need a writable home
(setenv "HOME" (getcwd))))
(replace 'check
(lambda* (#:key tests? #:allow-other-keys)
(when tests?
(invoke "python" "-m" "pytest" "--pyargs" "astroquery"
;; Skip tests that require online data.
"-m" "not remote_data")))))))
(list
#:test-flags
#~(list "--pyargs" "astroquery"
"-m" "not remote_data")
#:phases
#~(modify-phases %standard-phases
(add-before 'check 'prepare-test-environment
(lambda _
(setenv "HOME" (getcwd)) ; some tests need a writable home
;; To solve pytest/conftest issue. Pytest tries to load all
;; files with word 'test' in them.
;;
;; ImportError while loading conftest ...
;; _pytest.pathlib.ImportPathMismatchError: ...
;;
(call-with-output-file "pytest.ini"
(lambda (port)
(format port "[pytest]
python_files = test_*.py"))))))))
(propagated-inputs
(list python-astropy
python-beautifulsoup4
@ -1636,12 +1644,13 @@ (define-public python-astroquery
python-pyvo
python-requests))
(native-inputs
(list python-flask
python-jinja2
(list python-astropy-healpix
python-matplotlib
;; python-mocpy : Not packed yet, optional
python-pytest-astropy
python-pytest-dependency))
(home-page "https://www.astropy.org/astroquery/")
python-pytest-dependency
python-regions))
(home-page "https://astroquery.readthedocs.io/en/latest/index.html")
(synopsis "Access online astronomical data resources")
(description "Astroquery is a package that contains a collection of tools
to access online Astronomical data. Each web service has its own sub-package.")
@ -1726,13 +1735,13 @@ (define-public python-bayesicfitting
(define-public python-casa-formats-io
(package
(name "python-casa-formats-io")
(version "0.2.1")
(version "0.2.2")
(source (origin
(method url-fetch)
(uri (pypi-uri "casa-formats-io" version))
(sha256
(base32
"07cchih2ws6jf6q1a4xhkv0jk96s3w08kzxx9l1911wzqk0pw9pj"))))
"16qwr6yq86qgdb0lvnmfm5mn6g2d29b1vrmfv26v77kxm6szxr8h"))))
(build-system pyproject-build-system)
(arguments
(list
@ -1835,13 +1844,13 @@ (define-public python-cdflib
(define-public python-crds
(package
(name "python-crds")
(version "11.17.7")
(version "11.17.9")
(source (origin
(method url-fetch)
(uri (pypi-uri "crds" version))
(sha256
(base32
"10cxhb1xss21p992bfd5jm8bix1n12h0fd8m5sp6bcsgn6zs94v0"))))
"0ha7ibs5lmqs9pcr546jyxzgrmx1xyqps7fsp220rvlsbsisdgm0"))))
(build-system pyproject-build-system)
(arguments
(list
@ -1924,18 +1933,7 @@ (define-public python-drms
(uri (pypi-uri "drms" version))
(sha256
(base32 "0mkrmr55fgca441z7hvsyri6x9cjsh0sfas3hrj0k1k10k8vszbw"))))
(build-system python-build-system)
(arguments
(list
#:phases
#~(modify-phases %standard-phases
(replace 'check
(lambda* (#:key inputs outputs tests?
#:allow-other-keys)
(when tests?
(add-installed-pythonpath inputs outputs)
(setenv "JSOC_EMAIL" "jsoc@sunpy.org")
(invoke "python" "-m" "pytest" "-vv")))))))
(build-system pyproject-build-system)
(native-inputs
(list python-astropy
python-pytest-astropy
@ -2120,27 +2118,22 @@ (define-public python-poliastro
(build-system pyproject-build-system)
(arguments
(list
#:test-flags
#~(list "-m" "not remote_data"
;; TODO: Review failing tests later when any upstream
;; suggestions are provided:
;; https://github.com/poliastro/poliastro/issues/1618
"-k" (string-append "not test_czml_add_trajectory"
" and not test_czml_custom_packet"
" and not test_czml_ground_station"
" and not test_czml_groundtrack"
" and not test_czml_preamble"))
#:phases
#~(modify-phases %standard-phases
;; NOTE: Tests take about 7-10 minutes to pass.
(add-before 'check 'prepare-test-environment
(lambda _
(setenv "HOME" "/tmp")
;; TODO: Review failing tests later when any upstream
;; suggestions are provided:
;; https://github.com/poliastro/poliastro/issues/1618
(substitute* "tests/test_czml.py"
(("def test_czml_add_trajectory") "def __off_test_czml_add_trajectory")
(("def test_czml_custom_packet") "def __off_test_czml_custom_packet")
(("def test_czml_ground_station") "def __off_test_czml_ground_station")
(("def test_czml_groundtrack") "def __off_test_czml_groundtrack")
(("def test_czml_preamble") "def __off_test_czml_preamble"))))
(replace 'check
(lambda* (#:key tests? #:allow-other-keys)
(when tests?
(invoke "python" "-m" "pytest"
;; Skip tests that need remote data.
"-m" "not remote_data")))))))
(setenv "HOME" "/tmp"))))))
(native-inputs
(list python-coverage
python-hypothesis
@ -2373,13 +2366,13 @@ (define-public python-reproject
(define-public python-sgp4
(package
(name "python-sgp4")
(version "2.22")
(version "2.23")
(source
(origin
(method url-fetch)
(uri (pypi-uri "sgp4" version))
(sha256
(base32 "1yc6gcbhz80i875j0wf6ikx7rzs0m7m1qp72dmdhdjidmpma5w0p"))))
(base32 "0aalbmldks6ykgkcxwkvnp04q0avhv903m5zwvg8i7zvl99xrbfq"))))
(build-system python-build-system)
(propagated-inputs
(list python-numpy))
@ -2674,7 +2667,7 @@ (define-public python-stsci-imagestats
(sha256
(base32
"14457izlbnks84dyza75ib3nvx2w8nhlqm9vc1zb7hbhknb5gjvw"))))
(build-system python-build-system)
(build-system pyproject-build-system)
(arguments
(list #:tests? #f)) ;No tests
(propagated-inputs (list python-numpy))
@ -2702,11 +2695,23 @@ (define-public python-stsci-stimage
(build-system pyproject-build-system)
(arguments
(list
;; XXX: Fix failing tests. There are errors to load test files.
#:tests? #f))
#:phases
#~(modify-phases %standard-phases
;; Test steps are taken from GitHub Actions.
;; See https://github.com/spacetelescope/stsci.stimage/issues/27
(replace 'check
(lambda _
(copy-file (string-append
#$(this-package-native-input "python-waf") "/bin/waf")
"waf")
(invoke "python" "waf" "configure" "build" "do_tests"))))))
(propagated-inputs (list python-numpy))
(native-inputs (list python-codecov python-pytest python-pytest-cov
python-setuptools-scm))
(native-inputs
(list python-codecov
python-pytest
python-pytest-cov
python-setuptools-scm
python-waf))
(home-page "https://stscistimage.readthedocs.io/en/latest/")
(synopsis "STScI image processing")
(description "This package provides an astronomical Python package with
@ -2974,44 +2979,40 @@ (define-public libskry
(license license:gpl3+)))
(define-public libpasastro
;; NOTE: (Sharlatan-20210122T215921+0000): the version tag has a build
;; error on spice which is resolved with the latest commit.
(let ((commit "e3c218d1502a18cae858c83a9a8812ab197fcb60")
(revision "1"))
(package
(name "libpasastro")
(version (git-version "1.4.0" revision commit))
(source (origin
(method git-fetch)
(uri (git-reference
(url "https://github.com/pchev/libpasastro")
(commit commit)))
(file-name (git-file-name name version))
(sha256
(base32
"0asp2sn34nds5va2ghppwc41vb6j3d1mf049j949rgrll817kx47"))))
(build-system gnu-build-system)
(arguments
`(#:tests? #f
#:make-flags
(list
,(match (or (%current-target-system) (%current-system))
((or "aarch64-linux" "armhf-linux" "i686-linux" "x86_64-linux")
"OS_TARGET=linux")
(_ #f))
,(match (or (%current-target-system) (%current-system))
("i686-linux" "CPU_TARGET=i386")
("x86_64-linux" "CPU_TARGET=x86_64")
((or "armhf-linux" "aarch64-linux") "CPU_TARGET=armv7l")
(_ #f))
(string-append "PREFIX=" (assoc-ref %outputs "out")))
#:phases
(modify-phases %standard-phases
(delete 'configure))))
(home-page "https://github.com/pchev/libpasastro")
(synopsis "Interface to astronomy library for use from Pascal program")
(description
"This package provides shared libraries to interface Pascal program with
(package
(name "libpasastro")
(version "1.4.1")
(source
(origin
(method git-fetch)
(uri (git-reference
(url "https://github.com/pchev/libpasastro")
(commit (string-append "v" version))))
(file-name (git-file-name name version))
(sha256
(base32 "1h92p9ph3zi4w8krny1azd9wgwna2nf07ims983jcky1chkfm0is"))))
(build-system gnu-build-system)
(arguments
`(#:tests? #f
#:make-flags
(list
,(match (or (%current-target-system) (%current-system))
((or "aarch64-linux" "armhf-linux" "i686-linux" "x86_64-linux")
"OS_TARGET=linux")
(_ #f))
,(match (or (%current-target-system) (%current-system))
("i686-linux" "CPU_TARGET=i386")
("x86_64-linux" "CPU_TARGET=x86_64")
((or "armhf-linux" "aarch64-linux") "CPU_TARGET=armv7l")
(_ #f))
(string-append "PREFIX=" (assoc-ref %outputs "out")))
#:phases
(modify-phases %standard-phases
(delete 'configure))))
(home-page "https://github.com/pchev/libpasastro")
(synopsis "Interface to astronomy library for use from Pascal program")
(description
"This package provides shared libraries to interface Pascal program with
standard astronomy libraries:
@itemize
@ -3020,7 +3021,7 @@ (define-public libpasastro
@item @code{libpaswcs.so}: Interface with libwcs to work with FITS WCS.
@item @code{libpasspice.so}: To work with NAIF/SPICE kernel.
@end itemize\n")
(license license:gpl2+))))
(license license:gpl2+)))
(define-public libxisf
(package
@ -3153,23 +3154,21 @@ (define-public gpredict
(sha256
(base32 "0hwf97kng1zy8rxyglw04x89p0bg07zq30hgghm20yxiw2xc8ng7"))))
(build-system gnu-build-system)
(arguments
(list
#:configure-flags #~(list "CFLAGS=-O2 -g -fcommon")
#:phases
#~(modify-phases %standard-phases
(add-after 'unpack 'fix-tests
(lambda _
;; Remove reference to non-existent file.
(substitute* "po/POTFILES.in"
(("src/gtk-sat-tree\\.c") "")))))))
(native-inputs
`(("intltool" ,intltool)
("gettext" ,gettext-minimal)
("pkg-config" ,pkg-config)))
(list gettext-minimal intltool pkg-config))
(inputs
(list curl glib goocanvas gtk+))
(arguments
`(#:configure-flags '("CFLAGS=-O2 -g -fcommon")
#:phases
(modify-phases %standard-phases
(add-after 'unpack 'fix-tests
(lambda _
;; Remove reference to non-existent file.
(substitute* "po/POTFILES.in"
(("src/gtk-sat-tree\\.c")
""))
#t)))))
(home-page "http://gpredict.oz9aec.net/index.php")
(synopsis "Satellite tracking and orbit prediction application")
(description
"Gpredict is a real-time satellite tracking and orbit prediction
@ -3177,7 +3176,6 @@ (define-public gpredict
position and other data in lists, tables, maps, and polar plots (radar view).
Gpredict can also predict the time of future passes for a satellite, and
provide you with detailed information about each pass.")
(home-page "http://gpredict.oz9aec.net/index.php")
(license license:gpl2+)))
(define-public sgp4
@ -3393,13 +3391,13 @@ (define-public sunclock
(define-public python-jplephem
(package
(name "python-jplephem")
(version "2.19")
(version "2.20")
(source
(origin
(method url-fetch)
(uri (pypi-uri "jplephem" version))
(sha256
(base32 "1kvdzwyh0invinvcnwfr14r9zbqzcwkdh0cpzw1m4vkdcm64aqn1"))))
(base32 "1yp1l3n07849411099f976ps0pyv8jk8k5l9da9nhv54ir86v65v"))))
(build-system pyproject-build-system)
(arguments
(list
@ -3537,7 +3535,7 @@ (define-public python-pyerfa
(define-public python-pynbody
(package
(name "python-pynbody")
(version "1.4.1")
(version "1.4.2")
(source
(origin
(method git-fetch) ;PyPi doesn't have not prebuit version.
@ -3546,7 +3544,7 @@ (define-public python-pynbody
(commit (string-append "v" version))))
(file-name (git-file-name name version))
(sha256
(base32 "1vl1yif3bsazcil6saghrpa4qsg47fnr7xnkjpqnp44b7ipww27r"))
(base32 "1lwjs8vf3pc4a64c93fa5k6r276g1c60722swns2r10ig1s4wk0a"))
(modules '((guix build utils)))
(snippet
;; Symlink goes to not existing directory.
@ -3582,7 +3580,12 @@ (define-public python-pynbody
"--ignore=tests/sph_smooth_test.py"
"--ignore=tests/subfind_test.py"
"--ignore=tests/subfindhdf_gadget4_test.py"
"--ignore=tests/tipsy_test.py")))
"--ignore=tests/tipsy_test.py")
#:phases
#~(modify-phases %standard-phases
(add-before 'build 'set-compiler
(lambda _
(setenv "CC" #$(cc-for-target)))))))
(native-inputs
(list python-cython
python-pandas
@ -3721,9 +3724,21 @@ (define-public python-synphot
(build-system pyproject-build-system)
(arguments
(list
;; XXX: Test needs more love to pass.
;; ERROR collecting synphot/tests/test_utils.py
#:tests? #f))
#:phases
#~(modify-phases %standard-phases
(add-before 'check 'prepare-test-environment
(lambda _
(invoke "python" "setup.py" "build_ext" "--inplace")
;; To solve pytest/conftest issue. Pytest tries to load all
;; files with word 'test' in them.
;;
;; ImportError while loading conftest ...
;; _pytest.pathlib.ImportPathMismatchError: ...
;;
(call-with-output-file "pytest.ini"
(lambda (port)
(format port "[pytest]
python_files = test_*.py"))))))))
(propagated-inputs (list python-astropy python-numpy python-scipy))
(native-inputs (list python-pytest python-pytest-astropy
python-setuptools-scm))
@ -3772,13 +3787,13 @@ (define-public python-tweakwcs
(define-public python-asdf-3.0
(package
(name "python-asdf")
(version "3.0.0")
(version "3.0.1")
(source
(origin
(method url-fetch)
(uri (pypi-uri "asdf" version))
(sha256
(base32 "1a6lf75q9w8fsyq3hn6a7fyldkkyqxddlq21fwdfjwij40dzh3s8"))))
(base32 "1jsk7b4mx04l0a08j832vnl309dba3gjnha9mbd61dzs9ridrfna"))))
(build-system pyproject-build-system)
(native-inputs
(list python-fsspec
@ -4117,13 +4132,13 @@ (define-public python-gwcs
(define-public python-rad
(package
(name "python-rad")
(version "0.17.1")
(version "0.18.0")
(source (origin
(method url-fetch)
(uri (pypi-uri "rad" version))
(sha256
(base32
"11jhh3qmd00g8sn6hcfshbpb2qy1rfj0xkxn30pd63lqazg4ra3p"))))
"1wgnbhldgq0j55yzg33y11vd5k5nzwckiccxywvmq518qh19pky5"))))
(build-system pyproject-build-system)
(arguments
(list
@ -4179,13 +4194,13 @@ (define-public python-radio-beam
(define-public python-roman-datamodels
(package
(name "python-roman-datamodels")
(version "0.17.1")
(version "0.18.0")
(source (origin
(method url-fetch)
(uri (pypi-uri "roman_datamodels" version))
(sha256
(base32
"1y12cp8172i4a314gmhpi86jw6pfylz1adh0rzr5zqmvd3mrjqlj"))))
"0crlmd99p2nyqmrbykdqqng7v8zb4sibm8j9aqrq3ppak3r3r7q1"))))
(build-system pyproject-build-system)
(arguments
(list
@ -4223,7 +4238,7 @@ (define-public python-roman-datamodels
(define-public python-astroalign
(package
(name "python-astroalign")
(version "2.5.0")
(version "2.5.1")
(source
(origin
;; There are no tests in the PyPI tarball.
@ -4233,7 +4248,7 @@ (define-public python-astroalign
(commit (string-append "v" version))))
(file-name (git-file-name name version))
(sha256
(base32 "0br1v2l48jx214a1bcdr8wz1wggcswcbz4cqv8d19fd46fc4qlhy"))))
(base32 "1kr5cszcxvrdbksy7mvv3ps1h1jzrn4yamfr6x7whkbi6bpqf7xp"))))
(build-system pyproject-build-system)
(native-inputs
(list python-astropy
@ -4281,13 +4296,13 @@ (define-public python-skyfield
(define-public python-wiimatch
(package
(name "python-wiimatch")
(version "0.3.1")
(version "0.3.2")
(source (origin
(method url-fetch)
(uri (pypi-uri "wiimatch" version))
(sha256
(base32
"0x6p5z6a2cqinckwlpinjxagvmswl149s1jn6ihmdxk4k0h8rrz0"))))
"15kq7z30m9i286ncs9xvpaq3dq1p5fa47jz21prq146qwr7j6dm8"))))
(build-system pyproject-build-system)
(propagated-inputs (list python-numpy python-scipy))
(native-inputs (list python-codecov python-pytest python-pytest-cov

4
gnu/packages/benchmark.scm
View file

@ -137,7 +137,7 @@ (define-public fio
(define-public intel-mpi-benchmarks/openmpi
(package
(name "intel-mpi-benchmarks")
(version "2019.6")
(version "2021.3")
(source (origin
(method git-fetch)
(uri (git-reference
@ -146,7 +146,7 @@ (define-public intel-mpi-benchmarks/openmpi
(file-name (git-file-name name version))
(sha256
(base32
"02hxbk9g9nl59bk5qcfl3djj7b58vsqys340m1xdbyqwcrbnahh9"))
"04kczch2hlfzbgk929vcxx480kc6raba8rbz246j7d26k1z1zh8h"))
(modules '((guix build utils)))
(snippet
'(begin

12
gnu/packages/bioconductor.scm
View file

@ -12203,13 +12203,13 @@ (define-public r-ggtreeextra
(define-public r-ggpicrust2
(package
(name "r-ggpicrust2")
(version "1.7.2")
(version "1.7.3")
(source (origin
(method url-fetch)
(uri (cran-uri "ggpicrust2" version))
(sha256
(base32
"0yk62cc0vmv6dyfiwvvbgpsqlvp1cw61db60153xvzmcdvd077cl"))))
"0zjlsvzl2f74fvqw4ijnai23qwhlcpgd5p8z9dclnwnsgdbm6hcq"))))
(properties `((upstream-name . "ggpicrust2")))
(build-system r-build-system)
(propagated-inputs (list r-aldex2
@ -19027,14 +19027,14 @@ (define-public r-activedriverwgs
(define-public r-activepathways
(package
(name "r-activepathways")
(version "2.0.2")
(version "2.0.3")
(source
(origin
(method url-fetch)
(uri (cran-uri "ActivePathways" version))
(sha256
(base32
"1h0ih87pf6b5mdhmh65frv3nqx7v5adqv37wn2p3gkpszd6hwc79"))))
"0mgvxpqaq0jncr1kzmwhqkv3pajx2fz6vwhv5arw7fgla6w09p9h"))))
(properties
`((upstream-name . "ActivePathways")))
(build-system r-build-system)
@ -22029,14 +22029,14 @@ (define-public r-ldheatmap
(define-public r-abn
(package
(name "r-abn")
(version "3.0.2")
(version "3.0.3")
(source
(origin
(method url-fetch)
(uri (cran-uri "abn" version))
(sha256
(base32
"06n69cbkdqpwpxks8276h43132c9v57n4hg33vsjjyxjifwbwxwh"))))
"1yh9nhfphalxh77132r0fkpp71mqsfhb8jk11is4d5nvlvr5316z"))))
(build-system r-build-system)
(inputs
(list gsl))

11
gnu/packages/c.scm
View file

@ -3,7 +3,7 @@
;;; Copyright © 2016, 2017, 2018, 2019, 2021 Ricardo Wurmus <rekado@elephly.net>
;;; Copyright © 2018, 2020–2022 Tobias Geerinckx-Rice <me@tobias.gr>
;;; Copyright © 2018, 2019 Pierre Neidhardt <mail@ambrevar.xyz>
;;; Copyright © 2019, 2020, 2022 Efraim Flashner <efraim@flashner.co.il>
;;; Copyright © 2019, 2020, 2022, 2023 Efraim Flashner <efraim@flashner.co.il>
;;; Copyright © 2019, 2021 Guillaume Le Vaillant <glv@posteo.net>
;;; Copyright © 2019 Andreas Enge <andreas@enge.fr>
;;; Copyright © 2020 Jan (janneke) Nieuwenhuizen <janneke@gnu.org>
@ -1198,7 +1198,7 @@ (define-public aws-c-mqtt
(define-public mimalloc
(package
(name "mimalloc")
(version "2.0.9")
(version "2.1.2")
(source (origin
(method git-fetch)
(uri (git-reference
@ -1207,10 +1207,13 @@ (define-public mimalloc
(file-name (git-file-name name version))
(sha256
(base32
"19w0i28p6knjd192rrcw1ayc3x0qp6rcm48cwkls4kwn8fng81fj"))))
"1pyf05snc1ib7zjjm9kspvbmynd8lmxqw72qcpz8lcyzyywmz24i"))))
(build-system cmake-build-system)
(arguments
`(#:build-type "Release"))
`(#:build-type "Release"
,@(if (target-ppc32?)
`(#:configure-flags '("-DMI_USE_LIBATOMIC=ON"))
'())))
(synopsis "General purpose memory allocator")
(description "@code{mimalloc} is a drop-in replacement for @code{malloc}.")
(home-page "https://microsoft.github.io/mimalloc/")

33
gnu/packages/check.scm
View file

@ -2551,7 +2551,7 @@ (define-public python-pytest-pep8
(define-public python-pytest-perf
(package
(name "python-pytest-perf")
(version "0.12.0")
(version "0.13.1")
(source (origin
(method git-fetch)
(uri (git-reference
@ -2560,26 +2560,21 @@ (define-public python-pytest-perf
(file-name (git-file-name name version))
(sha256
(base32
"05mgknvrmyz1kmkgw8jzvisavc68wz1g2wxv69i6xvzgqxf17m9f"))))
(build-system python-build-system)
"1hrccvrbccqwba04pqj749hdzn4sgldmbpg74nf3fzz7wyg6jxqk"))))
(build-system pyproject-build-system)
(arguments
(list
#:phases
#~(modify-phases %standard-phases
(replace 'check
(lambda* (#:key tests? #:allow-other-keys)
(when tests?
(invoke "pytest" "-k"
(string-append
;; Do not test the myproject.toml build as it tries to pull
;; dependencies from the internet.
"not project "
;; The benchmark test attempts to install the
;; package, failing to pull its dependencies from the
;; network.
"and not BenchmarkRunner "
;; The upstream_url test requires networking.
"and not upstream_url"))))))))
#:test-flags '(list "-k"
(string-append
;; Do not test the myproject.toml build as it tries to pull
;; dependencies from the internet.
"not project "
;; The benchmark test attempts to install the
;; package, failing to pull its dependencies from the
;; network.
"and not BenchmarkRunner "
;; The upstream_url test requires networking.
"and not upstream_url"))))
(native-inputs
(list python-pytest
python-pytest-black

195
gnu/packages/cran.scm
View file

@ -147,13 +147,13 @@ (define-public r-aer
(define-public r-afpt
(package
(name "r-afpt")
(version "1.1.0.3")
(version "1.1.0.4")
(source (origin
(method url-fetch)
(uri (cran-uri "afpt" version))
(sha256
(base32
"18izncbr3ljckil97xx2w1y0y7qjykp06wm0ap8ismahqvia3xz3"))))
"15pa4p78p6r478l05481lzx6z4ahswj728s1sb3xp3pvn6rv4jfj"))))
(properties `((upstream-name . "afpt")))
(build-system r-build-system)
(native-inputs (list r-knitr))
@ -391,13 +391,13 @@ (define-public r-consort
(define-public r-collapse
(package
(name "r-collapse")
(version "2.0.3")
(version "2.0.6")
(source
(origin
(method url-fetch)
(uri (cran-uri "collapse" version))
(sha256
(base32 "16y4qxqr4k04690xn8s6c9fr3igpk34pgxygxkc41gc1na0ym37v"))))
(base32 "0azyl6667dzwns9knp3fplv6f9nav36wsrv42qzv90p5kzcaa872"))))
(properties `((upstream-name . "collapse")))
(build-system r-build-system)
(propagated-inputs (list r-rcpp))
@ -1490,14 +1490,14 @@ (define-public r-ruv
(define-public r-waldo
(package
(name "r-waldo")
(version "0.5.1")
(version "0.5.2")
(source
(origin
(method url-fetch)
(uri (cran-uri "waldo" version))
(sha256
(base32
"0inzdwna22axhjw0jdrk800g7zbkpcs7g1cmdi83r7j4zxn0ggs5"))))
"019fvypq36kwvr2znlr0fd9f2ihb08rgigf6ypdybry5n8daxkc2"))))
(properties `((upstream-name . "waldo")))
(build-system r-build-system)
(propagated-inputs
@ -2201,14 +2201,14 @@ (define-public r-ggalluvial
(define-public r-ggpp
(package
(name "r-ggpp")
(version "0.5.4")
(version "0.5.5")
(source
(origin
(method url-fetch)
(uri (cran-uri "ggpp" version))
(sha256
(base32
"05w74003jp7kprxxbni0plr7ydzyc5hzw8g39kn0qd4p7dksjpwr"))))
"0nysan87vgy0pbcks3bychm84zcwx9pf4p250b45ghimhvxh5cvm"))))
(properties `((upstream-name . "ggpp")))
(build-system r-build-system)
(propagated-inputs
@ -4080,24 +4080,26 @@ (define-public r-httpuv
(define-public r-httr2
(package
(name "r-httr2")
(version "0.2.3")
(version "1.0.0")
(source (origin
(method url-fetch)
(uri (cran-uri "httr2" version))
(sha256
(base32
"0gabjyv2699p7fb4225jsr2kkbarx1w01kha8ipqzwhjjl13481m"))))
"0jaajfr1hr6bzb1vz2nw2csl2l09kbq619vsq5yrlchcarpjv1fb"))))
(properties `((upstream-name . "httr2")))
(build-system r-build-system)
(propagated-inputs
(list r-cli
r-curl
r-glue
r-lifecycle
r-magrittr
r-openssl
r-r6
r-rappdirs
r-rlang
r-vctrs
r-withr))
(native-inputs (list r-knitr))
(home-page "https://httr2.r-lib.org")
@ -4227,13 +4229,13 @@ (define-public r-howmany
(define-public r-htmltools
(package
(name "r-htmltools")
(version "0.5.6.1")
(version "0.5.7")
(source (origin
(method url-fetch)
(uri (cran-uri "htmltools" version))
(sha256
(base32
"0km08kvg0j2h1d0v6wpxf09yjadhp2srjjnmqwcahfyh37w4xf09"))))
"11mkk26pjck6r2w2nv6niy90c6l13g64zi01s3j4jgq634kdic7c"))))
(build-system r-build-system)
(propagated-inputs
(list r-base64enc r-digest r-ellipsis r-fastmap r-rlang))
@ -5223,14 +5225,14 @@ (define-public r-sankeyd3
(define-public r-wesanderson
(package
(name "r-wesanderson")
(version "0.3.6")
(version "0.3.7")
(source
(origin
(method url-fetch)
(uri (cran-uri "wesanderson" version))
(sha256
(base32
"09mr6p2jmqdjq27cz974w5hyxgn929zp9z3inhxqmmh1582fmdi2"))))
"0kjyz5mrkrirg2glf57b0rhxj2fdp1m6q8zx947y0jg1w425cbn9"))))
(properties `((upstream-name . "wesanderson")))
(build-system r-build-system)
(home-page "https://github.com/karthik/wesanderson")
@ -5562,14 +5564,14 @@ (define-public r-mapdata
(define-public r-maps
(package
(name "r-maps")
(version "3.4.1")
(version "3.4.1.1")
(source
(origin
(method url-fetch)
(uri (cran-uri "maps" version))
(sha256
(base32
"0034114pdakxcx480b45qy9j4vq1v5ss961ssy92w4nqiqhsb4z6"))))
"06l58919kgks9adwzgfir44q6gnx46j3c7ah9c6d4dn36xsld7fk"))))
(build-system r-build-system)
(home-page "https://cran.r-project.org/web/packages/maps")
(synopsis "Draw geographical maps")
@ -5601,18 +5603,18 @@ (define-public r-mapproj
(define-public r-rgooglemaps
(package
(name "r-rgooglemaps")
(version "1.4.5.3")
(version "1.5.1")
(source
(origin
(method url-fetch)
(uri (cran-uri "RgoogleMaps" version))
(sha256
(base32
"02v8k0bw70q4qwx4lcdy8p25q7n3ql2ll46lfpqllxa1p26svmfi"))))
"197q5i2sky824dwq0x4hhrpkrsd1b6f9qg06mjlwb89mv4vnrzhl"))))
(properties `((upstream-name . "RgoogleMaps")))
(build-system r-build-system)
(propagated-inputs
(list r-png r-sp))
(list r-png))
(home-page "https://cran.r-project.org/web/packages/RgoogleMaps")
(synopsis "Use Google Maps in R")
(description "This package serves two purposes:
@ -7188,13 +7190,13 @@ (define-public r-rmpi
(define-public r-rmumps
(package
(name "r-rmumps")
(version "5.2.1-23")
(version "5.2.1-25")
(source
(origin
(method url-fetch)
(uri (cran-uri "rmumps" version))
(sha256
(base32 "1mypmf9j9fzaldpv56bqng5yhyxfc55hvzd98d1dk6w1m1sncn09"))))
(base32 "15yn5i6v3xz90gimvaqgvp805cfpvr439y9wpckyvwn1iwp2745y"))))
(properties `((upstream-name . "rmumps")))
(build-system r-build-system)
(inputs (list zlib))
@ -7942,14 +7944,14 @@ (define-public r-progressr
(define-public r-lava
(package
(name "r-lava")
(version "1.7.2.1")
(version "1.7.3")
(source
(origin
(method url-fetch)
(uri (cran-uri "lava" version))
(sha256
(base32
"0bpg75w0ri1mkf7cw9gbw1fjpy4mh9h48k019y772xjfgrf1yayl"))))
"023av1mz4hr1lqv8cpbx0j1y3c7ljyns35rm838c618b6pqps22f"))))
(build-system r-build-system)
(propagated-inputs
(list r-future-apply r-numderiv r-progressr r-squarem r-survival))
@ -9926,13 +9928,13 @@ (define-public r-seriation
(define-public r-xfun
(package
(name "r-xfun")
(version "0.40")
(version "0.41")
(source
(origin
(method url-fetch)
(uri (cran-uri "xfun" version))
(sha256
(base32 "1xvngh0kbd87cl39bzmjx5i57pmxik9gw50li8dh42j438cnma8y"))))
(base32 "00ivgr557ja8l33lvawrivfhgj1xbjmdi4dj07zybwa1y6wc6x13"))))
(build-system r-build-system)
(properties
;; knitr itself depends on xfun
@ -10494,13 +10496,13 @@ (define-public r-leaflet-providers
(define-public r-leaflet
(package
(name "r-leaflet")
(version "2.2.0")
(version "2.2.1")
(source
(origin
(method url-fetch)
(uri (cran-uri "leaflet" version))
(sha256
(base32 "0k0zplbhmvld6q1id17s827z1230kvnz16c4hlvp6jn9g26yy0dq"))
(base32 "1gfsf7bsmp418zv4gpk5i1xg5vvgqwpdkznnvj5x0mk4rcqk1i81"))
(snippet
'(for-each
delete-file
@ -10891,13 +10893,13 @@ (define-public r-extradistr
(define-public r-fbasics
(package
(name "r-fbasics")
(version "4031.95")
(version "4032.96")
(source (origin
(method url-fetch)
(uri (cran-uri "fBasics" version))
(sha256
(base32
"1d1pbyidng68fcc6vrm98ybklz6yzrinqc2dhg8q6f1pg3kkx6bj"))))
"14461d6ac8hcn1x3srh45a4s5imafqb0xy8bn5l6d0qwhw4njmg1"))))
(properties `((upstream-name . "fBasics")))
(build-system r-build-system)
(propagated-inputs
@ -12628,20 +12630,20 @@ (define-public r-rgexf
(define-public r-data-tree
(package
(name "r-data-tree")
(version "1.0.0")
(version "1.1.0")
(source
(origin
(method url-fetch)
(uri (cran-uri "data.tree" version))
(sha256
(base32
"0pizmx2312zsym4m42b97q2184bg3hibvbdrblcga05xln84qrs0"))))
"0qxd1g159phc6f18iddjljdg96sh09w63xqawjwbwyhg4blm9ddh"))))
(properties `((upstream-name . "data.tree")))
(build-system r-build-system)
(propagated-inputs
(list r-r6 r-stringi))
(native-inputs
(list r-knitr))
(list r-knitr r-rmarkdown))
(home-page "https://github.com/gluc/data.tree")
(synopsis "General purpose hierarchical data structure")
(description
@ -12688,14 +12690,14 @@ (define-public r-dtplyr
(define-public r-collapsibletree
(package
(name "r-collapsibletree")
(version "0.1.7")
(version "0.1.8")
(source
(origin
(method url-fetch)
(uri (cran-uri "collapsibleTree" version))
(sha256
(base32
"0b65pbp1wnpsrayqi630ds4r98jvcvynnlp6wxdqrnnr9nzw5343"))
"1i5nmw5w7m8xdgxzim8z8n4w321f42isxbvvajl8ii59pg7drilq"))
(snippet
'(begin
;; Delete minified JavaScript file
@ -12781,14 +12783,14 @@ (define-public r-rappdirs
(define-public r-rastervis
(package
(name "r-rastervis")
(version "0.51.5")
(version "0.51.6")
(source
(origin
(method url-fetch)
(uri (cran-uri "rasterVis" version))
(sha256
(base32
"18bsrw629p4pkyhrpjmiyhq73w882bhgpwmkih0gjnw3ywwgx7rs"))))
"12cl201gwah0bn14ji4nbygayd77w5fck9zkcikhrda5s0chvgb1"))))
(properties `((upstream-name . "rasterVis")))
(build-system r-build-system)
(propagated-inputs
@ -13618,14 +13620,14 @@ (define-public r-rbibutils
(define-public r-rdpack
(package
(name "r-rdpack")
(version "2.5")
(version "2.6")
(source
(origin
(method url-fetch)
(uri (cran-uri "Rdpack" version))
(sha256
(base32
"0xy8w3law1dn53f1gv4jd637pwssr928pvgchpbrpsqz8ghv4kad"))))
"02i21i85pb5aim529byjwhmyyz9jd82mi4j26a3kay0pcn6djxba"))))
(properties `((upstream-name . "Rdpack")))
(build-system r-build-system)
(propagated-inputs
@ -14360,14 +14362,14 @@ (define-public r-deriv
(define-public r-doby
(package
(name "r-doby")
(version "4.6.19")
(version "4.6.20")
(source
(origin
(method url-fetch)
(uri (cran-uri "doBy" version))
(sha256
(base32
"14hvbhf9zamqkjhr9jd8zjpm9xlc8hwqj04gy6ln32n2hzqqqr6v"))))
"08nsl9xzyi2k7xkwa9mn91fn77ji0z9z5lm388pfdmydbfmpy2ks"))))
(properties `((upstream-name . "doBy")))
(build-system r-build-system)
(propagated-inputs
@ -14469,14 +14471,14 @@ (define-public r-blockfest
(define-public r-proc
(package
(name "r-proc")
(version "1.18.4")
(version "1.18.5")
(source
(origin
(method url-fetch)
(uri (cran-uri "pROC" version))
(sha256
(base32
"0lqar1lbm461in4jb9rkdnpccl8lshrhig2qxr892m91mdxym46m"))))
"129cnh3kh9sr42nc7n9f14kr9svi3501834x40njynnzlr0wi4sm"))))
(properties `((upstream-name . "pROC")))
(build-system r-build-system)
(propagated-inputs
@ -15143,13 +15145,13 @@ (define-public r-qualv
(define-public r-mosaiccore
(package
(name "r-mosaiccore")
(version "0.9.2.1")
(version "0.9.4.0")
(source
(origin
(method url-fetch)
(uri (cran-uri "mosaicCore" version))
(sha256
(base32 "1yns15yxr6215xf9qsxfvl24a9zvh1chw49n31dql7fy1zr1dkmp"))))
(base32 "0v3xhv6yfk1hc6a40jjgp6vvq102qa1l4n787pfywx6jhzbhamp2"))))
(properties `((upstream-name . "mosaicCore")))
(build-system r-build-system)
(propagated-inputs
@ -15194,21 +15196,18 @@ (define-public r-labelled
(define-public r-ggformula
(package
(name "r-ggformula")
(version "0.10.4")
(version "0.12.0")
(source
(origin
(method url-fetch)
(uri (cran-uri "ggformula" version))
(sha256
(base32 "07d9sq0dqi0g5x9h58icfk1f4hgg1xz4mhbp2z2rxg9qgs74fvdj"))))
(base32 "0vbpivyxms46px3wqkbl1wq199mqdxq94gsiplv4i7lz0lzghsfm"))))
(build-system r-build-system)
(propagated-inputs
(list r-ggforce
r-ggplot2
(list r-ggplot2
r-ggridges
r-ggstance
r-labelled
r-magrittr
r-mosaiccore
r-rlang
r-scales
@ -15228,13 +15227,13 @@ (define-public r-ggformula
(define-public r-mosaicdata
(package
(name "r-mosaicdata")
(version "0.20.3")
(version "0.20.4")
(source
(origin
(method url-fetch)
(uri (cran-uri "mosaicData" version))
(sha256
(base32 "1s97yq24z7yhzmx0dpspfadpd8hndyhn7aiw0nslwrhvilhwa409"))))
(base32 "0y6ii234paknak0p8cm5wcjia4s4wh7iixjbbvdgp0w17c05dckh"))))
(properties `((upstream-name . "mosaicData")))
(build-system r-build-system)
(home-page "https://cran.r-project.org/web/packages/mosaicData/")
@ -15269,13 +15268,13 @@ (define-public r-raster
(define-public r-mosaic
(package
(name "r-mosaic")
(version "1.8.4.2")
(version "1.9.0")
(source
(origin
(method url-fetch)
(uri (cran-uri "mosaic" version))
(sha256
(base32 "12kpkb7vm54na9hjjkvzw6gm5plx0m6i0l9kihz2r30zanfx5jca"))))
(base32 "1dydqawljv5l9lmhdrhmr7wh3q1c2mnc61gc99jr0jbb1bmls327"))))
(build-system r-build-system)
(propagated-inputs
(list r-dplyr
@ -15288,6 +15287,7 @@ (define-public r-mosaic
r-mosaicdata
r-purrr
r-rlang
r-tibble
r-tidyr))
(native-inputs
(list r-knitr))
@ -21979,14 +21979,14 @@ (define-public r-zim
(define-public r-nor1mix
(package
(name "r-nor1mix")
(version "1.3-0")
(version "1.3-2")
(source
(origin
(method url-fetch)
(uri (cran-uri "nor1mix" version))
(sha256
(base32
"1817wcvlmxs70vs4db0jkxd7i037744zz8ay3c2a9949z29fxr4w"))))
"0252kqhdsp374isc59pm1c6dmsb16jibpnsp1bpyh4k5mg73cdj6"))))
(build-system r-build-system)
(home-page "https://cran.r-project.org/web/packages/nor1mix/")
(synopsis "Normal (1-d) mixture models")
@ -22290,14 +22290,14 @@ (define-public r-reinforcelearn
(define-public r-lemon
(package
(name "r-lemon")
(version "0.4.6")
(version "0.4.7")
(source
(origin
(method url-fetch)
(uri (cran-uri "lemon" version))
(sha256
(base32
"0v1kbyk64yzsk92h6yq03kp9alc9632qprznsws61r8firiskim5"))))
"1r33n7bkfhjpyi23j7gsi387qvyazcy9b912dsd3vg2yqir8s26p"))))
(build-system r-build-system)
(propagated-inputs
(list r-ggplot2
@ -25109,14 +25109,14 @@ (define-public r-rsparse
(define-public r-text2vec
(package
(name "r-text2vec")
(version "0.6.3")
(version "0.6.4")
(source
(origin
(method url-fetch)
(uri (cran-uri "text2vec" version))
(sha256
(base32
"1hi7ydb7xkgbff4lwnnz1biyl8m90w16hn3x5rrzvscvm53sj4y7"))))
"0sjlvp4zhzwc0ai7626fpw3ws8xv0xhl8gv8mrk24lrpk5nhin2h"))))
(properties `((upstream-name . "text2vec")))
(build-system r-build-system)
(propagated-inputs
@ -25218,14 +25218,14 @@ (define-public r-cyclocomp
(define-public r-lintr
(package
(name "r-lintr")
(version "3.1.0")
(version "3.1.1")
(source
(origin
(method url-fetch)
(uri (cran-uri "lintr" version))
(sha256
(base32
"1kb3jrzh1vn1fpj6phm2ni542yjgbbjmzgkn8w7khmh1sd9mj7pp"))))
"07c7h30nh1529wba8xkyg2sapj6r7jjckrxyzhrg2ssfwzs4dwdw"))))
(properties `((upstream-name . "lintr")))
(build-system r-build-system)
(propagated-inputs
@ -26489,13 +26489,13 @@ (define-public r-harmony
(define-public r-covr
(package
(name "r-covr")
(version "3.6.3")
(version "3.6.4")
(source
(origin
(method url-fetch)
(uri (cran-uri "covr" version))
(sha256
(base32 "17m2zzgfghr7gzcdgim21vsl12nd4714867dcp9xfb6ili31ikn0"))
(base32 "0al6n4gnnvgxk968skqnajpqpqyl6kpam3fmn782kihhcl1h8qib"))
(modules '((guix build utils)))
;; TODO: still need to replace highlight.js/highlight.pack.js
(snippet
@ -26616,14 +26616,14 @@ (define-public r-systemfonts
(define-public r-graphlayouts
(package
(name "r-graphlayouts")
(version "1.0.1")
(version "1.0.2")
(source
(origin
(method url-fetch)
(uri (cran-uri "graphlayouts" version))
(sha256
(base32
"0x777ixw2vvj1z3dams0zmyk25v7cdm4sx8v6knlb2mfkkg2gcyk"))))
"1mg0j9kcjp8dbpd8fy9vr5f35pz41v18vxc7q4pyl986pj859jam"))))
(properties `((upstream-name . "graphlayouts")))
(build-system r-build-system)
(propagated-inputs
@ -26767,14 +26767,14 @@ (define-public r-assertr
(define-public r-parameters
(package
(name "r-parameters")
(version "0.21.2")
(version "0.21.3")
(source
(origin
(method url-fetch)
(uri (cran-uri "parameters" version))
(sha256
(base32
"05ryyyibnm69hq1xa84r9n2gr1s1ifds70z4awmib2ch62098m43"))))
"091zpyq37v7xjicj4h4r4fqhrrc7d3hicgbdznsjn85sw4d7q595"))))
(properties `((upstream-name . "parameters")))
(build-system r-build-system)
(propagated-inputs
@ -26852,14 +26852,14 @@ (define-public r-insol
(define-public r-lifecycle
(package
(name "r-lifecycle")
(version "1.0.3")
(version "1.0.4")
(source
(origin
(method url-fetch)
(uri (cran-uri "lifecycle" version))
(sha256
(base32
"1hk9mblhap429fk77qpgc4hv0j91q5wpahi0y76w118m471zsnb4"))))
"1k4ibf2x90xgmzaq47vf9wrsh6a2fp2lg1l8bq89632bx33x795d"))))
(build-system r-build-system)
(propagated-inputs
(list r-cli r-glue r-rlang))
@ -26990,12 +26990,12 @@ (define-public r-pmcmrplus
(define-public r-pracma
(package
(name "r-pracma")
(version "2.4.2")
(version "2.4.4")
(source (origin
(method url-fetch)
(uri (cran-uri "pracma" version))
(sha256
(base32 "05lwx2yx7f45cr5amzbjv3b2p6ibspjxl0aglq2dga6rvxzk6l0x"))))
(base32 "0zxsqr7f4pcr1nmbbzliihyldv091ykzajv1mbdrkycp46pz6khs"))))
(build-system r-build-system)
(home-page "https://cran.r-project.org/web/packages/pracma/")
(synopsis "Practical numerical math functions")
@ -28997,14 +28997,14 @@ (define-public r-gdina
(define-public r-actcd
(package
(name "r-actcd")
(version "1.2-0")
(version "1.3-0")
(source
(origin
(method url-fetch)
(uri (cran-uri "ACTCD" version))
(sha256
(base32
"0mzjxxr2zfdidw8ibh6w8mvpkw3q3nvngqi05g9ind26ckvk053p"))))
"1a0gsznca5fv7i29xpcns4rkas5q88wv01rxvd4j66n64gw0ri4j"))))
(properties `((upstream-name . "ACTCD")))
(build-system r-build-system)
(propagated-inputs
@ -29403,14 +29403,14 @@ (define-public r-expint
(define-public r-actuar
(package
(name "r-actuar")
(version "3.3-3")
(version "3.3-4")
(source
(origin
(method url-fetch)
(uri (cran-uri "actuar" version))
(sha256
(base32
"0ji5p19vqnr3i3vfrql2qndhzcjnr57jrh0szil6gaz6bm56afc4"))))
"06693w4cwcchi0z64vgg7khc4k4209nw6m2x441nwix4x6rk1zjs"))))
(properties `((upstream-name . "actuar")))
(build-system r-build-system)
(propagated-inputs (list r-expint))
@ -31332,14 +31332,14 @@ (define-public r-rpf
(define-public r-openmx
(package
(name "r-openmx")
(version "2.21.8")
(version "2.21.10")
(source
(origin
(method url-fetch)
(uri (cran-uri "OpenMx" version))
(sha256
(base32
"1vvlb9q3w6i6g7kf0r5jnrlmdxskh3rbfss90icand046rl37qdz"))))
"1kll5iim5l71dxkjd8y9ma1494818j369gp92qdsy3x6lxy244ym"))))
(properties `((upstream-name . "OpenMx")))
(build-system r-build-system)
(propagated-inputs
@ -31532,14 +31532,14 @@ (define-public r-d3network
(define-public r-qgraph
(package
(name "r-qgraph")
(version "1.9.5")
(version "1.9.8")
(source
(origin
(method url-fetch)
(uri (cran-uri "qgraph" version))
(sha256
(base32
"1mi19bjx83zb42wmgb716a3l4gvwch3rmybdqmm8k3dl8xr2qnjc"))))
"1m019j5nxc0184p0r2zgdn457g555nxsp2s08maa053nydj1va0l"))))
(properties `((upstream-name . "qgraph")))
(build-system r-build-system)
(propagated-inputs
@ -34256,14 +34256,14 @@ (define-public r-rcppziggurat
(define-public r-rfast
(package
(name "r-rfast")
(version "2.0.9")
(version "2.1.0")
(source
(origin
(method url-fetch)
(uri (cran-uri "Rfast" version))
(sha256
(base32
"12jl5kqjn571zcqh4n351d7nx86b3jh46ds8krqz92f0z6fjmkzz"))))
"1zqq4k85i0nbzndkh0iiq3k83ly0mpl3pn4wkka6qxfvk6n6rr7r"))))
(properties `((upstream-name . "Rfast")))
(build-system r-build-system)
(propagated-inputs
@ -35147,14 +35147,14 @@ (define-public r-yardstick
(define-public r-warp
(package
(name "r-warp")
(version "0.2.0")
(version "0.2.1")
(source
(origin
(method url-fetch)
(uri (cran-uri "warp" version))
(sha256
(base32
"0s0acddc5h14245hi1faycxp0fyvw6nlgaz2df7da4fpyd2f638f"))))
"1gj65kgs7x63f6y2vnv13k293b52k4afbmdlcam635h9vs8da2h2"))))
(properties `((upstream-name . "warp")))
(build-system r-build-system)
(native-inputs (list r-knitr))
@ -36208,21 +36208,23 @@ (define-public r-seurat5object
(define-public r-seurat
(package
(name "r-seurat")
(version "4.4.0")
(version "5.0.0")
(source (origin
(method url-fetch)
(uri (cran-uri "Seurat" version))
(sha256
(base32
"1pdlvjh5xs1fyj2zic98sfz9zazbb45qywfqnhfzqb34jyaxy5qg"))))
"1hvqxfskwpw06dxc9hc9zvxqb73wr7qjxgrqgyjklxaq1xhr335v"))))
(properties `((upstream-name . "Seurat")))
(build-system r-build-system)
(propagated-inputs
(list r-cluster
r-cowplot
r-fastdummies
r-fitdistrplus
r-future
r-future-apply
r-generics
r-ggplot2
r-ggrepel
r-ggridges
@ -36233,6 +36235,7 @@ (define-public r-seurat
r-jsonlite
r-kernsmooth
r-leiden
r-lifecycle
r-lmtest
r-mass
r-matrix
@ -36249,10 +36252,12 @@ (define-public r-seurat
r-rcpp
r-rcppannoy
r-rcppeigen
r-rcpphnsw
r-rcppprogress
r-reticulate
r-rlang
r-rocr
r-rspectra
r-rtsne
r-scales
r-scattermore
@ -37008,14 +37013,14 @@ (define-public r-mlr3learners
(define-public r-bbotk
(package
(name "r-bbotk")
(version "0.7.2")
(version "0.7.3")
(source
(origin
(method url-fetch)
(uri (cran-uri "bbotk" version))
(sha256
(base32
"1gw0rkbiv93ifl9110r9sr0p9g4vg7qc11mznmmjq0a5vzmqgpm9"))))
"1ddr5w7n68d3imcrm0ipgk1waml8zj4szi566dmmiqvlpzpgdr3p"))))
(properties `((upstream-name . "bbotk")))
(build-system r-build-system)
(propagated-inputs
@ -37269,14 +37274,14 @@ (define-public r-highlight
(define-public r-clustree
(package
(name "r-clustree")
(version "0.5.0")
(version "0.5.1")
(source
(origin
(method url-fetch)
(uri (cran-uri "clustree" version))
(sha256
(base32
"1haam13aifak8fladyxwa0gz56anj1zfczfjgs07gbw90kf6azx8"))))
"05yizn8hcf4nsibypxahp2mz64sy10vli776mi0d2gvfb5p4kwmm"))))
(properties `((upstream-name . "clustree")))
(build-system r-build-system)
(propagated-inputs
@ -39346,14 +39351,14 @@ (define-public r-zoon
(define-public r-paws-common
(package
(name "r-paws-common")
(version "0.6.2")
(version "0.6.4")
(source
(origin
(method url-fetch)
(uri (cran-uri "paws.common" version))
(sha256
(base32
"1jgls5fks9s8m616qs6b7hvv0wf7nhzajyds15hnlasqwg387h3d"))))
"1pzgwljrk3maxcbmiy3yiccijm6c2ach8f9kzpqr7w5k5vkyhpvx"))))
(properties `((upstream-name . "paws.common")))
(build-system r-build-system)
(propagated-inputs
@ -40410,17 +40415,17 @@ (define-public r-logger
(define-public r-fasterize
(package
(name "r-fasterize")
(version "1.0.4")
(version "1.0.5")
(source
(origin
(method url-fetch)
(uri (cran-uri "fasterize" version))
(sha256
(base32 "1ckxi2iyxdahhgbliblcrkzziblfagzr54srjk27yp1lcgivvvs4"))))
(base32 "1d63q77hfbn2ly8cwsik4gaavdhidpi7idf7qj2y5bi9xhd10kyl"))))
(properties `((upstream-name . "fasterize")))
(build-system r-build-system)
(propagated-inputs
(list r-raster r-rcpp r-rcpparmadillo r-sp))
(list r-raster r-rcpp r-rcpparmadillo r-wk))
(native-inputs (list r-knitr))
(home-page "https://github.com/ecohealthalliance/fasterize")
(synopsis "Fast Polygon to Raster Conversion")

4
gnu/packages/databases.scm
View file

@ -5001,7 +5001,9 @@ (define-public soci
`(#:configure-flags
;; C++11 (-DSOCI_CXX11) is OFF by default. hyperledger-iroha needs it.
(list "-DCMAKE_CXX_STANDARD=17"
"-DSOCI_LIBDIR=lib")
"-DSOCI_LIBDIR=lib"
;; This is for relocation when linking statically
"-DCMAKE_CXX_FLAGS=-fPIE")
#:tests? #f)) ; may require running database management systems
(synopsis "C++ Database Access Library")
(description

12
gnu/packages/emacs-xyz.scm
View file

@ -8393,7 +8393,7 @@ (define-public emacs-flycheck-grammalecte
(inputs
(list grammalecte python))
(propagated-inputs
(list emacs-flycheck))
(list emacs-flycheck emacs-pkg-info))
(home-page "https://git.umaneti.net/flycheck-grammalecte/")
(synopsis "Integrate Grammalecte with Flycheck")
(description
@ -9992,8 +9992,8 @@ (define-public emacs-tagedit
(define-public emacs-slime
;; Update together with sbcl-slime-swank.
(let ((commit "0cc2e736112a0bc2a048ef6efd11dd67e3fbf7ad")
(revision "0"))
(let ((commit "735258a26bb97e85d25f39e4bef83c1f80c12f5d")
(revision "1"))
(package
(name "emacs-slime")
(version (git-version "2.28" revision commit))
@ -10005,7 +10005,7 @@ (define-public emacs-slime
(commit commit)))
(file-name (git-file-name name version))
(sha256
(base32 "0iq9r4007rrnabj290y79i926x2m4j20j6b0x701pkywz926sn02"))))
(base32 "0prskgzfqjmn8sc7p9nklnd0n1plwcvh40slgh23km31raplmzk7"))))
(build-system emacs-build-system)
(arguments
(list
@ -27115,7 +27115,7 @@ (define-public emacs-srfi
(define-public emacs-srht
(package
(name "emacs-srht")
(version "0.2")
(version "0.4")
(source (origin
(method git-fetch)
(uri (git-reference
@ -27124,7 +27124,7 @@ (define-public emacs-srht
(file-name (git-file-name name version))
(sha256
(base32
"10271yp9w9z27gjjpb7bnsqcrhqyvggrbmic6x1nlrn06vin1qkz"))))
"1kwc792r0kmnb7xhmggjgs8ii14c2rng9ci2k2zwy2zxqm0bynns"))))
(build-system emacs-build-system)
(arguments
(list

12
gnu/packages/engineering.scm
View file

@ -1092,7 +1092,7 @@ (define-public inspekt3d
(define-public kicad
(package
(name "kicad")
(version "7.0.8")
(version "7.0.9")
(source (origin
(method git-fetch)
(uri (git-reference
@ -1100,7 +1100,7 @@ (define-public kicad
(commit version)))
(sha256
(base32
"1gaj833hm3avyb7gyjnl4jk9cckcmj8084y6q45ysjvh283rxsy4"))
"1hq9rba1gcks14zwbr8nbicpsil4imslgfch6ll33fhizbks3fq4"))
(file-name (git-file-name name version))))
(build-system cmake-build-system)
(arguments
@ -1200,7 +1200,7 @@ (define-public kicad-doc
(file-name (git-file-name name version))
(sha256
(base32
"1ya9kwcbsh8cqbinjr1hr14sd0g6rls1awmvw8hwd7715f97x8fg"))))
"14dg99fvl6av9sn6gig6d6k1sdcf2svxy4fipqcz994z2khhz1sj"))))
(build-system cmake-build-system)
(arguments
`(#:configure-flags (list "-DBUILD_FORMATS=html")
@ -1234,7 +1234,7 @@ (define-public kicad-symbols
(file-name (git-file-name name version))
(sha256
(base32
"176zb7df25vz3wbhs94plmpabcgzxsnzbqmpdyssqr7m2wb2424a"))))
"0ynsnjq3z126cjkgm1fjbjvdvpc0walnr42ya9dv46l27kxy2j77"))))
(build-system cmake-build-system)
(arguments
`(#:tests? #f)) ; no tests exist
@ -1263,7 +1263,7 @@ (define-public kicad-footprints
(file-name (git-file-name name version))
(sha256
(base32
"1560m5mwwq0jrjhr8zdh2xrm1w7pgr250p81xzhdc4wj7zsb0rrp"))))
"16a4c2xs4i8wbm01a901yxabxk0qdsjkzlccfawddv82bkh4b87h"))))
(synopsis "Official KiCad footprint libraries")
(description "This package contains the official KiCad footprint libraries.")))
@ -1280,7 +1280,7 @@ (define-public kicad-packages3d
(file-name (git-file-name name version))
(sha256
(base32
"1ypy2nzs1x8i98jr5kmlxfd6y592qs22aq73yl8nq0s6640fc4kk"))))
"1cly28vc07i54v487zbb8d1h70nrd3naxvq146b0xnbrjwnd2q28"))))
(synopsis "Official KiCad 3D model libraries")
(description "This package contains the official KiCad 3D model libraries.")))

34
gnu/packages/fabric-management.scm
View file

@ -46,7 +46,7 @@ (define-module (gnu packages fabric-management)
(define-public opensm
(package
(name "opensm")
(version "3.3.22")
(version "3.3.24")
(source
(origin
(method url-fetch)
@ -54,7 +54,7 @@ (define-public opensm
(string-append "https://github.com/linux-rdma/opensm/releases/download/"
version "/opensm-" version ".tar.gz"))
(sha256
(base32 "19scwwpwqhqsyq4hbr5cflcmypss828lalxxd36yby7mbimca38y"))))
(base32 "0q74sx8y23h7picdzb4g5r84wcvc9hr9vzsdawkl812b38vmwcx3"))))
(build-system gnu-build-system)
(native-inputs
(list bison
@ -66,18 +66,20 @@ (define-public opensm
(inputs
(list rdma-core))
(arguments
`(#:configure-flags '("--disable-static")
#:phases
(modify-phases %standard-phases
(add-after 'install 'install-doc
(lambda* (#:key outputs #:allow-other-keys)
(let* ((base (assoc-ref outputs "out"))
(doc (string-append base "/share/doc/"
,name "-" ,version)))
(for-each (lambda (file)
(install-file file doc))
(find-files "doc"))
#t))))))
(list
#:configure-flags #~'("--disable-static")
#:phases
#~(modify-phases %standard-phases
(add-after 'install 'install-doc
(lambda* (#:key outputs #:allow-other-keys)
(let* ((base (assoc-ref outputs "out"))
(doc (string-append base "/share/doc/"
#$(package-name this-package)
"-"
#$(package-version this-package))))
(for-each (lambda (file)
(install-file file doc))
(find-files "doc"))))))))
(home-page "https://www.openfabrics.org/")
(synopsis "OpenIB InfiniBand Subnet Manager and management utilities")
(description "\
@ -183,7 +185,7 @@ (define-public ibutils
(define-public ucx
(package
(name "ucx")
(version "1.14.0")
(version "1.15.0")
(source (origin
(method git-fetch)
(uri (git-reference
@ -193,7 +195,7 @@ (define-public ucx
(patches (search-patches "ucx-tcp-iface-ioctl.patch"))
(sha256
(base32
"0ki2r768wqm92qv06wxrh3kv2nl2yj4ds9fz0s0b5rr2ycjiw9ir"))))
"1mk46vyfp8hsivk88s8gv0nf458jfs59fczpf66wwa3a9yp324jp"))))
(build-system gnu-build-system)
(arguments
(list

12
gnu/packages/gnuzilla.scm
View file

@ -546,9 +546,9 @@ (define all-mozilla-locales
;; XXXX: Workaround 'snippet' limitations.
(define computed-origin-method (@@ (guix packages) computed-origin-method))
(define %icecat-base-version "115.4.0")
(define %icecat-base-version "115.5.0")
(define %icecat-version (string-append %icecat-base-version "-guix0-preview1"))
(define %icecat-build-id "20231024000000") ;must be of the form YYYYMMDDhhmmss
(define %icecat-build-id "20231121000000") ;must be of the form YYYYMMDDhhmmss
;; 'icecat-source' is a "computed" origin that generates an IceCat tarball
;; from the corresponding upstream Firefox ESR tarball, using the 'makeicecat'
@ -568,12 +568,12 @@ (define icecat-source
"firefox-" upstream-firefox-version ".source.tar.xz"))
(sha256
(base32
"0ndf8b6qj0f178k5yq9s9mjgj9csb62f0igy74dzj28vlgrxn7y3"))))
"0a578r4kri7jdw8pkkzp7f1mm9idlk7sjxjghcb08k5p14172gyv"))))
;; The upstream-icecat-base-version may be older than the
;; %icecat-base-version.
(upstream-icecat-base-version "115.4.0")
(gnuzilla-commit "5b2ce0c4cefc73f996f260edfac368ecc3d86b24")
(upstream-icecat-base-version "115.5.0")
(gnuzilla-commit "bd66797f3bb057c9d051d4276d63843b4d7ee854")
(gnuzilla-source
(origin
(method git-fetch)
@ -585,7 +585,7 @@ (define icecat-source
(string-take gnuzilla-commit 8)))
(sha256
(base32
"13a0rv6b2vcf2mv7bfbb0rlx08pi0bz29dig0xrfdy3m1p39apla"))))
"0v3ckm8yv566f2y9a2bfzakbsk529f1ykr7dj69kb9k93dgny3ja"))))
;; 'search-patch' returns either a valid file name or #f, so wrap it
;; in 'assume-valid-file-name' to avoid 'local-file' warnings.

52
gnu/packages/haskell-apps.scm
View file

@ -294,13 +294,17 @@ (define-public ghcid
(define-public git-annex
(package
(name "git-annex")
(version "10.20230828")
(version "10.20230926")
(source
(origin
(method url-fetch)
(uri (hackage-uri "git-annex" version))
;; hackage release doesn't include everything needed for extra bits.
(method git-fetch)
(uri (git-reference
(url "https://git.joeyh.name/git/git-annex.git")
(commit version)))
(file-name (git-file-name name version))
(sha256
(base32 "0pb6834dwjs9kdki977rfkdyg58dfzy8wfwvswrz3n7h6bcnjd0b"))))
(base32 "0zsq686b0q7mlkybm1xrc0kpl32ymvf0ybar01p68wx800031b2b"))))
(build-system haskell-build-system)
(properties '((upstream-name . "git-annex")))
(arguments
@ -348,16 +352,7 @@ (define-public git-annex
(invoke "runhaskell" "PreConf.hs")))
(add-after 'build 'build-manpages
(lambda _
;; The Setup.hs rewrite above removed custom code for building
;; the man pages. In addition to that code, git-annex's source
;; tree has a file that's not included in the tarball but is used
;; by the Makefile to build man pages. Copy the core bits here.
(call-with-output-file "Build/MakeMans.hs"
(lambda (out)
(format out "module Main where~%")
(format out "import Build.Mans~%")
(format out "main = buildMansOrWarn~%")))
(invoke "runhaskell" "Build/MakeMans.hs")))
(invoke "make" "mans")))
(replace 'check
(lambda* (#:key tests? #:allow-other-keys)
;; We need to set the path so that Git recognizes
@ -373,13 +368,27 @@ (define-public git-annex
;; Undo `patch-shell-for-tests'.
(copy-file "/tmp/Shell.hs" "Utility/Shell.hs")
(apply (assoc-ref %standard-phases 'build) args)))
(add-after 'install 'install-manpages
(add-after 'install 'install-more
(lambda* (#:key outputs #:allow-other-keys)
(let ((man (string-append (assoc-ref outputs "out")
"/man/man1/")))
(mkdir-p man)
(for-each (lambda (file) (install-file file man))
(find-files "man")))))
(let* ((out (assoc-ref outputs "out"))
(bash (string-append out "/etc/bash_completions.d"))
(fish (string-append out "/share/fish/vendor_completions.d"))
(zsh (string-append out "/share/zsh/site-functions")))
(setenv "PREFIX" out)
(invoke "make" "install-mans")
(mkdir-p bash)
(copy-file "bash-completion.bash"
(string-append bash "/git-annex"))
(mkdir-p fish)
(with-output-to-file (string-append fish "/git-annex.fish")
(lambda _
(invoke (string-append out "/bin/git-annex")
"--fish-completion-script" "git-annex")))
(mkdir-p zsh)
(with-output-to-file (string-append zsh "/_git-annex")
(lambda _
(invoke (string-append out "/bin/git-annex")
"--zsh-completion-script" "git-annex"))))))
(add-after 'install 'install-symlinks
(lambda* (#:key outputs #:allow-other-keys)
(let* ((out (assoc-ref outputs "out"))
@ -406,13 +415,16 @@ (define-public git-annex
ghc-cryptonite
ghc-data-default
ghc-dav
ghc-dbus
ghc-disk-free-space
ghc-dlist
ghc-edit-distance
ghc-exceptions
ghc-fdo-notify
ghc-feed
ghc-filepath-bytestring
ghc-free
ghc-git-lfs
ghc-hinotify
ghc-http-client
ghc-http-client-tls

40
gnu/packages/haskell-xyz.scm
View file

@ -3913,6 +3913,27 @@ (define-public ghc-fast-logger
(description "This library provides a fast logging system for Haskell.")
(license license:bsd-3)))
(define-public ghc-fdo-notify
(package
(name "ghc-fdo-notify")
(version "0.3.1")
(source
(origin
(method url-fetch)
(uri (hackage-uri "fdo-notify" version))
(sha256
(base32 "1n4zk1i7g34w0wk5zy8n4r63xbglxf62h8j78kv5fc2yn95l30vh"))))
(build-system haskell-build-system)
(properties '((upstream-name . "fdo-notify")))
(inputs (list ghc-dbus))
(home-page "http://bitbucket.org/taejo/fdo-notify/")
(synopsis "Desktop Notifications client")
(description
"This package provides a library for issuing notifications using
@code{FreeDesktop.org's} Desktop Notifications protcol. This protocol is
supported by services such as Ubuntu's @code{NotifyOSD}.")
(license license:bsd-3)))
(define-public ghc-feed
(package
(name "ghc-feed")
@ -15683,6 +15704,25 @@ (define-public ghc-githash
<https://www.stackage.org/package/githash>")
(license license:bsd-3)))
(define-public ghc-git-lfs
(package
(name "ghc-git-lfs")
(version "1.2.0")
(source
(origin
(method url-fetch)
(uri (hackage-uri "git-lfs" version))
(sha256
(base32 "1iv3s1c7gwmsima9z3rsphjligpnf7h3vc5c96zgq9b71cx81lba"))))
(build-system haskell-build-system)
(properties '((upstream-name . "git-lfs")))
(inputs (list ghc-http-client ghc-http-types ghc-aeson ghc-network-uri
ghc-case-insensitive))
(home-page "http://hackage.haskell.org/package/git-lfs")
(synopsis "git-lfs protocol")
(description "An implementation of the git-lfs protocol.")
(license license:agpl3)))
(define-public ghc-nothunks
(package
(name "ghc-nothunks")

15
gnu/packages/linux.scm
View file

@ -6749,7 +6749,7 @@ (define-public ntfsfix/static
(define-public rdma-core
(package
(name "rdma-core")
(version "44.0")
(version "48.0")
(source (origin
(method url-fetch)
(uri (string-append "https://github.com/linux-rdma/rdma-core"
@ -6757,7 +6757,7 @@ (define-public rdma-core
version ".tar.gz"))
(sha256
(base32
"12w5v74wz1akac09frw7qk1yd06b00239zh7bvbvqyzjc0g61mi5"))))
"0h281dw2yph8pzfsr1wblqy6pb8nd9yj1pdf5c62zwc1l9b2fa3q"))))
(build-system cmake-build-system)
(arguments
`(#:tests? #f ;no tests
@ -8572,7 +8572,7 @@ (define-public procenv
(define-public libfabric
(package
(name "libfabric")
(version "1.11.2")
(version "1.19.0")
(source
(origin
(method url-fetch)
@ -8580,7 +8580,7 @@ (define-public libfabric
(string-append "https://github.com/ofiwg/libfabric/releases/download/v"
version "/libfabric-" version ".tar.bz2"))
(sha256
(base32 "1nnpfkwxhim2nqjkb1vwrb4wj4j3l6w6yvvy69fqam2snlhshazz"))))
(base32 "17pg0fb4fa77r1bmp0xk535m8n8fadpfdg93cb280ghhx55pck7i"))))
(build-system gnu-build-system)
(inputs `(("rdma-core" ,rdma-core)
,@(match (%current-system)
@ -8861,16 +8861,17 @@ (define-public mbpfan
(define-public psm2
(package
(name "psm2")
(version "11.2.230")
(version "12.0")
(source (origin
(method git-fetch)
(uri (git-reference
(url "https://github.com/intel/opa-psm2")
(commit (string-append "PSM2_" version))))
;; tag 'psm-v12.0' = commit ad5dd1b
(commit (string-append "psm-v" version))))
(file-name (git-file-name name version))
(sha256
(base32
"1bm7ndhi8qzmd0plnggj2h52yb34bab4k38530nsnkmv9smwdivl"))))
"04nar65ac11qqx41vkfs7iip8kfiah0zms7l4rmsxncpiz2iqfik"))))
(build-system gnu-build-system)
(arguments
(list #:make-flags

6
gnu/packages/lisp-check.scm
View file

@ -356,11 +356,11 @@ (define-public ecl-clunit
(sbcl-package->ecl-package sbcl-clunit))
(define-public sbcl-clunit2
(let ((commit "c3159275a6c5af166e60b592c3b7e22eaa69c048")
(let ((commit "b24c56851ee6ee6c4a9dc3725a634c06b604f207")
(revision "2"))
(package
(name "sbcl-clunit2")
(version (git-version "0.5.2" revision commit))
(version (git-version "0.6.1" revision commit))
(source
(origin
(method git-fetch)
@ -369,7 +369,7 @@ (define-public sbcl-clunit2
(commit commit)))
(file-name (git-file-name "cl-clunit2" version))
(sha256
(base32 "0n92z98dqfik3kfp25nz7yqycx4bpxlqbn69i5skcdnrj2ywmv01"))))
(base32 "03k4wc2zz31wcqcxy8fhq095i8xzcaxrzgrlrn2va10lcjs4v51b"))))
(build-system asdf-build-system/sbcl)
(synopsis "Unit testing framework for Common Lisp")
(description

74
gnu/packages/lisp-xyz.scm
View file

@ -3607,8 +3607,8 @@ (define-public ecl-pythonic-string-reader
(sbcl-package->ecl-package sbcl-pythonic-string-reader))
(define-public sbcl-slime-swank
(let ((commit "0cc2e736112a0bc2a048ef6efd11dd67e3fbf7ad")
(revision "0"))
(let ((commit "735258a26bb97e85d25f39e4bef83c1f80c12f5d")
(revision "1"))
(package
(name "sbcl-slime-swank")
(version (git-version "2.28" revision commit))
@ -3620,7 +3620,7 @@ (define-public sbcl-slime-swank
(url "https://github.com/slime/slime/")
(commit commit)))
(sha256
(base32 "0iq9r4007rrnabj290y79i926x2m4j20j6b0x701pkywz926sn02"))
(base32 "0prskgzfqjmn8sc7p9nklnd0n1plwcvh40slgh23km31raplmzk7"))
(modules '((guix build utils)))
(snippet
;; The doc folder drags `gawk' into the closure. Doc is already
@ -12132,6 +12132,50 @@ (define-public cl-jpeg
(define-public ecl-cl-jpeg
(sbcl-package->ecl-package sbcl-cl-jpeg))
(define-public sbcl-jpeg-turbo
(let ((commit "f79c646cc266c107bdace53572a31664754c6e0c")
(revision "1"))
(package
(name "sbcl-jpeg-turbo")
(version (git-version "1.0" revision commit))
(source
(origin
(method git-fetch)
(uri (git-reference
(url "https://github.com/shamazmazum/jpeg-turbo/")
(commit commit)))
(file-name (git-file-name "cl-jpeg-turbo" version))
(sha256
(base32 "1andd1ibbk3224idnpsnrn96flr5d1wm9ja3di57fs04wn577sag"))))
(build-system asdf-build-system/sbcl)
(arguments
(list #:phases
#~(modify-phases %standard-phases
(add-after 'unpack 'fix-lib-paths
(lambda* (#:key inputs #:allow-other-keys)
(substitute* "src/jpeg-turbo.lisp"
(("\"libturbojpeg\\.so\\.0\"")
(string-append "\""
(search-input-file inputs
"/lib/libturbojpeg.so")
"\""))))))))
(native-inputs
(list sbcl-fiveam))
(inputs
(list libjpeg-turbo sbcl-cffi))
(synopsis "Common Lisp wrapper for libjpeg-turbo")
(description
"This is a Common Lisp wrapper for libjpeg-turbo library which provides
TurboJPEG API for compressing and decompressing JPEG images.")
(home-page "https://github.com/shamazmazum/jpeg-turbo/")
(license license:bsd-2))))
(define-public cl-jpeg-turbo
(sbcl-package->cl-source-package sbcl-jpeg-turbo))
(define-public ecl-cl-jpeg-turbo
(sbcl-package->ecl-package sbcl-jpeg-turbo))
(define-public sbcl-png
(let ((commit "11b965fe378fd0561abe3616b18ff03af5179648")
(revision "1"))
@ -12206,11 +12250,11 @@ (define-public cl-svg
(sbcl-package->cl-source-package sbcl-cl-svg))
(define-public sbcl-nodgui
(let ((commit "b1d15fa9cca8550926f7823dbdd8be3b34387f1a")
(revision "2"))
(let ((commit "6baccf45371afd4dcc8cd3f38332b300614783b6")
(revision "1"))
(package
(name "sbcl-nodgui")
(version (git-version "0.4.8.5" revision commit))
(version (git-version "0.4.8.6" revision commit))
(source
(origin
(method git-fetch)
@ -12219,19 +12263,20 @@ (define-public sbcl-nodgui
(commit commit)))
(file-name (git-file-name "cl-nodgui" version))
(sha256
(base32 "1gsxg8igiavs8fr39vgw8ypa42wjqaq9sszwqiifpm7yvq54lls7"))))
(base32 "0fjz8362qmvkbzj9ylyllkdxg7vvj38l3y5qn4xi2gim92x4lx67"))))
(build-system asdf-build-system/sbcl)
(inputs
(list sbcl-alexandria
sbcl-bordeaux-threads
sbcl-cl-colors2
sbcl-cl-jpeg
sbcl-cl-ppcre-unicode
sbcl-cl-unicode
sbcl-clunit2
sbcl-esrap
sbcl-jpeg-turbo
sbcl-named-readtables
sbcl-parse-number
sbcl-pngload
tk
tklib))
(arguments
@ -18847,7 +18892,7 @@ (define-public cl-html-diff
(sbcl-package->cl-source-package sbcl-cl-html-diff))
(define-public sbcl-tooter
(let ((commit "2e1b22f0993419c1e7e6d10ead45d7bcafb5b6cb")
(let ((commit "2dcc2facddcacd79d0cce545a8c4b73c35826fc1")
(revision "4"))
(package
(name "sbcl-tooter")
@ -18860,10 +18905,13 @@ (define-public sbcl-tooter
(commit commit)))
(file-name (git-file-name "cl-tooter" version))
(sha256
(base32 "02ys58gzasvk7r84jmz6k522qcw2hkbgv8p0ax5i8dggjhr04cz2"))))
(base32 "1zisrmslj4rnibm02vxh7hbas2cfsjh6iizs2nfdg3a3pn7bhf6h"))))
(build-system asdf-build-system/sbcl)
(inputs
(list sbcl-cl-ppcre sbcl-documentation-utils sbcl-drakma
(list sbcl-alexandria
sbcl-cl-ppcre
sbcl-documentation-utils
sbcl-drakma
sbcl-yason))
(synopsis "Common Lisp client library for Mastodon instances")
(description
@ -18881,7 +18929,7 @@ (define-public cl-tooter
(define-public sbcl-croatoan
(package
(name "sbcl-croatoan")
(version "0.1")
(version "0.2")
(source
(origin
(method git-fetch)
@ -18890,7 +18938,7 @@ (define-public sbcl-croatoan
(commit (string-append "v" version))))
(file-name (git-file-name "cl-croatoan" version))
(sha256
(base32 "1whbvwc4df7zz0002xy3aczrpf4s3vk6kmyh9wydgwl112h060pd"))))
(base32 "0x2rlckyn8kn5mqy0fib8piggz694g3naarz2dvha1hsy4jhb1wg"))))
(build-system asdf-build-system/sbcl)
(arguments
'(#:phases

4
gnu/packages/lisp.scm
View file

@ -1247,7 +1247,7 @@ (define-public picolisp
(define-public janet
(package
(name "janet")
(version "1.29.1")
(version "1.32.1")
(source
(origin
(method git-fetch)
@ -1256,7 +1256,7 @@ (define-public janet
(commit (string-append "v" version))))
(file-name (git-file-name name version))
(sha256
(base32 "18684mxnb0jk63mkzi36zlmd8rjjv0msx3xxpmn67mhrnwz4x861"))))
(base32 "1nnqbpql6749597m0lp56i2zqm003pg690399l0g8kb9kwvpv1yv"))))
(build-system gnu-build-system)
(arguments
(list #:make-flags

65
gnu/packages/machine-learning.scm
View file

@ -1663,45 +1663,42 @@ (define-public python-tslearn
(define-public python-imbalanced-learn
(package
(name "python-imbalanced-learn")
(version "0.9.1")
(source (origin
(method url-fetch)
(uri (pypi-uri "imbalanced-learn" version))
(sha256
(base32
"0qnrmysnqpc8ii1w5n8mci20gcjhmjr7khvk7f2apdbqc2pgf52f"))))
(version "0.11.0")
(source
(origin
(method url-fetch)
(uri (pypi-uri "imbalanced-learn" version))
(sha256
(base32 "1p4gdgc8nsq0vjmw4y4d2bp9g0m1c23d0zgrzs90pnz6b24ax0km"))))
(build-system pyproject-build-system)
(arguments
(list
#:phases
'(modify-phases %standard-phases
(add-after 'unpack 'unbreak-tests
(lambda _
;; The doctests require tensorflow
(substitute* "setup.cfg"
(("--doctest-modules") ""))
;; Some tests require a home directory
(setenv "HOME" (getcwd))
;; We don't have keras
(delete-file "imblearn/keras/tests/test_generator.py")
;; We don't have tensorflow
(delete-file "imblearn/tensorflow/tests/test_generator.py"))))))
(propagated-inputs
(list python-joblib
python-numpy
python-scikit-learn
python-scipy
python-threadpoolctl))
(native-inputs
(list python-black
python-flake8
python-mypy
python-pandas
python-pytest
python-pytest-cov))
#:test-flags '(list "-k"
;; Although we cannot satify the Tensorflow and Keras requirements
;; (python-keras >= 2.4.3 and tensorflow >= 2.4.3), all tests
;; besides these pass.
"not balanced_batch_generator and not BalancedBatchGenerator")
#:phases '(modify-phases %standard-phases
(add-after 'unpack 'unbreak-tests
(lambda _
;; Some tests require a home directory
(setenv "HOME"
(getcwd)))))))
(propagated-inputs (list python-joblib python-numpy python-scikit-learn
python-scipy python-threadpoolctl))
(native-inputs (list python-black
python-flake8
python-keras
python-mypy
python-numpydoc
python-pandas
python-pytest
python-pytest-cov
tensorflow))
(home-page "https://github.com/scikit-learn-contrib/imbalanced-learn")
(synopsis "Toolbox for imbalanced dataset in machine learning")
(description "This is a Python package offering a number of re-sampling
(description
"This is a Python package offering a number of re-sampling
techniques commonly used in datasets showing strong between-class imbalance.
It is compatible with @code{scikit-learn}.")
(license license:expat)))

1
gnu/packages/mastodon.scm
View file

@ -119,6 +119,7 @@ (define-public tuba
(list gdk-pixbuf ; so pixbuf loader cache (for webp) is generated
gettext-minimal
`(,glib "bin") ; for glib-compile-resources
gsettings-desktop-schemas ; for the org.gnome.system.proxy schema
pkg-config))
(inputs
(list gst-plugins-bad

109
gnu/packages/maths.scm
View file

@ -7593,60 +7593,65 @@ (define-public elpa-openmpi
(synopsis "Eigenvalue solvers for symmetric matrices (with MPI support)")))
(define-public elemental
(package
(name "elemental")
(version "0.87.7")
(source (origin
(method git-fetch)
(uri (git-reference
(url "https://github.com/elemental/Elemental")
(commit (string-append "v" version))))
(file-name (git-file-name name version))
(sha256
(base32
"1687xpjjzig27y2pnqv7hv09smpijyfdpz7qjgmcxf4shfajlfkc"))))
(build-system cmake-build-system)
(home-page "https://github.com/elemental/Elemental")
(native-inputs
(list gfortran))
(inputs
`(("blas" ,openblas)
("gfortran:lib" ,gfortran "lib")
("gmp" ,gmp)
("lapack" ,lapack)
("metis" ,metis)
("mpc" ,mpc)
("mpfr" ,mpfr)
("mpi" ,openmpi)
("qd" ,qd)))
(arguments
`(#:build-type "Release" ;default RelWithDebInfo not supported
#:configure-flags `("-DEL_DISABLE_PARMETIS:BOOL=YES"
"-DEL_AVOID_COMPLEX_MPI:BOOL=NO"
"-DEL_CACHE_WARNINGS:BOOL=YES"
"-DEL_TESTS:BOOL=YES"
"-DCMAKE_INSTALL_LIBDIR=lib"
"-DGFORTRAN_LIB=gfortran")
#:phases (modify-phases %standard-phases
(add-before 'check 'mpi-setup
,%openmpi-setup)
(add-before 'check 'setup-tests
(lambda _
;; Parallelism is done at the MPI layer.
(setenv "OMP_NUM_THREADS" "1")
#t))
(add-after 'install 'remove-tests
(lambda* (#:key outputs #:allow-other-keys)
;; Tests are installed, with no easy configuration
;; switch to prevent this, so delete them.
(delete-file-recursively
(string-append (assoc-ref outputs "out") "/bin"))
#t)))))
(synopsis "Dense and sparse-direct linear algebra and optimization")
(description "Elemental is a modern C++ library for distributed-memory
;; The build of 0.87.7 is failed for a long time due to new version of GCC. The
;; latest commit has fixes.
;; See https://github.com/elemental/Elemental/issues/254
(let ((commit "6eb15a0da2a4998bf1cf971ae231b78e06d989d9")
(revision "0"))
(package
(name "elemental")
(version (git-version "0.87.7" revision commit))
(source (origin
(method git-fetch)
(uri (git-reference
(url "https://github.com/elemental/Elemental")
(commit commit)))
(file-name (git-file-name name version))
(sha256
(base32
"06xcs4ic60ndcf2hq19gr8yjwdsnphpcyhapab41rkw726z4lm7p"))))
(build-system cmake-build-system)
(arguments
(list
#:build-type "Release" ;default RelWithDebInfo not supported
#:configure-flags
#~(list "-DEL_DISABLE_PARMETIS:BOOL=YES"
"-DEL_AVOID_COMPLEX_MPI:BOOL=NO"
"-DEL_CACHE_WARNINGS:BOOL=YES"
"-DEL_TESTS:BOOL=YES"
"-DCMAKE_INSTALL_LIBDIR=lib"
"-DGFORTRAN_LIB=gfortran")
#:phases
#~(modify-phases %standard-phases
(add-before 'check 'mpi-setup
#$%openmpi-setup)
(add-before 'check 'setup-tests
(lambda _ ;; Parallelism is done at the MPI layer.
(setenv "OMP_NUM_THREADS" "1")))
(add-after 'install 'remove-tests
(lambda _
;; Tests are installed, with no easy configuration
;; switch to prevent this, so delete them.
(delete-file-recursively
(string-append #$output "/bin/test")))))))
(native-inputs
(list gfortran))
(inputs
(list `(,gfortran "lib")
gmp
lapack
metis
mpc
mpfr
openmpi
qd
openblas))
(home-page "https://github.com/elemental/Elemental")
(synopsis "Dense and sparse-direct linear algebra and optimization")
(description "Elemental is a modern C++ library for distributed-memory
dense and sparse-direct linear algebra, conic optimization, and lattice
reduction.")
(license license:bsd-2)))
(license license:bsd-2))))
(define-public mcrl2
(package

24
gnu/packages/mold.scm
View file

@ -1,5 +1,6 @@
;;; GNU Guix --- Functional package management for GNU
;;; Copyright © 2023 Zhu Zihao <all_but_last@163.com>
;;; Copyright © 2023 Efraim Flashner <efraim@flashner.co.il>
;;;
;;; This file is part of GNU Guix.
;;;
@ -34,7 +35,7 @@ (define-module (gnu packages mold)
(define-public mold
(package
(name "mold")
(version "1.10.1")
(version "2.3.2")
(source
(origin
(method git-fetch)
@ -43,10 +44,22 @@ (define-public mold
(commit (string-append "v" version))))
(file-name (git-file-name name version))
(sha256
(base32 "1bqv1a93n3nks38k8fdc5i7v7ca2sav8n4xxaph0ikaqw1mkjcg7"))
(base32 "1p6w92caysy9h0vkl26iv3viv0lvwzvbd357yykls0p13hnzlzkr"))
(modules '((guix build utils)))
(snippet
#~(begin
;; Fix detection of i686 systems.
;; This can be removed with the next release of mold.
(substitute* "test/elf/common.inc"
(("echo i386") "echo i686"))
(substitute* '("test/elf/common.inc"
"test/elf/global-offset-table.sh"
"test/elf/i386_tls-module-base.sh"
"test/elf/large-alignment-dso.sh"
"test/elf/large-alignment.sh"
"test/elf/nocopyreloc.sh"
"test/elf/range-extension-thunk.sh")
(("MACHINE = i386") "MACHINE = i686"))
(for-each
(lambda (x)
(delete-file-recursively (string-append "third-party/" x)))
@ -55,7 +68,8 @@ (define-public mold
(arguments
(list
#:configure-flags #~(list "-DMOLD_USE_SYSTEM_MIMALLOC=ON"
"-DMOLD_USE_SYSTEM_TBB=ON")
"-DMOLD_USE_SYSTEM_TBB=ON"
"-DBUILD_TESTING=ON")
#:phases
#~(modify-phases %standard-phases
(add-before 'configure 'force-system-xxhash
@ -69,6 +83,10 @@ (define-public mold
(("CC=\"\\$\\{TEST_CC:-cc\\}\"") "CC=gcc")
(("CXX=\"\\$\\{TEST_CXX:-c\\+\\+\\}\"")
"CXX=g++"))))
(add-before 'configure 'skip-tbb-lto-test
(lambda _
;; This test needs tbb 2021.9.0 or newer
(delete-file "test/elf/lto-version-script.sh")))
(add-before 'configure 'disable-rpath-test
(lambda _
;; This test fails because mold expect the RUNPATH as-is,

8
gnu/packages/mpi.scm
View file

@ -141,7 +141,7 @@ (define-public hwloc-1
(define-public hwloc-2
(package
(inherit hwloc-1)
(version "2.9.2")
(version "2.9.3")
(source (origin
(method url-fetch)
(uri (string-append "https://download.open-mpi.org/release/hwloc/v"
@ -149,7 +149,7 @@ (define-public hwloc-2
"/hwloc-" version ".tar.bz2"))
(sha256
(base32
"1kv0n3b9knb8aawf0hxaxn9wc9bbpwh676r2gmb0pc7qfzvgv1qa"))))
"1v0dzzgzp40slakdwdb8vy0hy4m2ff3gnzqpzi8k8vbgap764h2w"))))
;; libnuma is no longer needed.
(inputs (modify-inputs (package-inputs hwloc-1)
@ -184,7 +184,7 @@ (define-public hwloc
(define-public openmpi
(package
(name "openmpi")
(version "4.1.5")
(version "4.1.6")
(source
(origin
(method url-fetch)
@ -192,7 +192,7 @@ (define-public openmpi
(version-major+minor version)
"/downloads/openmpi-" version ".tar.bz2"))
(sha256
(base32 "1qyvc77diyrxmviirdwqpibgm32c4vkdlvw8g79rsf2pq9mrhh56"))
(base32 "05g4245v0pdqcyjmgn50519ry5v5q8ig26iinmiynvaihm29jh7p"))
(patches (search-patches "openmpi-mtl-priorities.patch"))))
(properties

32
gnu/packages/multiprecision.scm
View file

@ -10,6 +10,7 @@
;;; Copyright © 2021 Vinicius Monego <monego@posteo.net>
;;; Copyright © 2022 Maxim Cournoyer <maxim.cournoyer@gmail.com>
;;; Copyright © 2023 Janneke Nieuwenhuizen <janneke@gnu.org>
;;; Copyright © 2023 Sharlatan Hellseher <sharlatanus@gmail.com>
;;;
;;; This file is part of GNU Guix.
;;;
@ -251,30 +252,29 @@ (define-public irram
(define-public qd
(package
(name "qd")
(version "2.3.23")
(version "2.3.24")
(source
(origin
(method url-fetch)
(uri (string-append "https://crd-legacy.lbl.gov/~dhbailey/mpdist/qd-"
version ".tar.gz"))
(sha256
(base32 "09pfd77rmy370hy7qdqw84z21y9zpl3fcwzf93rhiv0kwhfg9smk"))))
(base32 "0f0fwsyh23p5zfyrj6n16q7b56g213fnhdc8dbl22r3fz1rnqyx4"))))
(build-system gnu-build-system)
(native-inputs
(list gfortran))
(native-inputs (list automake autoconf gfortran))
(arguments
`(#:configure-flags `("--disable-enable_fma" ;weird :/
"--disable-static"
"--enable-shared"
,,@(if (string-prefix? "aarch64"
(or (%current-target-system)
(%current-system)))
;; XXX: The qd_test test fails numerical
;; accuracy checks for 'dd_real::exp()' on
;; aarch64 with GCC 5.4 at -O2. Disabling
;; expensive optimizations lets it pass.
'("CXXFLAGS=-O3 -fno-expensive-optimizations")
'("CXXFLAGS=-O3")))))
(list
#:configure-flags
#~(list "--disable-enable_fma" ;weird :/
"--disable-static"
"--enable-shared"
#$@(if (target-aarch64?)
;; XXX: The qd_test test fails numerical
;; accuracy checks for 'dd_real::exp()' on
;; aarch64 with GCC 5.4 at -O2. Disabling
;; expensive optimizations lets it pass.
'("CXXFLAGS=-O3 -fno-expensive-optimizations")
'("CXXFLAGS=-O3")))))
(home-page "https://www.davidhbailey.com/dhbsoftware/")
(synopsis "Double-double and quad-double library")
(description "This package supports both a double-double

9
gnu/packages/music.scm
View file

@ -4982,7 +4982,7 @@ (define-public sfizz
(define-public musescore
(package
(name "musescore")
(version "4.0.2")
(version "4.1.1")
(source
(origin
(method git-fetch)
@ -4991,14 +4991,11 @@ (define-public musescore
(commit (string-append "v" version))))
(file-name (git-file-name name version))
(sha256
(base32 "1yri94xs4xw0lsvmk5q7bqnpgmdadchfn08r7bb2y07jsi8qgm6w"))
(base32 "12h26k9qnsq027gdpch579nchwrqva1ymwm2fj5xmlh0aayrwy4d"))
(modules '((guix build utils)))
(snippet
'(begin
;; Remove unused libraries...
(for-each delete-file-recursively
'("thirdparty/freetype"))
;; ... and precompiled binaries.
;; Delete precompiled binaries.
(delete-file-recursively "src/diagnostics/crashpad_handler")
(substitute* "src/diagnostics/CMakeLists.txt"
(("install") "#install"))))))

6
gnu/packages/package-management.scm
View file

@ -1510,8 +1510,8 @@ (define-public gwl/next
"0k9zkdyyzir3fvlbcfcqy17k28b51i20rpbjwlx2i1mwd2pw9cxc")))))))
(define-public guix-build-coordinator
(let ((commit "34463558e589aa260b15e53422652a37848aec95")
(revision "90"))
(let ((commit "c226d48d97ce3a248cf2d814c9b4c4f48e67511e")
(revision "91"))
(package
(name "guix-build-coordinator")
(version (git-version "0" revision commit))
@ -1522,7 +1522,7 @@ (define-public guix-build-coordinator
(commit commit)))
(sha256
(base32
"0fhy0l9js38byxwwb72qnjm358ai3k654jdnhwdcgk25pdsdzcpr"))
"0ig9hq483q2ir26gj6m9kj13a9hmq6sw18q0fiqvbvn31p4c8zvn"))
(file-name (string-append name "-" version "-checkout"))))
(build-system gnu-build-system)
(arguments

20
gnu/packages/parallel.scm
View file

@ -9,7 +9,7 @@
;;; Copyright © 2017, 2018 Rutger Helling <rhelling@mykolab.com>
;;; Copyright © 2018–2022 Tobias Geerinckx-Rice <me@tobias.gr>
;;; Copyright © 2018 Clément Lassieur <clement@lassieur.org>
;;; Copyright © 2019-2022 Ludovic Courtès <ludo@gnu.org>
;;; Copyright © 2019-2023 Ludovic Courtès <ludo@gnu.org>
;;; Copyright © 2020 Roel Janssen <roel@gnu.org>
;;; Copyright © 2021 Stefan Reichör <stefan@xsteve.at>
;;;
@ -185,7 +185,7 @@ (define-public xjobs
(define-public slurm
(package
(name "slurm")
(version "22.05.1")
(version "23.02.6")
(source (origin
(method url-fetch)
(uri (string-append
@ -193,7 +193,7 @@ (define-public slurm
version ".tar.bz2"))
(sha256
(base32
"0f3hhlki8g7slllsnyj1qikbsvr62i0hig85lcdcfnmsagzlhbyi"))
"08rz3r1rlnb3pmfdnbh542gm44ja0fdy8rkj4vm4lclc48cvqp2a"))
(modules '((guix build utils)))
(snippet
'(begin
@ -281,6 +281,20 @@ (define-public slurm
;; As noted in the link, YY.MM is the release scheme, and the 'maintenance'
;; digit does not introduce incompatibilities.
(define-public slurm-22.05
(package
(inherit slurm)
(version "22.05.1")
(source (origin
(inherit (package-source slurm))
(method url-fetch)
(uri (string-append
"https://download.schedmd.com/slurm/slurm-"
version ".tar.bz2"))
(sha256
(base32
"0f3hhlki8g7slllsnyj1qikbsvr62i0hig85lcdcfnmsagzlhbyi"))))))
(define-public slurm-21.08
(package
(inherit slurm)

105
gnu/packages/patches/ucx-tcp-iface-ioctl.patch
View file

@ -3,102 +3,121 @@ TCP network interfaces cannot be obtained via /sys/class/net. This patch
provides alternative code that uses the SIOCGIFCONF ioctl to get the
names of the available TCP network interfaces.
Initially submitted at <https://github.com/openucx/ucx/pull/4462>.
diff --git a/src/uct/tcp/tcp_iface.c b/src/uct/tcp/tcp_iface.c
index cad4a2709..7c1d2c9de 100644
index 6a6cd34fa..af32bb2e9 100644
--- a/src/uct/tcp/tcp_iface.c
+++ b/src/uct/tcp/tcp_iface.c
@@ -17,6 +17,8 @@
#include <sys/poll.h>
@@ -18,6 +18,8 @@
#include <netinet/tcp.h>
#include <dirent.h>
#include <float.h>
+#include <net/if.h>
+#include <sys/ioctl.h>
#define UCT_TCP_IFACE_NETDEV_DIR "/sys/class/net"
extern ucs_class_t UCS_CLASS_DECL_NAME(uct_tcp_iface_t);
@@ -586,6 +588,68 @@ static UCS_CLASS_DEFINE_NEW_FUNC(uct_tcp_iface_t, uct_iface_t, uct_md_h,
@@ -875,6 +877,85 @@ static UCS_CLASS_DEFINE_NEW_FUNC(uct_tcp_iface_t, uct_iface_t, uct_md_h,
uct_worker_h, const uct_iface_params_t*,
const uct_iface_config_t*);
+/* Fetch information about available network devices through an ioctl. */
+static ucs_status_t query_devices_ioctl(uct_md_h md,
+ uct_tl_device_resource_t **tl_devices_p,
+ unsigned *num_tl_devices_p)
+static ucs_status_t uct_tcp_query_devices_ioctl(uct_md_h md,
+ uct_tl_device_resource_t **devices_p,
+ unsigned *num_devices_p)
+{
+ int sock, err, i;
+ uct_tl_device_resource_t *resources, *tmp;
+ unsigned num_resources;
+ uct_tl_device_resource_t *devices, *tmp;
+ unsigned num_devices;
+ ucs_status_t status;
+ struct ifconf conf;
+ struct ifreq reqs[10];
+
+ conf.ifc_len = sizeof reqs;
+ conf.ifc_req = reqs;
+ conf.ifc_len = 0;
+ conf.ifc_req = NULL;
+
+ sock = socket(SOCK_STREAM, AF_INET, 0);
+ if (sock < 0) {
+ ucs_error("socket(2) failed: %m");
+ status = UCS_ERR_IO_ERROR;
+ goto out;
+ status = ucs_socket_create(AF_INET, SOCK_STREAM, &sock);
+ if (status != UCS_OK) {
+ goto out;
+ }
+
+ err = ioctl(sock, SIOCGIFCONF, &conf);
+ if (err < 0) {
+ ucs_error("SIOCGIFCONF ioctl failed: %m");
+ status = UCS_ERR_IO_ERROR;
+ goto out;
+ ucs_error("ioctl(SIOCGIFCONF) failed: %m");
+ status = UCS_ERR_IO_ERROR;
+ goto out;
+ }
+
+ resources = NULL;
+ num_resources = 0;
+ for (i = 0; i < conf.ifc_len / sizeof(struct ifreq); i++) {
+ const char *name = reqs[i].ifr_name;
+ conf.ifc_req = ucs_calloc(1, conf.ifc_len, "ifreq");
+ if (conf.ifc_req == NULL) {
+ ucs_error("memory alocation failed");
+ status = UCS_ERR_NO_MEMORY;
+ goto out;
+ }
+
+ if (!ucs_netif_is_active(name, AF_INET)) {
+ err = ioctl(sock, SIOCGIFCONF, &conf);
+ if (err < 0) {
+ ucs_error("ioctl(SIOCGIFCONF) failed: %m");
+ status = UCS_ERR_IO_ERROR;
+ goto out_free;
+ }
+
+ devices = NULL;
+ num_devices = 0;
+ for (i = 0; i < (conf.ifc_len / sizeof(struct ifreq)); i++) {
+ const char *name = conf.ifc_req[i].ifr_name;
+ sa_family_t family = conf.ifc_req[i].ifr_addr.sa_family;
+
+ if (!ucs_netif_is_active(name, family)) {
+ continue;
+ }
+
+ tmp = ucs_realloc(resources, sizeof(*resources) * (num_resources + 1),
+ "tcp resources");
+ tmp = ucs_realloc(devices, sizeof(*devices) * (num_devices + 1),
+ "tcp devices");
+ if (tmp == NULL) {
+ ucs_free(resources);
+ ucs_free(devices);
+ status = UCS_ERR_NO_MEMORY;
+ goto out;
+ goto out_free;
+ }
+ resources = tmp;
+ devices = tmp;
+
+ ucs_snprintf_zero(resources[i].name, sizeof(resources[i].name),
+ ucs_snprintf_zero(devices[num_devices].name,
+ sizeof(devices[num_devices].name),
+ "%s", name);
+ resources[i].type = UCT_DEVICE_TYPE_NET;
+ ++num_resources;
+ devices[num_devices].type = UCT_DEVICE_TYPE_NET;
+ ++num_devices;
+ }
+
+ *num_tl_devices_p = num_resources;
+ *tl_devices_p = resources;
+ status = UCS_OK;
+ *num_devices_p = num_devices;
+ *devices_p = devices;
+ status = UCS_OK;
+
+out_free:
+ ucs_free(conf.ifc_req);
+out:
+ if (sock >= 0) close(sock);
+ if (sock >= 0) {
+ close(sock);
+ }
+ return status;
+}
+
ucs_status_t uct_tcp_query_devices(uct_md_h md,
uct_tl_device_resource_t **devices_p,
unsigned *num_devices_p)
@@ -599,9 +663,9 @@ ucs_status_t uct_tcp_query_devices(uct_md_h md,
@@ -893,9 +974,9 @@ ucs_status_t uct_tcp_query_devices(uct_md_h md,
dir = opendir(UCT_TCP_IFACE_NETDEV_DIR);
if (dir == NULL) {
- ucs_error("opendir(%s) failed: %m", UCT_TCP_IFACE_NETDEV_DIR);
- status = UCS_ERR_IO_ERROR;
- goto out;
+ /* When /sys is unavailable, as can be the case in a container,
+ * resort to a good old 'ioctl'. */
+ return query_devices_ioctl(md, devices_p, num_devices_p);
+ /* When /sys is unavailable, as can be the case in a container,
+ * resort to a good old 'ioctl'. */
+ return uct_tcp_query_devices_ioctl(md, devices_p, num_devices_p);
}
devices = NULL;
@@ -655,7 +719,6 @@ ucs_status_t uct_tcp_query_devices(uct_md_h md,
@@ -963,7 +1044,6 @@ ucs_status_t uct_tcp_query_devices(uct_md_h md,
out_closedir:
closedir(dir);

33
gnu/packages/python-science.scm
View file

@ -22,6 +22,7 @@
;;; Copyright © 2022 Eric Bavier <bavier@posteo.net>
;;; Copyright © 2022 Antero Mejr <antero@mailbox.org>
;;; Copyright © 2022 jgart <jgart@dismail.de>
;;; Copyright © 2023 Troy Figiel <troy@troyfigiel.com>
;;;
;;; This file is part of GNU Guix.
;;;
@ -349,6 +350,38 @@ (define-public python-scikit-optimize
@code{skopt} aims to be accessible and easy to use in many contexts.")
(license license:bsd-3)))
(define-public python-tdda
(package
(name "python-tdda")
(version "2.0.9")
(source
(origin
(method url-fetch)
(uri (pypi-uri "tdda" version))
(sha256
(base32 "1xs91s8b7cshjcqw88qsrjh10xly799k5rf2ycawqfz2mw8sy3br"))))
(build-system pyproject-build-system)
(arguments
'(#:phases (modify-phases %standard-phases
(add-after 'unpack 'relax-requirements
(lambda _
(substitute* "setup.py"
(("pandas>=1.5.2")
"pandas"))))
(replace 'check
(lambda* (#:key tests? #:allow-other-keys)
(when tests?
(invoke "tdda" "test")))))))
(native-inputs (list python-numpy python-pandas))
(home-page "https://www.stochasticsolutions.com")
(synopsis "Test-driven data analysis library for Python")
(description
"The TDDA Python module provides command-line and Python API support
for the overall process of data analysis, through tools that peform
reference testing, constraint discovery for data, automatic inference
of regular expressions from text data and automatic test generation.")
(license license:expat))) ; MIT License
(define-public python-trimesh
(package
(name "python-trimesh")

35
gnu/packages/python-web.scm
View file

@ -5204,54 +5204,29 @@ (define-public python-google-auth-oauthlib
(define-public whoogle-search
(package
(name "whoogle-search")
(version "0.8.2")
(version "0.8.3")
(source (origin
(method url-fetch)
(uri (pypi-uri "whoogle-search" version))
(sha256
(base32
"1r6ymainwc3b8aar90b74mpnx3rsfscgzh0llwvsb03fbhiypw5g"))))
"09b9k97jflajvrs0npyz994rj8xkk400s98jw63b6vpsgw9q9nk4"))))
(build-system pyproject-build-system)
(arguments
(list
;; The tests need network access
#:tests? #f))
(propagated-inputs
(list python-attrs
python-beautifulsoup4
python-cachelib
python-certifi
python-cffi
(list python-beautifulsoup4
python-brotli
python-chardet
python-click
python-cryptography
python-cssutils
python-defusedxml
python-flask
python-flask-session
python-idna
python-itsdangerous
python-jinja2
python-markupsafe
python-more-itertools
python-packaging
python-pluggy
python-py
python-pycodestyle
python-pycparser
python-pyopenssl
python-pyparsing
python-pysocks
python-dateutil
python-dotenv
python-requests
python-soupsieve
python-stem
python-urllib3
python-waitress
python-wcwidth
python-werkzeug
python-dotenv))
python-waitress))
(home-page "https://github.com/benbusby/whoogle-search")
(synopsis "Self-hosted, ad-free, privacy-respecting metasearch engine")
(description

8
gnu/packages/python-xyz.scm
View file

@ -5045,13 +5045,13 @@ (define-public python-roman
(define-public python-rollbar
(package
(name "python-rollbar")
(version "0.16.3")
(version "1.0.0")
(source (origin
(method url-fetch)
(uri (pypi-uri "rollbar" version))
(sha256
(base32
"1qpd0j50wqli3867xmhwk65pm1cxjs60yg83mcvcf3kic3y3sc82"))))
"1bzkgp4r79d789q15vnjji2gcb34bnksx9l7q9pjkw12kzjbfiv3"))))
(build-system python-build-system)
(native-inputs (list python-pytest-runner python-unittest2))
(inputs (list python-requests python-six python-httpx python-blinker
@ -32573,13 +32573,13 @@ (define-public python-types-protobuf
(define-public python-types-pytz
(package
(name "python-types-pytz")
(version "2021.3.6")
(version "2023.3.1.1")
(source
(origin
(method url-fetch)
(uri (pypi-uri "types-pytz" version))
(sha256
(base32 "14yr5hg2ww8s4a0mz2bkd549fv8qgm538fnzxvqv92ld1pcpym3l"))))
(base32 "16mbinqac2fjjh4gqw2940q8ysjqwj0hrvj4p9mqz76l5hcx08yc"))))
(build-system python-build-system)
(home-page "https://github.com/python/typeshed")
(synopsis "Typing stubs for pytz")

66
gnu/packages/statistics.scm
View file

@ -672,14 +672,14 @@ (define-public r-lattice
(define-public r-matrix
(package
(name "r-matrix")
(version "1.6-1.1")
(version "1.6-3")
(source
(origin
(method url-fetch)
(uri (cran-uri "Matrix" version))
(sha256
(base32
"1hlcxr38p4ybb67n25cc1ssh2q2r8cj0flc59lid8hclzvqv27ik"))))
"094n9qf5j7bzi4cyxhm276qx2b2qp676ad8w9gql0qhzhfc889li"))))
(properties `((upstream-name . "Matrix")))
(build-system r-build-system)
(propagated-inputs
@ -1178,14 +1178,14 @@ (define-public r-sendmailr
(define-public r-stringi
(package
(name "r-stringi")
(version "1.7.12")
(version "1.8.1")
(source
(origin
(method url-fetch)
(uri (cran-uri "stringi" version))
(sha256
(base32
"02g0464sbprrbjlacx727p9ad1s5nbxl2mnvfmm9h7q000lsrs7g"))))
"0jm2f5wh231dzs46g7ic2k4633x9v9bd2a03dlpmq5rr46j299ay"))))
(build-system r-build-system)
(inputs (list icu4c))
(native-inputs (list pkg-config))
@ -1204,13 +1204,13 @@ (define-public r-stringi
(define-public r-stringr
(package
(name "r-stringr")
(version "1.5.0")
(version "1.5.1")
(source
(origin
(method url-fetch)
(uri (cran-uri "stringr" version))
(sha256
(base32 "0fk34ql5ak57f06l10ai300kxay6r7kkkyfanh8r24qaf3bmkcaj"))))
(base32 "1pj5xwg8kq2jllmszgkw96qj37wlb0x0vx4f3m5j211zpd8yrbd4"))))
(build-system r-build-system)
(propagated-inputs
(list r-cli r-glue r-lifecycle r-magrittr r-rlang r-stringi r-vctrs))
@ -1448,13 +1448,13 @@ (define-public r-bh
(define-public r-evaluate
(package
(name "r-evaluate")
(version "0.22")
(version "0.23")
(source (origin
(method url-fetch)
(uri (cran-uri "evaluate" version))
(sha256
(base32
"0sz4zimz4brbd9sawdazfgipkmfzzdmdq01b5m8pnrql5xrxhiwh"))))
"0p540jl6sixpgk08cp2h9470d28p7n66pfafiskvz3rba0vrrky9"))))
(build-system r-build-system)
(home-page "https://github.com/hadley/evaluate")
(synopsis "Parsing and evaluation tools for R")
@ -1782,13 +1782,13 @@ (define-public r-r6
(define-public r-rlang
(package
(name "r-rlang")
(version "1.1.1")
(version "1.1.2")
(source (origin
(method url-fetch)
(uri (cran-uri "rlang" version))
(sha256
(base32
"16fsibxbh4fy62x6fw358qbniw085qs1wjyr75n22xv9g6kwjpjy"))))
"14l0dz36wav2jbz0dd3w34va68lrhr7fgd9dqf1v4nawdvff23ia"))))
(build-system r-build-system)
(home-page "http://rlang.tidyverse.org")
(synopsis "Functions for base types, core R and Tidyverse features")
@ -3063,13 +3063,13 @@ (define-public r-readr
(define-public r-plotrix
(package
(name "r-plotrix")
(version "3.8-2")
(version "3.8-4")
(source (origin
(method url-fetch)
(uri (cran-uri "plotrix" version))
(sha256
(base32
"07xwq3505qb2yak7pfda22yqwifj6m78f8b5rm0ym74808qrawmv"))))
"1mp8mb79prgf5fzlaix4fvslr4q67hrzxqdv3kr7mik1mf9jv8p6"))))
(build-system r-build-system)
(home-page "https://cran.r-project.org/web/packages/plotrix")
(synopsis "Various plotting functions")
@ -3126,13 +3126,13 @@ (define-public r-latticeextra
(define-public r-rcpparmadillo
(package
(name "r-rcpparmadillo")
(version "0.12.6.4.0")
(version "0.12.6.6.0")
(source (origin
(method url-fetch)
(uri (cran-uri "RcppArmadillo" version))
(sha256
(base32
"1k7xq2yl4pkc7krz1bcdnx5kfj6n4zjmnm40nly2da2ji87agv49"))))
"171yflg07xi6570ich5gxhzsqqs7k3rxyhwg96amlkm1qn8v2pnk"))))
(properties `((upstream-name . "RcppArmadillo")))
(build-system r-build-system)
(propagated-inputs
@ -3195,14 +3195,14 @@ (define-public r-catools
(define-public r-rprojroot
(package
(name "r-rprojroot")
(version "2.0.3")
(version "2.0.4")
(source
(origin
(method url-fetch)
(uri (cran-uri "rprojroot" version))
(sha256
(base32
"15zq606s544wmbvk5dw13xq0sspr9dsxyxlvzvn0r48f8x3l4q2h"))))
"16bf6ga5fgm83j3m67plw5i54az2vdbvw5m99ixaqkd24pxn7x5m"))))
(build-system r-build-system)
(native-inputs
(list r-knitr))
@ -3340,13 +3340,13 @@ (define-public r-blob
(define-public r-rsqlite
(package
(name "r-rsqlite")
(version "2.3.2")
(version "2.3.3")
(source (origin
(method url-fetch)
(uri (cran-uri "RSQLite" version))
(sha256
(base32
"09vbx3akqws8a07ai6qbp3jn1w05qsmazl79wl2dyvvjpzs8b62x"))))
"0i1cjhqcclglv62j4dclxraaj5jmqdwyj4bs3qfbd8jd8v5d1c9j"))))
(properties `((upstream-name . "RSQLite")))
(build-system r-build-system)
(propagated-inputs
@ -3370,13 +3370,13 @@ (define-public r-rsqlite
(define-public r-rcurl
(package
(name "r-rcurl")
(version "1.98-1.12")
(version "1.98-1.13")
(source (origin
(method url-fetch)
(uri (cran-uri "RCurl" version))
(sha256
(base32
"1ci6lsxm0f13yzw712gcbq23syl54x5llvhs2w1b8wwm9vqgx0qs"))))
"01pkmip1sllislmp34c25i9m9mlrid9b48xfjbf93sml55ijz985"))))
(properties `((upstream-name . "RCurl")))
(build-system r-build-system)
(arguments
@ -3412,13 +3412,13 @@ (define-public r-rcurl
(define-public r-xml
(package
(name "r-xml")
(version "3.99-0.14")
(version "3.99-0.15")
(source (origin
(method url-fetch)
(uri (cran-uri "XML" version))
(sha256
(base32
"1ygi65ddgbsamxw2rm0p2clfak1xj44xyisgk48y72cd9ldaddic"))))
"0giv03bixc4kcq4dmcwzra7gp01i41hfr1710fd1v2hacya4d8cq"))))
(properties
`((upstream-name . "XML")))
(build-system r-build-system)
@ -4543,13 +4543,13 @@ (define-public r-mvtnorm
(define-public r-matrixstats
(package
(name "r-matrixstats")
(version "1.0.0")
(version "1.1.0")
(source (origin
(method url-fetch)
(uri (cran-uri "matrixStats" version))
(sha256
(base32
"0vxd7g1fm4x0f72bs1xfik1d4yklvpjdyg1hpx86pl8fwr86i1wl"))))
"0h85hjvsmc8s3hyjdj83fykb2vl8jc7pb9ynp2xsl0q9v1sihrxl"))))
(properties `((upstream-name . "matrixStats")))
(build-system r-build-system)
(arguments
@ -6014,18 +6014,18 @@ (define-public r-minqa
(define-public r-rcppeigen
(package
(name "r-rcppeigen")
(version "0.3.3.9.3")
(version "0.3.3.9.4")
(source
(origin
(method url-fetch)
(uri (cran-uri "RcppEigen" version))
(sha256
(base32
"0xhwgn77166ir7qnzl25mj0byskkqr0b36hihrpr2zaqsrzs8wsq"))))
"1faz1phvg7g14bchi88vizn5mfhgiwmsjg7jzkyf1yjg0f6vpsj1"))))
(properties `((upstream-name . "RcppEigen")))
(build-system r-build-system)
(propagated-inputs
(list r-rcpp r-matrix))
(list r-rcpp))
(home-page "http://eigen.tuxfamily.org")
(synopsis "Rcpp integration for the Eigen templated linear algebra library")
(description
@ -6060,14 +6060,14 @@ (define-public r-modelmetrics
(define-public r-matrixmodels
(package
(name "r-matrixmodels")
(version "0.5-2")
(version "0.5-3")
(source
(origin
(method url-fetch)
(uri (cran-uri "MatrixModels" version))
(sha256
(base32
"0ap3mfzb2psjwlksfjzs2ycl5598bllwzx5hfmf9db4yjsydn1hw"))))
"03zjfxjk4l2dl1117slz163w0ky675d23sjfni4d7fdhqq359ny2"))))
(properties `((upstream-name . "MatrixModels")))
(build-system r-build-system)
(propagated-inputs
@ -6142,14 +6142,14 @@ (define-public r-nloptr
(define-public r-lme4
(package
(name "r-lme4")
(version "1.1-34")
(version "1.1-35.1")
(source
(origin
(method url-fetch)
(uri (cran-uri "lme4" version))
(sha256
(base32
"1bbaxkrd5m3d40y6jdyrdr4vsjyzkfixbqjwj6c8inmks98f2wp8"))))
"0nzv1a22pfsf2ryw91h16ic4cb8y8g6wh0gx3msr7gv8dwwi3974"))))
(build-system r-build-system)
(propagated-inputs
(list r-boot
@ -6395,14 +6395,14 @@ (define-public r-tclust
(define-public r-ranger
(package
(name "r-ranger")
(version "0.15.1")
(version "0.16.0")
(source
(origin
(method url-fetch)
(uri (cran-uri "ranger" version))
(sha256
(base32
"0bibv9xf6w8k8nsc13f2yd4kx99aq0i758h3wfh089szgkpdjrad"))))
"12c52gqqwaaid5b062gad18ir1vala1z3a0z5j4af1xqzlxgk583"))))
(build-system r-build-system)
(propagated-inputs
(list r-rcpp r-matrix r-rcppeigen))

27
gnu/packages/tbb.scm
View file

@ -49,10 +49,33 @@ (define-public tbb
(build-system cmake-build-system)
(arguments
`(#:configure-flags
'(,@(if (target-riscv64?)
'(,@(if (or (target-riscv64?)
(target-ppc32?))
'("-DTBB_TEST_LINK_FLAGS=-latomic")
`())
"-DTBB_STRICT=OFF"))) ;; Don't fail on warnings
,@(if (or (target-arm32?)
(target-ppc32?))
'("-DTBB_TEST_COMPILE_FLAGS=-DTBB_TEST_LOW_WORKLOAD")
`())
"-DTBB_STRICT=OFF") ;; Don't fail on warnings
#:phases
(modify-phases %standard-phases
,@(cond
((target-arm32?)
`((add-after 'unpack 'adjust-test-suite
(lambda _
(substitute* "test/CMakeLists.txt"
;; Bus error, skipped on mips.
((".*test_malloc_pools.*") ""))))))
((target-ppc32?)
`((add-after 'unpack 'adjust-test-suite
(lambda _
(substitute* "test/CMakeLists.txt"
;; These tests hang forever.
((".*test_function_node.*") "")
((".*test_multifunction_node.*") "")
((".*test_async_node.*") ""))))))
(else '())))))
(home-page "https://www.threadingbuildingblocks.org")
(synopsis "C++ library for parallel programming")
(description

4
gnu/packages/tor.scm
View file

@ -63,14 +63,14 @@ (define-module (gnu packages tor)
(define-public tor
(package
(name "tor")
(version "0.4.8.8")
(version "0.4.8.9")
(source (origin
(method url-fetch)
(uri (string-append "https://dist.torproject.org/tor-"
version ".tar.gz"))
(sha256
(base32
"0140d0zcjxi4vijvr2gk3kmnd4xa80sjj9kdcc2gzazyr84fkfr1"))))
"0rfgn88izn74nh6gy42ggwmiicnylp73skrlwm61n4znj247vfsr"))))
(build-system gnu-build-system)
(arguments
(list #:configure-flags

21
gnu/packages/web-browsers.scm
View file

@ -95,6 +95,7 @@ (define-module (gnu packages web-browsers)
#:use-module (gnu packages qt)
#:use-module (gnu packages sdl)
#:use-module (gnu packages sqlite)
#:use-module (gnu packages tcl)
#:use-module (gnu packages tls)
#:use-module (gnu packages webkit)
#:use-module (gnu packages xorg))
@ -586,7 +587,7 @@ (define-public vimb
(define-public nyxt
(package
(name "nyxt")
(version "3.9.1")
(version "3.9.2")
(source
(origin
(method git-fetch)
@ -595,7 +596,7 @@ (define-public nyxt
(commit version)))
(sha256
(base32
"1x7ia43yh024hwwsh2a6g2daznkzgjlisnxvjfcb9sgvfqfa368i"))
"1v85jn46d9vacjig6n9z797fch88fw6vzwbfdzlqdkm86vvm8dwn"))
(file-name (git-file-name "nyxt" version))
(modules '((guix build utils)))
(snippet
@ -852,16 +853,16 @@ (define-public bombadillo
(define-public tinmop
(package
(name "tinmop")
(version "0.9.9.141")
(version "0.9.9.1414213")
(source
(origin
(method git-fetch)
(uri (git-reference
(url "https://notabug.org/cage/tinmop")
(url "https://codeberg.org/cage/tinmop")
(commit (string-append "v" version))))
(file-name (git-file-name name version))
(sha256
(base32 "0hx52kaq0q9iccalkxk50q1v3mf9ypardjgv56d5sdrbhfqyashl"))))
(base32 "0rlgnqld6ls46452xvcr8k4ji4lwmlsrxib5ii9l9clkm0s477wv"))))
(build-system gnu-build-system)
(native-inputs
(list autoconf
@ -872,6 +873,7 @@ (define-public tinmop
nano
openssl
sbcl
tk
unzip
xdg-utils))
(inputs
@ -893,10 +895,12 @@ (define-public tinmop
sbcl-crypto-shortcuts
sbcl-drakma
sbcl-esrap
sbcl-flexi-streams
sbcl-ieee-floats
sbcl-local-time
sbcl-log4cl
sbcl-marshal
sbcl-nodgui
sbcl-osicat
sbcl-parse-number
sbcl-percent-encoding
@ -907,6 +911,7 @@ (define-public tinmop
sbcl-trivial-clipboard
sbcl-unix-opts
sbcl-usocket
sbcl-yason
sqlite))
(arguments
`(#:tests? #f
@ -937,10 +942,10 @@ (define-public tinmop
"--eval \"(push \\\"$$(pwd)/\\\" asdf:*central-registry*)\" "))))
#t)))))
(synopsis
"Gemini, gopher, kami and pleroma client with a terminal interface")
"Gemini, gopher, kami and mastodon/pleroma client with a terminal interface")
(description
"This package provides a Gemini, gopher, kami and pleroma client with a
terminal interface.")
"This package provides a Gemini, gopher, kami and mastodon/pleroma client
with a terminal interface, for Gemini also a GUI is available.")
(home-page "https://www.autistici.org/interzona/tinmop.html")
(license license:gpl3+)))

30
gnu/packages/web.scm
View file

@ -64,6 +64,7 @@
;;; Copyright © 2023 David Thompson <dthompson2@worcester.edu>
;;; Copyright © 2023 Christopher Howard <christopher@librehacker.com>
;;; Copyright © 2023 Felix Lechner <felix.lechner@lease-up.com>
;;; Copyright © 2023 Evgeny Pisemsky <evgeny@pisemsky.com>
;;;
;;; This file is part of GNU Guix.
;;;
@ -7910,6 +7911,35 @@ (define-public geomyidae
@end enumerate\n")
(license license:expat)))
(define-public monsterid
(let ((commit "5597f177b473343ff5cad9a6e0e5b255312c6096")
(revision "0"))
(package
(name "monsterid")
(version (git-version "0" revision commit))
(source
(origin
(method git-fetch)
(uri (git-reference
(url "https://github.com/splitbrain/monsterID")
(commit commit)))
(file-name (git-file-name name version))
(sha256
(base32 "0ixyrrcbw96plcdna2rx1pqwisqy9hnr57kvamgj13lzlv2whdb3"))))
(build-system copy-build-system)
(arguments
'(#:install-plan '(("monsterid.php" "share/web/monsterid/")
("parts/" "share/web/monsterid/parts/"
#:include-regexp ("\\.png$")))))
(home-page "https://www.splitbrain.org/projects/monsterid")
(synopsis "The original MonsterID implementation")
(description
"MonsterID is a method to generate a unique monster image based upon a
certain identifier (IP address, email address, whatever). It can be
used to automatically provide personal avatar images in blog comments
or other community services.")
(license license:expat))))
(define-public cat-avatar-generator
(let ((commit "9360ea33f79d1dad3e43494b09878b5e3f6b41fa")
(revision "1"))

9
gnu/packages/xdisorg.scm
View file

@ -2796,9 +2796,16 @@ (define-public wl-clipboard
#~(list (string-append "-Dzshcompletiondir=" #$output
"/share/zsh/site-functions")
(string-append "-Dfishcompletiondir=" #$output
"/share/fish/completions"))
"/share/fish/vendor_completions.d"))
#:phases
#~(modify-phases %standard-phases
(add-after 'unpack 'fix-bash-completion-dir
(lambda _
(substitute* "completions/bash/meson.build"
(("bash_completion_dir =.*")
(string-append "bash_completion_dir = "
"join_paths(get_option('sysconfdir'), "
"'bash_completion.d')\n")))))
(add-after 'unpack 'patch-file-names
(lambda* (#:key inputs #:allow-other-keys)
(substitute* (find-files "src" "\\.c$")

4
guix/build-system/clojure.scm
View file

@ -83,8 +83,8 @@ (define* (lower name
#:clojure #:jdk #:zip)))
(if target
(error "No cross-compilation for clojure-build-system yet: LOWER"
target) ; FIXME
#f ; FIXME: No cross-compilation for
; clojure-build-system yet
(bag (name name)
(system system)
(host-inputs `(,@(if source

13
guix/build/guile-build-system.scm
View file

@ -28,6 +28,7 @@ (define-module (guix build guile-build-system)
#:use-module (ice-9 format)
#:use-module (guix build utils)
#:export (target-guile-effective-version
target-guile-scm+go
%standard-phases
guile-build))
@ -44,7 +45,17 @@ (define* (target-guile-effective-version #:optional guile)
(string? line)
line)))
(define (file-sans-extension file) ;TODO: factorize
(define* (target-guile-scm+go output #:optional guile)
"Return paths under `output' for scm and go files for effective version of
GUILE or whichever `guile' is in $PATH. Raises an error if they cannot be
determined."
(let* ((version (or (target-guile-effective-version guile)
(error "Cannot determine the effective target guile version.")))
(scm (string-append output "/share/guile/site/" version))
(go (string-append output "/lib/guile/" version "/site-ccache")))
(values scm go)))
(define (file-sans-extension file) ;TODO: factorize
"Return the substring of FILE without its extension, if any."
(let ((dot (string-rindex file #\.)))
(if dot

2
guix/scripts/locate.scm
View file

@ -657,7 +657,7 @@ (define* (populate-database database clear?)
files)))
(()
(if (null? files)
(unless update?
(unless (or update? (assoc-ref opts 'clear?))
(leave (G_ "no files to search for~%")))
(leave (N_ "file~{ '~a'~} not found in database '~a'~%"
"files~{ '~a'~} not found in database '~a'~%"

6
tests/guix-locate.sh
View file

@ -70,3 +70,9 @@ then
$cmd_store guile | grep "$(guix build guile-bootstrap)/bin/guile"
$cmd_store boot-9.scm | grep ^guile-bootstrap
fi
# The command below is an error: "no files to search for"...
guix locate && false
# ... but this one is fine.
guix locate --clear