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* 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 Courtès2018-06-14
* 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 Courtès2018-06-14
* gnu: libgcrypt: Fix CVE-2018-0495.•••* gnu/packages/gnupg.scm (libgcrypt)[replacement]: New field. (libgcrypt/fixed): New package. Efraim Flashner2018-06-14
* gnu: Add python-dns-lexicon.•••* gnu/packages/python.scm (python-dns-lexicon, python2-dns-lexicon): New variables. Clément Lassieur2018-06-14
* gnu: Add python-pynamecheap.•••* gnu/packages/python.scm (python-pynamecheap, python2-pynamecheap): New variables. Clément Lassieur2018-06-14
* gnu: Add python-tldextract.•••* gnu/packages/python.scm (python-tldextract, python2-tldextract): New variables. Clément Lassieur2018-06-14
* gnu: Add python-requests-file.•••* gnu/packages/python.scm (python-requests-file, python2-requests-file): New variables. Clément Lassieur2018-06-14
* gnu: Add tmate.•••* gnu/packages/terminals.scm (tmate): New variable. Arun Isaac2018-06-14
* services: tor: Mark end of auto-generated configuration block.•••* gnu/services/networking.scm (tor-configuration->torrc): Clearly demarcate auto-generated lines. Tobias Geerinckx-Rice2018-06-14
* Fix typo in (gnu packages gtk) header.•••* gnu/packages/gtk.scm: Fix ‘Coypright’ typo. Tobias Geerinckx-Rice2018-06-14
* gnu: python-gnupg: Return #t from phase.•••* gnu/packages/gnupg.scm (python-gnupg)[arguments]: Substitute INVOKE for SYSTEM*. Tobias Geerinckx-Rice2018-06-14
* 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-Rice2018-06-14
* gnu: sssd: Update to 1.16.2.•••* gnu/packages/sssd.scm (sssd): Update to 1.16.2. [native-inputs]: Add libxml2. Tobias Geerinckx-Rice2018-06-14
* gnu: pigx-scrnaseq: Update to 0.0.5.•••* gnu/packages/bioinformatics.scm (pigx-scrnaseq): Update to 0.0.5. [inputs]: Add python-magic. Ricardo Wurmus2018-06-13
* gnu: emacs-orgalist: Update to 1.8.•••* gnu/packages/emacs.scm (emacs-orgalist): Update to 1.8. Nicolas Goaziou2018-06-13
* 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 Kebreau2018-06-13
* gnu: r-factoextra: Fix syntax error.•••* gnu/packages/cran.scm (r-factoextra)[description]: Fix syntax error. Ricardo Wurmus2018-06-13
* 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 Wurmus2018-06-13
* gnu: r-s4vectors: Update to 0.18.3.•••* gnu/packages/bioinformatics.scm (r-s4vectors): Update to 0.18.3. Ricardo Wurmus2018-06-13
* gnu: r-biocviews: Update to 1.48.1.•••* gnu/packages/bioinformatics.scm (r-biocviews): Update to 1.48.1. Ricardo Wurmus2018-06-13
* gnu: r-rjson: Update to 0.2.20.•••* gnu/packages/web.scm (r-rjson): Update to 0.2.20. Ricardo Wurmus2018-06-13
* gnu: r-zoo: Update to 1.8-2.•••* gnu/packages/statistics.scm (r-zoo): Update to 1.8-2. Ricardo Wurmus2018-06-13
* gnu: r-rmarkdown: Update to 1.10.•••* gnu/packages/statistics.scm (r-rmarkdown): Update to 1.10. [propagated-inputs]: Add r-tinytex. Ricardo Wurmus2018-06-13
* gnu: r-highr: Update to 0.7.•••* gnu/packages/statistics.scm (r-highr): Update to 0.7. Ricardo Wurmus2018-06-13
* gnu: r-stringi: Update to 1.2.3.•••* gnu/packages/statistics.scm (r-stringi): Update to 1.2.3. Ricardo Wurmus2018-06-13
* gnu: r-munsell: Update to 0.5.0.•••* gnu/packages/statistics.scm (r-munsell): Update to 0.5.0. Ricardo Wurmus2018-06-13
* gnu: r-rgooglemaps: Update to 1.4.2.•••* gnu/packages/geo.scm (r-rgooglemaps): Update to 1.4.2. Ricardo Wurmus2018-06-13
* gnu: r-reticulate: Update to 1.8.•••* gnu/packages/cran.scm (r-reticulate): Update to 1.8. Ricardo Wurmus2018-06-13
* gnu: r-later: Update to 0.7.3.•••* gnu/packages/cran.scm (r-later): Update to 0.7.3. Ricardo Wurmus2018-06-13
* 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 Wurmus2018-06-13
* gnu: r-cubature: Update to 1.3-13.•••* gnu/packages/cran.scm (r-cubature): Update to 1.3-13. Ricardo Wurmus2018-06-13
* gnu: r-extradistr: Update to 1.8.9.•••* gnu/packages/cran.scm (r-extradistr): Update to 1.8.9. Ricardo Wurmus2018-06-13
* 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 Wurmus2018-06-13
* gnu: r-stringdist: Update to 0.9.5.1.•••* gnu/packages/cran.scm (r-stringdist): Update to 0.9.5.1. Ricardo Wurmus2018-06-13
* gnu: r-rcpproll: Update to 0.3.0.•••* gnu/packages/cran.scm (r-rcpproll): Update to 0.3.0. Ricardo Wurmus2018-06-13
* gnu: r-extremes: Update to 2.0-9.•••* gnu/packages/cran.scm (r-extremes): Update to 2.0-9. Ricardo Wurmus2018-06-13
* gnu: r-sp: Update to 1.3-1.•••* gnu/packages/cran.scm (r-sp): Update to 1.3-1. Ricardo Wurmus2018-06-13
* gnu: r-getoptlong: Update to 0.1.7.•••* gnu/packages/cran.scm (r-getoptlong): Update to 0.1.7. Ricardo Wurmus2018-06-13
* gnu: r-circlize: Update to 0.4.4.•••* gnu/packages/cran.scm (r-circlize): Update to 0.4.4. Ricardo Wurmus2018-06-13
* gnu: r-globaloptions: Update to 0.1.0.•••* gnu/packages/cran.scm (r-globaloptions): Update to 0.1.0. Ricardo Wurmus2018-06-13
* gnu: Add r-writexl.•••* gnu/packages/cran.scm (r-writexl): New variable. Ricardo Wurmus2018-06-13
* gnu: Add r-hdf5r.•••* gnu/packages/cran.scm (r-hdf5r): New variable. Ricardo Wurmus2018-06-13
* gnu: Add r-nbclust.•••* gnu/packages/cran.scm (r-nbclust): New variable. Ricardo Wurmus2018-06-13
* gnu: Add r-factoextra.•••* gnu/packages/cran.scm (r-factoextra): New variable. Ricardo Wurmus2018-06-13
* gnu: Add r-factominer.•••* gnu/packages/cran.scm (r-factominer): New variable. Ricardo Wurmus2018-06-13
* gnu: Add r-flashclust.•••* gnu/packages/cran.scm (r-flashclust): New variable. Ricardo Wurmus2018-06-13
* gnu: Add r-ellipse.•••* gnu/packages/cran.scm (r-ellipse): New variable. Ricardo Wurmus2018-06-13
* gnu: Add r-ggpubr.•••* gnu/packages/cran.scm (r-ggpubr): New variable. Ricardo Wurmus2018-06-13
* gnu: Add r-ggsignif.•••* gnu/packages/cran.scm (r-ggsignif): New variable. Ricardo Wurmus2018-06-13
* gnu: Add r-ggsci.•••* gnu/packages/cran.scm (r-ggsci): New variable. Ricardo Wurmus2018-06-13
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