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* gnu/packages/bioinformatics.scm (python-scikit-bio): Update to 0.5.9.
[source]: Add patch.
[arguments]: Disable one test via #:test-flags; adjust 'compatibility phase;
update 'check phase.
[propagated-inputs]: Remove python-cachecontrol, python-lockfile, and
python-scikit-learn; add python-requests.
* gnu/packages/patches/python-scikit-bio-1887.patch: New file.
* gnu/local.mk (dist_patch_DATA): Add it.
Change-Id: Ie57b0256cf695e5ea088545cd2102335303a93e7
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* gnu/packages/ssh.scm (openssh)[source]:
Use 'openssh-gcc-13-ppc64le-fzero-call-used-regs.patch'.
* gnu/packages/patches/openssh-gcc-13-ppc64le-fzero-call-used-regs.patch:
New file.
* gnu/local.mk (dist_patch_DATA): Add it.
Reported-by: Marcel van der Boom <marcel@van-der-boom.nl>.
Change-Id: I41b1350b2cdd1487a8fd69b13b64f63c0dc166c9
Signed-off-by: Ludovic Courtès <ludo@gnu.org>
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Apply two upstream commits that allow building with Python 3.9 or newer and
running with Python 3.10.
* gnu/packages/patches/unknown-horizons-python-3.9.patch: New file.
* gnu/packages/patches/unknown-horizons-python-3.10.patch: New file.
* gnu/local.mk (dist_patch_DATA): Add them.
* gnu/packages/games.scm (unknown-horizons)[source]: Apply them.
Change-Id: Icbc8b698b913be01465b09ab26afb29e5fd62a87
Signed-off-by: Liliana Marie Prikler <liliana.prikler@gmail.com>
Fixes: Unknown Horizons fails to start <https://bugs.gnu.org/54815>
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* gnu/packages/patches/fifengine-python-3.9-compat.patch: New file.
* gnu/local.mk (dist_patch_DATA): Add it.
* gnu/packages/games.scm (fifengine)[source]: Apply it.
Change-Id: I61001d6b87db00c71f1e2e6ca3bac8581e941451
Signed-off-by: Liliana Marie Prikler <liliana.prikler@gmail.com>
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Change-Id: I4ec6ad695392c76c389224255477819fa686eecb
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* gnu/packages/patches/sbcl-fix-riscv-build.patch: New file.
* gnu/local.mk (dist_patch_DATA): Register it.
* gnu/packages/lisp.scm (sbcl)[source]: Use it.
Change-Id: I63f1b9a7a7b6f3a1961d0a0cb31189b74a60abc3
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Fixes <https://issues.guix.gnu.org/68333>, as well.
This is a companion to commit 5c0f77f4241c9beac0c82deae946bfdc70b49ff0.
* gnu/packages/java.scm (openjdk10)[source]: Add patch.
* gnu/packages/patches/openjdk-currency-time-bomb2.patch: New file.
* gnu/local.mk (dist_patch_DATA): Add it.
Change-Id: I42fc14d305883f672cd6764a0ee6462852e41a5b
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This is a follow-up to commit db7488a7fbd829d25b0b5c5e53b1c680b67832b1.
* gnu/local.mk (dist_patch_DATA): Restore "packages/" prefix.
Change-Id: I1f8e420e75c3f4e1927dac935c2de337fd1306eb
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Fixes <https://issues.guix.gnu.org/68333>, as well.
This is a companion to commit 5c0f77f4241c9beac0c82deae946bfdc70b49ff0.
* gnu/packages/java.scm (openjdk9)[source]: Add patch.
* gnu/packages/patches/openjdk-currency-time-bomb.patch: New file.
* gnu/local.mk (dist_patch_DATA): Add it.
Change-Id: I45ca1fe5bad922307eba64d46a330a8f233c0f55
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Fixes <https://issues.guix.gnu.org/68333>.
* gnu/packages/java.scm (icedtea-7)[drop]: Add optional ‘patches’
parameter and honor it.
[native-inputs]: Add patch for “jdk-drop”.
(icedtea-8): Likewise.
* gnu/packages/patches/jdk-currency-time-bomb.patch,
gnu/packages/patches/jdk-currency-time-bomb2.patch: New files.
* gnu/local.mk (dist_patch_DATA): Add them.
Change-Id: I3b4cf562ce4bedb87ce0e7c289e431fbb0dbb6f8
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Change-Id: I6c2ce53e782a00861c3adf01c2505099daef7728
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* gnu/packages/jami.scm (%jami-version): Rename to...
(%jami-nightly-version): ... this. Update to 20231222.2.
(%jami-daemon-commit): New variable.
(%jami-sources): Delete variable.
(libjami) Adjust source to use %jami-nightly-version, %jami-daemon-commit.
[source]: Fetch from git. Apply libjami-ac-config-files.patch.
[arguments] <make-flags>: Skip ut_media_player test.
<phases>: Add extend-scheduler-test-timeout and extend-scheduler-test-timeout
phases.
[inputs]: Replace dbus-c++ with sdbus-c++.
Add dhtnet. Replace libgit2 with libgit2-1.6.
(jami): Set version to %jami-nightly-version.
[source]: Fetch from git. Apply new jami-qml-tests-discovery.patch,
jami-skip-tests-requiring-internet.patch and jami-unbundle-dependencies.patch
patches.
[arguments] <configure-flags>: Add -DWITH_DAEMON_SUBMODULE=OFF.
<phases>: Delete change-directory/maybe.
Adjust check phase. Add fake-x11-environment,
copy-3rdparty-source-dependencies and disable-problematic-tests phases.
[inputs]: Add md4c and tidy-html.
* gnu/packages/patches/jami-qml-tests-discovery.patch: New file.
* gnu/packages/patches/libjami-ac-config-files.patch: Likewise.
* gnu/packages/patches/jami-skip-tests-requiring-internet.patch: Likewise.
* gnu/packages/patches/jami-unbundle-dependencies.patch: Likewise.
* gnu/packages/patches/jami-libjami-headers-search.patch: Delete file.
* gnu/local.mk (dist_patch_DATA): Update accordingly.
* gnu/packages/patches/jami-disable-integration-tests.patch: Adjust patch.
Series-changes: 2
- Update Jami to latest nightly version (20231222.2)
Change-Id: If30f1178bdfa29c4ea3e54dbb7997e360788adae
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To avoid Guile module dependency cycles, inherited packages must be defined in
the same module. Use this opportunity to simplify the patches applying
mechanism, versioning custom patches the same as for other packages.
* gnu/packages/patches/ffmpeg-jami-change-RTCP-ratio.patch: New file.
* gnu/packages/patches/ffmpeg-jami-rtp_ext_abs_send_time.patch: Likewise.
* gnu/packages/patches/ffmpeg-jami-libopusdec-enable-FEC.patch: Likewise.
* gnu/packages/patches/ffmpeg-jami-libopusenc-enable-FEC.patch: Likewise.
* gnu/packages/patches/ffmpeg-jami-libopusenc-reload-packet-loss-at-encode.patch:
Likewise.
* gnu/packages/patches/ffmpeg-jami-remove-mjpeg-log.patch: Likewise.
* gnu/packages/patches/ffmpeg-jami-screen-sharing-x11-fix.patch: Likewise.
* gnu/local.mk (dist_patch_DATA): Register them.
* gnu/packages/jami.scm (jami-apply-custom-patches): Delete procedure.
(%ffmpeg-default-configure-flags): Delete variable.
(ffmpeg-compose-configure-flags): Delete procedure.
(ffmpeg-jami): Move to...
* gnu/packages/video.scm (ffmpeg-jami): ... here. Apply patches to origin and
repatriate configure flags.
Change-Id: Id374fae18240cd76b224915d80b61422635ccb77
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* gnu/packages/patches/python-pyreadstat-link-libiconv.patch: New file.
* gnu/local.mk (dist_patch_DATA): Add it.
* gnu/packages/statistics.scm (python-pyreadstat): New variable.
Signed-off-by: Mathieu Othacehe <othacehe@gnu.org>
Change-Id: I361df91487412e4bfd26fb728a6999752e6343e5
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* gnu/packages/patches/sbcl-fix-ppc64-build.patch: New file.
* gnu/local.mk: Register it.
* gnu/packages/lisp.scm (sbcl)[source]: Use it.
Change-Id: If81321bc7e4075ac7ec63f7b8d623011b4b975d5
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* gnu/packages/patches/guile-fibers-libevent-timeout.patch: New file.
* gnu/local.mk (dist_patch_DATA): Add it.
* gnu/packages/guile-xyz.scm (guile-fibers)[source]: Use it.
Change-Id: I872ffe5b193087234d29eed399d6db518c5af4d5
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Enable the python bindings and switch to the meson build system that handles
the python bindings better than the Makefile build system here.
* gnu/packages/patches/dtc-meson-cell-overflow.patch: New file
* gnu/local.mk (dist_patch_DATA): Add it.
* gnu/packages/bootloaders.scm (dtc): Update to 1.7.0.
[build-system]: Switch to the meson-build-system.
[arguments]: Remove #:make-flags. Add a new 'preparations phase. Do not edit
the Makefile in the 'patch-pkg-config phase. Remove the 'configure phase.
Change-Id: Ie61c920829ab3a8c32f4924c694dba6bda807711
Signed-off-by: Mathieu Othacehe <othacehe@gnu.org>
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* gnu/packages/graphviz.scm (python-uqbar): Update to 0.5.9.
[source]: Add patch for Python 3.10 compatibility.
[arguments]: Remove outdated patch phase.
Change-Id: I81d83efd69bd07fe12790981c48a6e82297908f0
Signed-off-by: Ludovic Courtès <ludo@gnu.org>
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* gnu/packages/statistics.scm (emacs-ess): Update to 18.10.2-1.3691ecc.
[arguments]: Skip failing tests.
* gnu/packages/patches/emacs-ess-fix-obsolete-function-alias.patch: Delete file.
* gnu/local.mk: Apply file removal.
Change-Id: If8cd54c32c44cd2465f2cdb78317e8f8339f6bc3
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* gnu/packages/golang-web.scm: New file.
* gnu/local.mk: Add to gnu/packages/golang-web.scm scope.
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* gnu/packages/emacs-xyz.scm (emacs-haskell-mode): Update to 17.5.
* gnu/packages/patches/emacs-haskell-mode-no-redefine-builtin.patch: Delete
file.
* gnu/local.mk (dist_patch_DATA): Apply file deletion.
Change-Id: Ic7d11737af87995610ecf2c3178320901991423d
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* gnu/packages/machine-learning.scm (python-pytorch-for-r-torch): Update to 2.0.1.
* gnu/packages/patches/python-pytorch2-system-libraries.patch: New file.
* gnu/local.mk (dist_patch_DATA): Add it.
Change-Id: I97551d543e50f6e511aa0529c097d156cf3f96de
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* gnu/packages/machine-learning.scm (onnx-for-torch2): New variable.
* gnu/packages/patches/onnx-1.13.1-use-system-googletest.patch: New file.
* gnu/local.mk (dist_patch_DATA): Add it.
Change-Id: I8a46b9a8096a33bcf949bc4f5d497e22902ab301
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* gnu/packages/machine-learning.scm (xnnpack-for-torch2): New variable.
* gnu/packages/patches/xnnpack-for-torch2-system-libraries.patch: New file.
* gnu/local.mk (dist_patch_DATA): Add it.
Change-Id: I1c35f5fbd064fcc6732b924d7cafaa1a7d03ce04
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* gnu/packages/bittorrent.scm (transmission): Update to 4.0.5.
[source]: Use 'transmission-4.0.5-fix-build.patch'.
* gnu/packages/patches/transmission-4.0.5-fix-build.patch: New file.
* gnu/local.mk (dist_patch_DATA): Add it.
Change-Id: I8e9486dca07f01628e7886e7ac5757d511056cb7
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Removes nano.scm and places the `nano' package within text-editors.scm.
* gnu/local.mk (GNU_SYSTEM_MODULES): Remove nano.scm from build.
* gnu/packages/nano.scm: Delete file.
* gnu/packages/text-editors.scm (nano): New variable.
[copyright header]: Transfer copyright notices from nano.scm to text-editors.scm.
Change-Id: I257f68a3072481f556db208bd1bd34e6eec79b47
Signed-off-by: Mathieu Othacehe <othacehe@gnu.org>
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Remove ed.scm and move the `ed' package to text-editors.scm.
* gnu/local.mk (GNU_SYSTEM_MODULES): Remove ed.scm from build.
* gnu/packages/ed.scm: Delete file.
* gnu/packages/text-editors.scm (ed): New variable.
[copyright header]: Transfer copyright notices from ed.scm to text-editors.scm.
Change-Id: I827a2943f4849085186f2a25a9c8676cf4b6a7fd
Signed-off-by: Mathieu Othacehe <othacehe@gnu.org>
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* gnu/packages/display-managers.scm (slim)[version]: Update to 1.4.0.
[inputs]: Remove input label.
[arguments]: Use gexp and remove fix-0-pointer-comparison.
[home-pages]: Update to slim-fork's url.
* gnu/packages/patches/slim-config.patch: Port to slim-1.4.0.
* gnu/packages/patches/slim-display.patch: Port to slim-1.4.0.
* gnu/packages/patches/slim-reset.patch: Deleted, no ablilty to port this
patch for big change in v1.4.0.
* gnu/packages/patches/slim-session.patch: Deleted. seem to work without this
patch, further observation is needed.
* gnu/packages/patches/slim-sigusr1.patch: Deleted, fixed in upstream.
* gnu/local.mk: Remove slim-reset.patch, slim-session.patch, slim-sigur1.patch.
Signed-off-by: Ludovic Courtès <ludo@gnu.org>
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* gnu/local.mk: Register image.
* gnu/system/images/orangepi-r1-plus-lts-rk3328.scm: New file.
* gnu/system/install.scm (orangepi-r1-plus-lts-rk3328-installation-os):
New variable.
Signed-off-by: Vagrant Cascadian <vagrant@debian.org>
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* gnu/local.mk: De-register patches.
* gnu/packages/bootloaders.scm (u-boot): Update to 2023.10.
[source]: Remove patches.
(u-boot-documentation)[inputs]: Add python-sphinx-prompt.
* gnu/packages/patches/u-boot-allow-disabling-openssl.patch: Refresh.
* gnu/packages/patches/u-boot-fix-build-python-3.10.patch: Delete file.
* gnu/packages/patches/u-boot-fix-u-boot-lib-build.patch: Delete file.
* gnu/packages/patches/u-boot-rk3399-enable-emmc-phy.patch: Delete file.
* gnu/packages/patches/u-boot-rockchip-inno-usb.patch: Refresh.
* gnu/packages/patches/u-boot-sifive-prevent-reloc-initrd-fdt.patch:
Delete file.
Modifed-by: Vagrant Cascadian <vagrant@debian.org>
Signed-off-by: Vagrant Cascadian <vagrant@debian.org>
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Fixes <https://issues.guix.gnu.org/63250>.
Dante uses dlopen which doesn't work with libc.so but libc.so.6.
This fixes socksify, which is patched to skip invoking uname needlessly.
* gnu/packages/networking.scm (dante): Enable preloading support.
* gnu/packages/patches/dante-non-darwin.patch: New file.
* gnu/local.mk (dist_patch_DATA): Add it.
References: https://github.com/NixOS/nixpkgs/pull/68418#discussion_r343625853
Change-Id: I03a5b6b6e11cf6a0453a4968ff00c6dd627249a8
Signed-off-by: Ludovic Courtès <ludo@gnu.org>
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* gnu/packages/php-xyz.scm: New file.
* gnu/local.mk (GNU_SYSTEM_MODULES): Add it.
Signed-off-by: Ludovic Courtès <ludo@gnu.org>
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* gnu/packages/image.scm (freeimage)[source]: Add patches.
* gnu/packages/patches/freeimage-CVE-2020-21428.patch,
gnu/packages/patches/freeimage-CVE-2020-22524.patch: New files.
* gnu/local.mk (dist_patch_DATA): Register them.
Change-Id: Iec114f2295cafbc8b55e81c0d8e4a361fd653152
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* gnu/local.mk (GNU_SYSTEM_MODULES): Register gnu/packages/elixir-xyz.scm.
* Makefile.am (MODULES): Register guix/build-system/mix.scm,
guix/build/mix-build-system.scm.
Change-Id: I69c8fbaa6b16d658d5f6a43d1d39d680dd28ffe9
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* gnu/packages/pascal.scm (fpc)[source]: Add patch.
* gnu/packages/patches/fpc-glibc-2.34-compat.patch: New file.
* gnu/local.mk (dist_patch_DATA): Register it.
Change-Id: I6fde62de63171d7e16754b36db460f4073b1979d
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* gnu/packages/patches/racket-backport-8.10-rktboot.patch: Delete file.
* gnu/packages/patches/racket-backport-8.11-layered-docs.patch: New file.
* gnu/local.mk (dist_patch_DATA): Update accordingly.
* gnu/packages/racket/scm (%racket-origin)[patches]: Likewise.
(%racket-version): Update to 8.11.1.
(%zuo-version): Update to 1.7.
(racket)[inputs]<deinprogramm, draw, drracket, games, gui, htdp>
<parser-tools, plot, rackunit, redex, scribble, slideshow, typed-racket>
<srfi, string-constants, syntax-color, web-server, xrepl>: Update hashes.
<quickscript>: Likewise, and add snippet.
* gnu/packages/chez.scm (chez-scheme-for-racket): Update to
9.9.9-pre-release.18.
Signed-off-by: Ludovic Courtès <ludo@gnu.org>
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* gnu/local.mk (GNU_SYSTEM_MODULES): Add cross-toolchain.scm.
* gnu/packages/cross-toolchain.scm (gcc-cross-avr-toolchain): New variable.
Change-Id: Ie768d5cc0663dd57753af1d4ac631b3cafbf9e8c
Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
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* gnu/packages/game-development.scm (openmw): Update to 0.48.0.
* gnu/packages/graphics.scm (openmw-openscenegraph): Update to commit 68c5c5.
Change-Id: I5e1ae0d59ead8de7976714cb82e8d514c308f19a
Signed-off-by: Ludovic Courtès <ludo@gnu.org>
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* gnu/packages/maths.scm (python-accupy): New variable.
* gnu/packages/patches/python-accupy-fix-use-of-perfplot.patch: New
file.
* gnu/packages/patches/python-accupy-use-matplotx.patch: New file.
* gnu/local.mk (dist_patch_DATA): Add new patch files.
Change-Id: I0222665d54a36830844b3b33e3dcb546741cfaa1
Signed-off-by: Ludovic Courtès <ludo@gnu.org>
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* gnu/packages/admin.scm (igt-gpu-tools): Update to 1.28.
[source]: Remove patch.
[inputs]: Add python.
* gnu/packages/patches/igt-gpu-tools-Use-libproc2.patch: Remove.
* gnu/local.mk (dist_patch_DATA): Remove it.
Change-Id: I5dccd7d5a5df0084fabf713949940775671aecd7
Co-authored-by: Ludovic Courtès <ludo@gnu.org>
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* gnu/packages/patches/zig-use-baseline-cpu-by-default.patch: Add file.
* gnu/packages/zig.scm (zig-0.10.1): Apply patch above.
* gnu/local/mk (dist_patch_DATA): Register it.
Change-Id: I40bd28071c97c0dd0a907c704072b52b26d2de28
Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
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* gnu/packages/graph.scm (igraph): Update to 0.10.7.
[source]: Use git-fetch. Apply patch.
<snippet>: Remove the entire "vendor" and "src/isomorphism/bliss" directories.
Patch CMakeLists.txt to not build and use vendored dependencies.
[arguments]: Add -DIGRAPH_INTEGER_SIZE=64 to #:configure-flags. Add phases to
use unbundled libraries and build documentation.
[native-inputs]: Add bison, docbook-xml-4.3, docbook-xsl, flex, pcg-c, python,
source-highlight and xmlto.
[inputs]: Remove gmp and libxml2. Add bliss and suitesparse-cxsparse.
* gnu/packages/patches/igraph-fix-varargs-integer-size.patch: New file.
* gnu/local.mk (dist_patch_DATA): Register it.
Signed-off-by: Ludovic Courtès <ludo@gnu.org>
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docutils>=0.19 broke the tests, which upstream fixed in a newer
commit. Cherry-pick it.
* gnu/packages/patches/python-sphinx-prompt-docutils-0.19.patch: New file.
* gnu/local.mk (dist_patch_DATA): Register it.
* gnu/packages/sphinx.scm (python-sphinx-prompt)[origin]: Use it.
Change-Id: I597387a35e6a1da01063b4812e0f919788a13b54
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* gnu/packages/patches/plasp-fix-normalization.patch: New file.
* gnu/packages/patches/plasp-include-iostream.patch: New file.
* gnu/local.mk (dist_patch_DATA): Register them here.
* gnu/packages/potassoc.scm (plasp): New variable.
Change-Id: I0d8d64153b180a7d1d8d81888f843458efdf5e51
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* gnu/packages/php.scm (php): Update to 8.2.13.
[source]: Remove patch.
[arguments]: Adjust the 'prepare-tests phase to skip fewer tests.
[inputs]: Replace openssl-1.1 with openssl.
* gnu/packages/patches/php-fix-streams-copy-length.patch: Remove file.
* gnu/local.mk (dist_patch_DATA): Remove it.
Change-Id: I29892deda457fdbaa6dd5e01515e97583951836d
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Change-Id: Ide02272218e76dfae6dc9f8748871c8d61704260
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* gnu/packages/golang.scm (go-gopkg-in-yaml-v3)[source]: Add patch.
* gnu/packages/patches/go-gopkg-in-yaml-v3-32bit.patch: New file.
* gnu/local.mk (dist_patch_DATA): Register it.
Change-Id: Ia8a96b15d37a3d2f133da9374cac1e58e38f2d2c
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* gnu/packages/bittorrent.scm (aria2)[source]: Add snippet to delete
configure script and remove bundled dependency. Add a patch.
[native-inputs]: Add autoconf, automake, gettext-minimal, libtool.
[inputs]: Add wslay.
* gnu/packages/patches/aria2-unbundle-wslay.patch: New file.
* gnu/local.mk (dist_patch_DATA): Register it.
Change-Id: I92390a872454726ff9587518bb535d2105c44ef3
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* gnu/packages/clifm.scm (clifm): New variable
* gnu/local.mk (GNU_SYSTEM_MODULES): Add it.
Co-authored-by: Ludovic Courtès <ludo@gnu.org>
Change-Id: Iba6929365aabdc779d42dcde08e826efc7288664
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* gnu/packages/haskell-xyz.scm (ghc-persistent)[source]: Add patch.
* gnu/packages/patches/ghc-persistent-fix-32bit.patch: New file.
* gnu/local.mk (dist_patch_DATA): Register it.
Change-Id: I1b2c8419f3136d6c9df772d7c7abdc83a80d6112
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