| Commit message (Collapse) | Author | Age |
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* gnu/packages/python-xyz.scm (snakemake)[propagated-inputs]: Add
python-nbformat, python-pulp, and python-toposort.
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* gnu/packages/python-xyz.scm (python-toposort): New variable.
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* gnu/packages/python-xyz.scm (python-pulp): New variable.
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* gnu/packages/python-xyz.scm (python-amply): New variable.
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* gnu/packages/emacs-xyz.scm (emacs-easy-kill): Update to 0.9.4.
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* gnu/packages/emacs-xyz.scm (emacs-leaf): Update to 4.4.0.
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* gnu/packages/python-xyz.scm (python-pikepdf): Update to 2.9.0.
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* gnu/packages/plotutils.scm (asymptote): Update to 2.70.
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* gnu/packages/version-control.scm (b4)[source]: Add snippet to not
require too specific of a version.
Reported-by: Kyle Meyer <kyle@kyleam.com>
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* 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>
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* 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.
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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.
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This is a follow-up to commit ab9629b7c91ff7d6392a03512cfe442823267777.
* gnu/packages/version-control.scm (git)[native-inputs]: Fix git-manpages's
hash.
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* gnu/packages/version-control.scm (git): Update to 2.31.0.
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* gnu/packages/python-web.scm (python2-urllib3)[base]: Base off of
python-urllib3/fixed.
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* gnu/packages/python-web.scm (python-urllib3/fixed): New variable.
(python-urllib3)[replacement]: Graft.
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* 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>
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* gnu/packages/python-xyz.scm (glances): Update to 3.1.6.
Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
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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))
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* gnu/packages/bioconductor.scm (r-biocparallel)[arguments]: Add phase
"make-reproducible".
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* gnu/packages/bioinformatics.scm (r-delayedarray): Move from here...
* gnu/packages/bioconductor.scm (r-delayedarray): ...to here.
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* gnu/packages/bioinformatics.scm (r-rsamtools): Move from here...
* gnu/packages/bioconductor.scm (r-rsamtools): ...to here.
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* gnu/packages/bioinformatics.scm (r-biostrings): Move from here...
* gnu/packages/bioconductor.scm (r-biostrings): ...to here.
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* gnu/packages/bioinformatics.scm (r-biocparallel): Move from here...
* gnu/packages/bioconductor.scm (r-biocparallel): ...to here.
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* gnu/packages/bioinformatics.scm (r-biomart): Move from here...
* gnu/packages/bioconductor.scm (r-biomart): ...to here.
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* gnu/packages/bioinformatics.scm (r-annotationdbi): Move from here...
* gnu/packages/bioconductor.scm (r-annotationdbi): ...to here.
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* gnu/packages/bioinformatics.scm (r-biobase): Move from here...
* gnu/packages/bioconductor.scm (r-biobase): ...to here.
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* gnu/packages/bioinformatics.scm (r-genomicranges): Move from here...
* gnu/packages/bioconductor.scm (r-genomicranges): ...to here.
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* gnu/packages/bioinformatics.scm (r-xvector): Move from here...
* gnu/packages/bioconductor.scm (r-xvector): ...to here.
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* gnu/packages/bioinformatics.scm (r-limma): Move from here...
* gnu/packages/bioconductor.scm (r-limma): ...to here.
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* gnu/packages/glib.scm (dbus-c++)[description]: Fix command prefix in
description, and mention the second command installed as well.
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* 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>
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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.
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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.
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* gnu/packages/glib.scm (glib-static): New variable.
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* gnu/packages/virtualization.scm (qemu): Fix indentation and remove
trailing #t, appeasing 'guix lint'.
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This is a follow-up to commit e4d4046999304a3693da80cf0fdfe5fd5753b2b7
* gnu/packages/cran.scm (r-seurat)[arguments]: Patch NAMESPACE file.
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* gnu/packages/xorg.scm (xterm)[arguments]: Add a 'patch-file-names
phase.
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* gnu/packages/admin.scm (sudo): Update to 1.9.6p1.
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* 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+.
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* gnu/packages/ibus.scm (libpinyin): Update to 2.6.0.
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* gnu/packages/bioinformatics.scm (r-genomicfeatures): Update to 1.42.2.
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* gnu/packages/bioinformatics.scm (r-delayedarray): Update to 0.16.2.
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* gnu/packages/bioconductor.scm (r-scater): Update to 1.18.6.
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* gnu/packages/bioconductor.scm (r-cytoml): Update to 2.2.2.
[inputs]: Add zlib.
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* gnu/packages/bioconductor.scm (r-diffbind): Update to 3.0.14.
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* gnu/packages/bioconductor.scm (r-reportingtools): Update to 2.30.2.
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* gnu/packages/bioconductor.scm (r-genomeinfodb): Update to 1.26.4.
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* gnu/packages/bioconductor.scm (r-deseq2): Update to 1.30.1.
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* 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.
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