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.
* 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.
Ludovic Courtès