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2019-05-06guix: Update to Bioconductor 3.9....* guix/build-system/r.scm (bioconductor-uri): Use 3.9 archive URL. * guix/import/cran.scm (%bioconductor-version): Update to 3.9. Ricardo Wurmus
2019-05-02Merge branch 'version-1.0.0'Ludovic Courtès
2019-05-01build: Change default substitute server to "ci.guix.gnu.org"....* config-daemon.ac: Replace "ci.guix.info" with "ci.guix.gnu.org". * doc/guix.texi (SUBSTITUTE-SERVER): Likewise. * etc/substitutes/ci.guix.gnu.org.pub: New file. * Makefile.am (dist_pkgdata_DATA): Add it. * guix/scripts/build.scm (%default-log-urls): Update. * guix/scripts/substitute.scm (%default-substitute-urls): Likewise. * guix/store.scm (%default-substitute-urls): Likewise. * guix/self.scm (miscellaneous-files): Add "ci.guix.gnu.org". Ludovic Courtès
2019-04-30guix: Fix another typo in another docstring....* guix/build/clojure-utils.scm (include-list\exclude-list)<docstring>: Fix typo. Tobias Geerinckx-Rice
2019-04-30guix: Fix typo in docstring....* guix/build/syscalls.scm (device-in-use?)<docstring>: Fix typo. Tobias Geerinckx-Rice
2019-04-29processes: Gracefully handle daemons without clients....Fixes <https://bugs.gnu.org/34716>. Reported by Mark H Weaver <mhw@netris.org>. The problem could be reproduced by running, on one hand: sh -c 'exec -a guix-daemon sleep 777' and on the other hand: guix processes If there is no process with PID 777, 'guix processes' would barf as it stumbles upon a <daemon-session> record whose client is #f. * guix/scripts/processes.scm (daemon-sessions)[child-process->session]: New procedure, with lambda formerly passed to 'map'. Handle #f returns from 'lookup-process'. Call 'child-process->session' within 'filter-map', not just 'map'. Ludovic Courtès
2019-04-29processes: 'process-open-files' ignores disappeared /proc/PID/fd entries....Previously, 'process-open-files' would throw ENOENT if an entry had vanished after the 'scandir' call and before the 'readlink' call. * guix/scripts/processes.scm (process-open-files): Catch ENOENT errors from 'readlink'. Ludovic Courtès
2019-04-29guix package: Add 'guix search' alias....* guix/scripts/search.scm: New file. * Makefile.am (MODULES): Add it. * po/guix/POTFILES.in: Add it. * tests/guix-package-aliases.sh: Add test. * doc/guix.texi (Invoking guix package): Document it and use it in a couple of examples. Ludovic Courtès
2019-04-29file-systems: Support the 'no-atime' flag....* guix/build/syscalls.scm (MS_NOATIME): New variable. * gnu/build/file-systems.scm (mount-flags->bit-mask): Support it. * doc/guix.texi (File Systems): Document it and add cross-references to the relevant documentation. Co-authored-by: Ludovic Courtès <ludo@gnu.org> rendaw
2019-04-29guix package: Add 'install', 'remove', and 'upgrade' aliases....* guix/scripts/install.scm, guix/scripts/remove.scm, guix/scripts/upgrade.scm, tests/guix-package-aliases.sh: New files. * Makefile.am (MODULES, SH_TESTS): Add them. * po/guix/POTFILES.in: Add them. * guix/scripts/package.scm (guix-package): Split with... (guix-package*): ... this. New procedure. * doc/guix.texi (Invoking guix package): Document them. (Binary Installation, Application Setup, Package Management) (Packages with Multiple Outputs, Package Modules) (X.509 Certificates, Installing Debugging Files): Use 'guix install' in simple examples. * etc/completion/bash/guix (_guix_complete): Handle "install", "remove", and "upgrade". Ludovic Courtès
2019-04-28describe: Provide a hint when origin detection fails....* guix/scripts/describe.scm (display-checkout-info): Add call to 'display-hint' in the error case. Ludovic Courtès
2019-04-28Merge branch 'staging'Ludovic Courtès
2019-04-27self: Rebuild translated manuals....* guix/self.scm (info-manual): Run po4a and related commands to generate translated texi files before building translated manuals. * guix/build/po.scm: New file. * Makefile.am (MODULES_NOT_COMPILED): Add it. Julien Lepiller
2019-04-25gnu: ocaml@4.02: Remove the package, affected by a CVE, and its dependent...packages. This fixes <https://bugs.gnu.org/27462>. * gnu/packages/ocaml.scm (ocaml-4.02, camlp4-4.02, ocaml4.02-menhir) (ocaml4.02-lablgtk, ocaml4.02-findlib, ocaml4.02-ounit) (ocaml4.02-camlzip, ocaml4.02-ocamlmod, ocaml4.02-zarith) (ocaml4.02-qcheck, ocaml4.02-qtest, ocaml4.02-stringext) (ocaml4.02-bisect, ocaml4.02-bitstring, ocaml4.02-result) (ocaml4.02-topkg, ocaml4.02-rresult, ocaml4.02-sqlite3, ocaml4.02-csv) (ocaml4.02-mtime, ocaml4.02-cmdliner, ocaml4.02-fmt, ocaml4.02-astring) (ocaml4.02-alcotest, ocaml4.02-ppx-tools, ocaml4.02-react, ocaml4.02-ssl) (ocaml4.02-lwt, ocaml4.02-lwt-log, ocaml4.02-logs, ocaml4.02-fpath) (ocaml4.02-bos, ocaml4.02-xmlm, ocaml4.02-ulex, ocaml4.02-uchar) (ocaml4.02-uutf, ocaml4.02-jsonm, ocaml4.02-ocurl, ocaml4.02-base64) (ocaml4.02-omake, ocaml4.02-batteries, ocaml4.02-pcre, ocaml4.02-oasis) (ocaml4.02-js-build-tools, ocaml4.02-bin-prot, ocaml4.02-fieldslib) (ocaml4.02-ppx-core, ocaml4.02-ppx-optcomp, ocaml4.02-ppx-driver) (ocaml4.02-cppo, ocaml4.02-ppx-deriving, ocaml4.02-ppx-type-conv) (ocaml4.02-ppx-inline-test, ocaml4.02-ppx-bench, ocaml4.02-ppx-compare) (ocaml4.02-sexplib, ocaml4.02-typerep, ocaml4.02-variantslib) (ocaml4.02-ppx-sexp-conv, ocaml4.02-ppx-variants-conv) (ocaml4.02-ppx-here, ocaml4.02-ppx-assert, ocaml4.02-ppx-enumerate) (ocaml4.02-ppx-let, ocaml4.02-ppx-typerep-conv, ocaml4.02-ppx-sexp-value) (ocaml4.02-ppx-pipebang, ocaml4.02-ppx-bin-prot, ocaml4.02-ppx-fail) (ocaml4.02-ppx-custom-printf, ocaml4.02-ppx-sexp-message) (ocaml4.02-ppx-fields-conv, ocaml4.02-seq, ocaml4.02-re) (ocaml4.02-ppx-expect, ocaml4.02-ppx-jane, ocaml4.02-core-kernel) (ocaml4.02-async-kernel, ocaml4.02-async-rpc-kernel, ocaml4.02-core) (ocaml4.02-async-unix, ocaml4.02-async-extra, ocaml4.02-async) (ocaml4.02-ocplib-endian, ocaml4.02-easy-format, optcomp) (ocaml4.02-piqilib, ocaml4.02-uuidm, ocaml4.02-graph, ocaml4.02-piqi) (ocaml4.02-camomile, ocaml4.02-zed, ocaml4.02-lambda-term): Remove variables. * guix/build-system/ocaml.scm (default-ocaml4.02) (default-ocaml4.02-findlib, package-with-ocaml4.02) (strip-ocaml4.02-variant): Remove variables. Julien Lepiller
2019-04-25gnu, guix: Yearly ritual purging of the filesystems....* gnu/packages/android.scm (android-ext4-utils)[synopsis]: Fix ‘file system’ spelling. * gnu/packages/disk.scm (rmlint)[synopsis, description]: Likewise. * gnu/packages/golang.scm (go-github-com-kr-fs)[synopsis, description]: Likewise & edit for grammar. * gnu/packages/ipfs.scm (gx, go-ipfs)[description]: Likewise. * /gnu/packages/java.scm (java-commons-vfs)[synopsis]: Likewise. * gnu/packages/linux.scm (fuseiso)[description]: Likewise. (genext2fs)[synopsis, description]: Likewise. * gnu/packages/package-management.scm (libostree)[description]: Likewise. * gnu/packages/python-xyz.scm (python-requests-file)[description]: Likewise & mark up. * gnu/packages/rails.scm (ruby-with-advisory-lock)[description]: Likewise. * gnu/packages/ruby.scm (ruby-rerun)[description]: Likewise. * guix/build/go-build-system.scm (setup-go-environment)<docstring>: Likewise. * guix/store/deduplication.scm (get-temp-link)<docstring>: Likewise. Tobias Geerinckx-Rice
2019-04-25self: Install 'guix.zh_CN.info'....Reported by Julien Lepiller. * guix/self.scm (info-manual): Adjust file name regexp so that it matches *.zh_CN.texi. Ludovic Courtès
2019-04-23guix system: Compute 'bootcfg' only for 'init' and 'reconfigure'....Previously, 'guix system vm' would start by computing the bootcfg derivation, which itself depended on an incorrect OS derivation (for the original OS instead of the one passed through 'virtualized-operating-system'.) That added overhead and would force the user's config file to define a root file system, for example, even though it makes no sense in the case of a VM. * guix/scripts/system.scm (perform-action)[bootcfg]: Limit to the 'init' and 'reconfigure' actions. Ludovic Courtès
2019-04-23Merge branch 'master' into stagingMarius Bakke
2019-04-22pull: Create profile after the store connection has been opened....Fixes <https://bugs.gnu.org/35341>. Reported by Florian Pelz <pelzflorian@pelzflorian.de>. Previously, we'd call 'ensure-default-profile' before the connection to the daemon has been opened. On the first connection, the daemon ensures that /var/guix/profiles/per-user is world-writable. Since we were calling 'ensure-default-profile' before that, /var/guix/profiles/per-user was typically non-writable (555 and root-owned), and thus 'guix pull' would error out. * guix/scripts/pull.scm (guix-pull): Call 'ensure-default-profile' within 'with-store'. Ludovic Courtès
2019-04-22pull: Add '--news'....Suggested by Tobias Geerinckx-Rice <me@tobias.gr>. * guix/scripts/pull.scm (%options, show-help): Add '--news'. (display-profile-news): Add #:current-is-newer? and #:concise?. Honor them. (build-and-install): Pass #:concise? #t. (display-new/upgraded-packages)[concise/max-item-count]: New variable. Add call to 'display-hint'. (process-query): Add clause for 'display-news'. * doc/guix.texi (Invoking guix pull): Add '--news'. Ludovic Courtès
2019-04-19guix build: Accept multiple '-s' options....* guix/scripts/build.scm (%default-options): Remove 'system'. (%options) <--system>: Keep previous occurrences of 'system in RESULT. (options->derivations)[system]: Remove. [systems, things-to-build]: New variables. [compute-derivation]: New procedure. Iterate on all of SYSTEMS to compute the derivations of THINGS-TO-BUILD. * tests/guix-build.sh: Add test for one and multiple '-s' flags. * doc/guix.texi (Additional Build Options): Document this behavior. Ludovic Courtès
2019-04-18guile-build-system: Support building in parallel....* guix/build/guile-build-system.scm (build): Use invoke-each, instead of for-each, to use multiple cores if available. (invoke-each, report-build-process): New procedures. Christopher Baines
2019-04-18lint: 'check-github-url' uses our own 'open-connection-for-uri'....Fixes <https://bugs.gnu.org/35053>. Reported by Efraim Flashner <efraim@flashner.co.il>. Previously 'check-github-url' would let Guile 2.2's (web client) module take care of opening the connection. Consequently, it wouldn't use the TLS priority strings that we use in (guix build download), 'open-connection-for-uri'. In particular, it would not disable TLSv1.3, which would trigger <https://bugs.gnu.org/34102> for github.com. * guix/scripts/lint.scm (check-github-url): Add #:timeout parameter. [follow-redirect]: Change parameter name to 'url' and pass it to 'string->uri'. Call 'guix:open-connection-for-uri' to open the connection and pass it to 'http-head' via #:port. Ludovic Courtès
2019-04-17pull: '--url', '--commit', and '--branch' apply to the 'guix' channel....Suggested by pkill9 <pkill9@runbox.com>. * guix/scripts/pull.scm (channel-list): Apply REF and URL to the 'guix' channel. * doc/guix.texi (Invoking guix pull): Adjust accordingly. Ludovic Courtès
2019-04-17build: No longer substitute 'LIBGCRYPT'....This had become useless since ca719424455465fca4b872c371daf2a46de88b33. * configure.ac (LIBGCRYPT): Remove. * guix/config.scm.in (%libgcrypt): Remove. Ludovic Courtès
2019-04-17self: Remove unused variable....This variable is unused since commit 45779fa676419de8838cb26b6c7a24678a2be1cd. * guix/self.scm (%dependency-variables): Remove. * build-aux/build-self.scm (%dependency-variables): Remove. Ludovic Courtès
2019-04-17Merge branch 'master' into stagingMarius Bakke
2019-04-16store: Add "add-data-to-store-cache" profiling component....* guix/store.scm (add-data-to-store): Define 'lookup' and use it instead of 'hash-ref'. Ludovic Courtès
2019-04-16derivations: Reduce 'valid-path?' RPCs in 'derivation-prerequisites-to-build'....On a profile with 280 packages, this reduces the number of 'valid-paths?' RPCs made by 'guix package -nu' from 6K to 500. * guix/derivations.scm (derivation-prerequisites-to-build)[built?]: Memoize 'valid-path?' calls. Ludovic Courtès
2019-04-16store: Memoize 'built-in-builders' call directly in <store-connection>....The caching strategy introduced in 40cc850aebb497faed0a11d867d8fcee729023df was ineffective since we regularly start from an empty object cache. For example, "guix build inkscape -n" would make 241 'built-in-builders' RPCs. * guix/store.scm (<store-connection>)[built-in-builders]: New field. (open-connection): Adjust '%make-store-connection' call accordingly. (port->connection): Likewise. (built-in-builders): Rename to... (%built-in-builders): ... this. (built-in-builders): New procedure. * guix/download.scm (built-in-builders*): Remove 'mcached' call. Ludovic Courtès
2019-04-15guix build: Fix relative file name canonicalization for '--root'....Fixes <https://bugs.gnu.org/35271>. Reported by rendaw <7e9wc56emjakcm@s.rendaw.me>. * guix/scripts/build.scm (register-root): When ROOT is a relative file name, append the basename of ROOT, not ROOT itself. * tests/guix-build.sh: Add test. Ludovic Courtès
2019-04-14ui: Highlight heading of generation lists....* guix/ui.scm (display-generation): Highlight the "Generation" heading. Ludovic Courtès
2019-04-14colors: Add 'highlight'....* guix/colors.scm (%highlight-color): New variable. (highlight): New procedure. * guix/ui.scm (%highlight-argument)[highlight]: Remove. (%highlight-color): Remove. Ludovic Courtès
2019-04-12build-system/linux-module: Configure module like the kernel....* guix/build/linux-module-build-system.scm (configure): New procedure. (%standard-phases): Add "configure" phase. Danny Milosavljevic
2019-04-12build-system/linux-module: Support module source versioning....* guix/build-system/linux-module.scm (make-linux-module-builder) [native-inputs]: Add linux. [arguments]<#:phases>[install]: Install "System.map" and "Module.symvers". * guix/build/linux-module-build-system.scm (configure): Delete procedure. (%standard-phases): Delete "configure" phase. Danny Milosavljevic
2019-04-11colors: Add 'colorize-matches'....* guix/colors.scm (colorize-matches): New procedure. (color-rules): Rewrite in terms of 'colorize-matches'. Ludovic Courtès
2019-04-11colors: Introduce a disjoint type and pre-compute ANSI escapes....* guix/colors.scm (color-table, color): Remove. (<color>): New record type. (print-color): New procedure. (define-color-table, color): New macros. (color-codes->ansi): New procedure. (%reset): New variable. (colorize-string): Rewrite accordingly. (color-rules): Adjust accordingly. * guix/status.scm (print-build-event): Adjust to new 'colorize-string' interface. * guix/ui.scm (%highlight-argument): Likewise. (%warning-colors, %info-colors, %error-colors, %hint-colors) (%highlight-colors): Remove. (%warning-color, %info-color, %error-color, %hint-color) (%highlight-color): New variables. Ludovic Courtès
2019-04-11guix gc: '-d' does not attempt to delete non-user-owned roots....* guix/scripts/gc.scm (guix-gc)[delete-generations]: Limit to user-owned roots, unless we're running as root. Ludovic Courtès
2019-04-11Add (guix build-system linux-module)....* guix/build/linux-module-build-system.scm: New file. * guix/build-system/linux-module.scm: New file. * doc/guix.texi (Build Systems): Document it. * Makefile.am (MODULES): Add them. Danny Milosavljevic
2019-04-10import: opam: Use dune-build-system when possible....* guix/import/opam.scm (opam->guix-package): Detect when dune can be used. Julien Lepiller
2019-04-10import: opam: Add more patterns to opam file parser....* guix/import/opam.scm: Add more patterns to peg parser. (choice-pat choice condition-not condition-paren): New patterns. (ground-value condition-content condition-var): Update patterns. Julien Lepiller
2019-04-10scripts: GC hint suggests 'guix gc -d 1m'....* guix/scripts.scm (warn-about-disk-space): Suggest 'guix gc -d'. Ludovic Courtès
2019-04-10guix gc: Add '--delete-generations'....* guix/scripts/gc.scm (show-help, %options): Add '--delete-generations'. Change '--delete' shorthand to '-D'. (delete-old-generations): New procedure. (guix-gc)[delete-generations]: New procedure. Call it when ACTION is 'collect-garbage' and OPTS contains 'delete-generations. * doc/guix.texi (Invoking guix gc): Document it. Ludovic Courtès
2019-04-10profiles: Add 'generation-profile'....* guix/profiles.scm (%profile-generation-rx): New variable. (generation-profile): New procedure. Ludovic Courtès
2019-04-10guix gc: Add '--list-roots'....* guix/scripts/gc.scm (show-help, %options): Add '--list-roots'. (guix-gc)[list-roots]: New procedure. Handle '--list-roots'. * tests/guix-gc.sh: Test it. * doc/guix.texi (Invoking guix gc): Document it. Ludovic Courtès
2019-04-10Add (guix store roots)....* guix/store/roots.scm, tests/store-roots.scm: New files. * Makefile.am (STORE_MODULES): Add guix/store/roots.scm. (SCM_TESTS): Add tests/store-roots.scm. Ludovic Courtès
2019-04-10pull: Remove duplicate '--dry-run' description....Reported by pkill9. * guix/scripts/pull.scm (show-help): Remove duplicate '--dry-run' description. Ludovic Courtès
2019-04-10ui: Highlight diagnostic format string arguments....* guix/ui.scm (highlight-argument): New macro. (%highlight-argument): New procedure. (define-diagnostic): Use 'highlight-argument'. Ludovic Courtès
2019-04-10ui: Colorize hints....* guix/ui.scm (%info-colors): Remove CYAN. (%hint-colors): New variable. (display-hint): Adjust so that the "hint:" prefix is colorized. Ludovic Courtès
2019-04-10ui: Colorize diagnostics....* guix/ui.scm (define-diagnostic): Add 'colors' parameter and pass it to 'print-diagnostic-prefix'. (warning, info, report-error): Add extra argument. (%warning-colors, %info-colors, %error-colors): New variables. (print-diagnostic-prefix): Add #:colors parameter and honor it. Ludovic Courtès