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* gnu: Add r-riboseqr.Ricardo Wurmus2018-06-15
| | | | * gnu/packages/bioconductor.scm (r-riboseqr): New variable.
* gnu: Add r-riboprofiling.Ricardo Wurmus2018-06-15
| | | | * gnu/packages/bioconductor.scm (r-riboprofiling): New variable.
* gnu: Add r-chipcomp.Ricardo Wurmus2018-06-15
| | | | * gnu/packages/bioconductor.scm (r-chipcomp): New variable.
* gnu: Add r-bsgenome-mmusculus-ucsc-mm9-masked.Ricardo Wurmus2018-06-15
| | | | | * gnu/packages/bioconductor.scm (r-bsgenome-mmusculus-ucsc-mm9-masked): New variable.
* gnu: Add r-bsgenome-hsapiens-ucsc-hg19-masked.Ricardo Wurmus2018-06-15
| | | | | * gnu/packages/bioconductor.scm (r-bsgenome-hsapiens-ucsc-hg19-masked): New variable.
* gnu: Add r-bsgenome-dmelanogaster-ucsc-dm3-masked.Ricardo Wurmus2018-06-15
| | | | | * gnu/packages/bioconductor.scm (r-bsgenome-dmelanogaster-ucsc-dm3-masked): New variable.
* gnu: Add r-bayseq.Ricardo Wurmus2018-06-15
| | | | * gnu/packages/bioconductor.scm (r-bayseq): New variable.
* gnu: certbot, python-acme: Update to 0.25.1.Leo Famulari2018-06-14
| | | | | | | * 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.
* gnu: Go 1.10: Update to 1.10.3.Leo Famulari2018-06-14
| | | | * gnu/packages/golang.scm (go-1.10): Update to 1.10.3.
* gnu: Go 1.9: Update to 1.9.7.Leo Famulari2018-06-14
| | | | * gnu/packages/golang.scm (go-1.9): Update to 1.9.7.
* linux-initrd: Module check correctly handles hyphen vs. underscore.Ludovic Courtès2018-06-14
| | | | | | | | | | 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.
* gnu: emacs-racket-mode: Update and bug fix.Konrad Hinsen2018-06-14
| | | | | | | | | * 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>
* gnu: Add vowpal-wabbit.Fis Trivial2018-06-14
| | | | | | * gnu/packages/machine-learning.scm (vowpal-wabbit): New variable. Signed-off-by: Ludovic Courtès <ludo@gnu.org>
* gnu: Add lightgbm.Fis Trivial2018-06-14
| | | | | | * gnu/packages/machine-learning.scm (lightgbm): New variable. Signed-off-by: Ludovic Courtès <ludo@gnu.org>
* self: Add 'guix-daemon' to the result.Ludovic Courtès2018-06-14
| | | | | | * 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'.
* gnu: libressl: Update to 2.7.4 [fixes CVE-2018-{0495,0732}].Gábor Boskovits2018-06-14
| | | | | | * gnu/packages/tls.scm (libressl): Update to 2.7.4. Signed-off-by: Leo Famulari <leo@famulari.name>
* gnu: botan: Update to 2.6.0 [fixes CVE-2018-{9127,9860}].Leo Famulari2018-06-14
| | | | * gnu/packages/crypto.scm (botan): Update to 2.6.0.
* gnu: vdirsyncer: Update to 0.6.6.Leo Famulari2018-06-14
| | | | | * gnu/packages/dav.scm (vdirsyncer): Update to 0.6.6. [arguments]: Simplify the man-page building.
* gnu: python-click-log: Update to 0.3.2.Leo Famulari2018-06-14
| | | | * gnu/packages/python.scm (python-click-log): Update to 0.3.2.
* gnu: GnuPG 1.4: Update to 1.4.23.Leo Famulari2018-06-14
| | | | | | | * 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.
* gnu: python-freezegun: Update to 0.3.10.Tobias Geerinckx-Rice2018-06-14
| | | | * gnu/packages/check.scm (python-freezegun): Update to 0.3.10.
* gnu: python-freezegun: Return #t from phase.Tobias Geerinckx-Rice2018-06-14
| | | | | * gnu/packages/check.scm (python-freezegun)[arguments]: Substitute INVOKE for SYSTEM*.
* gnu: cppcheck: Update to 1.84.Tobias Geerinckx-Rice2018-06-14
| | | | * gnu/packages/check.scm (cppcheck): Update to 1.84.
* gnu: qrencode: Update to 4.0.2.Tobias Geerinckx-Rice2018-06-14
| | | | * gnu/packages/aidc.scm (qrencode): Update to 4.0.2.
* gnu: perl-dbi: Update to 1.641.Tobias Geerinckx-Rice2018-06-14
| | | | * gnu/packages/databases.scm (perl-dbi): Update to 1.641.
* gnu: python-nose-timer: Update to 0.7.2.Tobias Geerinckx-Rice2018-06-14
| | | | | | | | * 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.
* gnu: openrct2: Downgrade to 0.1.1.Rutger Helling2018-06-14
| | | | | | | | * 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.
* gnu: emacs-password-store: Update to 1.7.2.Clément Lassieur2018-06-14
| | | | | * gnu/packages/emacs.scm (emacs-password-store): Update to 1.7.2. [propagated-inputs]: Add emacs-with-editor.
* gnu: password-store: Update to 1.7.2.Clément Lassieur2018-06-14
| | | | | | | * 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.
* gnu: fio: Update to 3.7.Ricardo Wurmus2018-06-14
| | | | * gnu/packages/benchmark.scm (fio): Update to 3.7.
* gnu: Add minimap2.Ricardo Wurmus2018-06-14
| | | | * gnu/packages/bioinformatics.scm (minimap2): New variable.
* gnu: pigx-bsseq: Update to 0.0.9.Ricardo Wurmus2018-06-14
| | | | * gnu/packages/bioinformatics.scm (pigx-bsseq): Update to 0.0.9.
* Remove 'guix-register' and its traces.Ludovic Courtès2018-06-14
| | | | | | | | | | | | | | | | | | | * 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.
* database: Allow for deterministic database construction.Ludovic Courtès2018-06-14
| | | | | | | | | | 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.
* install: Use 'reset-timestamps' from (guix store database).Ludovic Courtès2018-06-14
| | | | | * gnu/build/install.scm (reset-timestamps): Remove. * gnu/build/vm.scm: Use 'reset-timestamps' from (guix store database).
* database: Add 'register-items'.Ludovic Courtès2018-06-14
| | | | | | | | * 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'.
* install: Use (guix store database) instead of 'guix-register'.Ludovic Courtès2018-06-14
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | * 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).
* vm: 'expression->derivation-in-linux-vm' code can now use dlopen.Ludovic Courtès2018-06-14
| | | | | | | | | * 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'.
* build: Require Guile-SQLite3.Ludovic Courtès2018-06-14
| | | | | | | | | | | | | | | The next commits make (sqlite3) an indirect dependency of (gnu build install), which is itself used by (guix scripts system), hence this new requirement. * configure.ac: Error out when $guix_cv_have_recent_guile_sqlite3 is false. Remove HAVE_GUILE_SQLITE3 Automake conditional. * Makefile.am (MODULES, SCM_TESTS): Remove HAVE_GUILE_SQLITE3 conditions. * doc/guix.texi (Requirements): Add Guile-SQLite3. * README: Ditto. * gnu/packages/package-management.scm (guix)[propagated-inputs]: Add GUILE-SQLITE3. [arguments]: In 'wrap-program' phase, take guile-sqlite3 into account.
* store-copy: 'read-reference-graph' returns a list of records.Ludovic Courtès2018-06-14
| | | | | | | | | | | | | | The previous implementation of 'read-reference-graph' was good enough for many use cases, but it discarded the graph structure, which is useful information in some cases. * guix/build/store-copy.scm (<store-info>): New record type. (read-reference-graph): Rewrite to return a list of <store-info>. (closure-size, populate-store): Adjust accordingly. * gnu/services/base.scm (references-file): Adjust accordingly. * gnu/system/vm.scm (system-docker-image): Likewise. * guix/scripts/pack.scm (squashfs-image, docker-image): Likewise. * tests/gexp.scm ("gexp->derivation #:references-graphs"): Likewise.
* gnu: libgcrypt: Fix CVE-2018-0495.Efraim Flashner2018-06-14
| | | | | * gnu/packages/gnupg.scm (libgcrypt)[replacement]: New field. (libgcrypt/fixed): New package.
* gnu: Add python-dns-lexicon.Clément Lassieur2018-06-14
| | | | | * gnu/packages/python.scm (python-dns-lexicon, python2-dns-lexicon): New variables.
* gnu: Add python-pynamecheap.Clément Lassieur2018-06-14
| | | | | * gnu/packages/python.scm (python-pynamecheap, python2-pynamecheap): New variables.
* gnu: Add python-tldextract.Clément Lassieur2018-06-14
| | | | | * gnu/packages/python.scm (python-tldextract, python2-tldextract): New variables.
* gnu: Add python-requests-file.Clément Lassieur2018-06-14
| | | | | * gnu/packages/python.scm (python-requests-file, python2-requests-file): New variables.
* gnu: Add tmate.Arun Isaac2018-06-14
| | | | * gnu/packages/terminals.scm (tmate): New variable.
* services: tor: Mark end of auto-generated configuration block.Tobias Geerinckx-Rice2018-06-14
| | | | | * gnu/services/networking.scm (tor-configuration->torrc): Clearly demarcate auto-generated lines.
* Fix typo in (gnu packages gtk) header.Tobias Geerinckx-Rice2018-06-14
| | | | * gnu/packages/gtk.scm: Fix ‘Coypright’ typo.
* gnu: python-gnupg: Return #t from phase.Tobias Geerinckx-Rice2018-06-14
| | | | | * gnu/packages/gnupg.scm (python-gnupg)[arguments]: Substitute INVOKE for SYSTEM*.
* gnu: python-gnupg: Update to 0.4.3.Tobias Geerinckx-Rice2018-06-14
| | | | | * gnu/packages/gnupg.scm (python-gnupg): Update to 0.4.3. [arguments]: Remove obsolete substitution.
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