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* 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. Ludovic Courtès2018-06-142-10/+12
* database: 'register-path' creates the database directory if needed.•••* guix/store/database.scm (register-path): Call 'mkdir-p'. Ludovic Courtès2018-06-141-0/+2
* database: Provide a way to specify the schema location.•••* guix/store/database.scm (sqlite-register): Add #:schema. Parameterize 'sql-schema' based on this. (register-path): Add #:schema and pass it to 'sqlite-register'. Ludovic Courtès2018-06-141-13/+17
* build: Require Guile-SQLite3.•••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. Ludovic Courtès2018-06-145-17/+14
* store-copy: 'read-reference-graph' returns a list of records.•••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. Ludovic Courtès2018-06-145-30/+128
* database: Fail registration when encountering unregistered references.•••* 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. Ludovic Courtès2018-06-142-7/+31
* database: 'with-database' can now initialize new databases.•••* 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. Ludovic Courtès2018-06-146-7/+73
* gnu: libgcrypt: Fix CVE-2018-0495.•••* gnu/packages/gnupg.scm (libgcrypt)[replacement]: New field. (libgcrypt/fixed): New package. Efraim Flashner2018-06-141-0/+14
* gnu: Add python-dns-lexicon.•••* gnu/packages/python.scm (python-dns-lexicon, python2-dns-lexicon): New variables. Clément Lassieur2018-06-141-0/+33
* gnu: Add python-pynamecheap.•••* gnu/packages/python.scm (python-pynamecheap, python2-pynamecheap): New variables. Clément Lassieur2018-06-141-0/+25
* gnu: Add python-tldextract.•••* gnu/packages/python.scm (python-tldextract, python2-tldextract): New variables. Clément Lassieur2018-06-141-0/+33
* gnu: Add python-requests-file.•••* gnu/packages/python.scm (python-requests-file, python2-requests-file): New variables. Clément Lassieur2018-06-141-0/+27
* gnu: Add tmate.•••* gnu/packages/terminals.scm (tmate): New variable. Arun Isaac2018-06-141-0/+34
* services: tor: Mark end of auto-generated configuration block.•••* gnu/services/networking.scm (tor-configuration->torrc): Clearly demarcate auto-generated lines. Tobias Geerinckx-Rice2018-06-141-1/+5
* Fix typo in (gnu packages gtk) header.•••* gnu/packages/gtk.scm: Fix ‘Coypright’ typo. Tobias Geerinckx-Rice2018-06-141-1/+1
* gnu: python-gnupg: Return #t from phase.•••* gnu/packages/gnupg.scm (python-gnupg)[arguments]: Substitute INVOKE for SYSTEM*. Tobias Geerinckx-Rice2018-06-141-2/+2
* gnu: python-gnupg: Update to 0.4.3.•••* gnu/packages/gnupg.scm (python-gnupg): Update to 0.4.3. [arguments]: Remove obsolete substitution. Tobias Geerinckx-Rice2018-06-141-4/+2
* gnu: sssd: Update to 1.16.2.•••* gnu/packages/sssd.scm (sssd): Update to 1.16.2. [native-inputs]: Add libxml2. Tobias Geerinckx-Rice2018-06-141-2/+3
* pull: Add '--list-generations'.•••* guix/scripts/pull.scm (show-help, %options): Add '--list-generations'. (display-profile-content, process-query): New procedures. (guix-pull): Honor '--list-generations'. Ludovic Courtès2018-06-132-49/+144
* gnu: pigx-scrnaseq: Update to 0.0.5.•••* gnu/packages/bioinformatics.scm (pigx-scrnaseq): Update to 0.0.5. [inputs]: Add python-magic. Ricardo Wurmus2018-06-131-2/+3
* gnu: emacs-orgalist: Update to 1.8.•••* gnu/packages/emacs.scm (emacs-orgalist): Update to 1.8. Nicolas Goaziou2018-06-131-2/+2
* gnu: emacspeak: Update to 48.0.•••* 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. Kei Kebreau2018-06-131-15/+21
* nls: Update 'fr' translation.Julien Lepiller2018-06-131-14832/+3549
* gnu: r-factoextra: Fix syntax error.•••* gnu/packages/cran.scm (r-factoextra)[description]: Fix syntax error. Ricardo Wurmus2018-06-131-3/+3
* gnu: r-seurat: Update to 2.3.2.•••* gnu/packages/bioinformatics.scm (r-seurat): Update to 2.3.2. [propagated-inputs]: Add r-hdf5r. Ricardo Wurmus2018-06-131-2/+3
* gnu: r-s4vectors: Update to 0.18.3.•••* gnu/packages/bioinformatics.scm (r-s4vectors): Update to 0.18.3. Ricardo Wurmus2018-06-131-2/+2
* gnu: r-biocviews: Update to 1.48.1.•••* gnu/packages/bioinformatics.scm (r-biocviews): Update to 1.48.1. Ricardo Wurmus2018-06-131-2/+2
* gnu: r-rjson: Update to 0.2.20.•••* gnu/packages/web.scm (r-rjson): Update to 0.2.20. Ricardo Wurmus2018-06-131-2/+2
* gnu: r-zoo: Update to 1.8-2.•••* gnu/packages/statistics.scm (r-zoo): Update to 1.8-2. Ricardo Wurmus2018-06-131-2/+2
* gnu: r-rmarkdown: Update to 1.10.•••* gnu/packages/statistics.scm (r-rmarkdown): Update to 1.10. [propagated-inputs]: Add r-tinytex. Ricardo Wurmus2018-06-131-2/+3
* gnu: r-highr: Update to 0.7.•••* gnu/packages/statistics.scm (r-highr): Update to 0.7. Ricardo Wurmus2018-06-131-2/+2
* gnu: r-stringi: Update to 1.2.3.•••* gnu/packages/statistics.scm (r-stringi): Update to 1.2.3. Ricardo Wurmus2018-06-131-2/+2
* gnu: r-munsell: Update to 0.5.0.•••* gnu/packages/statistics.scm (r-munsell): Update to 0.5.0. Ricardo Wurmus2018-06-131-2/+2
* gnu: r-rgooglemaps: Update to 1.4.2.•••* gnu/packages/geo.scm (r-rgooglemaps): Update to 1.4.2. Ricardo Wurmus2018-06-131-2/+2
* gnu: r-reticulate: Update to 1.8.•••* gnu/packages/cran.scm (r-reticulate): Update to 1.8. Ricardo Wurmus2018-06-131-2/+2
* gnu: r-later: Update to 0.7.3.•••* gnu/packages/cran.scm (r-later): Update to 0.7.3. Ricardo Wurmus2018-06-131-2/+2
* gnu: r-radiant-data: Update to 0.9.5.•••* gnu/packages/cran.scm (r-radiant-data): Update to 0.9.5. [propagated-inputs]: Remove r-plyr; add r-glue, r-plotly, r-readxl, r-rlang, and r-writexl. Ricardo Wurmus2018-06-131-4/+8
* gnu: r-cubature: Update to 1.3-13.•••* gnu/packages/cran.scm (r-cubature): Update to 1.3-13. Ricardo Wurmus2018-06-131-2/+2
* gnu: r-extradistr: Update to 1.8.9.•••* gnu/packages/cran.scm (r-extradistr): Update to 1.8.9. Ricardo Wurmus2018-06-131-2/+2
* gnu: r-statnet-common: Update to 4.1.2.•••* gnu/packages/cran.scm (r-statnet-common): Update to 4.1.2. [propagated-inputs]: Add r-coda. Ricardo Wurmus2018-06-131-2/+4
* gnu: r-stringdist: Update to 0.9.5.1.•••* gnu/packages/cran.scm (r-stringdist): Update to 0.9.5.1. Ricardo Wurmus2018-06-131-2/+2
* gnu: r-rcpproll: Update to 0.3.0.•••* gnu/packages/cran.scm (r-rcpproll): Update to 0.3.0. Ricardo Wurmus2018-06-131-2/+2
* gnu: r-extremes: Update to 2.0-9.•••* gnu/packages/cran.scm (r-extremes): Update to 2.0-9. Ricardo Wurmus2018-06-131-2/+2
* gnu: r-sp: Update to 1.3-1.•••* gnu/packages/cran.scm (r-sp): Update to 1.3-1. Ricardo Wurmus2018-06-131-2/+2
* gnu: r-getoptlong: Update to 0.1.7.•••* gnu/packages/cran.scm (r-getoptlong): Update to 0.1.7. Ricardo Wurmus2018-06-131-2/+2
* gnu: r-circlize: Update to 0.4.4.•••* gnu/packages/cran.scm (r-circlize): Update to 0.4.4. Ricardo Wurmus2018-06-131-2/+2
* gnu: r-globaloptions: Update to 0.1.0.•••* gnu/packages/cran.scm (r-globaloptions): Update to 0.1.0. Ricardo Wurmus2018-06-131-2/+2
* gnu: Add r-writexl.•••* gnu/packages/cran.scm (r-writexl): New variable. Ricardo Wurmus2018-06-131-0/+20
* gnu: Add r-hdf5r.•••* gnu/packages/cran.scm (r-hdf5r): New variable. Ricardo Wurmus2018-06-131-0/+29
* gnu: Add r-nbclust.•••* gnu/packages/cran.scm (r-nbclust): New variable. Ricardo Wurmus2018-06-131-0/+21
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