| Commit message (Collapse) | Author | Age |
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* gnu/packages/xml.scm (perl-xml-xpath)[inputs]: Rename this...
[propagated-inputs]: ...to this.
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* gnu/packages/xml.scm (perl-xml-atom)[inputs]: Rename to...
[propagated-inputs]: ...this, and...
[native-inputs]: ...remove duplicate packages from here.
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* gnu/packages/nickle.scm (nickle): Update to 2.81.
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* gnu/packages/cran.scm (r-cubature): Update to 1.4.
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* gnu/packages/admin.scm (neofetch): Update to 4.0.2.
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* gnu/packages/bioconductor.scm (r-genomicinteractions): New variable.
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* gnu/packages/bioconductor.scm (r-interactionset): New variable.
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* gnu/packages/compression.scm (innoextract): Update to 1.7.
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* gnu/packages/bioconductor.scm (r-riboseqr): New variable.
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* gnu/packages/bioconductor.scm (r-riboprofiling): New variable.
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* gnu/packages/bioconductor.scm (r-chipcomp): New variable.
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* gnu/packages/bioconductor.scm (r-bsgenome-mmusculus-ucsc-mm9-masked): New
variable.
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* gnu/packages/bioconductor.scm (r-bsgenome-hsapiens-ucsc-hg19-masked): New
variable.
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* gnu/packages/bioconductor.scm (r-bsgenome-dmelanogaster-ucsc-dm3-masked):
New variable.
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* gnu/packages/bioconductor.scm (r-bayseq): New variable.
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* 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.
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* gnu/packages/golang.scm (go-1.10): Update to 1.10.3.
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* gnu/packages/golang.scm (go-1.9): Update to 1.9.7.
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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.
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* 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>
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* gnu/packages/machine-learning.scm (vowpal-wabbit): New variable.
Signed-off-by: Ludovic Courtès <ludo@gnu.org>
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* gnu/packages/machine-learning.scm (lightgbm): New variable.
Signed-off-by: Ludovic Courtès <ludo@gnu.org>
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* 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'.
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* gnu/packages/tls.scm (libressl): Update to 2.7.4.
Signed-off-by: Leo Famulari <leo@famulari.name>
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* gnu/packages/crypto.scm (botan): Update to 2.6.0.
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* gnu/packages/dav.scm (vdirsyncer): Update to 0.6.6.
[arguments]: Simplify the man-page building.
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* gnu/packages/python.scm (python-click-log): Update to 0.3.2.
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* 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.
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* gnu/packages/check.scm (python-freezegun): Update to 0.3.10.
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* gnu/packages/check.scm (python-freezegun)[arguments]: Substitute
INVOKE for SYSTEM*.
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* gnu/packages/check.scm (cppcheck): Update to 1.84.
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* gnu/packages/aidc.scm (qrencode): Update to 4.0.2.
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* gnu/packages/databases.scm (perl-dbi): Update to 1.641.
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* 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.
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* 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.
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* gnu/packages/emacs.scm (emacs-password-store): Update to 1.7.2.
[propagated-inputs]: Add emacs-with-editor.
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* 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.
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* gnu/packages/benchmark.scm (fio): Update to 3.7.
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* gnu/packages/bioinformatics.scm (minimap2): New variable.
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* gnu/packages/bioinformatics.scm (pigx-bsseq): Update to 0.0.9.
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* 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.
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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.
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* gnu/build/install.scm (reset-timestamps): Remove.
* gnu/build/vm.scm: Use 'reset-timestamps' from (guix store database).
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* 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'.
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* 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).
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* 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'.
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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.
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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.
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* gnu/packages/gnupg.scm (libgcrypt)[replacement]: New field.
(libgcrypt/fixed): New package.
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* gnu/packages/python.scm (python-dns-lexicon, python2-dns-lexicon): New
variables.
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