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2018-11-14gnu: Add python-fenics-ufl....* gnu/packages/simulation.scm (python-fenics-ufl): New variable. Signed-off-by: Ludovic Courtès <ludo@gnu.org> Paul Garlick
2018-11-14gnu: Add python-fenics-dijitso....* gnu/packages/simulation.scm (python-fenics-dijitso): New varaible. Signed-off-by: Ludovic Courtès <ludo@gnu.org> Paul Garlick
2018-11-14gnu: Add python-slepc4py....* gnu/packages/maths.scm (python-slepc4py): New variable. Signed-off-by: Ludovic Courtès <ludo@gnu.org> Paul Garlick
2018-11-14gnu: Add python-petsc4py....* gnu/packages/maths.scm (python-petsc4py): New variable. Signed-off-by: Ludovic Courtès <ludo@gnu.org> Paul Garlick
2018-11-14gnu: Add python-mpi4py....* gnu/packages/mpi.scm (python-mpi4py): New variable. Signed-off-by: Ludovic Courtès <ludo@gnu.org> Paul Garlick
2018-11-14daemon: Install 'authenticate' script under LIBEXECDIR/guix....That way it is handled in the same way as other helper scripts. * nix/scripts/guix-authenticate.in: Rename to... * nix/scripts/authenticate.in: ... this. * config-daemon.ac: Adjust accordingly. * nix/local.mk (libstore_a_CPPFLAGS): Remove -DOPENSSL_PATH. (nodist_libexec_SCRIPTS): Remove. (nodist_pkglibexec_SCRIPTS): New variable. * nix/nix-daemon/guix-daemon.cc (main): Remove 'setenv' call for "PATH". * nix/libstore/local-store.cc (runAuthenticationProgram): New function. (LocalStore::exportPath, LocalStore::importPath): Use it instead of 'runProgram' and OPENSSL_PATH. Ludovic Courtès
2018-11-14gnu: guix-daemon: Install 'guix-authenticate'....Fixes <https://bugs.gnu.org/33368>. Reported by Konrad Hinsen <konrad.hinsen@fastmail.net>. * gnu/packages/package-management.scm (guix-daemon)[arguments]: In 'install' phase, build "install-nodist_libexecSCRIPTS" target to install 'guix-authenticate'. Ludovic Courtès
2018-11-14download: Access content-addressed mirrors over HTTPS....Bug <http://bugs.gnu.org/22774> is no longer relevant now that we use "builtin:download" exclusively. * guix/download.scm (%content-addressed-mirrors): Use "https", not "http". Ludovic Courtès
2018-11-14download: Add Software Heritage as a content-addressed mirror....* guix/download.scm (%content-addressed-mirrors): Add Software Heritage. Ludovic Courtès
2018-11-14gnu: xf86-video-r128: Update to 6.12.0....* gnu/packages/xorg.scm (xf86-video-r128): Update to 6.12.0. Marius Bakke
2018-11-14gnu: mtools: Update to 4.0.20....* gnu/packages/mtools.scm (mtools): Update to 4.0.20. [source](uri): Change to 'bz2' compressed tarball. Marius Bakke
2018-11-14gnu: nano: Update to 3.2....* gnu/packages/nano.scm (nano): Update to 3.2. Marius Bakke
2018-11-14gnu: sudo: Update to 1.8.26....* gnu/packages/admin.scm (sudo): Update to 1.8.26. Marius Bakke
2018-11-14gnu: feh: Update to 3.0....* gnu/packages/image-viewers.scm (feh): Update to 3.0. Marius Bakke
2018-11-14gnu: Add jamm....* gnu/packages/bioinformatics.scm (jamm): New variable. Ricardo Wurmus
2018-11-14gnu: Add r-ouch....* gnu/packages/cran.scm (r-ouch): New variable. Ricardo Wurmus
2018-11-14gnu: Add r-activity....* gnu/packages/cran.scm (r-activity): New variable. Ricardo Wurmus
2018-11-14gnu: Add r-circular....* gnu/packages/cran.scm (r-circular): New variable. Ricardo Wurmus
2018-11-14gnu: Add r-overlap....* gnu/packages/cran.scm (r-overlap): New variable. Ricardo Wurmus
2018-11-14gnu: Add r-acdm....* gnu/packages/cran.scm (r-acdm): New variable. Ricardo Wurmus
2018-11-14gnu: Add r-acd....* gnu/packages/cran.scm (r-acd): New variable. Ricardo Wurmus
2018-11-14gnu: Add r-abn....* gnu/packages/cran.scm (r-abn): New variable. Ricardo Wurmus
2018-11-14gnu: Add r-rjags....* gnu/packages/cran.scm (r-rjags): New variable. Ricardo Wurmus
2018-11-14gnu: Add jags....* gnu/packages/statistics.scm (jags): New variable. Ricardo Wurmus
2018-11-13gnu: r-txdb-mmusculus-ucsc-mm10-knowngene: Update to 3.4.4....* gnu/packages/bioinformatics.scm (r-txdb-mmusculus-ucsc-mm10-knowngene): Update to 3.4.4. Ricardo Wurmus
2018-11-13gnu: r-org-mm-eg-db: Update to 3.7.0....* gnu/packages/bioinformatics.scm (r-org-mm-eg-db): Update to 3.7.0. Ricardo Wurmus
2018-11-13gnu: r-org-dm-eg-db: Update to 3.7.0....* gnu/packages/bioinformatics.scm (r-org-dm-eg-db): Update to 3.7.0. Ricardo Wurmus
2018-11-13gnu: r-org-ce-eg-db: Update to 3.7.0....* gnu/packages/bioinformatics.scm (r-org-ce-eg-db): Update to 3.7.0. Ricardo Wurmus
2018-11-13gnu: r-org-hs-eg-db: Update to 3.7.0....* gnu/packages/bioinformatics.scm (r-org-hs-eg-db): Update to 3.7.0. Ricardo Wurmus
2018-11-13gnu: r-genomationdata: Update to 1.14.0....* gnu/packages/bioinformatics.scm (r-genomationdata): Update to 1.14.0. Ricardo Wurmus
2018-11-13gnu: r-go-db: Update to 3.7.0....* gnu/packages/bioinformatics.scm (r-go-db): Update to 3.7.0. Ricardo Wurmus
2018-11-13gnu: r-genomeinfodbdata: Update to 1.2.0....* gnu/packages/bioinformatics.scm (r-genomeinfodbdata): Update to 1.2.0. Ricardo Wurmus
2018-11-13gnu: spice-vdagent: Fix typo in desktop file....Fixes <https://bugs.gnu.org/33346>. * gnu/packages/spice.scm (spice-vdagent)[arguments]: Fix typo in 'patch-spice-vdagent.desktop' phase. Taegil Bae
2018-11-14gnu: ImageMagick: Update to 6.9.10-14....* gnu/packages/imagemagick.scm (imagemagick): Update to 6.9.10-14. Alex Vong
2018-11-13gnu: libssh: Fetch source over HTTPS....* gnu/packages/ssh.scm (libssh)[source]: Use HTTPS URL. Leo Famulari
2018-11-13gnu: direnv: Build with Go 1.9....* gnu/packages/shellutils.scm (direnv)[native-inputs]: Remove go. [inputs]: Add go-1.9. Leo Famulari
2018-11-13gnu: Poppler: Fix CVE-2018-19149....* gnu/packages/patches/poppler-CVE-2018-19149.patch: New file. * gnu/local.mk (dist_patch_DATA): Add it. * gnu/packages/pdf.scm (poppler)[replacement]: New field. (poppler/fixed): New variable. (poppler-qt4, poppler-qt5): Use package/inherit. Leo Famulari
2018-11-13gnu: certbot, python-acme: Update to 0.28.0....* gnu/packages/tls.scm (certbot, python-acme): Update to 0.28.0. Leo Famulari
2018-11-13gnu: guix: Update to f5a2724....* gnu/packages/package-management.scm (guix): Update to f5a2724. Ludovic Courtès
2018-11-13deduplication: Restore directory mtime and permissions after deduplication....Fixes <https://bugs.gnu.org/33361>. * guix/store/deduplication.scm (replace-with-link): Call 'set-file-time' and 'chmod' after 'rename-file'. * tests/nar.scm ("restore-file-set with directories (signed, valid)"): New test. Ludovic Courtès
2018-11-13tests: Check file canonicalization for 'restore-file-set'....* guix/tests.scm (canonical-file?): New procedure. * tests/nar.scm ("restore-file-set (signed, valid)"): Check that every item of FILES matches 'canonical-file?'. Ludovic Courtès
2018-11-13tests: Remove check for a feature that appeared in Guile 2.0.10....* tests/nar.scm: Remove test for 'open-sha256-input-port'. Ludovic Courtès
2018-11-13services: nscd: Add 'invalidate' and 'statistics' actions....* gnu/services/base.scm (nscd-action-procedure, nscd-actions): New procedures. (nscd-shepherd-service): Add 'modules' and 'actions' fields. * gnu/tests/base.scm (run-basic-test)["nscd invalidate action"] ["nscd invalidate action, wrong table"]: New tests. * doc/guix.texi (Services): Mention 'herd doc nscd action'. (Base Services): Document the actions. Ludovic Courtès
2018-11-13services: mcron: Fix typo in comment....* gnu/services/mcron.scm (shepherd-schedule-action): Fix typo in comment. Ludovic Courtès
2018-11-13nar: Access the database instead of connecting to the daemon....* guix/store/database.scm (%default-database-file): New variable. (path-id): Export. * guix/nar.scm (finalize-store-file): Use 'with-database' instead of 'with-store', and use 'path-id' instead of 'valid-path?'. Ludovic Courtès
2018-11-13gnu: restic: Fix build phase....* gnu/packages/backup.scm (restic)[arguments]: Set "HOME" environment variable in build phase. Oleg Pykhalov
2018-11-13gnu: c-toxcore: Fetch sources from git....* gnu/packages/messaging.scm (c-toxcore)[source]: Fetch from git. Ricardo Wurmus
2018-11-13gnu: wine-staging: Update to 3.20....* gnu/packages/wine.scm (wine-staging-patchset-data): Update to 3.20. * gnu/packages/wine.scm (wine-staging): Update to 3.20. Rutger Helling
2018-11-12gnu: php: Update to 7.2.12....* gnu/packages/php.scm (php): Update to 7.2.12. Julien Lepiller
2018-11-12store: Add a functional object cache and use it in 'lower-object'....This leads to ~25% improvements on things like: guix system build desktop.tmpl --no-grafts -d * guix/store.scm (<nix-server>)[object-cache]: New field. * guix/store.scm (open-connection): Initialize it. (cache-object-mapping, lookup-cached-object, %mcached): New procedures. (mcached): New macro. * guix/gexp.scm (lower-object): Use it. * guix/grafts.scm (grafting?): New procedure. Ludovic Courtès
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