maint: Add gnupg to the manifest.

* manifest.scm: Add gnupg.

Change-Id: Id5e90f87e5c3a07aa3e49afa97cc0b6d3ce71b41

channels: ‘latest-channel-instances’ traverses user-provided channels first.

Previously, ‘latest-channel-instances’ would perform a depth-first
traversal of channels.  Since dependencies specified in ‘.guix-channel’
are usually less specific that those provided by the user, this would
lead to the use of instances corresponding to those less specific specs,
which in turn might declare dependencies that do not exist for the more
specific instances.

This commit changes ‘latest-channel-instances’ to perform a
breadth-first traversal, thereby giving user-supplied channels higher
precedence over dependencies found via ‘.guix-channel’.

Fixes <https://issues.guix.gnu.org/68822>.

* guix/channels.scm (latest-channel-instances)[ignore?]: Remove.
[instance-name, same-named?, more-specific?]: New procedures.
Rewrite as a breadth-first traversal using a regular loop.
* tests/channels.scm ("latest-channel-instances reads dependencies from most-specific instance"):
New test.

Change-Id: Iba518145cfd209f04293a56246dbfee3b714650b

channels: Tweak test.

* tests/channels.scm ("latest-channel-instances excludes duplicate channel dependencies"):
Use ‘equal?’ rather than ‘string=?’ since we can get #f.

Change-Id: I437b9d7e23200cf0c98b1593e68b1d355bc2de01

gnu: torbrowser: Copy buildID from the official build.

* gnu/packages/tor.scm (%moz-build-date): Update to 20240115174022.

Reported-by: André Batista <nandre@riseup.net>
Change-Id: Ia057d6efe9db9e04ece03d994ee226ecdbc6cc04

Revert "gnu: Add minify."

This reverts commit f8c2d8141efef4565d12d8247bade069889b720e.

Fixes: error: go-github-com-tdewolff-minify-v2: unbound variable
<https://ci.guix.gnu.org/eval/1086875/log/raw>

Change-Id: I26e02842980cf09e924ac1cae8f3a6421a005276

teams: go: Add golang-xyz.scm to scope.

* etc/teams.scm (go): Add "gnu/packages/golang-xyz.scm".

Change-Id: I580eadf52b631c6582e256a2900786b53483a466

gnu: Add minify.

* gnu/packages/web.scm (minify): New variable.

Co-authored-by: Sharlatan Hellseher <sharlatanus@gmail.com>
Co-authored-by: Hilton Chain <hako@ultrarare.space>
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
Change-Id: I7289c77a17f63501b6c7771606d396241333ac3a

gnu: Add go-github-com-matryer-try.

* gnu/packages/golang-check.scm (go-github-com-matryer-try): New variable.

Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
Change-Id: Ic354425938374fcd29e871a597da63a7a390cfa1

gnu: Add go-github-com-djherbis-atime.

* gnu/packages/golang-xyz.scm (go-github-com-djherbis-atime): New variable.

Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
Change-Id: I320070d68e7f590f830060904f5cbdf59d839d1d

gnu: Add (gnu packages golang-xyz) module.

* gnu/packages/golang-xyz.scm: New file.
* gnu/local.mk: Add to gnu/packages/golang-xyz.scm scope.

Change-Id: I25e434de1adc29c2f08146f040755287c63632d6

gnu: go-github-com-go-jose-go-jose-v3: Move to (gnu packages golang-web).

Drop inheritance from go-gopkg-in-square-go-jose-v2 as it's archived by
the owner on Feb 27, 2023.

* gnu/packages/golang.scm (go-github-com-go-jose-go-jose-v3): Move from
here ...
* gnu/packages/golang-web.scm: ... to here.

Change-Id: I67838e18a43d93e5ae3b62e9645b7d22cf474103

gnu: axoloti-patcher: Add missing headers.

* gnu/packages/axoloti.scm (axoloti-patcher)[arguments]: Include generic
headers in search paths.

Change-Id: I2e1819966eb657ba4a7e0c823e6686de8599dd9a

gnu: axoloti-patcher: Use G-expression.

* gnu/packages/axoloti.scm (axoloti-patcher)[arguments]: Use G-expression;
delete 'make-git-checkout-writable phase.

Change-Id: I4f9b98351f1752391211f1aed84d484184d32771

gnu: yggdrasil: Update to 0.5.5.

* gnu/packages/networking.scm (yggdrasil): Update to 0.5.5.

Change-Id: Iba086d544e8225ec1b08de80f0fc3f01aa1f17b3
Signed-off-by: Ricardo Wurmus <rekado@elephly.net>

gnu: guile-hoot: Update to 0.3.0.

* gnu/packages/guile-xyz.scm (guile-hoot): Update to 0.3.0.

Change-Id: I355d4b11bdd45bf87e3d7227f259907b1e7d57bd

gnu: r-scran: Update to 1.30.2.

* gnu/packages/bioconductor.scm (r-scran): Update to 1.30.2.

Change-Id: I49388f6307f88cb671b0a721cc4c82a4804312c6

gnu: r-bioccheck: Update to 1.38.2.

* gnu/packages/bioconductor.scm (r-bioccheck): Update to 1.38.2.
[propagated-inputs]: Remove r-httr; add r-httr2 and r-rvest.

Change-Id: I5bcf99f2e3e93141fe502f061c2f347d4f0783bc

gnu: r-flowcore: Update to 2.14.1.

* gnu/packages/bioconductor.scm (r-flowcore): Update to 2.14.1.

Change-Id: I7a8002206aaab85a722463a81939d7cea7d61644

gnu: r-rsubread: Update to 2.16.1.

* gnu/packages/bioconductor.scm (r-rsubread): Update to 2.16.1.

Change-Id: Id01d956d2f76347270d05961dba13f65b268862a

gnu: r-edger: Update to 4.0.12.

* gnu/packages/bioconductor.scm (r-edger): Update to 4.0.12.

Change-Id: If99f10f80fb7c085863d2da79cfce2b94af71543