* 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.
* 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'.
Ricardo Wurmus