| Age | Commit message (Expand) | Author |
|---|
| 2021-03-15 | 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.
| zimoun |
| 2021-03-15 | 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.
| Maxim Cournoyer |
| 2021-03-15 | 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>
| Leo Famulari |
| 2021-03-15 | 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.
| Maxim Cournoyer |
| 2021-03-15 | 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.
| Maxim Cournoyer |
| 2021-03-15 | gnu: Add glib-static....* gnu/packages/glib.scm (glib-static): New variable.
| Maxim Cournoyer |
| 2021-03-15 | gnu: qemu: Fix indentation and remove trailing #t....* gnu/packages/virtualization.scm (qemu): Fix indentation and remove
trailing #t, appeasing 'guix lint'.
| Maxim Cournoyer |
| 2021-03-15 | gnu: r-seurat: Fix build....This is a follow-up to commit e4d4046999304a3693da80cf0fdfe5fd5753b2b7
* gnu/packages/cran.scm (r-seurat)[arguments]: Patch NAMESPACE file.
| Ricardo Wurmus |
| 2021-03-15 | gnu: xterm: Fix uxterm in pure environments....* gnu/packages/xorg.scm (xterm)[arguments]: Add a 'patch-file-names
phase.
| Tobias Geerinckx-Rice |
| 2021-03-15 | gnu: sudo: Update to 1.9.6p1....* gnu/packages/admin.scm (sudo): Update to 1.9.6p1.
| Tobias Geerinckx-Rice |
| 2021-03-15 | 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+.
| Ricardo Wurmus |
| 2021-03-15 | gnu: libpinyin: Update to 2.6.0....* gnu/packages/ibus.scm (libpinyin): Update to 2.6.0.
| Ricardo Wurmus |
| 2021-03-15 | gnu: r-genomicfeatures: Update to 1.42.2....* gnu/packages/bioinformatics.scm (r-genomicfeatures): Update to 1.42.2.
| Ricardo Wurmus |
| 2021-03-15 | gnu: r-delayedarray: Update to 0.16.2....* gnu/packages/bioinformatics.scm (r-delayedarray): Update to 0.16.2.
| Ricardo Wurmus |
| 2021-03-15 | gnu: r-scater: Update to 1.18.6....* gnu/packages/bioconductor.scm (r-scater): Update to 1.18.6.
| Ricardo Wurmus |
| 2021-03-15 | gnu: r-cytoml: Update to 2.2.2....* gnu/packages/bioconductor.scm (r-cytoml): Update to 2.2.2.
[inputs]: Add zlib.
| Ricardo Wurmus |
| 2021-03-15 | gnu: r-diffbind: Update to 3.0.14....* gnu/packages/bioconductor.scm (r-diffbind): Update to 3.0.14.
| Ricardo Wurmus |
| 2021-03-15 | gnu: r-reportingtools: Update to 2.30.2....* gnu/packages/bioconductor.scm (r-reportingtools): Update to 2.30.2.
| Ricardo Wurmus |
| 2021-03-15 | gnu: r-genomeinfodb: Update to 1.26.4....* gnu/packages/bioconductor.scm (r-genomeinfodb): Update to 1.26.4.
| Ricardo Wurmus |
| 2021-03-15 | gnu: r-deseq2: Update to 1.30.1....* gnu/packages/bioconductor.scm (r-deseq2): Update to 1.30.1.
| Ricardo Wurmus |
| 2021-03-15 | 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.
| Efraim Flashner |
| 2021-03-15 | 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.
| Efraim Flashner |
| 2021-03-15 | 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.
| Efraim Flashner |
| 2021-03-15 | 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.
| Efraim Flashner |
| 2021-03-15 | 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.
| Efraim Flashner |
| 2021-03-15 | 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.
| Efraim Flashner |
| 2021-03-15 | 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.
| Efraim Flashner |
| 2021-03-15 | 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.
| Efraim Flashner |
| 2021-03-15 | 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.
| Efraim Flashner |
| 2021-03-15 | 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.
| Efraim Flashner |
| 2021-03-15 | 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.
| Efraim Flashner |
| 2021-03-15 | 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.
| Efraim Flashner |
| 2021-03-15 | 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.
| Efraim Flashner |
| 2021-03-15 | 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.
| Efraim Flashner |
| 2021-03-15 | 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.
| Efraim Flashner |
| 2021-03-15 | 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.
| Efraim Flashner |
| 2021-03-15 | 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.
| Efraim Flashner |
| 2021-03-15 | 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.
| Efraim Flashner |
| 2021-03-15 | 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.
| Efraim Flashner |
| 2021-03-15 | 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.
| Efraim Flashner |
| 2021-03-15 | 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.
| Efraim Flashner |
| 2021-03-15 | gnu: rust-quote-1: Update to 1.0.9....* gnu/packages/crates-io.scm (rust-quote-1): Update to 1.0.9.
| Efraim Flashner |
| 2021-03-15 | 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.
| zimoun |
| 2021-03-15 | 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.
| zimoun |
| 2021-03-15 | 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.
| zimoun |
| 2021-03-15 | 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'.
| zimoun |
| 2021-03-15 | gnu: r-iranges: Move to (gnu packages bioconductor)....* gnu/packages/bioinformatics.scm (r-iranges): Move from here...
* gnu/packages/bioconductor.scm (r-iranges): ...to here.
| zimoun |
| 2021-03-15 | gnu: r-s4vectors: Move to (gnu packages bioconductor)....* gnu/packages/bioinformatics.scm (r-s4vectors): Move from here...
* gnu/packages/bioconductor.scm (r-s4vectors): ...to here.
| zimoun |
| 2021-03-15 | gnu: r-bioccheck: Move to (gnu packages bioconductor)....* gnu/packages/bioinformatics.scm (r-bioccheck): Move from here...
* gnu/packages/bioconductor.scm (r-bioccheck): ...to here.
| zimoun |
| 2021-03-15 | gnu: r-grohmm: Move to (gnu packages bioconductor)....* gnu/packages/bioinformatics.scm (r-grohmm): Move from here...
* gnu/packages/bioconductor.scm (r-grohmm): ...to here.
| zimoun |
