diff options
| author | John Kehayias <john.kehayias@protonmail.com> | 2023-11-21 18:11:10 -0500 |
|---|---|---|
| committer | John Kehayias <john.kehayias@protonmail.com> | 2023-11-21 18:11:30 -0500 |
| commit | 8d2a5a36af4c36dfa08c7ee75d7a06ebb7a8225a (patch) | |
| tree | 0e0f0cc9d5fa5a3c783451d12b10ebdb4c0aafe9 /gnu | |
| parent | d1b786fe629ae9a80f37f64fdf48b9d7c132cd11 (diff) | |
| parent | 42be8fa560a7554ac35801b46c3a0a007fd742ce (diff) | |
| download | guix-8d2a5a36af4c36dfa08c7ee75d7a06ebb7a8225a.tar.gz | |
Merge branch 'master' into mesa-updates
Change-Id: I94c6874e5fdf916e3eb911f1a7df610cd3275474
Diffstat (limited to 'gnu')
37 files changed, 840 insertions, 591 deletions
diff --git a/gnu/packages/admin.scm b/gnu/packages/admin.scm index afbcf7fda6..17225863d7 100644 --- a/gnu/packages/admin.scm +++ b/gnu/packages/admin.scm @@ -4432,6 +4432,9 @@ late.") " *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 @@ late.") 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 @@ launch daemons into the relevant nodes.") (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 @@ launch daemons into the relevant nodes.") (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 diff --git a/gnu/packages/astronomy.scm b/gnu/packages/astronomy.scm index 47913a1282..c063285b52 100644 --- a/gnu/packages/astronomy.scm +++ b/gnu/packages/astronomy.scm @@ -589,13 +589,13 @@ mining in astronomy.") (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 @@ image formats.") (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 @@ image formats.") (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 @@ any arbitrary astrometric projection defined in the WCS standard.") (define-public celestia (package (name "celestia") - (version "1.6.3") + (version "1.6.4") (source (origin (method git-fetch) @@ -1394,7 +1394,7 @@ any arbitrary astrometric projection defined in the WCS standard.") (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 @@ astronomy and astrophysics.") (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 @@ astronomy and astrophysics.") 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 @@ Herschel.") (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 @@ attempting to maintain ISTP compliance (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 @@ Cesium.") (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 @@ of astronomical sources.") (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 @@ changing the pixel resolution, orientation, coordinate system.") (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 @@ Science Institute} image array manipulation functions.") (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 @@ task}.") (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 @@ low quality ones") (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 @@ standard astronomy libraries: @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 @@ Mercator, Mollweide, Peters, polyconic, orthographic and rectangular.") (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 @@ application. It can track a large number of satellites and display their 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 @@ Moon position, etc.") (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 @@ functions, so that they can be called with scalar or array inputs.") (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 @@ functions, so that they can be called with scalar or array inputs.") (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 @@ functions, so that they can be called with scalar or array inputs.") "--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 @@ datetime object.") (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 @@ between image and reference catalogs. Currently only aligning images with (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 @@ default) to world coordinates.") (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 @@ channels (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 @@ pipelines.") (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 @@ pipelines.") (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 @@ orbit around the Earth.") (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 diff --git a/gnu/packages/benchmark.scm b/gnu/packages/benchmark.scm index 4d92457e59..08fece6e91 100644 --- a/gnu/packages/benchmark.scm +++ b/gnu/packages/benchmark.scm @@ -137,7 +137,7 @@ is to write a job file matching the I/O load one wants to simulate.") (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 @@ is to write a job file matching the I/O load one wants to simulate.") (file-name (git-file-name name version)) (sha256 (base32 - "02hxbk9g9nl59bk5qcfl3djj7b58vsqys340m1xdbyqwcrbnahh9")) + "04kczch2hlfzbgk929vcxx480kc6raba8rbz246j7d26k1z1zh8h")) (modules '((guix build utils))) (snippet '(begin diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index ee5a94c461..7ff364ee55 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -12203,13 +12203,13 @@ rectangular layout tree built by ggtree with the grammar of ggplot2.") (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 @@ using whole genome sequencing data.") (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 @@ on the plot.") (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)) diff --git a/gnu/packages/c.scm b/gnu/packages/c.scm index ea58c68262..da0d11e8f7 100644 --- a/gnu/packages/c.scm +++ b/gnu/packages/c.scm @@ -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 @@ Telemetry Transport (MQTT) publish-subscribe messaging protocol.") (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 @@ Telemetry Transport (MQTT) publish-subscribe messaging protocol.") (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/") diff --git a/gnu/packages/check.scm b/gnu/packages/check.scm index cf26196a24..1f5b886977 100644 --- a/gnu/packages/check.scm +++ b/gnu/packages/check.scm @@ -2551,7 +2551,7 @@ mypy plugins.") (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 @@ mypy plugins.") (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 diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 11bc4aee50..221a81612c 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -147,13 +147,13 @@ the vignette \"AER\" for a package overview.)") (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 @@ labels on the node can also be achieved.") (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 @@ RUV-I, and RUV-III, along with various supporting algorithms.") (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 @@ variables.") (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 @@ particularly easy to create complete web applications using httpuv alone.") (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 @@ a list of p-values.") (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 @@ in R and Shiny via the D3 visualization library.") (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 @@ and/or higher-resolution databases.") (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 @@ coordinates.") (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 @@ provides an interactive R manager and worker environment.") (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 @@ these progress updates.") (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 @@ iVAT).") (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 @@ information between package updates.") (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 @@ multivariate distributions.") (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 @@ JavaScript library) and interact with the igraph package.") (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 @@ automatically translated to the equivalent, but usually much faster, (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 @@ Python's @url{https://github.com/ActiveState/appdirs,Appdirs} to R.") (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 @@ implemented in bibutils.") (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 @@ the work.") (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 @@ containing one or more SNPs that evolved under directional selection.") (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 @@ subsequence} (LCS) using a dynamic programming algorithm.") (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 @@ haven package.") (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 @@ while providing the intuitive capabilities of @code{r-ggplot2}.") (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 @@ Processing of very large files is supported.") (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 @@ Processing of very large files is supported.") r-mosaicdata r-purrr r-rlang + r-tibble r-tidyr)) (native-inputs (list r-knitr)) @@ -21979,14 +21979,14 @@ numbers from ZIP and ZINB distributions.") (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 @@ can be used with function approximation, eligibility traces (Singh & Sutton, (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 @@ Row} (CSR) format.") (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 @@ provides tools to compute this metric.") (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 @@ function and interfaces to external frameworks.") (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 @@ be used further by e.g. graphic devices.") (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 @@ in pipelines.") (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 @@ atmospheric physics.") (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 @@ to ODEs by numerical differencing.") (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 @@ be conducted. A graphical user interface is also provided.") (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 @@ API; see the package vignette for details.") (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 @@ Complete access to optimized C functions is made available with (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 @@ network, tree, dendrogram, and Sankey graphs from R using data frames.") (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 @@ aggregation for comparing different implementations in order to provide a (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 @@ and regression metrics (e.g., RMSE).") (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 @@ other R users.") (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 @@ other R users.") r-jsonlite r-kernsmooth r-leiden + r-lifecycle r-lmtest r-mass r-matrix @@ -36249,10 +36252,12 @@ other R users.") 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 @@ vector machines, and gradient boosting.") (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 @@ chunks.") (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 @@ fully reproducible.") (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 @@ formatting and delivering log messages with low overhead.") (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") diff --git a/gnu/packages/databases.scm b/gnu/packages/databases.scm index 3eeee9fadf..f0ea100c3b 100644 --- a/gnu/packages/databases.scm +++ b/gnu/packages/databases.scm @@ -5001,7 +5001,9 @@ The drivers officially supported by @code{libdbi} are: `(#: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 diff --git a/gnu/packages/emacs-xyz.scm b/gnu/packages/emacs-xyz.scm index be7ffd1f37..90fe9fceeb 100644 --- a/gnu/packages/emacs-xyz.scm +++ b/gnu/packages/emacs-xyz.scm @@ -8393,7 +8393,7 @@ for Flow files.") (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 @@ in @code{html-mode}.") (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 @@ in @code{html-mode}.") (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 @@ them in your web browser.") (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 @@ them in your web browser.") (file-name (git-file-name name version)) (sha256 (base32 - "10271yp9w9z27gjjpb7bnsqcrhqyvggrbmic6x1nlrn06vin1qkz")))) + "1kwc792r0kmnb7xhmggjgs8ii14c2rng9ci2k2zwy2zxqm0bynns")))) (build-system emacs-build-system) (arguments (list diff --git a/gnu/packages/engineering.scm b/gnu/packages/engineering.scm index b43e058af4..c533997027 100644 --- a/gnu/packages/engineering.scm +++ b/gnu/packages/engineering.scm @@ -1092,7 +1092,7 @@ Emacs).") (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 @@ Emacs).") (commit version))) (sha256 (base32 - "1gaj833hm3avyb7gyjnl4jk9cckcmj8084y6q45ysjvh283rxsy4")) + "1hq9rba1gcks14zwbr8nbicpsil4imslgfch6ll33fhizbks3fq4")) (file-name (git-file-name name version)))) (build-system cmake-build-system) (arguments @@ -1200,7 +1200,7 @@ electrical diagrams), gerbview (viewing Gerber files) and others.") (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 @@ electrical diagrams), gerbview (viewing Gerber files) and others.") (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 @@ libraries.") (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 @@ libraries.") (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."))) diff --git a/gnu/packages/fabric-management.scm b/gnu/packages/fabric-management.scm index b6b2e5176c..f41b4e99ed 100644 --- a/gnu/packages/fabric-management.scm +++ b/gnu/packages/fabric-management.scm @@ -46,7 +46,7 @@ (define-public opensm (package (name "opensm") - (version "3.3.22") + (version "3.3.24") (source (origin (method url-fetch) @@ -54,7 +54,7 @@ (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 @@ (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 @@ testing InfiniBand networks.") (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 @@ testing InfiniBand networks.") (patches (search-patches "ucx-tcp-iface-ioctl.patch")) (sha256 (base32 - "0ki2r768wqm92qv06wxrh3kv2nl2yj4ds9fz0s0b5rr2ycjiw9ir")))) + "1mk46vyfp8hsivk88s8gv0nf458jfs59fczpf66wwa3a9yp324jp")))) (build-system gnu-build-system) (arguments (list diff --git a/gnu/packages/gnuzilla.scm b/gnu/packages/gnuzilla.scm index 6a93ab933e..e5d0c4ea9b 100644 --- a/gnu/packages/gnuzilla.scm +++ b/gnu/packages/gnuzilla.scm @@ -546,9 +546,9 @@ variable defined below. It requires guile-json to be installed." ;; 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 @@ variable defined below. It requires guile-json to be installed." "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 @@ variable defined below. It requires guile-json to be installed." (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. diff --git a/gnu/packages/haskell-apps.scm b/gnu/packages/haskell-apps.scm index ac22082088..3288b0d0a9 100644 --- a/gnu/packages/haskell-apps.scm +++ b/gnu/packages/haskell-apps.scm @@ -294,13 +294,17 @@ to @code{cabal repl}).") (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 @@ to @code{cabal repl}).") (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 @@ to @code{cabal repl}).") ;; 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 @@ to @code{cabal repl}).") 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 diff --git a/gnu/packages/haskell-xyz.scm b/gnu/packages/haskell-xyz.scm index 676cdfa912..5d9e5757a0 100644 --- a/gnu/packages/haskell-xyz.scm +++ b/gnu/packages/haskell-xyz.scm @@ -3913,6 +3913,27 @@ when used with GHC versions which already provide the (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 @@ purposes. See the <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") diff --git a/gnu/packages/linux.scm b/gnu/packages/linux.scm index 641d1cd113..2024163a08 100644 --- a/gnu/packages/linux.scm +++ b/gnu/packages/linux.scm @@ -6749,7 +6749,7 @@ from the ntfs-3g package. It is meant to be used in initrds.") (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 @@ from the ntfs-3g package. It is meant to be used in initrds.") version ".tar.gz")) (sha256 (base32 - "12w5v74wz1akac09frw7qk1yd06b00239zh7bvbvqyzjc0g61mi5")))) + "0h281dw2yph8pzfsr1wblqy6pb8nd9yj1pdf5c62zwc1l9b2fa3q")))) (build-system cmake-build-system) (arguments `(#:tests? #f ;no tests @@ -8572,7 +8572,7 @@ comparing system environments.") (define-public libfabric (package (name "libfabric") - (version "1.11.2") + (version "1.19.0") (source (origin (method url-fetch) @@ -8580,7 +8580,7 @@ comparing system environments.") (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 @@ privileges.") (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 diff --git a/gnu/packages/lisp-check.scm b/gnu/packages/lisp-check.scm index cbbc8c3979..63a16d608c 100644 --- a/gnu/packages/lisp-check.scm +++ b/gnu/packages/lisp-check.scm @@ -356,11 +356,11 @@ experience.") (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 @@ experience.") (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 diff --git a/gnu/packages/lisp-xyz.scm b/gnu/packages/lisp-xyz.scm index 7f00a08203..4bc3c71a54 100644 --- a/gnu/packages/lisp-xyz.scm +++ b/gnu/packages/lisp-xyz.scm @@ -3607,8 +3607,8 @@ writing code that contains string literals that contain code themselves.") (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 @@ writing code that contains string literals that contain code themselves.") (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 @@ for reading and writing JPEG image files.") (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 @@ Scalable Vector Graphics files.") (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 @@ Scalable Vector Graphics files.") (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 @@ HTML documents.") (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 @@ HTML documents.") (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 @@ protocol for Mastodon.") (define-public sbcl-croatoan (package (name "sbcl-croatoan") - (version "0.1") + (version "0.2") (source (origin (method git-fetch) @@ -18890,7 +18938,7 @@ protocol for Mastodon.") (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 diff --git a/gnu/packages/lisp.scm b/gnu/packages/lisp.scm index f26362c79f..8fccee94dc 100644 --- a/gnu/packages/lisp.scm +++ b/gnu/packages/lisp.scm @@ -1247,7 +1247,7 @@ including a built-in database engine and a GUI system.") (define-public janet (package (name "janet") - (version "1.29.1") + (version "1.32.1") (source (origin (method git-fetch) @@ -1256,7 +1256,7 @@ including a built-in database engine and a GUI system.") (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 diff --git a/gnu/packages/machine-learning.scm b/gnu/packages/machine-learning.scm index a84377e1eb..7d833005bc 100644 --- a/gnu/packages/machine-learning.scm +++ b/gnu/packages/machine-learning.scm @@ -1663,45 +1663,42 @@ and forecasting.") (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))) diff --git a/gnu/packages/mastodon.scm b/gnu/packages/mastodon.scm index 44f8664997..cbeccdb402 100644 --- a/gnu/packages/mastodon.scm +++ b/gnu/packages/mastodon.scm @@ -119,6 +119,7 @@ Features include: (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 diff --git a/gnu/packages/maths.scm b/gnu/packages/maths.scm index ed1708c77b..34710fc65c 100644 --- a/gnu/packages/maths.scm +++ b/gnu/packages/maths.scm @@ -7593,60 +7593,65 @@ symmetric matrices.") (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 diff --git a/gnu/packages/mold.scm b/gnu/packages/mold.scm index 1e67f80081..4ce3741be2 100644 --- a/gnu/packages/mold.scm +++ b/gnu/packages/mold.scm @@ -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-public mold (package (name "mold") - (version "1.10.1") + (version "2.3.2") (source (origin (method git-fetch) @@ -43,10 +44,22 @@ (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 @@ (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 @@ (("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, diff --git a/gnu/packages/mpi.scm b/gnu/packages/mpi.scm index baf6ce11e0..85afc8cefc 100644 --- a/gnu/packages/mpi.scm +++ b/gnu/packages/mpi.scm @@ -141,7 +141,7 @@ bind processes, and much more.") (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 @@ bind processes, and much more.") "/hwloc-" version ".tar.bz2")) (sha256 (base32 - "1kv0n3b9knb8aawf0hxaxn9wc9bbpwh676r2gmb0pc7qfzvgv1qa")))) + "1v0dzzgzp40slakdwdb8vy0hy4m2ff3gnzqpzi8k8vbgap764h2w")))) ;; libnuma is no longer needed. (inputs (modify-inputs (package-inputs hwloc-1) @@ -184,7 +184,7 @@ bind processes, and much more.") (define-public openmpi (package (name "openmpi") - (version "4.1.5") + (version "4.1.6") (source (origin (method url-fetch) @@ -192,7 +192,7 @@ bind processes, and much more.") (version-major+minor version) "/downloads/openmpi-" version ".tar.bz2")) (sha256 - (base32 "1qyvc77diyrxmviirdwqpibgm32c4vkdlvw8g79rsf2pq9mrhh56")) + (base32 "05g4245v0pdqcyjmgn50519ry5v5q8ig26iinmiynvaihm29jh7p")) (patches (search-patches "openmpi-mtl-priorities.patch")))) (properties diff --git a/gnu/packages/multiprecision.scm b/gnu/packages/multiprecision.scm index 3aa5dccfab..0c6255c129 100644 --- a/gnu/packages/multiprecision.scm +++ b/gnu/packages/multiprecision.scm @@ -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 @@ error. Additionally, iRRAM uses the concept of multi-valued functions.") (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 diff --git a/gnu/packages/music.scm b/gnu/packages/music.scm index 85be6f6151..b5f7d882e4 100644 --- a/gnu/packages/music.scm +++ b/gnu/packages/music.scm @@ -4982,7 +4982,7 @@ includes LV2 plugins and a JACK standalone client.") (define-public musescore (package (name "musescore") - (version "4.0.2") + (version "4.1.1") (source (origin (method git-fetch) @@ -4991,14 +4991,11 @@ includes LV2 plugins and a JACK standalone client.") (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")))))) diff --git a/gnu/packages/package-management.scm b/gnu/packages/package-management.scm index 70a26c242a..4b585362a4 100644 --- a/gnu/packages/package-management.scm +++ b/gnu/packages/package-management.scm @@ -1510,8 +1510,8 @@ environments.") "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 @@ environments.") (commit commit))) (sha256 (base32 - "0fhy0l9js38byxwwb72qnjm358ai3k654jdnhwdcgk25pdsdzcpr")) + "0ig9hq483q2ir26gj6m9kj13a9hmq6sw18q0fiqvbvn31p4c8zvn")) (file-name (string-append name "-" version "-checkout")))) (build-system gnu-build-system) (arguments diff --git a/gnu/packages/parallel.scm b/gnu/packages/parallel.scm index 2ec87e751a..f3af1680b0 100644 --- a/gnu/packages/parallel.scm +++ b/gnu/packages/parallel.scm @@ -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 @@ when jobs finish.") (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 @@ when jobs finish.") version ".tar.bz2")) (sha256 (base32 - "0f3hhlki8g7slllsnyj1qikbsvr62i0hig85lcdcfnmsagzlhbyi")) + "08rz3r1rlnb3pmfdnbh542gm44ja0fdy8rkj4vm4lclc48cvqp2a")) (modules '((guix build utils))) (snippet '(begin @@ -281,6 +281,20 @@ by managing a queue of pending work.") ;; 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) diff --git a/gnu/packages/patches/ucx-tcp-iface-ioctl.patch b/gnu/packages/patches/ucx-tcp-iface-ioctl.patch index c441a0861a..2a0e4ce138 100644 --- a/gnu/packages/patches/ucx-tcp-iface-ioctl.patch +++ b/gnu/packages/patches/ucx-tcp-iface-ioctl.patch @@ -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; ++ ++ 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("ioctl(SIOCGIFCONF) failed: %m"); ++ status = UCS_ERR_IO_ERROR; ++ goto out; ++ } + -+ sock = socket(SOCK_STREAM, AF_INET, 0); -+ if (sock < 0) { -+ ucs_error("socket(2) failed: %m"); -+ status = UCS_ERR_IO_ERROR; -+ goto out; ++ 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; + } + + 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_free; + } + -+ resources = NULL; -+ num_resources = 0; -+ for (i = 0; i < conf.ifc_len / sizeof(struct ifreq); i++) { -+ const char *name = reqs[i].ifr_name; ++ 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, AF_INET)) { ++ 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); diff --git a/gnu/packages/python-science.scm b/gnu/packages/python-science.scm index 4063797a30..949cd11929 100644 --- a/gnu/packages/python-science.scm +++ b/gnu/packages/python-science.scm @@ -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 @@ implements several methods for sequential model-based optimization. @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") diff --git a/gnu/packages/python-web.scm b/gnu/packages/python-web.scm index 8d5af5bd46..9d8f3c156f 100644 --- a/gnu/packages/python-web.scm +++ b/gnu/packages/python-web.scm @@ -5204,54 +5204,29 @@ with 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 diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index e521c1580d..6a6f69e6bb 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -5045,13 +5045,13 @@ to Roman Numerals.") (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 @@ collection.") (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") diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm index d15732c839..95cc948d9f 100644 --- a/gnu/packages/statistics.scm +++ b/gnu/packages/statistics.scm @@ -672,14 +672,14 @@ also flexible enough to handle most nonstandard requirements.") (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 @@ solution for sending email, including attachments, from within R.") (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 @@ transliteration, concatenation, date-time formatting and parsing, etc.") (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 @@ for template use among CRAN packages.") (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 @@ defined in different packages.") (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 @@ disk (or a connection).") (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 @@ well as additional utilities such as panel and axis annotation functions.") (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 @@ encoder/decoder, round-off-error-free sum and cumsum, etc.") (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 @@ a column in data frame.") (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 @@ engine (version 3.8.8.2) is included.") (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 @@ ldap, and also supports cookies, redirects, authentication, etc.") (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 @@ t-probabilities, quantiles, random deviates and densities.") (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 @@ based on an interface to Fortran implementations by M. J. D. Powell.") (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 @@ metrics for evaluating models.") (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 @@ algorithms.") (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 @@ diagnostic tools (@code{ctlcurves} and @code{DiscrFact}).") (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)) diff --git a/gnu/packages/tbb.scm b/gnu/packages/tbb.scm index b2d276ac8b..ec630a029f 100644 --- a/gnu/packages/tbb.scm +++ b/gnu/packages/tbb.scm @@ -49,10 +49,33 @@ (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 diff --git a/gnu/packages/tor.scm b/gnu/packages/tor.scm index 71f32b3f43..d4bf27a790 100644 --- a/gnu/packages/tor.scm +++ b/gnu/packages/tor.scm @@ -63,14 +63,14 @@ (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 diff --git a/gnu/packages/web-browsers.scm b/gnu/packages/web-browsers.scm index e60661e493..553d003631 100644 --- a/gnu/packages/web-browsers.scm +++ b/gnu/packages/web-browsers.scm @@ -95,6 +95,7 @@ #: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 @@ driven and does not detract you from your daily work.") (define-public nyxt (package (name "nyxt") - (version "3.9.1") + (version "3.9.2") (source (origin (method git-fetch) @@ -595,7 +596,7 @@ driven and does not detract you from your daily work.") (commit version))) (sha256 (base32 - "1x7ia43yh024hwwsh2a6g2daznkzgjlisnxvjfcb9sgvfqfa368i")) + "1v85jn46d9vacjig6n9z797fch88fw6vzwbfdzlqdkm86vvm8dwn")) (file-name (git-file-name "nyxt" version)) (modules '((guix build utils))) (snippet @@ -852,16 +853,16 @@ http, and https via third-party applications.") (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 @@ http, and https via third-party applications.") nano openssl sbcl + tk unzip xdg-utils)) (inputs @@ -893,10 +895,12 @@ http, and https via third-party applications.") 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 @@ http, and https via third-party applications.") sbcl-trivial-clipboard sbcl-unix-opts sbcl-usocket + sbcl-yason sqlite)) (arguments `(#:tests? #f @@ -937,10 +942,10 @@ http, and https via third-party applications.") "--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+))) diff --git a/gnu/packages/web.scm b/gnu/packages/web.scm index 7363925aac..f06f0d6abf 100644 --- a/gnu/packages/web.scm +++ b/gnu/packages/web.scm @@ -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 @@ features include: @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$"))))) + (home-page "https://www.splitbrain.org/projects/monsterid") + (synopsis "The original MonsterID implementation") + (description + "MonsterID is a method to generate a unique monster image based upon a +certain identifier (IP address, email address, whatever). It can be +used to automatically provide personal avatar images in blog comments +or other community services.") + (license license:expat)))) + (define-public cat-avatar-generator (let ((commit "9360ea33f79d1dad3e43494b09878b5e3f6b41fa") (revision "1")) diff --git a/gnu/packages/xdisorg.scm b/gnu/packages/xdisorg.scm index 9de5cd24d2..f9bf42b721 100644 --- a/gnu/packages/xdisorg.scm +++ b/gnu/packages/xdisorg.scm @@ -2796,9 +2796,16 @@ Wayland and @code{wlroots} by leveraging @command{grim} and @command{slurp}.") #~(list (string-append "-Dzshcompletiondir=" #$output "/share/zsh/site-functions") (string-append "-Dfishcompletiondir=" #$output - "/share/fish/completions")) + "/share/fish/vendor_completions.d")) #:phases #~(modify-phases %standard-phases + (add-after 'unpack 'fix-bash-completion-dir + (lambda _ + (substitute* "completions/bash/meson.build" + (("bash_completion_dir =.*") + (string-append "bash_completion_dir = " + "join_paths(get_option('sysconfdir'), " + "'bash_completion.d')\n"))))) (add-after 'unpack 'patch-file-names (lambda* (#:key inputs #:allow-other-keys) (substitute* (find-files "src" "\\.c$") |