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guix/gnu/packages
History
Nicolas Graves ea99274af3 gnu: cnvkit: Update to 0.9.12. 
* gnu/packages/bioinformatics.scm (cnvkit): Update to 0.9.12.
[build-system]: Switch to pyproject.
[native-inputs]: Add python-setuptools, python-wheel.

Change-Id: Ia48f681ac2c45872c92214d685819579a40eae7a
Signed-off-by: Steve George <steve@futurile.net>
2025-04-16 11:46:31 +02:00
..
aux-files
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patches
gnu: python-bed-reader: Fix build and enable tests.
2025-04-16 11:46:28 +02:00
abduco.scm
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abiword.scm
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accessibility.scm
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acct.scm
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acl.scm
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ada.scm
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admin.scm
gnu: Update references to python3.10 directory.
2025-04-16 11:46:08 +02:00
adns.scm
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agda.scm
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aidc.scm
gnu: zbar: Update to 0.23.93.
2025-04-16 11:46:16 +02:00
algebra.scm
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android.scm
gnu: sdkmanager: Update python-urllib3.
2025-04-16 11:46:14 +02:00
animation.scm
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anthy.scm
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antivirus.scm
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apl.scm
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apparmor.scm
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appimage.scm
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apple.scm
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apr.scm
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arcan.scm
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aspell.scm
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assembly.scm
gnu: asm6f: Update license.
2025-04-14 10:34:51 +09:00
astronomy.scm
gnu: python-astroml: Disable more tests.
2025-04-16 11:46:22 +02:00
attr.scm
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audio.scm
gnu: guitarix: Make compatible with Python 3.11.
2025-04-16 11:46:19 +02:00
augeas.scm
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authentication.scm
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autogen.scm
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autotools.scm
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avahi.scm
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avr-xyz.scm
gnu: microscheme: Use gexps.
2025-04-14 17:27:10 +02:00
avr.scm
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axoloti.scm
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backup.scm
gnu: python-sip: Update to 6.10.0.
2025-04-16 11:46:25 +02:00
barrier.scm
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base.scm
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bash.scm
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batik.scm
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bdw-gc.scm
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benchmark.scm
gnu: python-locust: Update to 2.33.2.
2025-04-16 11:46:24 +02:00
bioconductor.scm
gnu: r-coregx: Disable three tests.
2025-04-16 11:01:12 +02:00
bioinformatics.scm
gnu: cnvkit: Update to 0.9.12.
2025-04-16 11:46:31 +02:00
bison.scm
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bittorrent.scm
gnu: qbittorrent-enhanced: Update to 5.0.4.10.
2025-04-05 08:45:23 +08:00
books.scm
gnu: book-sparc: Update to 4.0.0.
2025-04-06 23:38:49 +03:00
boost.scm
gnu: Add boost-numpy.
2025-04-08 13:24:38 +02:00
bootloaders.scm
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bootstrap.scm
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bqn.scm
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browser-extensions.scm
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build-tools.scm
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busybox.scm
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c2rust.scm
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c.scm
gnu: aws-c-mqtt: Downgrade to 0.12.2.
2025-04-15 23:01:05 +00:00
calcurse.scm
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calendar.scm
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ccache.scm
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cdrom.scm
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cedille.scm
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certs.scm
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check.scm
gnu: python-crosshair: Update to 0.0.84, fix build.
2025-04-16 11:46:22 +02:00
chemistry.scm
gnu: rdkit: Update to 2024.09.6.
2025-04-08 13:24:38 +02:00
chez.scm
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chicken.scm
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chromium.scm
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ci.scm
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cinnamon.scm
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clifm.scm
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clojure.scm
gnu: clojure: Update to 1.12.0.
2025-04-15 12:02:27 +02:00
cluster.scm
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cmake.scm
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cobol.scm
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code.scm
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commencement.scm
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compression.scm
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compton.scm
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configuration-management.scm
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conky.scm
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connman.scm
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containers.scm
gnu: buildah: Update to 1.39.4.
2025-04-07 17:34:44 +02:00
convmv.scm
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cook.scm
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coq.scm
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cpio.scm
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cpp.scm
gnu: Add string-view-lite.
2025-04-16 11:46:26 +02:00
cppi.scm
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cran.scm
gnu: r-quantreg: Move to (gnu packages cran).
2025-04-16 11:01:23 +02:00
crates-apple.scm
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crates-audio.scm
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crates-check.scm
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crates-compression.scm
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crates-crypto.scm
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crates-database.scm
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crates-graphics.scm
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crates-gtk.scm
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crates-io.scm
gnu: Add rust-notify-7.
2025-04-16 11:46:13 +02:00
crates-shell.scm
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crates-tls.scm
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crates-vcs.scm
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crates-web.scm
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crates-windows.scm
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cross-base.scm
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cross-toolchain.scm
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crypto.scm
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cryptsetup.scm
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cups.scm
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curl.scm
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cvassistant.scm
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cybersecurity.scm
gnu: pwntools: Update to 4.4.0.
2025-04-16 11:46:21 +02:00
cyrus-sasl.scm
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darwin.scm
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data-language.scm
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databases.scm
gnu: python-rq-scheduler: Update to 0.14.
2025-04-16 11:46:29 +02:00
datamash.scm
gnu: datamash: Update to 1.9.
2025-04-11 14:32:46 +08:00
datastructures.scm
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dav.scm
gnu: Add cadaver.
2025-04-15 10:47:04 +02:00
dbm.scm
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dc.scm
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debian.scm
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debug.scm
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decker.scm
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dejagnu.scm
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dezyne.scm
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dhall.scm
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dico.scm
gnu: dico: Remove a custom "check" phase.
2025-04-15 20:06:06 +03:00
dictd.scm
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dictionaries.scm
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diffoscope.scm
gnu: diffoscope: Update to 294.
2025-04-12 20:11:26 -07:00
digest.scm
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direct-connect.scm
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disk.scm
gnu: greaseweazle-host-tools: Update to 1.22.
2025-04-14 10:19:52 +02:00
display-managers.scm
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distributed.scm
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django.scm
gnu: python-django-rq: Update to 3.0.0.
2025-04-16 11:46:29 +02:00
djvu.scm
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dlang.scm
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dns.scm
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docbook.scm
gnu: inkscape/stable: Rename variable to inkscape/pinned.
2025-04-11 13:31:58 +01:00
docker.scm
gnu: cqfd: Update to 5.6.0.
2025-04-12 22:58:14 +03:00
documentation.scm
gnu: python-docrepr: Disable tests.
2025-04-16 11:46:23 +02:00
dotnet.scm
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dpdk.scm
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dvtm.scm
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easyrpg.scm
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ebook.scm
gnu: Update references to python3.10 directory.
2025-04-16 11:46:08 +02:00
education.scm
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efi.scm
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electronics.scm
gnu: packages/electronics: Sort variables.
2025-04-15 12:42:09 +01:00
elf.scm
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elixir-xyz.scm
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elixir.scm
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elm.scm
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emacs-xyz.scm
gnu: emacs-denote: Update to 4.0.0.
2025-04-15 23:47:14 -05:00
emacs.scm
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embedded.scm
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emulators.scm
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enchant.scm
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engineering.scm
gnu: python-lcapy: Add missing native-inputs.
2025-04-16 11:46:27 +02:00
enlightenment.scm
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entr.scm
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erlang-xyz.scm
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erlang.scm
gnu: erlang: Update to 27.3.2.
2025-04-08 18:17:19 +08:00
esolangs.scm
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fabric-management.scm
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fcitx5.scm
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fcitx.scm
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fediverse.scm
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figlet.scm
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file-systems.scm
gnu: python-dropbox: Move python-web.
2025-04-16 11:46:30 +02:00
file.scm
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finance.scm
gnu: python-duniterpy: Update to 1.2.1.
2025-04-16 11:46:28 +02:00
firmware.scm
gnu: fwupd: Check polkit actions at correct location
2025-04-15 10:21:01 +02:00
flashing-tools.scm
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flex.scm
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fltk.scm
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fonts.scm
gnu: font-adobe-source-serif-pro: Rename to font-adobe-source-serif.
2025-04-12 22:48:52 +08:00
fontutils.scm
gnu: python-cu2qu: Fix tests.
2025-04-16 11:46:25 +02:00
forth.scm
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fpga.scm
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freedesktop.scm
gnu: libei: Update to 1.4.0.
2025-04-16 11:46:25 +02:00
freeipmi.scm
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fribidi.scm
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fsf.scm
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ftp.scm
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fvwm.scm
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gambas.scm
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game-development.scm
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games.scm
gnu: moonlight-qt: Add wayland support.
2025-04-14 14:54:26 +02:00
gawk.scm
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gcal.scm
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gcc.scm
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gd.scm
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gdb.scm
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genealogy.scm
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genimage.scm
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geo.scm
gnu: Add python-obspy.
2025-04-13 20:54:13 +01:00
gettext.scm
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ghostscript.scm
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gimp.scm
gnu: gimp@3: Wrap GI_TYPELIB_PATH and GUIX_PYTHONPATH.
2025-04-13 14:48:57 +02:00
gkrellm.scm
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gl.scm
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glib.scm
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gnome-xyz.scm
gnu: inkscape/stable: Rename variable to inkscape/pinned.
2025-04-11 13:31:58 +01:00
gnome.scm
gnu: d-feet: Deprecate.
2025-04-16 11:46:13 +02:00
gnu-doc.scm
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gnu-pw-mgr.scm
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gnucash.scm
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gnunet.scm
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gnupg.scm
gnu: python-gpg: Fix build on 32-bit platforms.
2025-04-16 11:46:18 +02:00
gnustep.scm
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gnuzilla.scm
gnu: mozjs-78: Fix build with Python 3.11.
2025-04-16 11:46:11 +02:00
gobby.scm
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golang-build.scm
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golang-check.scm
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golang-compression.scm
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golang-crypto.scm
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golang-maths.scm
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golang-vcs.scm
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golang-web.scm
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golang-xyz.scm
gnu: Add go-github-com-wadey-gocovmerge.
2025-04-08 20:27:32 -04:00
golang.scm
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gperf.scm
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gpodder.scm
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gps.scm
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graph.scm
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graphics.scm
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graphviz.scm
gnu: python-uqbar: Update to 0.7.2.
2025-04-16 11:46:23 +02:00
groff.scm
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groovy.scm
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gsasl.scm
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gstreamer.scm
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gtk.scm
gnu: gtk: Update to 4.16.13.
2025-04-11 13:32:01 +01:00
guile-wm.scm
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guile-xyz.scm
gnu: Add guile-lsp-server.
2025-04-08 11:29:11 +02:00
guile.scm
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gv.scm
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gxmessage.scm
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hardware.scm
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haskell-apps.scm
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haskell-check.scm
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haskell-crypto.scm
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haskell-web.scm
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haskell-xyz.scm
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haskell.scm
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haxe.scm
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heads.scm
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hexedit.scm
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high-availability.scm
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hugs.scm
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hunspell.scm
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hurd.scm
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hyperledger.scm
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i2p.scm
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ibus.scm
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icu4c.scm
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idris.scm
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idutils.scm
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image-processing.scm
gnu: labelme: Add missing native-inputs.
2025-04-16 11:46:26 +02:00
image-viewers.scm
gnu: nsxiv: Update to 33.
2025-04-06 17:25:33 +01:00
image.scm
gnu: mypaint: Make compatible with Python 3.11.
2025-04-16 11:46:19 +02:00
imagemagick.scm
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inferno.scm
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inklingreader.scm
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inkscape.scm
gnu: inkscape/stable: Rename variable to inkscape/pinned.
2025-04-11 13:31:58 +01:00
installers.scm
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instrumentation.scm
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ipfs.scm
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irc.scm
gnu: Update references to python3.10 directory.
2025-04-16 11:46:08 +02:00
irods.scm
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iso-codes.scm
gnu: python-country-converter: Add missing native-input.
2025-04-16 11:46:29 +02:00
jami.scm
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java-bootstrap.scm
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java-compression.scm
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java-graphics.scm
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java-maths.scm
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java-rdf.scm
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java-xml.scm
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java.scm
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javascript.scm
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jemalloc.scm
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jose.scm
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julia-jll.scm
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julia-xyz.scm
gnu: Add julia-simpletropical.
2025-04-11 12:18:02 +02:00
julia.scm
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jupyter.scm
gnu: Remove python-anyio/without-dataclasses.
2025-04-16 11:46:18 +02:00
kawa.scm
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kde-frameworks.scm
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kde-games.scm
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kde-internet.scm
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kde-multimedia.scm
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kde-office.scm
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kde-pim.scm
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kde-plasma.scm
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kde-systemtools.scm
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kde-utils.scm
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kde.scm
gnu: krita: Fix build with xsimd 13.
2025-04-16 13:25:24 +08:00
kerberos.scm
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kodi.scm
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language.scm
gnu: liblouis: Fix library path for python extension.
2025-04-13 18:18:14 +02:00
lc0.scm
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ld-wrapper.in
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lean.scm
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lego.scm
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less.scm
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lesstif.scm
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libbsd.scm
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libcanberra.scm
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libdaemon.scm
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libedit.scm
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libevent.scm
gnu: libuv-for-node-lts: Update to 1.49.2.
2025-04-13 14:19:43 +02:00
libffcall.scm
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libffi.scm
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libftdi.scm
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libidn.scm
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libphidget.scm
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libreoffice.scm
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librewolf.scm
gnu: librewolf: Create lib/icecat so that ICECAT_SYSTEM_DIR is set.
2025-04-11 17:04:10 -07:00
libsigsegv.scm
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libunistring.scm
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libunwind.scm
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libusb.scm
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license.scm
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lighting.scm
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linphone.scm
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linux.scm
gnu: linux-libre 5.4: Update to 5.4.292.
2025-04-15 22:10:56 -04:00
lirc.scm
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lisp-check.scm
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lisp-xyz.scm
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lisp.scm
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llvm-meta.scm
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llvm.scm
gnu: make-llvm: Remove dynamic linker cache phase also with version 15.0.
2025-04-16 11:46:18 +02:00
logging.scm
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logo.scm
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loko.scm
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lout.scm
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lsof.scm
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lua.scm
gnu: luajit: Add riscv64 support.
2025-04-06 17:24:08 +01:00
lxde.scm
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lxqt.scm
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m4.scm
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machine-learning.scm
gnu: python-lap: Update to 0.5.12.
2025-04-16 11:46:30 +02:00
magic-wormhole.scm
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mail.scm
gnu: python-aiosmtpd: Update to 1.4.6.
2025-04-16 11:46:22 +02:00
make-bootstrap.scm
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man.scm
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markup.scm
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marst.scm
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mate.scm
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maths.scm
gnu: veusz: Update to 3.6.2.
2025-04-16 11:46:25 +02:00
matrix.scm
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maven-parent-pom.scm
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maven.scm
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mc.scm
gnu: mc: Update to 4.8.33.
2025-04-14 10:16:43 +02:00
mcrypt.scm
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medical.scm
gnu: openmolar: Fix build.
2025-04-16 11:46:26 +02:00
mercury.scm
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mes.scm
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messaging.scm
gnu: ngircd: Add debug output.
2025-04-14 10:34:51 +09:00
microcom.scm
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minetest.scm
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mingw.scm
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moe.scm
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mold.scm
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monitoring.scm
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moreutils.scm
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motti.scm
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mp3.scm
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mpd.scm
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mpi.scm
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mtools.scm
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multiprecision.scm
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music.scm
gnu: abjad-ext-rmakers: Adjust inputs.
2025-04-16 11:46:23 +02:00
musl.scm
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myrddin.scm
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ncdu.scm
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ncurses.scm
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netpbm.scm
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nettle.scm
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networking.scm
gnu: blueman: Use G-expressions.
2025-04-16 11:46:19 +02:00
nfs.scm
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nickle.scm
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nicotine.scm
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nim.scm
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ninja.scm
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node-xyz.scm
gnu: node-serialport-bindings: Fix build.
2025-04-13 14:19:43 +02:00
node.scm
gnu: node-lts: Skip test-debugger-heap-profiler on 32bit systems.
2025-04-13 14:19:43 +02:00
notcurses.scm
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noweb.scm
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nss.scm
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ntp.scm
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nushell.scm
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nutrition.scm
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nvi.scm
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nx.scm
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ocaml.scm
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ocr.scm
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onc-rpc.scm
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openbox.scm
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opencl.scm
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opencog.scm
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openkinect.scm
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openldap.scm
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openpgp.scm
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openstack.scm
gnu: Standardize python-oslo.* package names.
2025-04-16 11:46:21 +02:00
orange.scm
gnu: python-orange-canvas-core: Fix tests.
2025-04-16 11:46:30 +02:00
orpheus.scm
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ots.scm
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package-management.scm
gnu: conan: Update to 2.7.1.
2025-04-16 11:46:25 +02:00
pantheon.scm
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parallel.scm
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pascal.scm
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password-utils.scm
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patchutils.scm
gnu: meld: Update to 3.23.0.
2025-04-06 17:35:42 +01:00
patool.scm
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pciutils.scm
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pcre.scm
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pdf.scm
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pem.scm
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pep.scm
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perl6.scm
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perl-check.scm
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perl-compression.scm
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perl-maths.scm
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perl-web.scm
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perl.scm
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phabricator.scm
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photo.scm
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php-xyz.scm
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php.scm
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piet.scm
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pikchr.scm
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pkg-config.scm
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plan9.scm
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plotutils.scm
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poedit.scm
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polkit.scm
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popt.scm
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potassco.scm
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power.scm
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presentation.scm
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pretty-print.scm
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printers.scm
gnu: Add ptouch-print.
2025-04-15 10:21:01 +02:00
profiling.scm
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prolog.scm
gnu: trealla: Update to 2.68.11.
2025-04-12 11:20:00 -05:00
prometheus.scm
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protobuf.scm
gnu: python-protobuf: Update to 3.20.3.
2025-04-16 11:46:12 +02:00
pth.scm
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pulseaudio.scm
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pumpio.scm
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pure.scm
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purescript.scm
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pv.scm
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pypy.scm
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python-build.scm
gnu: Add python-poetry-core-next.
2025-04-16 11:46:28 +02:00
python-check.scm
gnu: Remove python-parameterizedtestcase.
2025-04-16 11:46:24 +02:00
python-compression.scm
gnu: Add python-unix-ar.
2025-04-16 11:46:21 +02:00
python-crypto.scm
gnu: python-pgpy: Fix tests.
2025-04-16 11:46:28 +02:00
python-graphics.scm
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python-science.scm
gnu: python-vaex-core: Update to 4.17.1.
2025-04-16 11:46:27 +02:00
python-web.scm
gnu: python-sanic: Update to 25.3.0.
2025-04-16 11:46:30 +02:00
python-xyz.scm
gnu: python-flufl-i18n: Update to 5.1.0.
2025-04-16 11:46:31 +02:00
python.scm
gnu: python-debug: Use G-Expressions.
2025-04-16 11:46:15 +02:00
qt.scm
gnu: python-sip: Update to 6.10.0.
2025-04-16 11:46:25 +02:00
quantum.scm
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racket.scm
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radio.scm
gnu: Remove python-pep8.
2025-04-16 11:46:15 +02:00
ragel.scm
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rails.scm
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raspberry-pi.scm
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ratpoison.scm
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rcm.scm
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rdesktop.scm
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rdf.scm
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re2c.scm
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readline.scm
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rednotebook.scm
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regex.scm
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robotics.scm
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rocm.scm
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rpc.scm
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rpm.scm
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rrdtool.scm
…
rsync.scm
…
ruby.scm
…
rush.scm
…
rust-apps.scm
gnu: speakersafetyd: Update to 1.1.2.
2025-04-14 13:47:56 +09:00
rust.scm
…
sagemath.scm
…
samba.scm
gnu: samba/pinned: Update to 4.18.1.
2025-04-11 12:42:47 +01:00
sawfish.scm
…
scanner.scm
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scheme.scm
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screen.scm
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scribus.scm
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scsi.scm
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sdl.scm
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search.scm
…
security-token.scm
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selinux.scm
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sequoia.scm
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serialization.scm
…
serveez.scm
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shells.scm
…
shellutils.scm
gnu: trash-cli: Update to 0.24.5.26.
2025-04-07 19:33:34 +01:00
simh.scm
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simulation.scm
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skarnet.scm
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skribilo.scm
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slang.scm
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smalltalk.scm
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sml.scm
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solidity.scm
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sourcehut.scm
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specifications.scm
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speech.scm
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sphinx.scm
gnu: python-sphinx: Skip one more test.
2025-04-16 11:46:08 +02:00
spice.scm
…
spreadsheet.scm
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sqlite.scm
…
squirrel.scm
…
ssh.scm
gnu: openssh: Update to 10.0p1
2025-04-15 10:21:01 +02:00
sssd.scm
gnu: sssd: Update to 2.9.6.
2025-04-14 15:13:10 -07:00
statistics.scm
gnu: python-pymc: Update to 5.21.0.
2025-04-16 11:46:30 +02:00
stb.scm
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stenography.scm
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storage.scm
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suckless.scm
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sugar.scm
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swig.scm
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sycl.scm
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sync.scm
gnu: onedrive: Update to 2.5.3-1
2025-04-15 10:21:01 +02:00
syncthing.scm
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syndication.scm
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synergy.scm
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task-management.scm
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task-runners.scm
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tbb.scm
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tcl.scm
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telegram.scm
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telephony.scm
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terminals.scm
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terraform.scm
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tex.scm
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texinfo.scm
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texlive.scm
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text-editors.scm
gnu: nano: Fix cross-compiling.
2025-04-08 22:28:24 +08:00
textutils.scm
…
time.scm
…
tls.scm
gnu: aws-lc: Downgrade to 1.48.5.
2025-04-15 22:55:18 +00:00
tmux.scm
…
toolkits.scm
…
tor-browsers.scm
…
tor.scm
…
toys.scm
…
tree-sitter.scm
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tryton.scm
gnu: python-proteus: Update to 7.4.1.
2025-04-16 11:46:10 +02:00
tv.scm
…
uglifyjs.scm
…
uml.scm
…
unicode.scm
…
unrtf.scm
…
upnp.scm
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usb-modeswitch.scm
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uucp.scm
…
valgrind.scm
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version-control.scm
gnu: gita: Improve package style.
2025-04-16 11:46:20 +02:00
video.scm
gnu: streamlink: Update to 7.1.2.
2025-04-16 11:46:11 +02:00
vim.scm
…
virtualization.scm
gnu: ganeti: Use python-bitarray-2.
2025-04-14 10:19:50 +02:00
vlang.scm
…
vnc.scm
gnu: wayvnc: Update to 0.9.1.
2025-04-15 23:25:30 +02:00
vpn.scm
…
vulkan.scm
…
w3m.scm
…
wdiff.scm
…
weather.scm
gnu: Add meteo-qt.
2025-04-14 14:59:50 +02:00
web-browsers.scm
gnu: qutebrowser: Update to 3.4.0.
2025-04-14 10:40:06 +02:00
web.scm
gnu: Remove python-rednose.
2025-04-16 11:46:14 +02:00
webkit.scm
gnu: webkitgtk: Update to 2.48.1.
2025-04-11 13:32:01 +01:00
wget.scm
…
wine.scm
…
wireservice.scm
…
wm.scm
gnu: Add sbcl-stumpwm-tomato.
2025-04-14 14:02:27 +02:00
wordnet.scm
…
wv.scm
…
wxwidgets.scm
…
xdisorg.scm
gnu: Remove duplicated package show-me-the-key.
2025-04-11 12:18:02 +02:00
xfce.scm
gnu: inkscape/stable: Rename variable to inkscape/pinned.
2025-04-11 13:31:58 +01:00
xfig.scm
…
xiph.scm
…
xml.scm
…
xnee.scm
…
xorg.scm
gnu: inkscape/stable: Rename variable to inkscape/pinned.
2025-04-11 13:31:58 +01:00
zig-xyz.scm
…
zig.scm
gnu: zig-0.14: Set max_rss to unlimited.
2025-04-05 08:45:23 +08:00
zile.scm
…
zwave.scm
…