* guix/import/cran.scm (%bioconductor-packages-list-url): Replace variable...
(bioconductor-packages-list-url): ...with this procedure.
(bioconductor-packages-list): Accept optional TYPE argument.
(latest-bioconductor-package-version): Same.
(fetch-description): Determine package type and use it in calls to
LATEST-BIOCONDUCTOR-PACKAGE-VERSION and BIOCONDUCTOR-URI.
(description->package): Pass package type to URI helper procedure; include
package type in annotation or experiment packages from Bioconducter.
* gnu/packages/patches/bash-4.4-linux-pgrp-pipe.patch: New file.
* gnu/local.mk (dist_patch_DATA): Add it.
* gnu/packages/make-bootstrap.scm (static-bash-for-bootstrap): New variable.
(%static-inputs): Use 'static-bash-for-bootstrap' instead of 'static-bash'.
* gnu/packages/make-bootstrap.scm (%bootstrap-tarballs)[inputs]: On i686-linux
and x86_64-linux, substitute linux-libre-headers, Mes, and MesCC, in place of
GCC, binutils, and glibc.
* gnu/packages/make-bootstrap.scm (%mes-minimal, %mes-minimal-stripped,
%mes-bootstrap-tarball): New variable.
Modified-By: Mark H Weaver <mhw@netris.org>
* gnu/packages/make-bootstrap.scm (%mescc-tools-static,
%mescc-tools-static-stripped, %mescc-tools-bootstrap-tarball): New variable.
Modified-By: Mark H Weaver <mhw@netris.org>
* guix/build/make-bootstrap.scm (copy-linux-headers): New procedure; extract
from make-stripped-libc and add headers for Mes bootstrap.
(make-stripped-libc): Use it.
This trivial package fails to build and has no reverse dependencies.
* gnu/packages/web.scm (python2-internetarchive): Remove variable.
(python-internetarchive)[properties]: Remove.
* guix/ssh.scm (remote-authorize-signing-key): New variable.
* gnu/machine/ssh.scm (deploy-managed-host): Authorize coordinator's
signing key before any invocations of 'remote-eval'.
(deploy-managed-host): Display an error if a signing key does not exist.
* doc/guix.texi (Invoking guix deploy): Remove section describing manual
signing key authorization.
(Invoking guix deploy): Add section describing the 'authorize?' field.
* gnu/machine.scm (roll-back-machine, &deploy-error, deploy-error?)
(deploy-error-should-roll-back)
(deploy-error-captured-args): New variable.
* gnu/machine/ssh.scm (roll-back-managed-host): New variable.
* guix/scripts/deploy.scm (guix-deploy): Roll-back systems when a
deployment fails.
* doc/guix.texi (Invoking guix deploy): Add section describing
prerequisites for deploying as a non-root user.
* guix/remote.scm (remote-pipe-for-gexp): New optional 'become-command'
argument.
(%remote-eval): New optional 'become-command' argument.
(remote-eval): New 'become-command' keyword argument.
* guix/ssh.scm (remote-inferior): New optional 'become-command'
argument.
(inferior-remote-eval): New optional 'become-command' argument.
(remote-authorize-signing-key): New optional 'become-command' argument.
* gnu/machine/ssh.scm (machine-become-command): New variable.
(managed-host-remote-eval): Invoke 'remote-eval' with the
'#:become-command' keyword.
(deploy-managed-host): Invoke 'remote-authorize-signing-key' with the
'#:become-command' keyword.
* gnu/services.scm (activation-script): Return a <program-file> rather
than a <scheme-file>.
* gnu/deploy.scm (guix-deploy): Remove handling for '--system'.
(show-help): Remove documentation for '--system'.
(%default-options): Remove default setting for 'system'.
* gnu/machine/ssh.scm (machine-ssh-configuration): Add 'system' field.
(managed-host-remote-eval): Pass 'system' field to 'remote-eval'.
(machine-check-building-for-appropriate-system): New variable.
(check-deployment-sanity): Add call to
'machine-check-building-for-appropriate-system'.
* doc/guix.texi (Invoking guix deploy): Describe new 'system' field.
* guix/ssh.scm (remote-system): New variable.
* guix/remote.scm (remote-eval): Use result of 'remote-system' when
lowering the G-Expression.
(remote-eval): Add 'system' keyword argument.
(trampoline): Return a <program-file> rather than a <scheme-file>.
This patch parameterizes previously hard-coded instances of
i686-w64-mingw32, adding support for x86_64-w64-mingw32.
* gnu/packages/mingw.scm (make-mingw-w64): New procedure.
(mingw-w64-i686, mingw-w64-x86_64): New variables.
(%mingw-triplet): Remove.
(mingw-w64): Update to point to 'mingw-w64-i686'.
* gnu/packages/cross-base.scm (cross-gcc): Use 'libc' keyword argument
if specified, instead of treating it as a boolean.
(native-libc): Return the correct mingw-w64 depending on machine
specified in target.
* gnu/packages/bootstrap.scm (glibc-dynamic-linker): Add "x86_64-mingw".
* gnu/build/cross-toolchain.scm (set-cross-path/mingw): Replace
hardcoded 'i686-w64-mingw32' instances with 'target' keyword argument.
(cross-gcc-build-phases): Update accordingly; use 'target-mingw?'
implementation of target checking and add commentary.
* gnu/ci.scm (%cross-targets): Add "x86_64-w64-mingw32".
* gnu/packages/tor.scm (onionshare): Upgrade to 2.1.
[arguments]: Rename "tests" phase to "check". Set home directory for tests.
Remove reference to closed upstream bug.
[inputs]: Add python-pycrypto and python-pysocks.
[license]: Remove bsd-3 license; relevant file no longer present.
Ricardo Wurmus