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Author SHA1 Message Date
Marius Bakke 7f1aa73b8c
gnu: guile: Update to 3.0.2. 
* gnu/packages/guile.scm (guile-3.0): Update to 3.0.2.
[source](patches): Remove.
* gnu/packages/patches/guile-3.0-crash.patch: Delete file.
* gnu/local.mk (dist_patch_DATA): Adjust accordingly.
 2020-03-27 19:21:49 +01:00
Ludovic Courtès 7cb77b7896
gnu: mailutils: Update to 3.9. 
* gnu/packages/mail.scm (mailutils): Update to 3.9.
[arguments]: In 'prepare-test-suite' phase, adjust name of the mda
'testsuite' files.
 2020-03-27 19:09:30 +01:00
Ludovic Courtès 2b6fe60599
packages: Use Guile 3.0 for grafts. 
* guix/packages.scm (guile-2.0): Rename to...
(guile-for-grafts): ... this, and adjust callers.  Refer to 'guile-3.0'
instead of 'guile-2.0'.
 2020-03-27 19:09:30 +01:00
Ludovic Courtès 3139739802
gnu: guile-next: Update to 3.0.2. 
* gnu/packages/guile.scm (guile-3.0): Update to 3.0.2.
* gnu/packages/patches/guile-3.0-crash.patch: Remove.
* gnu/local.mk (dist_patch_DATA): Remove it.
 2020-03-27 19:09:30 +01:00
Marius Bakke 5d446d6b6a
gnu: ovmf: Adapt to CPLUS_INCLUDE_PATH changes. 
* gnu/packages/firmware.scm (ovmf)[native-inputs]: Distinguish GCC-5.
[arguments]: Add phase to hide the default GCC from CPLUS_INCLUDE_PATH.
 2020-03-27 19:01:41 +01:00
Pierre Neidhardt eb5341c235
gnu: Add trivial-package-local-nicknames. 
* gnu/packages/lisp-xyz.scm (cl-trivial-package-local-nicknames,
  sbcl-trivial-package-local-nicknames): New variables.
 2020-03-27 18:40:21 +01:00
Ricardo Wurmus bc3fda5d2b
services/nfs: Replace nfs-version with nfs-versions. 
Instead of accepting a string for just one protocol version accept a list of
supported versions.

* gnu/services/nfs.scm (<nfs-configuration>)[nfs-version]: Remove field and
replace...
[nfs-versions]: ...with this new field.
(nfs-shepherd-services): Pass as many "--nfs-version" options as there are
supported versions.
* doc/guix.texi (Network File System): Document nfs-versions.
 2020-03-27 15:30:44 +01:00
Marius Bakke a3efa4f9eb
gnu: emacs: Fix format strings for compatibility with Guile 3. 
* gnu/packages/emacs.scm (emacs)[arguments]: In the 'patch-program-file-names'
and 'install-site-start' phases, specify port in the calls to FORMAT.
 2020-03-27 15:24:02 +01:00
Marius Bakke cfa6666921
gnu: mscgen: Fix build with gd >= 2.3.0. 
'gd' no longer provides 'libgd-config', so use 'pkg-config' instead.

* gnu/packages/graph.scm (mscgen)[native-inputs]: Add PKG-CONFIG.
 2020-03-27 15:16:22 +01:00
Jakub Kądziołka 9483782a61
gnu: rust: Add 1.39 
* gnu/packages/rust.scm (rust-1.39): New variable.
  (%cargo-reference-hash): Add a comment explaining the role of the
  variable.
 2020-03-27 14:28:11 +01:00
Jakub Kądziołka 444bc2ddf2
gnu: rust: Add 1.38 
All packages are still built with rustc 1.37, but users will see rustc
1.38 in their profiles, and packages that require newer compiler
versions will be possible to add.

* gnu/packages/rust.scm (rust-1.31): Factor out the
  patch-command-exec-tests phase to a separate procedure.
  (patch-command-exec-tests-phase): New procedure.
  (rust): Rename to rust-1.37, make rust an alias.
  (rust-1.38): New variable.
 2020-03-27 14:28:06 +01:00
Nicolas Goaziou 1a7247c629
gnu: asymptote: Update to 2.65. 
* gnu/packages/plotutils.scm (asymptote): Update to 2.65.
 2020-03-27 12:20:35 +01:00
Ricardo Wurmus 2ba5253044
gnu: r-multiassayexperiment: Update to 1.12.6. 
* gnu/packages/bioconductor.scm (r-multiassayexperiment): Update to 1.12.6.
 2020-03-27 11:21:13 +01:00
Ricardo Wurmus 37732212a3
gnu: r-locfit: Update to 1.5-9.4. 
* gnu/packages/statistics.scm (r-locfit): Update to 1.5-9.4.
 2020-03-27 11:21:13 +01:00
Ricardo Wurmus c99880320d
gnu: r-class: Update to 7.3-16. 
* gnu/packages/statistics.scm (r-class): Update to 7.3-16.
 2020-03-27 11:21:13 +01:00
Ricardo Wurmus 3345157fa6
gnu: r-xgboost: Update to 1.0.0.2. 
* gnu/packages/cran.scm (r-xgboost): Update to 1.0.0.2.
 2020-03-27 11:21:13 +01:00
Ricardo Wurmus 76d7ce4f45
gnu: r-rjava: Update to 0.9-12. 
* gnu/packages/cran.scm (r-rjava): Update to 0.9-12.
 2020-03-27 11:21:13 +01:00
Ricardo Wurmus 84b7c4aa17
gnu: r-sf: Update to 0.9-0. 
* gnu/packages/cran.scm (r-sf): Update to 0.9-0.
[native-inputs]: Add r-knitr.
 2020-03-27 11:21:13 +01:00
Ricardo Wurmus 498c887a96
gnu: r-bayestestr: Update to 0.5.3. 
* gnu/packages/cran.scm (r-bayestestr): Update to 0.5.3.
[native-inputs]: Add r-knitr.
 2020-03-27 11:21:13 +01:00
Ricardo Wurmus 9c189913e9
gnu: r-hdf5r: Update to 1.3.2. 
* gnu/packages/cran.scm (r-hdf5r): Update to 1.3.2.
[native-inputs]: Add r-knitr.
 2020-03-27 11:21:13 +01:00
Ricardo Wurmus 6232a36291
gnu: r-ggally: Update to 1.5.0. 
* gnu/packages/cran.scm (r-ggally): Update to 1.5.0.
 2020-03-27 11:21:13 +01:00
Marius Bakke 63bd6643c8
gnu: icu4c: Incorporate grafted changes. 
* gnu/packages/icu4c.scm (icu4c)[replacement]: Remove.
[source](patches, patch-flags): New fields.
(icu4c/fixed): Remove variable.
 2020-03-27 00:46:38 +01:00
Marius Bakke f605eef2d4
gnu: help2man: Remove version 1.47.12. 
* gnu/packages/man.scm (help2man): Update to 1.47.13.
(help2man/latest): Remove variable.
 2020-03-27 00:21:35 +01:00
Marius Bakke 20586ffdc7
gnu: Automake: Remove version 1.16.1. 
* gnu/packages/autotools.scm (automake): Update to 1.16.2.
[arguments]: Add phase "skip-test".
(automake-1.16.2): Remove variable.
 2020-03-27 00:21:10 +01:00
Marius Bakke 18af687037
Merge branch 'master' into core-updates 
Conflicts:
	gnu/packages/icu4c.scm
	gnu/packages/man.scm
	gnu/packages/python-xyz.scm
	guix/scripts/environment.scm
	guix/scripts/pack.scm
	guix/scripts/package.scm
	guix/scripts/pull.scm
	guix/store.scm
 2020-03-27 00:12:15 +01:00
Christopher Baines 0a76a4e073
gnu: guix-data-service: Update to 0.0.1-19.d1c243f. 
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.
 2020-03-26 22:51:36 +00:00
Lars-Dominik Braun 01d5f2c5cd
gnu: Add python-json5. 
* gnu/packages/python-xyz.scm (python-json5): New variable.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2020-03-26 23:45:41 +01:00
Lars-Dominik Braun aefcfecd84
gnu: Add python-pytest-check-links. 
* gnu/packages/python-xyz.scm (python-pytest-check-links): New variable.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2020-03-26 23:45:41 +01:00
Ludovic Courtès be6520e6a5
vm: Distinguish between success and failure of the guest code. 
Fixes <https://bugs.gnu.org/34276>.
Reported by Tobias Geerinckx-Rice <me@tobias.gr>.

* gnu/system/vm.scm (expression->derivation-in-linux-vm)[loader]:
Produce '/xchg/.exit-status' file upon success.
* gnu/build/vm.scm (load-in-linux-vm): Check for 'xchg/.exit-status'
once QEMU has completed and respond accordingly.
 2020-03-26 23:45:41 +01:00
Marius Bakke 0ab8ad4632
gnu: OpenSSL: Add upstream patch to preserve compatibility in EOF handling. 
This is a follow-up to ad8254c23a, which
unexpectedly caused a test failure in the Python test suite.

* gnu/packages/patches/openssl-1.1.1e-revert-detect-eof.patch: New file.
* gnu/local.mk (dist_patch_DATA): Adjust accordingly.
* gnu/packages/tls.scm (openssl)[source](patches): Add it.
 2020-03-26 23:09:15 +01:00
Jakub Kądziołka 60eee3e6de
gnu: Add ROPgadget. 
* gnu/packages/cybersecurity.scm: New file.
(ropgadget): New variable.
* gnu/local.mk (GNU_SYSTEM_MODULES): Register the file.
 2020-03-26 22:53:02 +01:00
Michael Rohleder b12acffbd0
gnu: xkbcomp: Update to 1.4.3. 
* gnu/packages/xorg.scm (xkbcomp): update to 1.4.3.

Signed-off-by: Marius Bakke <mbakke@fastmail.com>
 2020-03-26 22:35:37 +01:00
Marius Bakke 2c5bc95a19
gnu: ImageMagick: Build reproducibly. 
Fixes <https://bugs.gnu.org/38449>.

* gnu/packages/imagemagick.scm (imagemagick)[arguments]: In #:configure-flags,
add "--enable-reproducible-build".

(cherry picked from commit 87bc9f022c)
 2020-03-26 22:35:37 +01:00
Marius Bakke 0eb56ccbd6
gnu: libsigc++: Update to 2.10.3. 
* gnu/packages/glib.scm (libsigc++): Update to 2.10.3.
 2020-03-26 22:35:37 +01:00
Marius Bakke 2b9b854cd1
gnu: libgsf: Update to 1.14.47. 
* gnu/packages/gnome.scm (libgsf): Update to 1.14.47.
 2020-03-26 22:35:37 +01:00
Marius Bakke d9ff6ad88c
gnu: potrace: Update to 1.16. 
* gnu/packages/patches/potrace-tests.patch: Delete file.
* gnu/local.mk (dist_patch_DATA): Adjust accordingly.
* gnu/packages/fontutils.scm (potrace): Update to 1.16.
[source](patches): Remove.
 2020-03-26 22:35:36 +01:00
Marius Bakke bf115891dc
gnu: python-fonttools: Update to 4.6.0. 
* gnu/packages/python-xyz.scm (python-fonttools): Update to 4.6.0.
 2020-03-26 22:35:36 +01:00
Marius Bakke 447f9acf12
gnu: python-xmlschema: Update to 1.1.2. 
* gnu/packages/xml.scm (python-xmlschema): Update to 1.1.2.
 2020-03-26 22:35:36 +01:00
Marius Bakke eac7966f0d
gnu: libxcb: Update to 1.14. 
* gnu/packages/xorg.scm (libxcb): Update to 1.14.
[source](uri): Change to .xz tarball.
 2020-03-26 22:35:36 +01:00
Marius Bakke 814ad500ff
gnu: xcb-proto: Update to 1.14. 
* gnu/packages/xorg.scm (xcb-proto): Update to 1.14.
[source](uri): Change to .xz tarball.
 2020-03-26 22:35:36 +01:00
Marius Bakke 736d772b82
gnu: gd: Update to 2.3.0. 
* gnu/packages/patches/gd-fix-tests-on-i686.patch: Adjust context.
* gnu/packages/patches/gd-CVE-2018-1000222.patch,
gnu/packages/patches/gd-CVE-2018-5711.patch,
gnu/packages/patches/gd-CVE-2019-6977.patch,
gnu/packages/patches/gd-CVE-2019-6978.patch,
gnu/packages/patches/gd-freetype-test-failure.patch: Delete files.
* gnu/packages/patches/gd-brect-bounds.patch: New file.
* gnu/local.mk (dist_patch_DATA): Adjust accordingly
* gnu/packages/gd.scm (gd): Update to 2.3.0.
[source](patches): Remove obsolete.
* gnu/packages/gd.scm (gd):
[propagated-inputs]: Move LIBJPEG-TURBO and FONTCONFIG ...
[inputs]: ... here.
 2020-03-26 22:35:35 +01:00
Marius Bakke 8595c7b0bc
gnu: bison: Update to 3.5.3. 
* gnu/packages/bison.scm (bison): Update to 3.5.3.
 2020-03-26 22:35:35 +01:00
Marius Bakke daf87c72da
gnu: perl: Update to 5.30.2. 
* gnu/packages/perl.scm (perl): Update to 5.30.2.
 2020-03-26 22:35:35 +01:00
Marius Bakke 235a4d61d0
gnu: GLib: Update to 2.62.6. 
* gnu/packages/glib.scm (glib): Update to 2.62.6.
 2020-03-26 22:35:34 +01:00
Marius Bakke 159b62df5f
gnu: ghostscript: Update to 9.52. 
* gnu/packages/ghostscript.scm (ghostscript): Update to 9.52.
[arguments]: Remove obsolete phases.
 2020-03-26 22:35:34 +01:00
Marius Bakke ad8254c23a
gnu: OpenSSL: Remove replacement package. 
* gnu/packages/tls.scm (openssl): Update to 1.1.1e.
[replacement]: Remove.
(openssl-1.1.1e): Remove variable.
 2020-03-26 22:35:34 +01:00
Björn Höfling eebaed2b76
gnu: java-tomcat: Update to 8.5.53. 
This fixes CVE-2020-1938 ("Ghostcat").

* gnu/packages/web.scm (java-tomcat): Update to 8.5.53.
[properties]: Add cpe-name.
 2020-03-26 21:39:49 +01:00
Marius Bakke 3089b70d76
gnu: icu4c: Explicitly add patch flags in replacement package. 
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.
 2020-03-26 21:15:08 +01:00
Marius Bakke 9ea9ff6b0f
gnu: help2man: Update to 1.47.13. 
* gnu/packages/man.scm (help2man/latest): Update to 1.47.13.
 2020-03-26 20:20:48 +01:00
Alexandros Theodotou 9b0c95cc68
gnu: Add python-pywinrm. 
* gnu/packages/python-xyz.scm (python-pywinrm): New variable.

Signed-off-by: Christopher Baines <mail@cbaines.net>
 2020-03-26 19:14:44 +00:00