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
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
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
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
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
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
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
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
eab9807fb3
gnu: r-biocparallel: Move to (gnu packages bioconductor).
...
* 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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
3b6ec859c2
gnu: rust-wayland-cursor-0.28: Adapt for new build system.
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* gnu/packages/crates-graphics.scm (rust-wayland-cursor-0.28)
[arguments]: Don't skip build. Remove rust-wayland-client-0.28 from
cargo-inputs.
[inputs]: Add rust-nix-0.18, rust-wayland-client-0.28, rust-xcursor-0.3.
2021-03-15 15:53:15 +02:00
770e326fdb
gnu: rust-wayland-client-0.28: Adapt for new build system.
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* gnu/packages/crates-graphics.scm (rust-wayland-client-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-libc-0.2,
rust-nix-0.18, rust-scoped-tls-1, rust-wayland-commons-0.28,
rust-wayland-scanner-0.28, rust-wayland-sys-0.28.
(rust-wayland-client-0.23): Adjust accordingly.
2021-03-15 15:53:15 +02:00
f35ab79e03
gnu: rust-wayland-commons-0.28: Adapt for new build system.
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* gnu/packages/crates-graphics.scm (rust-wayland-commons-0.28)
[arguments]: Don't skip build. Remove rust-wayland-sys-0.28 from
cargo-inputs.
[inputs]: Add rust-nix-0.18, rust-once-cell-1, rust-smallvec-1,
rust-wayland-sys-0.28.
(rust-wayland-commons-0.23): Adjust accordingly.
2021-03-15 15:53:15 +02:00
b10c637e48
gnu: rust-libloading-0.6: Update to 0.6.7.
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* gnu/packages/crates-io.scm (rust-libloading-0.6): Update to 0.6.
[arguments]: Replace rust-cfg-if-0.1 with 1.
[inputs]: Add rust-cfg-if-1, rust-winapi-0.3.
2021-03-15 15:53:15 +02:00
Stefan Reichör
Chris Marusich
Leo Famulari
Ricardo Wurmus
zimoun
Maxim Cournoyer
Tobias Geerinckx-Rice
Efraim Flashner