* guix/import/cran.scm (%bioconductor-updater,
latest-bioconductor-release, bioconductor-package?): New procedures.
(cran->guix-package): Support repositories other than CRAN.
(%bioconductor-url, %bioconductor-svn-url): New variables.
(description->package): Update signature to distinguish between packages
from different repositories.
(latest-release): Rename procedure ...
(latest-cran-release): ... to this.
(cran-package?): Do not assume all R packages are available on CRAN.
* tests/cran.scm: Update tests.
* guix/scripts/import/cran.scm: Add "--archive" option and default to
CRAN.
* guix/scripts/refresh.scm (%updaters): Add "%bioconductor-updater".
* doc/guix.texi: Document Bioconductor importer and updater.
* guix/monad-repl.scm (store-monad-language): Add 'store' parameter and
use it. Remove call to 'open-connection'.
(enter-store-monad): Use 'with-store' and pass the store to
'store-monad-language.
Previously paths to the GEM_HOME of certain Ruby packages were
hard-coded, so packages failed to build when Ruby was updated to 2.3.0.
* guix/build/ruby-build-system.scm (gem-home): New procedure.
* gnu/packages/ruby.scm (ruby-metaclass, ruby-instantiator,
ruby-introspection, ruby-mocha, ruby-minitest-tu-shim): Use it.
The .gem file stored in GEM_HOME after install is both redundant and an
archive that stores timestamped files which makes builds
non-deterministic, so delete it after 'gem install'.
* guix/build/ruby-build-system.scm (install): Remove cached gem after
install.
This phase is inherited by other build systems, which ensures
'SOURCE_DATE_EPOCH' is always set in practice.
* guix/build/python-build-system.scm (set-SOURCE-DATE-EPOCH): Remove.
(%standard-phases): Don't add it.
* guix/build/gnu-build-system.scm (set-SOURCE-DATE-EPOCH): New
procedure.
(%standard-phases): Add it.
(gnu-build): Remove 'setenv' call for "SOURCE_DATE_EPOCH".
* guix/scripts/package.scm (find-packages-by-description): Change 'rx'
parameter to 'regexps'.
[matches-all?, matches-one?]: New procedures.
Use them.
(process-query): Collect regexps from all 'search' queries, and pass
them to 'find-packages-by-description'.
* tests/guix-package.sh: Add tests.
* doc/guix.texi (Invoking guix package): Document it.
Previously, the 'git checkout' invocation would remove sub-modules that
had been initialized by 'git clone --recursive'.
* guix/build/git.scm (git-fetch): Never use "git clone --recursive".
Invoke "git submodule update --init --recursive" after "git checkout".
Remove '.git' directories as the last step.
Before that it would include #f for most origins since that the default
value of 'origin-patch-guile'.
* guix/scripts/graph.scm (bag-node-edges): When 'origin-patch-guile'
returns #f, use (default-guile).
* tests/graph.scm ("bag DAG, including origins"): Check for an edge from
O to (default-guile).
Fixes <http://bugs.gnu.org/22280>.
Reported by Leo Famulari <leo@famulari.name>.
* guix/scripts/graph.scm (%bag-emerged-node-type)[edges]: Mimic
%BAG-NODE-TYPE. This is a followup to 38b92da.
This is a followup to 3eb34c6.
* guix/build-system/gnu.scm (gnu-build, gnu-cross-build): Use
"--enable-deterministic-archives" instead of "-D" to work around
Binutils bug <https://sourceware.org/bugzilla/show_bug.cgi?id=17671>.
* guix/build/gnu-build-system.scm (strip): Likewise.
* guix/packages.scm (package-transitive-native-search-paths): New
procedure.
* tests/packages.scm ("package-transitive-native-search-paths"): New
test.
Reported by Efraim Flashner <efraim@flashner.co.il>
at <https://lists.gnu.org/archive/html/guix-devel/2015-12/msg00202.html>.
* guix/gnu-maintenance.scm (latest-ftp-release): Call KEEP-FILE? on
directories too.
(latest-gnome-release)[even-minor-version?]: Protect again MINOR being
false; change pattern to match VERSION with two or more numbers. Remove
use of 'version-major+minor'.
[even-numbered-tarball?]: Rename to...
[even-numbered?]: ... this. Use 'package-name->name+version'. When
VERSION is #f, check NAME.
* guix/derivations.scm (substitution-oracle): Add #:mode parameter and
honor it.
(derivation-prerequisites-to-build): Likewise.
[derivation-built?]: Take it into account.
* guix/ui.scm (show-what-to-build): Add #:mode parameter. Pass it to
'substitute-oracle' and 'derivations-prerequisites-to-build'.
* tests/derivations.scm ("derivation-prerequisites-to-build in 'check'
mode"): New test.
Suggested by Efraim Flashner <efraim@flashner.co.il>.
* guix/gnu-maintenance.scm (latest-ftp-release): Add #:keep-file?
parameter and honor it.
(latest-gnome-release)[%not-dot]: New variable.
[even-minor-version?, even-numbered-tarball?]: New procedures.
Pass EVEN-NUMBERED-TARBALL? as #:keep-file? argument.
* guix/gnu-maintenance.scm (latest-ftp-release): Add #:file->signature
parameter. Honor it.
(latest-gnome-release): Pass #:file->signature.
* guix/upstream.scm (coalesce-sources): Keep 'signature-urls' as #f
unless both sources provide it.
With this, (latest-release "gcc") returns an <upstream-source> with URL:
ftp://ftp.gnu.org/gnu/gcc/gcc-5.3.0/gcc-5.3.0.tar.gz
Previous it would omit "gcc-5.3.0/" from the URL.
Fixes a regression introduced in 0a7c5a0.
* guix/gnu-maintenance.scm (latest-release)[file->url, file->source]:
Add 'directory' parameter. Update users.
* guix/store.scm (%protocol-version): Set minor to 15.
(build-mode): New enumerate type.
(build-things): Add 'mode' parameter; pass it to the RPC.
* tests/store.scm ("build-things, check mode"): New check.
Reported by Andreas Enge <andreas@enge.fr>
at <https://lists.gnu.org/archive/html/guix-devel/2015-11/msg00764.html>.
* guix/import/pypi.scm (&missing-source-error): New error type.
(latest-source-release): Raise it instead of using 'error'.
(pypi->guix-package): Guard against it and use 'leave' to report the
error.
(latest-release): Guard against it and return #f when caught.
* guix/scripts/build.scm (options/resolve-packages): Remove.
(options->things-to-build, transform-package-source): New procedure.
(%transformations): New variable.
(options->transformation): New procedure.
(options->derivations): Rewrite to use 'options->things-to-build' and
'options->transformation'.
* guix/scripts/package.scm (options->upgrade-predicate)
(store-item->manifest-entry): New procedures.
* guix/scripts/package.scm (options->installable): Use them. Remove the
'packages-to-upgrade' and 'packages-to-install' variables by getting rid
of a level of indirection.
* guix/scripts/package.scm (build-and-use-profile): New procedure.
Adapted and moved from...
(guix-package)[process-actions]: ... here. Adjust call sites.
* gnu/packages/python.scm (python-2)[arguments]: Set SOURCE_DATE_EPOCH
to 1 to match what the daemon does.
* guix/build/python-build-system.scm (set-SOURCE-DATE-EPOCH): Likewise.
* gnu/packages/patches/python-2.7-source-date-epoch.patch: New file.
* gnu/packages/python.scm (python-2)[source]: Use it.
[arguments]: Set SOURCE_DATE_EPOCH in 'patch-lib-shells' phase.
* guix/build/python-build-system.scm (set-SOURCE-DATE-EPOCH): New
procedure.
(%standard-phases): Add it.
* gnu-system.am (dist_patch_DATA): Add patch.
This is a followup to b68d2db, which added a check for updaters at
macro-expansion time. The problem is that, when running 'guix pull',
Guile-JSON is found, so the PyPi updater (say) is added to %UPDATERS,
but then at run time Guile-JSON might be missing.
Reported by orbea on #guix.
* guix/scripts/refresh.scm (maybe-updater): Rewrite as 'syntax-rules'.
Produce code that checks conditions at run time.
(list-updaters): Update docstring.
This fixes a bug whereby some options, such as #:substitute-urls, would
be passed to the daemon too late to have an effect.
* guix/scripts/environment.scm (build-inputs): Remove call to
'set-build-options-from-command-line*'.
(guix-environment): Add call to 'set-build-options-from-command-line' as
early as possible.
* guix/scripts/lint.scm (patch-file-name): New procedure.
(check-vulnerabilities): Use it to filter out patched vulnerabilities.
* tests/lint.scm ("cve: one patched vulnerability"): New test.
Suggested by Hynek Urban <hynek.urban@gmail.com>.
* guix/scripts/substitute.scm (fetch-narinfos): Move body to...
[do-fetch]: ... here. New procedure.
Emit a warning when CACHE-INFO's prefix does not match.
* guix/import/cabal.scm (is-test): Allow spaces between keyword and
parentheses.
(is-id): Add argument 'port'. Allow spaces between keyword and column.
(lex-word): Adjust call to 'is-id'.
* guix/import/cabal.scm (is-true, is-false, lex-true, lex-false): New procedures.
(lex-word): Use them.
(make-cabal-parser): Add TRUE and FALSE tokens.
(eval): Add entries for 'true and 'false symbols.
As measured with:
time sh -c 'for i in `seq 1 10` ; do guix package --search-paths ; done'
On my machine, when running:
strace -o ,,s guix package --search-paths
the number returned by:
grep -E '^(open|l?stat).*\.go' ,,s | wc -l
drops from 1610 to 837.
* guix/scripts/package.scm: Remove two unnecessary #:use-module forms.
Autoload (gnu packages ...) modules.
Fixes <http://bugs.gnu.org/21991>.
Reported by Jan Synáček <jan.synacek@gmail.com>.
* guix/scripts/download.scm (guix-download): Call 'leave' when OPTS does
not contain an 'argument' key.
* guix/ftp-client.scm (ftp-open): Change to use 'match' instead of
car/cdr, and fix off-by-one (was '(null? addresses)' instead of
'(null? (cdr addresses))'.)
Fixes <http://bugs.gnu.org/21958>.
* guix/scripts/environment.scm (status->exit-code): New procedure.
(exit/status, primitive-exit/status): Use it.
* tests/guix-environment-container.sh: Add test.
Fixes <http://bugs.gnu.org/21925>.
Regression introduced in 279ec1d.
Reported by Chris Marusich <cmmarusich@gmail.com>.
* guix/ftp-client.scm (ftp-open): Restrict sockets to
SOCK_STREAM/IPPROTO_IP.
* guix/build/graft.scm (rewrite-directory)[rewrite-leaf]: Change to take
a single parameter. Add call to 'lstat'. Factorize result of
'destination'.
Use 'find-files' instead of 'file-system-fold'.
* guix/scripts/lint.scm (probe-uri): Add #:timeout parameter. Pass it
to 'open-connection-for-uri' and 'ftp-open'.
(validate-uri): Pass #:timeout 3 to 'probe-uri'.
* guix/build/download.scm (open-socket-for-uri): Always pass
AI_ADDRCONFIG to 'getaddrinfo' as recommended in the fine Guile
manual.
* guix/ftp-client.scm (ftp-open): Ditto.
* guix/build/download.scm (ensure-uri): New procedure.
(current-http-proxy): New variable.
(open-socket-for-uri): Copy from Guile commit aaea5b2, but add #:timeout
parameter and use 'connect*' instead of 'connect'.
(open-connection-for-uri): Add #:timeout parameter and pass it to
'open-socket-for-uri'.
* guix/ftp-client.scm (catch-EINPROGRESS): New macro.
(connect*): New procedure.
(ftp-open): Add #:timeout parameter. Use 'connect*' instead of
'connect' and pass it TIMEOUT.
Fixes <http://bugs.gnu.org/21817>.
Reported by Petter Berntsen <petter@mykolab.ch>.
* guix/scripts/gc.scm (guix-gc)[assert-no-extra-arguments]: New
procedure.
Use it for actions 'collect-garbage', 'optimize', and 'verify'.
* tests/guix-gc.sh: Add tests.
Partly fixes <http://bugs.gnu.org/20255>.
* guix/scripts/package.scm (search-path-environment-variables): Change
'profile' to 'profiles'; expect it to be a list.
(display-search-paths): Likewise.
(%default-options): Remove 'profile' entry.
(%options) <--profile>: Keep previous values associated with 'profile'
in RESULT.
(guix-package)[process-actions, process-query]: Handle the possible
lack of 'profile' pair in OPTS.
Reported by Sleep_Walker and Mathieu Lirzin <mthl@gnu.org>.
* guix/scripts/refresh.scm (maybe-updater, list-updaters): New macros.
(%updaters): Use 'list-updaters' instead of 'list'. Make
%PYPI-UPDATER conditional.
Reported by Paul van der Walt <paul@denknerd.org>
in <http://bugs.gnu.org/21829>.
* guix/scripts/import/hackage.scm (guix-import-hackage): Add missing
argument in call to 'leave'.
* guix/scripts/container/exec.scm (partition-args): Reimplement such
that all args up to and including the PID are returned as the first of
the two values.
This is a followup to 0a7c5a0.
* guix/import/gnu.scm (preferred-archive-type): Use
'upstream-source-archive-types' instead of 'gnu-release-archive-types'.
(gnu-package->sexp): Use 'upstream-source-urls' et al. Update call to
'download-tarball'.
(gnu->guix-package): Use <upstream-source> instead of <gnu-release>.
* guix/upstream.scm (upstream-source-archive-types): Export.
Fixes <http://bugs.gnu.org/21068>.
Reported by Germano Gabbianelli <tyrion.mx@gmail.com>
and Mark H Weaver <mhw@netris.org>.
* guix/scripts/system.scm (perform-action): Always add GRUB.CFG to DRVS
for 'init' and 'reconfigure'.
Co-authored-by: Mark H Weaver <mhw@netris.org>
* gnu/services.scm (system-derivation): New procedure.
(system-service-type): New variable.
(boot-script-entry): New procedure.
(boot-service-type): Extend SYSTEM-SERVICE-TYPE.
(etc-entry): New procedure.
(etc-service-type): Extend SYSTEM-SERVICE-TYPE.
(fold-services): Change default #:target-type to SYSTEM-SERVICE-TYPE.
* gnu/system.scm (operating-system-directory-base-entries): New procedure.
(essential-services): Use it. Add an instance of
SYSTEM-SERVICE-TYPE.
(operating-system-boot-script): Pass #:target-type to 'fold-services'.
(operating-system-derivation): Rewrite in terms of 'fold-services'.
* gnu/system/linux-container.scm (system-container): Remove.
(container-script): Use 'operating-system-derivation'.
* guix/scripts/system.scm (export-extension-graph): Replace
BOOT-SERVICE-TYPE by SYSTEM-SERVICE-TYPE.
* doc/images/service-graph.dot: Add 'system' node and edges.
* doc/guix.texi (Service Composition): Mention SYSTEM-SERVICE-TYPE.
(Service Reference): Document it. Update 'fold-services'
documentation.
* guix/scripts/environment.scm (%default-options): Remove 'exec'
association.
(guix-environment): If the user didn't specify a command, use the
default shell, or use /bin/sh when a container is requested.
Benefits include: 'guix environment' more useful for ghc libraries, more
useful 'guix package --search-paths' for installed ghc libraries, cleaner
package recipes: no longer need to propagate runtime package dependencies.
* guix/build/haskell-build-system.scm (configure): Unset GHC_PACKAGE_PATH
around cabal configure.
(make-ghc-package-database): Use pattern directory search.
(register): Install complete package database for the current package.
* gnu/packages/haskell.scm (ghc): Add native-search-paths field.
This patch changes the --ad-hoc flag to be positional. That is, the
packages that appear before --ad-hoc are interpreted as packages whose
inputs should be in the environment; the packages that appear after are
interpreted as packages to be directly added to the environment.
* guix/scripts/environment.scm (tag-package-arg, compact): New
procedures.
(%options): Tweak the handlers for --load and --expression options.
(options/resolve-packages): Preserve package mode tag.
(parse-args): Tweak argument handler to use package tagging procedure.
(guix-environment): Apply ad-hoc behavior on a per package basis.
* tests/guix-environment.sh: Add test.
* doc/guix.texi ("invoking guix environment"): Document new behavior of
--ad-hoc.
Fixes <http://bugs.gnu.org/21773>.
Reported by Jan Synáček <jan.synacek@gmail.com>.
* guix/ui.scm (make-regexp*): New procedure.
* guix/scripts/package.scm (options->installable, guix-package): Use it
when processing user-provided regexps.
Partly fixes <http://bugs.gnu.org/20217>.
* guix/store.scm (set-build-options): Change #:substitute-urls to
default to #f. Send the 'substitute-urls' pair only if
SUBSTITUTE-URLS is true.
* guix/scripts/build.scm (set-build-options-from-command-line): Do not
default to %DEFAULT-SUBSTITUTE-URLS for #:substitute-urls.
* guix/scripts/size.scm (%default-options): Remove 'substitute-urls'.
* guix/scripts/substitute.scm (lookup-narinfos/diverse): New procedure.
(lookup-narinfo): Use it.
(process-query): Change #:cache-url to #:cache-urls.
[valid?]: Remove 'narinfo?' check, which is no longer necessary.
Use 'lookup-narinfos/diverse' instead of 'lookup-narinfos'.
(process-substitution): Change #:cache-url to #:cache-urls.
(%cache-url): Rename to...
(%cache-urls): ... this. Turn into a list.
(guix-substitute): Remove 'getaddrinfo' test with early exit. Adjust
calls to 'process-query' and 'process-substitution'.
* tests/substitute.scm: Change '%cache-url' to '%cache-urls'.
Ben Woodcroft