Léo Le Bouter
0ee5d4f7a8
gnu: git: Fix git-manpages native input's hash.
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This is a follow-up to commit ab9629b7c9
2021-03-16 10:58:36 +01:00
Léo Le Bouter
ab9629b7c9
gnu: git: Update to 2.31.0.
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* gnu/packages/version-control.scm (git): Update to 2.31.0.
2021-03-16 10:52:11 +01:00
Léo Le Bouter
db87d6ddaf
gnu: python2-urllib3: Update to 1.26.4 [fixes CVE-2021-28363].
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* gnu/packages/python-web.scm (python2-urllib3)[base]: Base off of
python-urllib3/fixed.
2021-03-16 09:25:02 +01:00
Léo Le Bouter
a01bfa7dee
gnu: python-urllib3: Update to 1.26.4 [fixes CVE-2021-28363].
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* gnu/packages/python-web.scm (python-urllib3/fixed): New variable.
(python-urllib3)[replacement]: Graft.
2021-03-16 08:59:38 +01:00
Stefan Reichör
e5fcfb82e0
gnu: tmsu: Improve installation.
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* gnu/packages/file-systems.scm (tmsu)[arguments]: Don't install go
source files. Install binary as tmsu instead of TMSU.
Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
2021-03-16 09:37:16 +02:00
Stefan Reichör
3679286bb4
gnu: glances: Update to 3.1.6.
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* gnu/packages/python-xyz.scm (glances): Update to 3.1.6.
Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
2021-03-16 09:34:41 +02:00
Chris Marusich
341dfe7eda
syscalls: mounts: Fix a matching bug.
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On some systems, the columns in /proc/self/mountinfo look like this:
23 28 0:21 / /proc rw,nosuid,nodev,noexec,relatime shared:11 - proc proc rw
Before this change, the mounts procedure was written with the assumption that
the type and source could always be found in columns 8 and 9, respectively.
However, the proc(5) man page explains that there can be zero or more optional
fields starting at column 7 (e.g., "shared:11" above), so this assumption is
false in some situations.
* guix/build/syscalls.scm (mounts): Update the match pattern to use ellipsis
to match zero or more optional fields followed by a single hyphen. Remove the
trailing ellipsis, since multiple ellipses are not allowed in the same level.
The proc(5) man page indicates that there are no additional columns, so it is
probably OK to match an exact number of columns at the end like this.
2021-03-15 21:22:43 -07:00
Leo Famulari
8ec0ca8faf
Revert some commits that caused guix pull to fail.
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This reverts commits 821e6439218f9fd9b70c
2021-03-15 19:52:34 -04:00
Ricardo Wurmus
8f9fd9b70c
gnu: r-biocparallel: Build reproducibly.
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* gnu/packages/bioconductor.scm (r-biocparallel)[arguments]: Add phase
"make-reproducible".
2021-03-15 23:31:58 +01:00
zimoun
d99a18252c
gnu: r-delayedarray: Move to (gnu packages bioconductor).
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* gnu/packages/bioinformatics.scm (r-delayedarray): Move from here...
* gnu/packages/bioconductor.scm (r-delayedarray): ...to here.
2021-03-15 23:30:26 +01:00
zimoun
adf45daae9
gnu: r-rsamtools: Move to (gnu packages bioconductor).
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* gnu/packages/bioinformatics.scm (r-rsamtools): Move from here...
* gnu/packages/bioconductor.scm (r-rsamtools): ...to here.
2021-03-15 23:30:26 +01:00
zimoun
b1a19ab6e2
gnu: r-biostrings: Move to (gnu packages bioconductor).
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* gnu/packages/bioinformatics.scm (r-biostrings): Move from here...
* gnu/packages/bioconductor.scm (r-biostrings): ...to here.
2021-03-15 23:30:26 +01:00
zimoun
eab9807fb3
gnu: r-biocparallel: Move to (gnu packages bioconductor).
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* gnu/packages/bioinformatics.scm (r-biocparallel): Move from here...
* gnu/packages/bioconductor.scm (r-biocparallel): ...to here.
2021-03-15 23:30:26 +01:00
zimoun
c11b541fba
gnu: r-biomart: Move to (gnu packages bioconductor).
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* gnu/packages/bioinformatics.scm (r-biomart): Move from here...
* gnu/packages/bioconductor.scm (r-biomart): ...to here.
2021-03-15 23:30:26 +01:00
zimoun
16c7e79ebb
gnu: r-annotationdbi: Move to (gnu packages bioconductor).
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* gnu/packages/bioinformatics.scm (r-annotationdbi): Move from here...
* gnu/packages/bioconductor.scm (r-annotationdbi): ...to here.
2021-03-15 23:30:26 +01:00
zimoun
457de7f401
gnu: r-biobase: Move to (gnu packages bioconductor).
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* gnu/packages/bioinformatics.scm (r-biobase): Move from here...
* gnu/packages/bioconductor.scm (r-biobase): ...to here.
2021-03-15 23:30:26 +01:00
zimoun
f3f09b99cd
gnu: r-genomicranges: Move to (gnu packages bioconductor).
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* gnu/packages/bioinformatics.scm (r-genomicranges): Move from here...
* gnu/packages/bioconductor.scm (r-genomicranges): ...to here.
2021-03-15 23:30:26 +01:00
zimoun
e56b3db82e
gnu: r-xvector: Move to (gnu packages bioconductor).
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* gnu/packages/bioinformatics.scm (r-xvector): Move from here...
* gnu/packages/bioconductor.scm (r-xvector): ...to here.
2021-03-15 23:30:26 +01:00
zimoun
821e643921
gnu: r-limma: Move to (gnu packages bioconductor).
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* gnu/packages/bioinformatics.scm (r-limma): Move from here...
* gnu/packages/bioconductor.scm (r-limma): ...to here.
2021-03-15 23:30:26 +01:00
Maxim Cournoyer
74fdd0fea0
gnu: dbus-c++: Fix command name in description.
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* gnu/packages/glib.scm (dbus-c++)[description]: Fix command prefix in
description, and mention the second command installed as well.
2021-03-15 18:03:17 -04:00
Maxim Cournoyer
1ea2c82355
news: Add news entry about changes to the QEMU binfmt service.
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* etc/news.scm: Add entry.
2021-03-15 18:03:16 -04:00
Leo Famulari
d15fdb66f3
gnu: qemu: Update to 5.2.0.
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* gnu/packages/virtualization.scm (qemu): Update to 5.2.0.
[source]: Re-indent and break long lines, to appease 'guix lint'.
[arguments]{disable-unusable-tests}: Adjust for the new Meson build
system. Remove patching for a test workaround that has been resolved in
5.2.0.
{patch-test-shebangs, patch-/bin/sh-references}: Combine into...
{patch-embedded-shebangs}: ... this new phase. Patch the SHELL variable in
the Makefile.
{fix-optionrom-makefile}: New phase.
{install-user-static}: Adjust as the binaries are now symbolic links pointing to their
actual build path.
[native-inputs]: Add ninja.
* gnu/packages/patches/qemu-build-info-manual.patch: Update patch.
Co-authored-by: Maxim Cournoyer <maxim.cournoyer@gmail.com>
Signed-off-by: Maxim Cournoyer <maxim.cournoyer@gmail.com>
2021-03-15 18:00:35 -04:00
Maxim Cournoyer
77c2f4e206
services/qemu-binfmt: Use the F flag and the static output of QEMU.
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Fixes <https://issues.guix.gnu.org/36117 >.
Before this change, the 'binfmt_misc' entries registered for QEMU would not be
usable in container contexts outside of guix-daemon (without manually bind
mounting file names).
For example:
$ docker run --rm arm32v7/debian true
standard_init_linux.go:207: exec user process caused "no such file or directory"
After this change, any container can make use of the QEMU binfmt_misc
registrations, as their corresponding QEMU static binaries are fully
pre-loaded by the kernel.
* gnu/services/virtualization.scm (<qemu-platform>): Define using
'define-record-type*'.
[flags]: New field, which defaults to "F" (fix binary).
(%i386, %i486, %alpha, %arm, %armeb, %sparc, %sparc32plus, %ppc, %ppc64)
(%ppc64le, %m68k, %mips, %mipsel, %mipsn32, %mipsn32el, %mips64, %mips64el)
(%riscv32, %riscv64, %sh4, %sh4eb, %s390x, %aarch64, %hppa): Adjust.
(qemu-binfmt-guix-chroot): Remove variable.
(qemu-binfmt-service-type): Remove the qemu-binfmt-guix-chroot extension.
* gnu/services/qemu-binfmt (qemu-platform->binfmt): Use the static output of
QEMU.
* doc/contributing.texi (Submitting Patches): Update doc.
* doc/guix.texi (Virtualization Services): Update doc.
2021-03-15 18:00:35 -04:00
Maxim Cournoyer
d184fd4216
gnu: qemu: Add a static output.
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The static output is equivalent to what other distributions commonly package
as 'qemu-user-static'.
* gnu/packages/virtualization.scm (qemu)[outputs]: Add a static output.
[phases]{configure}: Configure the main build as an out-of-source build. Move
all configure flags to ...
[configure-flags]: ... here. The options explicitly enabling optional
features are removed; the configure script does a good job at enabling all the
features available based on the inputs present and this allows reusing the
flags in variant packages such as qemu-minimal.
{configure-user-static, build-user-static, install-user-static}: New phases.
{patch-test-shebangs}: New phase, extracted from the configure phase.
[native-inputs]: Add glib-static, pcre:static and zlib:static.
(qemu-minimal)[arguments]: Reuse the configure-flags argument. Rewrite to use
match instead of cond.
2021-03-15 18:00:35 -04:00
Maxim Cournoyer
ce29866c01
gnu: Add glib-static.
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* gnu/packages/glib.scm (glib-static): New variable.
2021-03-15 18:00:35 -04:00
Maxim Cournoyer
3fe46eef57
gnu: qemu: Fix indentation and remove trailing #t.
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* gnu/packages/virtualization.scm (qemu): Fix indentation and remove
trailing #t, appeasing 'guix lint'.
2021-03-15 18:00:34 -04:00
Ricardo Wurmus
29e992c030
gnu: r-seurat: Fix build.
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This is a follow-up to commit e4d4046999
2021-03-15 22:06:57 +01:00
Tobias Geerinckx-Rice
fcb122b4ed
gnu: xterm: Fix uxterm in pure environments.
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* gnu/packages/xorg.scm (xterm)[arguments]: Add a 'patch-file-names
phase.
2021-03-15 20:31:24 +01:00
Tobias Geerinckx-Rice
20d090f435
gnu: sudo: Update to 1.9.6p1.
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* gnu/packages/admin.scm (sudo): Update to 1.9.6p1.
2021-03-15 20:31:24 +01:00
Ricardo Wurmus
266d55dc30
gnu: ibus-libpinyin: Update to 1.12.0.
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* gnu/packages/ibus.scm (ibus-libpinyin): Update to 1.12.0.
[arguments]: Enable opencc; include setup files on PYTHONPATH; override
PYTHONPATH instead of prefixing.
[inputs]: Add opencc; remove python-pyxdg.
[license]: Change to GPLv3+.
2021-03-15 15:24:01 +01:00
Ricardo Wurmus
f9e016baec
gnu: libpinyin: Update to 2.6.0.
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* gnu/packages/ibus.scm (libpinyin): Update to 2.6.0.
2021-03-15 15:23:50 +01:00
Ricardo Wurmus
14204d696c
gnu: r-genomicfeatures: Update to 1.42.2.
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* gnu/packages/bioinformatics.scm (r-genomicfeatures): Update to 1.42.2.
2021-03-15 15:03:08 +01:00
Ricardo Wurmus
f10f2745eb
gnu: r-delayedarray: Update to 0.16.2.
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* gnu/packages/bioinformatics.scm (r-delayedarray): Update to 0.16.2.
2021-03-15 15:03:08 +01:00
Ricardo Wurmus
1ada8ea96c
gnu: r-scater: Update to 1.18.6.
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* gnu/packages/bioconductor.scm (r-scater): Update to 1.18.6.
2021-03-15 15:03:08 +01:00
Ricardo Wurmus
fa6bb614c8
gnu: r-cytoml: Update to 2.2.2.
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* gnu/packages/bioconductor.scm (r-cytoml): Update to 2.2.2.
[inputs]: Add zlib.
2021-03-15 15:03:08 +01:00
Ricardo Wurmus
11dc49afc2
gnu: r-diffbind: Update to 3.0.14.
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* gnu/packages/bioconductor.scm (r-diffbind): Update to 3.0.14.
2021-03-15 15:03:07 +01:00
Ricardo Wurmus
ee61edb621
gnu: r-reportingtools: Update to 2.30.2.
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* gnu/packages/bioconductor.scm (r-reportingtools): Update to 2.30.2.
2021-03-15 15:03:07 +01:00
Ricardo Wurmus
fa227c9640
gnu: r-genomeinfodb: Update to 1.26.4.
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* gnu/packages/bioconductor.scm (r-genomeinfodb): Update to 1.26.4.
2021-03-15 15:03:07 +01:00
Ricardo Wurmus
b45c625f10
gnu: r-deseq2: Update to 1.30.1.
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* gnu/packages/bioconductor.scm (r-deseq2): Update to 1.30.1.
2021-03-15 15:03:07 +01:00
Efraim Flashner
4ce712aca4
gnu: alacritty: Use more packaged rust libraries.
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* gnu/packages/terminals.scm (alacritty)[arguments]: Move
rust-bitflags-1, rust-dirs-2, rust-libc-0.2, rust-unicode-width-0.1,
rust-winapi-0.3 from cargo-inputs ...
[inputs]: ... to here.
2021-03-15 15:53:17 +02:00
Efraim Flashner
ca3b97baaa
gnu: rust-dirs-2: Adapt for new build system.
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* gnu/packages/crates-io.scm (rust-dirs-2)[inputs]: Add rust-cfg-if-0.1,
rust-dirs-sys-0.3.
2021-03-15 15:53:17 +02:00
Efraim Flashner
a4bbebb2b3
gnu: rust-dirs-sys-0.3: Adapt for new build system.
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* gnu/packages/crates-io.scm (rust-dirs-sys-0.3)[inputs]: Add
rust-cfg-if-0.1, rust-libc-0.2, rust-redox-users-0.3, rust-winapi-0.3.
2021-03-15 15:53:17 +02:00
Efraim Flashner
647dfa788e
gnu: rust-lazy-static-1: Adapt for new build system.
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* gnu/packages/crates-io.scm (rust-lazy-static-1)[inputs]: Add
rust-spin-0.5.
2021-03-15 15:53:16 +02:00
Efraim Flashner
f69a3fe28c
gnu: alacritty: Use packaged rust-wayland-client.
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* gnu/packages/terminals.scm (alacritty)[arguments]: Remove
rust-wayland-client-0.28 from cargo-inputs. In custom
'add-absolute-library-references remove substitutions for
rust-wayland-client.
[inputs]: Add rust-wayland-client-0.28.
2021-03-15 15:53:16 +02:00
Efraim Flashner
190e94b278
gnu: rust-glutin-0.26: Adapt for new build system.
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* gnu/packages/crates-graphics.scm (rust-glutin-0.26)
[arguments]: Don't skip build. Remove rust-wayland-client-0.28 from
cargo-inputs.
[inputs]: Add rust-wayland-client-0.28, rust-wayland-egl-0.28.
2021-03-15 15:53:16 +02:00
Efraim Flashner
87d747860d
gnu: rust-winit-0.24: Adapt for new build system.
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* gnu/packages/crates-graphics.scm (rust-winit-0.24)[arguments]: Move
rust-wayland-client-0.28 from cargo-inputs ...
[inputs]: ... to here.
2021-03-15 15:53:16 +02:00
Efraim Flashner
6f655caf42
gnu: rust-wayland-server-0.28: Adapt for new build system.
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* gnu/packages/crates-graphics.scm (rust-wayland-server-0.28)
[arguments]: Don't skip build. Remove rust-wayland-commons-0.28,
rust-wayland-scanner-0.28, rust-wayland-sys-0.28 from cargo-inputs.
[inputs]: Add rust-bitflags-1, rust-downcast-rs-1, rust-lazy-static-1,
rust-libc-0.2, rust-nix-0.18, rust-parking-lot-0.18, rust-scoped-tls-1,
rust-wayland-commons-0.28, rust-wayland-scanner-0.28,
rust-wayland-sys-0.28.
(rust-wayland-server-0.23): Adjust accordingly.
2021-03-15 15:53:16 +02:00
Efraim Flashner
fb6f926193
gnu: rust-wayland-scanner-0.28: Adapt for new build system.
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* gnu/packages/crates-graphics.scm (rust-wayland-scanner-0.28):
[arguments]: Don't skip build. Remove cargo-inputs.
[inputs]: Add rust-proc-macro2-1, rust-quote-1, rust-xml-rs-0.8.
(rust-wayland-scanner-0.23): Adjust accordingly.
2021-03-15 15:53:16 +02:00
Efraim Flashner
facf27e08b
gnu: rust-wayland-protocols-0.28: Adapt for new build system.
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* gnu/packages/crates-graphics.scm (rust-wayland-protocols-0.28)
[arguments]: Don't skip build. Remove everything from cargo-inputs
except rust-bitflags-1.
[inputs]: Add rust-bitflags-1, rust-wayland-client-0.28,
rust-wayland-commons-0.28, rust-wayland-scanner-0.28,
rust-wayland-server-0.28.
(rust-wayland-protocols-0.23): Adjust accordingly.
2021-03-15 15:53:16 +02:00
Efraim Flashner
bb06a747b2
gnu: rust-wayland-egl-0.28: Adapt for new build system.
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* gnu/packages/crates-graphics.scm (rust-wayland-egl-0.28)
[arguments]: Don't skip build. Remove cargo-inputs.
[inputs]: Add rust-wayland-client-0.28, rust-wayland-sys-0.28.
[native-inputs]: Add pkg-config.
2021-03-15 15:53:15 +02:00
