gnu: guix: Update snapshot to 3fb6464.

* gnu/packages/package-management.scm (guix): Update to 3fb6464.

gnu: you-get: Update to 0.4.990.

* gnu/packages/video.scm (you-get): Update to 0.4.990.

Signed-off-by: Ricardo Wurmus <rekado@elephly.net>

ui: Tweak conflicting profile entry error message.

* guix/ui.scm (call-with-error-handling): Use 'manifest-entry-output*'
when reporting conflicting profile entries.

gnu: shepherd: Avoid "Bad file descriptor" warnings.

* gnu/packages/patches/shepherd-close-fds.patch: New file.
* gnu/local.mk (dist_patch_DATA): Add it.
* gnu/packages/admin.scm (shepherd)[source]: Use it.

profiles: Really disable deprecation warnings for 'profile-derivation'.

This is a followup to 2815fca1423cf72e6f3d0e774f1058bcbf8dfdbf.

* guix/profiles.scm (profile-derivation)[builder]: Remove
'debug-disable' call, which was ineffective.
Pass #:env-vars to 'gexp->derivation'.

scripts: Default to Guile 2.2 as the guile-for-build.

* guix/scripts/environment.scm (guix-environment): '%guile-for-build'
now defaults to GUILE-2.2 instead of GUILE-2.0.
* guix/scripts/package.scm (guix-package): Likewise.
* guix/scripts/pull.scm (guix-pull): Likewise.

gnu: samplv1: Update to 0.8.5.

* gnu/packages/music.scm (samplv1): Update to 0.8.5.

gnu: drumkv1: Update to 0.8.5.

* gnu/packages/music.scm (drumkv1): Update to 0.8.5.

gnu: synthv1: Update to 0.8.5.

* gnu/packages/music.scm (synthv1): Update to 0.8.5.

profile: Use _IO* but disable deprecation warning.

This fixes a regression introduced in
2f60084f77815f454d1521396c2a383390ea2865, 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.

install: Add colors in 'motd' and 'issue'.

* gnu/system/install.scm (%installation-services)[motd]: Add colors.
[services]: Use the "lat9u-16" font.
(%issue): Add colors.

profiles: Avoid _IO* in profile builder.

* guix/profiles.scm (profile-derivation)[builder]: Avoid the deprecated
_IO* constants.

doc: Link to work on bootstrapping.

* doc/guix.texi (Reducing the Set of Bootstrap Binaries): New section.

install: Add the prerequisites of 'profile-derivation' as GC roots.

* gnu/system/install.scm (%installation-services): Add
GLIBC-UTF8-LOCALES, TEXINFO, and GUILE-FINAL as GC roots.

profiles: Do not import the host's srfi-{19,26}.scm files.

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.

gnu: Add kallisto.

* gnu/packages/bioinformatics.scm (kallisto): New variable.

gnu: calf: Update to 0.90.0.

* gnu/packages/audio.scm (calf): Update to 0.90.0.

gnu: jack-2: Update to 1.9.11-RC1.

* gnu/packages/audio.scm (jack-2): Update to 1.9.11-RC1.

gnu: guitarix: Update to 0.36.1.

* gnu/packages/audio.scm (guitarix): Update to 0.36.1.

gnu: faust-2: Remove inherited phase.

* gnu/packages/audio.scm (faust-2)[arguments]: Remove build phase
"fix-permissions".