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2019-05-06guix: Update to Bioconductor 3.9.Ricardo Wurmus
* guix/build-system/r.scm (bioconductor-uri): Use 3.9 archive URL. * guix/import/cran.scm (%bioconductor-version): Update to 3.9.
2019-05-02Merge branch 'version-1.0.0'Ludovic Courtès
2019-05-01build: Change default substitute server to "ci.guix.gnu.org".Ludovic Courtès
* 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".
2019-04-30guix: Fix another typo in another docstring.Tobias Geerinckx-Rice
* guix/build/clojure-utils.scm (include-list\exclude-list)<docstring>: Fix typo.
2019-04-30guix: Fix typo in docstring.Tobias Geerinckx-Rice
* guix/build/syscalls.scm (device-in-use?)<docstring>: Fix typo.
2019-04-29processes: Gracefully handle daemons without clients.Ludovic Courtès
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'.
2019-04-29processes: 'process-open-files' ignores disappeared /proc/PID/fd entries.Ludovic Courtès
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'.
2019-04-29guix package: Add 'guix search' alias.Ludovic Courtès
* 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.
2019-04-29file-systems: Support the 'no-atime' flag.rendaw
* 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>
2019-04-29guix package: Add 'install', 'remove', and 'upgrade' aliases.Ludovic Courtès
* 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".
2019-04-28describe: Provide a hint when origin detection fails.Ludovic Courtès
* guix/scripts/describe.scm (display-checkout-info): Add call to 'display-hint' in the error case.
2019-04-28Merge branch 'staging'Ludovic Courtès
2019-04-27self: Rebuild translated manuals.Julien Lepiller
* 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.
2019-04-25gnu: ocaml@4.02: Remove the package, affected by a CVE, and its dependentJulien Lepiller
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.
2019-04-25gnu, guix: Yearly ritual purging of the filesystems.Tobias Geerinckx-Rice
* 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.
2019-04-25self: Install 'guix.zh_CN.info'.Ludovic Courtès
Reported by Julien Lepiller. * guix/self.scm (info-manual): Adjust file name regexp so that it matches *.zh_CN.texi.
2019-04-23guix system: Compute 'bootcfg' only for 'init' and 'reconfigure'.Ludovic Courtès
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.
2019-04-23Merge branch 'master' into stagingMarius Bakke
2019-04-22pull: Create profile after the store connection has been opened.Ludovic Courtès
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'.
2019-04-22pull: Add '--news'.Ludovic Courtès
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'.
2019-04-19guix build: Accept multiple '-s' options.Ludovic Courtès
* 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.
2019-04-18guile-build-system: Support building in parallel.Christopher Baines
* 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.
2019-04-18lint: 'check-github-url' uses our own 'open-connection-for-uri'.Ludovic Courtès
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.
2019-04-17pull: '--url', '--commit', and '--branch' apply to the 'guix' channel.Ludovic Courtès
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.
2019-04-17build: No longer substitute 'LIBGCRYPT'.Ludovic Courtès
This had become useless since ca719424455465fca4b872c371daf2a46de88b33. * configure.ac (LIBGCRYPT): Remove. * guix/config.scm.in (%libgcrypt): Remove.
2019-04-17self: Remove unused variable.Ludovic Courtès
This variable is unused since commit 45779fa676419de8838cb26b6c7a24678a2be1cd. * guix/self.scm (%dependency-variables): Remove. * build-aux/build-self.scm (%dependency-variables): Remove.
2019-04-17Merge branch 'master' into stagingMarius Bakke
2019-04-16store: Add "add-data-to-store-cache" profiling component.Ludovic Courtès
* guix/store.scm (add-data-to-store): Define 'lookup' and use it instead of 'hash-ref'.
2019-04-16derivations: Reduce 'valid-path?' RPCs in 'derivation-prerequisites-to-build'.Ludovic Courtès
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.
2019-04-16store: Memoize 'built-in-builders' call directly in <store-connection>.Ludovic Courtès
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.
2019-04-15guix build: Fix relative file name canonicalization for '--root'.Ludovic Courtès
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.
2019-04-14ui: Highlight heading of generation lists.Ludovic Courtès
* guix/ui.scm (display-generation): Highlight the "Generation" heading.
2019-04-14colors: Add 'highlight'.Ludovic Courtès
* guix/colors.scm (%highlight-color): New variable. (highlight): New procedure. * guix/ui.scm (%highlight-argument)[highlight]: Remove. (%highlight-color): Remove.
2019-04-12build-system/linux-module: Configure module like the kernel.Danny Milosavljevic
* guix/build/linux-module-build-system.scm (configure): New procedure. (%standard-phases): Add "configure" phase.
2019-04-12build-system/linux-module: Support module source versioning.Danny Milosavljevic
* 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.
2019-04-11colors: Add 'colorize-matches'.Ludovic Courtès
* guix/colors.scm (colorize-matches): New procedure. (color-rules): Rewrite in terms of 'colorize-matches'.
2019-04-11colors: Introduce a disjoint type and pre-compute ANSI escapes.Ludovic Courtès
* 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.
2019-04-11guix gc: '-d' does not attempt to delete non-user-owned roots.Ludovic Courtès
* guix/scripts/gc.scm (guix-gc)[delete-generations]: Limit to user-owned roots, unless we're running as root.
2019-04-11Add (guix build-system linux-module).Danny Milosavljevic
* 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.
2019-04-10import: opam: Use dune-build-system when possible.Julien Lepiller
* guix/import/opam.scm (opam->guix-package): Detect when dune can be used.
2019-04-10import: opam: Add more patterns to opam file parser.Julien Lepiller
* 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.
2019-04-10scripts: GC hint suggests 'guix gc -d 1m'.Ludovic Courtès
* guix/scripts.scm (warn-about-disk-space): Suggest 'guix gc -d'.
2019-04-10guix gc: Add '--delete-generations'.Ludovic Courtès
* 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.
2019-04-10profiles: Add 'generation-profile'.Ludovic Courtès
* guix/profiles.scm (%profile-generation-rx): New variable. (generation-profile): New procedure.
2019-04-10guix gc: Add '--list-roots'.Ludovic Courtès
* 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.
2019-04-10Add (guix store roots).Ludovic Courtès
* 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.
2019-04-10pull: Remove duplicate '--dry-run' description.Ludovic Courtès
Reported by pkill9. * guix/scripts/pull.scm (show-help): Remove duplicate '--dry-run' description.
2019-04-10ui: Highlight diagnostic format string arguments.Ludovic Courtès
* guix/ui.scm (highlight-argument): New macro. (%highlight-argument): New procedure. (define-diagnostic): Use 'highlight-argument'.
2019-04-10ui: Colorize hints.Ludovic Courtès
* guix/ui.scm (%info-colors): Remove CYAN. (%hint-colors): New variable. (display-hint): Adjust so that the "hint:" prefix is colorized.
2019-04-10ui: Colorize diagnostics.Ludovic Courtès
* 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.
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