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Author SHA1 Message Date
Tobias Geerinckx-Rice
beb37ea4ad
system: Use privileged-program-service-type by default. 
* gnu/system.scm (operating-system-default-essential-services)
(hurd-default-essential-services): Substitute
privileged-program-service-type for setuid-program-service-type.
 2024-08-11 02:00:00 +02:00
Tobias Geerinckx-Rice
d73ca7ecb6
services: Rename setuid-program-service-type. 
* gnu/services.scm (setuid-program->activation-gexp): Rename this…
(privileged-program->activation-gexp): …to this.
Operate on a list of <privileged-program> records.
(privileged-program-service-type): New variable, renamed from
setuid-program-service-type.  Rename the service-type accordingly.
(setuid-program-service-type): Redefine as an alias for the above.
 2024-08-11 02:00:00 +02:00
Tobias Geerinckx-Rice
f3b84be52d
build: Rename activate-setuid-programs. 
* gnu/build/activation.scm (activate-setuid-programs): Rename this…
(activate-privileged-programs): …to this.
Operate on a list of <privileged-program> records.
* gnu/services.scm (setuid-program->activation-gexp): Adjust caller.
 2024-08-11 02:00:00 +02:00
Tobias Geerinckx-Rice
9099f8bdcc
system: (gnu system setuid) wraps (gnu system privilege). 
* gnu/system/setuid.scm (setuid-program): Rewrite as syntax to create a
<privileged-program> record that is setuid by default.
(setuid-program?, setuid-program-program, setuid-program-setuid?)
(setuid-program-setgid?, setuid-program-user, setuid-program-group):
Alias their privileged-program equivalent.
 2024-08-11 02:00:00 +02:00
Tobias Geerinckx-Rice
39471f2627
system: Add (gnu system privilege). 
* gnu/system/privilege.scm: New file.
* gnu/local.mk (GNU_SYSTEM_MODULES): Add it.
 2024-08-11 02:00:00 +02:00
Tobias Geerinckx-Rice
902b15b24d
gnu: Replace (almost) all uses of /run/setuid-programs. 
…those good for master, anyway.

* gnu/packages/admin.scm (ktsuss, opendoas, hosts)
[arguments]: Replace /run/setuid-programs with /run/privileged/bin.
* gnu/packages/containers.scm (slirp4netns)[arguments]: Likewise.
* gnu/packages/debian.scm (pbuilder)[arguments]: Likewise.
* gnu/packages/disk.scm (udevil)[arguments]: Likewise.
* gnu/packages/enlightenment.scm (efl, enlightenment)
[arguments]: Likewise.
* gnu/packages/gnome.scm (gdm, gnome-control-center)
[arguments]: Likewise.
* gnu/packages/linux.scm (singularity)[arguments]: Likewise.
* gnu/packages/lxde.scm (spacefm)[arguments]: Likewise.
* gnu/packages/monitoring.scm (zabbix-agentd)[arguments]: Likewise.
* gnu/packages/virtualization.scm (ganeti)[arguments]: Likewise.
* gnu/packages/xdisorg.scm (xsecurelock)[arguments]: Likewise.
* gnu/services/dbus.scm (dbus-configuration-directory): Likewise.
* gnu/services/ganeti.scm (%default-ganeti-environment-variables):
Likewise.
* gnu/services/monitoring.scm (zabbix-agent-shepherd-service): Likewise.
* gnu/tests/ldap.scm (marionette): Likewise.
* gnu/tests/monitoring.scm (os): Likewise.
 2024-08-11 02:00:00 +02:00
Tobias Geerinckx-Rice
e364d1a494
system: Use /run/privileged/bin in search paths. 
* gnu/system.scm (operating-system-etc-service):
Substitute /run/privileged/bin for deprecated /run/setuid-programs.
 2024-08-11 02:00:00 +02:00
Tobias Geerinckx-Rice
d6c9754c56
services: setuid-program: Populate /run/privileged/bin. 
Create /run/setuid-programs compatibility symlinks so that we can
migrate all users (both package and human) piecemeal at our leisure.

Apart from being symlinks, this should be a user-invisible change.

* gnu/build/activation.scm (%privileged-program-directory): New variable.
[activate-setuid-programs]: Put privileged copies in
%PRIVILEGED-PROGRAM-DIRECTORY, with compatibility symlinks to each in
%SETUID-DIRECTORY.
* gnu/services.scm (setuid-program-service-type): Update docstring.
* doc/guix.texi (Setuid Programs): Update @file{} name accordingly.
 2024-08-11 02:00:00 +02:00
Tobias Geerinckx-Rice
0dffb851e0
system: Disallow file-like setuid-programs. 
It has been a warning for well over a year now.  Now, with
privileged-programs coming, don't let's support nested deprecation
hacks.

* gnu/system.scm (<operating-system>):
Don't ‘sanitize’ the setuid-programs field.
(ensure-setuid-program-list): Delete syntax.
(%ensure-setuid-program-list): Delete variable.
 2024-08-11 02:00:00 +02:00
Andrew Tropin
6c045f2c9e
gnu: kmonad: Update to 0.4.2-1.07cd1cb. 
* gnu/packages/haskell-apps.scm (kmonad): Update to 0.4.2-1.07cd1cb.

Change-Id: I8a8d36577804d2221b39b430d26e9fd17204c0de
 2024-08-18 08:36:35 +04:00
Ricardo Wurmus
41c44ffd56
gnu: r-dmrseq: Update to 1.24.1. 
* gnu/packages/bioconductor.scm (r-dmrseq): Update to 1.24.1.

Change-Id: I22fb49eee056e0dd5306fec4575fcb38cbe916aa
 2024-08-17 21:54:22 +02:00
Ricardo Wurmus
8bb976d4d6
gnu: r-bgeecall: Update to 1.20.1. 
* gnu/packages/bioconductor.scm (r-bgeecall): Update to 1.20.1.
[propagated-inputs]: Add r-txdbmaker.

Change-Id: Ia51c1ccdb0e49d8dc74a61f605f00c86718bc1f8
 2024-08-17 21:54:22 +02:00
Ricardo Wurmus
2e65b4811e
gnu: r-mscoreutils: Update to 1.16.1. 
* gnu/packages/bioconductor.scm (r-mscoreutils): Update to 1.16.1.

Change-Id: I233a01625f223c571dae863c977825d4a2909ee7
 2024-08-17 21:54:22 +02:00
Ricardo Wurmus
775ba94a50
gnu: r-scater: Update to 1.32.1. 
* gnu/packages/bioconductor.scm (r-scater): Update to 1.32.1.

Change-Id: I0232d463f243505a9b3706d64e6666eb245ceb1c
 2024-08-17 21:54:22 +02:00
Ricardo Wurmus
aa08111f38
gnu: r-hdf5array: Update to 1.32.1. 
* gnu/packages/bioconductor.scm (r-hdf5array): Update to 1.32.1.

Change-Id: Iebab45185f6f1fe3e6919a1e70e45127d9f1124f
 2024-08-17 21:54:22 +02:00
Ricardo Wurmus
7e83109d92
gnu: r-s4vectors: Update to 0.42.1. 
* gnu/packages/bioconductor.scm (r-s4vectors): Update to 0.42.1.

Change-Id: I58dc50344c5eb477da9d4ddd4447bcb41f456037
 2024-08-17 21:54:22 +02:00
Ricardo Wurmus
1d475e94d4
gnu: r-multiassayexperiment: Update to 1.30.3. 
* gnu/packages/bioconductor.scm (r-multiassayexperiment): Update to 1.30.3.

Change-Id: Iabbd0c74d7515f8f166827b8b99b2ac49b271c13
 2024-08-17 21:54:21 +02:00
Ricardo Wurmus
2a88a148fc
gnu: r-universalmotif: Update to 1.22.1. 
* gnu/packages/bioconductor.scm (r-universalmotif): Update to 1.22.1.

Change-Id: I60a617d120e5da046decb491b7641f1e10aac0cb
 2024-08-17 21:54:21 +02:00
Ricardo Wurmus
32a3206b4b
gnu: r-clusterprofiler: Update to 4.12.2. 
* gnu/packages/bioconductor.scm (r-clusterprofiler): Update to 4.12.2.

Change-Id: I17d837fb314c26fcb26c13240a01c91bc2da9797
 2024-08-17 21:54:21 +02:00
Ricardo Wurmus
91a56bc013
gnu: r-enrichplot: Update to 1.24.2. 
* gnu/packages/bioconductor.scm (r-enrichplot): Update to 1.24.2.

Change-Id: I188e7e908a09337d4bacf4802b1557ddd31048f3
 2024-08-17 21:54:21 +02:00
Ricardo Wurmus
ad1acb8114
gnu: r-dose: Update to 3.30.2. 
* gnu/packages/bioconductor.scm (r-dose): Update to 3.30.2.

Change-Id: Ic07fab82efcbda004d6c7ff21d4ed7b49cc426fb
 2024-08-17 21:54:21 +02:00
Ricardo Wurmus
7079d13d04
gnu: r-chippeakanno: Update to 3.38.1. 
* gnu/packages/bioconductor.scm (r-chippeakanno): Update to 3.38.1.

Change-Id: Ia4c89074674f3473e11f3b9e1f9ed828701591f6
 2024-08-17 21:54:21 +02:00
Ricardo Wurmus
efb25a259a
gnu: r-qfeatures: Update to 1.14.2. 
* gnu/packages/bioconductor.scm (r-qfeatures): Update to 1.14.2.

Change-Id: I93c4fc00d19b18a1e0981f21dd0950d1e1a81f37
 2024-08-17 21:54:21 +02:00
Ricardo Wurmus
20134ae2e4
gnu: r-seqarray: Update to 1.44.1. 
* gnu/packages/bioconductor.scm (r-seqarray): Update to 1.44.1.

Change-Id: I06bb0b45d1a4299e835f7a18c7ed70d847bdb565
 2024-08-17 21:54:21 +02:00
Ricardo Wurmus
f74e27f072
gnu: r-msa: Update to 1.36.1. 
* gnu/packages/bioconductor.scm (r-msa): Update to 1.36.1.

Change-Id: I91665d8ff4cd7570b5bcad27ff132611a09b8ecc
 2024-08-17 21:54:21 +02:00
Ricardo Wurmus
2a1a1738dd
gnu: r-limma: Update to 3.60.4. 
* gnu/packages/bioconductor.scm (r-limma): Update to 3.60.4.

Change-Id: Iaaf9317ab3921070f5b8e06a7948b42575bbe00b
 2024-08-17 21:54:21 +02:00
Ricardo Wurmus
0e0b349f6b
gnu: r-raggedexperiment: Update to 1.28.1. 
* gnu/packages/bioconductor.scm (r-raggedexperiment): Update to 1.28.1.

Change-Id: If7e8b60435413acda999f055bf9f104929e7f50f
 2024-08-17 21:54:21 +02:00
Ricardo Wurmus
43b84eeb84
gnu: r-edger: Update to 4.2.1. 
* gnu/packages/bioconductor.scm (r-edger): Update to 4.2.1.

Change-Id: Ia8cb57ada3f036f7fe45972ad1d3a8ff2e53c27b
 2024-08-17 21:54:21 +02:00
Ricardo Wurmus
e00e778eee
gnu: r-iranges: Update to 2.38.1. 
* gnu/packages/bioconductor.scm (r-iranges): Update to 2.38.1.

Change-Id: I95d34fb3f339590c1980b7a77093835baa0e0136
 2024-08-17 21:54:21 +02:00
Ricardo Wurmus
defb0e7676
gnu: r-dmrcate: Update to 3.0.5. 
* gnu/packages/bioconductor.scm (r-dmrcate): Update to 3.0.5.

Change-Id: I88768682f65b821e188f29c4dfee94927040cbbd
 2024-08-17 21:54:21 +02:00
Ricardo Wurmus
2dff160f09
gnu: r-degreport: Update to 1.40.1. 
* gnu/packages/bioconductor.scm (r-degreport): Update to 1.40.1.

Change-Id: I35e7284270c81cd10178e7d848dfa5872645405d
 2024-08-17 21:54:21 +02:00
Ricardo Wurmus
8d988b6bea
gnu: r-anvil: Update to 1.16.1. 
* gnu/packages/bioconductor.scm (r-anvil): Update to 1.16.1.

Change-Id: Ief1b321d44a3bd534c6107c4434957c0de2dd977
 2024-08-17 21:54:21 +02:00
Ricardo Wurmus
ef08d1330d
gnu: r-desctools: Update to 0.99.55. 
* gnu/packages/statistics.scm (r-desctools): Update to 0.99.55.

Change-Id: Ic6b6222e1702db59786ad2ab73645425645575a1
 2024-08-17 21:54:21 +02:00
Ricardo Wurmus
ea717b12d3
gnu: r-exact: Update to 3.3. 
* gnu/packages/statistics.scm (r-exact): Update to 3.3.

Change-Id: If388135e98d31308d6d6170f30038ea9b44c994f
 2024-08-17 21:54:21 +02:00
Ricardo Wurmus
8c0709893b
gnu: r-lme4: Update to 1.1-35.5. 
* gnu/packages/statistics.scm (r-lme4): Update to 1.1-35.5.

Change-Id: I886898d0158ba4a6d29e61e8a19a280ce387ee2e
 2024-08-17 21:54:21 +02:00
Ricardo Wurmus
811ba5c0de
gnu: r-rcppeigen: Update to 0.3.4.0.1. 
* gnu/packages/statistics.scm (r-rcppeigen): Update to 0.3.4.0.1.

Change-Id: I4b7b3569c414d57a1af788fedcdaaf1e59e42fe7
 2024-08-17 21:54:21 +02:00
Ricardo Wurmus
92e07c893e
gnu: r-pcapp: Update to 2.0-4-1. 
* gnu/packages/statistics.scm (r-pcapp): Update to 2.0-4-1.

Change-Id: I7a08f67e636843e36bc80af0d94778f6d2b202d6
 2024-08-17 21:54:21 +02:00
Ricardo Wurmus
595667be4d
gnu: r-sparsem: Update to 1.84-2. 
* gnu/packages/statistics.scm (r-sparsem): Update to 1.84-2.

Change-Id: Id2123705c08bab173a4c8da3029e9bbda4db3ceb
 2024-08-17 21:54:21 +02:00
Ricardo Wurmus
864e9d4e03
gnu: r-segmented: Update to 2.1-1. 
* gnu/packages/statistics.scm (r-segmented): Update to 2.1-1.

Change-Id: I754caaac1fca6903103b3c36f3d4894350c9a63d
 2024-08-17 21:54:21 +02:00
Ricardo Wurmus
30b84babc9
gnu: r-rcurl: Update to 1.98-1.16. 
* gnu/packages/statistics.scm (r-rcurl): Update to 1.98-1.16.

Change-Id: I7c1570708479711e32a98e586cf51ddf7958e4b6
 2024-08-17 21:54:20 +02:00
Ricardo Wurmus
bb4b4782d7
gnu: r-bitops: Update to 1.0-8. 
* gnu/packages/statistics.scm (r-bitops): Update to 1.0-8.

Change-Id: I0f5e97d07097a0ec13cce1b1d61e4633cdb9cd70
 2024-08-17 21:54:20 +02:00
Ricardo Wurmus
df62a81202
gnu: r-rcpparmadillo: Update to 14.0.0-1. 
* gnu/packages/statistics.scm (r-rcpparmadillo): Update to 14.0.0-1.

Change-Id: I9594cab48497f4767b2f5435828057704efdb01f
 2024-08-17 21:54:20 +02:00
Ricardo Wurmus
dc2c1bd1d9
gnu: r-withr: Update to 3.0.1. 
* gnu/packages/statistics.scm (r-withr): Update to 3.0.1.

Change-Id: Ic9302091cacb203a3d6e45183c871ba12276e3ba
 2024-08-17 21:54:20 +02:00
Ricardo Wurmus
e4bc7819d6
gnu: r-openssl: Update to 2.2.1. 
* gnu/packages/statistics.scm (r-openssl): Update to 2.2.1.

Change-Id: Id279140de607eb0f8324ab2e38ce248398110979
 2024-08-17 21:54:20 +02:00
Ricardo Wurmus
56e6495adc
gnu: r-checkmate: Update to 2.3.2. 
* gnu/packages/statistics.scm (r-checkmate): Update to 2.3.2.

Change-Id: I8dbd8ed86a5cc652da180c1bac951abc7ba82fb5
 2024-08-17 21:54:20 +02:00
Ricardo Wurmus
4524ade9d5
gnu: r-knitr: Update to 1.48. 
* gnu/packages/statistics.scm (r-knitr): Update to 1.48.

Change-Id: I87ec28f830230f8fd51f7a2701a6bc83c14bd3b6
 2024-08-17 21:54:20 +02:00
Ricardo Wurmus
fbbf69f501
gnu: r-yaml: Update to 2.3.10. 
* gnu/packages/statistics.scm (r-yaml): Update to 2.3.10.

Change-Id: I64802f3c68be2498ea48755608ddf55dc3adae3e
 2024-08-17 21:54:20 +02:00
Ricardo Wurmus
bb8bab522a
gnu: r-nlme: Update to 3.1-166. 
* gnu/packages/statistics.scm (r-nlme): Update to 3.1-166.

Change-Id: I7df0e68f3e685acb145d3c07f9de14ee1ab141a6
 2024-08-17 21:54:20 +02:00
Ricardo Wurmus
5520c9e8d1
gnu: r-webmockr: Update to 1.0.0. 
* gnu/packages/cran.scm (r-webmockr): Update to 1.0.0.

Change-Id: I732b25faa1d2cc6cf17fb8c9dfb9dbc7f194c0d9
 2024-08-17 21:54:20 +02:00
Ricardo Wurmus
d9064cd6f6
gnu: r-crul: Update to 1.5.0. 
* gnu/packages/cran.scm (r-crul): Update to 1.5.0.

Change-Id: Ic25ca2096424aa624eca983b68f622240e212b0a
 2024-08-17 21:54:20 +02:00