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2020-07-16gnu: r-r-rsp: Update to 0.44.0.Ricardo Wurmus
* gnu/packages/statistics.scm (r-r-rsp): Update to 0.44.0.
2020-07-16gnu: r-tibble: Update to 3.0.3.Ricardo Wurmus
* gnu/packages/statistics.scm (r-tibble): Update to 3.0.3.
2020-07-16gnu: r-rlang: Update to 0.4.7.Ricardo Wurmus
* gnu/packages/statistics.scm (r-rlang): Update to 0.4.7.
2020-07-16gnu: r-brms: Update to 2.13.3.Ricardo Wurmus
* gnu/packages/cran.scm (r-brms): Update to 2.13.3.
2020-07-16gnu: r-gamlss: Update to 5.1-7.Ricardo Wurmus
* gnu/packages/cran.scm (r-gamlss): Update to 5.1-7.
2020-07-16gnu: r-gamlss-dist: Update to 5.1-7.Ricardo Wurmus
* gnu/packages/cran.scm (r-gamlss-dist): Update to 5.1-7.
2020-07-16gnu: r-pillar: Update to 1.4.6.Ricardo Wurmus
* gnu/packages/cran.scm (r-pillar): Update to 1.4.6. [propagated-inputs]: Add r-ellipsis and r-lifecycle.
2020-07-16gnu: r-mice: Update to 3.10.0.Ricardo Wurmus
* gnu/packages/cran.scm (r-mice): Update to 3.10.0. [propagated-inputs]: Add r-generics.
2020-07-16gnu: r-broom: Update to 0.7.0.Ricardo Wurmus
* gnu/packages/cran.scm (r-broom): Update to 0.7.0. [propagated-inputs]: Remove r-nlme and r-reshape2; add r-ellipsis, r-glue, and r-rlang.
2020-07-16gnu: r-rhdf5lib: Update to 1.10.1.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-rhdf5lib): Update to 1.10.1.
2020-07-16gnu: r-qtl2: Update to 0.22-11.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-qtl2): Update to 0.22-11.
2020-07-16gnu: r-genomicfeatures: Update to 1.40.1.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-genomicfeatures): Update to 1.40.1.
2020-07-16gnu: r-summarizedexperiment: Update to 1.18.2.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-summarizedexperiment): Update to 1.18.2.
2020-07-16gnu: r-activepathways: Update to 1.0.2.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-activepathways): Update to 1.0.2. [propagated-inputs]: Remove r-metap.
2020-07-16gnu: r-rsubread: Update to 2.2.4.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-rsubread): Update to 2.2.4.
2020-07-16gnu: Add r-conquer.Ricardo Wurmus
* gnu/packages/cran.scm (r-conquer): New variable.
2020-07-16gnu: r-cairo: Update to 1.5-12.2.Ricardo Wurmus
* gnu/packages/statistics.scm (r-cairo): Update to 1.5-12.2.
2020-07-16gnu: r-gplots: Update to 3.0.4.Ricardo Wurmus
* gnu/packages/statistics.scm (r-gplots): Update to 3.0.4. [native-inputs]: Add r-knitr.
2020-07-16gnu: r-xml: Update to 3.99-0.4.Ricardo Wurmus
* gnu/packages/statistics.scm (r-xml): Update to 3.99-0.4.
2020-07-16gnu: r-tibble: Update to 3.0.2.Ricardo Wurmus
* gnu/packages/statistics.scm (r-tibble): Update to 3.0.2.
2020-07-16gnu: r-svglite: Update to 1.2.3.2.Ricardo Wurmus
* gnu/packages/statistics.scm (r-svglite): Update to 1.2.3.2. [native-inputs]: Add r-knitr.
2020-07-16gnu: r-rstan: Update to 2.21.1.Ricardo Wurmus
* gnu/packages/cran.scm (r-rstan): Update to 2.21.1. [propagated-inputs]: Add r-rcppparallel and r-v8. [native-inputs]: Add r-knitr.
2020-07-16gnu: r-loo: Update to 2.3.0.Ricardo Wurmus
* gnu/packages/cran.scm (r-loo): Update to 2.3.0. [native-inputs]: Add r-knitr.
2020-07-16gnu: r-rstantools: Update to 2.1.1.Ricardo Wurmus
* gnu/packages/cran.scm (r-rstantools): Update to 2.1.1. [propagated-inputs]: Add r-rcppparallel. [native-inputs]: Add r-knitr.
2020-07-16gnu: r-iheatmapr: Update to 0.5.0.Ricardo Wurmus
* gnu/packages/cran.scm (r-iheatmapr): Update to 0.5.0. [propagated-inputs]: Remove r-plyr and r-s4vectors. [native-inputs]: Add r-knitr.
2020-07-16gnu: r-quanteda: Update to 2.1.0.Ricardo Wurmus
* gnu/packages/cran.scm (r-quanteda): Update to 2.1.0. [propagated-inputs]: Add r-digest.
2020-07-16gnu: r-nonnest2: Update to 0.5-5.Ricardo Wurmus
* gnu/packages/cran.scm (r-nonnest2): Update to 0.5-5.
2020-07-16gnu: r-future: Update to 1.18.0.Ricardo Wurmus
* gnu/packages/cran.scm (r-future): Update to 1.18.0.
2020-07-16gnu: r-doby: Update to 4.6.7.Ricardo Wurmus
* gnu/packages/cran.scm (r-doby): Update to 4.6.7. [propagated-inputs]: Add r-dplyr and r-ggplot2.
2020-07-16gnu: r-cubature: Update to 2.0.4.1.Ricardo Wurmus
* gnu/packages/cran.scm (r-cubature): Update to 2.0.4.1. [native-inputs]: Add r-knitr.
2020-07-16gnu: r-getoptlong: Update to 1.0.2.Ricardo Wurmus
* gnu/packages/cran.scm (r-getoptlong): Update to 1.0.2.
2020-07-16gnu: r-rcpp: Update to 1.0.5.Ricardo Wurmus
* gnu/packages/cran.scm (r-rcpp): Update to 1.0.5.
2020-07-16gnu: r-delayedmatrixstats: Update to 1.10.1.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-delayedmatrixstats): Update to 1.10.1.
2020-07-16gnu: r-rhdf5: Update to 2.32.2.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-rhdf5): Update to 2.32.2.
2020-07-16gnu: r-variancepartition: Update to 1.18.2.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-variancepartition): Update to 1.18.2.
2020-07-16gnu: Add tao.Ricardo Wurmus
* gnu/packages/patches/tao-add-missing-headers.patch, gnu/packages/patches/tao-fix-parser-types.patch: New files. * gnu/local.mk (dist_patch_DATA): Add them. * gnu/packages/audio.scm (tao): New variable.
2020-07-15Revert "gnu: rust: Add SSL native search paths."Tobias Geerinckx-Rice
This reverts commit ba1e4ce2560d51c8ba935e5b5667ba3a0133c694.
2020-07-15gnu: Transmission: Update to 3.0.0.Leo Famulari
* gnu/packages/bittorrent.scm (transmission): Update to 3.0.0. [source]: Remove obsolete patch. * gnu/packages/patches/transmission-CVE-2018-10756.patch: Delete file. * gnu/local.mk (dist_patch_DATA): Remove it.
2020-07-15tests: zabbix: Fix typo in comment.Oleg Pykhalov
* gnu/tests/monitoring.scm (run-zabbix-server-test)[test]: Fix typo in comment.
2020-07-15gnu: zabbix-agentd: Update to 5.0.1.Oleg Pykhalov
* gnu/packages/monitoring.scm (zabbix-agentd): Update to 5.0.1. (arguments)[#:phases]<install-front-end>: Update front-end path.
2020-07-15gnu: bind: Update to 9.16.5.Tobias Geerinckx-Rice
* gnu/packages/dns.scm (isc-bind): Update to 9.16.5.
2020-07-15gnu: python-tinycss2: Fix test failure.Marius Bakke
Fixes <https://bugs.gnu.org/42372>. Reported by Michael Rohleder <mike@rohleder.de>. * gnu/packages/patches/python-tinycss2-flake8-compat.patch: New file. * gnu/local.mk (dist_patch_DATA): Adjust accordingly. * gnu/packages/python-web.scm (python-tinycss2)[source](patches): New field.
2020-07-15gnu: python-shiboken-2, python-pyside-2: Update to 5.14.2.3.Marius Bakke
* gnu/packages/patches/qtbase-absolute-runpath.patch: New file. * gnu/local.mk (dist_patch_DATA): Adjust accordingly. * gnu/packages/qt.scm (qtbase/next): New variable. * gnu/packages/qt.scm (python-shiboken-2): Update to 5.14.2.3. [source](uri): Adjust for tarball rename. [inputs]: Use the default CLANG-TOOLCHAIN. (python-pyside-2)[inputs]: Likewise. (python-pyside-2-tools)[inputs]: Change from QTBASE to QTBASE/NEXT.
2020-07-15gnu: gparted: Use the Glib-or-GTK build system.Tobias Geerinckx-Rice
Fixes <https://issues.guix.gnu.org/38544>. * gnu/packages/disk.scm (gparted)[build-system]: Use glib-or-gtk-build-system.
2020-07-15gnu: protobuf: Update to 3.12.3.Tobias Geerinckx-Rice
* gnu/packages/protobuf.scm (protobuf): Update to 3.12.3.
2020-07-15gnu: rust: Add SSL native search paths.Tobias Geerinckx-Rice
* gnu/packages/rust.scm (rust-1.19)[native-search-paths]: Add entries for SSL_CERT_DIR and SSL_CERT_FILE. Reported by Kimapr[m] in #guix.
2020-07-15gnu: Consistently use license: prefix in (gnu packages mail).Tobias Geerinckx-Rice
* gnu/packages/mail.scm: Don't #:select arbitrary variables from (guix licenses). (anubis, mailutils, nullmailer, fetchmail, mutt, neomutt, gmime) (bogofilter, offlineimap, emacs-mew, mu, alot, notifymuch, notmuch) (python-notmuch, muchsync, getmail, libetpan, compface, claws-mail) (msmtp, exim, dovecot, dovecot-trees, dovecot-libsodium-plugin, isync) (perl-email-abstract, perl-email-address, perl-email-address-xs) (perl-email-date-format, perl-email-messageid, perl-email-mime) (perl-email-mime-contenttype, perl-email-mime-encodings) (perl-email-sender, perl-email-simple, libesmtp, esmtp, fdm, procmail) (khard, perl-mail-spf, perl-mail-authenticationresults, perl-mail-dkim) (dkimproxy, mb2md, mpop, mhonarc, sendmail, opensmtpd, opensmtpd-extras) (python-mailmanclient, python2-django-mailman3, postorius, swaks, alpine) (balsa, afew, pan, urlscan, tnef, mumi, ytnef, public-inbox, sylpheed) [licenses]: Use a license: prefix instead.
2020-07-15gnu: opensmtpd-extras: Update to 6.7.1.Tobias Geerinckx-Rice
* gnu/packages/mail.scm (opensmtpd-extras): Update to 6.7.1. [native-inputs]: Remove bison, groff, automake, and autoconf. [inputs]: Remove libasr, perl, lua, and linux-pam. Add mysql. [arguments]: Remove obsolete or ineffective options. [license]: Update.
2020-07-15gnu: opensmtpd-extras: Don't use NAME in source URI.Tobias Geerinckx-Rice
* gnu/packages/mail.scm (opensmtpd-extras)[source]: Hard-code NAME.
2020-07-15system: 'operating-system-root-file-system' raises upon missing root.Ludovic Courtès
* gnu/system.scm (operating-system-root-file-system): Raise when 'find' returns #f.
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