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* gnu: tor: Update to 0.4.5.7 [security fixes].Efraim Flashner2021-03-16
| | | | * gnu/packages/tor.scm (tor): Update to 0.4.5.7.
* gnu: snakemake: Add missing inputs.Ricardo Wurmus2021-03-16
| | | | | * gnu/packages/python-xyz.scm (snakemake)[propagated-inputs]: Add python-nbformat, python-pulp, and python-toposort.
* gnu: Add python-toposort.Ricardo Wurmus2021-03-16
| | | | * gnu/packages/python-xyz.scm (python-toposort): New variable.
* gnu: Add python-pulp.Ricardo Wurmus2021-03-16
| | | | * gnu/packages/python-xyz.scm (python-pulp): New variable.
* gnu: Add python-amply.Ricardo Wurmus2021-03-16
| | | | * gnu/packages/python-xyz.scm (python-amply): New variable.
* gnu: emacs-easy-kill: Update to 0.9.4.Nicolas Goaziou2021-03-16
| | | | * gnu/packages/emacs-xyz.scm (emacs-easy-kill): Update to 0.9.4.
* gnu: emacs-leaf: Update to 4.4.0.Nicolas Goaziou2021-03-16
| | | | * gnu/packages/emacs-xyz.scm (emacs-leaf): Update to 4.4.0.
* gnu: python-pikepdf: Update to 2.9.0.Nicolas Goaziou2021-03-16
| | | | * gnu/packages/python-xyz.scm (python-pikepdf): Update to 2.9.0.
* gnu: asymptote: Update to 2.70.Nicolas Goaziou2021-03-16
| | | | * gnu/packages/plotutils.scm (asymptote): Update to 2.70.
* gnu: b4: Fix setup.py version incompatibility.Efraim Flashner2021-03-16
| | | | | | | * gnu/packages/version-control.scm (b4)[source]: Add snippet to not require too specific of a version. Reported-by: Kyle Meyer <kyle@kyleam.com>
* gnu: libmemcached: Disable test suite.Maxim Cournoyer2021-03-16
| | | | | | | | | | | * gnu/packages/databases.scm (libmemcached): Disable test suite. Removing trailing #t. [phases]{fix-configure}: Remove useless group in pattern. {disable-failing-tests}: Remove phase. {build-and-install-html-doc}: Order after the build phase. [home-page]: Please 'guix lint'. Reported-by: Simon Tournier <zimon.toutoune@gmail.com>
* gnu: hisat2: Update to 2.2.1.Ricardo Wurmus2021-03-16
| | | | | | | | | * gnu/packages/bioinformatics.scm (hisat2): Update to 2.2.1. [source]: Fetch from git repository on Github. [arguments]: Add phase to build manual; remove trailing #t from other phases. [native-inputs]: Remove unzip. [home-page]: Update. [inputs]: Add python-wrapper.
* gnu: Remove MongoDB.Léo Le Bouter2021-03-16
| | | | | | | | | | | | | | | | | | | | | | 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.
* gnu: git: Fix git-manpages native input's hash.Léo Le Bouter2021-03-16
| | | | | | | This is a follow-up to commit ab9629b7c91ff7d6392a03512cfe442823267777. * gnu/packages/version-control.scm (git)[native-inputs]: Fix git-manpages's hash.
* gnu: git: Update to 2.31.0.Léo Le Bouter2021-03-16
| | | | * gnu/packages/version-control.scm (git): Update to 2.31.0.
* gnu: python2-urllib3: Update to 1.26.4 [fixes CVE-2021-28363].Léo Le Bouter2021-03-16
| | | | | * gnu/packages/python-web.scm (python2-urllib3)[base]: Base off of python-urllib3/fixed.
* gnu: python-urllib3: Update to 1.26.4 [fixes CVE-2021-28363].Léo Le Bouter2021-03-16
| | | | | * gnu/packages/python-web.scm (python-urllib3/fixed): New variable. (python-urllib3)[replacement]: Graft.
* gnu: tmsu: Improve installation.Stefan Reichör2021-03-16
| | | | | | | * 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>
* gnu: glances: Update to 3.1.6.Stefan Reichör2021-03-16
| | | | | | * gnu/packages/python-xyz.scm (glances): Update to 3.1.6. Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
* syscalls: mounts: Fix a matching bug.Chris Marusich2021-03-15
| | | | | | | | | | | | | | | | | | 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.
* Revert some commits that caused `guix pull` to fail.Leo Famulari2021-03-15
| | | | | | | | | | | | | 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))
* gnu: r-biocparallel: Build reproducibly.Ricardo Wurmus2021-03-15
| | | | | * gnu/packages/bioconductor.scm (r-biocparallel)[arguments]: Add phase "make-reproducible".
* gnu: r-delayedarray: Move to (gnu packages bioconductor).zimoun2021-03-15
| | | | | * gnu/packages/bioinformatics.scm (r-delayedarray): Move from here... * gnu/packages/bioconductor.scm (r-delayedarray): ...to here.
* gnu: r-rsamtools: Move to (gnu packages bioconductor).zimoun2021-03-15
| | | | | * gnu/packages/bioinformatics.scm (r-rsamtools): Move from here... * gnu/packages/bioconductor.scm (r-rsamtools): ...to here.
* gnu: r-biostrings: Move to (gnu packages bioconductor).zimoun2021-03-15
| | | | | * gnu/packages/bioinformatics.scm (r-biostrings): Move from here... * gnu/packages/bioconductor.scm (r-biostrings): ...to here.
* gnu: r-biocparallel: Move to (gnu packages bioconductor).zimoun2021-03-15
| | | | | * gnu/packages/bioinformatics.scm (r-biocparallel): Move from here... * gnu/packages/bioconductor.scm (r-biocparallel): ...to here.
* gnu: r-biomart: Move to (gnu packages bioconductor).zimoun2021-03-15
| | | | | * gnu/packages/bioinformatics.scm (r-biomart): Move from here... * gnu/packages/bioconductor.scm (r-biomart): ...to here.
* gnu: r-annotationdbi: Move to (gnu packages bioconductor).zimoun2021-03-15
| | | | | * gnu/packages/bioinformatics.scm (r-annotationdbi): Move from here... * gnu/packages/bioconductor.scm (r-annotationdbi): ...to here.
* gnu: r-biobase: Move to (gnu packages bioconductor).zimoun2021-03-15
| | | | | * gnu/packages/bioinformatics.scm (r-biobase): Move from here... * gnu/packages/bioconductor.scm (r-biobase): ...to here.
* gnu: r-genomicranges: Move to (gnu packages bioconductor).zimoun2021-03-15
| | | | | * gnu/packages/bioinformatics.scm (r-genomicranges): Move from here... * gnu/packages/bioconductor.scm (r-genomicranges): ...to here.
* gnu: r-xvector: Move to (gnu packages bioconductor).zimoun2021-03-15
| | | | | * gnu/packages/bioinformatics.scm (r-xvector): Move from here... * gnu/packages/bioconductor.scm (r-xvector): ...to here.
* gnu: r-limma: Move to (gnu packages bioconductor).zimoun2021-03-15
| | | | | * gnu/packages/bioinformatics.scm (r-limma): Move from here... * gnu/packages/bioconductor.scm (r-limma): ...to here.
* gnu: dbus-c++: Fix command name in description.Maxim Cournoyer2021-03-15
| | | | | * gnu/packages/glib.scm (dbus-c++)[description]: Fix command prefix in description, and mention the second command installed as well.
* news: Add news entry about changes to the QEMU binfmt service.Maxim Cournoyer2021-03-15
| | | | * etc/news.scm: Add entry.
* gnu: qemu: Update to 5.2.0.Leo Famulari2021-03-15
| | | | | | | | | | | | | | | | | | | * 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>
* 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.
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