a32279ffb6
gnu: Add r-interactionset.
...
* gnu/packages/bioconductor.scm (r-interactionset): New variable.
2018-06-15 09:14:01 +02:00
056402220e
gnu: innoextract: Update to 1.7.
...
* gnu/packages/compression.scm (innoextract): Update to 1.7.
2018-06-15 09:10:35 +02:00
6ffdfe6a01
gnu: Add r-riboseqr.
...
* gnu/packages/bioconductor.scm (r-riboseqr): New variable.
2018-06-15 07:43:23 +02:00
0490f9de88
gnu: Add r-riboprofiling.
...
* gnu/packages/bioconductor.scm (r-riboprofiling): New variable.
2018-06-15 07:43:22 +02:00
609f4ad12f
gnu: Add r-chipcomp.
...
* gnu/packages/bioconductor.scm (r-chipcomp): New variable.
2018-06-15 07:43:22 +02:00
2bece692a6
gnu: Add r-bsgenome-mmusculus-ucsc-mm9-masked.
...
* gnu/packages/bioconductor.scm (r-bsgenome-mmusculus-ucsc-mm9-masked): New
variable.
2018-06-15 07:43:22 +02:00
6fbd759b13
gnu: Add r-bsgenome-hsapiens-ucsc-hg19-masked.
...
* gnu/packages/bioconductor.scm (r-bsgenome-hsapiens-ucsc-hg19-masked): New
variable.
2018-06-15 07:43:22 +02:00
dfac7eb917
gnu: Add r-bsgenome-dmelanogaster-ucsc-dm3-masked.
...
* gnu/packages/bioconductor.scm (r-bsgenome-dmelanogaster-ucsc-dm3-masked):
New variable.
2018-06-15 07:43:22 +02:00
bb15b581f7
gnu: Add r-bayseq.
...
* gnu/packages/bioconductor.scm (r-bayseq): New variable.
2018-06-15 07:43:22 +02:00
b494bbe466
gnu: certbot, python-acme: Update to 0.25.1.
...
* gnu/packages/tls.scm (certbot): Update 0.25.1.
(python-acme): Update to 0.25.1.
[native-inputs]: Add python-pytest.
[propagated-inputs]: Add python-requests-toolbelt.
2018-06-14 19:38:56 -04:00
9297fc61cc
gnu: Go 1.10: Update to 1.10.3.
...
* gnu/packages/golang.scm (go-1.10): Update to 1.10.3.
2018-06-14 17:49:56 -04:00
96fd9a0e62
gnu: Go 1.9: Update to 1.9.7.
...
* gnu/packages/golang.scm (go-1.9): Update to 1.9.7.
2018-06-14 17:49:53 -04:00
411959bef3
linux-initrd: Module check correctly handles hyphen vs. underscore.
...
Fixes <https://bugs.gnu.org/31714 >.
Reported by Vagrant Cascadian <vagrant@debian.org>
and Florian Pelz <pelzflorian@pelzflorian.de>.
* gnu/system/mapped-devices.scm (check-device-initrd-modules): Pass
LINUX-MODULES through 'normalize-module-name'.
* gnu/build/linux-modules.scm (normalize-module-name): Export.
2018-06-14 23:34:59 +02:00
a9a685cc00
offload: Gracefully handle invalid results from 'machines.scm'.
...
* guix/scripts/offload.scm (build-machines): Check the result of FILE.
Ignore it if it's not a list of <build-machine>.
2018-06-14 23:34:59 +02:00
565af91acc
gnu: emacs-racket-mode: Update and bug fix.
...
* gnu/packages/emacs.scm (emacs-racket-mode): Update and bug fix.
- Update to the current commit
- Bug fix: include Racket files in addition to Emacs Lisp files
Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2018-06-14 23:34:59 +02:00
a8fb82a8ab
gnu: Add vowpal-wabbit.
...
* gnu/packages/machine-learning.scm (vowpal-wabbit): New variable.
Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2018-06-14 23:34:59 +02:00
112c2c010b
gnu: Add lightgbm.
...
* gnu/packages/machine-learning.scm (lightgbm): New variable.
Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2018-06-14 23:34:59 +02:00
baed923682
self: Add 'guix-daemon' to the result.
...
* gnu/packages/package-management.scm (guix-daemon): New variable.
* guix/self.scm (whole-package): Add #:daemon and honor it.
(compiled-guix): Pass #:daemon to 'whole-package'.
2018-06-14 23:34:59 +02:00
0effadcad5
gnu: libressl: Update to 2.7.4 [fixes CVE-2018-{0495,0732}].
...
* gnu/packages/tls.scm (libressl): Update to 2.7.4.
Signed-off-by: Leo Famulari <leo@famulari.name>
2018-06-14 17:11:17 -04:00
e3173fe18e
gnu: botan: Update to 2.6.0 [fixes CVE-2018-{9127,9860}].
...
* gnu/packages/crypto.scm (botan): Update to 2.6.0.
2018-06-14 16:02:52 -04:00
af09bed7dc
guix: ui: Allow translation of dates.
...
* guix/ui.scm (display-generation): Allow translation of dates.
The format string will show dates as month day year, but some languages use a
different convention.
2018-06-14 21:53:12 +02:00
a4bae9af00
gnu: vdirsyncer: Update to 0.6.6.
...
* gnu/packages/dav.scm (vdirsyncer): Update to 0.6.6.
[arguments]: Simplify the man-page building.
2018-06-14 15:51:57 -04:00
44d1b9569b
gnu: python-click-log: Update to 0.3.2.
...
* gnu/packages/python.scm (python-click-log): Update to 0.3.2.
2018-06-14 15:51:56 -04:00
b6c675c693
gnu: GnuPG 1.4: Update to 1.4.23.
...
* gnu/packages/gnupg.scm (gnupg-1): Update to 1.4.23.
[source]: Remove patch.
* gnu/packages/patches/gnupg-1.4-CVE-2018-12020.patch: Delete file.
* gnu/local.mk (dist_patch_DATA): Remove it.
2018-06-14 15:35:23 -04:00
ef0d765605
gnu: python-freezegun: Update to 0.3.10.
...
* gnu/packages/check.scm (python-freezegun): Update to 0.3.10.
2018-06-14 18:55:52 +02:00
19611b7a0a
gnu: python-freezegun: Return #t from phase.
...
* gnu/packages/check.scm (python-freezegun)[arguments]: Substitute
INVOKE for SYSTEM*.
2018-06-14 18:55:52 +02:00
d518261f05
gnu: cppcheck: Update to 1.84.
...
* gnu/packages/check.scm (cppcheck): Update to 1.84.
2018-06-14 18:55:51 +02:00
6dd5f2ea63
gnu: qrencode: Update to 4.0.2.
...
* gnu/packages/aidc.scm (qrencode): Update to 4.0.2.
2018-06-14 18:55:51 +02:00
f71619648c
gnu: perl-dbi: Update to 1.641.
...
* gnu/packages/databases.scm (perl-dbi): Update to 1.641.
2018-06-14 18:55:51 +02:00
1ba7a62362
gnu: python-nose-timer: Update to 0.7.2.
...
* gnu/packages/check.scm (python-nose-timer): Update to 0.7.2.
[source]: Remove patch...
* gnu/packages/patches/python-nose-timer-drop-ordereddict.patch:
...delete file...
* gnu/local.mk (dist_patch_DATA): ...and remove it.
2018-06-14 18:55:46 +02:00
ecbac51a0c
gnu: openrct2: Downgrade to 0.1.1.
...
* gnu/packages/games.scm (openrct2): Downgrade to 0.1.1 due to audio not
working on 0.1.2+. Needs fixing before upgrade.
[arguments]: Add "-DDOWNLOAD_TITLE_SEQUENCES=OFF" configure-flag. Remove
'fixgcc7 and 'get-rid-of-errors phases.
[native-inputs]: Remove gcc@7.
2018-06-14 18:14:30 +02:00
43fa239717
gnu: emacs-password-store: Update to 1.7.2.
...
* gnu/packages/emacs.scm (emacs-password-store): Update to 1.7.2.
[propagated-inputs]: Add emacs-with-editor.
2018-06-14 17:37:04 +02:00
ab6f400531
gnu: password-store: Update to 1.7.2.
...
* gnu/packages/password-utils.scm (password-store): Update to 1.7.2.
[source]: Remove 'password-store-gnupg-compat.patch'.
* gnu/packages/patches/password-store-gnupg-compat.patch: Remove file.
* gnu/local.mk (dist_patch_DATA): Remove it.
2018-06-14 17:36:59 +02:00
f715f102e0
gnu: fio: Update to 3.7.
...
* gnu/packages/benchmark.scm (fio): Update to 3.7.
2018-06-14 15:41:09 +02:00
53131eab2d
gnu: Add minimap2.
...
* gnu/packages/bioinformatics.scm (minimap2): New variable.
2018-06-14 13:51:15 +02:00
ce573b1128
gnu: pigx-bsseq: Update to 0.0.9.
...
* gnu/packages/bioinformatics.scm (pigx-bsseq): Update to 0.0.9.
2018-06-14 12:56:49 +02:00
ea0a06cee2
Remove 'guix-register' and its traces.
...
* Makefile.am (SH_TESTS): Remove tests/guix-register.sh.
* build-aux/pre-inst-env.in (GUIX_REGISTER): Remove.
* gnu/build/install.scm (directives): Remove outdated comment.
* gnu/build/vm.scm (root-partition-initializer): Update comment.
* gnu/packages/package-management.scm (guix-register): Remove.
* guix/config.scm.in (%sbindir, %guix-register-program): Remove.
* guix/scripts/system.scm (install): Adjust docstring.
* guix/self.scm (make-config.scm): Remove #:guix. Do not generate
%sbindir and %guix-register-program.
(specification->package): Remove "guix".
* nix/guix-register/guix-register.cc: Remove.
* nix/libstore/store-api.cc (decodeValidPathInfo): Remove.
* nix/libstore/store-api.hh (decodeValidPathInfo): Remove declaration.
* nix/local.mk (sbin_PROGRAMS, guix_register_SOURCES)
(guix_register_CPPFLAGS, guix_register_LDFLAGS): Remove.
* tests/guix-register.sh: Remove.
2018-06-14 11:17:00 +02:00
df2f6400b1
store: Remove 'register-path'.
...
* guix/store.scm (register-path): Remove.
* guix/nar.scm: Use (guix store database).
* guix/scripts/system.scm: Likewise.
* tests/store-database.scm: Remove #:hide (register-path).
* tests/store.scm ("register-path"): Remove.
2018-06-14 11:17:00 +02:00
eb9fe97495
database: Allow for deterministic database construction.
...
Fixes <https://bugs.gnu.org/21073 >.
* guix/store/database.scm (sqlite-register): Add #:time.
(%epoch): New variable.
(register-items): Add #:registration-time. Pass #:time to
'sqlite-register'.
* gnu/build/install.scm (register-closure): Pass #:registration-time.
2018-06-14 11:17:00 +02:00
078c2329c0
install: Use 'reset-timestamps' from (guix store database).
...
* gnu/build/install.scm (reset-timestamps): Remove.
* gnu/build/vm.scm: Use 'reset-timestamps' from (guix store database).
2018-06-14 11:17:00 +02:00
31a63be878
database: Add 'register-items'.
...
* guix/build/store-copy.scm (store-info): Export.
* guix/store/database.scm (register-items): New procedure.
(register-path): Implement in terms of 'register-items'.
* gnu/build/install.scm (register-closure): Use 'register-items' instead
of 'for-each' and 'register-path'.
2018-06-14 11:17:00 +02:00
ef1297e8c7
database: 'sqlite-register' takes a database, not a file name.
...
* guix/store/database.scm (sqlite-register): Remove #:db-file and add
'db' parameter. Remove #:schema and 'parameterize'.
(register-path): Wrap 'sqlite-register' call in 'with-database' and in
'parameterize'.
* tests/store-database.scm ("new database")
("register-path with unregistered references"): Adjust accordingly.
2018-06-14 11:17:00 +02:00
c45477d2a1
install: Use (guix store database) instead of 'guix-register'.
...
* gnu/build/install.scm (register-closure): Add #:reset-timestamps? and
and #:schema; honor them. Rewrite in terms of 'register-path'.
(populate-single-profile-directory): Add #:schema and honor it. Make
/var/guix/profiles and /var/guix/gcroots.
* gnu/build/vm.scm (root-partition-initializer): Pass
#:reset-timestamps? to 'register-closure'.
* gnu/system/vm.scm (not-config?): New procedure.
(guile-sqlite3&co): New variable.
(expression->derivation-in-linux-vm)[config]: New variable.
[builder]: Use 'with-extensions'.
(iso9660-image)[schema, config]: New variables.
Wrap build expression in 'with-extensions'; add 'sql-schema' call.
Remove GUIX from INPUTS.
(qemu-image)[schema, config]: New variables.
Wrap body in 'with-extensions'.
(system-docker-image)[not-config?]: Remove.
[config]: Use 'make-config.scm'.
[schema]: New variable.
[build]: Use 'with-extensions'. Add call to 'sql-schema'. Remove GUIX
from INPUTS.
* gnu/system/file-systems.scm (%store-prefix): Check whether
'%store-prefix' is defined.
* guix/scripts/pack.scm (self-contained-tarball)[not-config?]
[libgcrypt, schema]: New variables.
[build]: Wrap in 'with-extensions'. Adjust imported module list to use
'make-config.scm' for (guix config).
2018-06-14 11:16:59 +02:00
be43c08b17
vm: 'expression->derivation-in-linux-vm' code can now use dlopen.
...
* gnu/system/vm.scm (expression->derivation-in-linux-vm)
[user-builder]: Define in non-monadic style as 'program-file'.
[loader]: Likewise, and 'execl' USER-BUILDER instead of loading it.
(system-docker-image): Pass BUILD as the second
argument to 'expression->derivation-in-linux-vm'.
(make-iso9660-image, qemu-image): Remove call to 'reboot'.
2018-06-14 11:16:59 +02:00
49c393ccaa
database: 'reset-timestamps' sets file permissions as well.
...
* guix/store/database.scm (reset-timestamps): Add 'chmod' calls.
2018-06-14 11:16:59 +02:00
122a6cad7d
database: Replace existing entries in Refs.
...
* guix/store/database.scm (add-reference-sql): Add "OR REPLACE".
2018-06-14 11:16:59 +02:00
4bd86f0d62
database: Add #:reset-timestamps? to 'register-path'.
...
* guix/store/database.scm (register-path): Add #:reset-timestamps? and
honor it.
2018-06-14 11:16:59 +02:00
b85e2ff484
database: Remove extra SQL parameter in 'update-or-insert'.
...
* guix/store/database.scm (update-or-insert): Remove extra #:path
parameter.
2018-06-14 11:16:59 +02:00
0d0438ed8c
deduplicate: Fix a couple of thinkos.
...
* guix/store/deduplication.scm (get-temp-link): Turn 'args' in the 'catch'
handler into a rest argument.
(deduplicate): Use 'lstat' instead of 'file-is-directory?' to properly
handle symlinks. When iterating over the result of 'scandir', exclude
the ".links" sub-directory.
* tests/store-deduplication.scm ("deduplicate"): Create sub-directories
and call 'deduplicate' directly on STORE.
2018-06-14 11:16:59 +02:00
866ee8c66a
database: 'register-path' creates the database directory if needed.
...
* guix/store/database.scm (register-path): Call 'mkdir-p'.
2018-06-14 11:16:59 +02:00
Ricardo Wurmus
Rutger Helling
Leo Famulari
Ludovic Courtès
Konrad Hinsen
Fis Trivial
Gábor Boskovits
Julien Lepiller
Tobias Geerinckx-Rice
Clément Lassieur