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Author SHA1 Message Date
Ricardo Wurmus b7f051db14
gnu: r-rhdf5lib: Update to 1.10.1. 
* gnu/packages/bioinformatics.scm (r-rhdf5lib): Update to 1.10.1.
 2020-07-16 10:08:05 +02:00
Ricardo Wurmus 82eafe32a2
gnu: r-qtl2: Update to 0.22-11. 
* gnu/packages/bioinformatics.scm (r-qtl2): Update to 0.22-11.
 2020-07-16 10:08:05 +02:00
Ricardo Wurmus 16e16586d2
gnu: r-genomicfeatures: Update to 1.40.1. 
* gnu/packages/bioinformatics.scm (r-genomicfeatures): Update to 1.40.1.
 2020-07-16 10:08:05 +02:00
Ricardo Wurmus 02f3a622e2
gnu: r-summarizedexperiment: Update to 1.18.2. 
* gnu/packages/bioinformatics.scm (r-summarizedexperiment): Update to 1.18.2.
 2020-07-16 10:08:05 +02:00
Ricardo Wurmus a9a912805a
gnu: r-activepathways: Update to 1.0.2. 
* gnu/packages/bioconductor.scm (r-activepathways): Update to 1.0.2.
[propagated-inputs]: Remove r-metap.
 2020-07-16 10:08:05 +02:00
Ricardo Wurmus 1a7d1c54d4
gnu: r-rsubread: Update to 2.2.4. 
* gnu/packages/bioconductor.scm (r-rsubread): Update to 2.2.4.
 2020-07-16 10:08:05 +02:00
Ricardo Wurmus ba663a331b
gnu: Add r-conquer. 
* gnu/packages/cran.scm (r-conquer): New variable.
 2020-07-16 10:08:05 +02:00
Ricardo Wurmus 021ad446fc
gnu: r-cairo: Update to 1.5-12.2. 
* gnu/packages/statistics.scm (r-cairo): Update to 1.5-12.2.
 2020-07-16 10:08:05 +02:00
Ricardo Wurmus 79f7cd99da
gnu: r-gplots: Update to 3.0.4. 
* gnu/packages/statistics.scm (r-gplots): Update to 3.0.4.
[native-inputs]: Add r-knitr.
 2020-07-16 10:08:05 +02:00
Ricardo Wurmus f12fd76912
gnu: r-xml: Update to 3.99-0.4. 
* gnu/packages/statistics.scm (r-xml): Update to 3.99-0.4.
 2020-07-16 10:08:04 +02:00
Ricardo Wurmus f7b05fb978
gnu: r-tibble: Update to 3.0.2. 
* gnu/packages/statistics.scm (r-tibble): Update to 3.0.2.
 2020-07-16 10:08:04 +02:00
Ricardo Wurmus 59b88ab39e
gnu: r-svglite: Update to 1.2.3.2. 
* gnu/packages/statistics.scm (r-svglite): Update to 1.2.3.2.
[native-inputs]: Add r-knitr.
 2020-07-16 10:08:04 +02:00
Ricardo Wurmus 0091d815ad
gnu: r-rstan: Update to 2.21.1. 
* gnu/packages/cran.scm (r-rstan): Update to 2.21.1.
[propagated-inputs]: Add r-rcppparallel and r-v8.
[native-inputs]: Add r-knitr.
 2020-07-16 10:08:04 +02:00
Ricardo Wurmus 67462c7be9
gnu: r-loo: Update to 2.3.0. 
* gnu/packages/cran.scm (r-loo): Update to 2.3.0.
[native-inputs]: Add r-knitr.
 2020-07-16 10:08:04 +02:00
Ricardo Wurmus 3cafe807b2
gnu: r-rstantools: Update to 2.1.1. 
* gnu/packages/cran.scm (r-rstantools): Update to 2.1.1.
[propagated-inputs]: Add r-rcppparallel.
[native-inputs]: Add r-knitr.
 2020-07-16 10:08:04 +02:00
Ricardo Wurmus 8aff0a206c
gnu: r-iheatmapr: Update to 0.5.0. 
* gnu/packages/cran.scm (r-iheatmapr): Update to 0.5.0.
[propagated-inputs]: Remove r-plyr and r-s4vectors.
[native-inputs]: Add r-knitr.
 2020-07-16 10:08:04 +02:00
Ricardo Wurmus e9d906748d
gnu: r-quanteda: Update to 2.1.0. 
* gnu/packages/cran.scm (r-quanteda): Update to 2.1.0.
[propagated-inputs]: Add r-digest.
 2020-07-16 10:08:04 +02:00
Ricardo Wurmus ed8c14589c
gnu: r-nonnest2: Update to 0.5-5. 
* gnu/packages/cran.scm (r-nonnest2): Update to 0.5-5.
 2020-07-16 10:08:04 +02:00
Ricardo Wurmus 215475907a
gnu: r-future: Update to 1.18.0. 
* gnu/packages/cran.scm (r-future): Update to 1.18.0.
 2020-07-16 10:08:04 +02:00
Ricardo Wurmus e1bfb22e6c
gnu: r-doby: Update to 4.6.7. 
* gnu/packages/cran.scm (r-doby): Update to 4.6.7.
[propagated-inputs]: Add r-dplyr and r-ggplot2.
 2020-07-16 10:08:04 +02:00
Ricardo Wurmus fbd4582a91
gnu: r-cubature: Update to 2.0.4.1. 
* gnu/packages/cran.scm (r-cubature): Update to 2.0.4.1.
[native-inputs]: Add r-knitr.
 2020-07-16 10:08:04 +02:00
Ricardo Wurmus 1fdd9ebf77
gnu: r-getoptlong: Update to 1.0.2. 
* gnu/packages/cran.scm (r-getoptlong): Update to 1.0.2.
 2020-07-16 10:08:03 +02:00
Ricardo Wurmus 1b5c263bfc
gnu: r-rcpp: Update to 1.0.5. 
* gnu/packages/cran.scm (r-rcpp): Update to 1.0.5.
 2020-07-16 10:08:03 +02:00
Ricardo Wurmus b80f141f86
gnu: r-delayedmatrixstats: Update to 1.10.1. 
* gnu/packages/bioinformatics.scm (r-delayedmatrixstats): Update to 1.10.1.
 2020-07-16 10:08:03 +02:00
Ricardo Wurmus 15597255e6
gnu: r-rhdf5: Update to 2.32.2. 
* gnu/packages/bioinformatics.scm (r-rhdf5): Update to 2.32.2.
 2020-07-16 10:08:03 +02:00
Ricardo Wurmus 2d9c897dd0
gnu: r-variancepartition: Update to 1.18.2. 
* gnu/packages/bioconductor.scm (r-variancepartition): Update to 1.18.2.
 2020-07-16 10:08:03 +02:00
Ricardo Wurmus f5340e0045
gnu: Add tao. 
* 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.
 2020-07-16 10:07:57 +02:00
Tobias Geerinckx-Rice 03f9a8c35b
Revert "gnu: rust: Add SSL native search paths." 
This reverts commit ba1e4ce256.
 2020-07-15 23:22:18 +02:00
Leo Famulari 7233b19fde
gnu: Transmission: Update to 3.0.0. 
* 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.
 2020-07-15 15:38:03 -04:00
Oleg Pykhalov 37fea3c30a
tests: zabbix: Fix typo in comment. 
* gnu/tests/monitoring.scm (run-zabbix-server-test)[test]: Fix typo in
comment.
 2020-07-15 22:15:50 +03:00
Oleg Pykhalov be6835765b
gnu: zabbix-agentd: Update to 5.0.1. 
* gnu/packages/monitoring.scm (zabbix-agentd): Update to 5.0.1.
(arguments)[#:phases]<install-front-end>: Update front-end path.
 2020-07-15 22:15:49 +03:00
Tobias Geerinckx-Rice 209bfe60ee
gnu: bind: Update to 9.16.5. 
* gnu/packages/dns.scm (isc-bind): Update to 9.16.5.
 2020-07-15 21:11:11 +02:00
Marius Bakke 1507636906
gnu: python-tinycss2: Fix test failure. 
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.
 2020-07-15 20:29:26 +02:00
Marius Bakke dec0217f6e
gnu: python-shiboken-2, python-pyside-2: Update to 5.14.2.3. 
* 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.
 2020-07-15 20:08:10 +02:00
Tobias Geerinckx-Rice b514478cb9
gnu: gparted: Use the Glib-or-GTK build system. 
Fixes <https://issues.guix.gnu.org/38544>.

* gnu/packages/disk.scm (gparted)[build-system]: Use
glib-or-gtk-build-system.
 2020-07-15 19:41:40 +02:00
Tobias Geerinckx-Rice 7af2b55d7b
gnu: protobuf: Update to 3.12.3. 
* gnu/packages/protobuf.scm (protobuf): Update to 3.12.3.
 2020-07-15 19:41:39 +02:00
Tobias Geerinckx-Rice ba1e4ce256
gnu: rust: Add SSL native search paths. 
* 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.
 2020-07-15 19:41:39 +02:00
Tobias Geerinckx-Rice 7e3b537c76
gnu: Consistently use license: prefix in (gnu packages mail). 
* 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.
 2020-07-15 19:41:39 +02:00
Tobias Geerinckx-Rice 4fdf4b6cfa
gnu: opensmtpd-extras: Update to 6.7.1. 
* 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.
 2020-07-15 19:41:39 +02:00
Tobias Geerinckx-Rice 6422615fc9
gnu: opensmtpd-extras: Don't use NAME in source URI. 
* gnu/packages/mail.scm (opensmtpd-extras)[source]: Hard-code NAME.
 2020-07-15 19:41:39 +02:00
Ludovic Courtès d7e9e0bbc9
system: 'operating-system-root-file-system' raises upon missing root. 
* gnu/system.scm (operating-system-root-file-system): Raise when 'find'
returns #f.
 2020-07-15 01:36:24 +02:00
Ludovic Courtès 9e12da319b
system: Add 'location' field to <operating-system>. 
This allows error messages to include source location info.

* gnu/system.scm (<operating-system>)[location]: New field.
 2020-07-15 01:36:24 +02:00
Ludovic Courtès a168c3e4f8
ui: 'with-error-handling' does not unwind the stack. 
Since a07d5e558b, we've been getting
useless backtraces upon unhandled errors, like this:

  Backtrace:
	     1 (primitive-load "/home/…/bin/guix")
  In guix/ui.scm:
    1953:12  0 (run-guix-command _ . _)

  guix/ui.scm:1953:12: In procedure run-guix-command:
  In procedure struct-vtable: Wrong type argument in position 1 (expecting struct): #f

This change finally gives us real backtraces back.

* guix/ui.scm (guard*): New macro.
(call-with-error-handling): Use it instead of 'guard'.
 2020-07-15 01:36:24 +02:00
Ludovic Courtès 8003a5adaf
news: Add ‘fr’ translation. 
* etc/news.scm: Add ‘fr’ translation.
 2020-07-15 01:36:24 +02:00
Ludovic Courtès b91a73a6a4
services: Add 'system-provenance' procedure. 
* gnu/services.scm (sexp->channel, system-provenance): New procedures.
* guix/scripts/system.scm (sexp->channel): Remove.
(display-system-generation): Use 'system-provenance' instead of parsing
the "provenance" file right here.
 2020-07-15 01:36:24 +02:00
Marius Bakke 0a72157271
gnu: Remove python2-pywavelets. 
This package no longer supports Python 2 since the update in
501d89d707 and has no dependents.

* gnu/packages/python-xyz.scm (python2-pywavelets): Remove variable.
 2020-07-14 22:01:35 +02:00
Marius Bakke f5e3f02fdd
gnu: python-pynacl: Update to 1.4.0. 
* gnu/packages/python-crypto.scm (python-pynacl): Update to 1.4.0.
[source](snippet): Adjust to fix spurious build requirement.
[arguments]: Add #:modules.  Replace check phase with custom pytest invocation.
 2020-07-14 21:41:39 +02:00
Marius Bakke 2008b8b7af
gnu: python-simplejson: Update to 3.17.0. 
* gnu/packages/python-xyz.scm (python-simplejson): Update to 3.17.0.
 2020-07-14 21:41:39 +02:00
Marius Bakke 784dadc0f7
gnu: python-paramiko: Update to 2.7.1. 
* gnu/packages/python-crypto.scm (python-paramiko): Update to 2.7.1.
 2020-07-14 21:41:38 +02:00
Marius Bakke ec6ee7d72e
gnu: python-bitarray: Update to 1.4.0. 
* gnu/packages/python-xyz.scm (python-bitarray): Update to 1.4.0.
 2020-07-14 21:41:38 +02:00