Fixes <https://bugs.gnu.org/29654>.
Reported by Ruud van Asseldonk <dev+guix@veniogames.com>.
This also speeds up database creation compared to "man-db
--create" (less than half the time, on a warm cache, for 19k pages.)
* guix/man-db.scm: New file.
* Makefile.am (MODULES_NOT_COMPILED): Add it.
* guix/profiles.scm (manual-database): Rewrite to use (guix man-db).
* guix/scripts/offload.scm (check-machine-status): New procedure.
(guix-offload): Call it when the argument is "status".
* doc/guix.texi (Daemon Offload Setup): Document it.
* guix/scripts/system.scm (show-help): Add expression option.
(%options): Ditto.
(guix-system): Allow commands taking a file as an argument to use an
expression instead.
(process-action): Read operating-system from expression or file.
* doc/guix.texi (Invoking guix system): Introduce the expression option.
* gnu/bootloader/extlinux.scm (install-extlinux): Factorize bootloader
writing in a new procedure write-file-on-device defined in (gnu build
bootloader).
* gnu/build/bootloader.scm: New file.
* gnu/local.mk (GNU_SYSTEM_MODULES): Add new file.
* gnu/system/vm.scm (qemu-img): Adapt to import and use (gnu build bootloader)
module during derivation building.
* gnu/scripts/system.scm (bootloader-installer-derivation): Ditto.
This reduces max RSS from 1.3G to 1.0G.
* guix/derivations.scm (invalidate-derivation-caches!): New procedure.
* build-aux/hydra/gnu-system.scm (hydra-jobs): Use it. Add 'format'
call.
This has little or no run-time impact and slightly reduces the memory
footprint.
* guix/derivations.scm (derivation-hash): Replace 'mlambda' with
'lambda'.
* guix/memoization.scm (<cache>): New record type.
(define-lookup-procedure, define-update-procedure): New macros.
(cache-ref, cacheq-ref, cache-set!, cacheq-set!): New procedures.
(cached/mv, cachedq/mv, cached, cachedq): Use them instead of 'hash-ref'
and 'hash-set!'.
(%make-hash-table*): When 'profiled?' returns true, return a <cache>
object.
(define-cache-procedure): Adjust to show cache lookups and hits.
* guix/memoization.scm (%memoization-tables): New variable.
(%make-hash-table*, show-memoization-tables): New procedures.
(make-hash-table*): New macro.
Add top-level call to 'register-profiling-hook!'.
(memoize): Adjust to pass the resulting procedure to
'make-hash-table*'.
(%mlambda): Likewise.
Fixes <https://bugs.gnu.org/29255>.
Reported by Ben Sturmfels <ben@sturm.com.au>.
* guix/ui.scm (display-collision-resolution-hint): New procedure.
(call-with-error-handling): Call it upon '&profile-collistion-error'.
* guix/scripts/lint.scm (check-vulnerabilities): Also check for CVEs
listed as mitigated in the package properties.
* tests/lint.scm ("cve: known safe from vulnerability"): New test.
'package-grafts' returns a list of potentially applicable grafts, which
'cumulative-grafts' then narrows by looking at store item references and
determining the subset of the grafts that's actually applicable.
Until now, 'package-grafts' would traverse native inputs and would thus
return a large superset of the applicable grafts, since native inputs
are not in the reference graph by definition. This patch fixes that by
having 'package-grafts' ignore entirely native inputs from the
dependency graph.
* guix/packages.scm (fold-bag-dependencies)[bag-direct-inputs*]: Add
special case for libc.
* guix/packages.scm (bag-grafts)[native-grafts, target-grafts]: Remove.
[grafts]: New procedure.
Use it.
* tests/packages.scm ("package-grafts, grafts of native inputs
ignored"): New test.
Previously recursive calls to 'loop' would always consider all the bag
inputs rather than those corresponding to NATIVE?.
* guix/packages.scm (fold-bag-dependencies)[bag-direct-inputs*]: New
procedure. Use it both in the 'match' expression and in its body.
This is a followup to 2815fca142.
* guix/profiles.scm (profile-derivation)[builder]: Remove
'debug-disable' call, which was ineffective.
Pass #:env-vars to 'gexp->derivation'.
This fixes a regression introduced in
2f60084f77, whereby the profile derivation
would fail to run on Guile 2.0 (as is the case with "guix package
--bootstrap").
Reported by Christopher Baines.
* guix/profiles.scm (profile-derivation)[builder]: Use _IO* but add
'debug-disable' call.
Previously the "manual-database" derivation would always import the
host's srfi-{19,26}.scm files in the build side. In practice this means
that different users could get different manual-database.drv depending
on the Guile version they're using in the host.
For example, the (gnu tests install) tests would fail if the host was
running Guile 2.2.3 because the guest is running 2.2.2, and thus has
different srfi-{19,26}.scm files. The manual-database.drv would need to
be built from source, which would fail because prerequisites were
missing.
Reported by Mathieu Othacehe <m.othacehe@gmail.com>
at <https://debbugs.gnu.org/cgi/bugreport.cgi?bug=29409#96>.
* guix/profiles.scm (manual-database): Do not pass #:modules to
'gexp->derivation'. Wrap 'build' gexp in 'with-imported-modules' form.
* guix/scripts/offload.scm (build-machines): Comment out
'(set! %fresh-auto-compile #t)' since with Guile 2.2.3 it could lead to
an actual rebuild of everything that gets loaded from there on. See
<https://bugs.gnu.org/29226>.
* guix/ui.scm (load*): Likewise.
Until now it would print the name of each store item being copied, which
was verbose and unhelpful.
* guix/scripts/system.scm (copy-closure): Use 'progress-reporter/bar'
and 'call-with-progress-reporter'.
(guix-system): Parameterize 'current-terminal-columns'.
* guix/scripts/system.scm (copy-item): Add 'references' argument and
remove 'references*' call. Turn into a non-monadic procedure.
(copy-closure): Remove initial call to 'references*'. Only pass ITEM to
'topologically-sorted*' since that's equivalent. Compute the list of
references corresponding to TO-COPY and pass it to 'copy-item'.
Previously things returned by 'program-file', such as %MODPROBE-WRAPPER
in (gnu services), would refer to 'guile-final'. This would introduce
'guile-final' in the system closure, which is otherwise absent. By
referring to 'guile-2.2' we remove that extra Guile.
* guix/gexp.scm (default-guile): Refer to GUILE-2.2 instead of
GUILE-FINAL.
This avoids repeated deprecation messages, particularly while running
'guix system build' or similar.
* guix/gexp.scm (gexp->derivation): Add #:deprecation-warnings. Pass it
to 'compiled-modules'.
(compiled-modules): Add #:deprecation-warnings and honor it.
* doc/guix.texi (G-Expressions): Update 'gexp->derivation'
documentation.
* guix/packages.scm (patch-and-repack): Pass #:deprecation-warnings #t.
Reported at <https://bugs.gnu.org/27943>
by Danny Milosavljevic <dannym@scratchpost.org>.
* guix/scripts/lint.scm (%distro-directory): New variable.
(check-patch-file-names): Add check for the file name length.
* tests/lint.scm ("patches: file name too long"): New test.
Fixes <https://bugs.gnu.org/25020>.
Reported by Hartmut Goebel <h.goebel@crazy-compilers.com>.
* guix/gnu-maintenance.scm (latest-ftp-release)[contains-digit?]: Remove.
Relax test as to whether to recurse into subdirectories.
Fixes <https://bugs.gnu.org/29358>.
Reported by Marius Bakke <mbakke@fastmail.com>.
* guix/ui.scm (known-variable-definition): Add 'visited' set to guard
against cycles on 2.0.
This reverts commit 5f93d97005.
'guix pull' would fail because (guix self) needs 'scheme-files'
from (guix discovery), which was not exported until now.
This mitigates <https://bugs.gnu.org/27284>.
* guix/self.scm: New file.
* Makefile.am (MODULES): Add it.
* build-aux/build-self.scm (libgcrypt, zlib, gzip, bzip2, xz)
(false-if-wrong-guile, package-for-current-guile, guile-json)
(guile-ssh, guile-git, guile-bytestructures): Remove.
(build): Rewrite to simply delegate to 'compiled-guix'.
* gnu/packages.scm (%distro-root-directory): Rewrite to try different
directories.
* guix/discovery.scm (guix): Export 'scheme-files'.
* guix/scripts/pull.scm (build-and-install): Split into...
(install-latest): ... this. New procedure. And...
(build-and-install): ... this, which now takes a monadic value argument.
(indirect-root-added): Remove.
(guix-pull): Call 'add-indirect-root'. Call 'build-from-source' and
pass the result to 'build-and-install'.
This makes 'latest-repository-commit' significantly more efficient and
reduces disk usage in the store.
* guix/git.scm (copy-to-store)[dot-git?]: New procedure.
Pass it as the #:select? argument to 'add-to-store'.
Fixes <https://bugs.gnu.org/29335>.
* guix/zlib.scm (close-procedure): Remove.
(make-gzip-input-port): Do (dup (fileno port)) to get a file descriptor
for 'gzdopen'. Close PORT before returning. Use 'gzclose' as the
'close' procedure of the returned port.
(make-gzip-output-port): Likewise.
* guix/workers.scm (worker-thunk): Add (const #f) as the 'catch'
handler, and move previous handler as pre-unwind handler. Protect
against 'make-stack' returning #f.
Fixes <https://bugs.gnu.org/28779>.
Reported by Eric Bavier <bavier@cray.com>.
* guix/workers.scm (<pool>)[busy]: New field.
(worker-thunk): Add #:idle and #:busy and use them.
(make-pool): Pass #:busy and #:idle to 'worker-thunk'. Pass a 'busy'
value to '%make-pool'.
* guix/workers.scm (pool-idle?): Check whether 'pool-busy' returns zero
and adjust docstring.
That way CVE fetching benefits from 'If-Modified-Since' handling.
* guix/http-client.scm (http-fetch/cached): Add #:write-cache and
#:cache-miss parameters and honor them.
* guix/cve.scm (%current-year-ttl, %past-year-ttl): Reduce.
(call-with-cve-port): Remove.
(write-cache): New procedure.
(fetch-vulnerabilities): Rewrite in terms of 'http-fetch/cached'.
This is another instance of <https://bugs.gnu.org/22966>.
The Microsoft-IIS/7.5 server at static.nvd.nist.gov would sometimes hang
when receiving our requests byte by byte.
* guix/build/download.scm (tls-wrap) [!guile-2.0]: Add 'setvbuf' call.
This ensures the timeout applies when connecting to the port returned by
PASV.
* guix/ftp-client.scm (ftp-list): Add #:timeout parameter. Use
'connect*' instead of 'connect' and pass TIMEOUT.
(ftp-retr): Likewise.
* guix/build/download.scm (ftp-fetch): Pass TIMEOUT to 'ftp-retr'.
* guix/build-system/r.scm (bioconductor-uri): Also return the archive URL.
* guix/import/cran.scm (latest-bioconductor-release, fetch-description):
Adjust because bioconductor-uri now returns a list.
* guix/import/cran.scm (%bioconductor-version,
%bioconductor-packages-list-url): New variables.
(bioconductor-packages-list, latest-bioconductor-package-version): New
procedures.
Suggested by Marius Bakke <mbakke@fastmail.com>
in <https://bugs.gnu.org/29177>.
* guix/scripts/refresh.scm (all-packages): Pass #:select? to
'fold-packages'.
Fixes <https://bugs.gnu.org/29091>.
Reported by Eric Bavier <bavier@cray.com>.
* guix/build/compile.scm (relative-file): New procedure.
(load-files): Use it before calling 'file-name->module-name'.
(compile-files): Likewise before calling 'scm->go'.
* guix/build/pull.scm (build-guix): Remove 'with-directory-excursion'
and file name hack from ce33c3af76.
Pass OUT to 'all-scheme-files'.
* guix/download.scm (%mirrors)[cpan]: Update the list of CPAN mirrors (of
which several are dead) with a more-or-less geographically diverse selection.
This is most often the need for perl module dependencies.
* guix/import/cpan.scm (cpan-module->sexp): 'inputs -> 'propagated-inputs.
* tests/cpan.scm ("cpan->guix-package"): Adjust accordingly.
Ludovic Courtès