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Author SHA1 Message Date
Ludovic Courtès
fbea62f829
gnu: emacs-gerbil-mode: Move to scheme.scm. 
This fixes a bug due to a top-level circular reference:

  $ guix show scheme48
  [...]
  ice-9/boot-9.scm:1685:16: In procedure raise-exception:
  error: gerbil: unbound variable

* gnu/packages/emacs-xyz.scm (emacs-gerbil-mode): Move to...
* gnu/packages/scheme.scm (emacs-gerbil-mode): ... here.
 2023-05-10 00:23:53 +02:00
Ludovic Courtès
1be5bf5604
tests: docker-system: Add missing import. 
This is a followup to f518882725.

* gnu/tests/docker.scm (run-docker-system-test)["load system image and
run it"]: Use (guix build utils).
 2023-05-10 00:23:52 +02:00
Ludovic Courtès
6a33f674b9
system: Fix reference to Hurd bug in comment. 
* gnu/system.scm (hurd-multiboot-modules): Fix bug reference in
comment.
 2023-05-10 00:23:52 +02:00
Mark H Weaver
7f89eee664
gnu: icecat: Update to 102.11.0-guix0-preview1 [security fixes]. 
Includes fixes for CVE-2023-32205, CVE-2023-32206, CVE-2023-32207,
CVE-2023-32211, CVE-2023-32212, CVE-2023-32213, CVE-2023-32214, and
CVE-2023-32215.

* gnu/packages/gnuzilla.scm (%icecat-base-version, %icecat-build-id): Update.
(icecat-source): Update gnuzilla commit, base version, and hashes.
 2023-05-09 14:45:39 -04:00
Liliana Marie Prikler
5b58608f56
gnu: Add python-clinguin. 
* gnu/packages/potassco.scm (python-clinguin): New variable.
 2023-05-09 19:54:27 +02:00
Ricardo Wurmus
a9bd722d67
gnu: python-fastapi: Do not delete tests, and add orjson. 
* gnu/packages/python-web.scm (python-fastapi)[arguments]: Remove all custom
phases; ignore two test files.
[propagated-inputs]: Add python-orjson.
 2023-05-09 19:54:27 +02:00
Liliana Marie Prikler
0f7d8a8305
gnu: Add python-fastapi. 
* gnu/packages/python-web.scm (python-fastapi): New variable.
 2023-05-09 19:43:44 +02:00
Liliana Marie Prikler
dd3ee6073e
gnu: python-databases: Revise description. 
* gnu/packages/databases.scm (python-databases)[synopsis]: Spell out
“Asynchronous”.
[description]: Mention that it's a wrapper around other libraries using
SQLAlchemy.
 2023-05-09 19:43:44 +02:00
Liliana Marie Prikler
8f01f084d3
gnu: python-databases: Update to 0.7.0. 
* gnu/packages/databases.scm (python-databases): Update to 0.7.0.
 2023-05-09 19:43:44 +02:00
Liliana Marie Prikler
966fd0bfdc
gnu: python-aiosqlite: Update to 0.18.0. 
* gnu/packages/databases.scm (python-aiosqlite): Update to 0.18.0.
[source]: Use git-fetch and git-reference.
[build-system]: Use pyproject-build-system.
[arguments]: Adjust accordingly.
[propagated-inputs]: Remove.
[native-inputs]: Remove python-aiounittest.
Add python-flit-core, python-coverage and python-mypy.
 2023-05-09 19:43:44 +02:00
Liliana Marie Prikler
3cc9e00473
gnu: python-aiomysql: Update to 0.1.1. 
* gnu/packages/databases.scm (python-aiomysql): Update to 0.1.1.
[build-system]: Change to pyproject-build-system.
 2023-05-09 19:43:43 +02:00
Liliana Marie Prikler
8d62db6b54
gnu: python-pymysql: Update to 1.0.2. 
* gnu/packages/databases.scm (python-pymysql): Update to 1.0.2.
 2023-05-09 19:43:43 +02:00
Ricardo Wurmus
b09e87be26
gnu: python-sqlalchemy: Use pyproject-build-system. 
* gnu/packages/databases.scm (python-sqlalchemy)[arguments]: Replace custom
'check phase with #:test-flags.
[build-system]: Use pyproject-build-system.
 2023-05-09 19:43:43 +02:00
Liliana Marie Prikler
98e943435f
gnu: python-sqlalchemy: Update to 1.4.42. 
* gnu/packages/databases.scm (python-sqlalchemy): Update to 1.4.42.
 2023-05-09 19:20:18 +02:00
Liliana Marie Prikler
851199ef57
gnu: python-starlette: Update to 0.25.0. 
* gnu/packages/python-web.scm (python-starlette): Update to 0.25.0.
[source]: Switch to git-fetch and git-reference.
[build-system]: Use pyproject-build-system.
[native-inputs]: Add python-hatchling, python-httpx, python-pytest, and
python-typing-extensions-next.
 2023-05-09 19:20:18 +02:00
Christopher Baines
a759cbffaf
services: guix-build-coordinator: Support extra environment vars. 
I'm looking at this because I need to do some debugging of Guile's GC, and
there are some useful environment variables for that, but it should be
generally useful.

* gnu/services/guix.scm (guix-build-coordinator-configuration-extra-environment-variables):
New procedure.
(guix-build-coordinator-shepherd-services): Pass the environment variables to
the shepherd.
* doc/guix.texi (Guix Services): Document it.
 2023-05-09 16:19:21 +01:00
Efraim Flashner
c1ffe2f21b
service: qemu-binfmt: Remove broken qemu targets. 
* gnu/services.virtualization.scm (%qemu-platforms): Remove %i486,
%aarch64be.
 2023-05-09 17:27:49 +03:00
Efraim Flashner
3f00f46ada
Revert "gnu: rust-bootstrap: Remove aarch64 as a supported architecture." 
This reverts commit c56d57110d.

rust-bootstrap *IS* supported on aarch64-linux, and the build farm will
catch up eventually.
 2023-05-09 16:54:29 +03:00
Ricardo Wurmus
7e421c1f5a
gnu: r-scran: Update to 1.28.1. 
* gnu/packages/bioconductor.scm (r-scran): Update to 1.28.1.
 2023-05-09 15:24:15 +02:00
Ricardo Wurmus
0880f325b7
gnu: r-scuttle: Update to 1.10.1. 
* gnu/packages/bioconductor.scm (r-scuttle): Update to 1.10.1.
 2023-05-09 15:24:15 +02:00
Ricardo Wurmus
8c7ddd3a44
gnu: r-chromvar: Update to 1.22.1. 
* gnu/packages/bioconductor.scm (r-chromvar): Update to 1.22.1.
 2023-05-09 15:24:15 +02:00
Ricardo Wurmus
d850b72346
gnu: r-hdf5array: Update to 1.28.1. 
* gnu/packages/bioconductor.scm (r-hdf5array): Update to 1.28.1.
[propagated-inputs]: Add r-s4arrays.
 2023-05-09 15:24:15 +02:00
Ricardo Wurmus
3bdd6fb256
gnu: r-s4vectors: Update to 0.38.1. 
* gnu/packages/bioconductor.scm (r-s4vectors): Update to 0.38.1.
 2023-05-09 15:24:15 +02:00
Ricardo Wurmus
da8638facb
gnu: r-preprocesscore: Update to 1.62.1. 
* gnu/packages/bioconductor.scm (r-preprocesscore): Update to 1.62.1.
 2023-05-09 15:24:15 +02:00
Ricardo Wurmus
6b2a0aab19
gnu: r-iclusterplus: Update to 1.36.1. 
* gnu/packages/bioconductor.scm (r-iclusterplus): Update to 1.36.1.
 2023-05-09 15:24:15 +02:00
Ricardo Wurmus
c96ebf4cf9
gnu: r-clusterprofiler: Update to 4.8.1. 
* gnu/packages/bioconductor.scm (r-clusterprofiler): Update to 4.8.1.
 2023-05-09 15:24:15 +02:00
Ricardo Wurmus
f7642f34d0
gnu: r-dose: Update to 3.26.1. 
* gnu/packages/bioconductor.scm (r-dose): Update to 3.26.1.
 2023-05-09 15:24:15 +02:00
Ricardo Wurmus
4228100215
gnu: r-linnorm: Update to 2.24.1. 
* gnu/packages/bioconductor.scm (r-linnorm): Update to 2.24.1.
 2023-05-09 15:24:15 +02:00
Ricardo Wurmus
c6c69d4cc6
gnu: r-dnacopy: Update to 1.74.1. 
* gnu/packages/bioconductor.scm (r-dnacopy): Update to 1.74.1.
 2023-05-09 15:24:15 +02:00
Ricardo Wurmus
c846a694a7
gnu: r-scaledmatrix: Update to 1.8.1. 
* gnu/packages/bioconductor.scm (r-scaledmatrix): Update to 1.8.1.
 2023-05-09 15:24:15 +02:00
Ricardo Wurmus
95d5a918a2
gnu: r-glmgampoi: Update to 1.12.1. 
* gnu/packages/bioconductor.scm (r-glmgampoi): Update to 1.12.1.
 2023-05-09 15:24:15 +02:00
Ricardo Wurmus
75869a8a94
gnu: r-oligo: Update to 1.64.1. 
* gnu/packages/bioconductor.scm (r-oligo): Update to 1.64.1.
 2023-05-09 15:24:15 +02:00
Ricardo Wurmus
a4b04c06ab
gnu: r-summarizedexperiment: Update to 1.30.1. 
* gnu/packages/bioconductor.scm (r-summarizedexperiment): Update to 1.30.1.
[propagated-inputs]: Add r-s4arrays.
 2023-05-09 15:24:15 +02:00
Ricardo Wurmus
c70787f552
gnu: r-scmap: Update to 1.22.1. 
* gnu/packages/bioconductor.scm (r-scmap): Update to 1.22.1.
 2023-05-09 15:24:15 +02:00
Ricardo Wurmus
0fd93c81be
gnu: r-rhdf5filters: Update to 1.12.1. 
* gnu/packages/bioconductor.scm (r-rhdf5filters): Update to 1.12.1.
 2023-05-09 15:24:15 +02:00
Ricardo Wurmus
4b7a06b839
gnu: r-pcaexplorer: Update to 2.26.1. 
* gnu/packages/bioconductor.scm (r-pcaexplorer): Update to 2.26.1.
 2023-05-09 15:24:15 +02:00
Ricardo Wurmus
37f44c278f
gnu: r-impute: Update to 1.74.1. 
* gnu/packages/bioconductor.scm (r-impute): Update to 1.74.1.
 2023-05-09 15:24:14 +02:00
Ricardo Wurmus
ef3ce37eeb
gnu: r-genefilter: Update to 1.82.1. 
* gnu/packages/bioconductor.scm (r-genefilter): Update to 1.82.1.
 2023-05-09 15:24:14 +02:00
Ricardo Wurmus
56524dc465
gnu: r-edger: Update to 3.42.2. 
* gnu/packages/bioconductor.scm (r-edger): Update to 3.42.2.
 2023-05-09 15:24:14 +02:00
Ricardo Wurmus
d9d920403a
gnu: r-deseq2: Update to 1.40.1. 
* gnu/packages/bioconductor.scm (r-deseq2): Update to 1.40.1.
 2023-05-09 15:24:14 +02:00
Ricardo Wurmus
7a9e68f103
gnu: r-biocparallel: Update to 1.34.1. 
* gnu/packages/bioconductor.scm (r-biocparallel): Update to 1.34.1.
 2023-05-09 15:24:14 +02:00
Ricardo Wurmus
69e954bb0a
gnu: r-annotationdbi: Update to 1.62.1. 
* gnu/packages/bioconductor.scm (r-annotationdbi): Update to 1.62.1.
 2023-05-09 15:24:14 +02:00
Ricardo Wurmus
931ac0735f
gnu: r-densvis: Update to 1.10.1. 
* gnu/packages/bioconductor.scm (r-densvis): Update to 1.10.1.
 2023-05-09 15:24:14 +02:00
Ricardo Wurmus
06b903963c
gnu: r-delayedarray: Update to 0.26.2. 
* gnu/packages/bioconductor.scm (r-delayedarray): Update to 0.26.2.
[propagated-inputs]: Add r-s4arrays.
 2023-05-09 15:24:14 +02:00
Ricardo Wurmus
01faf51999
gnu: r-bandits: Update to 1.16.1. 
* gnu/packages/bioconductor.scm (r-bandits): Update to 1.16.1.
 2023-05-09 15:24:14 +02:00
Ricardo Wurmus
13dde61328
gnu: r-bambu: Update to 3.2.2. 
* gnu/packages/bioconductor.scm (r-bambu): Update to 3.2.2.
 2023-05-09 15:24:14 +02:00
Ricardo Wurmus
6401f048cf
gnu: r-amplican: Update to 1.22.1. 
* gnu/packages/bioconductor.scm (r-amplican): Update to 1.22.1.
[propagated-inputs]: Remove r-clustercrit; add r-cluster.
 2023-05-09 15:24:14 +02:00
Ricardo Wurmus
0861bca905
gnu: r-affyplm: Update to 1.76.1. 
* gnu/packages/bioconductor.scm (r-affyplm): Update to 1.76.1.
 2023-05-09 15:24:14 +02:00
Ricardo Wurmus
7a58dc01d3
gnu: Add r-s4arrays. 
* gnu/packages/bioconductor.scm (r-s4arrays): New variable.
 2023-05-09 15:24:14 +02:00
Ricardo Wurmus
e2c47544a5
gnu: r-deoptimr: Update to 1.0-13. 
* gnu/packages/statistics.scm (r-deoptimr): Update to 1.0-13.
 2023-05-09 15:24:14 +02:00