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2020-03-27gnu: r-multiassayexperiment: Update to 1.12.6.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-multiassayexperiment): Update to 1.12.6.
2020-03-27gnu: r-locfit: Update to 1.5-9.4.Ricardo Wurmus
* gnu/packages/statistics.scm (r-locfit): Update to 1.5-9.4.
2020-03-27gnu: r-class: Update to 7.3-16.Ricardo Wurmus
* gnu/packages/statistics.scm (r-class): Update to 7.3-16.
2020-03-27gnu: r-xgboost: Update to 1.0.0.2.Ricardo Wurmus
* gnu/packages/cran.scm (r-xgboost): Update to 1.0.0.2.
2020-03-27gnu: r-rjava: Update to 0.9-12.Ricardo Wurmus
* gnu/packages/cran.scm (r-rjava): Update to 0.9-12.
2020-03-27gnu: r-sf: Update to 0.9-0.Ricardo Wurmus
* gnu/packages/cran.scm (r-sf): Update to 0.9-0. [native-inputs]: Add r-knitr.
2020-03-27gnu: r-bayestestr: Update to 0.5.3.Ricardo Wurmus
* gnu/packages/cran.scm (r-bayestestr): Update to 0.5.3. [native-inputs]: Add r-knitr.
2020-03-27gnu: r-hdf5r: Update to 1.3.2.Ricardo Wurmus
* gnu/packages/cran.scm (r-hdf5r): Update to 1.3.2. [native-inputs]: Add r-knitr.
2020-03-27gnu: r-ggally: Update to 1.5.0.Ricardo Wurmus
* gnu/packages/cran.scm (r-ggally): Update to 1.5.0.
2020-03-26gnu: guix-data-service: Update to 0.0.1-19.d1c243f.Christopher Baines
These changes support the guix-data-service-backup-database and guix-data-service-create-small-backup scripts. These are shell scripts, so require coreutils from the build environment at runtime as well as binaries from postgresql, ephemeralpg and optionally util-linux (for ionice and renice). * gnu/packages/web.scm (guix-data-service): Update to 0.0.1-19.d1c243f. [arguments]: Add (ice-9 ftw) and (ice-9 match) to #:modules, change the 'install phase to wrap all bin files with some inputs as well. [inputs]: Add util-linux, include ephemeralpg from native-inputs and switch postgresql for postgresql-11. [native-inputs]: Move ephemeralpg to inputs.
2020-03-26gnu: Add python-json5.Lars-Dominik Braun
* gnu/packages/python-xyz.scm (python-json5): New variable. Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2020-03-26gnu: Add python-pytest-check-links.Lars-Dominik Braun
* gnu/packages/python-xyz.scm (python-pytest-check-links): New variable. Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2020-03-26gnu: Add ROPgadget.Jakub Kądziołka
* gnu/packages/cybersecurity.scm: New file. (ropgadget): New variable. * gnu/local.mk (GNU_SYSTEM_MODULES): Register the file.
2020-03-26gnu: java-tomcat: Update to 8.5.53.Björn Höfling
This fixes CVE-2020-1938 ("Ghostcat"). * gnu/packages/web.scm (java-tomcat): Update to 8.5.53. [properties]: Add cpe-name.
2020-03-26gnu: icu4c: Explicitly add patch flags in replacement package.Marius Bakke
This is to prevent a build failure when this gets merged to 'core-updates' which does not have any patch-flags to inherit. * gnu/packages/icu4c.scm (icu4c/fixed)[source](patch-flags): New field.
2020-03-26gnu: help2man: Update to 1.47.13.Marius Bakke
* gnu/packages/man.scm (help2man/latest): Update to 1.47.13.
2020-03-26gnu: Add python-pywinrm.Alexandros Theodotou
* gnu/packages/python-xyz.scm (python-pywinrm): New variable. Signed-off-by: Christopher Baines <mail@cbaines.net>
2020-03-26gnu: Add python-requests_ntlm.Alexandros Theodotou
* gnu/packages/python-web.scm (python-requests_ntlm): New variable. Signed-off-by: Christopher Baines <mail@cbaines.net>
2020-03-26gnu: Add python-ntlm-auth.Alexandros Theodotou
* gnu/packages/python-crypto.scm (python-ntlm-auth): New variable. Signed-off-by: Christopher Baines <mail@cbaines.net>
2020-03-26gnu: Add python-kerberos.Alexandros Theodotou
* gnu/packages/python-crypto.scm (python-kerberos): New variable. Signed-off-by: Christopher Baines <mail@cbaines.net>
2020-03-26gnu: Update sambamba to 0.7.1.Roel Janssen
* gnu/packages/bioinformatics.scm (sambamba): Update to 0.7.1; Remove unneeded undead input.
2020-03-26gnu: Add 7kaa.Naga Malleswari
* gnu/packages/games.scm (7kaa): New variable.
2020-03-26gnu: boinc-client: Update to 7.16.5.Efraim Flashner
* gnu/packages/distributed.scm (boinc-client): Update to 7.16.5.
2020-03-26gnu: boinc-server: Fix build.Efraim Flashner
* gnu/packages/distributed.scm (boinc-server)[inputs]: Replace openssl with openssl-1.0, mariadb with mariadb:dev.
2020-03-26gnu: gnupg: Use ~/.guix-profile/bin/pinentry by default.Ludovic Courtès
Fixes <https://bugs.gnu.org/24076>. Reported by Danny Milosavljevic <dannym@scratchpost.org>. * gnu/packages/patches/gnupg-default-pinentry.patch: New file. * gnu/packages/gnupg.scm (gnupg)[source]: Use it. * gnu/local.mk (dist_patch_DATA): Add it.
2020-03-26gnu: youtube-viewer: Don't build gtk3 front-end.Efraim Flashner
* gnu/packages/video.scm (youtube-viewer)[arguments]: Update module-build-flags to only build gtk2 front-end.
2020-03-26gnu: youtube-viewer: Update to 3.7.5.Efraim Flashner
* gnu/packages/video.scm (youtube-viewer): Update to 3.7.5. [inputs]: Add perl-json-xs.
2020-03-26gnu: emacs-helm-exwm: Update to 0.0.2.Pierre Neidhardt
* gnu/packages/emacs-xyz.scm (emacs-helm-exwm): Update to 0.0.2.
2020-03-26gnu: r-argon2: Fix case in synopsis and use full sentence in description.Ricardo Wurmus
* gnu/packages/cran.scm (r-argon2)[synopsis]: Use lower case. [description]: Use full sentence.
2020-03-26gnu: r-getpass: Change case in synopsis and adjust indentation.Ricardo Wurmus
* gnu/packages/cran.scm (r-getpass): Adjust indentation. [synopsis]: Do not capitalize all words.
2020-03-26gnu: r-remoter: Fix indentation.Ricardo Wurmus
* gnu/packages/cran.scm (r-remoter): Fix indentation.
2020-03-26gnu: r-remoter: Use lower case in the synopsis.Ricardo Wurmus
* gnu/packages/cran.scm (r-remoter)[synopsis]: Do not capitalize all words.
2020-03-25gnu: linux-libre-5.4-source: Add patch to support pinebook pro.Vagrant Cascadian
* gnu/packages/patches/linux-libre-support-for-Pinebook-Pro.patch: New file. * gnu/local.mk (dist_patch_DATA): Update accordingly. * gnu/packages/linux (linux-libre-5.4-source): Add patch.
2020-03-25gnu: linux-libre: Update deblob scripts.Mark H Weaver
* gnu/packages/linux.scm (deblob-scripts-5.4): Update to 5.4.28.
2020-03-25gnu: linux-libre: Update to 5.4.28.Mark H Weaver
* gnu/packages/linux.scm (linux-libre-5.4-version): Update to 5.4.28. (linux-libre-5.4-pristine-source): Update hash.
2020-03-25gnu: linux-libre@4.19: Update to 4.19.113.Mark H Weaver
* gnu/packages/linux.scm (linux-libre-4.19-version): Update to 4.19.113. (linux-libre-4.19-pristine-source): Update hash.
2020-03-25gnu: icu4c: Fix CVE-2020-10531.Leo Famulari
* gnu/packages/patches/icu4c-CVE-2020-10531.patch: New file. * gnu/local.mk (dist_patch_DATA): Add it. * gnu/packages/icu4c.scm (icu4c)[replacement]: New field. (icu4c/fixed): New variable.
2020-03-25gnu: Add r-remoter.Todor Kondić
* gnu/packages/cran.scm (r-remoter): New variable. Signed-off-by: Leo Famulari <leo@famulari.name>
2020-03-25gnu: Add r-getpass.Todor Kondić
* gnu/packages/cran.scm (r-getpass): New variable. Signed-off-by: Leo Famulari <leo@famulari.name>
2020-03-25gnu: Add r-argon2.Todor Kondić
* gnu/packages/cran.scm (r-argon2): New variable. Signed-off-by: Leo Famulari <leo@famulari.name>
2020-03-25gnu: Add emacs-chronometrist.Nicolas Goaziou
* gnu/packages/emacs-xyz.scm (emacs-chronometrist): New variable.
2020-03-25gnu: abseil-cpp: Update to 20200225.1.Ricardo Wurmus
* gnu/packages/cpp.scm (abseil-cpp): Update to 20200225.1.
2020-03-25gnu: gnu-pw-mgr: Build reproducibly.Ludovic Courtès
* gnu/packages/gnu-pw-mgr.scm (gnu-pw-mgr)[native-inputs]: Remove AUTOGEN so that man pages are not regenerated with a fresh date.
2020-03-25gnu: electron-cash: Update to 4.0.14.Guillaume Le Vaillant
* gnu/packages/finance.scm (electron-cash): Update to 4.0.14.
2020-03-25gnu: r-shiny: Add missing inputs.Ricardo Wurmus
* gnu/packages/cran.scm (r-shiny)[propagated-inputs]: Add r-later, r-promises, r-rlang, and r-withr. [native-inputs]: Add gfortran.
2020-03-25gnu: r-mast: Add r-knitr to native inputs.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-mast)[native-inputs]: Add r-knitr.
2020-03-24gnu: poetry: Update to 1.0.5.Tanguy Le Carrour
* gnu/packages/python-xyz.scm (poetry): Update to 1.0.5. [propagated-inputs] Add python-clikit, python-importlib-metadata, python-keyring, and python-pexpect. Remove python-msgpack and python-glob2. [home-page] Update URL. [arguments] Remove 'patch-setup-py' phase, and adjust required versions of keyring, pyrsistent and importlib-metadata. Signed-off-by: Leo Famulari <leo@famulari.name>
2020-03-24gnu: python-cachy: Update to 0.3.0.Tanguy Le Carrour
* gnu/packages/python-xyz.scm (python-cachy): Update to 0.3.0. [arguments]: Replace the 'check' phase. [native-inputs]: Add memcached and python-pifpaf. Signed-off-by: Leo Famulari <leo@famulari.name>
2020-03-24gnu: Add python-pifpaf.Tanguy Le Carrour
* gnu/packages/python-xyz.scm (python-pifpaf): New variable. Signed-off-by: Leo Famulari <leo@famulari.name>
2020-03-24gnu: Add python-daiquiri.Tanguy Le Carrour
* gnu/packages/python-xyz.scm (python-daiquiri): New variable. Signed-off-by: Leo Famulari <leo@famulari.name>
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