* 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/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.
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.
* guix/packages.scm (package-transitive-native-search-paths): New
procedure.
* tests/packages.scm ("package-transitive-native-search-paths"): New
test.
* 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.
* 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.
* 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.
* gnu/services/dmd.scm (assert-no-duplicates): Rename to...
(assert-valid-graph): ... this.
[provisions]: New variable.
[assert-satisfied-requirements]: New procedure.
Use it.
* tests/guix-system.sh: Add test with unmet dmd requirements.
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/21410>.
Reported by Alex Vong <alexvong1995@gmail.com>.
* tests/guix-environment-container.sh: Exit with 77 when
'((@@ (guix scripts environment) assert-container-features))' fails.
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.
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.
* 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'.
* guix/scripts/system.scm (specification->file-system-mapping): Move from
here...
* guix/ui.scm (specification->file-system-mapping): ... to here.
* guix/scripts/enviroment.scm (show-help): Show help for new options.
(%options): Add --container --network, --expose, and --share options.
(%network-configuration-files): New variable.
(launch-environment, launch-environment/container, requisites*,
inputs->requisites): New procedures.
(guix-environment): Spawn new process in a container when requested.
* doc/guix.texi (Invoking guix environment): Document it.
* tests/guix-environment-container.sh: New file.
* Makefile.am (SH_TESTS): Add it.
* guix/scripts/archive.scm (show-help, %options): Add --extract.
(guix-archive): Honor it.
* tests/guix-archive.sh: Test it.
* doc/guix.texi (Invoking guix archive): Document it.
This patch rewrites GuixSD services to make them extensible.
* gnu-system.am (GNU_SYSTEM_MODULES): Add gnu/services/dbus.scm.
* gnu/services.scm (<service>): Replace with new record type.
(<service-extension>, <service-type>): New record types.
(write-service-type, compute-boot-script, second-argument): New
procedures.
(%boot-service, boot-service-type): New variables.
(file-union, directory-union, modprobe-wrapper,
activation-service->script, activation-script,
gexps->activation-gexp): New procedures.
(activation-service-type, %activation-service): New variables.
(etc-directory, files->etc-directory, etc-service): New procedures.
(etc-service-type, setuid-program-service, firmware-service-type): New
variables.
(firmware->activation-gexp): New procedure.
(&service-error, &missing-target-service-error,
&ambiguous-target-service-error): New condition types.
(service-back-edges, fold-services): New procedures.
* gnu/services/avahi.scm (<avahi-configuration>): New record type.
(configuration-file): Replace keyword parameters with a single
'config' parameter.
(%avahi-accounts, %avahi-activation, avahi-service-type): New
variables.
(avahi-dmd-service): New procedure.
(avahi-service): Rewrite using 'service' and 'avahi-configuration'.
* gnu/services/base.scm (%root-file-system-dmd-service,
root-file-system-service-type): New variables.
(root-file-system-service): Use them.
(file-system->dmd-service-name): New procedure.
(file-system-service-type): New variable.
(file-system-service): Use it. Replace keyword parameters with a
single 'file-system' object.
(user-unmount-service-type): New variable.
(user-unmount-service): Use it.
(user-processes-service-type): New variable.
(user-processes-service): Use it.
(host-name-service-type): New variable.
(host-name-service): Use it.
(console-keymap-service-type): New variable.
(console-keymap-service): Use it.
(console-font-service-type): New variable.
(console-font-service): Use it.
(mingetty-pam-service, mingetty-dmd-service): New procedures.
(mingetty-service-type): New variable.
(mingetty-service): Use it.
(nscd-dmd-service): New procedure.
(nscd-activation, nscd-service-type): New variables.
(nscd-service): Use the latter.
(syslog-service-type): New variable.
(syslog-service): Use it.
(<guix-configuration>): New record type.
(%default-guix-configuration): New variable.
(guix-dmd-service, guix-accounts, guix-activation): New procedures.
(guix-service-type): New variable.
(guix-service): Replace list of keyword parameters with a single
'config' parameter. Rewrite using 'service'.
(<udev-configuration>): New record type.
(udev-dmd-service): New procedure.
(udev-service-type): New variable.
(udev-service): Use it.
(device-mapping-service-type): New variable.
(device-mapping-service): Use it.
(swap-service-type): New variable.
(swap-service): Use it.
* gnu/services/databases.scm (<postgresql-configuration>): New record
type.
(%postgresql-accounts, postgresql-activation): New variables.
(postgresql-dmd-service): New procedure.
(postgresql-service): Rewrite using 'service' and
'postgresql-configuration'.
* gnu/services/dbus.scm: New file.
* gnu/services/desktop.scm (dbus-configuration-directory, dbus-service):
Remove.
(wrapped-dbus-service): New procedure.
(<upower-configuration>): New record type.
(upower-configuration-file): Replace keyword parameters with single
<upower-configuration> parameter.
(%upower-accounts, %upower-activation): New variables.
(upower-dbus-service, upower-dmd-service): New procedures.
(upower-service-type): New variable.
(upower-service): Rewrite using 'service' and 'upower-configuration'.
(%colord-activation, %colord-accounts): New variables.
(colord-dmd-service): New procedure.
(colord-service-type): New variable.
(colord-service): Rewrite using 'service'.
(<geoclue-configuration>): New record type.
(geoclue-configuration-file): Replace keyword parameters with a single
'config' parameter.
(geoclue-dbus-service, geoclue-dmd-service): New procedures.
(%geoclue-accounts, geoclue-service-type): New variables.
(geoclue-service): Rewrite using 'service' and
'geoclue-configuration'.
(%polkit-accounts, %polkit-pam-services, polkit-service-type): New
variables.
(polkit-dmd-service): New procedure.
(polkit-service): Rewrite using 'service'.
(<elogind-configuration>)[elogind]: New field.
(elogind-dmd-service): New procedure.
(elogind-service-type): New variable.
(elogind-service): Rewrite using 'service'.
(%desktop-services): Remove argument to 'dbus-service'. Remove 'map'
over %BASE-SERVICES.
* gnu/services/dmd.scm (dmd-boot-gexp): New procedure.
(dmd-root-service-type, %dmd-root-service): New variables.
(dmd-service-type): New macro.
(<dmd-service>): New record type.
* gnu/services/lirc.scm (<lirc-configuration>): New record type.
(%lirc-activation): New variable.
(lirc-dmd-service): New procedure.
(lirc-service-type): New variable.
(lirc-service): Rewrite using 'service' and 'lirc-configuration'.
* gnu/services/networking.scm (<static-networking>): New record type.
(static-networking-service-type): New variable.
(static-networking-service): Rewrite using 'service' and
'static-networking'.
(dhcp-client-service-type): New variable.
(dhcp-client-service): Rewrite using 'service'.
(<ntp-configuration>): New record type.
(ntp-dmd-service): New procedure.
(ntp-service-type): New variable.
(ntp-service): New procedure.
(%tor-accounts, tor-service-type): New variable.
(tor-dmd-service): New procedure.
(tor-service): Rewrite using 'service'.
(<bitlbee-configuration>): New record type.
(bitlbee-dmd-service): New procedure.
(%bitlbee-accounts, %bitlbee-activation, bitlbee-service-type): New
variables.
(bitlbee-service): Rewrite using 'service'.
(%wicd-activation): New variable.
(wicd-dmd-service): New procedure.
(wicd-service-type): New variable.
(wicd-service): Rewrite using 'service'.
* gnu/services/ssh.scm (<lsh-configuration>): New record type.
(activation): Rename to...
(lsh-initialization): ... this.
(lsh-activation, lsh-dmd-service, lsh-pam-services): New procedures.
(lsh-service-type): New variable.
(lsh-service): Rewrite using 'service' and 'lsh-configuration'.
* gnu/services/web.scm (<nginx-configuration>): New record type.
(%nginx-accounts): New variable.
(nginx-activation, nginx-dmd-service): New procedures.
(nginx-service-type): New variable.
(nginx-service): Rewrite using 'service' and 'nginx-configuration'.
* gnu/services/xorg.scm (<slim-configuration>): New record type.
(slim-pam-service, slim-dmd-service): New procedures.
(slim-service-type): New variable.
(slim-service): Rewrite using 'service' and 'slim-configuration'.
* gnu/system.scm (file-union): Remove.
(other-file-system-services): Adjust to new 'file-system-service'
signature.
(essential-services): Add #:container? parameter. Add
%DMD-ROOT-SERVICE, %ACTIVATION-SERVICE, and calls to
'pam-root-service', 'account-service', 'operating-system-etc-service',
and a SETUID-PROGRAM-SERVICE instance.
(operating-system-services): Pass #:container? to 'essential-services.
(etc-directory): Remove.
(operating-system-etc-service): New procedure. Rewrite as a call to
'etc-service'.
(operating-system-accounts): Change to not return accounts required by
services.
(operating-system-etc-directory): Rewrite as a call to 'fold-services'
and 'etc-directory'.
(user-group->gexp, user-account->gexp, modprobe-wrapper): Remove.
(operating-system-activation-script): Rewrite as a call to
'fold-services' and 'activation-service->script'.
(operating-system-boot-script): Likewise.
(operating-system-derivation): Add call to 'lower-object'.
(emacs-site-file, emacs-site-directory, shells-file): Change to use
'computed-file' and 'scheme-file' instead of the monadic procedures.
* gnu/system/install.scm (cow-store-service-type): New variable.
(cow-store-service): Rewrite using 'service'.
(/etc/configuration-files): New procedure.
(configuration-template-service-type,
%configuration-template-service): New variables.
(configuration-template-service): Remove.
(installation-services): Adjust accordingly. Adjust argument to
'guix-service'.
* gnu/system/linux.scm (/etc-entry, pam-root-service): New procedures.
(pam-root-service-type): New variable.
* gnu/system/shadow.scm (user-group->gexp, user-account->gexp,
account-activation, etc-skel, account-service): New procedures.
(account-service-type): New variable.
* tests/services.scm: New file.
* doc/guix.texi (Base Services, Desktop Services): Adjust accordingly.
(Defining Services): Rewrite.
* doc/images/service-graph.dot: New file.
* doc.am (DOT_FILES): Add it.
* po/guix/POTFILES.in: Add gnu/services.scm.
* guix/scripts/system.scm (perform-action): Add #:derivations-only?
parameter and honor it.
(show-help, %options): Add '--derivation'.
(guix-system): Pass #:derivations-only? to 'perform-action'.
* tests/guix-system.sh: Test it.
* doc/guix.texi (Invoking guix system): Document it.
* guix/gexp.scm (<scheme-file>): New record type.
(scheme-file, scheme-file-compiler): New procedures.
* tests/gexp.scm ("scheme-file"): New test.
* doc/guix.texi (G-Expressions): Document 'scheme-file'.
* guix/gexp.scm (<program-file>): New record type.
(program-file, program-file-compiler): New procedures.
* tests/gexp.scm ("program-file"): New test.
* doc/guix.texi (G-Expressions): Document it.
Before, call-with-clean-exit would *always* return an exit code of 1.
* gnu/build/linux-container.scm (call-with-clean-exit): Exit with status
code of 0 if thunk does not throw an exception.
* tests/containers.scm: Add test.
This allows for direct program invokation without needing a shell to act
as a command interpreter.
* guix/scripts/environment.scm (%default-shell): New variable.
(show-help): Adjust description. Remove '--exec' reference.
(%default-options): Use '%default-shell'.
(%options): Adjust '--exec' to run command via the default shell.
(parse-args): New procedure.
(guix-environment): Use 'parse-args'. Use 'system*' instead of
'system'.
* tests/guix-environment.sh: Add test for '--' command invokation.
* doc/guix.texi ("Invoking guix environment"): Use new syntax. Remove
'--exec' documentation.
Suggested by Mark H Weaver <mhw@netris.org>.
* guix/store.scm (query-failed-paths, clear-failed-paths): New
procedures.
* tests/guix-daemon.sh: Add test with daemon started with
--cache-failures.
Fixes <http://bugs.gnu.org/21536>.
Reported by Alex Kost <alezost@gmail.com>.
* guix/ui.scm (texi->plain-text): Wrap body in 'with-fluids'.
* tests/ui.scm ("package-description-string vs. Unicode"): New test.
* guix/scripts/lint.scm (%hanging-paren-rx): New variable.
(report-lone-parentheses): New procedure.
(%formatting-reporters): Use it.
* tests/lint.scm ("formatting: lonely parentheses"): New test.
Reported by Andy Wingo <wingo@igalia.com>.
* guix/monads.scm (define-lift) <fallback case>: Add missing #'. Remove
extra formal parameter.
* tests/monads.scm ("lift"): Add test with 'lift1' as a procedure.
* guix/import/gem.scm (make-gem-sexp): Properly handle an empty list of
licenses. When rendering a list of licenses, cons 'list onto the front of
the expression.
* tests/gem.scm: New file.
* Makefile.am (SCM_TESTS): Add it.
Reported by Eric Hanchrow <eric.hanchrow@gmail.com>
in <http://bugs.gnu.org/21354>.
* tests/syscalls.scm ("set-network-interface-address"): Skip when (getuid)
returns zero.
* guix/gexp.scm (lower-object): New procedure.
(lower-inputs, lower-references, gexp->sexp): Use it.
* tests/gexp.scm ("lower-object"): New test.
* doc/guix.texi (G-Expressions): Document it.
Fixes <http://bugs.gnu.org/21280>.
Reported by Leo Famulari <leo@famulari.name>.
* tests/nar.scm (file-tree-equal?): Use #t as the initial result. Btrfs would
set nlink to 1 instead of 2 for an empty directory, thereby leading
'file-tree-equal?' to return #f.
* guix/scripts/package.scm (show-help): Add help text for --install-from-file
option.
(%options): Add --install-from-file option.
* tests/guix-package.sh: Test it.
* doc/guix.texi ("invoking guix package"): Document it.
* doc/package-hello.scm: New file.
* doc.am (EXTRA_DIST): Add it.
Fixes bug #21226.
Linux 3.19 introduced a fix for a security vulnerability in user namespaces.
This fix introduced a new proc file called 'setgroups' and was backported to
many older kernels. However, some users run a kernel that is new enough to
support user namespaces yet old enough to not include the patch, so we must
skip the tests.
* tests/containers.scm: Skip all tests if /proc/self/setgroups does not exist.
It's not always possible to map 65536 uids when creating a container as the
root user within another user namespace. This is true when building Guix
within the build daemon's container. By using a uid range of 1 by default,
even as the root user, the tests now pass.
* gnu/build/linux-container.scm (initialize-user-namespace, run-container):
Add 'host-uids' argument.
(call-with-container): Add #:host-uids keyword argument.
* tests/containers.scm ("container-excursion"): Update 'run-container' call.
Based on discussions with Rohan Prinja <rohan.prinja@gmail.com>.
* guix/build/syscalls.scm (<interface>): New record type.
(write-interface, values->interface, unfold-interface-list,
network-interfaces, free-ifaddrs): New procedures.
(ifaddrs): New C struct.
(%struct-ifaddrs-type, %sizeof-ifaddrs): New macros.
* tests/syscalls.scm ("network-interfaces returns one or more interfaces",
"network-interfaces returns \"lo\""): New tests.
* tests/gexp.scm ("gexp->derivation #:references-graphs"): Use 'lset=' instead
of 'equal?' since the order in which references are listed in not
guaranteed.
Fixes <http://bugs.gnu.org/19778>.
Reported by Mark H Weaver <mhw@netris.org>.
* gnu/system/file-systems.scm (%uuid-rx): New variable.
(string->uuid): New procedure.
(uuid): New macro.
* tests/file-systems.scm: New file.
* Makefile.am (SCM_TESTS): Add it.
* doc/guix.texi (File Systems): Give an example of UUID.
* guix/scripts/substitute.scm (or*): New macro.
(%cache-url): Honor "untrusted-substitute-urls".
* guix/tests.scm (%test-substitute-urls): New variable.
(open-connection-for-tests): Use it.
* tests/derivations.scm ("derivation-prerequisites-to-build and substitutes",
"derivation-prerequisites-to-build and substitutes, non-substitutable
build", "derivation-prerequisites-to-build and substitutes, local build"):
Pass it to 'set-build-options'.
* tests/guix-daemon.sh: Likewise.
* tests/store.scm ("substitute query, alternating URLs"): New test.
("substitute query", "substitute", "substitute + build-things with output
path", "substitute, corrupt output hash", "substitute --fallback"): Pass
#:substitute-urls to 'set-build-options'.
This ensures that switching between different substitute servers doesn't lead
to a polluted narinfo cache.
* guix/scripts/substitute.scm (narinfo-cache-file): Add 'cache-url'
parameter. Add the base32 of CACHE-URL as a sub-directory under
%NARINFO-CACHE-DIRECTORY. Update callers.
(cached-narinfo): Likewise. Call 'mkdir-p' on the dirname of the cache
file. Update callers.
(remove-expired-cached-narinfos): Add 'directory' parameter and use it
instead of %NARINFO-CACHE-DIRECTORY.
(narinfo-cache-directories): New procedure.
(maybe-remove-expired-cached-narinfo): Call 'remove-expired-cached-narinfos'
for each item returned by 'narinfo-cache-directories'.
There were two issues:
1. Use of 'delete-duplicates', which is quadratic, was a serious problem for
closures with lots of propagated inputs, such as that of the 'hydra'
package (several minutes for 'guix build hydra -n'!).
2. The 'delete-duplicates' call essentially had no effect since duplicate
inputs typically had a different label and were thus kept. For
instance, (bag-transitive-inputs (package->bag inkscape)) would return
216 items whereas (delete-duplicates (map cdr THAT)) contains only 67
items.
The new implementation returns 67 items in this case. For 'hydra', we're
down from 42211 items to 361, and roughly 13s for 'guix build hydra'.
* guix/packages.scm (transitive-inputs): Rewrite as a breadth-first
traversal. Remove duplicate propagated inputs.
* tests/packages.scm ("package-transitive-inputs", "package->bag, propagated
inputs"): Adjust to use simple labels for propagated inputs, without "/".
("package-transitive-inputs, no duplicates"): New test.
This is a followup to commit 5d6792f ("gnu: bootstrap: Create a wrapper for
guile to set the system load path.")
* tests/size.scm ("store-profile"): Expect profile of 'bash' bootstrap binary.
* tests/gexp.scm ("gexp->derivation #:references-graphs"): Expect GUILE-DRV to
depend on 'bash' bootstrap binary.
* gnu/build/linux-container.scm: New file.
* gnu-system.am (GNU_SYSTEM_MODULES): Add it.
* .dir-locals.el: Add Scheme indent rules for 'call-with-container', and
'container-excursion'.
* tests/containers.scm: New file.
* Makefile.am (SCM_TESTS): Add it.
Ricardo Wurmus