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2018-06-14gnu: Add minimap2.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (minimap2): New variable.
2018-06-14gnu: pigx-bsseq: Update to 0.0.9.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (pigx-bsseq): Update to 0.0.9.
2018-06-14Remove 'guix-register' and its traces.Ludovic Courtès
* 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 * gnu/build/install.scm (directives): Remove outdated comment.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.
2018-06-14store: Remove 'register-path'.Ludovic Courtès
* 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.
2018-06-14database: Allow for deterministic database construction.Ludovic Courtès
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.
2018-06-14install: Use 'reset-timestamps' from (guix store database).Ludovic Courtès
* gnu/build/install.scm (reset-timestamps): Remove. * gnu/build/vm.scm: Use 'reset-timestamps' from (guix store database).
2018-06-14database: Add 'register-items'.Ludovic Courtès
* 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'.
2018-06-14database: 'sqlite-register' takes a database, not a file name.Ludovic Courtès
* 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.
2018-06-14install: Use (guix store database) instead of 'guix-register'.Ludovic Courtès
* 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).
2018-06-14vm: 'expression->derivation-in-linux-vm' code can now use dlopen.Ludovic Courtès
* 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'.
2018-06-14database: 'reset-timestamps' sets file permissions as well.Ludovic Courtès
* guix/store/database.scm (reset-timestamps): Add 'chmod' calls.
2018-06-14database: Replace existing entries in Refs.Ludovic Courtès
* guix/store/database.scm (add-reference-sql): Add "OR REPLACE".
2018-06-14database: Add #:reset-timestamps? to 'register-path'.Ludovic Courtès
* guix/store/database.scm (register-path): Add #:reset-timestamps? and honor it.
2018-06-14database: Remove extra SQL parameter in 'update-or-insert'.Ludovic Courtès
* guix/store/database.scm (update-or-insert): Remove extra #:path parameter.
2018-06-14deduplicate: Fix a couple of thinkos.Ludovic Courtès
* 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.
2018-06-14database: 'register-path' creates the database directory if needed.Ludovic Courtès
* guix/store/database.scm (register-path): Call 'mkdir-p'.
2018-06-14database: Provide a way to specify the schema location.Ludovic Courtès
* guix/store/database.scm (sqlite-register): Add #:schema. Parameterize 'sql-schema' based on this. (register-path): Add #:schema and pass it to 'sqlite-register'.
2018-06-14build: Require Guile-SQLite3.Ludovic Courtès
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.
2018-06-14store-copy: 'read-reference-graph' returns a list of records.Ludovic Courtès
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.
2018-06-14database: Fail registration when encountering unregistered references.Ludovic Courtès
* guix/store/database.scm (add-reference-sql): Remove nested SELECT. (add-references): Expect REFERENCES to be a list of ids. (sqlite-register): Call 'path-id' for each of REFERENCES and pass it to 'add-references'. * tests/store-database.scm ("register-path with unregistered references"): New test.
2018-06-14database: 'with-database' can now initialize new databases.Ludovic Courtès
* nix/libstore/schema.sql: Rename to... * guix/store/schema.sql: ... this. * Makefile.am (nobase_dist_guilemodule_DATA): Add it. * nix/local.mk (%D%/libstore/schema.sql.hh): Adjust accordingly. * guix/store/database.scm (sql-schema): New variable. (sqlite-exec, initialize-database, call-with-database): New procedures. (with-database): Rewrite in terms of 'call-with-database'. * tests/store-database.scm ("new database"): New test. * guix/self.scm (compiled-guix)[*core-modules*]: Add 'schema.sql' to #:extra-files.
2018-06-14gnu: libgcrypt: Fix CVE-2018-0495.Efraim Flashner
* gnu/packages/gnupg.scm (libgcrypt)[replacement]: New field. (libgcrypt/fixed): New package.
2018-06-14gnu: Add python-dns-lexicon.Clément Lassieur
* gnu/packages/python.scm (python-dns-lexicon, python2-dns-lexicon): New variables.
2018-06-14gnu: Add python-pynamecheap.Clément Lassieur
* gnu/packages/python.scm (python-pynamecheap, python2-pynamecheap): New variables.
2018-06-14gnu: Add python-tldextract.Clément Lassieur
* gnu/packages/python.scm (python-tldextract, python2-tldextract): New variables.
2018-06-14gnu: Add python-requests-file.Clément Lassieur
* gnu/packages/python.scm (python-requests-file, python2-requests-file): New variables.
2018-06-14gnu: Add tmate.Arun Isaac
* gnu/packages/terminals.scm (tmate): New variable.
2018-06-14services: tor: Mark end of auto-generated configuration block.Tobias Geerinckx-Rice
* gnu/services/networking.scm (tor-configuration->torrc): Clearly demarcate auto-generated lines.
2018-06-14Fix typo in (gnu packages gtk) header.Tobias Geerinckx-Rice
* gnu/packages/gtk.scm: Fix ‘Coypright’ typo.
2018-06-14gnu: python-gnupg: Return #t from phase.Tobias Geerinckx-Rice
* gnu/packages/gnupg.scm (python-gnupg)[arguments]: Substitute INVOKE for SYSTEM*.
2018-06-14gnu: python-gnupg: Update to 0.4.3.Tobias Geerinckx-Rice
* gnu/packages/gnupg.scm (python-gnupg): Update to 0.4.3. [arguments]: Remove obsolete substitution.
2018-06-14gnu: sssd: Update to 1.16.2.Tobias Geerinckx-Rice
* gnu/packages/sssd.scm (sssd): Update to 1.16.2. [native-inputs]: Add libxml2.
2018-06-13pull: Add '--list-generations'.Ludovic Courtès
* guix/scripts/pull.scm (show-help, %options): Add '--list-generations'. (display-profile-content, process-query): New procedures. (guix-pull): Honor '--list-generations'.
2018-06-13gnu: pigx-scrnaseq: Update to 0.0.5.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (pigx-scrnaseq): Update to 0.0.5. [inputs]: Add python-magic.
2018-06-13gnu: emacs-orgalist: Update to 1.8.Nicolas Goaziou
* gnu/packages/emacs.scm (emacs-orgalist): Update to 1.8.
2018-06-13gnu: emacspeak: Update to 48.0.Kei Kebreau
* gnu/packages/emacs.scm (emacspeak): Update to 48.0. [arguments]: Use 'invoke'. In the 'install' phase, add additional installation directories and fix the launch script substitution. [inputs]: Add emacs and perl. [native-inputs]: Remove emacs-minimal.
2018-06-13nls: Update 'fr' translation.Julien Lepiller
2018-06-13gnu: r-factoextra: Fix syntax error.Ricardo Wurmus
* gnu/packages/cran.scm (r-factoextra)[description]: Fix syntax error.
2018-06-13gnu: r-seurat: Update to 2.3.2.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-seurat): Update to 2.3.2. [propagated-inputs]: Add r-hdf5r.
2018-06-13gnu: r-s4vectors: Update to 0.18.3.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-s4vectors): Update to 0.18.3.
2018-06-13gnu: r-biocviews: Update to 1.48.1.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-biocviews): Update to 1.48.1.
2018-06-13gnu: r-rjson: Update to 0.2.20.Ricardo Wurmus
* gnu/packages/web.scm (r-rjson): Update to 0.2.20.
2018-06-13gnu: r-zoo: Update to 1.8-2.Ricardo Wurmus
* gnu/packages/statistics.scm (r-zoo): Update to 1.8-2.
2018-06-13gnu: r-rmarkdown: Update to 1.10.Ricardo Wurmus
* gnu/packages/statistics.scm (r-rmarkdown): Update to 1.10. [propagated-inputs]: Add r-tinytex.
2018-06-13gnu: r-highr: Update to 0.7.Ricardo Wurmus
* gnu/packages/statistics.scm (r-highr): Update to 0.7.
2018-06-13gnu: r-stringi: Update to 1.2.3.Ricardo Wurmus
* gnu/packages/statistics.scm (r-stringi): Update to 1.2.3.
2018-06-13gnu: r-munsell: Update to 0.5.0.Ricardo Wurmus
* gnu/packages/statistics.scm (r-munsell): Update to 0.5.0.
2018-06-13gnu: r-rgooglemaps: Update to 1.4.2.Ricardo Wurmus
* gnu/packages/geo.scm (r-rgooglemaps): Update to 1.4.2.
2018-06-13gnu: r-reticulate: Update to 1.8.Ricardo Wurmus
* gnu/packages/cran.scm (r-reticulate): Update to 1.8.
2018-06-13gnu: r-later: Update to 0.7.3.Ricardo Wurmus
* gnu/packages/cran.scm (r-later): Update to 0.7.3.
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