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* gnu: Remove MongoDB.•••mongodb 3.4.10 has unpatched CVEs and mongodb 3.4.24 has some files in the release tarball under the SSPL, therefore we cannot provide mongodb while upholding to good security standards. It turns out feff80cec3c97a3df2c20d300be12d67f79d4f22 was right since while the main license file wasnt altered to SSPL, some files in the tree contain SSPL headers. * gnu/packages/databases.scm (go-gopkg.in-mgo.v2): Remove. * gnu/packages/databases.scm (mongo-tools): Remove. * doc/guix.texi (mongodb-service-type): Remove. * gnu/tests/databases.scm (%test-mongodb, %mongodb-os, run-mongodb-test): Remove. * gnu/services/databases.scm (mongodb-configuration, mongodb-configuration?, mongodb-configuration-mongodb, mongodb-configuration-config-file, mongodb-configuration-data-directory, mongodb-service-type, %default-mongodb-configuration-file, %mongodb-accounts, mongodb-activation, mongodb-shepherd-service): Remove. * gnu/packages/databases.scm (mongodb): Remove. Léo Le Bouter2021-03-16
* gnu: git: Fix git-manpages native input's hash.•••This is a follow-up to commit ab9629b7c91ff7d6392a03512cfe442823267777. * gnu/packages/version-control.scm (git)[native-inputs]: Fix git-manpages's hash. Léo Le Bouter2021-03-16
* gnu: git: Update to 2.31.0.•••* gnu/packages/version-control.scm (git): Update to 2.31.0. Léo Le Bouter2021-03-16
* gnu: python2-urllib3: Update to 1.26.4 [fixes CVE-2021-28363].•••* gnu/packages/python-web.scm (python2-urllib3)[base]: Base off of python-urllib3/fixed. Léo Le Bouter2021-03-16
* gnu: python-urllib3: Update to 1.26.4 [fixes CVE-2021-28363].•••* gnu/packages/python-web.scm (python-urllib3/fixed): New variable. (python-urllib3)[replacement]: Graft. Léo Le Bouter2021-03-16
* gnu: tmsu: Improve installation.•••* 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> Stefan Reichör2021-03-16
* gnu: glances: Update to 3.1.6.•••* gnu/packages/python-xyz.scm (glances): Update to 3.1.6. Signed-off-by: Efraim Flashner <efraim@flashner.co.il> Stefan Reichör2021-03-16
* Revert some commits that caused `guix pull` to fail.•••This reverts commits 821e6439212f8e94580674eaaff2ce6752cd3b18 through 8f9fd9b70c7bf166d96a4b1dc8b427f8cdf040b5. Specifically, these commits caused the build failure of guix-package-cache.drv like this: ------ (repl-version 0 1 1) Generating package cache for '/gnu/store/vyz7q26kxxd4z70m24rkkqqhaizdla7g-profile'... (exception unbound-variable (value #f) (value "Unbound variable: ~S") (value (r-biobase)) (value #f)) Leo Famulari2021-03-15
* gnu: r-biocparallel: Build reproducibly.•••* gnu/packages/bioconductor.scm (r-biocparallel)[arguments]: Add phase "make-reproducible". Ricardo Wurmus2021-03-15
* gnu: r-delayedarray: Move to (gnu packages bioconductor).•••* gnu/packages/bioinformatics.scm (r-delayedarray): Move from here... * gnu/packages/bioconductor.scm (r-delayedarray): ...to here. zimoun2021-03-15
* gnu: r-rsamtools: Move to (gnu packages bioconductor).•••* gnu/packages/bioinformatics.scm (r-rsamtools): Move from here... * gnu/packages/bioconductor.scm (r-rsamtools): ...to here. zimoun2021-03-15
* gnu: r-biostrings: Move to (gnu packages bioconductor).•••* gnu/packages/bioinformatics.scm (r-biostrings): Move from here... * gnu/packages/bioconductor.scm (r-biostrings): ...to here. zimoun2021-03-15
* 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. zimoun2021-03-15
* gnu: r-biomart: Move to (gnu packages bioconductor).•••* gnu/packages/bioinformatics.scm (r-biomart): Move from here... * gnu/packages/bioconductor.scm (r-biomart): ...to here. zimoun2021-03-15
* gnu: r-annotationdbi: Move to (gnu packages bioconductor).•••* gnu/packages/bioinformatics.scm (r-annotationdbi): Move from here... * gnu/packages/bioconductor.scm (r-annotationdbi): ...to here. zimoun2021-03-15
* gnu: r-biobase: Move to (gnu packages bioconductor).•••* gnu/packages/bioinformatics.scm (r-biobase): Move from here... * gnu/packages/bioconductor.scm (r-biobase): ...to here. zimoun2021-03-15
* 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. zimoun2021-03-15
* 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. zimoun2021-03-15
* 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. zimoun2021-03-15
* 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 Cournoyer2021-03-15
* 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 Famulari2021-03-15
* 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 Cournoyer2021-03-15
* 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 Cournoyer2021-03-15
* gnu: Add glib-static.•••* gnu/packages/glib.scm (glib-static): New variable. Maxim Cournoyer2021-03-15
* gnu: qemu: Fix indentation and remove trailing #t.•••* gnu/packages/virtualization.scm (qemu): Fix indentation and remove trailing #t, appeasing 'guix lint'. Maxim Cournoyer2021-03-15
* gnu: r-seurat: Fix build.•••This is a follow-up to commit e4d4046999304a3693da80cf0fdfe5fd5753b2b7 * gnu/packages/cran.scm (r-seurat)[arguments]: Patch NAMESPACE file. Ricardo Wurmus2021-03-15
* gnu: xterm: Fix uxterm in pure environments.•••* gnu/packages/xorg.scm (xterm)[arguments]: Add a 'patch-file-names phase. Tobias Geerinckx-Rice2021-03-15
* gnu: sudo: Update to 1.9.6p1.•••* gnu/packages/admin.scm (sudo): Update to 1.9.6p1. Tobias Geerinckx-Rice2021-03-15
* 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 Wurmus2021-03-15
* gnu: libpinyin: Update to 2.6.0.•••* gnu/packages/ibus.scm (libpinyin): Update to 2.6.0. Ricardo Wurmus2021-03-15
* gnu: r-genomicfeatures: Update to 1.42.2.•••* gnu/packages/bioinformatics.scm (r-genomicfeatures): Update to 1.42.2. Ricardo Wurmus2021-03-15
* gnu: r-delayedarray: Update to 0.16.2.•••* gnu/packages/bioinformatics.scm (r-delayedarray): Update to 0.16.2. Ricardo Wurmus2021-03-15
* gnu: r-scater: Update to 1.18.6.•••* gnu/packages/bioconductor.scm (r-scater): Update to 1.18.6. Ricardo Wurmus2021-03-15
* gnu: r-cytoml: Update to 2.2.2.•••* gnu/packages/bioconductor.scm (r-cytoml): Update to 2.2.2. [inputs]: Add zlib. Ricardo Wurmus2021-03-15
* gnu: r-diffbind: Update to 3.0.14.•••* gnu/packages/bioconductor.scm (r-diffbind): Update to 3.0.14. Ricardo Wurmus2021-03-15
* gnu: r-reportingtools: Update to 2.30.2.•••* gnu/packages/bioconductor.scm (r-reportingtools): Update to 2.30.2. Ricardo Wurmus2021-03-15
* gnu: r-genomeinfodb: Update to 1.26.4.•••* gnu/packages/bioconductor.scm (r-genomeinfodb): Update to 1.26.4. Ricardo Wurmus2021-03-15
* gnu: r-deseq2: Update to 1.30.1.•••* gnu/packages/bioconductor.scm (r-deseq2): Update to 1.30.1. Ricardo Wurmus2021-03-15
* 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 Flashner2021-03-15
* 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 Flashner2021-03-15
* 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 Flashner2021-03-15
* 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 Flashner2021-03-15
* 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 Flashner2021-03-15
* 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 Flashner2021-03-15
* 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 Flashner2021-03-15
* 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 Flashner2021-03-15
* 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 Flashner2021-03-15
* 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 Flashner2021-03-15
* 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 Flashner2021-03-15
* 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 Flashner2021-03-15
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