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* services/qemu-binfmt: Use the F flag and the static output of QEMU.Maxim Cournoyer2021-03-15
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | 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.
* gnu: qemu: Add a static output.Maxim Cournoyer2021-03-15
| | | | | | | | | | | | | | | | | | 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.
* gnu: Add glib-static.Maxim Cournoyer2021-03-15
| | | | * gnu/packages/glib.scm (glib-static): New variable.
* gnu: qemu: Fix indentation and remove trailing #t.Maxim Cournoyer2021-03-15
| | | | | * gnu/packages/virtualization.scm (qemu): Fix indentation and remove trailing #t, appeasing 'guix lint'.
* gnu: r-seurat: Fix build.Ricardo Wurmus2021-03-15
| | | | | | This is a follow-up to commit e4d4046999304a3693da80cf0fdfe5fd5753b2b7 * gnu/packages/cran.scm (r-seurat)[arguments]: Patch NAMESPACE file.
* gnu: xterm: Fix uxterm in pure environments.Tobias Geerinckx-Rice2021-03-15
| | | | | * gnu/packages/xorg.scm (xterm)[arguments]: Add a 'patch-file-names phase.
* gnu: sudo: Update to 1.9.6p1.Tobias Geerinckx-Rice2021-03-15
| | | | * gnu/packages/admin.scm (sudo): Update to 1.9.6p1.
* gnu: ibus-libpinyin: Update to 1.12.0.Ricardo Wurmus2021-03-15
| | | | | | | | * 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+.
* gnu: libpinyin: Update to 2.6.0.Ricardo Wurmus2021-03-15
| | | | * gnu/packages/ibus.scm (libpinyin): Update to 2.6.0.
* gnu: r-genomicfeatures: Update to 1.42.2.Ricardo Wurmus2021-03-15
| | | | * gnu/packages/bioinformatics.scm (r-genomicfeatures): Update to 1.42.2.
* gnu: r-delayedarray: Update to 0.16.2.Ricardo Wurmus2021-03-15
| | | | * gnu/packages/bioinformatics.scm (r-delayedarray): Update to 0.16.2.
* gnu: r-scater: Update to 1.18.6.Ricardo Wurmus2021-03-15
| | | | * gnu/packages/bioconductor.scm (r-scater): Update to 1.18.6.
* gnu: r-cytoml: Update to 2.2.2.Ricardo Wurmus2021-03-15
| | | | | * gnu/packages/bioconductor.scm (r-cytoml): Update to 2.2.2. [inputs]: Add zlib.
* gnu: r-diffbind: Update to 3.0.14.Ricardo Wurmus2021-03-15
| | | | * gnu/packages/bioconductor.scm (r-diffbind): Update to 3.0.14.
* gnu: r-reportingtools: Update to 2.30.2.Ricardo Wurmus2021-03-15
| | | | * gnu/packages/bioconductor.scm (r-reportingtools): Update to 2.30.2.
* gnu: r-genomeinfodb: Update to 1.26.4.Ricardo Wurmus2021-03-15
| | | | * gnu/packages/bioconductor.scm (r-genomeinfodb): Update to 1.26.4.
* gnu: r-deseq2: Update to 1.30.1.Ricardo Wurmus2021-03-15
| | | | * gnu/packages/bioconductor.scm (r-deseq2): Update to 1.30.1.
* gnu: alacritty: Use more packaged rust libraries.Efraim Flashner2021-03-15
| | | | | | | * 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.
* gnu: rust-dirs-2: Adapt for new build system.Efraim Flashner2021-03-15
| | | | | * gnu/packages/crates-io.scm (rust-dirs-2)[inputs]: Add rust-cfg-if-0.1, rust-dirs-sys-0.3.
* gnu: rust-dirs-sys-0.3: Adapt for new build system.Efraim Flashner2021-03-15
| | | | | * 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.
* gnu: rust-lazy-static-1: Adapt for new build system.Efraim Flashner2021-03-15
| | | | | * gnu/packages/crates-io.scm (rust-lazy-static-1)[inputs]: Add rust-spin-0.5.
* gnu: alacritty: Use packaged rust-wayland-client.Efraim Flashner2021-03-15
| | | | | | | | * 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.
* gnu: rust-glutin-0.26: Adapt for new build system.Efraim Flashner2021-03-15
| | | | | | | * 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.
* gnu: rust-winit-0.24: Adapt for new build system.Efraim Flashner2021-03-15
| | | | | | * gnu/packages/crates-graphics.scm (rust-winit-0.24)[arguments]: Move rust-wayland-client-0.28 from cargo-inputs ... [inputs]: ... to here.
* gnu: rust-wayland-server-0.28: Adapt for new build system.Efraim Flashner2021-03-15
| | | | | | | | | | | * 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.
* gnu: rust-wayland-scanner-0.28: Adapt for new build system.Efraim Flashner2021-03-15
| | | | | | | * 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.
* gnu: rust-wayland-protocols-0.28: Adapt for new build system.Efraim Flashner2021-03-15
| | | | | | | | | | * 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.
* gnu: rust-wayland-egl-0.28: Adapt for new build system.Efraim Flashner2021-03-15
| | | | | | | * 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.
* gnu: rust-wayland-cursor-0.28: Adapt for new build system.Efraim Flashner2021-03-15
| | | | | | | * 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.
* gnu: rust-wayland-client-0.28: Adapt for new build system.Efraim Flashner2021-03-15
| | | | | | | | | | * 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.
* gnu: rust-wayland-commons-0.28: Adapt for new build system.Efraim Flashner2021-03-15
| | | | | | | | | * 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.
* gnu: rust-libloading-0.6: Update to 0.6.7.Efraim Flashner2021-03-15
| | | | | | * 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.
* gnu: dlib-0.4: Update to 0.4.2.Efraim Flashner2021-03-15
| | | | | | * 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.
* gnu: rust-proc-macro2-1: Adapt for new build system.Efraim Flashner2021-03-15
| | | | | * gnu/packages/crates-io.scm (rust-proc-macro2-1)[inputs]: Add rust-unicode-xid-0.2.
* gnu: rust-winapi-0.3: Adjust for new build system.Efraim Flashner2021-03-15
| | | | | * gnu/packages/crates-io.scm (rust-winapi-0.3)[inputs]: Add rust-winapi-i686-pc-windows-gnu, rust-winapi-x86-64-pc-windows-gnu.
* gnu: rust-pkg-config-0.3: Hardcode location of pkg-config.Efraim Flashner2021-03-15
| | | | | * gnu/packages/crates-io.scm (rust-pkg-config-0.3)[arguments]: Add phase to hardcode location of pkg-config binary.
* gnu: rust-pkg-config-0.3: Update to 0.3.19.Efraim Flashner2021-03-15
| | | | * gnu/packages/crates-io.scm (rust-pkg-config-0.3): Update to 0.3.19.
* gnu: rust-wayland-sys-0.28: Adapt for new build system.Efraim Flashner2021-03-15
| | | | | | | | | * 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.
* gnu: rust-quote-1: Update to 1.0.9.Efraim Flashner2021-03-15
| | | | * gnu/packages/crates-io.scm (rust-quote-1): Update to 1.0.9.
* build-system/cargo: Don't clobber packaged crates while building.Efraim Flashner2021-03-15
| | | | | | | | 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.
* gnu: r-variantannotation: Move to (gnu packages bioconductor).zimoun2021-03-15
| | | | | * gnu/packages/bioinformatics.scm (r-variantannotation): Move from here... * gnu/packages/bioconductor.scm (r-variantannotation): ...to here.
* gnu: r-edger: Move to (gnu packages bioconductor).zimoun2021-03-15
| | | | | * gnu/packages/bioinformatics.scm (r-edger): Move from here... * gnu/packages/bioconductor.scm (r-edger): ...to here.
* gnu: r-genomeinfodb: Move to (gnu packages bioconductor).zimoun2021-03-15
| | | | | * gnu/packages/bioinformatics.scm (r-genomeinfodb): Move from here... * gnu/packages/bioconductor.scm (r-genomeinfodb): ...to here.
* gnu: r-genomeinfodbdata: Move to (gnu packages bioconductor).zimoun2021-03-15
| | | | | | * gnu/packages/bioinformatics.scm (r-genomeinfodbdata): Move from here... * gnu/packages/bioconductor.scm (r-genomeinfodbdata): ...to here. [source]: Use 'bioconductor-uri'.
* gnu: r-iranges: Move to (gnu packages bioconductor).zimoun2021-03-15
| | | | | * gnu/packages/bioinformatics.scm (r-iranges): Move from here... * gnu/packages/bioconductor.scm (r-iranges): ...to here.
* gnu: r-s4vectors: Move to (gnu packages bioconductor).zimoun2021-03-15
| | | | | * gnu/packages/bioinformatics.scm (r-s4vectors): Move from here... * gnu/packages/bioconductor.scm (r-s4vectors): ...to here.
* gnu: r-bioccheck: Move to (gnu packages bioconductor).zimoun2021-03-15
| | | | | * gnu/packages/bioinformatics.scm (r-bioccheck): Move from here... * gnu/packages/bioconductor.scm (r-bioccheck): ...to here.
* gnu: r-grohmm: Move to (gnu packages bioconductor).zimoun2021-03-15
| | | | | * gnu/packages/bioinformatics.scm (r-grohmm): Move from here... * gnu/packages/bioconductor.scm (r-grohmm): ...to here.
* gnu: r-biocstyle: Move to (gnu packages bioconductor).zimoun2021-03-15
| | | | | * gnu/packages/bioinformatics.scm (r-biocstyle): Move from here... * gnu/packages/bioconductor.scm (r-biocstyle): ...to here.
* gnu: r-biocviews: Move to (gnu packages bioconductor).zimoun2021-03-15
| | | | | * gnu/packages/bioinformatics.scm (r-biocviews): Move from here... * gnu/packages/bioconductor.scm (r-biocviews): ...to here.
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