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* daemon: Do not deduplicate files smaller than 8 KiB.Ludovic Courtès2021-11-16
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | Files smaller than 8 KiB typically represent ~70% of the entries in /gnu/store/.links but only contribute to ~4% of the space savings afforded by deduplication. Not considering these files for deduplication speeds up file insertion in the store and, more importantly, leaves 'removeUnusedLinks' with fewer entries to traverse, thereby speeding it up proportionally. Partly fixes <https://issues.guix.gnu.org/24937>. * config-daemon.ac: Remove symlink hard link check and CAN_LINK_SYMLINK definition. * guix/store/deduplication.scm (%deduplication-minimum-size): New variable. (deduplicate)[loop]: Do not recurse when FILE's size is below %DEDUPLICATION-MINIMUM-SIZE. (dump-port): New procedure. (dump-file/deduplicate)[hash]: Turn into... [dump-and-compute-hash]: ... this thunk. Call 'deduplicate' only when SIZE is greater than %DEDUPLICATION-MINIMUM-SIZE; otherwise call 'dump-port'. * nix/libstore/gc.cc (LocalStore::removeUnusedLinks): Drop files where st.st_size < deduplicationMinSize. * nix/libstore/local-store.hh (deduplicationMinSize): New declaration. * nix/libstore/optimise-store.cc (deduplicationMinSize): New variable. (LocalStore::optimisePath_): Return when PATH is a symlink or smaller than 'deduplicationMinSize'. * tests/derivations.scm ("identical files are deduplicated"): Produce files bigger than %DEDUPLICATION-MINIMUM-SIZE. * tests/nar.scm ("restore-file-set with directories (signed, valid)"): Likewise. * tests/store-deduplication.scm ("deduplicate, below %deduplication-minimum-size"): New test. ("deduplicate", "deduplicate, ENOSPC"): Produce files bigger than %DEDUPLICATION-MINIMUM-SIZE. * tests/store.scm ("substitute, deduplication"): Likewise.
* tests: Factorize 'file=?'.Ludovic Courtès2021-11-16
| | | | | | | * guix/tests.scm (file=?): Add optional 'stat' parameter. Add fast patch comparing inode numbers. * tests/gexp.scm ("imported-files with file-like objects"): Remove 'file=?' procedure and use the one from (guix tests).
* services: openssh: Collect all keys for all users.Vivien Kraus2021-11-16
| | | | | | | | Fixes <https://issues.guix.gnu.org/51487> * gnu/services/ssh.scm (extend-openssh-authorized-keys): ensure that no key is forgotten. Co-authored-by: Ludovic Courtès <ludo@gnu.org>
* Revert "home-services: Demonadify 'on-first-login' handling."Efraim Flashner2021-11-16
| | | | | | | | This commit breaks building guix home guix home: error: reference to invalid output 'out' of derivation \ '/gnu/store/86zc4rijsswmfqnaq8rwixcxjl2zyl1c-on-first-login.drv' This reverts commit 4dcec60fa6a93dbc93bef2cdb91e3633c705579e.
* gnu: Add julia-sundials-jullJean-Baptiste Volatier2021-11-16
| | | | | | | * gnu/packages/julia-jll.scm (julia-sundials-jll): New variable. * gnu/packages/maths.scm (sundials-julia): New variable. Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
* Revert "gnu: Add cl-https-everywhere."Efraim Flashner2021-11-16
| | | | | | | | With thanks to jlicht on IRC: sbcl-package->cl-source-package assumes all inputs are packages which isn't the case here. This reverts commit e31d48d8db09e723727eeadbeea22d677f5d1d52.
* gnu: julia-pycall: Update to 1.92.5.Efraim Flashner2021-11-16
| | | | * gnu/packages/julia-xyz.scm (julia-pycall): Update to 1.92.5.
* build-system/julia: Enable Julia Pkg to find installed packages.Jean-Baptiste Volatier2021-11-16
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | Julia's built-in package manager (Pkg) looks for packages in JULIA_DEPOT_PATH/packages/PACKAGENAME/XXXX, where XXXX is a string encoding package UUID and SHA1 of files. The link-depot phase creates a link at the correct location to allow Pkg to find packages that were already installed by Guix. * guix/build/julia-build-system.scm (link-depot): New phase. (%package-path): Modified package path from packages/ to loadpath/. (project.toml->uuid): New procedure, retrive package uuid from TOML file. (precompile, check): Adjust to the change in paths. (%standard-phases): Add link-depot phase. (julia-build): Add julia-package-uuid keyword. * guix/build-system/julia.scm (julia-build): Also use the julia-package-uuid keyword. * gnu/packages/julia-jll.scm (julia-bzip2-jll, julia-cairo-jll, julia-compilersupportlibraries-jll, julia-expat-jll, julia-ffmpeg-jll, julia-fontconfig-jll, julia-freetype2-jll, julia-fribidi-jll, julia-gettext-jll, julia-glib-jll, julia-gr-jll, julia-gumbo-jll, julia-imagemagick-jll, julia-jllwrappers-jll, julia-jpegturbo-jll, julia-lame-jll, julia-libass-jll, julia-libfdk-aac-jll, julia-libffi-jll, julia-libgcrypt-jll, julia-libglvnd-jll, julia-libgpg-error-jll, juli-libiconv-jll, julia-libmount-jll, julia-libpng-jll, julia-libsass-jll, julia-libtiff-jll, julia-libuuid-jll, julia-libvorbis-jll, julia-lzo-jll, julia-mbedtls-jll, julia-ogg-jll, julia-openspecfun-jll, julia-openssl-jll, julia-opus-jll, julia-pcre-jll, julia-pixman-jll, julia-qt5base-jll, julia-wayland-jll, julia-wayland-protocols-jll, julia-x264-jll, julia-x265-jll, julia-xkbcommon-jll, julia-xml2-jll, julia-xorg-libpthread-stubs-jll, julia-xorg-libx11-jll, julia-xorg-libxau-jll, julia-xorg-libxcb-jll, julia-xorg-libxcursor-jll, julia-xorg-libxdmcp-jll, julia-xorg-libxext-jll, julia-xorg-libxfixes-jll, julia-xorg-libxi-jll, julia-xorg-libxinerama-jll, julia-xorg-libxkbfile-jll, julia-xorg-libxrandr-jll, julia-xorg-libxrender-jll, julia-xorg-xcb-util-jll, julia-xorg-xcb-util-keysyms-jll, julia-xorg-xcb-util-renderutil-jll, julia-xorg-xcb-util-wm-jll, julia-xorg-xkbcomp-jll, julia-xorg-xkeyboard-config-jll, julia-xorg-xtrans-jll, julia-xslt-jll, julia-zlib-jll, julia-zstd-jll) [argument]: Adjust the order of the phases to the change in the julia-build-system. * gnu/packages/julia-xyz.scm (julia-bufferedstreams, julia-calculus, julia-dataframes, julia-datavalues, julia-distances, julia-documenter, julia-dualnumbers, julia-ellipsisnotation, julia-expronicon, julia-fileio, julia-fixedpointnumbers, julia-functionwrappers, julia-fuzzycompletions, julia-genericlinearalgebra, julia-genericschur, julia-geometrybasics, julia-imagemagick, julia-infinity, julia-matrixfactorizations, julia-media, julia-missings, julia-nnlib, julia-optimtestproblems, julia-orderedcollections, julia-prettytables, julia-pycall, julia-quadmath, julia-safetests, julia-stackviews) [arguments]: Correct paths to reflect change of %package-path modify order of phases as link-depot needs to run on an unmodified src directory add package-name-uuid keyword argument to packages without Project.toml file. * gnu/packages/julia.scm (julia)[native-search-paths]: Correct paths to reflect change of %package-path modify order of phases as link-depot needs to run on an unmodified src directory. Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
* gnu: Add cl-https-everywhere.Pierre Neidhardt2021-11-16
| | | | | * gnu/packages/lisp-xyz.scm (cl-https-everywhere, sbcl-cl-https-everywhere): New variables.
* gnu: Add vernacular.Pierre Neidhardt2021-11-16
| | | | * gnu/packages/lisp-xyz.scm (cl-vernacular, sbcl-vernacular): New variables.
* gnu: Add fxml.Pierre Neidhardt2021-11-16
| | | | * gnu/packages/lisp-xyz.scm (cl-fxml, sbcl-fxml): New variables.
* gnu: Add xpath.Pierre Neidhardt2021-11-16
| | | | * gnu/packages/lisp-xyz.scm (cl-xpath, sbcl-xpath): New variables.
* gnu: Add overlord.Pierre Neidhardt2021-11-16
| | | | * gnu/packages/lisp-xyz.scm (cl-overlord, sbcl-overlord): New variables.
* gnu: Add cxml-rng.Pierre Neidhardt2021-11-16
| | | | * gnu/packages/lisp-xyz.scm (cl-cxml-rng, sbcl-cxml-rng): New variables.
* gnu: Add bit-smasher.Pierre Neidhardt2021-11-16
| | | | * gnu/packages/lisp-xyz.scm (cl-bit-smasher, ecl-bit-smasher, sbcl-bit-smasher): New variables.
* gnu: Add cl-base58.Pierre Neidhardt2021-11-16
| | | | * gnu/packages/lisp-xyz.scm (cl-base58, ecl-cl-base58, sbcl-cl-base58): New variables.
* gnu: Add exit-hooks.Pierre Neidhardt2021-11-16
| | | | | * gnu/packages/lisp-xyz.scm (cl-exit-hooks, ecl-exit-hooks, sbcl-exit-hooks): New variables.
* gnu: Add cl-strftime.Pierre Neidhardt2021-11-16
| | | | | * gnu/packages/lisp-xyz.scm (cl-strftime, ecl-cl-strftime, sbcl-cl-strftime): New variables.
* gnu: Add sbcl-cl-tld.Pierre Neidhardt2021-11-16
| | | | * gnu/packages/lisp-xyz.scm (sbcl-cl-tld): New variable.
* gnu: sbcl-cl-webkit: Update to 3.2.0.Pierre Neidhardt2021-11-16
| | | | * gnu/packages/lisp-xyz.scm (sbcl-cl-webkit): Update to 3.2.0.
* gnu: sbcl-cmd: Update to 20211009.Pierre Neidhardt2021-11-16
| | | | * gnu/packages/lisp-xyz.scm (sbcl-cmd): Update to 20211009.
* services: cups: Update default timeouts.Tobias Geerinckx-Rice2021-11-16
| | | | | | | | Upstream raised these back in 2019 with CUPS 2.3.0. * gnu/services/cups.scm (<cups-configuration>): Raise default ‘multiple-operation-timeout’ and ‘timeout’ from 300 to 900 seconds. * doc/guix.texi (Printing Services): Adjust accordingly.
* doc: Remove obsolete example module import.Tobias Geerinckx-Rice2021-11-16
| | | | | | | This follows up on commit a247f5c7537df7e0c09051ba22d5c95eb08f48b9. * doc/guix.texi (X Window): Remove unused (srfi srfi-1) from the modify-services example.
* gnu: guix-build-coordinator: Update to 0-37.200ffe7.Christopher Baines2021-11-15
| | | | | * gnu/packages/package-management.scm (guix-build-coordinator): Update to 0-37.200ffe7.
* gnu: libuv-for-node: Update to 1.42.0.Jelle Licht2021-11-15
| | | | * gnu/packages/libevent.scm (libuv-for-node): Update to 1.42.0.
* gnu: node-lts: Update to 14.18.1 [security fixes].Jelle Licht2021-11-15
| | | | | | | | | * gnu/packages/node.scm (node-lts): Update to 14.18.1. [native-inputs]: Replace c-ares with c-ares-for-node. [inputs]: Replace c-ares with c-ares-for-node. Includes fixes for CVE-2021-22918, CVE-2021-22930, CVE-2021-22931, CVE-2021-22939, and CVE-2021-22940.
* gnu: llhttp-bootstrap: Update to 2.1.4 [security-fixes].Jelle Licht2021-11-15
| | | | | | * gnu/packages/node.scm (llhttp-bootstrap): Update to 2.1.4. Includes fixes for CVE-2021-22959 and CVE-2021-22960.
* gnu: Add c-ares-for-node.Jelle Licht2021-11-15
| | | | | | * gnu/packages/adns.scm (c-ares-for-node): New variable. Co-authored-by: Marius Bakke <marius@gnu.org>
* gnu: node: Add cpe-name.Jelle Licht2021-11-15
| | | | * gnu/packages/node.scm (node)[properties]: Add cpe-name.
* gnu: taskwarrior: Update to 2.6.1.Lenny Händler2021-11-15
| | | | | | * gnu/packages/task-management.scm (taskwarrior): Update to 2.6.1. Signed-off-by: Nicolas Goaziou <mail@nicolasgoaziou.fr>
* gnu: emacs-helm: Update to 3.8.1.Nicolas Goaziou2021-11-15
| | | | * gnu/packages/emacs-xyz.scm (emacs-helm): Update to 3.8.1.
* gnu: pdfarranger: Update to 1.8.0.Nicolas Goaziou2021-11-15
| | | | * gnu/packages/pdf.scm (pdfarranger): Update to 1.8.0.
* gnu: julia: Fix llvm-julia version.Jean-Baptiste Volatier2021-11-15
| | | | | | | | | | | | | | | | | | | | | LLVM bundled in the binary julia distributed by upstream has its version with a "jl" suffix. The llvm-julia package does not have this suffix, which causes some packages (e. g. LLVM.jl) to fail to load. LLVM.jl does this in order to be sure that it is loading a LLVM as patched for julia and not LLVM from the distribution which will lack the correct patches on distribs other than GUIX. I guess there might be other packages that rely on this, so we should fix our llvm-julia package. * gnu/packages/julia.scm (llvm) [source]: Add missing upstream patch [arguments]: Add configure-flag to set a "jl" suffix to llvm version (julia)[arguments]: Symlink llvm to llvm-11jl.so Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
* gnu: emacs-consult: Update to 0.13.Nicolas Goaziou2021-11-15
| | | | * gnu/packages/emacs-xyz.scm (emacs-consult): Update to 0.13.
* gnu: emacs-exwm: Update to 0.26.Nicolas Goaziou2021-11-15
| | | | * gnu/packages/emacs-xyz.scm (emacs-exwm): Update to 0.26.
* gnu: emacs-rustic: Update to 2.1.Nicolas Goaziou2021-11-15
| | | | * gnu/packages/emacs-xyz.scm (emacs-rustic): Update to 2.1.
* gnu: emacs-marginalia: Update to 0.10.Nicolas Goaziou2021-11-15
| | | | * gnu/packages/emacs-xyz.scm (emacs-marginalia): Update to 0.10.
* gnu: borgmatic: Fix typo in description.Nicolas Goaziou2021-11-15
| | | | * gnu/packages/backup.scm (borgmatic): Fix typo, "software" being a mass noun.
* gnu: hpcguix-web: Update to 0.2.0.Ludovic Courtès2021-11-15
| | | | | | | | | | | | * gnu/packages/web.scm (hpcguix-web): Update to 0.2.0. [arguments]: In 'wrap-program' phase, add guile-zlib to DEPS. [native-inputs]: Add GUILE. [inputs]: Add GUILE-ZLIB, GUILE-COMMONMARK, and GUILE-JSON. [propagated-inputs]: Remove. These were pointless. * gnu/services/web.scm (<hpcguix-web-configuration>)[address, port]: New fields. * doc/guix.texi (Web Services): Document them. * gnu/tests/web.scm (%hpcguix-web-os): Add 'address'.
* gnu: python-pytorch: Update to 1.10.0.Ludovic Courtès2021-11-15
| | | | | * gnu/packages/machine-learning.scm (python-pytorch): Update to 1.10.0. * gnu/packages/patches/python-pytorch-system-libraries.patch: Adjust.
* gnu: Add python-minikanren.Ryan Prior2021-11-15
| | | | | | * gnu/packages/python-xyz.scm (python-minikanren): New variable. Signed-off-by: Ludovic Courtès <ludo@gnu.org>
* gnu: Add python-etuples.Ryan Prior2021-11-15
| | | | | | * gnu/packages/python-xyz.scm (python-etuples): New variable. Signed-off-by: Ludovic Courtès <ludo@gnu.org>
* gnu: Add python-cons.Ryan Prior2021-11-15
| | | | | | * gnu/packages/python-xyz.scm (python-cons): New variable. Signed-off-by: Ludovic Courtès <ludo@gnu.org>
* gnu: Add python-logical-unification.Ryan Prior2021-11-15
| | | | | | * gnu/packages/python-xyz.scm (python-logical-unification): New variable. Signed-off-by: Ludovic Courtès <ludo@gnu.org>
* gnu: Add python-multipledispatch.Ryan Prior2021-11-15
| | | | | | * gnu/packages/python-xyz.scm (python-multipledispatch): New variable. Signed-off-by: Ludovic Courtès <ludo@gnu.org>
* gnu: clang-toolchain: Add libomp.Ludovic Courtès2021-11-15
| | | | * gnu/packages/llvm.scm (make-clang-toolchain)[inputs]: Add LIBOMP.
* gnu: Add python-rtree.Vinicius Monego2021-11-15
| | | | | | * gnu/packages/geo.scm (python-rtree): New variable. Signed-off-by: Guillaume Le Vaillant <glv@posteo.net>
* gnu: Add python-ta-lib.Foo Chuan Wei2021-11-15
| | | | | | * gnu/packages/finance.scm (python-ta-lib): New variable. Signed-off-by: Guillaume Le Vaillant <glv@posteo.net>
* gnu: Add cl-chemboy.Foo Chuan Wei2021-11-15
| | | | | | | * gnu/packages/lisp-xyz.scm (cl-chemboy, ecl-chemboy, sbcl-chemboy): New variables. Signed-off-by: Guillaume Le Vaillant <glv@posteo.net>
* gnu: Add cl-chemical-compounds.Foo Chuan Wei2021-11-15
| | | | | | | * gnu/packages/lisp-xyz.scm (cl-chemical-compounds, ecl-chemical-compounds, sbcl-chemical-compounds): New variables. Signed-off-by: Guillaume Le Vaillant <glv@posteo.net>
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