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2018-06-14gnu: fio: Update to 3.7.•••* gnu/packages/benchmark.scm (fio): Update to 3.7. Ricardo Wurmus
2018-06-14gnu: Add minimap2.•••* gnu/packages/bioinformatics.scm (minimap2): New variable. Ricardo Wurmus
2018-06-14gnu: pigx-bsseq: Update to 0.0.9.•••* gnu/packages/bioinformatics.scm (pigx-bsseq): Update to 0.0.9. Ricardo Wurmus
2018-06-14Remove 'guix-register' and its traces.•••* 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 * gnu/build/install.scm (directives): Remove outdated comment.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. Ludovic Courtès
2018-06-14database: Allow for deterministic database construction.•••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. Ludovic Courtès
2018-06-14install: Use 'reset-timestamps' from (guix store database).•••* gnu/build/install.scm (reset-timestamps): Remove. * gnu/build/vm.scm: Use 'reset-timestamps' from (guix store database). Ludovic Courtès
2018-06-14database: Add 'register-items'.•••* 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'. Ludovic Courtès
2018-06-14install: Use (guix store database) instead of 'guix-register'.•••* 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). Ludovic Courtès
2018-06-14vm: 'expression->derivation-in-linux-vm' code can now use dlopen.•••* 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'. Ludovic Courtès
2018-06-14build: 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 Courtès
2018-06-14store-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 Courtès
2018-06-14gnu: libgcrypt: Fix CVE-2018-0495.•••* gnu/packages/gnupg.scm (libgcrypt)[replacement]: New field. (libgcrypt/fixed): New package. Efraim Flashner
2018-06-14gnu: Add python-dns-lexicon.•••* gnu/packages/python.scm (python-dns-lexicon, python2-dns-lexicon): New variables. Clément Lassieur
2018-06-14gnu: Add python-pynamecheap.•••* gnu/packages/python.scm (python-pynamecheap, python2-pynamecheap): New variables. Clément Lassieur
2018-06-14gnu: Add python-tldextract.•••* gnu/packages/python.scm (python-tldextract, python2-tldextract): New variables. Clément Lassieur
2018-06-14gnu: Add python-requests-file.•••* gnu/packages/python.scm (python-requests-file, python2-requests-file): New variables. Clément Lassieur
2018-06-14gnu: Add tmate.•••* gnu/packages/terminals.scm (tmate): New variable. Arun Isaac
2018-06-14services: tor: Mark end of auto-generated configuration block.•••* gnu/services/networking.scm (tor-configuration->torrc): Clearly demarcate auto-generated lines. Tobias Geerinckx-Rice
2018-06-14Fix typo in (gnu packages gtk) header.•••* gnu/packages/gtk.scm: Fix ‘Coypright’ typo. Tobias Geerinckx-Rice
2018-06-14gnu: python-gnupg: Return #t from phase.•••* gnu/packages/gnupg.scm (python-gnupg)[arguments]: Substitute INVOKE for SYSTEM*. Tobias Geerinckx-Rice
2018-06-14gnu: python-gnupg: Update to 0.4.3.•••* gnu/packages/gnupg.scm (python-gnupg): Update to 0.4.3. [arguments]: Remove obsolete substitution. Tobias Geerinckx-Rice
2018-06-14gnu: sssd: Update to 1.16.2.•••* gnu/packages/sssd.scm (sssd): Update to 1.16.2. [native-inputs]: Add libxml2. Tobias Geerinckx-Rice
2018-06-13gnu: pigx-scrnaseq: Update to 0.0.5.•••* gnu/packages/bioinformatics.scm (pigx-scrnaseq): Update to 0.0.5. [inputs]: Add python-magic. Ricardo Wurmus
2018-06-13gnu: emacs-orgalist: Update to 1.8.•••* gnu/packages/emacs.scm (emacs-orgalist): Update to 1.8. Nicolas Goaziou
2018-06-13gnu: 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 Kebreau
2018-06-13gnu: r-factoextra: Fix syntax error.•••* gnu/packages/cran.scm (r-factoextra)[description]: Fix syntax error. Ricardo Wurmus
2018-06-13gnu: r-seurat: Update to 2.3.2.•••* gnu/packages/bioinformatics.scm (r-seurat): Update to 2.3.2. [propagated-inputs]: Add r-hdf5r. Ricardo Wurmus
2018-06-13gnu: r-s4vectors: Update to 0.18.3.•••* gnu/packages/bioinformatics.scm (r-s4vectors): Update to 0.18.3. Ricardo Wurmus
2018-06-13gnu: r-biocviews: Update to 1.48.1.•••* gnu/packages/bioinformatics.scm (r-biocviews): Update to 1.48.1. Ricardo Wurmus
2018-06-13gnu: r-rjson: Update to 0.2.20.•••* gnu/packages/web.scm (r-rjson): Update to 0.2.20. Ricardo Wurmus
2018-06-13gnu: r-zoo: Update to 1.8-2.•••* gnu/packages/statistics.scm (r-zoo): Update to 1.8-2. Ricardo Wurmus
2018-06-13gnu: r-rmarkdown: Update to 1.10.•••* gnu/packages/statistics.scm (r-rmarkdown): Update to 1.10. [propagated-inputs]: Add r-tinytex. Ricardo Wurmus
2018-06-13gnu: r-highr: Update to 0.7.•••* gnu/packages/statistics.scm (r-highr): Update to 0.7. Ricardo Wurmus
2018-06-13gnu: r-stringi: Update to 1.2.3.•••* gnu/packages/statistics.scm (r-stringi): Update to 1.2.3. Ricardo Wurmus
2018-06-13gnu: r-munsell: Update to 0.5.0.•••* gnu/packages/statistics.scm (r-munsell): Update to 0.5.0. Ricardo Wurmus
2018-06-13gnu: r-rgooglemaps: Update to 1.4.2.•••* gnu/packages/geo.scm (r-rgooglemaps): Update to 1.4.2. Ricardo Wurmus
2018-06-13gnu: r-reticulate: Update to 1.8.•••* gnu/packages/cran.scm (r-reticulate): Update to 1.8. Ricardo Wurmus
2018-06-13gnu: r-later: Update to 0.7.3.•••* gnu/packages/cran.scm (r-later): Update to 0.7.3. Ricardo Wurmus
2018-06-13gnu: 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 Wurmus
2018-06-13gnu: r-cubature: Update to 1.3-13.•••* gnu/packages/cran.scm (r-cubature): Update to 1.3-13. Ricardo Wurmus
2018-06-13gnu: r-extradistr: Update to 1.8.9.•••* gnu/packages/cran.scm (r-extradistr): Update to 1.8.9. Ricardo Wurmus
2018-06-13gnu: 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 Wurmus
2018-06-13gnu: r-stringdist: Update to 0.9.5.1.•••* gnu/packages/cran.scm (r-stringdist): Update to 0.9.5.1. Ricardo Wurmus
2018-06-13gnu: r-rcpproll: Update to 0.3.0.•••* gnu/packages/cran.scm (r-rcpproll): Update to 0.3.0. Ricardo Wurmus
2018-06-13gnu: r-extremes: Update to 2.0-9.•••* gnu/packages/cran.scm (r-extremes): Update to 2.0-9. Ricardo Wurmus
2018-06-13gnu: r-sp: Update to 1.3-1.•••* gnu/packages/cran.scm (r-sp): Update to 1.3-1. Ricardo Wurmus
2018-06-13gnu: r-getoptlong: Update to 0.1.7.•••* gnu/packages/cran.scm (r-getoptlong): Update to 0.1.7. Ricardo Wurmus
2018-06-13gnu: r-circlize: Update to 0.4.4.•••* gnu/packages/cran.scm (r-circlize): Update to 0.4.4. Ricardo Wurmus
2018-06-13gnu: r-globaloptions: Update to 0.1.0.•••* gnu/packages/cran.scm (r-globaloptions): Update to 0.1.0. Ricardo Wurmus
2018-06-13gnu: Add r-writexl.•••* gnu/packages/cran.scm (r-writexl): New variable. Ricardo Wurmus
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