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zimoun
f3f09b99cd
gnu: r-genomicranges: Move to (gnu packages bioconductor). 
* 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). 
* 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). 
* 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. 
* 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. 
* etc/news.scm: Add entry.
 2021-03-15 18:03:16 -04:00
Leo Famulari
d15fdb66f3
gnu: qemu: Update to 5.2.0. 
* 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. 
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. 
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. 
* 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. 
* 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. 
This is a follow-up to commit e4d4046999

* gnu/packages/cran.scm (r-seurat)[arguments]: Patch NAMESPACE file.
 2021-03-15 22:06:57 +01:00
Tobias Geerinckx-Rice
fcb122b4ed
gnu: xterm: Fix uxterm in pure environments. 
* 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. 
* 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. 
* 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. 
* 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. 
* 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. 
* 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. 
* 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. 
* 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. 
* 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. 
* 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. 
* 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. 
* 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. 
* 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. 
* 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. 
* 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. 
* 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. 
* 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. 
* 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. 
* 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. 
* 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. 
* 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. 
* 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. 
* 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
Efraim Flashner
3b6ec859c2
gnu: rust-wayland-cursor-0.28: Adapt for new build system. 
* 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
Efraim Flashner
770e326fdb
gnu: rust-wayland-client-0.28: Adapt for new build system. 
* 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
Efraim Flashner
f35ab79e03
gnu: rust-wayland-commons-0.28: Adapt for new build system. 
* 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
Efraim Flashner
b10c637e48
gnu: rust-libloading-0.6: Update to 0.6.7. 
* 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
Efraim Flashner
bafeee4f6d
gnu: dlib-0.4: Update to 0.4.2. 
* gnu/packages/crates-io.scm (rust-dlib-0.4): Update to 0.4.2.
[arguments]: Replace rust-libloading-0.5 with 0.6.
[inputs]: Add rust-libloading-0.6.
 2021-03-15 15:53:15 +02:00
Efraim Flashner
358f5d9b1b
gnu: rust-proc-macro2-1: Adapt for new build system. 
* gnu/packages/crates-io.scm (rust-proc-macro2-1)[inputs]: Add
rust-unicode-xid-0.2.
 2021-03-15 15:53:15 +02:00
Efraim Flashner
c805bdd550
gnu: rust-winapi-0.3: Adjust for new build system. 
* gnu/packages/crates-io.scm (rust-winapi-0.3)[inputs]: Add
rust-winapi-i686-pc-windows-gnu, rust-winapi-x86-64-pc-windows-gnu.
 2021-03-15 15:53:14 +02:00
Efraim Flashner
12c699572c
gnu: rust-pkg-config-0.3: Hardcode location of pkg-config. 
* gnu/packages/crates-io.scm (rust-pkg-config-0.3)[arguments]: Add phase
to hardcode location of pkg-config binary.
 2021-03-15 15:53:14 +02:00
Efraim Flashner
d499911432
gnu: rust-pkg-config-0.3: Update to 0.3.19. 
* gnu/packages/crates-io.scm (rust-pkg-config-0.3): Update to 0.3.19.
 2021-03-15 15:53:14 +02:00
Efraim Flashner
4363b542f2
gnu: rust-wayland-sys-0.28: Adapt for new build system. 
* gnu/packages/crates-graphics.scm (rust-wayland-sys-0.28)[arguments]:
Don't skip build. Add phase to refer explicitly to wayland libraries.
[inputs]: Add rust-dlib-0.4, rust-lazy-static-1, rust-libc-0.2,
rust-pkg-config-0.3.
[propagated-inputs]: Add wayland.
(rust-wayland-sys-0.23): Adjust accordingly.
 2021-03-15 15:53:14 +02:00
Efraim Flashner
69c757c45a
gnu: rust-quote-1: Update to 1.0.9. 
* gnu/packages/crates-io.scm (rust-quote-1): Update to 1.0.9.
 2021-03-15 15:53:14 +02:00
Efraim Flashner
78e7e178a3
build-system/cargo: Don't clobber packaged crates while building. 
This fixes an issue where two packages share a common dependent.

* guix/build/cargo-build-system.scm (unpack-rust-crates): Only copy rust
crates into the target directory if there isn't one already there with
the same name.
 2021-03-15 15:53:11 +02:00
zimoun
bf612ead76
gnu: r-variantannotation: Move to (gnu packages bioconductor). 
* gnu/packages/bioinformatics.scm (r-variantannotation): Move from here...
* gnu/packages/bioconductor.scm (r-variantannotation): ...to here.
 2021-03-15 14:06:24 +01:00
zimoun
082f3c5433
gnu: r-edger: Move to (gnu packages bioconductor). 
* gnu/packages/bioinformatics.scm (r-edger): Move from here...
* gnu/packages/bioconductor.scm (r-edger): ...to here.
 2021-03-15 14:06:16 +01:00
zimoun
35b62c044e
gnu: r-genomeinfodb: Move to (gnu packages bioconductor). 
* gnu/packages/bioinformatics.scm (r-genomeinfodb): Move from here...
* gnu/packages/bioconductor.scm (r-genomeinfodb): ...to here.
 2021-03-15 14:05:56 +01:00
zimoun
8d6d75ff39
gnu: r-genomeinfodbdata: Move to (gnu packages bioconductor). 
* gnu/packages/bioinformatics.scm (r-genomeinfodbdata): Move from here...
* gnu/packages/bioconductor.scm (r-genomeinfodbdata): ...to here.
[source]: Use 'bioconductor-uri'.
 2021-03-15 14:05:47 +01:00