* 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.
* guix/import/elpa.scm (elpa-fetch-archive): Use 'http-fetch/cached'
directly instead of 'call-with-downloaded-file'. This ensures we don't
just abort when networking access is lacking, which is required to allow
'guix refresh -c refresh' to proceed.
* guix/scripts/lint.scm (call-with-networking-fail-safe): New procedure.
(with-networking-fail-safe): New macro.
(current-vulnerabilities*): Rewrite in terms of 'with-networking-fail-safe'.
* guix/scripts/challenge.scm (summarize-report-list): New procedure.
(guix-challenge): Use it.
* doc/guix.texi (Invoking guix challenge): Adjust command output in
example.
Fixes <https://bugs.gnu.org/28731>.
Reported by Jan Nieuwenhuizen <janneke@gnu.org>.
* guix/scripts/substitute.scm (at-most): New procedure.
(http-multiple-get): Use it to send at most 1000 requests at once.
Fixes <https://bugs.gnu.org/28956>.
Reported by Leo Famulari <leo@famulari.name>.
* build-aux/build-self.scm (build): Add (guix build compile) to
#:modules.
* guix/build/pull.scm (build-guix): Wrap 'compile-files' call in
'with-directory-excursion'. Strip "./" from FILES when passing it to
'compile-files'.
Among other things, this removes (guix utils), (guix ui), (guix config),
etc. from the closure of (guix build download), as was the case since
798648515b.
* guix/utils.scm (<progress-reporter>, call-with-progress-reporter):
Move to...
* guix/progress.scm: ... here. New file.
* Makefile.am (MODULES): Add it.
* guix/build/download.scm (current-terminal-columns)
(nearest-exact-integer, duration->seconds, seconds->string)
(byte-count->string, progress-bar, string-pad-middle)
(rate-limited, progress-reporter/file, dump-port*)
(time-monotonic): Move to progress.scm.
* guix/scripts/download.scm: Adjust accordingly.
* guix/scripts/substitute.scm: Likewise.
* guix/build/download.scm (http-fetch): Remove 'file' parameter. Change
to return an input port and the content-length. Make public.
(url-fetch): Adjust accordingly.
This is a followup to 36626c556e.
* guix/build/download.scm (http-fetch): Rename 'port-or-bv' to 'port'.
Assume (port? port) is always true, and remove other branch.
Fixes <https://bugs.gnu.org/28756>.
* guix/utils.scm (filtered-port): Close the 'input' port for the current
process, and close it upon exit in the child process.
* guix/scripts/substitute.scm (progress-substitution): Display "\n\n" after
the reporter has finished.
Previously the regex would match from /bin/ to a closing quote. However, this
is greedy, so will match up until the last ". This causes problems when there
are several quotes on the same line, for example:
org-effectiveness.el:
196: (call-process "/bin/bash" nil t nil "-c" strplot)
Therefore, change . to \S so that it doesn't include whitespace
characters. Changing to a lazy quantifier would be an option, if that were
supported.
* guix/build/emacs-build-system.scm (patch-el-files): Change the regular
expression used.
Previously the string-append here would error, which isn't useful as it
doesn't tell you which command couldn't be found. To make the error
actionable, catch it earlier, and explicitly error.
* guix/build/emacs-build-system.scm (patch-el-files): Handle (which cmd)
returning #f.
Previously we would call 'machine-load' once per machine, which was very
costly when there were many machines. Now we arrange to call it only
once on average (when all the machines have the same 'speed' value).
* guix/scripts/offload.scm (random-seed, shuffle): New procedures.
(choose-build-machine)[machines+slots+loads]: Rename to...
[machines+slots]: ... this. Remove load from the tuples therein.
[undecorate]: Adjust accordingly.
[machine-less-loaded-or-faster?]: Remove.
[machine-faster?]: New procedure.
Sort MACHINES+SLOTS according to 'machine-faster?'. Call
'machine-load?' as the last thing.
Fixes <https://bugs.gnu.org/28784>.
This mostly reverts 81a0f1cdf1, which
introduced a regression: revealed ports are *never* GC'd (contrary to
what Guile's manual suggests).
In addition to the revert, 'close-procedure' now explicitly swallows
EBADF errors when 'close-port' is called.
* guix/zlib.scm (close-procedure): New procedure.
(make-gzip-input-port)[gzfile]: Use 'fileno' instead of 'port->fdes'.
Use 'close-procedure' instead of 'gzclose'.
(make-gzip-output-port): Likewise.
* tests/zlib.scm ("compression/decompression pipe"): Use 'port-closed?'
to determine whether PARENT has been closed.
* guix/import/cpan.scm: Remove dependency on (gnu packages perl).
(perl-package): New procedure.
(%corelist, core-module?): Use it instead of referring to 'perl'.
Suggested by Ricardo Wurmus.
Works around <https://bugs.gnu.org/28295>.
* guix/ui.scm (report-load-error): Add case for 'read-error'.
* tests/guix-system.sh: Test missing-closing-paren errors.
* guix/scripts/lint.scm (check-for-updates): New procedure.
(%checkers): Add it.
* guix/scripts/refresh.scm (importer-modules, %updaters): Move
from here ...
* guix/upstream.scm: ... to here.
Fixes <https://bugs.gnu.org/28664>.
Reported by Maxim Cournoyer <maxim.cournoyer@gmail.com>.
* guix/scripts/publish.scm (bake-narinfo+nar): When COMPRESSION is
'none, write NAR instead of doing nothing.
(make-request-handler): Use 'render-nar/cached' for /nar URLs with no
compression.
* tests/publish.scm ("with cache", "with cache, uncompressed"): Adjust
expected result accordingly.
* guix/build-system/ant.scm: Add #:test-include and #:test-exclude
arguments.
* guix/build/ant-build-system.scm: Generate test list from arguments.
* doc/guix.texi (Build Systems): Document it.
* guix/build-system/ant.scm: New #:main-class argument
* guix/build/ant-build-system.scm: Generate a manifest file with
additional properties.
* doc/guix.texi (Build Systems): Document it.
This is a follow-up to commit fb1db38547.
* guix/scripts/build.scm (lazy-util): Remove procedure.
(options->things-to-build): Remove special case for files with ".json"
extension.
* guix/utils.scm (<progress-reporter>): New record type.
(call-with-progress-reporter): New procedure.
* guix/build/download.scm (dump-port*, rate-limited, progress-reporter/file):
New procedures.
(ftp-fetch, http-fetch): Use 'dump-port*'.
(progress-proc): Remove procedure.
* guix/scripts/substitute.scm (progress-report-port): Rewrite in terms of
<progress-reporter>.
(process-substitution): Adjust accordingly.
* guix/http-client.scm (http-fetch/cached)[update-cache]: Add
'cache-port' parameter. Check its mtime and compute 'if-modified-since'
header accordingly. Guard 'http-get-error?' and honor 304.
Adjust callers of 'update-cache'.
* guix/gnu-maintenance.scm (ftp.gnu.org-files): Set #:ttl to 15m.
The perl-license definition is intended to avoid circular dependencies, so
use this as a default when importing packages from CPAN.
* guix/import/cpan.scm (string->license): Replace '(package-license perl) with
'perl-license.
* guix/gnu-maintenance.scm (latest-gnu-release): Return a list of
matching tarballs instead of just the first one. This gives us .tar.gz,
.tar.xz, etc.
* guix/gnu-maintenance.scm (latest-gnu-release): Add calls to
'sans-extension'. This fixes version comparison, which could be fooled
with the ".tar.gz" extension.
This allows substitutes to be downloaded from unauthorized servers, as
long as they advertise the same hash and references as one of the
authorized servers.
* guix/scripts/substitute.scm (assert-valid-narinfo): Remove.
(valid-narinfo?): Add #:verbose?. Handle each case of
'signature-case'.
(equivalent-narinfo?): New procedure.
(lookup-narinfos/diverse): Add 'authorized?' parameter and honor it.
[select-hit]: New procedure.
(lookup-narinfo): Add 'authorized?' parameter and pass it.
(process-query): Adjust callers accordingly.
(process-substitution): Remove call to 'assert-valid-narinfo'. Check
whether 'lookup-narinfo' returns true and call 'leave' if not.
* tests/substitute.scm (%main-substitute-directory)
(%alternate-substitute-directory): New variables.
(call-with-narinfo): Make 'narinfo-directory' a parameter. Call
'mkdir-p' to create it. Change unwind handler to check whether
CACHE-DIRECTORY exists before deleting it.
(with-narinfo*): New macro.
("substitute, no signature")
("substitute, invalid hash")
("substitute, unauthorized key"): Change expected error message to "no
valid substitute".
("substitute, unauthorized narinfo comes first")
("substitute, unsigned narinfo comes first")
("substitute, first narinfo is unsigned and has wrong hash")
("substitute, first narinfo is unsigned and has wrong refs")
("substitute, unsigned narinfo comes first")
("substitute, two invalid narinfos"): New tests.
* doc/guix.texi (Substitutes): Explain the new behavior.
* guix/scripts/substitute.scm (%cache-urls): Rename to...
(%default-substitute-urls): ... this.
(substitute-urls): New variable.
(guix-substitute): Use it instead of %CACHE-URLS.
* tests/substitute.scm: Likewise.
* guix/build/download.scm (http-fetch): Complete the hard-coded list of HTTP
redirection status codes.
* guix/http-client.scm (http-fetch): Likewise.
* guix/scripts/lint.scm (probe-uri): Likewise.
When current-processor-count is used without (ice-9 threads) being used, Guile
complains with the following warning:
Import (ice-9 threads) to have access to `current-processor-count'.
* guix/store.scm: Use (ice-9 threads).
Partly fixes <https://bugs.gnu.org/28159>.
Suggested by Hartmut Goebel <h.goebel@crazy-compilers.com>.
* guix/gnu-maintenance.scm (%gnu-file-list-uri): New variable.
(ftp.gnu.org-files, latest-gnu-release): New procedures.
(%gnu-updater)[pred]: Change to GNU-HOSTED?.
[latest]: Change to LATEST-GNU-RELEASE.
(%gnu-ftp-updater): New variable.
Previously (mlambda () (define foo 2) bar) would trigger a syntax error.
* guix/memoization.scm (%mlambda): In the zero-argument case, move
BODY... to a lambda to allow for inner 'define' and such.
Detecting when no files were installed was broken when switching to use
cond. Test with (not (null? ...)) to fix this.
* guix/build/emacs-build-system.scm (install): Fix detecting when no files
were installed.
Modify the install phase to detect when nothing has been installed, and error
if this happens. This is preferable to continuing, and allowing the next phase
to fail.
Also, when nothing can be found to be installed, print out each file that was
considered, along with the regular expressions that were used to include and
exclude it.
* gnu/build/emacs-build-system.scm (install-file?): Add additional error
checking and logging.
Fixes <http://bugs.gnu.org/27157>.
Having a finite default `max-silent-time' value for scripts such as 'guix
environment' could lead to timeouts when building subtitutes; this was
undesirable.
This change also fixes client behavior to match the documentation, which
is that by default the daemon's settings are honored.
* guix/scripts/archive.scm (%default-options): Remove max-silent-time entry.
* guix/scripts/copy.scm (%default-options): Likewise.
* guix/scripts/environment.scm (%default-options): Likewise.
* guix/scripts/pack.scm (%default-options): Likewise.
* guix/scripts/package.scm (%default-options): Likewise.
* guix/scripts/pull.scm (%default-options): Likewise.
* guix/scripts/system.scm (%default-options): Likewise.
Signed-off-by: Ludovic Courtès <ludo@gnu.org>
* guix/download.scm (%mirrors)[sourceforge]: Remove
nbtelecom.dl.sourceforge.net, which never returns 404 responses. This causes
download failures due to hash mismatch, effectively preventing secondary
source URLs from being queried.
Fixes <http://bugs.gnu.org/28212>.
Reported by Leo Famulari <leo@famulari.name>.
* guix/build/graft.scm (replace-store-references): When I >= END, check
whether WRITTEN > END and call 'get-bytevector-n!' when it is.
* tests/grafts.scm (buffer-size): New variable.
("replace-store-references, <http://bugs.gnu.org/28212>"): New test.
Ricardo Wurmus