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* gnu/packages/bioinformatics.scm (pbtranscript-tofu): Update to 2.2.3.
[source]: Remove bundled Cython sources in a snippet. Replace
".tar.gz" extension in file-name field with "-checkout".
[arguments]: Replace "enter-directory-and-clean-up" phase with
"enter-directory" phase, and add "patch-setuppy" phase.
[inputs]: Add python2-h5py. Move python2-cython ...
[native-inputs]: ... to this field.
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* gnu/packages/algebra.scm (pari-gp)[inputs]: Add libx11, which enables
plotting functions.
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* tests/guix-environment-container.sh: Print the content of
$tmpdir/mounts.
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Fixes <http://bugs.gnu.org/21773>.
Reported by Jan Synáček <jan.synacek@gmail.com>.
* guix/ui.scm (make-regexp*): New procedure.
* guix/scripts/package.scm (options->installable, guix-package): Use it
when processing user-provided regexps.
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* gnu/build/linux-container.scm (namespaces->bit-mask): Remove
CLONE_CHILD_CLEARTID and CLONE_CHILD_SETTID, which are unneeded.
Discussed at <http://bugs.gnu.org/21694>.
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Partly fixes <http://bugs.gnu.org/20217>.
* guix/store.scm (set-build-options): Change #:substitute-urls to
default to #f. Send the 'substitute-urls' pair only if
SUBSTITUTE-URLS is true.
* guix/scripts/build.scm (set-build-options-from-command-line): Do not
default to %DEFAULT-SUBSTITUTE-URLS for #:substitute-urls.
* guix/scripts/size.scm (%default-options): Remove 'substitute-urls'.
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* gnu/packages/image.scm (leptonica)[arguments]: Add 'disable-failing-tests' phase.
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* guix/scripts/build.scm (show-help): Add help text for --file option.
(%options): Add --file option.
(options/resolve-packages): Handle 'file' options.
* tests/guix-build.sh: Add tests.
* doc/guix.texi ("invoking guix build"): Add doc.
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* gnu/packages/python.scm (python-debian): Use @enumerate instead of
@itemize.
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* guix/scripts/substitute.scm (lookup-narinfos/diverse): New procedure.
(lookup-narinfo): Use it.
(process-query): Change #:cache-url to #:cache-urls.
[valid?]: Remove 'narinfo?' check, which is no longer necessary.
Use 'lookup-narinfos/diverse' instead of 'lookup-narinfos'.
(process-substitution): Change #:cache-url to #:cache-urls.
(%cache-url): Rename to...
(%cache-urls): ... this. Turn into a list.
(guix-substitute): Remove 'getaddrinfo' test with early exit. Adjust
calls to 'process-query' and 'process-substitution'.
* tests/substitute.scm: Change '%cache-url' to '%cache-urls'.
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* guix/scripts/substitute.scm (lookup-narinfos): Filter out #f values
from CACHED, such that the end result is exactly a list of narinfos,
not interspersed with #f.
* guix/scripts/challenge.scm (discrepancies): Assume REMOTE is a list of
narinfos.
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* guix/scripts/substitute.scm (http-multiple-get): Add 'seed'
parameter. Call PROC in 'fold' style.
(fetch-narinfos)[handle-narinfo-response]: Adjust accordingly.
Update 'http-multiple-get' call accordingly.
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* gnu/packages/grub.scm (grub)[native-inputs]: Add help2man and texinfo.
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* gnu/packages/grub.scm (grub)[arguments]: Use modify-phases. Return #t from
'patch-stuff' phase. Add 'patch-stuff' phase after 'unpack' instead of
before 'patch-source-shebangs'.
[inputs]: Add comment noting that 'fuse' would be a desirable input.
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* doc/contributing.texi (Building from Git): Add GNU Texinfo to the list of
additional requirements.
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* gnu/packages/linux.scm (linux-libre)[install-phase]: Add vmlinuz to the list
of file names to be copied.
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* gnu/packages/linux.scm (linux-libre)[build-phase]: When setting ARCH, add a
case for MIPS.
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* gnu/packages/linux.scm (linux-libre)[supported-systems]: New field.
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* gnu/packages/linux.scm (linux-libre): Update to 4.2.5.
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* gnu/system/linux-initrd.scm (base-initrd)[linux-modules]: Include
"pata_acpi", "pata_atiixp", and "isci" on Intel systems only.
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* gnu/system/grub.scm (eye-candy): Accept additional 'system' argument. Add
local 'setup-gfxterm-body' variable. Replace the 'load_video' grub function
with 'setup_gfxterm', which includes everything in the 'if loadfont' form on
Intel systems, but is empty on non-Intel.
(grub-configuration-file): Pass 'system' to 'eye-candy.
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* gnu/system/grub.scm (grub-configuration-file): Add 'linux-image-name'
internal procedure. Use it from 'entry->gexp'.
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* gnu/packages/package-management.scm (diffoscope): New variable.
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* gnu/packages/python.scm (python-chardet, python2-chardet): New
variables.
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* gnu/packages/python.scm (python-debian, python2-debian): New
variables.
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* gnu/packages/qt.scm (qt): Update to 5.5.1.
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* guix/scripts/refresh.scm (list-updaters-and-exit): New procedure.
(%options, show-help): Add '--list-updaters' option.
* doc/guix.texi (Invoking guix refresh): Document it.
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Suggested by Ludovic Courtès <ludo@gnu.org>.
* guix/upstream.scm (<upstream-updater>): Use 'define-record-type*'.
[description]: New field.
(lookup-updater): Adjust accordingly.
* guix/gnu-maintenance.scm (%gnu-updater): Likewise.
* guix/import/cran.scm (%cran-updater): Likewise.
* guix/import/elpa.scm (%elpa-updater): Likewise.
* po/guix/POTFILES.in: Add guix/scripts/import/cran.scm and
guix/gnu-maintenance.scm.
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This is a followup to commit 06d45f4566469364b4c1fe6d3c71ecf58f5d4838.
* emacs/guix-base.el (guix-switch-to-generation): Replace
'switch-to-generation' with 'switch-to-generation*'.
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* emacs/guix-command.el (guix-command-rest-argument): Add "challenge".
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* emacs/guix-pcomplete.el (guix-pcomplete-complete-command-arg): Add
"challenge" to complete package names for it.
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* gnu/packages/gcc.scm (gcj)[native-inputs]: Add dejagnu.
[arguments]: Enable tests and set test target to
"check-target-libjava".
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* gnu/packages/guile.scm (guile-next): Update to 20151025.e5bccb6.
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* gnu/packages/image.scm (leptonica): Update to 1.72.
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* gnu/packages/audio.scm (jalv)[arguments],
gnu/packages/gtk.scm (ganv)[arguments],
gnu/packages/music.scm (non-sequencer)[arguments],
gnu/packages/pulseaudio.scm (pavucontrol)[arguments]: Set
'CXXFLAGS' to '-std=c++11'.
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* gnu/packages/bioinformatics.scm (subread)[arguments]: Override CC and
CCFLAGS conditionally dependent on target system.
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* gnu/packages/bioinformatics.scm (crossmap): Update to 0.2.1.
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* gnu/packages/mail.scm (%mu-gtester-patch): New variable.
(mu)[source]: Use it.
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* gnu/packages/gtk.scm (gtkmm)[native-inputs]: Add glib:bin.
(gtkmm-2)[native-inputs]: New field.
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* gnu/packages/xdisorg.scm (libwacom)[inputs]: Add LIBGUDEV.
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* gnu/packages/password-utils.scm (yapet): New variable.
Signed-off-by: Ludovic Courtès <ludo@gnu.org>
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* gnu/packages/xorg.scm (xcompmgr): New variable.
Signed-off-by: Ludovic Courtès <ludo@gnu.org>
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* guix/scripts/package.scm (delete-generations): Use
'delete-generation*' instead of 'delete-generation'.
(guix-package)[process-actions]: Use 'roll-back*' instead of
'roll-back' and 'switch-to-generation*' instead of
'switch-to-generation'.
(link-to-empty-profile, switch-to-generation,
switch-to-previous-generation, roll-back, delete-generation): Move
to...
* guix/profiles.scm: ... here. Adjust to not print messages and to
return values that can be used by user interfaces.
* guix/ui.scm (display-generation-change, roll-back*,
switch-to-generation*, delete-generation*): New procedures.
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* guix/ui.scm (switch-symlinks): Move to...
* guix/utils.scm: ... here. New procedure.
* guix/scripts/pull.scm: Use it.
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* guix/scripts/system.scm (display-system-generation, list-generations):
New procedures.
(process-action): Clarify docstring.
(process-command): New procedure.
(guix-system)[parse-sub-command]: Add 'list-generations'
Call 'process-command' instead of 'process-action'.
* doc/guix.texi (Using the Configuration System): Mention generations,
rollback, and 'list-generations'.
(Invoking guix system): Document 'list-generations'.
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* guix/scripts/system.scm (<boot-parameters>): New record type.
(read-boot-parameters): New procedure.
(previous-grub-entries)[system->grub-entry]: Use it.
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* guix/scripts/package.scm (guix-package)[process-query](list-generations):
Move part of the body to 'delete-generation' and
'display-profile-content'.
* guix/ui.scm (display-generation, display-profile-content): New
procedures.
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* guix/scripts/package.scm (readlink*): Move to...
* guix/utils.scm (readlink*): ... here. New procedure.
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* guix/scripts/system.scm (process-action): New procedure. Extracted
from...
(guix-system): ... here. Use it.
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* guix/scripts/package.scm (matching-generations): Move to...
* guix/ui.scm (matching-generations): ... here.
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