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10 Commits
| Author | SHA1 | Date | |
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d3a0108415 | ||
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1a7e8d47e3 | ||
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927469313c | ||
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5043ec49c5 | ||
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5660474bfa | ||
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5bef6564ba | ||
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c781426226 |
@@ -16,8 +16,6 @@
|
||||
( ;; primary: "D0C2 EAC1 3310 822D 98DE B57C E9C5 A2D9 0898 A02F"
|
||||
"01FD 85F4 1A7B 7F82 0583 06A5 935E BE07 36DC 857E"
|
||||
(name "avp"))
|
||||
("5D54 CF25 57B2 38E8 8DC1 80A2 2D22 3241 0AB7 4043"
|
||||
(name "baleine"))
|
||||
( ;; primary: "34FF 38BC D151 25A6 E340 A0B5 3453 2F9F AFCA 8B8E"
|
||||
"A3A4 B419 0074 087C A7DE 5698 BC45 CA67 E2F8 D007"
|
||||
(name "bavier"))
|
||||
|
||||
@@ -179,7 +179,6 @@ guix/scripts/import/elpa\.scm @guix/emacs
|
||||
tests/import/elpa\.scm @guix/emacs
|
||||
|
||||
gnu/packages/bootloaders\.scm @guix/embedded
|
||||
gnu/packages/coreboot\.scm @guix/embedded
|
||||
gnu/packages/firmware\.scm @guix/embedded
|
||||
|
||||
gnu/packages/emulators\.scm @guix/games
|
||||
@@ -274,7 +273,6 @@ guix/build-system/ant\.scm @guix/java
|
||||
guix/build-system/clojure\.scm @guix/java
|
||||
guix/build-system/maven\.scm @guix/java
|
||||
|
||||
gnu/packages/javascript\.scm @guix/javascript
|
||||
gnu/packages/node-xyz\.scm @guix/javascript
|
||||
gnu/packages/node\.scm @guix/javascript
|
||||
guix/build-system/node\.scm @guix/javascript
|
||||
@@ -320,7 +318,6 @@ gnu/packages/tor-browsers\.scm @guix/mozilla
|
||||
|
||||
gnu/packages/ocaml\.scm @guix/ocaml
|
||||
gnu/packages/coq\.scm @guix/ocaml
|
||||
gnu/packages/rocq\.scm @guix/ocaml
|
||||
guix/build/ocaml-build-system\.scm @guix/ocaml
|
||||
guix/build/dune-build-system\.scm @guix/ocaml
|
||||
guix/build-system/ocaml\.scm @guix/ocaml
|
||||
|
||||
@@ -1667,9 +1667,6 @@ can be turned into a version string via @code{git-version}, for example
|
||||
@code{rust-pipewire-0.8.0.fd3d8f7} and @code{rust-pubgrub-0.3.0.b70cf70}.
|
||||
@end table
|
||||
|
||||
When contributing Rust packages, we should have all modifications to these
|
||||
two modules, in the same commit as the package we are contributing.
|
||||
|
||||
To avoid merge conflicts with changes from multiple branches, these two modules
|
||||
are maintained by the Rust team (@pxref{Teams}).
|
||||
|
||||
@@ -1699,68 +1696,6 @@ tree.
|
||||
@xref{Packaging Rust Crates,,, guix-cookbook, GNU Guix Cookbook}, for
|
||||
packaging workflow.
|
||||
|
||||
@subsubsection Commit messages
|
||||
|
||||
The commit message must have a general brief mention to entry changes
|
||||
in @code{(gnu packages rust-crates)}. For changes in @code{(gnu packages
|
||||
rust-sources)}, the commit message must explicitly mention all changes to the
|
||||
packages.
|
||||
|
||||
Here are some examples for different situations:
|
||||
|
||||
@itemize
|
||||
|
||||
@item
|
||||
Adding a new Rust package:
|
||||
|
||||
@example
|
||||
gnu: Add catppuccin-whiskers.
|
||||
|
||||
* gnu/packages/rust-apps.scm (catppuccin-whiskers): New variable.
|
||||
* gnu/packages/rust-crates.scm (lookup-cargo-inputs)
|
||||
[catppuccin-whiskers]: New entry.
|
||||
@end example
|
||||
|
||||
@item
|
||||
Updating a simple package:
|
||||
|
||||
@example
|
||||
gnu: watchexec: Update to 2.3.2.
|
||||
|
||||
* gnu/packages/rust-apps.scm (watchexec): Update to 2.3.2.
|
||||
* gnu/packages/rust-crates.scm (lookup-cargo-inputs)[watchexec]:
|
||||
Update entry.
|
||||
@end example
|
||||
|
||||
@item
|
||||
Updating a package with sources:
|
||||
|
||||
@example
|
||||
gnu: typst: Update to 0.14.0.
|
||||
|
||||
* gnu/packages/rust-apps.scm (typst): Update to 0.14.0.
|
||||
[arguments]<#:rust>: Use rust-1.88.
|
||||
* gnu/packages/rust-crates.scm (lookup-cargo-inputs)[typst]: Update
|
||||
entry.
|
||||
[rust-syntect-5]: Rename to rust-syntect-5.2.
|
||||
[rust-syntect-5.3]: New entry.
|
||||
* gnu/packages/rust-sources.scm (rust-hypher-0.1): Update to 0.1.6.
|
||||
(rust-syntect-5): Rename to rust-syntect-5.2.
|
||||
[inputs]: Rename cargo-inputs rust-syntect-5 to rust-syntect-5.2.
|
||||
(rust-syntect-5.3): New variable.
|
||||
@end example
|
||||
|
||||
@end itemize
|
||||
|
||||
@subsubsection Resolving merge conflicts in Pull Requests
|
||||
|
||||
For Rust crates, the recommended way to solve merge conflicts is to drop all
|
||||
changes to @code{gnu/packages/rust-crates.scm}, rebase onto the desired branch
|
||||
and run the lockfile importer again, manually adding back all relevant snippets
|
||||
(if any).
|
||||
|
||||
@xref{Common Workflow for Resolving Merge Conflicts on Existing Pull Requests,,, guix-cookbook, GNU Guix Cookbook} for
|
||||
a suggested workflow on resolving merge conflicts.
|
||||
|
||||
@node Elm Packages
|
||||
@subsection Elm Packages
|
||||
@@ -2715,7 +2650,6 @@ applications settings page}, granting read/write access to the
|
||||
|
||||
@cindex decision making
|
||||
@cindex consensus seeking
|
||||
Every contribution to the project involves a form of decision making.
|
||||
It is expected from all contributors, and even more so from committers,
|
||||
to help build consensus and make decisions based on consensus. By using
|
||||
consensus, we are committed to finding solutions that everyone can live
|
||||
@@ -2730,26 +2664,6 @@ resolve the deadlock. To learn what consensus decision making means and
|
||||
understand its finer details, you are encouraged to read
|
||||
@url{https://www.seedsforchange.org.uk/consensus}.
|
||||
|
||||
Day-to-day decision making, for instance discussions about pull requests
|
||||
(@pxref{Reviewing the Work of Others}), happens informally among
|
||||
interested parties such as contributors and members of the relevant
|
||||
teams (@pxref{Teams}).
|
||||
|
||||
@cindex GCD, Guix Consensus Documents
|
||||
@cindex Guix Consensus Documents (GCD)
|
||||
Decisions that are expected to have an impact on most contributors
|
||||
and/or on the broader user community---e.g., changes to project-wide
|
||||
policies, to core functionality, and so on---are made following the
|
||||
@acronym{GCD, Guix Consensus Document} process. The process provides a
|
||||
framework to formalize proposals and draw attention to them, to leave
|
||||
time for interested parties to discuss them, and to collectively accept
|
||||
or withdraw them based on input from participating team members. It is
|
||||
defined in
|
||||
@uref{https://consensus.guix.gnu.org/gcd/001-gcd-process.html,
|
||||
GCD@tie{}001}. Past GCDs can be seen at
|
||||
@uref{https://consensus.guix.gnu.org}, and discussions take place at
|
||||
@uref{https://codeberg.org/guix/guix-consensus-documents}.
|
||||
|
||||
@node Commit Access
|
||||
@section Commit Access
|
||||
|
||||
|
||||
@@ -146,8 +146,6 @@ Packaging Rust Crates
|
||||
* Common Workflow for Rust Packaging::
|
||||
* Cargo Workspaces and Development Snapshots::
|
||||
* Using Rust Libraries in Other Build Systems::
|
||||
* Common Workflow for Updating Existing Rust Packages::
|
||||
* Common Workflow for Resolving Merge Conflicts on Existing Pull Requests::
|
||||
|
||||
System Configuration
|
||||
|
||||
@@ -1649,8 +1647,6 @@ $ guix shell rust rust:cargo cargo-audit cargo-license
|
||||
* Common Workflow for Rust Packaging::
|
||||
* Cargo Workspaces and Development Snapshots::
|
||||
* Using Rust Libraries in Other Build Systems::
|
||||
* Common Workflow for Updating Existing Rust Packages::
|
||||
* Common Workflow for Resolving Merge Conflicts on Existing Pull Requests::
|
||||
@end menu
|
||||
|
||||
@node Common Workflow for Rust Packaging
|
||||
@@ -1709,15 +1705,6 @@ $ cargo audit
|
||||
$ cargo license
|
||||
@end example
|
||||
|
||||
@quotation Note
|
||||
Before running @command{cargo generate-lockfile}, make sure you have checked
|
||||
out the correct tag for the version you are packaging. This ensures that
|
||||
@code{Cargo.toml} matches the file used in the packages's @code{source} field.
|
||||
To make sure, you can obtain the exact source with @command{./pre-inst-env guix
|
||||
build --source <package>} and only then run @command{cargo generate-lockfile} on
|
||||
that source tree.
|
||||
@end quotation
|
||||
|
||||
@command{cargo generate-lockfile} updates dependencies to compatible versions.
|
||||
Applying it to all Rust applications helps reduce a great number of Rust
|
||||
libraries we need to check later. Although sometimes libraries may fail to
|
||||
@@ -2000,316 +1987,6 @@ method, one of the most popular choices for Traditional Chinese users.")
|
||||
(license license:lgpl2.1+)))
|
||||
@end lisp
|
||||
|
||||
@node Common Workflow for Updating Existing Rust Packages
|
||||
@subsubsection Common Workflow for Updating Existing Rust Packages
|
||||
|
||||
For this example, we'll update @code{niri}. The package definition looks like
|
||||
this initially:
|
||||
|
||||
@lisp
|
||||
(define-public niri
|
||||
(package
|
||||
(name "niri")
|
||||
(version "25.08")
|
||||
(source (origin
|
||||
(method git-fetch)
|
||||
(uri (git-reference
|
||||
(url "https://github.com/YaLTeR/niri")
|
||||
(commit (string-append "v" version))))
|
||||
(file-name (git-file-name name version))
|
||||
(sha256
|
||||
(base32
|
||||
"09nsxd211mly8r1ys2lq6ia4jxgb980h1axrbgw748r0knfbbj7n"))))
|
||||
(build-system cargo-build-system)
|
||||
...
|
||||
@end lisp
|
||||
|
||||
We start by running the usual @command{guix refresh -u niri}.
|
||||
|
||||
The @command{-u} flag will update in place the version and hash for the
|
||||
@code{niri} package.
|
||||
|
||||
The package definition will then look like this:
|
||||
|
||||
@lisp
|
||||
(define-public niri
|
||||
(package
|
||||
(name "niri")
|
||||
(version "25.11")
|
||||
(source (origin
|
||||
(method git-fetch)
|
||||
(uri (git-reference
|
||||
(url "https://github.com/YaLTeR/niri")
|
||||
(commit (string-append "v" version))))
|
||||
(file-name (git-file-name name version))
|
||||
(sha256
|
||||
(base32
|
||||
"0752qm245wc2gak0jhp0fnr0rdj3z54m2h97k3cxbjym9pcn658n"))))
|
||||
(build-system cargo-build-system)
|
||||
...
|
||||
@end lisp
|
||||
|
||||
This means the source field was updated successfully, thus we can now proceed to
|
||||
get the updated source with @command{guix build --source niri} as follows:
|
||||
|
||||
@example shell
|
||||
$ cp -r $(./pre-inst-env guix build --source niri) /tmp
|
||||
$ cd /tmp/<hash>-niri-25.11-checkout/
|
||||
@end example
|
||||
|
||||
@quotation Note
|
||||
In this specific example, the source is a git checkout, thus a directory. If the
|
||||
package source is a compressed archive, you would at this point extract it to a
|
||||
directory to proceed.
|
||||
@end quotation
|
||||
|
||||
Now, given that we have access to the @code{Cargo.toml} file, we can now run
|
||||
the following inside the checkout:
|
||||
|
||||
@example shell
|
||||
$ guix shell rust rust:cargo -- cargo generate-lockfile
|
||||
$ guix shell rust rust:cargo -- cargo audit
|
||||
$ guix shell rust rust:cargo -- cargo license
|
||||
@end example
|
||||
|
||||
@quotation Note
|
||||
Sometimes the package will require a more up-to-date version of rust, that is
|
||||
not yet the default rust on guix. For these cases you can use:
|
||||
@example shell
|
||||
$ guix shell -e "(@ (gnu packages rust) rust-1.90)" \
|
||||
-e '`(,(@ (gnu packages rust) rust-1.90) "cargo")'
|
||||
@end example
|
||||
@end quotation
|
||||
|
||||
The first command will ensure that all cargo dependencies are up to date
|
||||
and semver compatible, while also providing some other benefits, as further
|
||||
explained in @ref{Common Workflow for Rust Packaging}.
|
||||
|
||||
The following command will warn if there are any known vulnerabilities in the
|
||||
crates being imported. The last one will output the license information of all
|
||||
the dependent crates.
|
||||
|
||||
If everything looks good, we can now replace the contents of the @code{niri}
|
||||
indentifier, located inside the @code{lookup-cargo-inputs} variable on the
|
||||
bottom of the @file{gnu/packages/rust-crates.scm} module, with the newer updated
|
||||
crates by running the importer on the lockfile as follows:
|
||||
|
||||
@example shell
|
||||
$ guix import -i /path/to/gnu/packages/rust-crates.scm \
|
||||
crate -f Cargo.lock niri
|
||||
@end example
|
||||
|
||||
@quotation Note
|
||||
For the purpose of contributing a package to Guix (@pxref{Contributing,,,
|
||||
guix, GNU Guix Reference Manual}), there is no need to cleanup the leftover
|
||||
crates as a result of the package update. This is tasked to the rust-team
|
||||
(@pxref{Teams,,, guix, GNU Guix Reference Manual}) to periodically run a
|
||||
convenient script in @code{etc/teams/rust} to cleanup unused crates from
|
||||
@file{gnu/packages/rust-crates.scm}.
|
||||
@end quotation
|
||||
|
||||
We then need to check whether the importer has placed some TODOs for us,
|
||||
inside @file{gnu/packages/rust-crates.scm} (you can use @command{git diff --
|
||||
gnu/packages/rust-crates.scm} for this purpose).
|
||||
|
||||
There are a few types of TODO messages that you might encounter during this
|
||||
step, each type requiring you to perform a different action.
|
||||
|
||||
The first one we encounter in our example is:
|
||||
|
||||
@lisp
|
||||
(define rust-libdisplay-info-sys-0.3.0
|
||||
;; TODO REVIEW: Check bundled sources.
|
||||
(crate-source "libdisplay-info-sys" "0.3.0"
|
||||
"07xmkc2aqcdn6d58321y87rd3gzdr4nx3ncm1mmrr7w1p1ahsn96"))
|
||||
@end lisp
|
||||
|
||||
This specific TODO message tells us that there is a high probability of
|
||||
encountering bundled sources within a crate definition generated by the
|
||||
importer.
|
||||
|
||||
We then check if there are any bundled sources within the
|
||||
@code{rust-libdisplay-info-sys-0.3.0} crate. Since there are none (in our
|
||||
example), we can simply remove the TODO line, and continue to the next TODO.
|
||||
|
||||
If there were any bundled sources inside the crate, we would have to patch
|
||||
it with a snippet, in order to unbundle it. You can see some examples on
|
||||
how to unbundle inside @file{gnu/packages/rust-crates.scm} (search for the
|
||||
@code{#:snippet} keyword).
|
||||
|
||||
@quotation Note
|
||||
If the unbundle is considered too difficult to be executed (e.g. the effort
|
||||
needed to unbundle is unreasonable), the @code{TODO REVIEW} line should be
|
||||
converted to a regular TODO comment explicitly stating the unbundle was not done
|
||||
(e.g. @code{TODO: Unbundle rust-libdisplay-info-sys.}).
|
||||
@end quotation
|
||||
|
||||
Continuing, another TODO message we encounter in this example is the following:
|
||||
|
||||
@lisp
|
||||
(define rust-smithay-0.7.0.d743e1a
|
||||
;; TODO REVIEW: Define standalone package if this is a workspace.
|
||||
(origin
|
||||
(method git-fetch)
|
||||
(uri (git-reference (url "https://github.com/Smithay/smithay.git")
|
||||
(commit "d743e1a317fa0f01d1c4cadd96d277a1ec7b59d9")))
|
||||
(file-name (git-file-name "rust-smithay" "0.7.0.d743e1a"))
|
||||
(sha256 (base32 "11327mhxxf844bs0v5bw1g9bzjssnzhidsissywy6kwng16x727v"))))
|
||||
@end lisp
|
||||
|
||||
This specific TODO message tells us that there is a high probability of the
|
||||
@code{rust-smithay-0.7.0.d743e1a} crate being a workspace.
|
||||
|
||||
After verifying that it is indeed a workspace, we now need to make it an
|
||||
actual package in @file{gnu/packages/rust-sources.scm}, referencing it in the
|
||||
crate-source definition (see @ref{Common Workflow for Rust Packaging} for more
|
||||
details).
|
||||
|
||||
@quotation Note
|
||||
You can verify if a crate is a workspace by cloning the crate repository (in
|
||||
this case @code{https://github.com/Smithay/smithay.git}), checking out the
|
||||
specific revision (in this case @command{git checkout d743e1a}), and looking
|
||||
for @code{[workspace]} in its main @file{Cargo.toml} file. If it does not have a
|
||||
TOML @code{[workspace]} section, then it is not a workspace.
|
||||
@end quotation
|
||||
|
||||
After defining the separate source package for the workspace in
|
||||
@file{gnu/packages/rust-sources.scm} (see @ref{Common Workflow for Rust
|
||||
Packaging} for more details on how to do this), the crate definition for
|
||||
@code{rust-smithay-0.7.0.d743e1a} would then become the following (notice we
|
||||
also remove the TODO line):
|
||||
|
||||
@lisp
|
||||
(define rust-smithay-0.7.0.d743e1a package:rust-smithay-0.7.0.d743e1a)
|
||||
@end lisp
|
||||
|
||||
If @code{rust-smithay-0.7.0.d743e1a} was not a workspace, we would simply remove
|
||||
the TODO line and move on.
|
||||
|
||||
We then try to build the package with @command{guix build niri}, and make sure
|
||||
whether it builds successfully, which it does.
|
||||
|
||||
As a good practice, we can further check the output of the
|
||||
@code{check-for-pregenerated-files} phase to ensure there are no extraneous
|
||||
pregenerated files inside the crates. If there are any, it is important to
|
||||
snippet them out, like these:
|
||||
|
||||
@lisp
|
||||
(define rust-winapi-x86-64-pc-windows-gnu-0.4.0
|
||||
(crate-source "winapi-x86_64-pc-windows-gnu" "0.4.0"
|
||||
"0gqq64czqb64kskjryj8isp62m2sgvx25yyj3kpc2myh85w24bki"
|
||||
#:snippet '(delete-file-recursively "lib")))
|
||||
|
||||
(define rust-flate2-1.1.4
|
||||
(crate-source "flate2" "1.1.4"
|
||||
"1a8a3pk2r2dxays4ikc47ygydhpd1dcxlgqdi3r9kiiq9rb4wnnw"
|
||||
#:snippet '(for-each delete-file-recursively '("examples" "tests"))))
|
||||
|
||||
(define rust-flo-curves-0.3.1
|
||||
(crate-source "flo_curves" "0.3.1"
|
||||
"16x293dp8825jh465kgms4yyvl4960j26gh37h3skflq9zxpy8hw"
|
||||
#:snippet '(for-each delete-file '("logo-small.png" "logo.png"))))
|
||||
|
||||
(define rust-interception-sys-0.1.3
|
||||
(crate-source "interception-sys" "0.1.3"
|
||||
"1lgwbml7gzq5a5rriy708w68gx6yiw9cdg7xy2c5vsrrck7pbs5b"
|
||||
#:snippet '(for-each delete-file (find-files "." "\\.(dll|lib)$"))))
|
||||
@end lisp
|
||||
|
||||
@node Common Workflow for Resolving Merge Conflicts on Existing Pull Requests
|
||||
@subsubsection Common Workflow for Resolving Merge Conflicts on Existing Pull Requests
|
||||
|
||||
Whenever a Rust package change is merged into our target branch from a different
|
||||
Pull Request, we often encounter many merge conflicts in @code{(gnu packages
|
||||
rust-crates)} when rebasing the Pull Request on top of the target branch. Since
|
||||
we should avoid modifying the rust-crates file manually (e.g. using the git
|
||||
interface to solve merge conflicts), it is recommended (and often much faster)
|
||||
to drop all changes to @code{(gnu packages rust-crates)} and run the lockfile
|
||||
importer once again, manually adding back all the manual changes.
|
||||
|
||||
This workflow describes one of many ways to do the described procedure.
|
||||
|
||||
In this example we'll update the @code{codeberg-cli} package, which has produced
|
||||
some merge conflicts in @file{gnu/packages/rust-crates.scm} when we tried a git
|
||||
pull rebase.
|
||||
|
||||
Before starting, make sure we're not in a rebase environment, by aborting the
|
||||
rebase we tried previously (the one which created the merge conflicts by git
|
||||
pulling):
|
||||
|
||||
@example
|
||||
$ git rebase --abort
|
||||
@end example
|
||||
|
||||
@cindex git rebase --interactive
|
||||
@cindex interactive rebase
|
||||
To begin, we interactively rebase our PR branch by marking as
|
||||
@code{edit} the commit we want to edit, which is the one containing the
|
||||
@file{gnu/packages/rust-crates.scm} changes:
|
||||
|
||||
@example
|
||||
# Change 1 to the number of relevant commits
|
||||
$ git rebase -i HEAD~1
|
||||
@end example
|
||||
|
||||
In our example, we would mark the @code{codeberg-cli} commit like so:
|
||||
|
||||
@example
|
||||
edit 6ef4f1ad043 # gnu: codeberg-cli: Update to 0.5.4.
|
||||
@end example
|
||||
|
||||
After that, we'll be in rebase mode, where we can restore the changes made to
|
||||
@file{gnu/packages/rust-crates.scm}:
|
||||
|
||||
@quotation Note
|
||||
Notice that we will lose all manual changes we have previously made to
|
||||
@file{gnu/packages/rust-crates.scm} (e.g. snippets, deleting TODO comments,
|
||||
if there were any). We'll need to manually add them back after we run the guix
|
||||
lockfile importer once again, so make sure you have them saved somewhere, for
|
||||
example in your PR link under the @code{Files changed} tab.
|
||||
@end quotation
|
||||
|
||||
@example
|
||||
$ git restore --source=HEAD~ gnu/packages/rust-crates.scm
|
||||
@end example
|
||||
|
||||
Having restored the file, we can stage the changes, commit, finish the rebase
|
||||
and pull rebase from the target branch:
|
||||
|
||||
@example
|
||||
$ git add gnu/packages/rust-crates.scm
|
||||
$ git commit --amend --no-edit
|
||||
$ git rebase --continue
|
||||
$ git pull <remote> <target branch>
|
||||
@end example
|
||||
|
||||
We then proceed to run the guix lockfile importer:
|
||||
|
||||
@quotation Note
|
||||
Remember to checkout the correct tag you're packaging in the package repository
|
||||
checkout. Don't forget to run @code{cargo generate-lockfile} before running
|
||||
the lockfile importer, see @ref{Common Workflow for Rust Packaging} for more
|
||||
detailed steps on what to do before running the guix lockfile importer.
|
||||
@end quotation
|
||||
|
||||
@example
|
||||
$ guix import --insert=gnu/packages/rust-crates.scm \
|
||||
crate --lockfile=/path/to/Cargo.lock codeberg-cli
|
||||
@end example
|
||||
|
||||
Now is the time we manually add back the snippets and remove the relevant TODOs
|
||||
we have already checked (if there are any).
|
||||
|
||||
After running the lockfile importer and checking if there are any changes to
|
||||
manually add back, we can finally:
|
||||
|
||||
@example
|
||||
$ git add gnu/packages/rust-crates.scm
|
||||
# Our target commit is the last one:
|
||||
$ git commit --amend --no-edit
|
||||
@end example
|
||||
|
||||
We now have a non-conflicting tree, from which we can now update our PR with.
|
||||
|
||||
@c *********************************************************************
|
||||
@node System Configuration
|
||||
|
||||
131
doc/guix.texi
131
doc/guix.texi
@@ -2658,13 +2658,12 @@ bootloaders.
|
||||
|
||||
Once you are done partitioning the target hard disk drive, you have to
|
||||
create a file system on the relevant partition(s)@footnote{Currently
|
||||
Guix System can mount only ext4, btrfs, JFS, F2FS, and XFS file systems
|
||||
at boot time. In particular, code that reads file system UUIDs and
|
||||
labels works only for these file system types. The code for bcachefs is
|
||||
in place, but support for loading out-of-tree kernel modules in the
|
||||
initrd is not.}.
|
||||
|
||||
For the ESP, if you have one and assuming it is @file{/dev/sda1}, run:
|
||||
Guix System supports only ext4, btrfs, bcachefs, JFS, F2FS, and XFS
|
||||
file systems. In particular, code that reads file system UUIDs and
|
||||
labels works only for these file system types. For bcachefs, also add
|
||||
the @code{bcachefs-linux-module} to your @code{operating-system}'s
|
||||
@code{initrd-modules}.}. For the ESP, if you have one and assuming it is
|
||||
@file{/dev/sda1}, run:
|
||||
|
||||
@example
|
||||
mkfs.fat -F32 /dev/sda1
|
||||
@@ -8844,12 +8843,12 @@ dependencies than the original package. For example, the default
|
||||
optional dependency, you can define a variant that removes that
|
||||
dependency like so:
|
||||
|
||||
@findex package/inherit
|
||||
@lisp
|
||||
(use-modules (gnu packages gdb)) ;for 'gdb'
|
||||
|
||||
(define gdb-sans-guile
|
||||
(package/inherit gdb
|
||||
(package
|
||||
(inherit gdb)
|
||||
(inputs (modify-inputs inputs
|
||||
(delete "guile")))))
|
||||
@end lisp
|
||||
@@ -8857,23 +8856,6 @@ dependency like so:
|
||||
In the body of the @code{inputs} field above, @code{inputs} is bound to
|
||||
the inherited value. Thus, the @code{modify-inputs} form above removes
|
||||
the @code{"guile"} package from the @code{inputs} field of @code{gdb}.
|
||||
|
||||
@quotation Note
|
||||
The example above uses @code{(package/inherit gdb @dots{})} instead of
|
||||
the usual @code{(package (inherit gdb) @dots{})}. While the latter
|
||||
would work, @code{package/inherit} does extra work: if @code{gdb} has a
|
||||
@code{replacement} field (@pxref{Security Updates}),
|
||||
@code{package/inherit} propagates the @code{inputs} changes of this
|
||||
variant to the replacement.
|
||||
|
||||
In other words, @code{package/inherit} ensures the variant gets a
|
||||
consistent @code{replacement} when the original package has one. Thus,
|
||||
one should generally use @code{package/inherit} when creating a variant
|
||||
for the same version, but not when targeting a different version, as in
|
||||
the @code{hello} example we saw earlier, where the replacement may be
|
||||
incorrect.
|
||||
@end quotation
|
||||
|
||||
The @code{modify-inputs} macro is a helper that can prove useful anytime
|
||||
you want to remove, add, or replace package inputs.
|
||||
|
||||
@@ -15552,7 +15534,7 @@ gnu/packages/qt.scm:452:13: qtbase would be upgraded from 5.15.8 to 5.15.10
|
||||
@end example
|
||||
|
||||
@cindex partial version specification, guix refresh
|
||||
A per-package equivalent to @option{--target-version} is made available by
|
||||
A per-package equivalent to --target-version is made available by
|
||||
prefixing the version specification with the @samp{~} (tilde) character.
|
||||
For example:
|
||||
|
||||
@@ -16113,7 +16095,7 @@ it unchanged.
|
||||
@item git-source
|
||||
If the @code{home-page} is a Git repository (as per
|
||||
@code{git-repository-url?}), and the actual Git repository is tagged
|
||||
with a version string, possibly prefixed by ``v'', change the
|
||||
with @code{version} or @code{(string-append ``v'' version)}, change the
|
||||
package origin to the @code{git-fetch} method
|
||||
(@pxref{origin Reference}). Consider this example:
|
||||
|
||||
@@ -16142,16 +16124,14 @@ its @code{source} field like to:
|
||||
(inherit guile-json-3)
|
||||
(name "guile-json")
|
||||
(version "4.7.3")
|
||||
(source
|
||||
(origin
|
||||
(method git-fetch)
|
||||
(uri (git-reference
|
||||
(url "https://github.com/aconchillo/guile-json")
|
||||
(commit version)))
|
||||
(file-name (git-file-name name version))
|
||||
(sha256
|
||||
(base32
|
||||
"0akhm8xjv8fl55fyq0w6c9c6hi5j7mifjx01w07np7qg1cjl9f06"))))))
|
||||
(source (origin
|
||||
(method git-fetch)
|
||||
(uri (git-reference (url
|
||||
"https://github.com/aconchillo/guile-json")
|
||||
(commit version)))
|
||||
(file-name (git-file-name name version))
|
||||
(sha256 (base32
|
||||
"0akhm8xjv8fl55fyq0w6c9c6hi5j7mifjx01w07np7qg1cjl9f06"))))))
|
||||
@end lisp
|
||||
|
||||
@end table
|
||||
@@ -19216,7 +19196,7 @@ Partitioning}, for an example.
|
||||
|
||||
When using GRUB as the bootloader, the LUKS password is only requested
|
||||
once: GRUB passes the master key to the initial RAM disk automatically.
|
||||
@xref{grub-luks-root-device-key, Automatic LUKS Master Key Passing}, for
|
||||
@xref{Bootloader Configuration, Automatic LUKS Master Key Passing}, for
|
||||
details.
|
||||
|
||||
@end defvar
|
||||
@@ -27268,28 +27248,6 @@ Package object for GVfs.
|
||||
@end table
|
||||
@end deftp
|
||||
|
||||
@defvar kmonad-service-type
|
||||
This is the type of the service that runs
|
||||
@uref{https://github.com/kmonad/kmonad, KMonad}. Its value is a
|
||||
@code{kmonad-configuration} object. This service allows spawning
|
||||
@command{kmonad} configurations to manage keyboards.
|
||||
|
||||
@deftp {Data Type} kmonad-configuration
|
||||
Configuration record for the KMonad service.
|
||||
|
||||
@table @asis
|
||||
@item @code{kmonad} (default: @code{kmonad})
|
||||
The KMonad package to use.
|
||||
|
||||
@item @code{keymaps}
|
||||
A list of files with KMonad configurations. One shepherd service will be
|
||||
created to control each configuration. Each configuration should target
|
||||
a distinct input device as KMonad operates on a per-input basis.
|
||||
|
||||
@end table
|
||||
@end deftp
|
||||
@end defvar
|
||||
|
||||
@defvar colord-service-type
|
||||
This is the type of the service that runs @command{colord}, a system
|
||||
service with a D-Bus
|
||||
@@ -45251,12 +45209,6 @@ Extra command line options for @code{guix-data-service}.
|
||||
@item @code{extra-process-jobs-options} (default: @var{'()})
|
||||
Extra command line options for @code{guix-data-service-process-jobs}.
|
||||
|
||||
@item @code{extra-environment-variables} (default: @var{'()})
|
||||
Extra environment variables for @code{guix-data-service}.
|
||||
|
||||
@item @code{extra-process-jobs-environment-variables} (default: @var{'()})
|
||||
Extra environment variables for @code{guix-data-service-process-jobs}.
|
||||
|
||||
@item @code{git-repositories} (default: @var{#f})
|
||||
List of git-repository information to insert into the database.
|
||||
|
||||
@@ -48966,28 +48918,8 @@ This option in enabled by default. In some cases involving the
|
||||
in RAM, it can be handy to disable the option by setting it to
|
||||
@code{#f}.
|
||||
|
||||
@item @code{extra-initrd} (default: @code{#f})
|
||||
File name of an additional initrd to load during the boot. It may or
|
||||
may not point to a file in the store, but the main use case is for
|
||||
out-of-store files containing secrets.
|
||||
@subsubheading Automatic LUKS Master Key Passing
|
||||
|
||||
For any use case not involving secrets, you should use regular initrd
|
||||
(@pxref{operating-system Reference, @code{initrd}}) instead.
|
||||
|
||||
Be careful when using this option, since pointing to a file that is not
|
||||
readable by the grub while booting will cause the boot to fail and
|
||||
require a manual edit of the initrd line in the grub menu.
|
||||
|
||||
Currently only supported by GRUB.
|
||||
@end table
|
||||
|
||||
@end deftp
|
||||
|
||||
@anchor{grub-luks-root-device-key}
|
||||
@unnumberedsubsec Automatic LUKS Master Key Passing
|
||||
|
||||
@cindex LUKS, root file system encryption
|
||||
@cindex passphrase, for LUKS-encrypted root
|
||||
When booting from a LUKS-encrypted device using GRUB, the password is
|
||||
normally requested twice: once by GRUB to access @file{/boot}, and a
|
||||
second time by the initial RAM disk to mount the root file system.
|
||||
@@ -49028,7 +48960,22 @@ No configuration is required: GRUB's @code{procfs} and @code{luks}
|
||||
modules are loaded automatically when encrypted devices are declared
|
||||
via @code{luks-device-mapping} (@pxref{Mapped Devices}).
|
||||
|
||||
@unnumberedsubsec Additional Boot Entries
|
||||
@item @code{extra-initrd} (default: @code{#f})
|
||||
File name of an additional initrd to load during the boot. It may or
|
||||
may not point to a file in the store, but the main use case is for
|
||||
out-of-store files containing secrets.
|
||||
|
||||
For any use case not involving secrets, you should use regular initrd
|
||||
(@pxref{operating-system Reference, @code{initrd}}) instead.
|
||||
|
||||
Be careful when using this option, since pointing to a file that is not
|
||||
readable by the grub while booting will cause the boot to fail and
|
||||
require a manual edit of the initrd line in the grub menu.
|
||||
|
||||
Currently only supported by GRUB.
|
||||
@end table
|
||||
|
||||
@end deftp
|
||||
|
||||
@cindex dual boot
|
||||
@cindex boot menu
|
||||
@@ -49157,13 +49104,9 @@ example of chainloading a different GNU/Linux system.
|
||||
@end table
|
||||
@end deftp
|
||||
|
||||
@unnumberedsubsec Themes
|
||||
|
||||
@cindex HDPI
|
||||
@cindex HiDPI
|
||||
@cindex resolution
|
||||
@cindex themes, for GRUB
|
||||
@cindex bootloader themes
|
||||
@c FIXME: Write documentation once it's stable.
|
||||
For now only GRUB has theme support. GRUB themes are created using
|
||||
the @code{grub-theme} form, which is not fully documented yet.
|
||||
@@ -49183,7 +49126,7 @@ Return the default GRUB theme used by the operating system if no
|
||||
@code{theme} field is specified in @code{bootloader-configuration}
|
||||
record.
|
||||
|
||||
It comes with a fancy background image displaying the Guix
|
||||
It comes with a fancy background image displaying the GNU and Guix
|
||||
logos.
|
||||
@end deffn
|
||||
|
||||
|
||||
@@ -16,7 +16,6 @@ exec $pre_inst_env_maybe guix repl -- "$0" "$@"
|
||||
;;; Copyright © 2025 Cayetano Santos <csantosb@inventati.org>
|
||||
;;; Copyright © 2025-2026 Ludovic Courtès <ludo@gnu.org>
|
||||
;;; Copyright © 2025 jgart <jgart@dismail.de>
|
||||
;;; Copyright © 2026 Denis 'GNUtoo' Carikli <GNUtoo@cyberdimension.org>
|
||||
;;;
|
||||
;;; This file is part of GNU Guix.
|
||||
;;;
|
||||
@@ -691,7 +690,6 @@ ecosystem."
|
||||
(team 'embedded
|
||||
#:name "Embedded"
|
||||
#:scope (list "gnu/packages/bootloaders.scm"
|
||||
"gnu/packages/coreboot.scm"
|
||||
"gnu/packages/firmware.scm")))
|
||||
|
||||
(define-team games
|
||||
@@ -844,8 +842,7 @@ and the maven-build-system."
|
||||
#:name "JavaScript team"
|
||||
#:description
|
||||
"JavaScript/Node.js packages, the node build system."
|
||||
#:scope (list "gnu/packages/javascript.scm"
|
||||
"gnu/packages/node-xyz.scm"
|
||||
#:scope (list "gnu/packages/node-xyz.scm"
|
||||
"gnu/packages/node.scm"
|
||||
"guix/build-system/node.scm"
|
||||
"guix/build/node-build-system.scm"
|
||||
@@ -946,7 +943,6 @@ importer, and the ocaml-build-system."
|
||||
#:scope
|
||||
(list "gnu/packages/ocaml.scm"
|
||||
"gnu/packages/coq.scm"
|
||||
"gnu/packages/rocq.scm"
|
||||
"guix/build/ocaml-build-system.scm"
|
||||
"guix/build/dune-build-system.scm"
|
||||
"guix/build-system/ocaml.scm"
|
||||
@@ -1250,11 +1246,6 @@ the \"texlive\" importer."
|
||||
"jonsger")
|
||||
mozilla)
|
||||
|
||||
(define-member (person "Denis Carikli"
|
||||
"GNUtoo@cyberdimension.org"
|
||||
"GNUtoo")
|
||||
embedded)
|
||||
|
||||
(define-member (person "Ludovic Courtès"
|
||||
"ludo@gnu.org"
|
||||
"civodul")
|
||||
|
||||
@@ -1,6 +1,6 @@
|
||||
#!/usr/bin/env -S gawk -f
|
||||
# GNU Guix --- Functional package management for GNU
|
||||
# Copyright © 2025, 2026 Efraim Flashner <efraim@flashner.co.il>
|
||||
# Copyright © 2025 Efraim Flashner <efraim@flashner.co.il>
|
||||
#
|
||||
# This file is part of GNU Guix.
|
||||
#
|
||||
@@ -21,22 +21,20 @@
|
||||
# ./etc/teams/rust/audit-rust-crates ./path/to/file.scm
|
||||
# Prints the output of cargo-audit to the shell.
|
||||
|
||||
# Make sure we have cargo-audit in our PATH
|
||||
BEGIN {
|
||||
"which cargo-audit" | getline cargoAudit
|
||||
close("which cargo-audit")
|
||||
cargoAudit = cargoAudit " audit --file -"
|
||||
|
||||
if (system("which cargo-audit 1> /dev/null"))
|
||||
exit 1;
|
||||
# Parse a record at a time.
|
||||
RS = "\n\n"
|
||||
cargoAudit = "cargo-audit audit --file -"
|
||||
}
|
||||
|
||||
# Check the crate-source origin-only inputs, like in rust-crates.scm
|
||||
# Check the crate-source origin-only inputs
|
||||
/crate-source/ {
|
||||
for(i=3; i <= NF-2; i++) {
|
||||
if($i == "(crate-source") {
|
||||
crateName = $(i+1)
|
||||
crateVersion = $(i+2)
|
||||
cargoLock = cargoLock "[[package]]\nname = " crateName "\nversion = " crateVersion "\n"
|
||||
cargoLock = cargoLock "[[package]]\nname = " $(i+1) "\nversion = " $(i+2) "\n"
|
||||
next
|
||||
}
|
||||
}
|
||||
@@ -46,64 +44,27 @@ BEGIN {
|
||||
/crate-uri/ {
|
||||
for(i=3; i <= NF; i++) {
|
||||
if($i == "(version")
|
||||
crateVersion = $(i+1)
|
||||
crateVersion = $(i+1)
|
||||
if($i == "(crate-uri")
|
||||
crateName = $(i+1)
|
||||
crateName = $(i+1)
|
||||
}
|
||||
gsub(/)/, "", crateVersion)
|
||||
cargoLock = cargoLock "[[package]]\nname = " crateName "\nversion = " crateVersion "\n"
|
||||
next
|
||||
}
|
||||
|
||||
# Parse the crates created from packages using 'cargo package'
|
||||
/package:rust/ {
|
||||
pkg = $2
|
||||
split(pkg, name_version, "-")
|
||||
crateVersion = name_version[length(name_version)]
|
||||
crateName = substr(pkg, 6, (length(pkg) - length(crateVersion) - 6))
|
||||
split(crateVersion, versionDots, ".")
|
||||
if(crateVersion && (crateVersion != "(git-version") && (length(versionDots) == 3) && crateName) {
|
||||
cargoLock = cargoLock "[[package]]\nname = \"" crateName "\"\nversion = \"" crateVersion "\"\n"
|
||||
} else {
|
||||
untested++
|
||||
#print("Unable to test " $0)
|
||||
}
|
||||
next
|
||||
}
|
||||
# The xxxx-cargo-input variables have a set style
|
||||
# TODO: Replace the last dash between the name and the version with a space!
|
||||
# This doesn't take into account swapping between "-" and "_" so we skip it.
|
||||
#( $2 ~ /-cargo-inputs/ ) {
|
||||
# sub(/-cargo-inputs/, "", $2)
|
||||
# gsub(/)/, "", $0)
|
||||
# gsub(/rust-/, "", $0)
|
||||
# #gensub(/([[:alpha:]])-([[:digit:]]+)/, "\\1 \\2", "g", $i)
|
||||
# print "[[package]]\nname = \"" $2 "\"\nversion = \"1.0.0\"\ndependencies = ["
|
||||
# for (i = 4; i <= NF; i++) {
|
||||
# print "\"" $i "\","
|
||||
# }
|
||||
# print "]"
|
||||
#}
|
||||
|
||||
# We make an attempt to create the crate name from the package name otherwise
|
||||
/git-reference/ {
|
||||
for(i=3; i <= NF; i++) {
|
||||
if($i == "(version")
|
||||
crateVersion = $(i+1)
|
||||
if($i == "(name")
|
||||
crateName = $(i+1)
|
||||
if($i == "(git-file-name") {
|
||||
crateName = $(i+1)
|
||||
crateVersion = $(i+2)
|
||||
}
|
||||
}
|
||||
gsub(/)/, "", crateVersion)
|
||||
gsub(/)/, "", crateName)
|
||||
sub(/rust-/, "", crateName)
|
||||
# The crate version MUST be major.minor.patch
|
||||
split(crateVersion, versionParts, ".")
|
||||
if(crateVersion && (crateVersion != "(git-version") && (length(versionParts) == 3) && crateName) {
|
||||
cargoLock = cargoLock "[[package]]\nname = " crateName "\nversion = " crateVersion "\n"
|
||||
} else {
|
||||
untested++
|
||||
#print("Unable to test " $0)
|
||||
}
|
||||
next
|
||||
}
|
||||
|
||||
# Note those which we were unable to parse
|
||||
/define rust/ {
|
||||
if($3 == "#f)")
|
||||
next
|
||||
print("Unable to parse " $0)
|
||||
}
|
||||
|
||||
{ untested++ }
|
||||
|
||||
END { print("Number of crates untested: " untested); print cargoLock | cargoAudit }
|
||||
END { print cargoLock | cargoAudit }
|
||||
|
||||
@@ -445,14 +445,10 @@ load path must be adjusted as needed."
|
||||
;; Behave like an init process: create a sub-process that calls
|
||||
;; THUNK, and wait for child processes. Furthermore, forward
|
||||
;; RELAYED-SIGNALS to the child process.
|
||||
;; We presently use `safe-clone` here due to a bug in the interaction
|
||||
;; between Guix and `primitive-fork` in Guile 3.0.11:
|
||||
;; https://codeberg.org/guix/guix/issues/7690#issuecomment-12744123
|
||||
(safe-clone
|
||||
SIGCHLD
|
||||
(lambda ()
|
||||
(match (primitive-fork)
|
||||
(0
|
||||
(call-with-clean-exit thunk))
|
||||
(lambda (pid)
|
||||
(pid
|
||||
(install-signal-handlers pid)
|
||||
(let loop ()
|
||||
(match (wait-child-process)
|
||||
|
||||
26
gnu/local.mk
26
gnu/local.mk
@@ -610,7 +610,6 @@ GNU_SYSTEM_MODULES = \
|
||||
%D%/packages/rocm-apps.scm \
|
||||
%D%/packages/rocm-libs.scm \
|
||||
%D%/packages/rocm-tools.scm \
|
||||
%D%/packages/rocq.scm \
|
||||
%D%/packages/rpc.scm \
|
||||
%D%/packages/rpm.scm \
|
||||
%D%/packages/rrdtool.scm \
|
||||
@@ -1131,10 +1130,9 @@ dist_patch_DATA = \
|
||||
%D%/packages/patches/clucene-gcc-14.patch \
|
||||
%D%/packages/patches/clucene-pkgconfig.patch \
|
||||
%D%/packages/patches/coda-use-system-libs.patch \
|
||||
%D%/packages/patches/codex-acp-0.11.1-disable-code-mode.patch \
|
||||
%D%/packages/patches/codex-acp-0.11.1-remove-patch-sections.patch \
|
||||
%D%/packages/patches/codex-acp-0.9.2-remove-patch-sections.patch \
|
||||
%D%/packages/patches/codex-acp-0.9.2-replace-result-flatten.patch \
|
||||
%D%/packages/patches/codex-0.98.0-remove-patch-sections.patch \
|
||||
%D%/packages/patches/rust-codex-0.117.0-remove-patch-sections.patch \
|
||||
%D%/packages/patches/cogl-fix-double-free.patch \
|
||||
%D%/packages/patches/collada-dom-boost.patch \
|
||||
%D%/packages/patches/collectd-5.11.0-noinstallvar.patch \
|
||||
@@ -1468,6 +1466,7 @@ dist_patch_DATA = \
|
||||
%D%/packages/patches/ghostscript-no-header-creationdate.patch \
|
||||
%D%/packages/patches/gimp-fix-metadata-editor.patch \
|
||||
%D%/packages/patches/gimp-fix-tiff-load.patch \
|
||||
%D%/packages/patches/git-clar-path-max.patch \
|
||||
%D%/packages/patches/git-filter-repo-generate-doc.patch \
|
||||
%D%/packages/patches/gklib-suitesparse.patch \
|
||||
%D%/packages/patches/glib-appinfo-watch.patch \
|
||||
@@ -1617,6 +1616,7 @@ dist_patch_DATA = \
|
||||
%D%/packages/patches/hurd-refcounts-assert.patch \
|
||||
%D%/packages/patches/hurd-rumpdisk-no-hd.patch \
|
||||
%D%/packages/patches/hurd-startup.patch \
|
||||
%D%/packages/patches/hwloc-1-test-btrfs.patch \
|
||||
%D%/packages/patches/hwloc-add-with-opencl.patch \
|
||||
%D%/packages/patches/i3lock-blur-fix-build-on-gcc-10.patch \
|
||||
%D%/packages/patches/i7z-gcc-10.patch \
|
||||
@@ -1652,7 +1652,6 @@ dist_patch_DATA = \
|
||||
%D%/packages/patches/id3lib-CVE-2007-4460.patch \
|
||||
%D%/packages/patches/id3lib-UTF16-writing-bug.patch \
|
||||
%D%/packages/patches/ilmbase-fix-tests.patch \
|
||||
%D%/packages/patches/inetutils-drop-test.patch \
|
||||
%D%/packages/patches/inferno-fix-crash.patch \
|
||||
%D%/packages/patches/iniparser-remove-fetchcontent-usage.patch \
|
||||
%D%/packages/patches/inkscape-libxml2.patch \
|
||||
@@ -1699,6 +1698,7 @@ dist_patch_DATA = \
|
||||
%D%/packages/patches/libcss-check-format.patch \
|
||||
%D%/packages/patches/libeb-gcc-14.patch \
|
||||
%D%/packages/patches/libextractor-tidy-support.patch \
|
||||
%D%/packages/patches/libfossil-skip-amalgamation.patch \
|
||||
%D%/packages/patches/libftdi-fix-paths-when-FTDIPP-set.patch \
|
||||
%D%/packages/patches/libgeotiff-fix-tests-with-proj-9.1.1.patch \
|
||||
%D%/packages/patches/libgeotiff-fix-tests-with-proj-9.3.0.patch \
|
||||
@@ -1713,7 +1713,6 @@ dist_patch_DATA = \
|
||||
%D%/packages/patches/libretro-dolphin-emu-libusb-assert.patch \
|
||||
%D%/packages/patches/libretro-dolphin-emu-vulkan-headers.patch \
|
||||
%D%/packages/patches/libretranslate-use-flasgger.patch \
|
||||
%D%/packages/patches/librewolf-150.0-encoding_rs-rust-fix.patch \
|
||||
%D%/packages/patches/librewolf-add-store-to-rdd-allowlist.patch \
|
||||
%D%/packages/patches/librewolf-compare-paths.patch \
|
||||
%D%/packages/patches/librewolf-neuter-locale-download.patch \
|
||||
@@ -2349,16 +2348,8 @@ dist_patch_DATA = \
|
||||
%D%/packages/patches/renpy-fix-integer-slots.patch \
|
||||
%D%/packages/patches/reposurgeon-add-missing-docbook-files.patch \
|
||||
%D%/packages/patches/rdkit-unbundle-external-dependencies.patch \
|
||||
%D%/packages/patches/r-biostrings-r4.6.0-compat.patch \
|
||||
%D%/packages/patches/r-h5mread-0001-h5mread-1.3.2-Get-rid-of-non-API-calls-to-R.patch \
|
||||
%D%/packages/patches/r-httpuv-1.6.6-unvendor-libuv.patch \
|
||||
%D%/packages/patches/r-mscoreutils-0001-fix-non-API-call-to-R-SETLENGTH-by-using-lengthgets.patch \
|
||||
%D%/packages/patches/r-rsamtools-r-4.6.0-compat.patch \
|
||||
%D%/packages/patches/r-snpstats-0001-fixed-non-API-except-for-IS_S4_OBJECT.patch \
|
||||
%D%/packages/patches/r-snpstats-0002-fixed-IS_S4_OBJECT.patch \
|
||||
%D%/packages/patches/r-sapa-lapack.patch \
|
||||
%D%/packages/patches/r-shortread-0001-ShortRead-1.69.3-Get-rid-of-non-API-calls-to-R.patch \
|
||||
%D%/packages/patches/r-sparsearray-r-4.6.0-compat.patch \
|
||||
%D%/packages/patches/ripperx-missing-file.patch \
|
||||
%D%/packages/patches/rpcbind-CVE-2017-8779.patch \
|
||||
%D%/packages/patches/rtosc-0.3.1-fix-invalid-comparison-operator.patch \
|
||||
@@ -2403,13 +2394,6 @@ dist_patch_DATA = \
|
||||
%D%/packages/patches/rust-codex-0.98.0-test-shebangs.patch \
|
||||
%D%/packages/patches/rust-codex-0.98.0-test-timeout.patch \
|
||||
%D%/packages/patches/rust-codex-0.98.0-windows-sandbox-protocol-version.patch \
|
||||
%D%/packages/patches/rust-codex-0.117.0-core-remove-self-dep.patch \
|
||||
%D%/packages/patches/rust-codex-0.120.0-core-remove-self-dep.patch \
|
||||
%D%/packages/patches/rust-codex-0.120.0-connectors-cache-test-race.patch \
|
||||
%D%/packages/patches/rust-codex-0.120.0-remove-libwebrtc.patch \
|
||||
%D%/packages/patches/rust-codex-0.120.0-test-timeout.patch \
|
||||
%D%/packages/patches/rust-codex-0.124.0-code-mode-stub-toolname.patch \
|
||||
%D%/packages/patches/rust-codex-0.124.0-remove-patch-sections.patch \
|
||||
%D%/packages/patches/rust-ring-0.17-ring-core.patch \
|
||||
%D%/packages/patches/rw-igraph-0.10.patch \
|
||||
%D%/packages/patches/rxvt-unicode-fix-cursor-position.patch \
|
||||
|
||||
@@ -1,5 +1,5 @@
|
||||
;;; GNU Guix --- Functional package management for GNU
|
||||
;;; Copyright © 2012-2026 Ludovic Courtès <ludo@gnu.org>
|
||||
;;; Copyright © 2012-2025 Ludovic Courtès <ludo@gnu.org>
|
||||
;;; Copyright © 2013 Cyril Roelandt <tipecaml@gmail.com>
|
||||
;;; Copyright © 2014, 2015, 2016, 2018, 2019, 2020 Mark H Weaver <mhw@netris.org>
|
||||
;;; Copyright © 2014, 2015-2018, 2020-2023 Eric Bavier <bavier@posteo.net>
|
||||
@@ -1158,7 +1158,7 @@ on memory usage on GNU/Linux systems.")
|
||||
(define-public htop
|
||||
(package
|
||||
(name "htop")
|
||||
(version "3.5.0")
|
||||
(version "3.4.1")
|
||||
(source
|
||||
(origin
|
||||
(method git-fetch)
|
||||
@@ -1166,7 +1166,7 @@ on memory usage on GNU/Linux systems.")
|
||||
(url "https://github.com/htop-dev/htop")
|
||||
(commit version)))
|
||||
(sha256
|
||||
(base32 "1r07ri0dl9xz0jn1hc2g8q3l0q4clvnxs05yagpzsz0zigp4flj5"))
|
||||
(base32 "058y4a4mvx9m179dyr4wi8mlm6i4ybywshadaj4cvfn9fv0r0nkx"))
|
||||
(file-name (git-file-name name version))))
|
||||
(build-system gnu-build-system)
|
||||
(arguments
|
||||
@@ -1309,8 +1309,7 @@ re-executing them as necessary.")
|
||||
version ".tar.gz"))
|
||||
(sha256
|
||||
(base32
|
||||
"11n01vsd51r7qraaaylhhx04hq4s6vcq0896zkz0yp1wvqfbwmm1"))
|
||||
(patches (search-patches "inetutils-drop-test.patch"))))
|
||||
"11n01vsd51r7qraaaylhhx04hq4s6vcq0896zkz0yp1wvqfbwmm1"))))
|
||||
(build-system gnu-build-system)
|
||||
(arguments
|
||||
(list
|
||||
@@ -3442,7 +3441,7 @@ modules and plugins that extend Ansible.")
|
||||
(list ansible
|
||||
bash-minimal
|
||||
encfs
|
||||
fuse
|
||||
fuse-2
|
||||
util-linux ;; for umount
|
||||
findutils
|
||||
git
|
||||
@@ -3751,68 +3750,59 @@ summarizes network bandwidth by process and remote host.")
|
||||
(define-public munge
|
||||
(package
|
||||
(name "munge")
|
||||
(version "0.5.18")
|
||||
(version "0.5.14")
|
||||
(source (origin
|
||||
(method git-fetch)
|
||||
(uri (git-reference
|
||||
(url "https://github.com/dun/munge")
|
||||
(commit (string-append "munge-" version))))
|
||||
(file-name (git-file-name name version))
|
||||
(method url-fetch)
|
||||
(uri (string-append "https://github.com/dun/munge/releases/"
|
||||
"download/munge-" version "/munge-"
|
||||
version ".tar.xz"))
|
||||
(sha256
|
||||
(base32
|
||||
"1b7gm680dlvmgvj9vxy7n0cqmnv1rl9n4563vasxdxx54f78j30s"))
|
||||
"0h06sghb4rqvv1ywyd6mzsmbcgh712v6ygrff0gzm440y4ca41k6"))
|
||||
(modules '((guix build utils)))
|
||||
(snippet
|
||||
;; Don't insist on write access to /var.
|
||||
#~(substitute* "src/etc/Makefile.am"
|
||||
(("\\$\\(MKDIR_P\\) .*(local|run)statedir.*" all)
|
||||
(string-append ": " all))))))
|
||||
'(begin
|
||||
;; Don't insist on write access to /var.
|
||||
(substitute* "src/etc/Makefile.in"
|
||||
(("\\$\\(INSTALL\\)(.*)localstatedir" _ middle)
|
||||
(string-append "-$(INSTALL)" middle "localstatedir"))
|
||||
(("\\$\\(MKDIR_P\\) .*(local|run)statedir.*")
|
||||
""))
|
||||
#t))))
|
||||
(inputs
|
||||
(list openssl libgcrypt))
|
||||
(native-inputs
|
||||
(list autoconf
|
||||
automake
|
||||
libtool
|
||||
procps)) ;for tests
|
||||
(build-system gnu-build-system)
|
||||
(arguments
|
||||
(list #:configure-flags
|
||||
#~(list "--localstatedir=/var"
|
||||
"--disable-static"
|
||||
#$@(if (%current-target-system)
|
||||
;; Assume yes on pipes when cross compiling.
|
||||
`("ac_cv_file__dev_spx=yes"
|
||||
"x_ac_cv_check_fifo_recvfd=yes")
|
||||
'())
|
||||
|
||||
;; The '.pc' file is not installed when omitting this flag.
|
||||
(string-append "--with-pkgconfigdir="
|
||||
#$output "/lib/pkgconfig"))
|
||||
#:phases
|
||||
#~(modify-phases %standard-phases
|
||||
(add-before 'bootstrap 'pre-bootstrap
|
||||
(lambda _
|
||||
(for-each patch-shebang (find-files "build-aux"))))
|
||||
(add-after 'unpack 'skip-failing-tests
|
||||
(lambda _
|
||||
;; Pass '--force' to 'munged'; without it, it fails with "Socket
|
||||
;; is inaccessible" due to the build directory not being
|
||||
;; world-readable.
|
||||
(substitute* "tests/sharness.d/03-munged.sh"
|
||||
(("--group-update-time=-1" all)
|
||||
(string-append all " --force")))
|
||||
|
||||
;; The tests below invoke 'sudo' or have special expectations
|
||||
;; about network interfaces.
|
||||
(for-each (lambda (test)
|
||||
(substitute* "tests/Makefile.am"
|
||||
(((string-append test "\\.t "))
|
||||
"")))
|
||||
(list "0100-munged-lock"
|
||||
"0101-munged-security-socket"
|
||||
"0102-munged-security-keyfile"
|
||||
"0103-munged-security-logfile"
|
||||
"0110-munged-origin-addr")))))))
|
||||
`(#:configure-flags
|
||||
(list "--localstatedir=/var"
|
||||
(string-append "--with-pkgconfigdir="
|
||||
(assoc-ref %outputs "out") "/lib/pkgconfig")
|
||||
(string-append "--with-libgcrypt-prefix="
|
||||
(assoc-ref %build-inputs "libgcrypt"))
|
||||
,@(if (%current-target-system)
|
||||
;; Assume yes on pipes when cross compiling.
|
||||
`("ac_cv_file__dev_spx=yes"
|
||||
"x_ac_cv_check_fifo_recvfd=yes")
|
||||
'()))
|
||||
#:phases
|
||||
(modify-phases %standard-phases
|
||||
;; XXX Many test series fail. Some might be fixable, others do no-no
|
||||
;; things like invoking ‘sudo’.
|
||||
(add-after 'unpack 'skip-failing-tests
|
||||
(lambda _
|
||||
(for-each (lambda (test)
|
||||
(substitute* "t/Makefile.in"
|
||||
(((string-append test "\\.t ")) "")))
|
||||
(list "0100-munged-lock"
|
||||
"0010-basic"
|
||||
"0011-munged-cmdline"
|
||||
"0012-munge-cmdline"
|
||||
"0013-unmunge-cmdline"
|
||||
"0101-munged-security-socket"
|
||||
"0102-munged-security-keyfile"
|
||||
"0103-munged-security-logfile"
|
||||
"0110-munged-origin-addr"))
|
||||
#t)))))
|
||||
(home-page "https://dun.github.io/munge/")
|
||||
(synopsis "Cluster computing authentication service")
|
||||
(description
|
||||
@@ -7179,35 +7169,6 @@ stored in an SQL database.")
|
||||
(connects via USB OTG).")
|
||||
(license license:expat)))
|
||||
|
||||
(define-public yoctofetch
|
||||
(package
|
||||
(name "yoctofetch")
|
||||
(version "2.0.0")
|
||||
(source
|
||||
(origin
|
||||
(method git-fetch)
|
||||
(uri (git-reference
|
||||
(url "https://codeberg.org/Phosphenius/yoctofetch.git")
|
||||
(commit (string-append "v" version))))
|
||||
(file-name (git-file-name name version))
|
||||
(sha256
|
||||
(base32 "0smkaydv74p2231gafibvqbwsy469w56hya8gz8wq0gw7m2l7zh3"))))
|
||||
; Support for other platforms not available per upstream:
|
||||
; https://codeberg.org/Phosphenius/yoctofetch#supported-platforms
|
||||
(supported-systems '("x86_64-linux" "aarch64-linux"))
|
||||
(build-system gnu-build-system)
|
||||
(arguments
|
||||
(list
|
||||
#:tests? #f)) ; No tests available.
|
||||
(home-page "https://codeberg.org/Phosphenius/yoctofetch")
|
||||
(synopsis "Fast and low footprint system fetch tool for the Linux UAPI")
|
||||
(description
|
||||
"This package provides a system fetch tool, similar to
|
||||
@command{neofetch}, @command{fastfetch}, etc. It is lightweight and
|
||||
has a focus on performance. It can be used as a greeter by starting
|
||||
it from @file{~/.bashrc} for example.")
|
||||
(license license:agpl3+)))
|
||||
|
||||
(define-public zzz
|
||||
(package
|
||||
(name "zzz")
|
||||
|
||||
@@ -6529,23 +6529,22 @@ on the ALSA software PCM plugin.")
|
||||
(define-public snd
|
||||
(package
|
||||
(name "snd")
|
||||
(version "26.3")
|
||||
(source
|
||||
(origin
|
||||
(method url-fetch)
|
||||
(uri (string-append "https://ccrma.stanford.edu/software/snd/snd-"
|
||||
version ".tar.gz"))
|
||||
(sha256
|
||||
(base32
|
||||
"1d573mjlrn9rhl9g0a3d1rkar34q60ln8mwlbibfalpn8lsz59a0"))))
|
||||
(version "25.2")
|
||||
(source (origin
|
||||
(method url-fetch)
|
||||
(uri (string-append "ftp://ccrma-ftp.stanford.edu/pub/Lisp/"
|
||||
"snd-" version ".tar.gz"))
|
||||
(sha256
|
||||
(base32
|
||||
"0fgxqk0byxdj6059mb9d5qic2dqjabz49j0szsrn2y3c9nz6iyq4"))))
|
||||
(build-system gnu-build-system)
|
||||
(arguments
|
||||
(list
|
||||
#:tests? #f ; No tests.
|
||||
#:out-of-source? #f ; Required by 'install-doc'.
|
||||
#:tests? #f ; no tests
|
||||
#:out-of-source? #f ; for the 'install-doc' phase
|
||||
#:configure-flags
|
||||
#~(let
|
||||
((docdir (string-append #$output "/share/doc/snd-" #$version)))
|
||||
#~(let ((docdir (string-append #$output "/share/doc/"
|
||||
#$name "-" #$version)))
|
||||
(list "--with-alsa"
|
||||
"--with-jack"
|
||||
"--with-gmp"
|
||||
@@ -6553,20 +6552,18 @@ on the ALSA software PCM plugin.")
|
||||
(string-append "--with-doc-dir=" docdir)))
|
||||
#:phases
|
||||
#~(modify-phases %standard-phases
|
||||
(add-after 'install 'install-s7-h
|
||||
(add-after 'install 'install-s7
|
||||
(lambda _
|
||||
(install-file "s7.h" (string-append #$output
|
||||
"/include"))))
|
||||
(install-file "s7.h" (string-append #$output "/include"))))
|
||||
(add-after 'install 'install-doc
|
||||
(lambda _
|
||||
(let
|
||||
((docdir (string-append #$output "/share/doc/snd-"
|
||||
#$version)))
|
||||
(let ((doc (string-append #$output "/share/doc/"
|
||||
#$name "-" #$version)))
|
||||
(for-each
|
||||
(lambda (f)
|
||||
(install-file f docdir))
|
||||
(install-file f doc))
|
||||
(find-files "." "\\.html$"))
|
||||
(copy-recursively "pix" (string-append docdir "/pix"))))))))
|
||||
(copy-recursively "pix" (string-append doc "/pix"))))))))
|
||||
(native-inputs
|
||||
(list pkg-config))
|
||||
(inputs
|
||||
@@ -6585,16 +6582,13 @@ on the ALSA software PCM plugin.")
|
||||
timidity++
|
||||
vorbis-tools
|
||||
wavpack))
|
||||
(home-page "https://ccrma.stanford.edu/software/snd/snd/snd.html")
|
||||
(synopsis "Sound editor")
|
||||
(home-page "https://ccrma.stanford.edu/software/snd/")
|
||||
(description
|
||||
"Snd is a sound editor modelled loosely after Emacs. It can be
|
||||
customized and extended using either the s7 Scheme implementation (included in
|
||||
the Snd sources), Ruby, or Forth.")
|
||||
(license
|
||||
;; INFO: pkgsrc classifies this as `esdl-license', a license not included
|
||||
;; in OSI or FSF lists, despite being similar to ISC.
|
||||
(license:non-copyleft "file://COPYING"))))
|
||||
(license (license:non-copyleft "file://COPYING"))))
|
||||
|
||||
(define-public libspecbleach
|
||||
(package
|
||||
|
||||
@@ -341,7 +341,7 @@ runtime.")
|
||||
("java-jgit" ,java-jgit-4.2)
|
||||
("axoloti-runtime" ,axoloti-runtime)))
|
||||
(native-inputs
|
||||
(list ant zip ; for repacking the jar
|
||||
(list ant/java7 zip ; for repacking the jar
|
||||
unzip))
|
||||
(description
|
||||
"The Axoloti patcher offers a “patcher” environment similar to Pure Data
|
||||
@@ -647,7 +647,7 @@ This package provides the runtime.")
|
||||
("java-slf4j-api" ,java-slf4j-api)
|
||||
("ksoloti-runtime" ,ksoloti-runtime)))
|
||||
(native-inputs
|
||||
(list ant zip ;for repacking the jar
|
||||
(list ant/java7 zip ;for repacking the jar
|
||||
unzip))
|
||||
(description
|
||||
"Ksoloti is an environment for generating and processing digital audio.
|
||||
|
||||
File diff suppressed because it is too large
Load Diff
@@ -913,7 +913,7 @@ suite native in R.")
|
||||
(define-public r-bpcells
|
||||
(package
|
||||
(name "r-bpcells")
|
||||
(version "0.3.1")
|
||||
(version "0.3.0")
|
||||
(source
|
||||
(origin
|
||||
(method git-fetch)
|
||||
@@ -922,7 +922,7 @@ suite native in R.")
|
||||
(commit (string-append "v" version))))
|
||||
(file-name (git-file-name name version))
|
||||
(sha256
|
||||
(base32 "0yqgcajq83g25mznwcngaw7pi6vcqxqdnynpgb95yci57k3wrp6j"))
|
||||
(base32 "12h1di45fg06nhsliii7v0h1z567pkpis1xm4ar1qr8ns1n8iljw"))
|
||||
(modules '((guix build utils)))
|
||||
(snippet
|
||||
'(delete-file-recursively "r/src/vendor/highway"))))
|
||||
@@ -931,15 +931,13 @@ suite native in R.")
|
||||
(arguments
|
||||
(list
|
||||
#:phases
|
||||
`(modify-phases %standard-phases
|
||||
'(modify-phases %standard-phases
|
||||
(add-after 'unpack 'chdir
|
||||
(lambda _ (chdir "r")))
|
||||
,@(if (target-x86-32?)
|
||||
'((add-after 'chdir 'require-sse2
|
||||
;; This avoids falling back to the scalar backend in
|
||||
;; highway, which fails to build.
|
||||
(lambda _ (setenv "CFLAGS" "-msse2"))))
|
||||
'()))))
|
||||
(lambda _
|
||||
(substitute* "r/configure"
|
||||
(("tools/hwy-test.cpp" m)
|
||||
(string-append m " $HWY_LIBS $HWY_CFLAGS")))
|
||||
(chdir "r"))))))
|
||||
(propagated-inputs
|
||||
(list r-dplyr
|
||||
r-ggplot2
|
||||
@@ -9285,7 +9283,7 @@ VCF.")
|
||||
;; [testng] Exception in thread "main" java.lang.NoClassDefFoundError: com/beust/jcommander/ParameterException
|
||||
#:tests? #f
|
||||
#:jdk ,icedtea-8
|
||||
#:ant ,ant/java8
|
||||
#:ant ,ant
|
||||
;; This is only used for tests.
|
||||
#:make-flags
|
||||
(list "-Dsamjdk.intel_deflater_so_path=lib/jni/libIntelDeflater.so")
|
||||
@@ -9355,11 +9353,10 @@ VCF.")
|
||||
(list java-snappy-1
|
||||
java-commons-jexl-2
|
||||
java-cofoja
|
||||
ant/java8 ;for bzip2 support at runtime
|
||||
ant ;for bzip2 support at runtime
|
||||
zlib))
|
||||
(native-inputs
|
||||
`(("ant-apache-bcel" ,ant-apache-bcel)
|
||||
("ant-junit" ,ant-junit)
|
||||
("java-testng" ,java-testng)
|
||||
("java-commons-bcel" ,java-commons-bcel)
|
||||
("java-jcommander" ,java-jcommander)
|
||||
@@ -22351,6 +22348,37 @@ combinatorial configurations.\", G. Ehrlich - Journal of the ACM (JACM),
|
||||
1973. (Algorithm 7.)")
|
||||
(license license:expat)))
|
||||
|
||||
(define-public fsom
|
||||
(let ((commit "a6ef318fbd347c53189384aef7f670c0e6ce89a3"))
|
||||
(package
|
||||
(name "fsom")
|
||||
(version (git-version "0.0.0" "1" commit))
|
||||
(source (origin
|
||||
(method git-fetch)
|
||||
(uri (git-reference
|
||||
(url "https://github.com/ekg/fsom/")
|
||||
(commit commit)))
|
||||
(file-name (git-file-name name version))
|
||||
(sha256
|
||||
(base32 "0gw1lpvr812pywg9y546x0h1hhj261xwls41r6kqhddjlrcjc0pi"))))
|
||||
(build-system gnu-build-system)
|
||||
(arguments
|
||||
`(#:tests? #f ; There are no tests to run.
|
||||
#:phases
|
||||
(modify-phases %standard-phases
|
||||
(delete 'configure) ; There is no configure phase.
|
||||
(replace 'install
|
||||
(lambda* (#:key outputs #:allow-other-keys)
|
||||
(let ((bin (string-append (assoc-ref outputs "out") "/bin")))
|
||||
(install-file "fsom" bin)))))))
|
||||
(native-inputs
|
||||
(list gcc-6))
|
||||
(home-page "https://github.com/ekg/fsom")
|
||||
(synopsis "Manage SOM (Self-Organizing Maps) neural networks")
|
||||
(description "A tiny C library for managing SOM (Self-Organizing Maps)
|
||||
neural networks.")
|
||||
(license license:gpl3))))
|
||||
|
||||
(define-public fastahack
|
||||
(package
|
||||
(name "fastahack")
|
||||
|
||||
@@ -275,14 +275,14 @@ generate such a compilation database.")
|
||||
(define-public bmake
|
||||
(package
|
||||
(name "bmake")
|
||||
(version "20260406")
|
||||
(version "20260313")
|
||||
(source
|
||||
(origin
|
||||
(method url-fetch)
|
||||
(uri (string-append
|
||||
"http://www.crufty.net/ftp/pub/sjg/bmake-" version ".tar.gz"))
|
||||
(sha256
|
||||
(base32 "09nzd9v12n2pwxmf67056kzjnvxcpk5q2x1fs5qkrsk1ssh5yvpd"))
|
||||
(base32 "0xgryknmv625idw37rq89mpl5rymwdb15j5w8zxwy1gf8b6z7j3n"))
|
||||
(patches (search-patches "bmake-run-check-separately.patch"))))
|
||||
(build-system gnu-build-system)
|
||||
(inputs
|
||||
|
||||
@@ -23,7 +23,7 @@
|
||||
;;; Copyright © 2023, 2024 David Elsing <david.elsing@posteo.net>
|
||||
;;; Copyright @ 2022, Kitzman <kitzman@disroot.org>
|
||||
;;; Copyright @ 2025 Dariqq <dariqq@posteo.net>
|
||||
;;; Copyright © 2025, 2026 Ashish SHUKLA <ashish.is@lostca.se>
|
||||
;;; Copyright © 2025 Ashish SHUKLA <ashish.is@lostca.se>
|
||||
;;; Copyright © 2026 Cayetano Santos <csantosb@inventati.org>
|
||||
;;; Copyright © 2026 Sharlatan Hellseher <sharlatanus@gmail.com>
|
||||
;;;
|
||||
@@ -1762,7 +1762,7 @@ string.h, but with a utf8* prefix instead of the str* prefix.")
|
||||
(define-public simdutf
|
||||
(package
|
||||
(name "simdutf")
|
||||
(version "9.0.0")
|
||||
(version "7.7.1")
|
||||
(source
|
||||
(origin
|
||||
(method git-fetch)
|
||||
@@ -1771,7 +1771,7 @@ string.h, but with a utf8* prefix instead of the str* prefix.")
|
||||
(commit (string-append "v" version))))
|
||||
(file-name (git-file-name name version))
|
||||
(sha256
|
||||
(base32 "0f5ccvqj7pfa69m9y1kxp2v1lybx6x8i9pykdqfkr7dydqbhrhx6"))))
|
||||
(base32 "0kw4j4qqcfjaii667xa745pklj50m70nqq8cj5agj714acczbk7y"))))
|
||||
(build-system cmake-build-system)
|
||||
(arguments (list #:configure-flags #~(list "-DBUILD_SHARED_LIBS=ON")))
|
||||
(synopsis "SIMD Unicode validation and transcoding")
|
||||
|
||||
@@ -3131,7 +3131,7 @@ time by mocking the datetime module.")
|
||||
(define-public python-flaky
|
||||
(package
|
||||
(name "python-flaky")
|
||||
(version "3.8.1") ; On bump, remove some skipped tests in python-cherrypy.
|
||||
(version "3.8.1")
|
||||
(source (origin
|
||||
(method url-fetch)
|
||||
(uri (pypi-uri "flaky" version))
|
||||
@@ -3719,6 +3719,30 @@ system. The code under test requires no modification to work with pyfakefs.")
|
||||
directories and files.")
|
||||
(license license:expat)))
|
||||
|
||||
(define-public python-pytest-tornado5
|
||||
(package
|
||||
(name "python-pytest-tornado5")
|
||||
(version "2.0.0")
|
||||
(source (origin
|
||||
(method url-fetch)
|
||||
(uri (pypi-uri "pytest-tornado5" version))
|
||||
(sha256
|
||||
(base32
|
||||
"0qb62jw2w0xr6y942yp0qxiy755bismjfpnxaxjjm05gy2pymr8d"))))
|
||||
(build-system pyproject-build-system)
|
||||
(arguments
|
||||
;; Tests require pytest < 6
|
||||
(list #:tests? #f))
|
||||
(propagated-inputs (list python-pytest python-tornado))
|
||||
(native-inputs (list python-setuptools python-wheel))
|
||||
(home-page "https://github.com/vidartf/pytest-tornado")
|
||||
(synopsis
|
||||
"Fixtures and markers to simplify testing of Tornado applications")
|
||||
(description
|
||||
"This package provides a @code{py.test} plugin supplying fixtures and
|
||||
markers to simplify testing of asynchronous tornado applications.")
|
||||
(license license:asl2.0)))
|
||||
|
||||
(define-public guile-proba
|
||||
(package
|
||||
(name "guile-proba")
|
||||
|
||||
@@ -580,7 +580,7 @@ stored with user-specified precision.")
|
||||
python-sphinx))
|
||||
(inputs
|
||||
(list fftwf
|
||||
`(,hwloc "lib")
|
||||
`(,hwloc-2 "lib")
|
||||
libtirpc
|
||||
lmfit
|
||||
muparser
|
||||
|
||||
@@ -18,10 +18,10 @@
|
||||
|
||||
;;; This module is separate from (gnu packages rust-apps) to avoid a
|
||||
;;; circular module dependency: (gnu packages rust-sources), which
|
||||
;;; defines rust-codex-0.124.0, transitively loads (gnu packages
|
||||
;;; defines rust-codex-0.98.0, transitively loads (gnu packages
|
||||
;;; rust-apps) through its #:use-module chain. If the codex package
|
||||
;;; lived in rust-apps.scm, loading rust-sources would trigger loading
|
||||
;;; rust-apps before rust-codex-0.124.0 is defined, causing an unbound
|
||||
;;; rust-apps before rust-codex-0.98.0 is defined, causing an unbound
|
||||
;;; variable error.
|
||||
|
||||
(define-module (gnu packages codex)
|
||||
@@ -36,46 +36,33 @@
|
||||
#:use-module (gnu packages base)
|
||||
#:use-module (gnu packages cmake)
|
||||
#:use-module (gnu packages compression)
|
||||
#:use-module (gnu packages linux)
|
||||
#:use-module (gnu packages libunwind)
|
||||
#:use-module (gnu packages llvm)
|
||||
#:use-module (gnu packages lsof)
|
||||
#:use-module (gnu packages perl)
|
||||
#:use-module (gnu packages pkg-config)
|
||||
#:use-module (gnu packages python)
|
||||
#:use-module (gnu packages rust-sources)
|
||||
#:use-module (gnu packages sqlite)
|
||||
#:use-module (gnu packages textutils)
|
||||
#:use-module (gnu packages nss)
|
||||
#:use-module (gnu packages tls)
|
||||
#:use-module (gnu packages version-control)
|
||||
#:use-module (gnu packages virtualization))
|
||||
#:use-module (gnu packages version-control))
|
||||
|
||||
(define-public codex
|
||||
(package
|
||||
(name "codex")
|
||||
(version (package-version rust-codex-0.124.0))
|
||||
(version (package-version rust-codex-0.98.0))
|
||||
(source
|
||||
(origin
|
||||
(inherit (package-source rust-codex-0.124.0))
|
||||
(inherit (package-source rust-codex-0.98.0))
|
||||
(patches (search-patches
|
||||
"codex-acp-0.11.1-disable-code-mode.patch"
|
||||
"rust-codex-0.124.0-code-mode-stub-toolname.patch"
|
||||
"rust-codex-0.124.0-remove-patch-sections.patch"
|
||||
"rust-codex-0.120.0-remove-libwebrtc.patch"
|
||||
"codex-0.98.0-remove-patch-sections.patch"
|
||||
"rust-codex-0.98.0-test-shebangs.patch"
|
||||
"rust-codex-0.120.0-test-timeout.patch"))))
|
||||
"rust-codex-0.98.0-test-timeout.patch"))))
|
||||
(build-system cargo-build-system)
|
||||
(arguments
|
||||
(list
|
||||
#:install-source? #f
|
||||
;; exec-server is library-only in 0.124 (no [[bin]] in
|
||||
;; exec-server/Cargo.toml); cargo install --path exec-server fails
|
||||
;; with "no packages found with binaries or examples". Drop it
|
||||
;; from the install paths -- the library is consumed via the
|
||||
;; workspace by other binaries here, not installed standalone.
|
||||
#:cargo-install-paths '(list "cli" "exec"
|
||||
"linux-sandbox" "mcp-server"
|
||||
#:cargo-install-paths '(list "cli" "exec" "exec-server"
|
||||
"linux-sandbox" "mcp-server" "network-proxy"
|
||||
"app-server" "tui")
|
||||
;; schema_fixtures_match_generated (upstream fixture is stale:
|
||||
;; FileChange::Update in codex-protocol gained old_content,
|
||||
@@ -84,55 +71,72 @@
|
||||
#:cargo-test-flags '(list "--workspace"
|
||||
"--exclude" "codex-app-server-protocol"
|
||||
"--"
|
||||
;;; BEGIN Landlock returns NotEnforced
|
||||
;;; in the build container; the sandbox
|
||||
;;; binary panics instead of cleanly
|
||||
;;; denying filesystem access.
|
||||
;; Sandbox denial and escalation tests.
|
||||
;; These tests exercise sandbox denial and
|
||||
;; escalation, which requires Landlock to
|
||||
;; cleanly deny filesystem access. Inside the
|
||||
;; build container Landlock returns NotEnforced
|
||||
;; and the sandbox binary panics instead.
|
||||
;; Disabling Landlock would not help either,
|
||||
;; since these tests need a working sandbox to
|
||||
;; have anything to deny and escalate.
|
||||
"--skip" "sandbox_denied_shell_returns_original_output"
|
||||
;; Sandbox denial and escalation tests.
|
||||
"--skip" "shell_escalated_permissions_rejected_then_ok"
|
||||
;; Sandbox denial and escalation tests.
|
||||
"--skip" "unified_exec_runs_under_sandbox"
|
||||
;; codex-exec: spawn_command_under_linux_sandbox
|
||||
;; panics with LandlockRestrict (exit 101).
|
||||
;; These tests (in codex-exec) directly call
|
||||
;; spawn_command_under_linux_sandbox to verify
|
||||
;; that python and bash work correctly inside
|
||||
;; the Landlock sandbox. The sandbox binary
|
||||
;; (codex-exec) panics with LandlockRestrict
|
||||
;; (exit code 101) before the inner command
|
||||
;; even starts.
|
||||
"--skip" "python_getpwuid_works_under_sandbox"
|
||||
;; Same as above.
|
||||
"--skip" "python_multiprocessing_lock_works_under_sandbox"
|
||||
;; Same as above.
|
||||
"--skip" "sandbox_distinguishes_command_and_policy_cwds"
|
||||
;; linux-sandbox: process_exec_tool_call
|
||||
;; invokes Landlock; same panic.
|
||||
;; These linux-sandbox tests directly invoke
|
||||
;; the Landlock sandbox via
|
||||
;; process_exec_tool_call; same root cause.
|
||||
"--skip" "test_writable_root"
|
||||
;; Same as above.
|
||||
"--skip" "test_timeout"
|
||||
;; Same as above.
|
||||
"--skip" "test_root_read"
|
||||
;; Same as above.
|
||||
"--skip" "test_dev_null_write"
|
||||
;; Same as above.
|
||||
"--skip" "test_no_new_privs_is_enabled"
|
||||
;; One scenario runs through Landlock
|
||||
;; which panics; cargo --skip cannot
|
||||
;; target individual scenarios.
|
||||
;; This test iterates many approval scenarios;
|
||||
;; one of them
|
||||
;; (danger_full_access_on_request_allows_network)
|
||||
;; runs a command through the Landlock sandbox
|
||||
;; binary, which panics with LandlockRestrict
|
||||
;; inside the build container. Cargo --skip
|
||||
;; cannot target individual scenarios, so we
|
||||
;; skip the entire matrix.
|
||||
"--skip" "approval_matrix_covers_all_modes"
|
||||
;; Landlock panic triggers escalation-retry
|
||||
;; which interferes with the approval cache.
|
||||
;; This test verifies session-level patch
|
||||
;; approval caching: approve once, skip
|
||||
;; future prompts for the same file. When
|
||||
;; Landlock is unavailable (as in the Guix
|
||||
;; build container) the sandbox binary panics,
|
||||
;; triggering the escalation-retry path, which
|
||||
;; interferes with the approval cache and
|
||||
;; causes a spurious re-prompt on the second
|
||||
;; patch.
|
||||
"--skip" "approving_apply_patch_for_session_skips_future_prompts_for_same_file"
|
||||
;; These tests expect to interrupt a
|
||||
;; long-running 'sleep 60' and receive
|
||||
;; TurnAborted. What happens:
|
||||
;; TurnAborted. Default test config is
|
||||
;; OnRequest + ReadOnly. What happens:
|
||||
;;
|
||||
;; 1. ReadOnly wraps the command with
|
||||
;; codex-linux-sandbox (Landlock-based).
|
||||
;; 2. Landlock is unavailable, so the
|
||||
;; sandbox binary exits instantly.
|
||||
;; 2. Landlock is unavailable in the Guix
|
||||
;; build container, so the sandbox
|
||||
;; binary exits instantly (~1 ms).
|
||||
;; 3. Orchestrator gets SandboxErr::Denied.
|
||||
;; wants_no_sandbox_approval(OnRequest)
|
||||
;; returns false, so no escalation --
|
||||
;; denial returned directly.
|
||||
;; returns false (sandboxing.rs:222),
|
||||
;; so no escalation -- denial returned
|
||||
;; directly.
|
||||
;; 4. ToolEmitter::finish sends the error
|
||||
;; to the mock model.
|
||||
;; to the mock model as
|
||||
;; function_call_output.
|
||||
;; 5. Second mock SSE response fires,
|
||||
;; turn finishes with TurnComplete.
|
||||
;; 6. Op::Interrupt arrives 100 ms later,
|
||||
@@ -146,370 +150,74 @@
|
||||
;; has only one mock response (so the turn
|
||||
;; cannot complete first).
|
||||
"--skip" "interrupt_persists_turn_aborted_marker_in_next_request"
|
||||
;; Same causal chain as above.
|
||||
"--skip" "interrupt_tool_records_history_entries"
|
||||
;; WorkspaceWrite sandbox policy wraps
|
||||
;; commands with codex-linux-sandbox;
|
||||
;; Landlock panics, command never runs,
|
||||
;; exit_code is None instead of Some(0).
|
||||
"--skip" "request_permissions_grants_apply_to_later_exec_command_calls"
|
||||
;; Same root cause.
|
||||
"--skip" "request_permissions_grants_apply_to_later_shell_command_calls"
|
||||
;; Same root cause.
|
||||
"--skip" "partial_request_permissions_grants_do_not_preapprove_new_permissions"
|
||||
;;; END Landlock
|
||||
;;; BEGIN mcp_process.rs initialize
|
||||
;;; assertion expects "version":"0.0.0"
|
||||
;;; but the server returns "0.120.0".
|
||||
;; Upstream bug: test hardcodes "0.0.0" in the
|
||||
;; expected user-agent string but the workspace
|
||||
;; version is "0.98.0".
|
||||
"--skip" "get_user_agent_returns_current_codex_user_agent"
|
||||
;; Same upstream bug: mcp-server tests
|
||||
;; check the initialize response which
|
||||
;; includes "version": "0.0.0" but the
|
||||
;; server returns "0.98.0".
|
||||
"--skip" "test_codex_tool_passes_base_instructions"
|
||||
"--skip" "test_shell_command_approval_triggers_elicitation"
|
||||
"--skip" "test_patch_approval_triggers_elicitation"
|
||||
;;; END version mismatch
|
||||
;;; BEGIN Test isolation bug:
|
||||
;;; unique_temp_dir() in
|
||||
;;; state/src/runtime.rs names dirs
|
||||
;;; using nanosecond timestamps, so
|
||||
;;; parallel tests can collide. The
|
||||
;;; SQLite migration runs CREATE TABLE
|
||||
;;; threads (without IF NOT EXISTS),
|
||||
;;; so the second init panics with
|
||||
;;; "table threads already exists".
|
||||
;; These codex-exec-server tests need
|
||||
;; "dotslash", a Meta tool that lazily
|
||||
;; downloads pre-built binaries from a
|
||||
;; JSON manifest. The test helper
|
||||
;; create_transport runs
|
||||
;; `dotslash -- fetch <path>` to obtain a
|
||||
;; custom bash binary described in
|
||||
;; exec-server/tests/suite/bash.
|
||||
;; dotslash is not available in the build
|
||||
;; container.
|
||||
"--skip" "list_tools"
|
||||
"--skip" "accept_elicitation_for_prompt_rule"
|
||||
;;; Test isolation bug: each test in
|
||||
;;; state/src/runtime.rs calls
|
||||
;;; unique_temp_dir() to get its own
|
||||
;;; temporary directory (and thus its
|
||||
;;; own SQLite database). That function
|
||||
;;; names directories using the current
|
||||
;;; nanosecond timestamp, so when tests
|
||||
;;; run in parallel several can receive
|
||||
;;; the same name and open the same
|
||||
;;; database. The initial SQLite
|
||||
;;; migration runs CREATE TABLE threads
|
||||
;;; (without IF NOT EXISTS), so any init
|
||||
;;; after the first panics with "table
|
||||
;;; threads already exists". Any of
|
||||
;;; these tests
|
||||
;;; can be the victim.
|
||||
"--skip" "init_removes_legacy_state_db_files"
|
||||
"--skip" "upsert_and_get_thread_memory"
|
||||
"--skip" "get_last_n_thread_memories_for_cwd_matches_exactly"
|
||||
"--skip" "upsert_thread_memory_errors_for_unknown_thread"
|
||||
"--skip" "get_last_n_thread_memories_for_cwd_zero_returns_empty"
|
||||
"--skip" "get_last_n_thread_memories_for_cwd_does_not_prefix_match"
|
||||
"--skip" "deleting_thread_cascades_thread_memory"
|
||||
;;; END SQLite test isolation
|
||||
;; The test spawns 'sh' after
|
||||
;; env_clear() with an empty env map;
|
||||
;; glibc execvp uses confstr(_CS_PATH)
|
||||
;; ("/bin:/usr/bin") when PATH is
|
||||
;; unset, but /bin/sh does not exist
|
||||
;; in the build container.
|
||||
"--skip" "cancellation_expiration_keeps_process_alive_until_terminated"
|
||||
;; Proxy baseline_policy returns 403
|
||||
;; "not_allowed_local" for example.com;
|
||||
;; test expects 200.
|
||||
"--skip" "managed_network_proxy_decider_survives_full_access_start"
|
||||
;;; BEGIN bash_snapshot_script() uses
|
||||
;;; "compgen -e" to list exports but
|
||||
;;; bash-minimal lacks programmable
|
||||
;;; completion; export section is empty.
|
||||
;; stdout.contains("VALID_NAME") fails.
|
||||
"--skip" "bash_snapshot_filters_invalid_exports"
|
||||
;; stdout.contains("MULTILINE_CERT") fails.
|
||||
"--skip" "bash_snapshot_preserves_multiline_exports"
|
||||
;; snapshot.contains("PATH") fails.
|
||||
"--skip" "linux_bash_snapshot_includes_sections"
|
||||
;;; END compgen
|
||||
;; substitute* patches PAGER to store
|
||||
;; path of cat; test expects bare "cat".
|
||||
"--skip" "unified_exec_env_injects_defaults"
|
||||
;;; BEGIN V8 disabled (codex-code-mode
|
||||
;;; default-features = false).
|
||||
"--skip" "suite::code_mode::"
|
||||
"--skip" "suite::js_repl::"
|
||||
"--skip" "suite::view_image::js_repl_"
|
||||
;;; END V8 disabled
|
||||
;;; BEGIN same compgen root cause:
|
||||
;;; assert_posix_snapshot_sections
|
||||
;;; asserts snapshot.contains("PATH").
|
||||
"--skip" "linux_shell_command_uses_shell_snapshot"
|
||||
"--skip" "linux_unified_exec_uses_shell_snapshot"
|
||||
"--skip" "shell_command_snapshot_still_intercepts_apply_patch"
|
||||
;;; END compgen / shell snapshot
|
||||
;;; BEGIN These sandbox tests set
|
||||
;;; exclude_slash_tmp: true which makes
|
||||
;;; bwrap exclude /tmp from its mount
|
||||
;;; namespace. Since Guix builds under
|
||||
;;; /tmp, the codex-linux-sandbox binary
|
||||
;;; becomes invisible to bwrap even though
|
||||
;;; the test adds the helper dir as a
|
||||
;;; filesystem carve-out -- the parent /tmp
|
||||
;;; bind-mount is absent so the carve-out
|
||||
;;; has nothing to carve out of.
|
||||
"--skip" "sandbox_reenables_writable_subpaths_under_unreadable_parents"
|
||||
"--skip" "managed_proxy_mode_routes_through_bridge_and_blocks_direct_egress"
|
||||
;;; END exclude_slash_tmp
|
||||
;; Expects 3 TerminalInteraction events
|
||||
;; across timed poll windows; under CPU
|
||||
;; contention events merge into 2.
|
||||
"--skip" "unified_exec_terminal_interaction_captures_delayed_output"
|
||||
;;; BEGIN assert_parallel_duration
|
||||
;;; requires < 1600 ms for parallel ops.
|
||||
;; Two 300 ms test_sync_tool calls.
|
||||
"--skip" "read_file_tools_run_in_parallel"
|
||||
;; Two "sleep 0.25" shell commands.
|
||||
"--skip" "shell_tools_run_in_parallel"
|
||||
;; One test_sync_tool + one shell sleep.
|
||||
"--skip" "mixed_parallel_tools_run_in_parallel"
|
||||
;;; END assert_parallel_duration
|
||||
;; Asserts elapsed >= 4500 ms and
|
||||
;; < 5800 ms for a 5 s timeout; under
|
||||
;; contention elapsed drifts past 5800.
|
||||
"--skip" "remote_models_request_times_out_after_5s"
|
||||
;; Queued inter-agent mail must be
|
||||
;; injected between the reasoning/
|
||||
;; commentary item and the gate release;
|
||||
;; under contention the gate fires before
|
||||
;; the mail is processed, so the snapshot
|
||||
;; shows the stale function_call instead
|
||||
;; of the expected mail message.
|
||||
"--skip" "queued_inter_agent_mail_triggers_follow_up_after_commentary_message_item"
|
||||
;; Same root cause: snapshot mismatch at
|
||||
;; pending_input.rs assert_two_responses_
|
||||
;; input_snapshot; expects mail at position
|
||||
;; 04 but gets function_call/shell instead.
|
||||
"--skip" "queued_inter_agent_mail_triggers_follow_up_after_reasoning_item"
|
||||
;;; BEGIN DNS for hostnames like
|
||||
;;; example.com fails in the build
|
||||
;;; sandbox. host_resolves_to_non_
|
||||
;;; public_ip() in runtime.rs treats
|
||||
;;; failed DNS as non-public and
|
||||
;;; returns NotAllowedLocal, so tests
|
||||
;;; expecting Allowed or Decider get
|
||||
;;; Deny/BaselinePolicy instead.
|
||||
"--skip" "host_blocked_requires_allowlist_match"
|
||||
"--skip" "add_allowed_domain_removes_matching_deny_entry"
|
||||
"--skip" "host_blocked_subdomain_wildcards_exclude_apex"
|
||||
"--skip" "host_blocked_global_wildcard_allowlist_allows_public_hosts_except_denylist"
|
||||
"--skip" "evaluate_host_policy_emits_domain_event_for_decider_ask"
|
||||
"--skip" "evaluate_host_policy_emits_domain_event_for_decider_allow_override"
|
||||
"--skip" "http_connect_accept_blocks_in_limited_mode"
|
||||
"--skip" "http_connect_accept_allows_allowlisted_host_in_full_mode"
|
||||
"--skip" "mitm_policy_blocks_disallowed_method_and_records_telemetry"
|
||||
;;; END DNS failure / NotAllowedLocal
|
||||
;;; BEGIN Flaky: wiremock mock expects
|
||||
;;; 1 POST to /codex/safety/arc but
|
||||
;;; receives 0. Passes in some builds,
|
||||
;;; fails in others with identical code
|
||||
;;; and env. The identical custom_
|
||||
;;; variant always passes; only the
|
||||
;;; CODEX_APPS_MCP_SERVER_NAME variant
|
||||
;;; flakes, suggesting a timing race
|
||||
;;; in the async POST under contention.
|
||||
"--skip" "approve_mode_blocks_when_arc_returns_interrupt_for_model"
|
||||
"--skip" "approve_mode_blocks_when_arc_returns_interrupt_without_annotations"
|
||||
;;; END ARC monitor flake
|
||||
;;; BEGIN nss-certs sets SSL_CERT_FILE
|
||||
;;; which makes build_reqwest_client load
|
||||
;;; 171 CA certs via add_root_certificate.
|
||||
;;; This changes the reqwest TLS backend
|
||||
;;; configuration; the ARC safety POST to
|
||||
;;; the localhost mock server never arrives
|
||||
;;; (wiremock expects 1 request, gets 0).
|
||||
"--skip" "approve_mode_blocks_when_arc_returns_interrupt_for_model"
|
||||
"--skip" "approve_mode_blocks_when_arc_returns_interrupt_without_annotations"
|
||||
;;; END nss-certs / ARC monitor
|
||||
;; Upstream bug: JsonRpcConnection has
|
||||
;; no websocket keepalive or read timeout.
|
||||
;; When the exec-server is killed, the
|
||||
;; client's reader task blocks on
|
||||
;; websocket_reader.next() forever because
|
||||
;; TCP doesn't detect the dead peer without
|
||||
;; a write or keepalive probe. Previously
|
||||
;; masked because empty env made "sleep 10"
|
||||
;; fail instantly; with PATH the process
|
||||
;; lives long enough to hit the deadlock.
|
||||
"--skip" "remote_exec_process_reports_transport_disconnect"
|
||||
;; 500 ms timeout on MCP list response
|
||||
;; (mcp_server_status.rs timeout at
|
||||
;; Duration::from_millis(500)). With
|
||||
;; nss-certs TLS now works, so the
|
||||
;; startup plugin sync HTTP requests
|
||||
;; (chatgpt.com, api.github.com) wait
|
||||
;; for TCP timeout instead of failing
|
||||
;; instantly at TLS, eating the budget.
|
||||
"--skip" "mcp_server_status_list_tools_and_auth_only_skips_slow_inventory_calls"
|
||||
;;; BEGIN Stack overflow in 'current_thread'
|
||||
;;; tokio runtime. The sibling tests in
|
||||
;;; tracing_tests.rs use the local helper
|
||||
;;; run_current_thread_test_with_stack
|
||||
;;; (4 MiB) but this one uses bare
|
||||
;;; #[tokio::test] on the 2 MiB default
|
||||
;;; test-thread stack, and TurnStart's
|
||||
;;; future graph exceeds it. With
|
||||
;;; RUST_MIN_STACK raised the overflow is
|
||||
;;; gone but the test then deterministically
|
||||
;;; times out waiting for a span tagged
|
||||
;;; codex.op = "user_input" on the remote
|
||||
;;; trace that upstream never emits on that
|
||||
;;; trace in our environment.
|
||||
"--skip" "turn_start_jsonrpc_span_parents_core_turn_spans"
|
||||
;;; END tracing test stack/timeout
|
||||
;;; BEGIN The upstream loader resolves the
|
||||
;;; MCP OAuth credentials store mode by
|
||||
;;; calling
|
||||
;;; resolve_mcp_oauth_credentials_store_mode
|
||||
;;; with env!("CARGO_PKG_VERSION") -- which
|
||||
;;; in the released 0.124.0 tarball is
|
||||
;;; "0.124.0". These fixture tests
|
||||
;;; construct the expected Config by
|
||||
;;; passing the LOCAL_DEV_BUILD_VERSION
|
||||
;;; constant ("0.0.0") to the same
|
||||
;;; resolver, and the resolver only returns
|
||||
;;; File for "0.0.0" -- Auto otherwise.
|
||||
;;; Upstream CI builds from a checkout
|
||||
;;; still carrying version = "0.0.0" so the
|
||||
;;; tests pass there; they cannot pass
|
||||
;;; against a released tag.
|
||||
"--skip" "test_precedence_fixture_with_gpt3_profile"
|
||||
"--skip" "test_precedence_fixture_with_gpt5_profile"
|
||||
"--skip" "test_precedence_fixture_with_o3_profile"
|
||||
"--skip" "test_precedence_fixture_with_zdr_profile"
|
||||
;;; END LOCAL_DEV_BUILD_VERSION fixture mismatch
|
||||
;;; BEGIN Verifies that Codex's user-shell
|
||||
;;; spawn produces a child where
|
||||
;;; CODEX_SANDBOX_NETWORK_DISABLED is unset
|
||||
;;; (asserts stdout == "not-set"). We
|
||||
;;; deliberately set that env var at the
|
||||
;;; check phase to trigger upstream's
|
||||
;;; skip_if_no_network! guards; the var then
|
||||
;;; leaks into the spawned shell and the
|
||||
;;; assertion fails. The guix skip is a
|
||||
;;; direct cost of the network-gate fix --
|
||||
;;; trading one broken test for two that
|
||||
;;; now skip cleanly.
|
||||
"--skip" "user_shell_command_does_not_set_network_sandbox_env_var"
|
||||
;;; END CODEX_SANDBOX_NETWORK_DISABLED leak
|
||||
;;; BEGIN The exec-server/tests/file_system
|
||||
;;; integration tests invoke the real
|
||||
;;; system bwrap, which tries to execvp the
|
||||
;;; test binary at the cargo target path
|
||||
;;; under the build dir. Same root cause
|
||||
;;; as the existing
|
||||
;;; sandbox_reenables_writable_subpaths_under_unreadable_parents
|
||||
;;; skip: guix builds live under /tmp but
|
||||
;;; bwrap's mount namespace excludes /tmp,
|
||||
;;; making the binary invisible inside the
|
||||
;;; namespace.
|
||||
"--skip" "file_system_copy_preserves_symlink_source"
|
||||
"--skip" "file_system_copy_rejects_symlink_escape_destination"
|
||||
"--skip" "file_system_copy_rejects_symlink_escape_source"
|
||||
"--skip" "file_system_create_directory_rejects_symlink_escape"
|
||||
"--skip" "file_system_read_directory_rejects_symlink_escape"
|
||||
"--skip" "file_system_remove_rejects_symlink_escape"
|
||||
"--skip" "file_system_remove_removes_symlink_not_target"
|
||||
"--skip" "file_system_sandboxed_read_allows_readable_root"
|
||||
"--skip" "file_system_sandboxed_read_rejects_symlink_escape"
|
||||
"--skip" "file_system_sandboxed_read_rejects_symlink_parent_dotdot_escape"
|
||||
"--skip" "file_system_sandboxed_write_allows_additional_write_root"
|
||||
"--skip" "file_system_sandboxed_write_rejects_symlink_escape"
|
||||
"--skip" "file_system_sandboxed_write_rejects_unwritable_path"
|
||||
;;; END bwrap-cant-see-/tmp file_system tests
|
||||
;;; BEGIN Landlock is unavailable on Guix,
|
||||
;;; so the sandbox cannot deny network
|
||||
;;; syscalls. These tests expect
|
||||
;;; SandboxErr::Denied for the nc, ping,
|
||||
;;; ssh, getent, and dev_tcp_redirection
|
||||
;;; commands but those commands instead
|
||||
;;; block on connect() until the test's 2s
|
||||
;;; timeout fires (Timeout, exit 124).
|
||||
;;; Same root cause as the Landlock skips
|
||||
;;; at the top of this list; new test names
|
||||
;;; in 0.124.
|
||||
"--skip" "sandbox_blocks_nc"
|
||||
"--skip" "sandbox_blocks_ping"
|
||||
"--skip" "sandbox_blocks_dev_tcp_redirection"
|
||||
"--skip" "sandbox_blocks_getent"
|
||||
"--skip" "sandbox_blocks_ssh"
|
||||
;;; END Landlock network block
|
||||
;;; BEGIN Requires github.com network access.
|
||||
;;; With no "extraKnownMarketplaces" entry
|
||||
;;; in settings.json,
|
||||
;;; collect_marketplace_import_sources
|
||||
;;; inserts a fallback entry for the
|
||||
;;; "claude-plugins-official" marketplace
|
||||
;;; pointing at the github shorthand
|
||||
;;; "anthropics/claude-plugins-official".
|
||||
;;; add_marketplace -> parse_marketplace_source
|
||||
;;; expands that to a github.com/.git URL
|
||||
;;; and clone_git_source runs 'git clone'.
|
||||
;;; The Guix build sandbox has no network,
|
||||
;;; so the clone fails and the marketplace
|
||||
;;; lands in failed_marketplaces. No mock
|
||||
;;; cloner is injected via
|
||||
;;; ExternalAgentConfigService::new_for_test,
|
||||
;;; so there is no in-tree way to satisfy
|
||||
;;; the test offline.
|
||||
"--skip" "import_plugins_infers_claude_official_marketplace_when_missing_from_settings"
|
||||
;;; END github.com network access
|
||||
;;; BEGIN Async race between the rollout
|
||||
;;; writer task and a direct SQLite read.
|
||||
;;; The test calls
|
||||
;;; update_memory_settings_with_app_server,
|
||||
;;; which routes through the in-memory
|
||||
;;; thread path on the app-server's
|
||||
;;; ThreadMemoryModeSet handler ->
|
||||
;;; Session::set_thread_memory_mode ->
|
||||
;;; persist_thread_memory_mode_update,
|
||||
;;; which writes a RolloutItem::SessionMeta
|
||||
;;; with the new mode to the rollout file
|
||||
;;; via recorder.record_items + flush. The
|
||||
;;; rollout writer task then asynchronously
|
||||
;;; calls sync_thread_state_after_write,
|
||||
;;; which calls state_db::apply_rollout_items
|
||||
;;; to mirror the SessionMeta into SQLite.
|
||||
;;; flush() only awaits the rollout-file
|
||||
;;; write, not the subsequent SQLite sync.
|
||||
;;; The test opens a fresh StateRuntime and
|
||||
;;; reads get_thread_memory_mode
|
||||
;;; immediately, so it observes the creation
|
||||
;;; default of "enabled" written by
|
||||
;;; upsert_thread_with_creation_memory_mode
|
||||
;;; instead of the new "disabled". Upstream
|
||||
;;; CI wins this race; we lose.
|
||||
"--skip" "update_memory_settings_updates_current_thread_memory_mode"
|
||||
;;; END memory-mode rollout/sqlite race
|
||||
;;; BEGIN The Stopwatch::new constructor in
|
||||
;;; codex_shell_escalation anchors
|
||||
;;; T0 = Instant::now() at construction;
|
||||
;;; the spawned cancellation task fires at
|
||||
;;; T0 + limit. The test captures
|
||||
;;; start = Instant::now() at T1 > T0 (after
|
||||
;;; cancellation_token() returns) and
|
||||
;;; asserts start.elapsed() >= limit,
|
||||
;;; i.e. (T0 + limit) - T1 >= limit, which
|
||||
;;; is always false by the offset T1 - T0.
|
||||
;;; The test only passes when scheduler
|
||||
;;; jitter on the sleep wakeup happens to
|
||||
;;; exceed that offset. Upstream wins the
|
||||
;;; race; we don't always.
|
||||
"--skip" "cancellation_receiver_fires_after_limit"
|
||||
;;; END Stopwatch construction/start offset race
|
||||
)
|
||||
"--skip" "deleting_thread_cascades_thread_memory")
|
||||
#:cargo-package-crates
|
||||
''(;;; Tier 0: No internal deps.
|
||||
"codex-ansi-escape"
|
||||
"codex-async-utils"
|
||||
"codex-backend-openapi-models"
|
||||
"codex-client"
|
||||
"codex-execpolicy"
|
||||
"codex-file-search"
|
||||
"codex-git-utils"
|
||||
"codex-git"
|
||||
"codex-keyring-store"
|
||||
"codex-process-hardening"
|
||||
"codex-utils-absolute-path"
|
||||
"codex-utils-cache"
|
||||
"codex-utils-cargo-bin"
|
||||
"codex-utils-elapsed"
|
||||
"codex-utils-fuzzy-match"
|
||||
"codex-utils-home-dir"
|
||||
"codex-utils-json-to-toml"
|
||||
"codex-utils-path"
|
||||
"codex-utils-plugins"
|
||||
"codex-utils-pty"
|
||||
"codex-utils-readiness"
|
||||
"codex-utils-rustls-provider"
|
||||
"codex-utils-sleep-inhibitor"
|
||||
"codex-utils-stream-parser"
|
||||
"codex-utils-string"
|
||||
"codex-utils-template"
|
||||
;;; Tier 1.
|
||||
"codex-backend-openapi-models"
|
||||
"codex-process-hardening"
|
||||
"codex-ansi-escape"
|
||||
;;; Tier 1: Depends on tier 0.
|
||||
"codex-utils-image"
|
||||
"codex-utils-output-truncation"
|
||||
"codex-apply-patch"
|
||||
"codex-protocol"
|
||||
"codex-windows-sandbox"
|
||||
@@ -518,69 +226,35 @@
|
||||
"codex-secrets"
|
||||
"codex-execpolicy-legacy"
|
||||
"codex-debug-client"
|
||||
"codex-analytics"
|
||||
"codex-rollout"
|
||||
"codex-rollout-trace"
|
||||
"codex-terminal-detection"
|
||||
"codex-utils-approval-presets"
|
||||
"codex-utils-cli"
|
||||
"codex-uds"
|
||||
"codex-install-context"
|
||||
"codex-device-key"
|
||||
;;; Tier 2.
|
||||
"codex-app-server-protocol"
|
||||
"codex-rmcp-client"
|
||||
"codex-otel"
|
||||
"codex-thread-store"
|
||||
"codex-state"
|
||||
"codex-features"
|
||||
"codex-model-provider"
|
||||
"codex-config"
|
||||
"codex-agent-identity"
|
||||
"codex-aws-auth"
|
||||
"codex-hooks"
|
||||
"codex-code-mode"
|
||||
"codex-feedback"
|
||||
"codex-skills"
|
||||
"codex-test-binary-support"
|
||||
"codex-core"
|
||||
"codex-core-plugins"
|
||||
"codex-utils-sandbox-summary"
|
||||
"codex-linux-sandbox"
|
||||
"codex-sandboxing"
|
||||
"codex-connectors"
|
||||
"codex-core-skills"
|
||||
"codex-feedback"
|
||||
;;; Tier 3.
|
||||
"codex-arg0"
|
||||
"codex-lmstudio"
|
||||
"codex-login"
|
||||
"codex-ollama"
|
||||
"codex-utils-oss"
|
||||
"codex-common"
|
||||
"codex-mcp-server"
|
||||
"codex-backend-client"
|
||||
"codex-responses-api-proxy"
|
||||
"codex-shell-command"
|
||||
"codex-shell-escalation"
|
||||
"codex-plugin"
|
||||
"codex-model-provider-info"
|
||||
"codex-models-manager"
|
||||
;;; Tier 4.
|
||||
"codex-cloud-requirements"
|
||||
"codex-exec"
|
||||
"codex-exec-server"
|
||||
"codex-network-proxy"
|
||||
"codex-stdio-to-uds"
|
||||
"codex-network-proxy"
|
||||
"codex-chatgpt"
|
||||
"codex-cloud-tasks-client"
|
||||
"codex-cloud-tasks-mock-client"
|
||||
"codex-tools"
|
||||
"codex-mcp"
|
||||
"codex-collaboration-mode-templates"
|
||||
;;; Tier 5.
|
||||
"codex-app-server"
|
||||
"codex-app-server-test-client"
|
||||
"codex-tui"
|
||||
"codex-response-debug-context"
|
||||
;;; Tier 6.
|
||||
"codex-cloud-tasks"
|
||||
;; The main executable.
|
||||
@@ -596,7 +270,7 @@
|
||||
;; Update them to match the actual package version.
|
||||
(let ((snap-files (find-files "." "\\.snap$")))
|
||||
(substitute* snap-files
|
||||
(("\\(v0\\.0\\.0\\) ") "(v0.124.0) ")))))
|
||||
(("\\(v0\\.0\\.0\\) ") "(v0.98.0)")))))
|
||||
(add-after 'chdir-to-workspace 'patch-git-deps-to-vendor
|
||||
(lambda _
|
||||
;; Replace git dependencies with version references so cargo
|
||||
@@ -605,57 +279,23 @@
|
||||
(("nucleo = \\{ git = [^}]+\\}")
|
||||
"nucleo = \"0.5.0\"")
|
||||
(("runfiles = \\{ git = [^}]+\\}")
|
||||
"runfiles = \"0.1.0\""))
|
||||
;; Remove workspace members that have unbuildable deps
|
||||
;; (v8-poc requires V8). code-mode stays a workspace member
|
||||
;; so its codex-protocol resolves to the same local copy as
|
||||
;; the rest of the build; disabling its default features
|
||||
;; (below) avoids pulling in V8.
|
||||
(substitute* "Cargo.toml"
|
||||
(("\"v8-poc\",") ""))
|
||||
;; Disable V8 runtime in codex-code-mode by turning off
|
||||
;; default features. Keep path= so code-mode is resolved
|
||||
;; from the local source tree and shares codex-protocol
|
||||
;; (and other workspace crates) with the rest of the build;
|
||||
;; resolving it from the vendor instead introduces a
|
||||
;; duplicate codex-protocol and causes E0308 type
|
||||
;; mismatches in codex-tools.
|
||||
(substitute* "Cargo.toml"
|
||||
(("codex-code-mode = \\{ path = \"code-mode\" \\}")
|
||||
"codex-code-mode = { path = \"code-mode\", default-features = false }"))
|
||||
;; cargo build at workspace root ignores per-dep
|
||||
;; default-features=false and builds code-mode with its
|
||||
;; own default features, which include v8-runtime and
|
||||
;; would pull in V8. Make the default feature empty.
|
||||
(substitute* "code-mode/Cargo.toml"
|
||||
(("^default = \\[\"v8-runtime\"\\]") "default = []"))))
|
||||
(add-after 'patch-git-deps-to-vendor 'add-version-to-workspace-deps
|
||||
"runfiles = \"0.1.0\""))))
|
||||
(add-after 'chdir-to-workspace 'add-version-to-workspace-deps
|
||||
(lambda _
|
||||
;; cargo package requires all dependencies to have versions.
|
||||
;; Add version = "0.124.0" to internal path dependencies.
|
||||
;; cargo package requires all dependencies to have versions.
|
||||
;; Add version = "0.98.0" to internal path dependencies.
|
||||
(let ((cargo-files (find-files "." "^Cargo\\.toml$")))
|
||||
(substitute* cargo-files
|
||||
;; Handle inline deps: name = { path = "..." }
|
||||
(("(codex-[a-z0-9-]+) = \\{ path = " all name)
|
||||
(string-append name " = { version = \"0.124.0\", path = "))
|
||||
(string-append name " = { version = \"0.98.0\", path = "))
|
||||
;; Handle inline deps with package: name = { package = "...", path = "..." }
|
||||
(("(codex-[a-z0-9-]+) = \\{ package = " all name)
|
||||
(string-append name " = { version = \"0.124.0\", package = "))
|
||||
(string-append name " = { version = \"0.98.0\", package = "))
|
||||
;; Handle section deps: [dependencies.X] with path = "..."
|
||||
(("^(path = \"\\.\\./[^\"]*\")" all path-line)
|
||||
(string-append path-line "\nversion = \"0.124.0\""))))))
|
||||
(add-after 'chdir-to-workspace 'use-gnu-store-in-sandbox
|
||||
(lambda _
|
||||
;; LINUX_PLATFORM_DEFAULT_READ_ROOTS in linux-sandbox/src/
|
||||
;; bwrap.rs is the read-only baseline that codex's bwrap
|
||||
;; sandbox bind-mounts so commands can read /usr/bin/ls,
|
||||
;; libc, etc. Upstream lists "/nix/store" for NixOS;
|
||||
;; Guix's equivalent is "/gnu/store". Without this swap,
|
||||
;; the codex sandbox cannot locate any binaries on a Guix
|
||||
;; system because every "system" path resolves into
|
||||
;; /gnu/store/<hash>-pkg/bin/...
|
||||
(substitute* "linux-sandbox/src/bwrap.rs"
|
||||
(("\"/nix/store\"") "\"/gnu/store\""))))
|
||||
(string-append path-line "\nversion = \"0.98.0\""))))))
|
||||
(add-after 'chdir-to-workspace 'patch-hardcoded-paths
|
||||
(lambda* (#:key inputs #:allow-other-keys)
|
||||
(let ((bash-bin (string-append
|
||||
@@ -685,14 +325,6 @@
|
||||
(string-append "\"" bash-bin "/bash "))
|
||||
(("\"/bin/sh ")
|
||||
(string-append "\"" bash-bin "/sh "))
|
||||
;; Single-quoted paths in test assertion strings,
|
||||
;; e.g. "exec '/bin/bash' -c ...". Must match the
|
||||
;; double-quoted substitutions above so both sides
|
||||
;; of assert_eq!/contains use the store path.
|
||||
(("'/bin/bash'")
|
||||
(string-append "'" bash-bin "/bash'"))
|
||||
(("'/bin/sh'")
|
||||
(string-append "'" bash-bin "/sh'"))
|
||||
;; coreutils.
|
||||
(("\"/bin/(cat|cp|date|echo|head|ls|rm|sleep|true|touch)\"" all cmd)
|
||||
(string-append "\"" coreutils-bin "/" cmd "\""))
|
||||
@@ -707,132 +339,28 @@
|
||||
(string-append "\"" git-bin "/git\""))
|
||||
(("\"/usr/bin/sed\"")
|
||||
(string-append "\"" sed-bin "/sed\"")))
|
||||
;; Bare Command::new("git") and Command::new("ls")
|
||||
;; in codex source files that exec internally.
|
||||
(substitute* (find-files "git-utils" "\\.rs$")
|
||||
(("Command::new\\(\"git\"\\)")
|
||||
(string-append "Command::new(\"" git-bin "/git\")")))
|
||||
(substitute* "tui/src/get_git_diff.rs"
|
||||
(("Command::new\\(\"git\"\\)")
|
||||
(string-append "Command::new(\"" git-bin "/git\")")))
|
||||
(substitute* "core/src/turn_diff_tracker.rs"
|
||||
(("Command::new\\(\"git\"\\)")
|
||||
(string-append "Command::new(\"" git-bin "/git\")")))
|
||||
(substitute* "cloud-tasks/src/env_detect.rs"
|
||||
(("Command::new\\(\"git\"\\)")
|
||||
(string-append "Command::new(\"" git-bin "/git\")")))
|
||||
(substitute* "core/src/plugins/startup_sync.rs"
|
||||
(("\"git\",")
|
||||
(string-append "\"" git-bin "/git\",")))
|
||||
(substitute* "file-search/src/lib.rs"
|
||||
(("Command::new\\(\"ls\"\\)")
|
||||
(string-append "Command::new(\"" coreutils-bin "/ls\")")))
|
||||
;; Neutralize pager with absolute path to cat.
|
||||
(substitute* "core/src/unified_exec/process_manager.rs"
|
||||
(("\"PAGER\", \"cat\"")
|
||||
(string-append "\"PAGER\", \"" coreutils-bin "/cat\""))
|
||||
(("\"GIT_PAGER\", \"cat\"")
|
||||
(string-append "\"GIT_PAGER\", \"" coreutils-bin "/cat\""))
|
||||
(("\"GH_PAGER\", \"cat\"")
|
||||
(string-append "\"GH_PAGER\", \"" coreutils-bin "/cat\"")))
|
||||
;; Bare /bin/sleep inside a format! string
|
||||
;; (no surrounding double quotes, so the main
|
||||
;; pattern does not match).
|
||||
(substitute*
|
||||
"shell-escalation/src/unix/escalate_server.rs"
|
||||
(("/bin/sleep")
|
||||
(string-append coreutils-bin "/sleep")))
|
||||
;; @SHELL@ placeholder from test-shebangs patch
|
||||
(substitute*
|
||||
(list "rmcp-client/src/program_resolver.rs"
|
||||
"tui/src/external_editor.rs")
|
||||
(("@SHELL@")
|
||||
(string-append bash-bin "/sh")))
|
||||
;; Shebangs inside raw string literals (r#"..."#)
|
||||
;; that are written to scripts at runtime. The
|
||||
;; main "/bin/sh" patterns only match double-quoted
|
||||
;; occurrences; these shebangs have no surrounding
|
||||
;; double quotes.
|
||||
;; shebang in test-only file
|
||||
(substitute*
|
||||
(list "core/src/plugins/startup_sync_tests.rs"
|
||||
"core/src/tools/runtimes/shell/unix_escalation_tests.rs"
|
||||
"core/tests/suite/client.rs"
|
||||
"core/tests/suite/js_repl.rs"
|
||||
"core/tests/suite/skill_approval.rs"
|
||||
"core/tests/suite/user_notification.rs"
|
||||
"exec-server/tests/file_system.rs"
|
||||
"login/src/auth/auth_tests.rs"
|
||||
"models-manager/src/manager_tests.rs"
|
||||
"sandboxing/src/bwrap_tests.rs")
|
||||
"core/tests/suite/user_notification.rs"
|
||||
(("#!/bin/bash")
|
||||
(string-append "#!" bash-bin "/bash"))
|
||||
(("#!/bin/sh")
|
||||
(string-append "#!" bash-bin "/sh")))
|
||||
;; Test helpers pass env: Default::default() to the
|
||||
;; spawn code which calls env_clear(), leaving
|
||||
;; processes with no PATH. Inject the build-time
|
||||
;; PATH so tests find coreutils, bash, etc.
|
||||
(substitute* (find-files "." "\\.rs$")
|
||||
(("env: Default::default\\(\\)")
|
||||
(string-append
|
||||
"env: std::env::var(\"PATH\")"
|
||||
".into_iter()"
|
||||
".map(|p| (\"PATH\".to_string(), p))"
|
||||
".collect()")))
|
||||
;; Test-only absolute path; bare name works via PATH.
|
||||
(substitute* "exec-server/tests/exec_process.rs"
|
||||
(("\"/usr/bin/python3\"")
|
||||
"\"python3\""))
|
||||
;; Same empty-env issue but in JSON literals
|
||||
;; (serde_json::json! macro).
|
||||
(substitute* "exec-server/tests/process.rs"
|
||||
(("\"env\": \\{\\}")
|
||||
(string-append
|
||||
"\"env\": {\"PATH\": \""
|
||||
(getenv "PATH")
|
||||
"\"}"))))))
|
||||
(add-before 'build 'set-bubblewrap-source
|
||||
(lambda* (#:key inputs #:allow-other-keys)
|
||||
(setenv "CODEX_BWRAP_SOURCE_DIR"
|
||||
(string-append
|
||||
(assoc-ref inputs "bubblewrap-source")
|
||||
"/"))))
|
||||
(add-before 'build 'create-node-version-file
|
||||
(lambda _
|
||||
(call-with-output-file "guix-vendor/node-version.txt"
|
||||
(lambda (port)
|
||||
(display "22.22.0" port)))))
|
||||
(string-append "#!" bash-bin "/bash"))))))
|
||||
(add-before 'check 'set-home
|
||||
(lambda _
|
||||
;; HOME must not be a prefix of /tmp, otherwise
|
||||
;; the TUI's path shortener replaces /tmp/... with
|
||||
;; ~/... and 30 snapshot tests fail.
|
||||
(setenv "HOME" "/tmp/guix-home")
|
||||
(mkdir-p "/tmp/guix-home")
|
||||
(setenv "USER" "nixbld")
|
||||
;; Default libtest thread stack is 2 MiB, which is not
|
||||
;; enough for tokio current_thread tests that drive
|
||||
;; codex-core's full turn pipeline. Upstream gates such
|
||||
;; tests through run_current_thread_test_with_stack (4 MiB)
|
||||
;; in app-server/src/message_processor/tracing_tests.rs;
|
||||
;; raise the global default so future additions that
|
||||
;; forget the wrapper still pass.
|
||||
(setenv "RUST_MIN_STACK" "8388608")
|
||||
;; Disable network access.
|
||||
(setenv "CODEX_SANDBOX_NETWORK_DISABLED" "1"))))))
|
||||
(native-inputs `(("bubblewrap" ,bubblewrap) ;tests need bwrap on PATH
|
||||
("clang" ,clang)
|
||||
("cmake-minimal" ,cmake-minimal)
|
||||
("libunwind" ,libunwind)
|
||||
("lsof" ,lsof) ;app-server tests
|
||||
("nss-certs-for-test" ,nss-certs-for-test) ;OTLP gRPC TLS
|
||||
("perl" ,perl)
|
||||
("procps" ,procps) ;tests use ps
|
||||
("python-minimal" ,python-minimal)
|
||||
("pkg-config" ,pkg-config)
|
||||
("bubblewrap-source" ,(package-source bubblewrap))))
|
||||
(setenv "HOME" "/tmp")
|
||||
(setenv "USER" "nixbld"))))))
|
||||
(native-inputs (list clang ;bindgen uses libclang to parse BoringSSL's C headers
|
||||
cmake-minimal ;BoringSSL is compiled from C source
|
||||
libunwind ;BoringSSL tests verify stack unwinding in assembly
|
||||
perl python-minimal ;for tests
|
||||
pkg-config))
|
||||
(inputs (cons* bash-minimal coreutils git-minimal sed
|
||||
libcap oniguruma openssl sqlite zlib `(,zstd "lib")
|
||||
openssl sqlite `(,zstd "lib")
|
||||
(cargo-inputs 'codex)))
|
||||
(home-page "https://github.com/openai/codex")
|
||||
(synopsis "AI-assisted coding CLI and TUI")
|
||||
@@ -840,15 +368,13 @@
|
||||
"Codex is an AI-powered coding assistant that runs in the terminal.
|
||||
It provides an interactive TUI for conversations with AI models, with
|
||||
support for shell command execution, file editing, and code generation.
|
||||
Configure providers via @file{~/.codex/config.toml}.
|
||||
|
||||
codex-code-mode's V8 Javascript executor is disabled.")
|
||||
Configure providers via @file{~/.codex/config.toml}.")
|
||||
(license license:asl2.0)))
|
||||
|
||||
(define-public codex-acp
|
||||
(package
|
||||
(name "codex-acp")
|
||||
(version "0.11.1")
|
||||
(version "0.9.2")
|
||||
(source
|
||||
(origin
|
||||
(method git-fetch)
|
||||
@@ -857,8 +383,9 @@ codex-code-mode's V8 Javascript executor is disabled.")
|
||||
(commit (string-append "v" version))))
|
||||
(file-name (git-file-name name version))
|
||||
(sha256
|
||||
(base32 "1rlgkbvrbdl5jhf49sjn2mifn2rq6z0vwf0gard23y1bz6sr3wmr"))
|
||||
(patches (search-patches "codex-acp-0.11.1-remove-patch-sections.patch"))))
|
||||
(base32 "190sq6s6jfz8dkj1y8305r7x6ln86qqr2j1bnfjci7f1x2wyzmsj"))
|
||||
(patches (search-patches "codex-acp-0.9.2-remove-patch-sections.patch"
|
||||
"codex-acp-0.9.2-replace-result-flatten.patch"))))
|
||||
(build-system cargo-build-system)
|
||||
(arguments
|
||||
(list
|
||||
@@ -866,43 +393,13 @@ codex-code-mode's V8 Javascript executor is disabled.")
|
||||
#:phases
|
||||
#~(modify-phases %standard-phases
|
||||
(add-after 'unpack 'patch-codex-deps
|
||||
(lambda* (#:key inputs #:allow-other-keys)
|
||||
(lambda _
|
||||
;; Rewrite git dependencies to use vendored sources from rust-codex
|
||||
(substitute* "Cargo.toml"
|
||||
(("git = \"https://github.com/openai/codex\", tag = \"rust-v0.117.0\"")
|
||||
"version = \"0.117.0\""))
|
||||
;; Disable V8 runtime in codex-code-mode (transitive dep).
|
||||
(let ((port (open-file "Cargo.toml" "a")))
|
||||
(display "
|
||||
[dependencies.codex-code-mode]
|
||||
version = \"0.117.0\"
|
||||
default-features = false
|
||||
" port)
|
||||
(close-port port))
|
||||
;; Point codex-linux-sandbox at system bubblewrap source.
|
||||
(setenv "CODEX_BWRAP_SOURCE_DIR"
|
||||
(string-append
|
||||
(assoc-ref inputs "bubblewrap-source")
|
||||
"/"))))
|
||||
(add-before 'check 'set-home
|
||||
(lambda _
|
||||
(setenv "HOME" "/tmp")
|
||||
(setenv "USER" "nixbld")))
|
||||
(add-before 'build 'create-node-version-file
|
||||
(lambda _
|
||||
;; codex-core's js_repl uses include_str! to read
|
||||
;; node-version.txt four directories up from its source;
|
||||
;; create it where the vendored crate expects it.
|
||||
(call-with-output-file "guix-vendor/node-version.txt"
|
||||
(lambda (port)
|
||||
(display "22.22.0" port))))))))
|
||||
(native-inputs
|
||||
`(("cmake-minimal" ,cmake-minimal)
|
||||
("clang" ,clang)
|
||||
("pkg-config" ,pkg-config)
|
||||
("bubblewrap-source" ,(package-source bubblewrap))))
|
||||
(inputs (cons* libcap openssl sqlite zlib `(,zstd "lib")
|
||||
(cargo-inputs 'codex-acp)))
|
||||
(("git = \"https://github.com/zed-industries/codex\", branch = \"acp\"")
|
||||
"version = \"0.0.0\"")))))))
|
||||
(native-inputs (list pkg-config))
|
||||
(inputs (cons* openssl sqlite `(,zstd "lib") (cargo-inputs 'codex-acp)))
|
||||
(home-page "https://github.com/zed-industries/codex-acp")
|
||||
(synopsis "ACP-compatible agent bridging Zed Codex with ACP clients")
|
||||
(description
|
||||
|
||||
@@ -150,7 +150,7 @@ as created by Podman, CRI-O and containerd.")))
|
||||
(define-public crun
|
||||
(package
|
||||
(name "crun")
|
||||
(version "1.26")
|
||||
(version "1.25.1")
|
||||
(source
|
||||
(origin
|
||||
(method url-fetch)
|
||||
@@ -160,7 +160,7 @@ as created by Podman, CRI-O and containerd.")))
|
||||
"/crun-" version ".tar.gz"))
|
||||
(sha256
|
||||
(base32
|
||||
"1hdwk5dpsz9danxiyfli07b7sqid6hr34qmhs5qjl2dcc00is89j"))))
|
||||
"02kksvnja234k8mpq5j7yms8npbpvh8iz3k03h21lwcqzqsb88rx"))))
|
||||
(build-system gnu-build-system)
|
||||
(arguments
|
||||
(list
|
||||
|
||||
@@ -44,7 +44,7 @@
|
||||
;;; Copyright © 2024 Jakob Kirsch <jakob.kirsch@web.de>
|
||||
;;; Copyright © 2025 Sharlatan Hellseher <sharlatanus@gmail.com>
|
||||
;;; Copyright © 2025 Sergio Pastor Pérez <sergio.pastorperez@gmail.com>
|
||||
;;; Copyright © 2025, 2026 Ashish SHUKLA <ashish.is@lostca.se>
|
||||
;;; Copyright © 2025 Ashish SHUKLA <ashish.is@lostca.se>
|
||||
;;; Copyright © 2025 Nicolas Graves <ngraves@ngraves.fr>
|
||||
;;; Copyright © 2025 Romain Garbage <romain.garbage@inria.fr>
|
||||
;;; Copyright © 2024, 2025 Janneke Nieuwenhuizen <janneke@gnu.org>
|
||||
@@ -3360,7 +3360,7 @@ which can evaluate Jsonnet files and expressions.")))
|
||||
(define-public simdjson
|
||||
(package
|
||||
(name "simdjson")
|
||||
(version "4.6.3")
|
||||
(version "3.13.0")
|
||||
(source (origin
|
||||
(method git-fetch)
|
||||
(uri (git-reference
|
||||
@@ -3369,7 +3369,7 @@ which can evaluate Jsonnet files and expressions.")))
|
||||
(file-name (git-file-name name version))
|
||||
(sha256
|
||||
(base32
|
||||
"0729mxnc2wjb94gr4znwlzfmgw5w2v9kd8glvn3vnjhkdnd87zry"))))
|
||||
"005yli56nrkvlyx9g9cq8dczk42r9a18l162i2s5k81lj3y7mcrp"))))
|
||||
(build-system cmake-build-system)
|
||||
(arguments
|
||||
'(#:tests? #f ; tests require downloading dependencies
|
||||
@@ -3608,7 +3608,7 @@ std::wstring, etc).")
|
||||
(define-public fast-float
|
||||
(package
|
||||
(name "fast-float")
|
||||
(version "8.2.5")
|
||||
(version "8.0.2")
|
||||
(source (origin
|
||||
(method git-fetch)
|
||||
(uri (git-reference
|
||||
@@ -3617,7 +3617,7 @@ std::wstring, etc).")
|
||||
(file-name (git-file-name name version))
|
||||
(sha256
|
||||
(base32
|
||||
"1l13nsl4sgq71m7aifrmmmfyl14vp48vqdh7pb50hxqq6f8bq2b5"))))
|
||||
"19x1yklf641yrpad6lk4cq3jmird10d5ig8hicm3p9lxh92k78cl"))))
|
||||
(build-system cmake-build-system)
|
||||
(arguments
|
||||
(list
|
||||
@@ -3628,10 +3628,12 @@ std::wstring, etc).")
|
||||
(add-after 'unpack 'patch-cmake-tests
|
||||
(lambda* (#:key inputs native-inputs #:allow-other-keys)
|
||||
(substitute* "tests/CMakeLists.txt"
|
||||
(("FetchContent_MakeAvailable\\(supplemental_test_files.*")
|
||||
(("FetchContent_GetProperties\\(supplemental_test_files.*")
|
||||
"")
|
||||
(("if\\(NOT supplemental_test_files_POPULATED.*")
|
||||
(string-append
|
||||
"set(supplemental_test_files_BINARY_DIR "
|
||||
#$fast-float-test-files ")\n"))))))))
|
||||
#$fast-float-test-files ")\nif(0)\n"))))))))
|
||||
(native-inputs (list doctest fast-float-test-files))
|
||||
(home-page "https://github.com/fastfloat/fast_float")
|
||||
(synopsis "Floating point number parser for C++")
|
||||
|
||||
File diff suppressed because it is too large
Load Diff
@@ -276,17 +276,18 @@ Ed448-Goldilocks and Curve448, using the Decaf encoding.")
|
||||
(define-public libsodium
|
||||
(package
|
||||
(name "libsodium")
|
||||
(version "1.0.22")
|
||||
(source
|
||||
(origin
|
||||
(method git-fetch)
|
||||
(uri (git-reference
|
||||
(url "https://github.com/jedisct1/libsodium")
|
||||
(commit (string-append version "-RELEASE"))))
|
||||
(file-name (git-file-name name version))
|
||||
(sha256
|
||||
(base32
|
||||
"05lqdn6nzldsia5mv5a9xfvc5k0kybh9snwv7qsb135gva4bpjwk"))))
|
||||
(version "1.0.18")
|
||||
(source (origin
|
||||
(method url-fetch)
|
||||
(uri (list (string-append
|
||||
"https://download.libsodium.org/libsodium/"
|
||||
"releases/libsodium-" version ".tar.gz")
|
||||
(string-append
|
||||
"https://download.libsodium.org/libsodium/"
|
||||
"releases/old/libsodium-" version ".tar.gz")))
|
||||
(sha256
|
||||
(base32
|
||||
"1h9ncvj23qbbni958knzsli8dvybcswcjbx0qjjgi922nf848l3g"))))
|
||||
(build-system gnu-build-system)
|
||||
(synopsis "Portable NaCl-based crypto library")
|
||||
(description
|
||||
|
||||
@@ -70,7 +70,6 @@
|
||||
;;; Copyright © 2025 bdunahu <bdunahu@operationnull.com>
|
||||
;;; Copyright © 2026 Spencer King <spencer.king@wustl.edu>
|
||||
;;; Copyright © 2026 Peter Polidoro <peter@polidoro.io>
|
||||
;;; Copyright © 2026 Josep Bigorra <jjbigorra@gmail.com>
|
||||
;;;
|
||||
;;; This file is part of GNU Guix.
|
||||
;;;
|
||||
@@ -127,7 +126,6 @@
|
||||
#:use-module (gnu packages gperf)
|
||||
#:use-module (gnu packages gtk)
|
||||
#:use-module (gnu packages guile)
|
||||
#:use-module (gnu packages guile-xyz)
|
||||
#:use-module (gnu packages icu4c)
|
||||
#:use-module (gnu packages jemalloc)
|
||||
#:use-module (gnu packages language)
|
||||
@@ -200,7 +198,6 @@
|
||||
#:use-module (guix build-system emacs)
|
||||
#:use-module (guix build-system gnu)
|
||||
#:use-module (guix build-system go)
|
||||
#:use-module (guix build-system guile)
|
||||
#:use-module (guix build-system meson)
|
||||
#:use-module (guix build-system perl)
|
||||
#:use-module (guix build-system pyproject)
|
||||
@@ -5049,54 +5046,6 @@ postgresql = postgresql://nixbld@/yoyo_test~%")))
|
||||
files or Python scripts that define a list of migration steps.")
|
||||
(license license:asl2.0)))
|
||||
|
||||
(define-public mutastructura
|
||||
(package
|
||||
(name "mutastructura")
|
||||
(version "0.6.0")
|
||||
(source
|
||||
(origin
|
||||
(method git-fetch)
|
||||
(uri (git-reference
|
||||
(url "https://codeberg.org/jjba23/mutastructura")
|
||||
(commit (string-append "v" version))))
|
||||
(file-name (git-file-name name version))
|
||||
(sha256
|
||||
(base32 "08vzlc5imavqf3bdzgbh70c7z44xjhf05gr7i2g5ksl49lv39gzh"))))
|
||||
(build-system guile-build-system)
|
||||
(arguments
|
||||
(list
|
||||
#:source-directory "src"
|
||||
#:phases
|
||||
#~(modify-phases %standard-phases
|
||||
(add-before 'build 'install-program-files
|
||||
(lambda _
|
||||
(let* ((bin (string-append #$output "/bin"))
|
||||
(share (string-append #$output "/share")))
|
||||
(copy-recursively "resources"
|
||||
(string-append share "/resources"))
|
||||
(install-file "scripts/mutastructura" bin)
|
||||
(install-file "scripts/log.bash"
|
||||
(string-append share "/scripts/"))
|
||||
(chmod (string-append bin "/mutastructura") #o755)))))))
|
||||
(native-inputs (list guile-3.0))
|
||||
(propagated-inputs (list guile-dbi
|
||||
guile-dbd-mysql
|
||||
guile-dbd-sqlite3
|
||||
guile-dbd-postgresql
|
||||
guile-gcrypt))
|
||||
(inputs (list guile-3.0 bash-minimal))
|
||||
(home-page "https://codeberg.org/jjba23/mutastructura")
|
||||
(synopsis "Relational database schema migrations powered by Guile Scheme")
|
||||
(description
|
||||
"Mutastructura provides a familiar, declarative and transactional
|
||||
approach to managing database states. It exposes a user-friendly
|
||||
@acronym{CLI, command-line interface} and has support for PostgreSQL, MySQL, and SQLite.
|
||||
It also exposes library functions and can be imported and used directly from other Guile code.
|
||||
|
||||
Features include executing migrations transactionally and computing SHA256
|
||||
checksums to track schema evolution in a @code{migrations_history} table.")
|
||||
(license license:agpl3+)))
|
||||
|
||||
(define-public python-mysqlclient
|
||||
(package
|
||||
(name "python-mysqlclient")
|
||||
|
||||
@@ -31,7 +31,7 @@
|
||||
;;; Copyright © 2023 Zheng Junjie <873216071@qq.com>
|
||||
;;; Copyright © 2024-2025 Sharlatan Hellseher <sharlatanus@gmail.com>
|
||||
;;; Copyright © 2025 Ashish SHUKLA <ashish.is@lostca.se>
|
||||
;;; Copyright © 2025, 2026 Vinicius Monego <monego@posteo.net>
|
||||
;;; Copyright © 2025 Vinicius Monego <monego@posteo.net>
|
||||
;;; Copyright © 2025 Grigory Shepelev <shegeley@gmail.com>
|
||||
;;; Copyright © 2026 Luis Guilherme Coelho <lgcoelho@disroot.org>
|
||||
|
||||
@@ -94,8 +94,6 @@
|
||||
#:use-module (gnu packages gnome)
|
||||
#:use-module (gnu packages gnupg)
|
||||
#:use-module (gnu packages golang-build)
|
||||
#:use-module (gnu packages golang-check)
|
||||
#:use-module (gnu packages golang-compression)
|
||||
#:use-module (gnu packages golang-xyz)
|
||||
#:use-module (gnu packages graphics)
|
||||
#:use-module (gnu packages gtk)
|
||||
@@ -422,49 +420,6 @@ tables, and it understands a variety of different formats.")
|
||||
similarity.")
|
||||
(license license:gpl3+)))
|
||||
|
||||
(define-public gdu
|
||||
(package
|
||||
(name "gdu")
|
||||
(version "5.35.0")
|
||||
(source
|
||||
(origin
|
||||
(method git-fetch)
|
||||
(uri (git-reference
|
||||
(url "https://github.com/dundee/gdu")
|
||||
(commit (string-append "v" version))))
|
||||
(file-name (git-file-name name version))
|
||||
(sha256
|
||||
(base32 "051xf3wncdiavjwyl9djmni5vd2dqjgn6drkw2nm21c9l0rjfv6d"))))
|
||||
(build-system go-build-system)
|
||||
(arguments
|
||||
(list
|
||||
#:install-source? #f
|
||||
#:import-path "github.com/dundee/gdu/v5/cmd/gdu"
|
||||
#:unpack-path "github.com/dundee/gdu/v5"))
|
||||
(native-inputs
|
||||
(list go-github-com-dgraph-io-badger-v4
|
||||
go-github-com-fatih-color
|
||||
go-github-com-gdamore-tcell-v2
|
||||
go-github-com-h2non-filetype
|
||||
go-github-com-maruel-natural
|
||||
go-github-com-mattn-go-isatty
|
||||
go-github-com-pkg-errors
|
||||
go-github-com-rivo-tview
|
||||
go-github-com-sirupsen-logrus
|
||||
go-github-com-spf13-cobra
|
||||
go-github-com-stretchr-testify
|
||||
go-github-com-ulikunitz-xz
|
||||
go-golang-org-x-sys
|
||||
go-golang-org-x-text
|
||||
go-gopkg-in-yaml-v3
|
||||
go-modernc-org-sqlite))
|
||||
(home-page "https://github.com/dundee/gdu")
|
||||
(synopsis "Disk usage analyzer")
|
||||
(description "Gdu is a disk usage analyzer written in Go. It is intended
|
||||
primarily for SSD disks where it can fully utilize parallel processing, but it
|
||||
also works on HDDs.")
|
||||
(license license:expat)))
|
||||
|
||||
(define-public gpart
|
||||
;; The latest (0.3) release is from 2015 and is missing a crash fix.
|
||||
(let ((commit "ec03350a01ad69708b5a3e2d47b8e002b0eba6c9")
|
||||
|
||||
@@ -201,13 +201,13 @@ your project into different processes.")
|
||||
(define-public python-django
|
||||
(package
|
||||
(name "python-django")
|
||||
(version "5.2.13")
|
||||
(version "5.2.11")
|
||||
(source
|
||||
(origin
|
||||
(method url-fetch)
|
||||
(uri (pypi-uri "django" version))
|
||||
(sha256
|
||||
(base32 "1i1vlffzhwbzp6r6y8ycvwklc45diy4c6i897z379l48a7dqj5d3"))))
|
||||
(base32 "1lq2dynfw6jmvzrzgfrlij2qnxcksaxgnrfr0pj3bvmrv0m2jbbz"))))
|
||||
(build-system pyproject-build-system)
|
||||
(arguments
|
||||
'(#:test-flags
|
||||
|
||||
@@ -148,13 +148,13 @@ system.")
|
||||
(define-public r-duckdb
|
||||
(package
|
||||
(name "r-duckdb")
|
||||
(version "1.5.2")
|
||||
(version "1.5.1")
|
||||
(source
|
||||
(origin
|
||||
(method url-fetch)
|
||||
(uri (cran-uri "duckdb" version))
|
||||
(sha256
|
||||
(base32 "1dldlfwvc33czvlxfmwaj4p9y6sjjj5iqy98yda47a8kclrqmyam"))
|
||||
(base32 "177621m08whqqk4yhj3zrr08l3d9hhlqh3gm9jzhi5cplg47cksq"))
|
||||
;; This package bundles the duckdb sources and builds a custom variant
|
||||
;; of duckdb. I'd be happy to link it with our duckdb library instead,
|
||||
;; but it does not seem possible to do that.
|
||||
|
||||
@@ -2331,7 +2331,7 @@ Automation}, portable and vendor neutral FPGA place and route tool.")
|
||||
(define-public nvc
|
||||
(package
|
||||
(name "nvc")
|
||||
(version "1.20.1")
|
||||
(version "1.19.3")
|
||||
(source (origin
|
||||
(method git-fetch)
|
||||
(uri (git-reference
|
||||
@@ -2340,7 +2340,7 @@ Automation}, portable and vendor neutral FPGA place and route tool.")
|
||||
(file-name (git-file-name name version))
|
||||
(sha256
|
||||
(base32
|
||||
"1b38x2ch468s4p6mrq6c8s0d95vb84p6w4v8in79l4w7sfy8jnr0"))))
|
||||
"1zizz2dafm53lzpjayy6vig5pz5ri9cszdivg0jzzh8s3ggkpy1i"))))
|
||||
(build-system gnu-build-system)
|
||||
(arguments
|
||||
(list #:out-of-source? #t
|
||||
@@ -3461,7 +3461,7 @@ form of AXI, AXI lite, and AXI stream modules.")
|
||||
(define-public python-edalize
|
||||
(package
|
||||
(name "python-edalize")
|
||||
(version "0.6.8")
|
||||
(version "0.6.6")
|
||||
(source
|
||||
(origin
|
||||
(method git-fetch)
|
||||
@@ -3470,7 +3470,7 @@ form of AXI, AXI lite, and AXI stream modules.")
|
||||
(commit (string-append "v" version))))
|
||||
(file-name (git-file-name name version))
|
||||
(sha256
|
||||
(base32 "04m2lhkclw9fj92k43c06j003qnq9i1yhy2131fvcnkkr0d9438m"))))
|
||||
(base32 "115nc15n2cx4x9irjim07zkg0287418djqd6ja7rm8jrnyldvln9"))))
|
||||
(build-system pyproject-build-system)
|
||||
(arguments
|
||||
(list
|
||||
@@ -4516,7 +4516,7 @@ unique design feature of Trilinos is its focus on packages.")
|
||||
(define-public verilator
|
||||
(package
|
||||
(name "verilator")
|
||||
(version "5.048")
|
||||
(version "5.046")
|
||||
(source
|
||||
(origin
|
||||
(method git-fetch)
|
||||
@@ -4525,7 +4525,7 @@ unique design feature of Trilinos is its focus on packages.")
|
||||
(commit (string-append "v" version))))
|
||||
(file-name (git-file-name name version))
|
||||
(sha256
|
||||
(base32 "16c1x66kqmc5ldqjij81kypj471fibfihcqn6kz4wbxvnn0smyn6"))))
|
||||
(base32 "1gr1qhxvl4856hnmnx46dqd2qp0jhdh959zm2qfmxzzh19np7xkm"))))
|
||||
(native-inputs
|
||||
(list autoconf
|
||||
automake
|
||||
|
||||
@@ -290,7 +290,7 @@ based upon the Common Locale Data Repository (CLDR).")
|
||||
(package
|
||||
(inherit elixir-ex-cldr-minimal)
|
||||
(name "elixir-ex-cldr")
|
||||
(version "2.47.2")
|
||||
(version "2.43.2")
|
||||
(source
|
||||
(origin
|
||||
;; The hex.pm package ships only the en locale.
|
||||
@@ -300,7 +300,7 @@ based upon the Common Locale Data Repository (CLDR).")
|
||||
(commit (string-append "v" version))))
|
||||
(file-name (git-file-name name version))
|
||||
(sha256
|
||||
(base32 "1rivy61aq0c9zfklm4bpvvkj7lzjgy316rwxl8qz92xqp6xa292y"))))
|
||||
(base32 "1wgwp74ya0gkvd5pk4qv9s38p85r5yw370y4wv7jywy3hrbrj9f5"))))
|
||||
(arguments
|
||||
(list
|
||||
#:phases
|
||||
|
||||
@@ -303,17 +303,7 @@ purposes. Its goal is to be as close as possible to
|
||||
(list
|
||||
#:test-flags
|
||||
;; These tests require network access to badssl.com.
|
||||
#~(list "--exclude" "network")
|
||||
#:phases
|
||||
#~(modify-phases %standard-phases
|
||||
(add-after 'unpack 'make-reproducible
|
||||
(lambda _
|
||||
;; Buffer size has been increased in OTP 28+. For more info see:
|
||||
;; https://github.com/erlang/otp/issues/9722#issuecomment-2808683303
|
||||
(substitute* "test/httpoison_test.exs"
|
||||
(("stream/20") "stream/100")
|
||||
(("<= expected_length") "<= expected_length * 1.1")
|
||||
((">= max_length") ">= max_length * 0.9")))))))
|
||||
#~(list "--exclude" "network")))
|
||||
(native-inputs
|
||||
(list erlang-cowboy
|
||||
elixir-earmark
|
||||
|
||||
@@ -56,7 +56,7 @@
|
||||
;;; Copyright © 2019 Jelle Licht <jlicht@fsfe.org>
|
||||
;;; Copyright © 2019 Björn Höfling <bjoern.hoefling@bjoernhoefling.de>
|
||||
;;; Copyright © 2019 Stephen Webber <montokapro@gmail.com>
|
||||
;;; Copyright © 2019, 2021—2026 Liliana Marie Prikler <liliana.prikler@gmail.com>
|
||||
;;; Copyright © 2019, 2021 Liliana Marie Prikler <liliana.prikler@gmail.com>
|
||||
;;; Copyright © 2019 David Wilson <david@daviwil.com>
|
||||
;;; Copyright © 2020 Paul Garlick <pgarlick@tourbillion-technology.com>
|
||||
;;; Copyright © 2020 Robert Smith <robertsmith@posteo.net>
|
||||
@@ -147,7 +147,7 @@
|
||||
;;; Copyright © 2024 Artyom V. Poptsov <poptsov.artyom@gmail.com>
|
||||
;;; Copyright © 2024, 2025 Spencer King <spencer.king@wustl.edu>
|
||||
;;; Copyright © 2024 emma thompson <bigbookofbug@proton.me>
|
||||
;;; Copyright © 2024-2026 Liam Hupfer <liam@hpfr.net>
|
||||
;;; Copyright © 2024-2025 Liam Hupfer <liam@hpfr.net>
|
||||
;;; Copyright © 2024-2025 Alvin Hsu <aurtzy@gmail.com>
|
||||
;;; Copyright © 2024 Olivier Rojon <o.rojon@posteo.net>
|
||||
;;; Copyright © 2024 Divya Ranjan Pattanaik <divya@subvertising.org>
|
||||
@@ -656,30 +656,6 @@ supported algorithm is chosen to ensure interoperability with
|
||||
Emacs Lisp.")
|
||||
(license license:gpl3)))
|
||||
|
||||
(define-public emacs-org-arbeitszeit
|
||||
(package
|
||||
(name "emacs-org-arbeitszeit")
|
||||
(version "0.0.5")
|
||||
(source
|
||||
(origin
|
||||
(method git-fetch)
|
||||
(uri (git-reference
|
||||
(url "https://github.com/bkaestner/org-arbeitszeit")
|
||||
(commit (string-append "v" version))))
|
||||
(file-name (git-file-name name version))
|
||||
(sha256
|
||||
(base32 "0krxainwpn7bnnvbrrhivmh302i9dyfixs6l5wb7xw7qpjgwqzc8"))))
|
||||
(build-system emacs-build-system)
|
||||
(arguments (list #:tests? #f)) ; no tests
|
||||
(home-page "https://github.com/bkaestner/org-arbeitszeit")
|
||||
(synopsis "Calculate your worktime")
|
||||
(description
|
||||
"This package provides a new dynamic block for Org called \"arbeitszeit\"
|
||||
(German for \"working hours\"). The dynamic block collects all clocked hours and
|
||||
provides a weekly table to quickly see your accumulated overtime. To insert a
|
||||
new block, use @samp{M-x org-dynamic-block-insert-dblock}.")
|
||||
(license license:gpl3+)))
|
||||
|
||||
(define-public emacs-perl-doc
|
||||
(package
|
||||
(name "emacs-perl-doc")
|
||||
@@ -781,54 +757,6 @@ balance windows (keeping them roughly the same size) whenever the window
|
||||
configuration changes, e.g. after splitting or deleting a window.")
|
||||
(license license:bsd-3))))
|
||||
|
||||
(define-public emacs-ben
|
||||
(package
|
||||
(name "emacs-ben")
|
||||
(version "0.12.11")
|
||||
(source
|
||||
(origin
|
||||
(method git-fetch)
|
||||
(uri (git-reference
|
||||
(url "https://codeberg.org/pastor/ben.el")
|
||||
(commit (string-append "v" version))))
|
||||
(file-name (git-file-name name version))
|
||||
(sha256
|
||||
(base32 "0iqrk87dl567vwpwm8rmplrpva475a04s6c34rm24xfy2m7wrwk6"))))
|
||||
(build-system emacs-build-system)
|
||||
(arguments
|
||||
(list
|
||||
#:phases
|
||||
#~(modify-phases %standard-phases
|
||||
(add-after 'unpack 'set-environment
|
||||
(lambda _
|
||||
;; Since the testsuite uses `direnv', the build needs a home
|
||||
;; directory so `direnv' can allow the contents of the `.envrc`
|
||||
;; files generated for the different tests.
|
||||
(setenv "HOME" "/tmp")
|
||||
(setenv "OFFLINE" "1") ;Enable offline tests.
|
||||
(emacs-substitute-variables "ben.el"
|
||||
("ben-direnv-executable"
|
||||
#$(file-append (this-package-input "direnv")
|
||||
"/bin/direnv"))))))))
|
||||
(inputs (list direnv))
|
||||
(propagated-inputs (list emacs-inheritenv))
|
||||
(home-page "https://codeberg.org/pastor/ben.el")
|
||||
(synopsis "Asynchronous buffer-local environments via @command{direnv}")
|
||||
(description
|
||||
"This package allows you to load environments buffer locally. The
|
||||
package is named @command{ben}, which stands for Buffer ENvironments.
|
||||
|
||||
The project relies on @uref{https://direnv.net, direnv} which allows setting
|
||||
per-directory environments through @file{.envrc} files.
|
||||
|
||||
The main improvement of @command{ben} over @command{envrc} is the asynchronous
|
||||
processing of environments, which prevents Emacs from freezing. This is
|
||||
especially useful while loading computationally heavy environments, such when
|
||||
loading @file{.envrc} files that rely on Guix. In these cases, computations
|
||||
can take hours to complete. This package aims to facilitate loading such
|
||||
environments in the background.")
|
||||
(license license:gpl3+)))
|
||||
|
||||
(define-public emacs-bookmark-plus
|
||||
(package
|
||||
(name "emacs-bookmark-plus")
|
||||
@@ -906,7 +834,7 @@ input via a small child-frame spawned at the position of the cursor.")
|
||||
(define-public emacs-arei
|
||||
(package
|
||||
(name "emacs-arei")
|
||||
(version "0.9.7")
|
||||
(version "0.9.6")
|
||||
(source
|
||||
(origin
|
||||
(method git-fetch)
|
||||
@@ -916,13 +844,10 @@ input via a small child-frame spawned at the position of the cursor.")
|
||||
(file-name (git-file-name name version))
|
||||
(sha256
|
||||
(base32
|
||||
"1fp4l8rzfd7cds80p8c9jgwwlb7rsw35djh0hs50g89h937w5s02"))))
|
||||
"1m8ic5pcshz2y2maxvbgg70n4k2kgxvj98zisqal15j7djz0hzji"))))
|
||||
(build-system emacs-build-system)
|
||||
(arguments
|
||||
(list #:lisp-directory "lisp"
|
||||
#:tests? #f)) ; no tests
|
||||
(propagated-inputs
|
||||
(list emacs-consult emacs-eros emacs-sesman emacs-queue))
|
||||
(arguments (list #:tests? #f)) ; no tests
|
||||
(propagated-inputs (list emacs-eros emacs-sesman emacs-queue))
|
||||
(home-page "https://git.sr.ht/~abcdw/emacs-arei")
|
||||
(synopsis "Asynchronous Reliable Extensible IDE")
|
||||
(description "Sleek Guile IDE for Emacs.")
|
||||
@@ -13593,8 +13518,8 @@ for compilation, debugging, documentation lookup, and so on.")
|
||||
(license (list license:gpl2+ license:public-domain))))
|
||||
|
||||
(define-public emacs-sliver
|
||||
(let ((commit "b4cb9cd2a810ba59c946e2592c4a4d56060a8d22")
|
||||
(revision "1"))
|
||||
(let ((commit "d08d41947bb943f25ee2de9573459a6c720e027f")
|
||||
(revision "0"))
|
||||
(package
|
||||
(name "emacs-sliver")
|
||||
;; No tagged releases. Version comes from source code.
|
||||
@@ -13607,7 +13532,7 @@ for compilation, debugging, documentation lookup, and so on.")
|
||||
(commit commit)))
|
||||
(file-name (git-file-name name version))
|
||||
(sha256
|
||||
(base32 "1wddivmp5f4m6fdib96vfylqp4kgcw3ipdsi4b9w50dqzvrqrfjh"))))
|
||||
(base32 "08qycim0mxyiqbik9hjlmzpdggl506bcsv1q1icxzd05bm73sh6n"))))
|
||||
(build-system emacs-build-system)
|
||||
(arguments
|
||||
(list
|
||||
@@ -15872,16 +15797,8 @@ versions utilizing Consult's internal API.")
|
||||
(arguments
|
||||
(list
|
||||
#:tests? #f ;no tests
|
||||
#:phases
|
||||
#~(modify-phases %standard-phases
|
||||
;; Move the extensions source files to the top level, which is
|
||||
;; included in the EMACSLOADPATH.
|
||||
(add-after 'unpack 'move-source-files
|
||||
(lambda _
|
||||
(let ((el-files (find-files "./extensions" ".*\\.el$")))
|
||||
(for-each (lambda (f)
|
||||
(rename-file f (basename f)))
|
||||
el-files)))))))
|
||||
#:include #~(cons "^extensions\\/consult-eglot-embark"
|
||||
%default-include)))
|
||||
(propagated-inputs (list emacs-consult emacs-eglot emacs-embark))
|
||||
(home-page "https://github.com/mohkale/consult-eglot")
|
||||
(synopsis "Consulting-read interface for eglot")
|
||||
@@ -25154,7 +25071,7 @@ lines, and @code{gc} to comment out the target of a motion.")
|
||||
(define-public emacs-eglot
|
||||
(package
|
||||
(name "emacs-eglot")
|
||||
(version "1.23")
|
||||
(version "1.21")
|
||||
(source
|
||||
(origin
|
||||
(method url-fetch)
|
||||
@@ -25162,7 +25079,7 @@ lines, and @code{gc} to comment out the target of a motion.")
|
||||
".tar"))
|
||||
(sha256
|
||||
(base32
|
||||
"1l83c90rdamlk576bd859jkg6406hgxi7w4c6ixlw509c66qr3s6"))))
|
||||
"03fx22rv8ijxq0jnn7xlfqhkpk2b109ygpjbcchp41sa4q7d6nbl"))))
|
||||
(build-system emacs-build-system)
|
||||
(propagated-inputs
|
||||
(list emacs-eldoc
|
||||
@@ -28599,7 +28516,7 @@ unstructured, meant for quick @code{JavaScript} experiments.")
|
||||
(define-public emacs-firefox-release-notes
|
||||
(package
|
||||
(name "emacs-firefox-release-notes")
|
||||
(version "1.8")
|
||||
(version "1.7")
|
||||
(source
|
||||
(origin
|
||||
(method git-fetch)
|
||||
@@ -28610,7 +28527,7 @@ unstructured, meant for quick @code{JavaScript} experiments.")
|
||||
(commit version)))
|
||||
(file-name (git-file-name name version))
|
||||
(sha256
|
||||
(base32 "13ymnx4vgiq5f3cjk3zddrq4xnv6116j5zzza67v98q7rsvzl049"))))
|
||||
(base32 "1i9ncnn0qys0v0bqw87jwx0sa2g31n1i1gfr9zqdml3hakyz8b5f"))))
|
||||
(build-system emacs-build-system)
|
||||
(arguments
|
||||
(list
|
||||
@@ -32121,31 +32038,6 @@ leverages the Parinfer Rust Emacs library to do most of the heavy lifting.")
|
||||
bookmarks and history.")
|
||||
(license license:gpl3+)))
|
||||
|
||||
(define-public emacs-shr-syntax-highlight
|
||||
(package
|
||||
(name "emacs-shr-syntax-highlight")
|
||||
(version "0.1.0")
|
||||
(source
|
||||
(origin
|
||||
(method git-fetch)
|
||||
(uri (git-reference
|
||||
(url "https://codeberg.org/coopi/emacs-shr-syntax-highlight")
|
||||
(commit (string-append "v" version))))
|
||||
(file-name (git-file-name name version))
|
||||
(sha256
|
||||
(base32 "04ax8svpw2s0085pp93dsz5xhhbqr58ghkr1ab2g38pczlsbz18s"))))
|
||||
(build-system emacs-build-system)
|
||||
(home-page "https://codeberg.org/coopi/emacs-shr-syntax-highlight")
|
||||
(synopsis "Syntax highlighting for code blocks rendered by shr")
|
||||
(description
|
||||
"This package adds syntax highlighting to @code{<pre>} code blocks
|
||||
rendered by @acronym{@code{shr}, Simple @acronym{HTML, HyperText Markup
|
||||
Language} Renderer}, used by @acronym{EWW, Emacs Web Wowser} and similar
|
||||
interfaces. It reads @acronym{CSS, Cascading Style Sheets} class annotations
|
||||
such as @code{language-python} and fontifies block contents using the
|
||||
corresponding Emacs major mode.")
|
||||
(license license:agpl3+)))
|
||||
|
||||
(define-public emacs-stumpwm-mode
|
||||
(let ((commit "920f8fc1488f7953f205e1dda4c2ecbbbda56d6")
|
||||
(revision "3"))
|
||||
@@ -39910,7 +39802,7 @@ user interfaces for various built-in modes.")
|
||||
(define-public emacs-calibredb
|
||||
(package
|
||||
(name "emacs-calibredb")
|
||||
(version "2.14.0")
|
||||
(version "2.13.0")
|
||||
(source
|
||||
(origin
|
||||
(method git-fetch)
|
||||
@@ -39919,40 +39811,31 @@ user interfaces for various built-in modes.")
|
||||
(commit version)))
|
||||
(file-name (git-file-name name version))
|
||||
(sha256
|
||||
(base32 "1g0jg6a6fgvxd5bsydckbqwf899d2d9732laz4k1k476mbws5dqy"))))
|
||||
(base32 "1a4gyc3gcq18j29pw2i296d70nvx5fbzlw9fdmqwzncciqz5as6m"))))
|
||||
(build-system emacs-build-system)
|
||||
(arguments
|
||||
(list
|
||||
#:include #~(cons "\\.py$" %default-include)
|
||||
#:tests? #f ;no tests
|
||||
#:phases
|
||||
#~(modify-phases %standard-phases
|
||||
(add-after 'unpack 'patch-paths
|
||||
(lambda* (#:key inputs #:allow-other-keys)
|
||||
(make-file-writable "calibredb-core.el")
|
||||
(let ((calibredb (search-input-file inputs "/bin/calibredb"))
|
||||
(fetch-ebook-metadata
|
||||
(search-input-file inputs "/bin/fetch-ebook-metadata"))
|
||||
(ebook-convert
|
||||
(search-input-file inputs "/bin/ebook-convert"))
|
||||
(calibre-debug
|
||||
(search-input-file inputs "/bin/calibre-debug"))
|
||||
(ebook-meta
|
||||
(search-input-file inputs "/bin/ebook-meta"))
|
||||
(folder-program
|
||||
(string-append #$output
|
||||
"/share/emacs/site-lisp/calibredb-"
|
||||
#$version "/calibredb-folder.py")))
|
||||
(search-input-file inputs "/bin/calibre-debug")))
|
||||
(emacs-substitute-variables "calibredb-core.el"
|
||||
("calibredb-fetch-metadata-program" fetch-ebook-metadata)
|
||||
("calibredb-program" calibredb)
|
||||
("calibredb-convert-program" ebook-convert)
|
||||
("calibredb-debug-program" calibre-debug)
|
||||
("calibredb-ebook-meta-program" ebook-meta)
|
||||
("calibredb-folder-program" folder-program))))))))
|
||||
("calibredb-debug-program" calibre-debug))))))))
|
||||
(inputs
|
||||
(list calibre))
|
||||
(propagated-inputs
|
||||
(list emacs-dash emacs-esxml emacs-request emacs-s))
|
||||
(list emacs-dash emacs-esxml emacs-s))
|
||||
(home-page "https://github.com/chenyanming/calibredb.el")
|
||||
(synopsis "Yet another calibre client for Emacs")
|
||||
(description "This package integrates calibre into Emacs.
|
||||
@@ -41550,65 +41433,17 @@ time.")
|
||||
(build-system emacs-build-system)
|
||||
(arguments
|
||||
(list
|
||||
#:test-command #~(list "make" "tests")
|
||||
#:phases
|
||||
#~(modify-phases %standard-phases
|
||||
;; Move the source files to the top level, which is
|
||||
;; included in the EMACSLOADPATH.
|
||||
(add-after 'unpack 'move-source-files
|
||||
(lambda _
|
||||
(let ((el-files (find-files "./lisp" ".*\\.el$")))
|
||||
(for-each (lambda (f)
|
||||
(rename-file f
|
||||
(basename f)))
|
||||
el-files))))
|
||||
(add-before 'check 'fix-tests
|
||||
(lambda _
|
||||
(substitute* "Makefile"
|
||||
(("cask") ""))
|
||||
(substitute* "test/ert-helper.el"
|
||||
(("lisp\\/") ""))))
|
||||
(add-before 'check 'skip-failing-tests
|
||||
(lambda _
|
||||
(let-syntax
|
||||
((disable-tests
|
||||
(syntax-rules ()
|
||||
((_ file ())
|
||||
(syntax-error "test names list must not be empty"))
|
||||
((_ file (test-name ...))
|
||||
(substitute* file
|
||||
(((string-append
|
||||
"^\\(ert-deftest " test-name ".*") all)
|
||||
(string-append all "(skip-unless nil)\n")) ...)))))
|
||||
(disable-tests
|
||||
"test/mastodon-profile-tests.el"
|
||||
("mastodon-profile--add-author-bylines"
|
||||
"mastodon-profile--make-author-buffer"))
|
||||
(disable-tests
|
||||
"test/mastodon-auth-tests.el"
|
||||
("mastodon-auth--handle-token-response--good"
|
||||
"mastodon-auth-plstore-token-check"))
|
||||
(disable-tests
|
||||
"test/mastodon-client-tests.el"
|
||||
("mastodon-client--make-user-active"
|
||||
"mastodon-client--store"
|
||||
"mastodon-client--store-access-token"))
|
||||
(disable-tests
|
||||
"test/mastodon-tl-tests.el"
|
||||
("mastodon-tl--byline-timestamp-has-relative-display"
|
||||
"mastodon-tl--next-tab-item--no-spaces-at-ends"
|
||||
"mastodon-tl--next-tab-item--with-spaces-at-ends"))
|
||||
(disable-tests
|
||||
"test/mastodon-media-tests.el"
|
||||
("mastodon-media--get-avatar-rendering"
|
||||
"mastodon-media--inline-images"
|
||||
"mastodon-media--load-image-from-url-avatar-with-imagemagic"
|
||||
"mastodon-media--load-image-from-url-avatar-without-imagemagic"
|
||||
"mastodon-media--load-image-from-url-media-link-with-imagemagic"
|
||||
"mastodon-media--load-image-from-url-media-link-without-imagemagic"
|
||||
"mastodon-media--load-image-from-url-url-fetching-fails"
|
||||
"mastodon-media--process-image-response"))))))))
|
||||
(native-inputs (list emacs-el-mock))
|
||||
#:tests? #f ; requires cask
|
||||
#:phases #~(modify-phases %standard-phases
|
||||
;; Move the source files to the top level, which is
|
||||
;; included in the EMACSLOADPATH.
|
||||
(add-after 'unpack 'move-source-files
|
||||
(lambda _
|
||||
(let ((el-files (find-files "./lisp" ".*\\.el$")))
|
||||
(for-each (lambda (f)
|
||||
(rename-file f
|
||||
(basename f)))
|
||||
el-files)))))))
|
||||
(propagated-inputs
|
||||
(list emacs-persist emacs-tp))
|
||||
(home-page "https://codeberg.org/martianh/mastodon.el")
|
||||
|
||||
@@ -3452,7 +3452,7 @@ This is a part of the TiLP project.")
|
||||
(define-public mame
|
||||
(package
|
||||
(name "mame")
|
||||
(version "0.287")
|
||||
(version "0.252")
|
||||
(source
|
||||
(origin
|
||||
(method git-fetch)
|
||||
@@ -3461,16 +3461,16 @@ This is a part of the TiLP project.")
|
||||
(commit (apply string-append "mame" (string-split version #\.)))))
|
||||
(file-name (git-file-name name version))
|
||||
(sha256
|
||||
(base32 "1p9v71gvaqiyj6sa1b0wkdksa9wnr6yr2a43ckycljjfas5s36kq"))
|
||||
(base32 "07qhcm1v47sy2wj30nx3cbhvcbgki0cl83gabr0miiw60fhgyn6j"))
|
||||
(modules '((guix build utils)))
|
||||
(snippet
|
||||
;; Remove bundled libraries.
|
||||
'(begin
|
||||
(with-directory-excursion "3rdparty"
|
||||
(for-each delete-file-recursively
|
||||
'("asio" "expat" "glm" "flac" "libjpeg" "lua"
|
||||
"portaudio" "portmidi" "pugixml" "rapidjson"
|
||||
"sqlite3" "utf8proc" "zlib")))))))
|
||||
'("asio" "expat" "glm" "libflac" "libjpeg" "lua"
|
||||
"portaudio" "portmidi" "pugixml" "rapidjson" "SDL2"
|
||||
"SDL2-override" "sqlite3" "utf8proc" "zlib")))))))
|
||||
(build-system gnu-build-system)
|
||||
(arguments
|
||||
(list
|
||||
@@ -3604,9 +3604,7 @@ This is a part of the TiLP project.")
|
||||
libjpeg-turbo
|
||||
libxi
|
||||
libxinerama
|
||||
;; MAME requires Lua compiled as C++ to work correctly.
|
||||
;; See https://www.mamedev.org/?p=523
|
||||
lua-5.4-for-c++
|
||||
lua
|
||||
portaudio
|
||||
portmidi
|
||||
pugixml
|
||||
|
||||
@@ -50,7 +50,7 @@
|
||||
(define-public erlang
|
||||
(package
|
||||
(name "erlang")
|
||||
(version "28.4.3")
|
||||
(version "27.3.4.6")
|
||||
(source (origin
|
||||
(method git-fetch)
|
||||
;; The tarball from http://erlang.org/download contains many
|
||||
@@ -62,7 +62,7 @@
|
||||
(file-name (git-file-name name version))
|
||||
(sha256
|
||||
(base32
|
||||
"1dsdmp2rccc0rhzy2w8r4amxmc6nr9hbi053j2s0bg9db30b48rc"))
|
||||
"0dhz2c7w28ss0ypj7jh88pfs3kc8hbwiiq91in1j2miy5sn4cp3x"))
|
||||
(patches (search-patches "erlang-man-path.patch"))))
|
||||
(build-system gnu-build-system)
|
||||
(native-inputs
|
||||
@@ -75,7 +75,7 @@
|
||||
"/OTP-" version "/otp_doc_man_" version ".tar.gz"))
|
||||
(sha256
|
||||
(base32
|
||||
"1g17wzv8j12g9272yvv55nj4wqs09hxkv3i0vnp7d6gcs24bmphi"))))))
|
||||
"1j1fcli7ma9vi4qyv67lq7yiznhpnfvcmh57bn8qxvha6ky2pngm"))))))
|
||||
(inputs
|
||||
(list ncurses openssl wxwidgets))
|
||||
(propagated-inputs
|
||||
|
||||
@@ -220,7 +220,6 @@ testing InfiniBand networks.")
|
||||
"--disable-assertions"
|
||||
"--disable-params-check"
|
||||
|
||||
"--enable-mt"
|
||||
(string-append "--with-verbs="
|
||||
#$(this-package-input "rdma-core"))
|
||||
|
||||
|
||||
@@ -165,7 +165,7 @@
|
||||
;; <https://bitcoincore.org/en/lifecycle/#schedule>.
|
||||
(package
|
||||
(name "bitcoin-core")
|
||||
(version "31.0")
|
||||
(version "30.2")
|
||||
(source (origin
|
||||
(method url-fetch)
|
||||
(uri
|
||||
@@ -173,7 +173,7 @@
|
||||
version "/bitcoin-" version ".tar.gz"))
|
||||
(sha256
|
||||
(base32
|
||||
"1qxkcyq8nwq6sw4qi660z8n8356mqdsf4jvpq5ndkvrsx9gfz80b"))))
|
||||
"1jw4djh22v0nih0n7irdbknfbqavlc4l3b8176b5qgc88a60pl3g"))))
|
||||
(build-system qt-build-system)
|
||||
(arguments
|
||||
(list #:qtbase qtbase
|
||||
@@ -197,7 +197,9 @@
|
||||
"python3" "./test/functional/test_runner.py" "--timeout-factor=2"
|
||||
(string-append "--jobs=" (number->string (parallel-job-count)))))))))
|
||||
(native-inputs
|
||||
(list pkg-config
|
||||
(list bash ; provides the sh command for system_tests
|
||||
coreutils ; provides the cat, echo and false commands for system_tests
|
||||
pkg-config
|
||||
python ; for the tests
|
||||
python-pyzmq ; for the tests
|
||||
qttools))
|
||||
|
||||
@@ -4658,6 +4658,46 @@ is a stylish type with a polished yet relaxed feel. Its versatility makes it
|
||||
suitable for a wide range of uses.")
|
||||
(license license:silofl1.1))))
|
||||
|
||||
(define-public font-cozette
|
||||
(package
|
||||
(name "font-cozette")
|
||||
(version "1.13.0")
|
||||
(source (origin
|
||||
(method git-fetch)
|
||||
(uri (git-reference
|
||||
(url "https://github.com/slavfox/Cozette")
|
||||
(commit (string-append "v." version))))
|
||||
(file-name (git-file-name name version))
|
||||
(sha256
|
||||
(base32
|
||||
"178i812n4sfsvid7jhnm683jlxqmrv4ck6qbb4nwyllhwg3gyq60"))))
|
||||
(build-system font-build-system)
|
||||
(arguments
|
||||
`(#:phases
|
||||
(modify-phases %standard-phases
|
||||
(add-after 'unpack 'dont-depend-on-git
|
||||
(lambda _
|
||||
(substitute* "build.py"
|
||||
;; Merely importing this module requires a git repository.
|
||||
;; We don't use get_changelog, so just disable the import.
|
||||
(("from cozette_builder\\.changeloggen import get_changelog")
|
||||
""))))
|
||||
(add-before 'install 'build
|
||||
(lambda _
|
||||
(invoke "python3" "build.py" "fonts"))))))
|
||||
(native-inputs
|
||||
(list fontforge
|
||||
python
|
||||
python-crayons
|
||||
python-fonttools
|
||||
python-numpy
|
||||
python-pillow))
|
||||
(home-page "https://github.com/slavfox/Cozette")
|
||||
(synopsis "Bitmap programming font")
|
||||
(description "Cozette is a 6x13px (bounding box) bitmap font based on Dina
|
||||
and heavily inspired by Creep.")
|
||||
(license license:expat)))
|
||||
|
||||
(define-public font-montserrat
|
||||
(package
|
||||
(name "font-montserrat")
|
||||
|
||||
@@ -3417,50 +3417,50 @@ interfaces.")
|
||||
(define-public xdg-desktop-portal-wlr
|
||||
(package
|
||||
(name "xdg-desktop-portal-wlr")
|
||||
(version "0.8.2")
|
||||
(source
|
||||
(origin
|
||||
(method git-fetch)
|
||||
(uri (git-reference
|
||||
(url "https://github.com/emersion/xdg-desktop-portal-wlr")
|
||||
(commit (string-append "v" version))))
|
||||
(file-name (git-file-name name version))
|
||||
(sha256
|
||||
(base32 "1jj0a9s3h3i04qsxkhcpxjzbb17hs9ngdy7wkypja09233zdz10w"))
|
||||
(patches (search-patches "xdg-desktop-portal-wlr-harcoded-length.patch"))))
|
||||
(version "0.7.1")
|
||||
(source (origin
|
||||
(method git-fetch)
|
||||
(uri (git-reference
|
||||
(url "https://github.com/emersion/xdg-desktop-portal-wlr")
|
||||
(commit (string-append "v" version))))
|
||||
(file-name (git-file-name name version))
|
||||
(sha256
|
||||
(base32
|
||||
"1mbq3czka9swwmfaasnaj89y2m254p3qa522ayclh688jdwh70hq"))
|
||||
(patches (search-patches "xdg-desktop-portal-wlr-harcoded-length.patch"))))
|
||||
(build-system meson-build-system)
|
||||
(arguments
|
||||
(list
|
||||
#:configure-flags
|
||||
#~(list "-Dsystemd=disabled"
|
||||
"-Dsd-bus-provider=libelogind")
|
||||
#:phases
|
||||
#~(modify-phases %standard-phases
|
||||
(add-after 'unpack 'hardcode-binaries
|
||||
(lambda* (#:key inputs #:allow-other-keys)
|
||||
(let ((sh (search-input-file inputs "/bin/sh"))
|
||||
(grim (search-input-file inputs "/bin/grim"))
|
||||
(slurp (search-input-file inputs "/bin/slurp")))
|
||||
(substitute* '("src/screencast/chooser.c"
|
||||
"src/screenshot/screenshot.c")
|
||||
(("grim") grim)
|
||||
(("slurp") slurp)
|
||||
(("/bin/sh") sh))
|
||||
(substitute* "src/screencast/screencast.c"
|
||||
(("execvp\\(\"sh")
|
||||
(format #f "execvp(\"~a" sh))))))
|
||||
(add-after 'install 'install-documentation
|
||||
(lambda _
|
||||
(install-file "../source/README.md"
|
||||
(string-append #$output "/share/doc/"
|
||||
#$name)))))))
|
||||
(native-inputs (list cmake-minimal pkg-config scdoc))
|
||||
(inputs (list bash-minimal
|
||||
elogind
|
||||
`(#:configure-flags
|
||||
'("-Dsystemd=disabled"
|
||||
"-Dsd-bus-provider=libelogind")
|
||||
#:phases
|
||||
(modify-phases %standard-phases
|
||||
(add-after 'unpack 'hardcode-binaries
|
||||
(lambda* (#:key inputs #:allow-other-keys)
|
||||
(let ((sh (search-input-file inputs "/bin/sh"))
|
||||
(grim (search-input-file inputs "/bin/grim"))
|
||||
(slurp (search-input-file inputs "/bin/slurp")))
|
||||
(substitute* "src/screenshot/screenshot.c"
|
||||
(("grim") grim)
|
||||
(("slurp") slurp)
|
||||
(("execl\\(\"/bin/sh\", \"/bin/sh\"")
|
||||
(string-append "execl(\"" sh "\", \"" sh "\"")))
|
||||
(substitute* "src/screencast/screencast.c"
|
||||
(("execvp\\(\"sh")
|
||||
(string-append "execvp(\"" sh))))))
|
||||
(add-after 'install 'install-documentation
|
||||
(lambda* (#:key outputs #:allow-other-keys)
|
||||
(install-file "../source/README.md"
|
||||
(string-append (assoc-ref outputs "out")
|
||||
"/share/doc/" ,name)))))))
|
||||
(native-inputs
|
||||
(list cmake-minimal pkg-config))
|
||||
(inputs (list elogind
|
||||
bash-minimal
|
||||
grim
|
||||
iniparser
|
||||
libinih
|
||||
mesa
|
||||
libinih
|
||||
pipewire
|
||||
slurp
|
||||
wayland
|
||||
|
||||
@@ -5534,13 +5534,23 @@ falling, themeable graphics and sounds, and replays.")
|
||||
(build-system cmake-build-system)
|
||||
(arguments
|
||||
(list #:tests? #f ;no test target
|
||||
#:configure-flags #~'("-DENABLE_SYSTEM_LUA=ON")))
|
||||
#:configure-flags #~'("-DENABLE_SYSTEM_LUA=ON")
|
||||
#:phases
|
||||
#~(modify-phases %standard-phases
|
||||
(add-before 'configure 'pre-configure
|
||||
(lambda _
|
||||
;; XXX: Our Lua doesn't have a C++ library, force C linkage.
|
||||
(substitute* '("src/lua/wrapper_lua.h"
|
||||
"src/lua/wrapper_lualib.h"
|
||||
"src/lua/wrapper_lauxlib.h")
|
||||
(("#include \"(lua|lualib|lauxlib)\\.h\"")
|
||||
"#include \"lua.hpp\"")))))))
|
||||
(inputs
|
||||
(list boost-1.83
|
||||
curl
|
||||
dbus
|
||||
libvorbis
|
||||
lua-5.4-for-c++
|
||||
lua-5.4
|
||||
openssl
|
||||
pango
|
||||
sdl2
|
||||
@@ -5927,7 +5937,7 @@ Transport Tycoon Deluxe.")
|
||||
(add-after 'unpack 'patch-sources
|
||||
(lambda* (#:key inputs #:allow-other-keys)
|
||||
(substitute* "src/music/fluidsynth.cpp"
|
||||
(("_default_soundfonts\\[\\] = \\{" all)
|
||||
(("default_sf\\[\\] = \\{" all)
|
||||
(string-append all "
|
||||
\t/* Guix hardcoded :P */
|
||||
\t\"" (search-input-file inputs "/share/soundfonts/FreePatsGM.sf2") "\",
|
||||
@@ -5954,7 +5964,7 @@ Transport Tycoon Deluxe.")
|
||||
(package
|
||||
(inherit openttd)
|
||||
(name "openttd-jgrpp")
|
||||
(version "0.71.1")
|
||||
(version "0.70.2")
|
||||
(source
|
||||
(origin
|
||||
(method git-fetch)
|
||||
@@ -5963,7 +5973,7 @@ Transport Tycoon Deluxe.")
|
||||
(commit (string-append "jgrpp-" version))))
|
||||
(file-name (git-file-name name version))
|
||||
(sha256
|
||||
(base32 "1cy1ghc1mc61hdz8lykx2ggs5nld30jdgj8y4vdli2v1ffhy7xy9"))))
|
||||
(base32 "1jzzvribf2cqvjl9cympyx9qpplljvmhqrrlw7aq4ckzl92d87z3"))))
|
||||
(inputs (modify-inputs inputs
|
||||
(append zstd harfbuzz)))
|
||||
(arguments
|
||||
|
||||
@@ -425,29 +425,14 @@ hierarchical hexagonal geospatial indexing system")
|
||||
(base32
|
||||
"00qdk9a4048pzfj2rhzkfw3lvm642znf6kr4x29i3d94494pxsnn"))))
|
||||
(build-system cmake-build-system)
|
||||
(arguments
|
||||
`(#:phases
|
||||
(modify-phases %standard-phases
|
||||
,@(if (or (target-x86-32?) (target-arm32?))
|
||||
'((add-after 'unpack 'disable-broken-tests
|
||||
(lambda _
|
||||
;; This test fails due to limited accuracy.
|
||||
(delete-file "tests/xmltester/tests/general/TestCentroid.xml")
|
||||
(with-directory-excursion "tests/unit"
|
||||
;; These also fail due to limited accuracy.
|
||||
(delete-file "algorithm/MinimumAreaRectangleTest.cpp")
|
||||
(delete-file "capi/GEOSMinimumRotatedRectangleTest.cpp")
|
||||
;; It is unclear why these fail, but I'm guessing:
|
||||
;; limited accuracy.
|
||||
(delete-file "linearref/LengthIndexedLineTest.cpp")
|
||||
(delete-file "math/DDTest.cpp")))))
|
||||
'())
|
||||
(add-after
|
||||
'unpack 'patch-test-shebangs
|
||||
(lambda _
|
||||
(substitute* '("tests/xmltester/testrunner.sh"
|
||||
"tests/xmltester/safe_to_xml.sh")
|
||||
(("/bin/sh") (which "sh"))))))))
|
||||
(arguments `(#:phases
|
||||
(modify-phases %standard-phases
|
||||
(add-after
|
||||
'unpack 'patch-test-shebangs
|
||||
(lambda _
|
||||
(substitute* '("tests/xmltester/testrunner.sh"
|
||||
"tests/xmltester/safe_to_xml.sh")
|
||||
(("/bin/sh") (which "sh"))))))))
|
||||
(inputs
|
||||
(list glib))
|
||||
(home-page "https://libgeos.org/")
|
||||
@@ -970,29 +955,6 @@ hydrology and waste deposition.")
|
||||
(base32
|
||||
"03r6mspfv22fs4x4jcgv25v9gsj5k6zy8incvyf94qf50g47s2bc"))))
|
||||
(build-system cmake-build-system)
|
||||
(arguments
|
||||
(if (target-32bit?)
|
||||
(list
|
||||
#:phases
|
||||
'(modify-phases %standard-phases
|
||||
(add-after 'unpack 'patch-tests
|
||||
(lambda _
|
||||
;; These regression tests fail due to accuracy problems.
|
||||
(substitute* "test/unit/test_factory.cpp"
|
||||
(("^TEST\\(factory, AuthorityFactory_createUnitOfMeasure_linear_us_survey_foot\\) \\{" m)
|
||||
(string-append m "\nGTEST_SKIP();\n")))
|
||||
(substitute* "test/unit/test_grids.cpp"
|
||||
(("^TEST_F\\(GridTest, VerticalShiftGridSet_gtx\\) \\{" m)
|
||||
(string-append m "\nGTEST_SKIP();\n")))
|
||||
(substitute* "test/unit/test_defmodel.cpp"
|
||||
(("^TEST\\(defmodel, evaluator_horizontal_unit_metre\\) \\{" m)
|
||||
(string-append m "\nGTEST_SKIP();\n")))
|
||||
;; These regression tests fail due to accuracy problems.
|
||||
(substitute* "test/CMakeLists.txt"
|
||||
(("proj_add_gie_test\\(\"4D-API-cs2cs-style\".+") "")
|
||||
(("proj_add_gie_test\\(\"Builtins\".+") "")
|
||||
(("proj_add_gie_test\\(\"peirce_q\".+") ""))))))
|
||||
'()))
|
||||
(native-inputs (list googletest pkg-config))
|
||||
(propagated-inputs (list curl libtiff sqlite)) ;required by proj.pc
|
||||
(home-page "https://proj.org/")
|
||||
@@ -1022,34 +984,7 @@ lets developers use the functionality of Proj in their own software.")
|
||||
version ".tar.gz"))
|
||||
(sha256
|
||||
(base32
|
||||
"1g0hkpiablvhsmw0kn5frwgdir3q7avc45p6lc1zhhhzkv5ikydh"))))
|
||||
(arguments
|
||||
(if (target-32bit?)
|
||||
(list
|
||||
#:phases
|
||||
'(modify-phases %standard-phases
|
||||
(add-after 'unpack 'patch-tests
|
||||
(lambda _
|
||||
;; These regression tests fail due to accuracy problems.
|
||||
(substitute* "test/unit/test_factory.cpp"
|
||||
(("^TEST\\(factory, AuthorityFactory_createUnitOfMeasure_linear_us_survey_foot\\) \\{" m)
|
||||
(string-append m "\nGTEST_SKIP();\n")))
|
||||
(substitute* "test/unit/test_grids.cpp"
|
||||
(("^TEST_F\\(GridTest, VerticalShiftGridSet_gtx\\) \\{" m)
|
||||
(string-append m "\nGTEST_SKIP();\n")))
|
||||
(substitute* "test/unit/test_defmodel.cpp"
|
||||
(("^TEST\\(defmodel, evaluator_horizontal_unit_metre\\) \\{" m)
|
||||
(string-append m "\nGTEST_SKIP();\n")))
|
||||
;; These regression tests fail due to accuracy problems.
|
||||
(substitute* "test/CMakeLists.txt"
|
||||
(("proj_add_gie_test\\(\"4D-API-cs2cs-style\".+") "")
|
||||
(("proj_add_gie_test\\(\"Builtins\".+") "")
|
||||
(("proj_add_gie_test\\(\"peirce_q\".+") "")
|
||||
(("proj_add_gie_test\\(\"adams_ws2\".+") ""))
|
||||
(substitute* "test/cli/CMakeLists.txt"
|
||||
(("proj_add_test_script_sh\\(\"testvarious\" CS2CS_BIN\\)") ""))))))
|
||||
'()))))
|
||||
|
||||
"1g0hkpiablvhsmw0kn5frwgdir3q7avc45p6lc1zhhhzkv5ikydh"))))))
|
||||
|
||||
(define-public python-obspy
|
||||
(package
|
||||
|
||||
@@ -1,4 +1,7 @@
|
||||
;;; GNU Guix --- Functional package management for GNU
|
||||
;;; Copyright © 2013 Andreas Enge <andreas@enge.fr>
|
||||
;;; Copyright © 2016 Efraim Flashner <efraim@flashner.co.il>
|
||||
;;; Copyright © 2018, 2020 Tobias Geerinckx-Rice <me@tobias.gr>
|
||||
;;;
|
||||
;;; This file is part of GNU Guix.
|
||||
;;;
|
||||
@@ -16,8 +19,44 @@
|
||||
;;; along with GNU Guix. If not, see <http://www.gnu.org/licenses/>.
|
||||
|
||||
(define-module (gnu packages gkrellm)
|
||||
#:use-module (gnu packages monitoring)
|
||||
#:use-module (guix deprecation))
|
||||
#:use-module (guix build-system gnu)
|
||||
#:use-module (guix download)
|
||||
#:use-module (guix gexp)
|
||||
#:use-module ((guix licenses) #:prefix license:)
|
||||
#:use-module (guix packages)
|
||||
#:use-module (guix utils)
|
||||
#:use-module (gnu packages gettext)
|
||||
#:use-module (gnu packages gtk)
|
||||
#:use-module (gnu packages pkg-config)
|
||||
#:use-module (gnu packages xorg))
|
||||
|
||||
(define-deprecated/public-alias gkrellm
|
||||
(@ (guix packages monitoring) gkrellm))
|
||||
(define-public gkrellm
|
||||
(package
|
||||
(name "gkrellm")
|
||||
(version "2.5.1")
|
||||
(source
|
||||
(origin
|
||||
(method url-fetch)
|
||||
(uri (string-append "https://gkrellm.srcbox.net/releases/gkrellm-"
|
||||
version ".tar.bz2"))
|
||||
(sha256
|
||||
(base32 "0qvy2xmwmfy5f0g09yn9lr262shnx82ba04r5il2wj4qscg3r7h8"))))
|
||||
(build-system gnu-build-system)
|
||||
(inputs (list gtk+-2 libsm))
|
||||
(native-inputs (list gettext-minimal pkg-config))
|
||||
(arguments
|
||||
(list
|
||||
#:tests? #f ;there is no check target
|
||||
#:phases
|
||||
#~(modify-phases %standard-phases
|
||||
(delete 'configure)) ;no configure script
|
||||
#:make-flags
|
||||
#~(list (string-append "INSTALLROOT=" #$output)
|
||||
(string-append "CC=" #$(cc-for-target)))))
|
||||
(home-page "https://gkrellm.srcbox.net/")
|
||||
(synopsis "System monitors")
|
||||
(description
|
||||
"GKrellM is a single process stack of system monitors which supports
|
||||
applying themes to match its appearance to your window manager, Gtk, or any
|
||||
other theme.")
|
||||
(license license:gpl3+)))
|
||||
|
||||
@@ -605,9 +605,9 @@ in the case of Firefox, it is browser/locales/all-locales."
|
||||
"zh-TW"))
|
||||
|
||||
;;; Please keep these versions in sync with icedove.
|
||||
(define %icecat-base-version "140.10.0")
|
||||
(define %icecat-base-version "140.9.1")
|
||||
(define %icecat-version (string-append %icecat-base-version "-gnu1"))
|
||||
(define %icecat-build-id "20260421000000") ;must be of the form YYYYMMDDhhmmss
|
||||
(define %icecat-build-id "20260414000000") ;must be of the form YYYYMMDDhhmmss
|
||||
|
||||
;; 'icecat-source' is a "computed" origin that generates an IceCat tarball
|
||||
;; from the corresponding upstream Firefox ESR tarball, using the 'makeicecat'
|
||||
@@ -627,9 +627,9 @@ in the case of Firefox, it is browser/locales/all-locales."
|
||||
"firefox-" upstream-firefox-version ".source.tar.xz"))
|
||||
(sha256
|
||||
(base32
|
||||
"06996548nfmn4r4mfw3wvgb1mp35majc5hjyhs1krgp33ck2m1f0"))))
|
||||
"1hld2kbzvrmr7pqq0r5hw639xl8kw29lm2hsbn0m4kxang1fdlj5"))))
|
||||
|
||||
(gnuzilla-commit "02125f31250c0240ee2ab1aa629ce66d4ffb9f30")
|
||||
(gnuzilla-commit "f3595923458a5255f61a3853bd83bb5f004dc3bc")
|
||||
(gnuzilla-source
|
||||
(origin
|
||||
(method git-fetch)
|
||||
@@ -640,7 +640,7 @@ in the case of Firefox, it is browser/locales/all-locales."
|
||||
(string-take gnuzilla-commit 8)))
|
||||
(sha256
|
||||
(base32
|
||||
"1hgx286gp0j46pklzzh5kvsnari1j3s0bff384m505m942k6l4hf"))))
|
||||
"03kc08cvmdv3sxihf5hfhw2k91mg1y6f46b3x47p7q98phgk03cv"))))
|
||||
|
||||
;; 'search-patch' returns either a valid file name or #f, so wrap it
|
||||
;; in 'assume-valid-file-name' to avoid 'local-file' warnings.
|
||||
@@ -1249,166 +1249,6 @@ testing.")
|
||||
(cpe-name . "firefox_esr")
|
||||
(cpe-version . ,(first (string-split version #\-)))))))
|
||||
|
||||
;;; TEMPORARY old version of icecat-source for use by icedove until it is updated.
|
||||
(define %icecat-140.9.1-base-version "140.9.1")
|
||||
(define %icecat-140.9.1-version (string-append %icecat-140.9.1-base-version "-gnu1"))
|
||||
(define icecat-140.9.1-source
|
||||
(let* ((major-version (first (string-split %icecat-140.9.1-base-version #\.)))
|
||||
(minor-version (second (string-split %icecat-140.9.1-base-version #\.)))
|
||||
(sub-version (third (string-split %icecat-140.9.1-base-version #\.)))
|
||||
|
||||
(upstream-firefox-version (string-append %icecat-140.9.1-base-version "esr"))
|
||||
(upstream-firefox-source
|
||||
(origin
|
||||
(method url-fetch)
|
||||
(uri (string-append
|
||||
"https://ftp.mozilla.org/pub/firefox/releases/"
|
||||
upstream-firefox-version "/source/"
|
||||
"firefox-" upstream-firefox-version ".source.tar.xz"))
|
||||
(sha256
|
||||
(base32
|
||||
"1hld2kbzvrmr7pqq0r5hw639xl8kw29lm2hsbn0m4kxang1fdlj5"))))
|
||||
|
||||
(gnuzilla-commit "f3595923458a5255f61a3853bd83bb5f004dc3bc")
|
||||
(gnuzilla-source
|
||||
(origin
|
||||
(method git-fetch)
|
||||
(uri (git-reference
|
||||
(url "git://git.savannah.gnu.org/gnuzilla.git")
|
||||
(commit gnuzilla-commit)))
|
||||
(file-name (git-file-name "gnuzilla"
|
||||
(string-take gnuzilla-commit 8)))
|
||||
(sha256
|
||||
(base32
|
||||
"03kc08cvmdv3sxihf5hfhw2k91mg1y6f46b3x47p7q98phgk03cv"))))
|
||||
|
||||
;; 'search-patch' returns either a valid file name or #f, so wrap it
|
||||
;; in 'assume-valid-file-name' to avoid 'local-file' warnings.
|
||||
(makeicecat-patch
|
||||
(local-file (assume-valid-file-name
|
||||
(search-patch "icecat-makeicecat.patch")))))
|
||||
|
||||
(origin
|
||||
(method computed-origin-method)
|
||||
(file-name (string-append "icecat-" %icecat-140.9.1-version ".tar.zst"))
|
||||
(sha256 #f)
|
||||
(uri
|
||||
(delay
|
||||
(with-imported-modules '((guix build utils))
|
||||
#~(begin
|
||||
(use-modules (guix build utils))
|
||||
(let ((firefox-dir
|
||||
(string-append "firefox-" #$%icecat-140.9.1-base-version))
|
||||
(icecat-dir
|
||||
(string-append "icecat-" #$%icecat-140.9.1-version)))
|
||||
|
||||
(set-path-environment-variable
|
||||
"PATH" '("bin")
|
||||
(list #+python
|
||||
#+(canonical-package bash)
|
||||
#+(canonical-package coreutils)
|
||||
#+(canonical-package findutils)
|
||||
#+(canonical-package patch)
|
||||
#+(canonical-package xz)
|
||||
#+(canonical-package zstd)
|
||||
#+(canonical-package sed)
|
||||
#+(canonical-package grep)
|
||||
#+(canonical-package bzip2)
|
||||
#+(canonical-package gzip)
|
||||
#+(canonical-package tar)))
|
||||
|
||||
(set-path-environment-variable
|
||||
"PYTHONPATH"
|
||||
(list #+(format #f "lib/python~a/site-packages"
|
||||
(version-major+minor
|
||||
(package-version python))))
|
||||
'#+(cons python-jsonschema
|
||||
(map second
|
||||
(package-transitive-propagated-inputs
|
||||
python-jsonschema))))
|
||||
|
||||
;; We copy the gnuzilla source directory because it is
|
||||
;; read-only in 'gnuzilla-source', and the makeicecat script
|
||||
;; uses "cp -a" to copy parts of it and assumes that the
|
||||
;; copies will be writable.
|
||||
(copy-recursively #+gnuzilla-source "/tmp/gnuzilla"
|
||||
#:log (%make-void-port "w"))
|
||||
|
||||
(with-directory-excursion "/tmp/gnuzilla"
|
||||
(make-file-writable "makeicecat")
|
||||
(invoke "patch" "--force" "--no-backup-if-mismatch"
|
||||
"-p1" "--input" #+makeicecat-patch)
|
||||
(patch-shebang "makeicecat")
|
||||
(substitute* "makeicecat"
|
||||
(("^readonly FFMAJOR=(.*)" all ffmajor)
|
||||
(unless (string=? #$major-version
|
||||
(string-trim-both ffmajor))
|
||||
;; The makeicecat script cannot be expected to work
|
||||
;; properly on a different version of Firefox, even if
|
||||
;; no errors occur during execution.
|
||||
(error "makeicecat major version mismatch"))
|
||||
(string-append "readonly FFMAJOR=" #$major-version "\n"))
|
||||
(("^readonly FFMINOR=.*")
|
||||
(string-append "readonly FFMINOR=" #$minor-version "\n"))
|
||||
(("^readonly FFSUB=.*")
|
||||
(string-append "readonly FFSUB=" #$sub-version "\n"))
|
||||
(("^readonly DATADIR=.*")
|
||||
"readonly DATADIR=/tmp/gnuzilla/data\n")
|
||||
(("^readonly SOURCEDIR=.*")
|
||||
(string-append "readonly SOURCEDIR=" icecat-dir "\n"))
|
||||
(("/bin/sed")
|
||||
#+(file-append (canonical-package sed) "/bin/sed"))))
|
||||
|
||||
(format #t "Unpacking upstream firefox tarball...~%")
|
||||
(force-output)
|
||||
(invoke "tar" "xf" #+upstream-firefox-source)
|
||||
(rename-file firefox-dir icecat-dir)
|
||||
|
||||
(with-directory-excursion icecat-dir
|
||||
(format #t "Populating l10n directory...~%")
|
||||
(force-output)
|
||||
(mkdir "l10n")
|
||||
(with-directory-excursion "l10n"
|
||||
(for-each
|
||||
(lambda (locale)
|
||||
(let ((locale-dir (string-append #+mozilla-l10n "/"
|
||||
locale)))
|
||||
(format #t " ~a~%" locale)
|
||||
(force-output)
|
||||
(copy-recursively locale-dir locale
|
||||
#:log (%make-void-port "w"))
|
||||
(for-each make-file-writable (find-files locale))
|
||||
(with-directory-excursion locale
|
||||
(mkdir-p "browser/chrome/browser/preferences")
|
||||
(call-with-output-file "browser/chrome/browser/\
|
||||
preferences/advanced-scripts.dtd"
|
||||
(lambda (port) #f)))))
|
||||
'#+%icecat-locales)
|
||||
(copy-recursively #+mozilla-compare-locales
|
||||
"compare-locales"
|
||||
#:log (%make-void-port "w"))
|
||||
(delete-file "compare-locales/.gitignore")))
|
||||
|
||||
(format #t "Running makeicecat script...~%")
|
||||
(force-output)
|
||||
(invoke "bash" "/tmp/gnuzilla/makeicecat")
|
||||
|
||||
(format #t "Packing IceCat source tarball...~%")
|
||||
(force-output)
|
||||
(setenv "ZSTD_NBTHREADS" (number->string (parallel-job-count)))
|
||||
(invoke "tar" "cfa" #$output
|
||||
;; Avoid non-determinism in the archive. We set the
|
||||
;; mtime of files in the archive to early 1980 because
|
||||
;; the build process fails if the mtime of source
|
||||
;; files is pre-1980, due to the creation of zip
|
||||
;; archives.
|
||||
"--mtime=@315619200" ; 1980-01-02 UTC
|
||||
"--owner=root:0"
|
||||
"--group=root:0"
|
||||
"--sort=name"
|
||||
icecat-dir)))))))))
|
||||
|
||||
|
||||
(define %icedove-build-id "20260403000000") ;must be of the form YYYYMMDDhhmmss
|
||||
;;; See <https://product-details.mozilla.org/1.0/thunderbird_versions.json>
|
||||
;;; for the source of truth regarding Thunderbird releases.
|
||||
@@ -1543,7 +1383,7 @@ preferences/advanced-scripts.dtd"
|
||||
;; Extract the base Icecat tarball, renaming its top-level
|
||||
;; directory.
|
||||
(invoke "tar" "--transform" (string-append "s,[^/]*," #$name ",")
|
||||
"-xf" #$icecat-140.9.1-source)
|
||||
"-xf" #$icecat-source)
|
||||
(chdir #$name)
|
||||
|
||||
;; Merge the Thunderdbird localization data.
|
||||
|
||||
@@ -245,55 +245,6 @@ go-fuzz-headers.")
|
||||
@end itemize")
|
||||
(license license:expat)))
|
||||
|
||||
(define-public go-github-com-alexkohler-prealloc
|
||||
(package
|
||||
(name "go-github-com-alexkohler-prealloc")
|
||||
(version "1.0.0")
|
||||
(source
|
||||
(origin
|
||||
(method git-fetch)
|
||||
(uri (git-reference
|
||||
(url "https://github.com/alexkohler/prealloc")
|
||||
(commit (string-append "v" version))))
|
||||
(file-name (git-file-name name version))
|
||||
(sha256
|
||||
(base32 "011i8yqzyjgwj17k44xvvg4bxfv8z20s0416r2d3yf4s3wqqygpq"))))
|
||||
(build-system go-build-system)
|
||||
(arguments
|
||||
(list
|
||||
#:import-path "github.com/alexkohler/prealloc"))
|
||||
(home-page "https://github.com/alexkohler/prealloc")
|
||||
(synopsis "Find slice declarations that could be preallocated")
|
||||
(description
|
||||
"This package is a Go static analysis tool to find slice declarations
|
||||
that could potentially be preallocated.")
|
||||
(license license:expat)))
|
||||
|
||||
(define-public go-github-com-alingse-asasalint
|
||||
(package
|
||||
(name "go-github-com-alingse-asasalint")
|
||||
(version "0.0.11")
|
||||
(source
|
||||
(origin
|
||||
(method git-fetch)
|
||||
(uri (git-reference
|
||||
(url "https://github.com/alingse/asasalint")
|
||||
(commit (string-append "v" version))))
|
||||
(file-name (git-file-name name version))
|
||||
(sha256
|
||||
(base32 "1avz33cx3gcpps26rxijv7ic0njfmsdkbcp2mqg5yxhdcpq57s0q"))))
|
||||
(build-system go-build-system)
|
||||
(arguments
|
||||
(list
|
||||
#:import-path "github.com/alingse/asasalint"))
|
||||
(propagated-inputs
|
||||
(list go-golang-org-x-tools))
|
||||
(home-page "https://github.com/alingse/asasalint")
|
||||
(synopsis "Lint pass any slice as any in variadic function")
|
||||
(description
|
||||
"Golang linter, lint that pass any slice as any in variadic function.")
|
||||
(license license:expat)))
|
||||
|
||||
(define-public go-github-com-andreyvit-diff
|
||||
(package
|
||||
(name "go-github-com-andreyvit-diff")
|
||||
|
||||
@@ -31,7 +31,6 @@
|
||||
;;; Copyright © 2025 Arthur Rodrigues <arthurhdrodrigues@proton.me>
|
||||
;;; Copyright © 2025 Patrick Norton <patrick.147.norton@gmail.com>
|
||||
;;; Copyright © 2025 Giacomo Leidi <therewasa@fishinthecalculator.me>
|
||||
;;; Copyright © 2026 Evgeny Pisemsky <mail@pisemsky.site>
|
||||
;;;
|
||||
;;; This file is part of GNU Guix.
|
||||
;;;
|
||||
@@ -1600,7 +1599,7 @@ RSA, RSA-PSS, and ECDSA, though hooks are present for adding your own.")
|
||||
(define-public go-github-com-google-go-tpm
|
||||
(package
|
||||
(name "go-github-com-google-go-tpm")
|
||||
(version "0.9.4")
|
||||
(version "0.9.1")
|
||||
(source
|
||||
(origin
|
||||
(method git-fetch)
|
||||
@@ -1609,7 +1608,7 @@ RSA, RSA-PSS, and ECDSA, though hooks are present for adding your own.")
|
||||
(commit (string-append "v" version))))
|
||||
(file-name (git-file-name name version))
|
||||
(sha256
|
||||
(base32 "1sp1mbr6vz36zy9w36iksirbsj5p2jslsl8zs1cdj8s4ig4lkd9d"))))
|
||||
(base32 "1c5j5cvwl45ka93nknmv454ivd7kp9n8yql19gr6z01z0s1ph7sg"))))
|
||||
(build-system go-build-system)
|
||||
(arguments
|
||||
(list
|
||||
@@ -2874,7 +2873,7 @@ package.")
|
||||
(define-public go-github-com-refraction-networking-utls
|
||||
(package
|
||||
(name "go-github-com-refraction-networking-utls")
|
||||
(version "1.8.2")
|
||||
(version "1.6.0")
|
||||
(source
|
||||
(origin
|
||||
(method git-fetch)
|
||||
@@ -2883,7 +2882,7 @@ package.")
|
||||
(commit (string-append "v" version))))
|
||||
(file-name (git-file-name name version))
|
||||
(sha256
|
||||
(base32 "03kgwxdm2lg28fn2w5q7ql2szsiwj2xjdf477h1g3a4a9y9j6zk0"))))
|
||||
(base32 "1iywar5vqsml4b177k2nkcxmjm8mw92g3p112yjsrpmikiwpwpyw"))))
|
||||
(build-system go-build-system)
|
||||
(arguments
|
||||
`(#:import-path "github.com/refraction-networking/utls"
|
||||
@@ -3641,39 +3640,6 @@ algorithm described in @url{https://rfc-editor.org/rfc/rfc2898.html,RFC 2898}
|
||||
and @url{https://rfc-editor.org/rfc/rfc8018.html,RFC 8018}.")
|
||||
(license license:asl2.0)))
|
||||
|
||||
(define-public go-github-com-xtls-reality
|
||||
(package
|
||||
(name "go-github-com-xtls-reality")
|
||||
(version "0.0.0-20260322125925-9234c772ba8f")
|
||||
(source
|
||||
(origin
|
||||
(method git-fetch)
|
||||
(uri (git-reference
|
||||
(url "https://github.com/xtls/reality")
|
||||
(commit (go-version->git-ref version))))
|
||||
(file-name (git-file-name name version))
|
||||
(sha256
|
||||
(base32 "1wncy5aph6nmq4814xjhj6b5p1wm2fyrqn83dw0xlyxvq2z6iqfs"))))
|
||||
(build-system go-build-system)
|
||||
(arguments
|
||||
(list
|
||||
#:import-path "github.com/xtls/reality"))
|
||||
(propagated-inputs
|
||||
(list go-github-com-cloudflare-circl
|
||||
go-github-com-juju-ratelimit
|
||||
go-github-com-pires-go-proxyproto
|
||||
go-github-com-refraction-networking-utls
|
||||
go-golang-org-x-crypto
|
||||
go-golang-org-x-sys))
|
||||
(home-page "https://github.com/xtls/reality")
|
||||
(synopsis "Implementation of REALITY protocol")
|
||||
(description
|
||||
"This package provides an implementation of REALITY protocol, which is
|
||||
intented to eliminate the detectable TLS fingerprint on the server side, while
|
||||
still maintain the secrecy. It achieves full real TLS that is
|
||||
undistingwishable with the specified SNI to the middleman.")
|
||||
(license (list license:bsd-3 license:mpl2.0))))
|
||||
|
||||
(define-public go-github-com-youmark-pkcs8
|
||||
(package
|
||||
(name "go-github-com-youmark-pkcs8")
|
||||
|
||||
@@ -456,29 +456,6 @@ penalization.")
|
||||
FFT (Schonhage-Strassen method for multiplying integers).")
|
||||
(license license:bsd-3)))
|
||||
|
||||
(define-public go-github-com-robinus2-golang-moving-average
|
||||
(package
|
||||
(name "go-github-com-robinus2-golang-moving-average")
|
||||
(version "1.0.0")
|
||||
(source
|
||||
(origin
|
||||
(method git-fetch)
|
||||
(uri (git-reference
|
||||
(url "https://github.com/RobinUS2/golang-moving-average")
|
||||
(commit (string-append "v" version))))
|
||||
(file-name (git-file-name name version))
|
||||
(sha256
|
||||
(base32 "02z3ad29653fz7whxkjjpq820ig9j8m68xj4kay14jyazkr5in1f"))))
|
||||
(build-system go-build-system)
|
||||
(arguments
|
||||
(list
|
||||
#:import-path "github.com/RobinUS2/golang-moving-average"))
|
||||
(home-page "https://github.com/RobinUS2/golang-moving-average")
|
||||
(synopsis "Moving average implementation for Go")
|
||||
(description
|
||||
"This package provides a moving average implementation for Go.")
|
||||
(license license:asl2.0)))
|
||||
|
||||
(define-public go-github-com-shopspring-decimal
|
||||
(package
|
||||
(name "go-github-com-shopspring-decimal")
|
||||
|
||||
File diff suppressed because it is too large
Load Diff
@@ -75,7 +75,6 @@
|
||||
;;; Copyright © 2026 Carlos Durán Domínguez <wurt@wurt.eu>
|
||||
;;; Copyright © 2026 Giacomo Leidi <therewasa@fishinthecalculator.me>
|
||||
;;; Copyright © 2026 Evgeny Pisemsky <mail@pisemsky.site>
|
||||
;;; Copyright © 2026 Vinicius Monego <monego@posteo.net>
|
||||
;;;
|
||||
;;; This file is part of GNU Guix.
|
||||
;;;
|
||||
@@ -525,35 +524,6 @@ file along with an index.html file.")
|
||||
"Package tcell provides a gruid Driver for making terminal apps.")
|
||||
(license license:isc)))
|
||||
|
||||
(define-public go-codeberg-org-chavacava-garif
|
||||
(package
|
||||
(name "go-codeberg-org-chavacava-garif")
|
||||
(version "0.2.0")
|
||||
(source
|
||||
(origin
|
||||
(method git-fetch)
|
||||
(uri (git-reference
|
||||
(url "https://codeberg.org/chavacava/garif.git")
|
||||
(commit (string-append "v" version))))
|
||||
(file-name (git-file-name name version))
|
||||
(sha256
|
||||
(base32 "0cz037yb9gnk9fd61pni6m0n9cbrwmlxxija5vm91mplyxlih05h"))))
|
||||
(build-system go-build-system)
|
||||
(arguments
|
||||
(list
|
||||
#:import-path "codeberg.org/chavacava/garif"))
|
||||
(native-inputs
|
||||
(list go-github-com-stretchr-testify))
|
||||
(home-page "https://codeberg.org/chavacava/garif")
|
||||
(synopsis "Create and manipulate SARIF logs")
|
||||
(description
|
||||
"This package defines all the Go structures required to model a log file.
|
||||
|
||||
SARIF, from Static Analysis Results Interchange Format, is a standard
|
||||
JSON-based format for the output of static analysis tools defined and promoted
|
||||
by @url{https://www.oasis-open.org/, OASIS}.")
|
||||
(license license:expat)))
|
||||
|
||||
(define-public go-codeberg-org-emersion-go-scfg
|
||||
(package
|
||||
(name "go-codeberg-org-emersion-go-scfg")
|
||||
@@ -642,33 +612,6 @@ recursively any exported one. It also won't merge structs inside
|
||||
maps (because they are not addressable using Go reflection).")
|
||||
(license license:bsd-3)))
|
||||
|
||||
(define-public go-fyne-io-systray
|
||||
(package
|
||||
(name "go-fyne-io-systray")
|
||||
(version "1.11.0")
|
||||
(source
|
||||
(origin
|
||||
(method git-fetch)
|
||||
(uri (git-reference
|
||||
(url "https://github.com/fyne-io/systray")
|
||||
(commit (string-append "v" version))))
|
||||
(file-name (git-file-name name version))
|
||||
(sha256
|
||||
(base32 "0yrd4f3n8wrqcqradmqq9w0b31hd5hali876xkynfhm3nhaz4j1i"))))
|
||||
(build-system go-build-system)
|
||||
(arguments
|
||||
(list
|
||||
#:import-path "fyne.io/systray"))
|
||||
(propagated-inputs
|
||||
(list go-github-com-godbus-dbus-v5
|
||||
go-golang-org-x-sys))
|
||||
(home-page "https://fyne.io/systray/")
|
||||
(synopsis "Place an icon and menu in the notification area")
|
||||
(description
|
||||
"This package is a cross-platform Go library to place an icon and menu in
|
||||
the notification area.")
|
||||
(license license:asl2.0)))
|
||||
|
||||
(define-public go-git-sr-ht-rjarry-go-opt
|
||||
(package
|
||||
(name "go-git-sr-ht-rjarry-go-opt")
|
||||
@@ -3037,38 +2980,6 @@ input from the terminal while not echoing the input back (similar to
|
||||
and is therefore compatible with cross-compiling.")
|
||||
(license license:expat)))
|
||||
|
||||
(define-public go-github-com-bitfield-script
|
||||
(package
|
||||
(name "go-github-com-bitfield-script")
|
||||
(version "0.24.1")
|
||||
(source
|
||||
(origin
|
||||
(method git-fetch)
|
||||
(uri (git-reference
|
||||
(url "https://github.com/bitfield/script")
|
||||
(commit (string-append "v" version))))
|
||||
(file-name (git-file-name name version))
|
||||
(sha256
|
||||
(base32 "1pzmz7n39sh9sprclzd0m0l0flf626286fh51m065yjhkqzrjw89"))))
|
||||
(build-system go-build-system)
|
||||
(arguments
|
||||
(list
|
||||
#:import-path "github.com/bitfield/script"
|
||||
#:test-flags #~(list "-vet=off")))
|
||||
(native-inputs
|
||||
(list go-github-com-google-go-cmp))
|
||||
(propagated-inputs
|
||||
(list go-github-com-itchyny-gojq
|
||||
go-github-com-rogpeppe-go-internal
|
||||
go-mvdan-cc-sh-v3))
|
||||
(home-page "https://github.com/bitfield/script")
|
||||
(synopsis "Making it easy to write shell-like scripts in Go")
|
||||
(description
|
||||
"Package script aims to make it easy to write shell-type scripts in Go,
|
||||
for general system administration purposes: reading files, counting lines,
|
||||
matching strings, and so on.")
|
||||
(license license:expat)))
|
||||
|
||||
(define-public go-github-com-bitly-go-hostpool
|
||||
(package
|
||||
(name "go-github-com-bitly-go-hostpool")
|
||||
@@ -4521,34 +4432,6 @@ over strings.")
|
||||
@code{https://en.wikipedia.org/wiki/WebP, WebP} images.")
|
||||
(license license:bsd-3)))
|
||||
|
||||
(define-public go-github-com-chainguard-dev-clog
|
||||
(package
|
||||
(name "go-github-com-chainguard-dev-clog")
|
||||
(version "1.8.0")
|
||||
(source
|
||||
(origin
|
||||
(method git-fetch)
|
||||
(uri (git-reference
|
||||
(url "https://github.com/chainguard-dev/clog")
|
||||
(commit (string-append "v" version))))
|
||||
(file-name (git-file-name name version))
|
||||
(sha256
|
||||
(base32 "0b95vw8czs2r9lscyi85vppbyqj672zm6z2n9siy1s9yv6fkys62"))))
|
||||
(build-system go-build-system)
|
||||
(arguments
|
||||
(list
|
||||
#:import-path "github.com/chainguard-dev/clog"))
|
||||
(home-page "https://github.com/chainguard-dev/clog")
|
||||
(synopsis "Context aware slog")
|
||||
(description
|
||||
"This package provides a context-aware Go std lib
|
||||
@url{https://pkg.go.dev/log/slog, @code{slog}}. The context Logger can be
|
||||
used to use Loggers from the context. This is sometimes preferred over the
|
||||
@url{https://github.com/chainguard-dev/clog#context-handler, Context Handler},
|
||||
since this can make it easier to use different loggers in different
|
||||
contexts (e.g. testing).")
|
||||
(license license:asl2.0)))
|
||||
|
||||
(define-public go-github-com-charlievieth-fastwalk
|
||||
(package
|
||||
(name "go-github-com-charlievieth-fastwalk")
|
||||
@@ -8153,7 +8036,7 @@ supports concurrent serializable transactions.")
|
||||
(package
|
||||
(inherit go-github-com-dgraph-io-badger)
|
||||
(name "go-github-com-dgraph-io-badger-v4")
|
||||
(version "4.9.1")
|
||||
(version "4.5.2")
|
||||
(source
|
||||
(origin
|
||||
(method git-fetch)
|
||||
@@ -8162,7 +8045,7 @@ supports concurrent serializable transactions.")
|
||||
(commit (string-append "v" version))))
|
||||
(file-name (git-file-name name version))
|
||||
(sha256
|
||||
(base32 "0a9lk7fw06yb89wy9rp4q50ircw5imm1cqzhyhs92d0cia5qbhh6"))))
|
||||
(base32 "0v4c69whypm3k40hrx8bw9rjrcb0swz43v056s0fadqr04j0ncwj"))))
|
||||
(arguments
|
||||
(list
|
||||
#:tests? #f ; TODO: tests hang, find out why.
|
||||
@@ -8175,8 +8058,7 @@ supports concurrent serializable transactions.")
|
||||
go-github-com-klauspost-compress
|
||||
go-github-com-pkg-errors
|
||||
go-github-com-spf13-cobra
|
||||
go-go-opentelemetry-io-contrib-zpages
|
||||
go-go-opentelemetry-io-otel
|
||||
go-go-opencensus-io
|
||||
go-golang-org-x-net
|
||||
go-golang-org-x-sys
|
||||
go-google-golang-org-protobuf))))
|
||||
@@ -9083,41 +8965,6 @@ sub-interfaces are also provided for cases where the full Channel interface
|
||||
cannot be met (for example, @code{InChannel} for write-only channels).")
|
||||
(license license:expat)))
|
||||
|
||||
(define-public go-github-com-eapache-go-resiliency
|
||||
(package
|
||||
(name "go-github-com-eapache-go-resiliency")
|
||||
(version "1.7.0")
|
||||
(source
|
||||
(origin
|
||||
(method git-fetch)
|
||||
(uri (git-reference
|
||||
(url "https://github.com/eapache/go-resiliency")
|
||||
(commit (string-append "v" version))))
|
||||
(file-name (git-file-name name version))
|
||||
(sha256
|
||||
(base32 "07a1r3c2spd37k3riy4fxz8v8ibxiprf8a3vw788whz4mlp6gm40"))))
|
||||
(build-system go-build-system)
|
||||
(arguments
|
||||
(list
|
||||
#:skip-build? #t
|
||||
#:import-path "github.com/eapache/go-resiliency"))
|
||||
(home-page "https://github.com/eapache/go-resiliency")
|
||||
(synopsis "Resiliency patterns for golang")
|
||||
(description
|
||||
"Resiliency patterns for golang. Based in part on
|
||||
@url{https://github.com/Netflix/Hystrix, Hystrix},
|
||||
@@url{https://github.com/Shopify/semian, Semian}, and others.
|
||||
|
||||
Currently implemented patterns include:
|
||||
@itemize
|
||||
@item circuit-breaker
|
||||
@item semaphore
|
||||
@item deadline/timeout
|
||||
@item batching
|
||||
@item retriable
|
||||
@end itemize")
|
||||
(license license:expat)))
|
||||
|
||||
(define-public go-github-com-eapache-queue
|
||||
(package
|
||||
(name "go-github-com-eapache-queue")
|
||||
@@ -17757,7 +17604,7 @@ implementing features like:
|
||||
(define-public go-github-com-maruel-natural
|
||||
(package
|
||||
(name "go-github-com-maruel-natural")
|
||||
(version "1.3.0")
|
||||
(version "1.1.1")
|
||||
(source
|
||||
(origin
|
||||
(method git-fetch)
|
||||
@@ -17766,7 +17613,7 @@ implementing features like:
|
||||
(commit (string-append "v" version))))
|
||||
(file-name (git-file-name name version))
|
||||
(sha256
|
||||
(base32 "1nr1ai3b7yvz4wz4k0jqvjq3978hpk9yxarn7g7i3d2sxbdc0g4q"))))
|
||||
(base32 "040aikizdd7c4zm8xindb2ps16s60i0fkf8gkll2rir7lwv6q7ks"))))
|
||||
(build-system go-build-system)
|
||||
(arguments
|
||||
(list
|
||||
@@ -22939,16 +22786,16 @@ it is capable of logging at some or all levels.")
|
||||
(define-public go-github-com-rivo-tview
|
||||
(package
|
||||
(name "go-github-com-rivo-tview")
|
||||
(version "0.42.0")
|
||||
(version "0.0.0-20241227133733-17b7edb88c57")
|
||||
(source
|
||||
(origin
|
||||
(method git-fetch)
|
||||
(uri (git-reference
|
||||
(url "https://github.com/rivo/tview")
|
||||
(commit (string-append "v" version))))
|
||||
(commit (go-version->git-ref version))))
|
||||
(file-name (git-file-name name version))
|
||||
(sha256
|
||||
(base32 "0jw47h92l0vp1lg6s5kng4hjv81hi8qxx9h5yilc7rzrr8l9ksd2"))))
|
||||
(base32 "1w59vyvs8k5mzl7k39zpwcwwdgam2pbz0rnrfnnjgvkld1rh81dc"))))
|
||||
(build-system go-build-system)
|
||||
(arguments
|
||||
(list #:import-path "github.com/rivo/tview"))
|
||||
@@ -30589,8 +30436,8 @@ The yaml package supports most of YAML 1.2, but preserves some behavior from
|
||||
;; to build NNCP and remove vendor) dependency for Golang. Full build depends
|
||||
;; on Bazel <https://bazel.build/>.
|
||||
(define-public go-gvisor-dev-gvisor
|
||||
(let ((commit "9414b50a5633100fd7299a5a7998742575dcb669")
|
||||
(revision "1"))
|
||||
(let ((commit "634ce95eed8d5b8e6b3e2ea30542c34cb30af148")
|
||||
(revision "0"))
|
||||
(package
|
||||
(name "go-gvisor-dev-gvisor")
|
||||
(version (git-version "0.0.0" revision commit))
|
||||
@@ -30602,7 +30449,7 @@ The yaml package supports most of YAML 1.2, but preserves some behavior from
|
||||
(commit commit)))
|
||||
(file-name (git-file-name name version))
|
||||
(sha256
|
||||
(base32 "0vqaclb2ignkcs7n463bj349m0xybdsv71i6afhzh8r05hdywzax"))))
|
||||
(base32 "1l3si6qlchwgsvaq6lxyvj8iq8n8pqxlayb1hbdf3pynxi52hfkw"))))
|
||||
(build-system go-build-system)
|
||||
(arguments
|
||||
(list
|
||||
|
||||
@@ -412,7 +412,7 @@ similar to javadoc."))))
|
||||
(inherit base)
|
||||
(arguments
|
||||
`(;#:tests? #f;Requires spock-framework which is a circular dependency
|
||||
#:ant ,ant/java8; ant is actually a dependency of this package, and we need 1.10
|
||||
#:ant ,ant; ant is actually a dependency of this package, and we need 1.10
|
||||
,@(substitute-keyword-arguments arguments
|
||||
((#:phases phases)
|
||||
`(modify-phases ,phases
|
||||
@@ -431,8 +431,7 @@ similar to javadoc."))))
|
||||
("java-asm-analysis" ,java-asm-analysis-8)
|
||||
,@(package-inputs base)))
|
||||
(native-inputs
|
||||
`(("ant-junit" ,ant-junit)
|
||||
("groovy-bootstrap" ,groovy-bootstrap)
|
||||
`(("groovy-bootstrap" ,groovy-bootstrap)
|
||||
("groovy-xml" ,groovy-xml)
|
||||
("groovy-test" ,groovy-test)
|
||||
("groovy-tests-bootstrap" ,groovy-tests-bootstrap)
|
||||
|
||||
@@ -60,7 +60,6 @@
|
||||
;;; Copyright © 2025 Andy Tai <atai@atai.org>
|
||||
;;; Copyright © 2025 Ekaitz Zarraga <ekaitz@elenq.tech>
|
||||
;;; Copyright © 2026 Matt Wette <matt.wette@gmail.com>
|
||||
;;; Copyright © 2026 Dzianis Jackievič <mail@miesta.by>
|
||||
;;;
|
||||
;;; This file is part of GNU Guix.
|
||||
;;;
|
||||
@@ -1168,7 +1167,7 @@ is not available for Guile 2.0.")
|
||||
(package
|
||||
(inherit guile-fibers-1.3)
|
||||
(name "guile-fibers")
|
||||
(version "1.4.3")
|
||||
(version "1.4.2")
|
||||
(source
|
||||
(origin (inherit (package-source guile-fibers-1.3))
|
||||
(file-name (git-file-name name version))
|
||||
@@ -1177,7 +1176,7 @@ is not available for Guile 2.0.")
|
||||
(commit (string-append "v" version))))
|
||||
(sha256
|
||||
(base32
|
||||
"1q0a9y0cc8rld1z7mcj61fkldhd0kn9n4yq25izxslbgg4g5h9j6"))
|
||||
"0qh0czz5qvk5mmrc8x2gmvl5psdfd22q2rhzj4jrpan6k3d55bl8"))
|
||||
(patches '())))
|
||||
(arguments
|
||||
(if (target-aarch64?)
|
||||
@@ -1257,8 +1256,30 @@ is not available for Guile 2.0.")
|
||||
(modify-inputs native-inputs
|
||||
(replace "guile" guile-2.2)))))
|
||||
|
||||
;; Deprecated on 2026-04-23
|
||||
(define-deprecated-package guile-fibers-next guile-fibers)
|
||||
(define-public guile-fibers-next
|
||||
(let ((commit "297359f0ad655378bcc3ff0d4e96101965ef39b4")
|
||||
(revision "0"))
|
||||
(package
|
||||
(inherit guile-fibers)
|
||||
(name "guile-fibers-next")
|
||||
(version (git-version "1.4.2"
|
||||
revision
|
||||
commit))
|
||||
(source (origin
|
||||
(method git-fetch)
|
||||
(uri (git-reference
|
||||
(url "https://codeberg.org/guile/fibers.git")
|
||||
(commit commit)))
|
||||
(file-name (git-file-name name version))
|
||||
(sha256
|
||||
(base32
|
||||
"0qh0czz5qvk5mmrc8x2gmvl5psdfd22q2rhzj4jrpan6k3d55bl8"))))
|
||||
(inputs
|
||||
(modify-inputs inputs
|
||||
(replace "guile" guile-next)))
|
||||
(native-inputs
|
||||
(modify-inputs native-inputs
|
||||
(replace "guile" guile-next))))))
|
||||
|
||||
(define-public guile-kracht
|
||||
(package
|
||||
@@ -1516,7 +1537,7 @@ order to provide IDE functionality for Guile Scheme.")
|
||||
(define-public guile-ares-rs
|
||||
(package
|
||||
(name "guile-ares-rs")
|
||||
(version "0.9.7")
|
||||
(version "0.9.6")
|
||||
(source
|
||||
(origin
|
||||
(method git-fetch)
|
||||
@@ -1526,42 +1547,35 @@ order to provide IDE functionality for Guile Scheme.")
|
||||
(file-name (git-file-name name version))
|
||||
(sha256
|
||||
(base32
|
||||
"1xbznh5zjswfydgqg53g50ya7zm0hidin74g2glk849l9j45szw3"))))
|
||||
"1vkww3vc0lsh5f8yh6fnh402rx3rsm0ss69rdkmplhzp4c7c4z1d"))))
|
||||
(build-system guile-build-system)
|
||||
(arguments
|
||||
(list
|
||||
#:source-directory "src/guile"
|
||||
#:phases
|
||||
#~(modify-phases %standard-phases
|
||||
(add-after 'build 'install-scripts
|
||||
(add-after 'build 'install-script
|
||||
(lambda _
|
||||
(define bin (string-append #$output "/bin"))
|
||||
(define site (string-append #$output "/share/guile/site/3.0"))
|
||||
(define ccache
|
||||
(string-append #$output "/lib/guile/3.0/site-ccache"))
|
||||
|
||||
(define (install-script name)
|
||||
(let ((oldpath
|
||||
(string-append site "/ares/scripts/" name ".scm"))
|
||||
(newpath
|
||||
(string-append bin "/" name)))
|
||||
(symlink oldpath newpath)
|
||||
(wrap-program newpath
|
||||
`("GUILE_LOAD_PATH" ":" =
|
||||
,(list "$GUILE_LOAD_PATH"
|
||||
site
|
||||
(getenv "GUILE_LOAD_PATH")))
|
||||
`("GUILE_LOAD_COMPILED_PATH" ":" =
|
||||
,(list "$GUILE_LOAD_COMPILED_PATH"
|
||||
ccache
|
||||
(getenv "GUILE_LOAD_COMPILED_PATH"))))
|
||||
;; Not needed since the wrapper followed the symlink.
|
||||
(delete-file (string-append bin "/." name "-real"))))
|
||||
|
||||
(mkdir bin)
|
||||
(for-each install-script '("ares-nrepl" "ares-suitbl")))))))
|
||||
(inputs (list bash-minimal guile-3.0-latest))
|
||||
(propagated-inputs (list guile-fibers))
|
||||
(let* ((bin (string-append #$output "/bin"))
|
||||
(oldpath (string-append
|
||||
#$output
|
||||
;; This file will be named ares-nrepl.scm for
|
||||
;; the next version.
|
||||
"/share/guile/site/3.0/ares/scripts/ares.scm"))
|
||||
(newpath (string-append bin "/ares-nrepl")))
|
||||
(mkdir bin)
|
||||
(symlink oldpath newpath)
|
||||
(wrap-program newpath
|
||||
`("GUILE_LOAD_PATH" ":" =
|
||||
,(list (string-append #$output "/share/guile/site/3.0")
|
||||
(getenv "GUILE_LOAD_PATH")))
|
||||
`("GUILE_LOAD_COMPILED_PATH" ":" =
|
||||
,(list (string-append #$output "/lib/guile/3.0/site-ccache")
|
||||
(getenv "GUILE_LOAD_COMPILED_PATH"))))
|
||||
;; Not needed since the wrapper followed the symlink.
|
||||
(delete-file (string-append bin "/.ares-nrepl-real"))))))))
|
||||
(inputs (list bash-minimal guile-3.0))
|
||||
(propagated-inputs (list guile-fibers guile-custom-ports))
|
||||
(home-page "https://git.sr.ht/~abcdw/guile-ares-rs")
|
||||
(synopsis "Asynchronous Reliable Extensible Sleek RPC Server for Guile")
|
||||
(description "Asynchronous Reliable Extensible Sleek RPC Server for
|
||||
@@ -5693,32 +5707,27 @@ perform geometrical transforms on JPEG images.")
|
||||
(license license:gpl3+))))
|
||||
|
||||
(define-public guile-jtd
|
||||
;; There are a few unreleased commits that include niceties such as warning
|
||||
;; that the debug VM must be used; use the latest commit until the next
|
||||
;; release comes.
|
||||
(let ((commit "425f86ae954d6445aaedacfd4ecd50aa0022e59d")
|
||||
(revision "0"))
|
||||
(package
|
||||
(name "guile-jtd")
|
||||
(version (git-version "220323a" revision commit))
|
||||
(source (origin
|
||||
(method git-fetch)
|
||||
(uri (git-reference
|
||||
(url "https://github.com/mwette/guile-jtd")
|
||||
(commit commit)))
|
||||
(file-name (git-file-name name version))
|
||||
(sha256
|
||||
(base32
|
||||
"1l8fyqhvksarvpbr903i3ss3432jzvyvhgcqa15j922ngqh4ds6f"))))
|
||||
(build-system guile-build-system)
|
||||
(native-inputs (list guile-3.0))
|
||||
(home-page "https://github.com/mwette/guile-jtd")
|
||||
(synopsis "Python's @code{pdb.set_trace()} but for Guile")
|
||||
(description
|
||||
"The @code{(jtd)} module for Guile provides a procedure
|
||||
(package
|
||||
(name "guile-jtd")
|
||||
(version "220323a")
|
||||
(source (origin
|
||||
(method git-fetch)
|
||||
(uri (git-reference
|
||||
(url "https://github.com/mwette/guile-jtd")
|
||||
(commit (string-append "v" version))))
|
||||
(file-name (git-file-name name version))
|
||||
(sha256
|
||||
(base32
|
||||
"1l8fyqhvksarvpbr903i3ss3432jzvyvhgcqa15j922ngqh4ds6f"))))
|
||||
(build-system guile-build-system)
|
||||
(native-inputs (list guile-3.0))
|
||||
(home-page "https://github.com/mwette/guile-jtd")
|
||||
(synopsis "Python's @code{pdb.set_trace()} but for Guile")
|
||||
(description
|
||||
"The @code{(jtd)} module for Guile provides a procedure
|
||||
@code{jump-to-debugger} for escaping to the Guile REPL for the purpose of
|
||||
debugging code.")
|
||||
(license license:lgpl2.1+))))
|
||||
(license license:lgpl2.1+)))
|
||||
|
||||
(define-public guile-png
|
||||
(package
|
||||
@@ -6390,88 +6399,6 @@ as signed sessions, multipart message support, etc.")
|
||||
(propagated-inputs
|
||||
(list guile2.2-irregex guile2.2-gcrypt))))
|
||||
|
||||
(define-public guile-compose
|
||||
(package
|
||||
(name "guile-compose")
|
||||
(version "0.1.2")
|
||||
(source
|
||||
(origin
|
||||
(method git-fetch)
|
||||
(uri (git-reference
|
||||
(url "https://codeberg.org/jadzi/guile-compose.git")
|
||||
(commit (string-append "v" version))))
|
||||
(file-name (git-file-name name version))
|
||||
(sha256
|
||||
(base32 "1g68gczs96nrb0vf1hv4n07zsp2516gpiwq1wwlhcq4rzynhf12h"))))
|
||||
(build-system gnu-build-system)
|
||||
(arguments
|
||||
(list
|
||||
#:make-flags
|
||||
#~'("GUILE_AUTO_COMPILE=0")))
|
||||
(inputs (list guile-3.0))
|
||||
(native-inputs (list autoconf-2.72 automake pkg-config guile-3.0 texinfo))
|
||||
(synopsis "Procedure composition utilities for Guile Scheme")
|
||||
(description
|
||||
"This tiny package provides some procedures and macros to extend
|
||||
Guile Scheme procedure composition facilities. For example, there is
|
||||
a @code{compose-top}, a reverse-order analog to native @code{compose}
|
||||
procedure. The @code{compose-cont} is a macro, utilizing some power of
|
||||
continuations to build really flexible flows.
|
||||
|
||||
This library is intended to stay basic and small, so it has no any
|
||||
external dependencies and can be a good base for other packages, like e.g.
|
||||
@code{guile-web-middleware}.")
|
||||
(license (list license:lgpl3+))
|
||||
(home-page "https://jadzi.codeberg.page/guile-compose")))
|
||||
|
||||
(define-public guile-web-middleware
|
||||
(package
|
||||
(name "guile-web-middleware")
|
||||
(version "0.11.1")
|
||||
(source
|
||||
(origin
|
||||
(method git-fetch)
|
||||
(uri (git-reference
|
||||
(url "https://codeberg.org/jadzi/guile-web-middleware.git")
|
||||
(commit (string-append "v" version))))
|
||||
(file-name (git-file-name name version))
|
||||
(sha256
|
||||
(base32 "01wb8v0lszphdv08ly4aqv59qm5h8yw2fgm025vkn61djspsq4j9"))))
|
||||
(build-system gnu-build-system)
|
||||
(arguments
|
||||
(list
|
||||
#:make-flags
|
||||
#~'("GUILE_AUTO_COMPILE=0")))
|
||||
(inputs (list guile-3.0))
|
||||
(propagated-inputs (list guile-compose))
|
||||
(native-inputs (list autoconf-2.72 automake pkg-config guile-3.0 texinfo))
|
||||
(synopsis "Web application middleware composition for Guile Scheme")
|
||||
(description
|
||||
"This package provides means to compose a web application by
|
||||
chaining procedures, a.k.a. middlewares. By those means, composed
|
||||
procedures form a standard request handler for any Guile's web server
|
||||
implementation.
|
||||
|
||||
Each middleware has its own limited responsibility in request
|
||||
processing. Also, middlewares are simple Scheme procedures, so they
|
||||
can be easily tested and shared among web applications.
|
||||
|
||||
Out of the box, this package provides several procedures for commonly
|
||||
required tasks. Among them:
|
||||
|
||||
@itemize
|
||||
@item Error handling with customizable page contents.
|
||||
@item Request filtering.
|
||||
@item Request logging.
|
||||
@item Serving static files, file URL generation.
|
||||
@item Request routing, handling parameters, route URL generation.
|
||||
@item Middleware nesting, composing whole apps.
|
||||
@end itemize
|
||||
|
||||
This package relies on @code{guile-compose} package as its only dependency.")
|
||||
(license (list license:lgpl3+))
|
||||
(home-page "https://jadzi.codeberg.page/guile-web-middleware")))
|
||||
|
||||
(define-public guile-web-driver-ng
|
||||
(package
|
||||
(name "guile-web-driver-ng")
|
||||
@@ -7764,8 +7691,8 @@ is an attempt to combine both into something useful.")
|
||||
(license license:asl2.0))))
|
||||
|
||||
(define-public guile-knots
|
||||
(let ((commit "49996c432a4616e03ecaf01cb42afc5fd78eafd5")
|
||||
(revision "35"))
|
||||
(let ((commit "f767eca066495e6582e89ba1b91907c0c5657878")
|
||||
(revision "34"))
|
||||
(package
|
||||
(name "guile-knots")
|
||||
(version (git-version "0.1" revision commit))
|
||||
@@ -7776,7 +7703,7 @@ is an attempt to combine both into something useful.")
|
||||
(commit commit)))
|
||||
(sha256
|
||||
(base32
|
||||
"0i6vk432shy7qmsq1hli71a9kmgf8yy9hx3bck0r9qzsldv1m3m9"))
|
||||
"18fqmpyrrxy8phxxm5b7d1qhhvc3rsrs243xiinkj2hn2ca1cqi8"))
|
||||
(file-name (git-file-name name version))))
|
||||
(build-system gnu-build-system)
|
||||
(arguments
|
||||
@@ -7789,13 +7716,13 @@ is an attempt to combine both into something useful.")
|
||||
(list pkg-config
|
||||
autoconf
|
||||
automake
|
||||
guile-3.0-latest
|
||||
guile-next
|
||||
guile-lib
|
||||
guile-fibers))
|
||||
guile-fibers-next))
|
||||
(inputs
|
||||
(list guile-3.0-latest))
|
||||
(list guile-next))
|
||||
(propagated-inputs
|
||||
(list guile-fibers))
|
||||
(list guile-fibers-next))
|
||||
(home-page "https://cbaines.codeberg.page/guile-knots/")
|
||||
(synopsis "Patterns and functionality to use with Guile Fibers")
|
||||
(description
|
||||
@@ -8091,14 +8018,14 @@ application to open a given file or URL based on given configurations.")
|
||||
(define-public guile-goblins
|
||||
(package
|
||||
(name "guile-goblins")
|
||||
(version "0.18.0")
|
||||
(version "0.17.0")
|
||||
(source
|
||||
(origin
|
||||
(method url-fetch)
|
||||
(uri (string-append "https://files.spritely.institute/releases"
|
||||
"/guile-goblins/guile-goblins-" version ".tar.gz"))
|
||||
(sha256
|
||||
(base32 "0gj5018wmq97ln1z7x03a13z3p35xc8762id9bl9fgkxwm01df1a"))))
|
||||
(base32 "16jkmfspsnza2fdk5jr05a5pfh7x856gpg031i21s1yvy43l8mi0"))))
|
||||
(build-system gnu-build-system)
|
||||
(arguments
|
||||
(list
|
||||
|
||||
@@ -653,10 +653,7 @@ GNU@tie{}Guile. Use the @code{(ice-9 readline)} module and call its
|
||||
(define (guile-variant-package-name prefix)
|
||||
(lambda (name)
|
||||
"Return NAME with PREFIX instead of \"guile-\", when applicable."
|
||||
(if (and (string-prefix? "guile-" name)
|
||||
|
||||
;; Don't rename guile-bootstrap@2.0.
|
||||
(not (string=? "guile-bootstrap" name)))
|
||||
(if (string-prefix? "guile-" name)
|
||||
(string-append prefix "-"
|
||||
(string-drop name
|
||||
(string-length "guile-")))
|
||||
@@ -903,8 +900,8 @@ type system, elevating types to first-class status.")
|
||||
(define-public guile-git
|
||||
(package
|
||||
(name "guile-git")
|
||||
(version "0.11.1")
|
||||
(home-page "https://codeberg.org/guile-git/guile-git.git")
|
||||
(version "0.11.0")
|
||||
(home-page "https://gitlab.com/guile-git/guile-git.git")
|
||||
(source (origin
|
||||
(method git-fetch)
|
||||
(uri (git-reference
|
||||
@@ -913,11 +910,11 @@ type system, elevating types to first-class status.")
|
||||
(file-name (git-file-name name version))
|
||||
(sha256
|
||||
(base32
|
||||
"0xpzchnglddphi3chv53xqaz2x6rpq3l4s023w7r4mmndb6lgz0b"))))
|
||||
"1yjyil6z4k80pjdps8v6h6lxikwxmjxvrslf2jrmq2rrfnajschz"))))
|
||||
(build-system gnu-build-system)
|
||||
(arguments
|
||||
`(#:make-flags '("GUILE_AUTO_COMPILE=0") ; to prevent guild warnings
|
||||
;; https://codeberg.org/guile-git/guile-git/issues/20
|
||||
;; https://gitlab.com/guile-git/guile-git/-/issues/20
|
||||
,@(if (target-ppc32?)
|
||||
`(#:phases
|
||||
(modify-phases %standard-phases
|
||||
@@ -925,7 +922,20 @@ type system, elevating types to first-class status.")
|
||||
(lambda _
|
||||
(substitute* "Makefile.am"
|
||||
((".*tests/blob\\.scm.*") ""))))))
|
||||
'())))
|
||||
'())
|
||||
,@(if (system-hurd?)
|
||||
(list
|
||||
#:phases
|
||||
#~(modify-phases %standard-phases
|
||||
(add-after 'unpack 'skip-tests/hurd
|
||||
(lambda _
|
||||
(substitute* "tests/proxy.scm"
|
||||
(("\\(test-begin.*" all)
|
||||
(string-append
|
||||
all
|
||||
"(when (string-ci= \"GNU\" (vector-ref (uname) 0))\n"
|
||||
" (test-skip 1))\n")))))))
|
||||
'())))
|
||||
(native-inputs
|
||||
(list pkg-config autoconf automake texinfo guile-3.0 guile-bytestructures))
|
||||
(inputs
|
||||
@@ -994,7 +1004,7 @@ Guile's foreign function interface.")
|
||||
(file-name (string-append "guile-lzlib-" version ".tar.gz"))
|
||||
(sha256
|
||||
(base32
|
||||
"1v1pfqp6hwl0rivs7swhqnfgznxlfnws9ldmn6avnhd10filfa3a"))
|
||||
"1whgmwkr1v8m63p4aaqn8blwl9vcrswwhbfv4bm0aghl5a6rryd7"))
|
||||
(patches (search-patches "guile-lzlib-gcc-14.patch"
|
||||
"guile-lzlib-hurd64.patch"))))
|
||||
(build-system gnu-build-system)
|
||||
|
||||
@@ -914,7 +914,7 @@ regular) Diffie Hellman key exchanges, and many extensions.")
|
||||
(list #:extra-directories (list "openssl")
|
||||
#:configure-flags
|
||||
#~(list "--ghc-options=-optc=-Wno-incompatible-pointer-types")))
|
||||
(inputs (list ghc-network openssl-3.0))
|
||||
(inputs (list ghc-network openssl))
|
||||
(home-page "https://github.com/haskell-cryptography/HsOpenSSL")
|
||||
(synopsis "Partial OpenSSL binding for Haskell")
|
||||
(description
|
||||
|
||||
@@ -489,22 +489,11 @@ lost.
|
||||
"0b9d2i22ghyjarwi1c596q5mf7gj1k04k784hnmrd2d4x9hgv9ax"))))
|
||||
(build-system gnu-build-system)
|
||||
(arguments
|
||||
(list #:configure-flags #~(list "--with-corosync"
|
||||
"--disable-static"
|
||||
"--localstatedir=/var"
|
||||
(list #:configure-flags #~(list "--with-corosync" "--disable-static"
|
||||
(string-append "--with-initdir="
|
||||
#$output "/etc/init.d")
|
||||
(string-append "--with-ocfdir="
|
||||
#$output "/lib"))
|
||||
#:phases
|
||||
#~(modify-phases %standard-phases
|
||||
(add-before 'configure 'pre-configure
|
||||
(lambda _
|
||||
;; Do not attempt to install /var.
|
||||
(substitute* '("Makefile.am"
|
||||
"daemons/schedulerd/Makefile.am")
|
||||
(("install-exec-local:")
|
||||
"install-exec-local-disabled:")))))))
|
||||
#$output "/lib"))))
|
||||
(native-inputs (list autoconf
|
||||
automake
|
||||
cmocka
|
||||
|
||||
@@ -339,6 +339,30 @@ coverage.")
|
||||
;; that list in further version.
|
||||
(supported-systems (list "x86_64-linux"))))
|
||||
|
||||
(define-public lttng-modules
|
||||
(package
|
||||
(name "lttng-modules")
|
||||
(version "2.13.14")
|
||||
(source (origin
|
||||
(method url-fetch)
|
||||
(uri (string-append "https://lttng.org/files/lttng-modules/"
|
||||
"lttng-modules-" version ".tar.bz2"))
|
||||
(sha256
|
||||
(base32
|
||||
"19jx1yz1hsbr4vwfp2nr6z52a5g50iimaak962k49diay5zryi66"))))
|
||||
(build-system linux-module-build-system)
|
||||
(arguments
|
||||
`(#:tests? #f ; no tests
|
||||
#:make-flags (list "CONFIG_LTTNG=m"
|
||||
"CONFIG_LTTNG_CLOCK_PLUGIN_TEST=m")))
|
||||
(home-page "https://lttng.org/")
|
||||
(synopsis "LTTng kernel modules for the LTTng tracer toolset")
|
||||
(description
|
||||
"LTTng kernel modules are Linux kernel modules which make
|
||||
LTTng kernel tracing possible. They include essential control modules and
|
||||
many probes which instrument numerous interesting parts of Linux.")
|
||||
(license (list license:lgpl2.1 license:gpl2 license:expat))))
|
||||
|
||||
(define-public lttng-ust
|
||||
(package
|
||||
(name "lttng-ust")
|
||||
|
||||
@@ -1,5 +1,5 @@
|
||||
;;; GNU Guix --- Functional package management for GNU
|
||||
;;; Copyright © 2014-2019, 2021, 2026 Ricardo Wurmus <rekado@elephly.net>
|
||||
;;; Copyright © 2014, 2015, 2016, 2017, 2018, 2019, 2021 Ricardo Wurmus <rekado@elephly.net>
|
||||
;;; Copyright © 2021, 2026 Ludovic Courtès <ludo@gnu.org>
|
||||
;;; Copyright © 2017 Leo Famulari <leo@famulari.name>
|
||||
;;; Copyright © 2017, 2022 Marius Bakke <marius@gnu.org>
|
||||
@@ -226,18 +226,6 @@ JNI.")
|
||||
(setenv "JAVACMD" (search-input-file inputs "/bin/jamvm"))
|
||||
(setenv "JAVAC" (search-input-file inputs "/bin/jikes"))
|
||||
(setenv "CLASSPATH" (search-input-file inputs "/lib/rt.jar"))))
|
||||
,@(if (target-x86-32?)
|
||||
;; XXX: On i686 isFile() always seems to return true. Patching
|
||||
;; this here is very ugly, but the effects are limited. None
|
||||
;; of these changes remain by the time we've built Icedtea and
|
||||
;; the other JDKs.
|
||||
'((add-after 'unpack 'disable-isFile-checks
|
||||
(lambda _
|
||||
(substitute* "src/main/org/apache/tools/ant/util/ResourceUtils.java"
|
||||
(("destFile = \\(\\(FileProvider\\).*") ""))
|
||||
(substitute* "src/main/org/apache/tools/ant/taskdefs/Mkdir.java"
|
||||
(("dir.isFile\\(\\)") "false")))))
|
||||
'())
|
||||
(replace 'build
|
||||
(lambda* (#:key inputs outputs #:allow-other-keys)
|
||||
;; Ant complains if this file doesn't exist.
|
||||
|
||||
@@ -55,12 +55,13 @@
|
||||
(modify-phases %standard-phases
|
||||
(add-after 'unpack 'make-git-checkout-writable
|
||||
(lambda _
|
||||
(for-each make-file-writable (find-files "."))))
|
||||
(for-each make-file-writable (find-files "."))
|
||||
#t))
|
||||
(add-before 'build 'remove-binaries
|
||||
(lambda _
|
||||
(delete-file "lib/org/xerial/snappy/OSInfo.class")
|
||||
(delete-file-recursively
|
||||
"src/main/resources/org/xerial/snappy/native")))
|
||||
(delete-file-recursively "src/main/resources/org/xerial/snappy/native")
|
||||
#t))
|
||||
(add-before 'build 'build-jni
|
||||
(lambda _
|
||||
;; Rebuild one of the binaries we removed earlier
|
||||
@@ -97,33 +98,36 @@
|
||||
(add-after 'build-jni 'copy-jni
|
||||
(lambda _
|
||||
(copy-recursively "src/main/resources/org/xerial/snappy/native"
|
||||
"build/classes/org/xerial/snappy/native")))
|
||||
"build/classes/org/xerial/snappy/native")
|
||||
#t))
|
||||
(add-before 'build 'set-test-memory-size
|
||||
(lambda _
|
||||
(substitute* "build.xml"
|
||||
(("<junit printsummary=")
|
||||
"<junit maxmemory=\"2G\" printsummary="))))
|
||||
(("<junit printsummary=") "<junit maxmemory=\"2G\" printsummary="))
|
||||
#t))
|
||||
(add-before 'check 'fix-failing
|
||||
(lambda _
|
||||
(with-directory-excursion "src/test/java/org/xerial/snappy"
|
||||
;; This package assumes maven build, which puts results in
|
||||
;; "target". We put them in "build" instead, so fix that.
|
||||
;; This package assumes maven build, which puts results in "target".
|
||||
;; We put them in "build" instead, so fix that.
|
||||
(substitute* "SnappyLoaderTest.java"
|
||||
(("target/classes") "build/classes"))
|
||||
;; This requires Hadoop, which is not in Guix yet.
|
||||
(delete-file "SnappyHadoopCompatibleOutputStreamTest.java")))))))
|
||||
(delete-file "SnappyHadoopCompatibleOutputStreamTest.java"))
|
||||
#t)))))
|
||||
(inputs
|
||||
(list java-osgi-framework))
|
||||
`(("osgi-framework" ,java-osgi-framework)))
|
||||
(propagated-inputs
|
||||
(list bitshuffle-for-snappy snappy))
|
||||
`(("bitshuffle" ,bitshuffle-for-snappy)
|
||||
("snappy" ,snappy)))
|
||||
(native-inputs
|
||||
(list java-junit
|
||||
java-hamcrest-core
|
||||
java-xerial-core
|
||||
java-plexus-classworlds
|
||||
java-commons-lang
|
||||
java-commons-io
|
||||
perl))
|
||||
`(("junit" ,java-junit)
|
||||
("hamcrest" ,java-hamcrest-core)
|
||||
("xerial-core" ,java-xerial-core)
|
||||
("classworlds" ,java-plexus-classworlds)
|
||||
("commons-lang" ,java-commons-lang)
|
||||
("commons-io" ,java-commons-io)
|
||||
("perl" ,perl)))
|
||||
(home-page "https://github.com/xerial/snappy-java")
|
||||
(synopsis "Compression/decompression algorithm in Java")
|
||||
(description "Snappy-java is a Java port of snappy, a fast C++
|
||||
@@ -152,13 +156,13 @@ compressor/decompressor.")
|
||||
(add-before 'build 'remove-binaries
|
||||
(lambda _
|
||||
(delete-file "lib/org/xerial/snappy/OSInfo.class")
|
||||
(delete-file-recursively
|
||||
"src/main/resources/org/xerial/snappy/native")))
|
||||
(delete-file-recursively "src/main/resources/org/xerial/snappy/native")
|
||||
#t))
|
||||
(add-before 'build 'build-jni
|
||||
(lambda _
|
||||
;; Rebuild one of the binaries we removed earlier
|
||||
(invoke "javac" "src/main/java/org/xerial/snappy/OSInfo.java"
|
||||
"-d" "lib")
|
||||
"-d" "lib")
|
||||
;; Link to the dynamic snappy, not the static ones
|
||||
(substitute* "Makefile.common"
|
||||
(("-shared") "-shared -lsnappy"))
|
||||
@@ -180,14 +184,16 @@ compressor/decompressor.")
|
||||
(add-after 'build-jni 'copy-jni
|
||||
(lambda _
|
||||
(copy-recursively "src/main/resources/org/xerial/snappy/native"
|
||||
"build/classes/org/xerial/snappy/native")))
|
||||
"build/classes/org/xerial/snappy/native")
|
||||
#t))
|
||||
(add-before 'check 'fix-tests
|
||||
(lambda _
|
||||
(mkdir-p "src/test/resources/org/xerial/snappy/")
|
||||
(copy-recursively "src/test/java/org/xerial/snappy/testdata"
|
||||
"src/test/resources/org/xerial/snappy/testdata")
|
||||
(install-file "src/test/java/org/xerial/snappy/alice29.txt"
|
||||
"src/test/resources/org/xerial/snappy/"))))))))
|
||||
"src/test/resources/org/xerial/snappy/")
|
||||
#t)))))))
|
||||
|
||||
(define-public java-iq80-snappy
|
||||
(package
|
||||
|
||||
@@ -75,7 +75,7 @@
|
||||
(inputs
|
||||
(list openblas))
|
||||
(native-inputs
|
||||
`(("ant" ,ant)
|
||||
`(("ant" ,ant/java7)
|
||||
("ruby" ,ruby) ; for configure script
|
||||
("gfortran" ,gfortran)
|
||||
("jdk" ,icedtea "jdk")))
|
||||
|
||||
@@ -1285,13 +1285,7 @@ new Date();"))))
|
||||
;; It looks like the "--disable-warnings-as-errors" option of
|
||||
;; the 'configure' phase is not working.
|
||||
(substitute* "make/autoconf/generated-configure.sh"
|
||||
(("-Werror") ""))))
|
||||
#$@(if (target-x86-32?)
|
||||
;; On i686 the C2 compiler sometimes crashes when importing
|
||||
;; certificates.
|
||||
#~((add-before 'install-keystore 'disable-C2-compiler
|
||||
(lambda _ (setenv "_JAVA_OPTIONS" "-XX:TieredStopAtLevel=1"))))
|
||||
#~())))
|
||||
(("-Werror") ""))))))
|
||||
((#:disallowed-references refs '())
|
||||
(cons* (this-package-native-input "openjdk")
|
||||
(gexp-input (this-package-native-input "openjdk") "jdk")
|
||||
@@ -1850,50 +1844,12 @@ blacklisted.certs.pem"
|
||||
(define-public openjdk24
|
||||
(make-openjdk
|
||||
openjdk23 "24.0.1"
|
||||
"0h6sbzbjyqg85iml41pswdh2z3d7h2hhb0sd5yll37r1mj5lsxmx"
|
||||
(arguments
|
||||
(substitute-keyword-arguments (package-arguments base)
|
||||
((#:configure-flags flags #~(list))
|
||||
(if (target-x86-32?)
|
||||
#~(cons* "--enable-deprecated-ports=yes" #$flags)
|
||||
flags))))))
|
||||
"0h6sbzbjyqg85iml41pswdh2z3d7h2hhb0sd5yll37r1mj5lsxmx"))
|
||||
|
||||
(define-public openjdk25
|
||||
(make-openjdk
|
||||
openjdk24 "25.0.2"
|
||||
"03aa34lscr3qbdl6qz3gqyp0nzkqfj02362mzmpkiq3y2g5xdnrj"
|
||||
(arguments
|
||||
(substitute-keyword-arguments (package-arguments base)
|
||||
((#:configure-flags flags #~(list))
|
||||
(if (target-x86-32?)
|
||||
;; Full builds on 32-bit x86 architectures are not supported as of
|
||||
;; this version. Best we can do is to build with the "zero" variant.
|
||||
#~(cons* "--with-jvm-variants=zero"
|
||||
"--disable-precompiled-headers"
|
||||
#$flags)
|
||||
flags))
|
||||
((#:phases phases #~%standard-phases)
|
||||
(if (target-x86-32?)
|
||||
#~(modify-phases #$phases
|
||||
(replace 'install
|
||||
(lambda _
|
||||
(let ((images (car (find-files "build" "-zero-release"
|
||||
#:directories? #t))))
|
||||
(copy-recursively (string-append images "/images/jdk")
|
||||
#$output:jdk)
|
||||
(copy-recursively (string-append images "/images/jre")
|
||||
#$output)
|
||||
(copy-recursively (string-append images "/images/docs")
|
||||
#$output:doc))))
|
||||
(replace 'install-libjvm
|
||||
(lambda _
|
||||
(let ((lib-out (string-append #$output "/lib"))
|
||||
(lib-jdk (string-append #$output:jdk "/lib")))
|
||||
(symlink (string-append lib-jdk "/zero/libjvm.so")
|
||||
(string-append lib-jdk "/libjvm.so"))
|
||||
(symlink (string-append lib-out "/zero/libjvm.so")
|
||||
(string-append lib-out "/libjvm.so"))))))
|
||||
phases))))))
|
||||
"03aa34lscr3qbdl6qz3gqyp0nzkqfj02362mzmpkiq3y2g5xdnrj"))
|
||||
|
||||
;;; Convenience alias to point to the latest version of OpenJDK.
|
||||
(define-public openjdk openjdk25)
|
||||
@@ -2008,8 +1964,7 @@ OpenJDK.")
|
||||
(home-page "https://www.jetbrains.com/")
|
||||
(license license:gpl2+)))
|
||||
|
||||
|
||||
(define-public ant/java8
|
||||
(define-public ant
|
||||
(package
|
||||
(name "ant")
|
||||
(version "1.10.15")
|
||||
@@ -2024,15 +1979,12 @@ OpenJDK.")
|
||||
(snippet
|
||||
'(begin
|
||||
(for-each delete-file
|
||||
(find-files "lib/optional" "\\.jar$"))
|
||||
#t))))
|
||||
(build-system gnu-build-system)
|
||||
(find-files "lib/optional" "\\.jar$"))))))
|
||||
(build-system ant-build-system)
|
||||
(arguments
|
||||
(list
|
||||
#:modules '((srfi srfi-1)
|
||||
(guix build gnu-build-system)
|
||||
(guix build utils))
|
||||
#:tests? #f ;no "check" target
|
||||
#:ant ant/java7
|
||||
#:test-target "test"
|
||||
#:phases
|
||||
#~(modify-phases %standard-phases
|
||||
(add-after 'unpack 'remove-scripts
|
||||
@@ -2042,11 +1994,100 @@ OpenJDK.")
|
||||
(for-each delete-file
|
||||
(find-files "src/script"
|
||||
"(.*\\.(bat|cmd)|runant.*|antRun.*)"))))
|
||||
(add-after 'unpack 'link-test-dependencies
|
||||
(lambda* (#:key inputs #:allow-other-keys)
|
||||
(for-each (lambda (file)
|
||||
(symlink file
|
||||
(string-append "lib/optional/"
|
||||
(basename file))))
|
||||
(append
|
||||
(find-files (assoc-ref inputs "java-hamcrest-core")
|
||||
"\\.jar$")
|
||||
(find-files (assoc-ref inputs "java-hamcrest-library")
|
||||
"\\.jar$")
|
||||
(find-files (assoc-ref inputs "java-junit")
|
||||
"\\.jar$")))))
|
||||
(add-before 'build 'fix-test-failures
|
||||
(lambda _
|
||||
;; Failure because the directory does not exist
|
||||
(substitute* "src/etc/testcases/taskdefs/exec/exec-with-redirector.xml"
|
||||
(("/usr/bin") (getcwd)))
|
||||
;; Failure because it cannot read root's name in the build
|
||||
;; container
|
||||
(delete-file "src/tests/junit/org/apache/tools/ant/types/selectors/OwnedBySelectorTest.java")
|
||||
;; Cause timestamp issue when trying to rollback time by a few
|
||||
;; seconds.
|
||||
(for-each (lambda (file) (utime file 5000))
|
||||
(find-files "src/etc/testcases/taskdefs" "" #:directories? #t))))
|
||||
(delete 'bootstrap)
|
||||
(delete 'configure)
|
||||
(replace 'build
|
||||
(lambda* (#:key inputs #:allow-other-keys)
|
||||
(setenv "JAVA_HOME" (assoc-ref inputs "jdk"))
|
||||
(invoke "bash" "bootstrap.sh"
|
||||
(string-append "-Ddist.dir=" #$output))))
|
||||
(add-after 'build 'fix-executables-paths
|
||||
(lambda* (#:key inputs #:allow-other-keys)
|
||||
(wrap-script (string-append #$output "/bin/ant")
|
||||
`("PATH" suffix
|
||||
(,(dirname (search-input-file inputs "/bin/sed"))
|
||||
,(dirname (search-input-file inputs "/bin/uname"))
|
||||
,(dirname (search-input-file inputs "/bin/which")))))
|
||||
(patch-shebang
|
||||
(string-append #$output "/bin/complete-ant-cmd.pl")
|
||||
(list (dirname (search-input-file inputs "/bin/perl"))))))
|
||||
(delete 'install))))
|
||||
(inputs
|
||||
(list coreutils-minimal
|
||||
guile-3.0/pinned
|
||||
java-hamcrest-core
|
||||
java-hamcrest-library
|
||||
java-junit
|
||||
perl
|
||||
sed
|
||||
which))
|
||||
(home-page "https://ant.apache.org")
|
||||
(synopsis "Build tool for Java")
|
||||
(description
|
||||
"Ant is a platform-independent build tool for Java. It is similar to
|
||||
make but is implemented using the Java language, requires the Java platform,
|
||||
and is best suited to building Java projects. Ant uses XML to describe the
|
||||
build process and its dependencies, whereas Make uses Makefile format.")
|
||||
(license license:asl2.0)))
|
||||
|
||||
;; The 1.9.x series is the last that can be built with GCJ. The 1.10.x series
|
||||
;; requires Java 8.
|
||||
(define-public ant/java7
|
||||
(package
|
||||
(name "ant")
|
||||
(version "1.9.15")
|
||||
(source (origin
|
||||
(method url-fetch)
|
||||
(uri (string-append "mirror://apache/ant/source/apache-ant-"
|
||||
version "-src.tar.gz"))
|
||||
(sha256
|
||||
(base32
|
||||
"1xy30f1w5gaqk6g3f0vw7ygix4rb6032qkcw42y4z8wd9jihgygd"))))
|
||||
(build-system gnu-build-system)
|
||||
(arguments
|
||||
`(#:modules ((srfi srfi-1)
|
||||
(guix build gnu-build-system)
|
||||
(guix build utils))
|
||||
#:tests? #f ; no "check" target
|
||||
#:phases
|
||||
(modify-phases %standard-phases
|
||||
(delete 'bootstrap)
|
||||
(delete 'configure)
|
||||
(add-after 'unpack 'remove-scripts
|
||||
;; Remove bat / cmd scripts for DOS as well as the antRun and runant
|
||||
;; wrappers.
|
||||
(lambda _
|
||||
(for-each delete-file
|
||||
(find-files "src/script"
|
||||
"(.*\\.(bat|cmd)|runant.*|antRun.*)"))))
|
||||
(replace 'build
|
||||
(lambda* (#:key inputs outputs #:allow-other-keys)
|
||||
(setenv "JAVA_HOME" (assoc-ref inputs "jdk"))
|
||||
|
||||
;; Disable tests to avoid dependency on hamcrest-core, which needs
|
||||
;; Ant to build. This is necessary in addition to disabling the
|
||||
@@ -2055,9 +2096,10 @@ OpenJDK.")
|
||||
(substitute* "build.xml"
|
||||
(("depends=\"jars,test-jar") "depends=\"jars"))
|
||||
(invoke "bash" "bootstrap.sh"
|
||||
(string-append "-Ddist.dir=" #$output))))
|
||||
(string-append "-Ddist.dir="
|
||||
(assoc-ref outputs "out")))))
|
||||
(add-after 'build 'strip-jar-timestamps ;based on ant-build-system
|
||||
(lambda _
|
||||
(lambda* (#:key outputs #:allow-other-keys)
|
||||
(define (repack-archive jar)
|
||||
(let* ((dir (mkdtemp "jar-contents.XXXXXX"))
|
||||
(manifest (string-append dir "/META-INF/MANIFESTS.MF")))
|
||||
@@ -2083,11 +2125,11 @@ OpenJDK.")
|
||||
(apply invoke command)))))
|
||||
(for-each repack-archive
|
||||
(find-files
|
||||
(string-append #$output "/lib")
|
||||
(string-append (assoc-ref %outputs "out") "/lib")
|
||||
"\\.jar$"))))
|
||||
(delete 'install))))
|
||||
(native-inputs
|
||||
`(("jdk" ,icedtea-8 "jdk")
|
||||
`(("jdk" ,icedtea-7 "jdk")
|
||||
("zip" ,zip)
|
||||
("unzip" ,unzip)))
|
||||
(home-page "https://ant.apache.org")
|
||||
@@ -2099,131 +2141,12 @@ and is best suited to building Java projects. Ant uses XML to describe the
|
||||
build process and its dependencies, whereas Make uses Makefile format.")
|
||||
(license license:asl2.0)))
|
||||
|
||||
;; The 1.9.x series is the last that can be built with GCJ. The 1.10.x series
|
||||
;; requires Java 8.
|
||||
(define-public ant
|
||||
(package (inherit ant/java8)
|
||||
(version "1.9.15")
|
||||
(source (origin
|
||||
(method url-fetch)
|
||||
(uri (string-append "mirror://apache/ant/source/apache-ant-"
|
||||
version "-src.tar.gz"))
|
||||
(sha256
|
||||
(base32
|
||||
"1xy30f1w5gaqk6g3f0vw7ygix4rb6032qkcw42y4z8wd9jihgygd"))))
|
||||
;; XXX: we do this to avoid a rebuild. This mess will be cleaned up
|
||||
;; later.
|
||||
(arguments
|
||||
(substitute-keyword-arguments
|
||||
`(#:modules ((srfi srfi-1)
|
||||
(guix build gnu-build-system)
|
||||
(guix build utils))
|
||||
#:tests? #f ; no "check" target
|
||||
#:phases
|
||||
(modify-phases %standard-phases
|
||||
(delete 'bootstrap)
|
||||
(delete 'configure)
|
||||
(add-before 'build 'define-java-environment-variables
|
||||
(lambda* (#:key inputs #:allow-other-keys)
|
||||
;; First, set environment variables (eases debugging on -K).
|
||||
(setenv "JAVA_HOME" (assoc-ref inputs "jamvm"))
|
||||
(setenv "JAVACMD" (search-input-file inputs "/bin/jamvm"))
|
||||
(setenv "JAVAC" (search-input-file inputs "/bin/jikes"))
|
||||
(setenv "CLASSPATH" (search-input-file inputs "/lib/rt.jar"))))
|
||||
(replace 'build
|
||||
(lambda* (#:key inputs outputs #:allow-other-keys)
|
||||
;; Ant complains if this file doesn't exist.
|
||||
(setenv "HOME" "/tmp")
|
||||
(with-output-to-file "/tmp/.ant.properties"
|
||||
(lambda _ (display "")))
|
||||
|
||||
;; Use jikes instead of javac for <javac ...> tags in build.xml
|
||||
(setenv "ANT_OPTS" "-Dbuild.compiler=jikes")
|
||||
|
||||
;; jikes produces lots of warnings, but they are not very
|
||||
;; interesting, so we silence them.
|
||||
(setenv "$BOOTJAVAC_OPTS" "-nowarn")
|
||||
|
||||
;; Without these JamVM options the build may freeze.
|
||||
(substitute* "bootstrap.sh"
|
||||
(("^\"\\$\\{JAVACMD\\}\" " m)
|
||||
,@(if (string-prefix? "armhf" (or (%current-system)
|
||||
(%current-target-system)))
|
||||
`((string-append m "-Xnocompact "))
|
||||
`((string-append m "-Xnocompact -Xnoinlining ")))))
|
||||
|
||||
;; Disable tests because we are bootstrapping and thus don't have
|
||||
;; any of the dependencies required to build and run the tests.
|
||||
(substitute* "build.xml"
|
||||
(("depends=\"jars,test-jar\"") "depends=\"jars\""))
|
||||
(invoke "bash" "bootstrap.sh"
|
||||
(string-append "-Ddist.dir="
|
||||
(assoc-ref outputs "out")))))
|
||||
(add-after 'build 'strip-jar-timestamps ;based on ant-build-system
|
||||
(lambda* (#:key outputs #:allow-other-keys)
|
||||
(define (repack-archive jar)
|
||||
(let* ((dir (mkdtemp "jar-contents.XXXXXX"))
|
||||
(manifest (string-append dir "/META-INF/MANIFESTS.MF")))
|
||||
(with-directory-excursion dir
|
||||
(invoke "unzip" jar))
|
||||
(delete-file jar)
|
||||
;; XXX: copied from (gnu build install)
|
||||
(for-each (lambda (file)
|
||||
(let ((s (lstat file)))
|
||||
(unless (eq? (stat:type s) 'symlink)
|
||||
(utime file 0 0 0 0))))
|
||||
(find-files dir #:directories? #t))
|
||||
;; It is important that the manifest appears first.
|
||||
(with-directory-excursion dir
|
||||
(let* ((files (find-files "." ".*" #:directories? #t))
|
||||
;; To ensure that the reference scanner can
|
||||
;; detect all store references in the jars
|
||||
;; we disable compression with the "-0" option.
|
||||
(command (if (file-exists? manifest)
|
||||
`("zip" "-0" "-X" ,jar ,manifest
|
||||
,@files)
|
||||
`("zip" "-0" "-X" ,jar ,@files))))
|
||||
(apply invoke command)))))
|
||||
(for-each repack-archive
|
||||
(find-files
|
||||
(string-append (assoc-ref %outputs "out") "/lib")
|
||||
"\\.jar$"))))
|
||||
(delete 'install)))
|
||||
((#:phases phases)
|
||||
`(modify-phases ,phases
|
||||
(delete 'define-java-environment-variables)
|
||||
(add-after 'unpack 'remove-scripts
|
||||
;; Remove bat / cmd scripts for DOS as well as the antRun and runant
|
||||
;; wrappers.
|
||||
(lambda _
|
||||
(for-each delete-file
|
||||
(find-files "src/script"
|
||||
"(.*\\.(bat|cmd)|runant.*|antRun.*)"))
|
||||
#t))
|
||||
(replace 'build
|
||||
(lambda* (#:key inputs outputs #:allow-other-keys)
|
||||
(setenv "JAVA_HOME" (assoc-ref inputs "jdk"))
|
||||
|
||||
;; Disable tests to avoid dependency on hamcrest-core, which needs
|
||||
;; Ant to build. This is necessary in addition to disabling the
|
||||
;; "check" phase, because the dependency on "test-jar" would always
|
||||
;; result in the tests to be run.
|
||||
(substitute* "build.xml"
|
||||
(("depends=\"jars,test-jar") "depends=\"jars"))
|
||||
(invoke "bash" "bootstrap.sh"
|
||||
(string-append "-Ddist.dir="
|
||||
(assoc-ref outputs "out")))))))))
|
||||
(native-inputs
|
||||
`(("jdk" ,icedtea-7 "jdk")
|
||||
("zip" ,zip)
|
||||
("unzip" ,unzip)))))
|
||||
|
||||
(define-public ant-apache-bcel
|
||||
(package
|
||||
(inherit ant/java8)
|
||||
(inherit ant)
|
||||
(name "ant-apache-bcel")
|
||||
(arguments
|
||||
(substitute-keyword-arguments (package-arguments ant/java8)
|
||||
(substitute-keyword-arguments (package-arguments ant)
|
||||
((#:phases phases)
|
||||
#~(modify-phases #$phases
|
||||
(add-after 'unpack 'link-bcel
|
||||
@@ -2244,37 +2167,11 @@ build process and its dependencies, whereas Make uses Makefile format.")
|
||||
(delete-file-recursively bin)
|
||||
(delete-file-recursively lib))))))))
|
||||
(inputs
|
||||
(modify-inputs (package-inputs ant/java8)
|
||||
(modify-inputs (package-inputs ant)
|
||||
(prepend java-commons-bcel)))))
|
||||
|
||||
(define-public ant-junit
|
||||
(package
|
||||
(inherit ant/java8)
|
||||
(name "ant-junit")
|
||||
(arguments
|
||||
(substitute-keyword-arguments (package-arguments ant/java8)
|
||||
((#:phases phases)
|
||||
#~(modify-phases #$phases
|
||||
(add-after 'unpack 'link-junit
|
||||
(lambda* (#:key inputs #:allow-other-keys)
|
||||
(for-each (lambda (file)
|
||||
(symlink file
|
||||
(string-append "lib/optional/"
|
||||
(basename file))))
|
||||
(find-files (assoc-ref inputs "java-junit")
|
||||
"\\.jar$"))))
|
||||
(add-after 'build 'install
|
||||
(lambda _
|
||||
(let ((share (string-append #$output "/share/java"))
|
||||
(bin (string-append #$output "/bin"))
|
||||
(lib (string-append #$output "/lib")))
|
||||
(mkdir-p share)
|
||||
(install-file (string-append lib "/ant-junit.jar") share)
|
||||
(delete-file-recursively bin)
|
||||
(delete-file-recursively lib))))))))
|
||||
(inputs
|
||||
(modify-inputs (package-inputs ant/java8)
|
||||
(prepend java-junit)))))
|
||||
(define-deprecated-package ant-junit
|
||||
ant)
|
||||
|
||||
(define-public libantlr3c
|
||||
(package
|
||||
@@ -3381,6 +3278,9 @@ is implemented.")
|
||||
`(;; Tests require junit
|
||||
#:tests? #f
|
||||
#:jar-name "qdox.jar"
|
||||
;; Explicitely use an ant version that includes the junit tasks, since
|
||||
;; it is a dependency of junit.
|
||||
#:ant ,ant/java7
|
||||
#:phases
|
||||
(modify-phases %standard-phases
|
||||
(replace 'unpack
|
||||
@@ -3489,6 +3389,9 @@ documentation tools.")
|
||||
`(;; Tests require junit, which ultimately depends on this package.
|
||||
#:tests? #f
|
||||
#:build-target "jar"
|
||||
;; Explicitely use an ant version that includes the junit tasks, since
|
||||
;; it is a dependency of junit.
|
||||
#:ant ,ant/java7
|
||||
#:phases
|
||||
(modify-phases %standard-phases
|
||||
(add-before 'build 'do-not-use-bundled-asm
|
||||
@@ -3587,6 +3490,9 @@ testing frameworks, mocking libraries and UI validation rules.")
|
||||
(build-system ant-build-system)
|
||||
(arguments
|
||||
`(#:tests? #f ; Tests require junit
|
||||
;; Explicitely use an ant version that includes the junit tasks, since
|
||||
;; it is a dependency of junit.
|
||||
#:ant ,ant/java7
|
||||
#:modules ((guix build ant-build-system)
|
||||
(guix build java-utils)
|
||||
(guix build utils)
|
||||
@@ -3672,6 +3578,9 @@ testing frameworks, mocking libraries and UI validation rules.")
|
||||
(native-inputs '())
|
||||
(arguments
|
||||
`(#:tests? #f
|
||||
;; Explicitely use an ant version that includes the junit tasks, since
|
||||
;; it is a dependency of junit.
|
||||
#:ant ,ant/java7
|
||||
#:phases
|
||||
(modify-phases %standard-phases
|
||||
(delete 'configure)
|
||||
@@ -3713,7 +3622,7 @@ testing frameworks, mocking libraries and UI validation rules.")
|
||||
(define-public java-junit
|
||||
(package
|
||||
(name "java-junit")
|
||||
(version "4.12")
|
||||
(version "4.13.2")
|
||||
(source (origin
|
||||
(method git-fetch)
|
||||
(uri (git-reference
|
||||
@@ -3722,7 +3631,7 @@ testing frameworks, mocking libraries and UI validation rules.")
|
||||
(file-name (git-file-name name version))
|
||||
(sha256
|
||||
(base32
|
||||
"1j8avi91px1z8rjc89cfikwrvfifdmmsarwiyrcnr59ynvpz0v8h"))
|
||||
"1r7k4zzscc8019np3is3bzfigw8fxd6s3259cbhzzh02q6d5p9h3"))
|
||||
(modules '((guix build utils)))
|
||||
(snippet
|
||||
'(begin
|
||||
@@ -3734,6 +3643,9 @@ testing frameworks, mocking libraries and UI validation rules.")
|
||||
`(#:jar-name "junit.jar"
|
||||
#:source-dir "src/main/java"
|
||||
#:test-dir "src/test"
|
||||
;; Explicitely use an ant version that includes the junit tasks, so
|
||||
;; we can run the tests.
|
||||
#:ant ,ant/java7
|
||||
#:test-exclude (list "**/SimpleTest.java" "**/StackTracesTest.java"
|
||||
"**/RuleChainTest.java" "**/TestWatchmanTest.java")
|
||||
#:phases
|
||||
@@ -3774,7 +3686,13 @@ sharing common test data, and test runners for running tests.")
|
||||
`(#:jar-name "junitparams.jar"
|
||||
#:source-dir "src/main/java"
|
||||
#:test-dir "src/test"
|
||||
#:test-exclude (list "**/SuperclassTest.java")))
|
||||
#:test-exclude (list
|
||||
;; Abstract class: no tests
|
||||
"**/SuperclassTest.java"
|
||||
;; Incompatible tests with junit 4.13.2
|
||||
"**/BeforeAfterClassTest.java"
|
||||
"**/FilterableTest.java"
|
||||
"**/RulesTest.java")))
|
||||
(inputs
|
||||
(list java-junit))
|
||||
(native-inputs
|
||||
@@ -5243,6 +5161,9 @@ complex transformations and code analysis tools.")
|
||||
(build-system ant-build-system)
|
||||
(arguments
|
||||
`(#:tests? #f
|
||||
;; Explicitely use an ant version that includes the junit tasks, since
|
||||
;; it is a dependency of junit.
|
||||
#:ant ,ant/java7
|
||||
#:phases
|
||||
(modify-phases %standard-phases
|
||||
(delete 'unpack)
|
||||
@@ -5264,6 +5185,9 @@ including java-asm.")
|
||||
(properties '((hidden? . #t)))
|
||||
(arguments
|
||||
(substitute-keyword-arguments (package-arguments java-asm)
|
||||
;; Explicitely use an ant version that includes the junit tasks, since
|
||||
;; it is a dependency of junit.
|
||||
((#:ant _ ant/java7) ant/java7)
|
||||
((#:tests? _) #f)))
|
||||
(native-inputs `())))
|
||||
|
||||
|
||||
@@ -22,7 +22,6 @@
|
||||
;;; Copyright © 2024, 2025 Nicolas Graves <ngraves@ngraves.fr>
|
||||
;;; Copyright © 2024-2025 Sharlatan Hellseher <sharlatanus@gmail.com>
|
||||
;;; Copyright © 2025 Ghislain Vaillant <ghislain.vaillant@inria.fr>
|
||||
;;; Copyright © 2026 Vinicius Monego <monego@posteo.net>
|
||||
;;;
|
||||
;;; This file is part of GNU Guix.
|
||||
;;;
|
||||
@@ -53,9 +52,7 @@
|
||||
#:use-module (gnu packages bash)
|
||||
#:use-module (gnu packages check)
|
||||
#:use-module (gnu packages cpp)
|
||||
#:use-module (gnu packages databases)
|
||||
#:use-module (gnu packages docker)
|
||||
#:use-module (gnu packages freedesktop)
|
||||
#:use-module (gnu packages linux)
|
||||
#:use-module (gnu packages monitoring)
|
||||
#:use-module (gnu packages networking)
|
||||
@@ -1713,13 +1710,13 @@ analyzing Jupyter Notebooks.")
|
||||
(define-public python-qtconsole
|
||||
(package
|
||||
(name "python-qtconsole")
|
||||
(version "5.7.2")
|
||||
(version "5.7.0")
|
||||
(source
|
||||
(origin
|
||||
(method url-fetch)
|
||||
(uri (pypi-uri "qtconsole" version))
|
||||
(sha256
|
||||
(base32 "088m56fav6xlcw55srxz96yf7rj2ndmycy4f3m69498r2swqbd17"))))
|
||||
(base32 "0w9i0s70dm39cxgn3vh4wcaxdywzp9j0ac7f49q4qmggx4f3fcqd"))))
|
||||
(build-system pyproject-build-system)
|
||||
(arguments
|
||||
(list
|
||||
@@ -1767,67 +1764,6 @@ analyzing Jupyter Notebooks.")
|
||||
rich media output.")
|
||||
(license license:bsd-3)))
|
||||
|
||||
(define-public python-spyder-kernels
|
||||
(package
|
||||
(name "python-spyder-kernels")
|
||||
(version "3.1.4")
|
||||
(source
|
||||
(origin
|
||||
(method git-fetch)
|
||||
(uri (git-reference
|
||||
(url "https://github.com/spyder-ide/spyder-kernels")
|
||||
(commit (string-append "v" version))))
|
||||
(file-name (git-file-name name version))
|
||||
(sha256
|
||||
(base32 "0yhrifh148g93qkwx9ggsh2kr9789apzlw91ais4dyas5yf1xj8w"))))
|
||||
(build-system pyproject-build-system)
|
||||
(arguments
|
||||
(list
|
||||
#:test-flags
|
||||
#~(list "-k" (string-append
|
||||
;; Avoid pulling Django for a single test.
|
||||
"not test_django_settings"
|
||||
;; AssertionError.
|
||||
" and not test_umr_reload_modules"))
|
||||
#:phases
|
||||
#~(modify-phases %standard-phases
|
||||
(add-before 'check 'redirect-HOME
|
||||
(lambda _
|
||||
(setenv "HOME" "/tmp"))))))
|
||||
(propagated-inputs (list python-cloudpickle
|
||||
python-ipykernel
|
||||
python-ipython
|
||||
python-jupyter-client
|
||||
python-packaging
|
||||
python-pyxdg
|
||||
python-pyzmq
|
||||
python-traitlets
|
||||
python-wurlitzer))
|
||||
(native-inputs (list python-anyio
|
||||
python-cython
|
||||
python-dask
|
||||
python-h5py
|
||||
python-matplotlib
|
||||
python-numpy
|
||||
python-pandas
|
||||
python-pillow
|
||||
python-polars
|
||||
python-pyarrow
|
||||
python-pydicom
|
||||
python-pytest
|
||||
python-scipy
|
||||
python-setuptools
|
||||
python-xarray))
|
||||
(home-page "https://github.com/spyder-ide/spyder-kernels")
|
||||
(synopsis "Jupyter kernels for Spyder's console")
|
||||
(description "This package provides Jupyter kernels for use with the
|
||||
consoles of Spyder, the Scientific Python Development Environment.
|
||||
|
||||
These kernels can be launched either through Spyder itself or in an
|
||||
independent Python session, and allow for interactive or file-based execution
|
||||
of Python code inside Spyder.")
|
||||
(license license:expat)))
|
||||
|
||||
(define-public python-voila
|
||||
(package
|
||||
(name "python-voila")
|
||||
|
||||
@@ -1191,42 +1191,37 @@ CDs.")
|
||||
(define-public plasmatube
|
||||
(package
|
||||
(name "plasmatube")
|
||||
(version "26.04.0")
|
||||
(source
|
||||
(origin
|
||||
(method url-fetch)
|
||||
(uri (string-append "mirror://kde/stable/release-service/" version
|
||||
"/src/plasmatube-" version ".tar.xz"))
|
||||
(sha256
|
||||
(base32 "0dby9wypbrhg6g03kvl8fc40zpnri03hf3kk3vi1z16pwc7sn093"))))
|
||||
(version "25.12.2")
|
||||
(source (origin
|
||||
(method url-fetch)
|
||||
(uri (string-append "mirror://kde/stable/release-service/" version
|
||||
"/src/plasmatube-" version ".tar.xz"))
|
||||
(sha256
|
||||
(base32
|
||||
"1jc6iqcxz0zyai26vx80nyfr818r4cj8lpw0b1pbvb1vya12v8zy"))))
|
||||
(build-system qt-build-system)
|
||||
(native-inputs (list extra-cmake-modules pkg-config python-minimal))
|
||||
(inputs
|
||||
(list kconfig
|
||||
kcoreaddons
|
||||
kdbusaddons
|
||||
kdeclarative ; for org.kde.kquickcontrolsaddons
|
||||
ki18n
|
||||
kirigami
|
||||
kirigami-addons
|
||||
kitemmodels
|
||||
ki18n
|
||||
kwindowsystem
|
||||
mpvqt
|
||||
purpose
|
||||
qqc2-desktop-style ; for org.kde.desktop
|
||||
qtdeclarative
|
||||
qtkeychain-qt6
|
||||
qtmultimedia
|
||||
qtsvg
|
||||
qtkeychain-qt6
|
||||
qtwayland
|
||||
sonnet
|
||||
yt-dlp))
|
||||
(arguments (list #:qtbase qtbase))
|
||||
(home-page "https://apps.kde.org/plasmatube/")
|
||||
(synopsis "YouTube and PeerTube video player")
|
||||
(description
|
||||
"Plasmatube is a YouTube video player that uses Invidious and Piped
|
||||
APIs. It can also play videos from PeerTube sources.")
|
||||
(synopsis "Kirigami YouTube video player")
|
||||
(description "This package provides YouTube video player based
|
||||
on QtMultimedia and @command{yt-dlp}.")
|
||||
(license license:gpl3+)))
|
||||
|
||||
(define-public rattlesnake
|
||||
|
||||
@@ -125,14 +125,14 @@
|
||||
;; ex:
|
||||
;; tar xf /gnu/store/...-firefox-123.4.source.tar.xz -O \
|
||||
;; firefox-123.4/browser/locales/l10n-changesets.json | grep revision
|
||||
(let ((commit "fefe280d909d0eee8d60edd2a6db7d969df56c5b"))
|
||||
(let ((commit "0245ffb160688061f0e0c67ea488bcdfdacbeca4"))
|
||||
(origin
|
||||
(method git-fetch)
|
||||
(uri (git-reference
|
||||
(url "https://github.com/mozilla-l10n/firefox-l10n.git")
|
||||
(commit commit)))
|
||||
(file-name (git-file-name "firefox-l10n" commit))
|
||||
(sha256 (base32 "0z1ksvspbn4bbzxdl2w4x7bg36j4rwhaby8g37apg4393frh558i")))))
|
||||
(sha256 (base32 "0y8xdxql04yys0wj685v4yp3kmx1ivnndg6z11vam8vszh0j7ak6")))))
|
||||
|
||||
(define* (make-librewolf-source #:key version firefox-hash librewolf-hash l10n)
|
||||
(let* ((ff-src (firefox-source-origin
|
||||
@@ -205,8 +205,7 @@
|
||||
(search-patches
|
||||
"librewolf-compare-paths.patch"
|
||||
"librewolf-use-system-wide-dir.patch"
|
||||
"librewolf-add-store-to-rdd-allowlist.patch"
|
||||
"librewolf-150.0-encoding_rs-rust-fix.patch"))
|
||||
"librewolf-add-store-to-rdd-allowlist.patch"))
|
||||
;; Slim down the tarball by removing unbundled libraries and 75 Mo (800+
|
||||
;; Mo uncompressed) of unused tests.
|
||||
;; TODO: Unbundle security/nss and media/libpng.
|
||||
@@ -245,17 +244,17 @@
|
||||
;; It's used for cache validation and therefore can lead to strange bugs.
|
||||
;; ex: date '+%Y%m%d%H%M%S'
|
||||
;; or: (format-time-string "%Y%m%d%H%M%S")
|
||||
(define %librewolf-build-id "20260421153818")
|
||||
(define %librewolf-build-id "20260409162101")
|
||||
|
||||
(define-public librewolf
|
||||
(package
|
||||
(name "librewolf")
|
||||
(version "150.0-1")
|
||||
(version "149.0.2-2")
|
||||
(source
|
||||
(make-librewolf-source
|
||||
#:version version
|
||||
#:firefox-hash "151rxzl80dm8jsxl6fwzgbirwq4zpms5adwwnbjcwdd1r3s3vr7v"
|
||||
#:librewolf-hash "0iw9v3zc1fxc93yyhldqarxaypgmbndh2ylsy330kcbpb6p1gnmr"
|
||||
#:firefox-hash "1kkhg3lgyakinn5ankxrlxbf39wi61mqbhwrj1l4q5l7y0n1m4va"
|
||||
#:librewolf-hash "1bai8g2kc9snck2f724al29q6r57vkj3d7v58rf0mgzpqzvwnw5f"
|
||||
#:l10n firefox-l10n))
|
||||
(build-system gnu-build-system)
|
||||
(arguments
|
||||
@@ -353,18 +352,18 @@
|
||||
(cdr pref)))
|
||||
`(("extensions.getAddons.search.browseURL"
|
||||
,(string-append
|
||||
"https://gnuzilla.gnu.org/"
|
||||
"https://gnuzilla.gnu.org/mozzarella/"
|
||||
"search.php?q=%TERMS%"))
|
||||
("extensions.getAddons.get.url" .
|
||||
"https://gnuzilla.gnu.org")
|
||||
"https://gnuzilla.gnu.org/mozzarella")
|
||||
("extensions.getAddons.link.url" .
|
||||
"https://gnuzilla.gnu.org")
|
||||
"https://gnuzilla.gnu.org/mozzarella")
|
||||
("extensions.getAddons.discovery.api_url" .
|
||||
"https://gnuzilla.gnu.org")
|
||||
"https://gnuzilla.gnu.org/mozzarella")
|
||||
("extensions.getAddons.langpacks.url" .
|
||||
"https://gnuzilla.gnu.org")
|
||||
"https://gnuzilla.gnu.org/mozzarella")
|
||||
("lightweightThemes.getMoreURL" .
|
||||
"https://gnuzilla.gnu.org")))))))
|
||||
"https://gnuzilla.gnu.org/mozzarella")))))))
|
||||
(add-after 'patch-source-shebangs 'patch-cargo-checksums
|
||||
(lambda _
|
||||
(use-modules (guix build cargo-utils))
|
||||
|
||||
@@ -87,7 +87,6 @@
|
||||
;;; Copyright © 2025 John Kehayias <john.kehayias@protonmail.com>
|
||||
;;; Copyright © 2025 Arjan Adriaanse <arjan@adriaan.se>
|
||||
;;; Copyright © 2026 Justin Veilleux <terramorpha@cock.li>
|
||||
;;; Copyright © 2026 Simen Endsjø <contact@simendsjo.me>
|
||||
;;;
|
||||
;;; This file is part of GNU Guix.
|
||||
;;;
|
||||
@@ -2768,6 +2767,32 @@ This package provides the @command{corefreqd} data collection daemon, the
|
||||
(supported-systems (list "x86_64-linux"))
|
||||
(license license:gpl2)))
|
||||
|
||||
(define-public librem-ec-acpi-linux-module
|
||||
(package
|
||||
(name "librem-ec-acpi-linux-module")
|
||||
(version "0.9.2")
|
||||
(source
|
||||
(origin
|
||||
(method git-fetch)
|
||||
(uri (git-reference
|
||||
(url "https://source.puri.sm/nicole.faerber/librem-ec-acpi-dkms")
|
||||
(commit (string-append "v" version))))
|
||||
(file-name (git-file-name name version))
|
||||
(sha256
|
||||
(base32 "0m8hamf0550083jnk5q4hv20l8lfiardnkxbib4hhvqghpzzbxl0"))))
|
||||
(build-system linux-module-build-system)
|
||||
(arguments
|
||||
(list #:tests? #f)) ; no test suite
|
||||
(home-page "https://source.puri.sm/nicole.faerber/librem-ec-acpi-dkms")
|
||||
(synopsis "Linux kernel module to control the Librem Embedded Controller")
|
||||
(description
|
||||
"This is the Linux kernel @acronym{ACPI, Advanced Configuration and Power
|
||||
Interface} platform driver for the @acronym{EC, Embedded Controller} firmware
|
||||
on Purism Librem laptop computers. It allows user-space control over the
|
||||
battery charging thresholds, keyboard backlight, fans and thermal monitors,
|
||||
and the notification, WiFi, and Bluetooth LED.")
|
||||
(license license:gpl2)))
|
||||
|
||||
(define-public tuxedo-keyboard
|
||||
(package
|
||||
(name "tuxedo-keyboard")
|
||||
@@ -2801,7 +2826,7 @@ module is also needed for the @code{tuxedo-control-center} (short tcc) package."
|
||||
(define-public evdi
|
||||
(package
|
||||
(name "evdi")
|
||||
(version "1.14.15") ;inherited by libevdi
|
||||
(version "1.14.8") ;inherited by libevdi
|
||||
(source
|
||||
(origin
|
||||
(method git-fetch)
|
||||
@@ -2810,20 +2835,14 @@ module is also needed for the @code{tuxedo-control-center} (short tcc) package."
|
||||
(commit (string-append "v" version))))
|
||||
(file-name (git-file-name name version))
|
||||
(sha256
|
||||
(base32 "065mfwmb4nw71s0f0ax9si8xpbr1sah1bhxvq1k81yicvi83wsxn"))))
|
||||
(base32 "18n8kk4gbbj252a2dqb7mbpscfb437x42flh1fsl4g5c8brczc77"))))
|
||||
(build-system linux-module-build-system)
|
||||
(arguments
|
||||
(list #:tests? #f ;no test suite
|
||||
#:phases #~(modify-phases %standard-phases
|
||||
(add-after 'unpack 'chdir
|
||||
(lambda _
|
||||
(chdir "module")))
|
||||
;; Looks like the value is only there to detect RHEL
|
||||
;; derivatives, so we can safely delete the include.
|
||||
(add-after 'unpack 'embed-/etc/os-release
|
||||
(lambda _
|
||||
(substitute* "module/Makefile"
|
||||
(("include /etc/os-release") "")))))))
|
||||
(chdir "module"))))))
|
||||
(home-page "https://github.com/DisplayLink/evdi")
|
||||
(synopsis
|
||||
"@acronym{EVDI, Extensible Virtual Display Interface} Linux kernel module")
|
||||
@@ -2836,7 +2855,7 @@ and receive screen updates.
|
||||
|
||||
The EVDI driver uses the standard Linux @acronym{DRM, Direct Rendering Manager}.
|
||||
Its displays can be controlled by standard tools such as @command{xrandr} and
|
||||
display settings applets in graphical environments.")
|
||||
display settings applets in graphical environments")
|
||||
(license license:gpl2)))
|
||||
|
||||
(define-public libevdi
|
||||
@@ -2893,6 +2912,62 @@ registers of the @acronym{EC, Embedded Controller} supported by the
|
||||
@code{ec_sys} Linux driver.")
|
||||
(license license:gpl2)))
|
||||
|
||||
(define-public lkrg
|
||||
(package
|
||||
(name "lkrg")
|
||||
(version "0.9.7")
|
||||
(source (origin
|
||||
(method git-fetch)
|
||||
(uri (git-reference
|
||||
(url "https://github.com/lkrg-org/lkrg")
|
||||
(commit (string-append "v" version))))
|
||||
(file-name (git-file-name name version))
|
||||
(sha256
|
||||
(base32
|
||||
"0k0z9caj48nqjwk3bapgfcdzi1lkizxcjj4r1dvkvwsk38mbk1c4"))))
|
||||
(build-system linux-module-build-system)
|
||||
(arguments
|
||||
(list #:linux linux-libre
|
||||
#:tests? #f
|
||||
#:make-flags #~(list (string-append "CC="
|
||||
#$(cc-for-target))
|
||||
(string-append "SYSSRC="
|
||||
(assoc-ref %build-inputs
|
||||
"linux-module-builder")
|
||||
"/lib/modules/build"))))
|
||||
(inputs (list bash-minimal))
|
||||
(home-page "https://lkrg.org/")
|
||||
(synopsis "Linux Kernel Runtime Guard")
|
||||
(description
|
||||
"This package performs runtime integrity checking of the Linux kernel and
|
||||
detection of security vulnerability exploits against the kernel.")
|
||||
(license license:gpl2)))
|
||||
|
||||
(define-public vhba-module
|
||||
(package
|
||||
(name "vhba-module")
|
||||
(version "20211218")
|
||||
(source
|
||||
(origin
|
||||
(method url-fetch)
|
||||
(uri (string-append
|
||||
"http://downloads.sourceforge.net/cdemu/vhba-module/vhba-module-"
|
||||
version ".tar.xz"))
|
||||
(sha256
|
||||
(base32 "1dkprnnya0i8121p7ip4g8cww99drk7fzbwcxx65x02jqk0siibj"))))
|
||||
(build-system linux-module-build-system)
|
||||
(arguments
|
||||
(list #:tests? #f)) ; no test suite
|
||||
(home-page "https://cdemu.sourceforge.io/")
|
||||
(synopsis "Linux kernel module that emulates SCSI devices")
|
||||
(description
|
||||
"The @acronym{VHBA, Virtual SCSI Host Bus Adapter} module is the link
|
||||
between the CDemu user-space daemon and the kernel Linux. It acts as a
|
||||
low-level SCSI driver that emulates a virtual SCSI adapter which can have
|
||||
multiple virtual devices attached to it. Its typical use with CDEmu is to
|
||||
emulate optical devices such as DVD and CD-ROM drives.")
|
||||
(license license:gpl2+)))
|
||||
|
||||
(define-public bbswitch-module
|
||||
;; Use "develop" branch since stable release does not build on Linux >= 5.6.
|
||||
;; See https://github.com/Bumblebee-Project/bbswitch/issues/205.
|
||||
@@ -3089,6 +3164,36 @@ Linux kernel module, it also contains a modprobe configuration and udev rules,
|
||||
which need to be installed separately.")
|
||||
(license license:gpl3+)))
|
||||
|
||||
(define-public vendor-reset-linux-module
|
||||
(let ((commit "4b466e92a2d9f76ce1082cde982c7be0be91e248")
|
||||
(revision "0"))
|
||||
(package
|
||||
(name "vendor-reset-linux-module")
|
||||
(version (git-version "0.1.0" revision commit))
|
||||
(source (origin
|
||||
(method git-fetch)
|
||||
(uri (git-reference
|
||||
(url "https://github.com/gnif/vendor-reset")
|
||||
(commit commit)))
|
||||
(file-name (git-file-name name version))
|
||||
(sha256
|
||||
(base32
|
||||
"1gaf4j20grng689c9fylcqri3j9ycnhr2bsva2z6qcdqvzl6yxbi"))))
|
||||
(build-system linux-module-build-system)
|
||||
(arguments
|
||||
(list #:tests? #f)) ;no test suite
|
||||
(home-page "https://github.com/gnif/vendor-reset")
|
||||
(synopsis
|
||||
"Kernel module that resets GPUs that are affected by the reset bug")
|
||||
(description
|
||||
"This package provides a kernel module that is capable of
|
||||
resetting hardware devices into a state where they can be
|
||||
re-initialized or passed through into a virtual machine (VFIO).
|
||||
While it would be great to have these in the kernel as PCI quirks,
|
||||
some of the reset procedures are very complex and would never be
|
||||
accepted as a quirk (ie AMD Vega 10).")
|
||||
(license license:gpl2))))
|
||||
|
||||
|
||||
;;;
|
||||
;;; Pluggable authentication modules (PAM).
|
||||
@@ -11989,7 +12094,7 @@ provides user-space tools for creating EROFS file systems.")
|
||||
(define-public rasdaemon
|
||||
(package
|
||||
(name "rasdaemon")
|
||||
(version "0.8.4")
|
||||
(version "0.8.3")
|
||||
(source
|
||||
(origin
|
||||
(method git-fetch)
|
||||
@@ -11998,17 +12103,9 @@ provides user-space tools for creating EROFS file systems.")
|
||||
(commit (string-append "v" version))))
|
||||
(file-name (git-file-name name version))
|
||||
(sha256
|
||||
(base32 "1930g35igfdw5bzcd6diy59rm1q4yirpjgqznfqfsichnmk04kmf"))))
|
||||
(base32 "0vfw4vf75fnpbxnfsmpdwdzhplnccz24j23bg6nsb3b4wa8hv4sa"))))
|
||||
(native-inputs (list autoconf automake libtool pkg-config))
|
||||
(inputs
|
||||
(list bash-minimal
|
||||
dmidecode
|
||||
kmod
|
||||
libtraceevent
|
||||
pciutils
|
||||
perl
|
||||
perl-dbd-sqlite
|
||||
sqlite))
|
||||
(inputs (list bash-minimal libtraceevent perl perl-dbd-sqlite sqlite dmidecode kmod))
|
||||
(arguments
|
||||
(list
|
||||
#:configure-flags
|
||||
|
||||
@@ -22847,6 +22847,16 @@ specification}, a toolkit for writing GUIs in Common Lisp.")
|
||||
(define-public cl-mcclim
|
||||
(sbcl-package->cl-source-package sbcl-mcclim))
|
||||
|
||||
(define-public ecl-mcclim
|
||||
(let ((pkg (sbcl-package->ecl-package sbcl-mcclim)))
|
||||
(package
|
||||
(inherit pkg)
|
||||
(arguments
|
||||
(substitute-keyword-arguments arguments
|
||||
;; Tests fail with "FUNCTION: Not a valid argument (R1
|
||||
;; (GENERATE-REGION))." on ECL.
|
||||
((#:tests? _ #f) #f))))))
|
||||
|
||||
(define-public sbcl-md5
|
||||
(package
|
||||
(name "sbcl-md5")
|
||||
@@ -29757,7 +29767,7 @@ the Processing language and shares some of the API.")
|
||||
;; Update together with emacs-slime.
|
||||
(package
|
||||
(name "sbcl-slime-swank")
|
||||
(version "2.32")
|
||||
(version "2.31")
|
||||
(source
|
||||
(origin
|
||||
(file-name (git-file-name "cl-slime-swank" version))
|
||||
@@ -29766,7 +29776,7 @@ the Processing language and shares some of the API.")
|
||||
(url "https://github.com/slime/slime/")
|
||||
(commit (string-append "v" version))))
|
||||
(sha256
|
||||
(base32 "0s7m7j7y1p8fb6ncpxcxdrrrxp5aw67xl7wrqy8zjjvwzljbs548"))
|
||||
(base32 "0nv99wq2vz053p0rn9953rhmyz4g40zdl01mz7z9xbklxzbsx6x7"))
|
||||
(modules '((guix build utils)))
|
||||
(snippet
|
||||
;; The doc folder drags `gawk' into the closure. Doc is already
|
||||
|
||||
@@ -89,7 +89,6 @@
|
||||
#:use-module (gnu packages wget)
|
||||
#:use-module (gnu packages xml)
|
||||
#:use-module (gnu packages xorg)
|
||||
#:use-module (ice-9 match)
|
||||
#:use-module ((srfi srfi-1) #:hide (zip)))
|
||||
|
||||
(define (lua-search-paths version)
|
||||
@@ -171,22 +170,6 @@ for configuration, scripting, and rapid prototyping.")
|
||||
"lua-5.4-search-paths.patch"))))
|
||||
(native-search-paths (lua-search-paths "5.4"))))
|
||||
|
||||
|
||||
(define-public lua-5.4-for-c++
|
||||
(let ((lua-pkg lua-5.4))
|
||||
(hidden-package
|
||||
(package/inherit lua-pkg
|
||||
(name (string-append (package-name lua-pkg) "-for-c++"))
|
||||
(arguments
|
||||
(substitute-keyword-arguments (package-arguments lua-pkg)
|
||||
((#:make-flags old-flags)
|
||||
(map
|
||||
(match-lambda
|
||||
((string-append "CC=" _)
|
||||
`(string-append "CC=" ,(cxx-for-target)))
|
||||
(else else))
|
||||
old-flags))))))))
|
||||
|
||||
(define-public lua-5.2
|
||||
(package (inherit lua)
|
||||
(version "5.2.4")
|
||||
|
||||
@@ -1355,7 +1355,7 @@ security functionality including PGP, S/MIME, SSH, and SSL.")
|
||||
(define-public mu
|
||||
(package
|
||||
(name "mu")
|
||||
(version "1.14.1")
|
||||
(version "1.14.0")
|
||||
(source
|
||||
(origin
|
||||
(method git-fetch)
|
||||
@@ -1364,7 +1364,7 @@ security functionality including PGP, S/MIME, SSH, and SSL.")
|
||||
(commit (string-append "v" version))))
|
||||
(file-name (git-file-name name version))
|
||||
(sha256
|
||||
(base32 "0dv27pq2jmgqlzsy2gcmh7vddiwiwd55j299blb9k8g0xhkg8riz"))))
|
||||
(base32 "1fhnnm58ndfd6hzdagrsgcdcm2qlcjlda13vyx5d9lclhxgdn0vf"))))
|
||||
(build-system meson-build-system)
|
||||
(native-inputs
|
||||
(list pkg-config
|
||||
|
||||
@@ -2475,9 +2475,6 @@ similar to MATLAB, GNU Octave or SciPy.")
|
||||
;; "--enable-doxygen"
|
||||
"--enable-dot"
|
||||
"--enable-netcdf-4"
|
||||
#$@(if (or (target-x86-32?) (target-arm32?))
|
||||
'("CFLAGS=-Wno-error=incompatible-pointer-types")
|
||||
'())
|
||||
(string-append "--with-plugin-dir=" #$output "/lib/hdf5-plugins"))
|
||||
#:phases
|
||||
#~(modify-phases %standard-phases
|
||||
@@ -2489,15 +2486,7 @@ similar to MATLAB, GNU Octave or SciPy.")
|
||||
(("testurl.sh") ""))
|
||||
(substitute* "nczarr_test/Makefile.in"
|
||||
(("/bin/bash")
|
||||
(search-input-file inputs "bin/bash")))
|
||||
;; This test fails on 32 bit platforms.
|
||||
#$@(if (or (target-x86-32?) (target-arm32?))
|
||||
'((substitute* '("ncdump/tst_netcdf4_4.sh"
|
||||
"ncdump/tst_nccopy4.sh")
|
||||
(("#!/bin/sh" m) (string-append m "\nexit 0\n")))
|
||||
(substitute* "ncdump/Makefile.in"
|
||||
(("tst_netcdf4_4.log") "")))
|
||||
'())))
|
||||
(search-input-file inputs "bin/bash")))))
|
||||
(add-before 'configure 'fix-source-date
|
||||
(lambda _
|
||||
;; As we ${SOURCE_DATE_EPOCH} evaluates to "1" in the build
|
||||
@@ -9658,7 +9647,7 @@ researchers and developers alike to get started on SAT.")
|
||||
(define-public kissat
|
||||
(package
|
||||
(name "kissat")
|
||||
(version "4.0.4")
|
||||
(version "4.0.1")
|
||||
(source
|
||||
(origin
|
||||
(method git-fetch)
|
||||
@@ -9668,7 +9657,7 @@ researchers and developers alike to get started on SAT.")
|
||||
(file-name (git-file-name name version))
|
||||
(sha256
|
||||
(base32
|
||||
"1snimig4cp97p570nin2i38my72zvwypldyhr125i1z6cd9pa046"))))
|
||||
"0acg61cfcjg13if2i375cyl4xvwmabhfhi9z8pnw971046am6bzv"))))
|
||||
(build-system gnu-build-system)
|
||||
(inputs (list xz gzip lzip bzip2 p7zip))
|
||||
(arguments
|
||||
@@ -9679,10 +9668,6 @@ researchers and developers alike to get started on SAT.")
|
||||
#~(modify-phases %standard-phases
|
||||
(add-after 'unpack 'patch-source
|
||||
(lambda* (#:key inputs #:allow-other-keys)
|
||||
(substitute* "test/testfile.c"
|
||||
;; Don't check if /etc/passwd isn't writable.
|
||||
;; When building in a container/chroot, this fails spuriously.
|
||||
((".*/etc/passwd.*") ""))
|
||||
(substitute* "scripts/generate-build-header.sh"
|
||||
;; by default BUILD includes the build date which
|
||||
;; makes the build not reproducible.
|
||||
@@ -11469,7 +11454,7 @@ expression parsing and evaluation.")
|
||||
(define-public highs
|
||||
(package
|
||||
(name "highs")
|
||||
(version "1.14.0")
|
||||
(version "1.10.0")
|
||||
(source
|
||||
(origin
|
||||
(method git-fetch)
|
||||
@@ -11478,14 +11463,14 @@ expression parsing and evaluation.")
|
||||
(commit (string-append "v" version))))
|
||||
(file-name (git-file-name name version))
|
||||
(sha256
|
||||
(base32 "16y664rzvxd8785195k0srz0842zvl0zdkf6qi103p503pj81afh"))))
|
||||
(base32 "19q99nkk6r6k91gxp8a5rjil1399qyfgfc6jqlg2gd82vpcw8c8b"))))
|
||||
(build-system cmake-build-system)
|
||||
(home-page "https://highs.dev")
|
||||
(synopsis "High performance software for linear optimization")
|
||||
(description
|
||||
"HiGHS provides serial and parallel solvers for large-scale sparse
|
||||
linear programming (LP), mixed-integer programming (MIP), and quadratic
|
||||
programming (QP) models.")
|
||||
programming (QP) models")
|
||||
(license license:expat)))
|
||||
|
||||
(define-public trilinos-zoltan
|
||||
|
||||
@@ -1151,7 +1151,7 @@ simultaneously and therefore appear under the same nickname on IRC.")
|
||||
(define-public python-nbxmpp
|
||||
(package
|
||||
(name "python-nbxmpp")
|
||||
(version "7.2.0")
|
||||
(version "7.1.0")
|
||||
(source
|
||||
(origin
|
||||
(method git-fetch)
|
||||
@@ -1160,7 +1160,7 @@ simultaneously and therefore appear under the same nickname on IRC.")
|
||||
(commit version)))
|
||||
(file-name (git-file-name name version))
|
||||
(sha256
|
||||
(base32 "1dyf4jh76ffbl45x4cpk6rsn1r4wck54b3d8wfd2swxaqq4p7lis"))))
|
||||
(base32 "1n7b6yv2k89hsmhmx9pi7m8l3aq97xppaz3hm7mvqgvxnlw0c1kr"))))
|
||||
(build-system pyproject-build-system)
|
||||
(arguments (list #:test-backend #~'unittest))
|
||||
(propagated-inputs
|
||||
@@ -1184,7 +1184,7 @@ of xmpppy.")
|
||||
(define-public gajim
|
||||
(package
|
||||
(name "gajim")
|
||||
(version "2.4.6")
|
||||
(version "2.4.5")
|
||||
(source
|
||||
(origin
|
||||
(method url-fetch)
|
||||
@@ -1192,7 +1192,7 @@ of xmpppy.")
|
||||
(version-major+minor version)
|
||||
"/gajim-" version ".tar.gz"))
|
||||
(sha256
|
||||
(base32 "0ilpgkzw45scjlnag94p8v6np629v7w0ihci5a2w5d742gpqvq6c"))
|
||||
(base32 "1rkxzf1pfd29rip5bw4730fl7b2xk12zpiwnfkyzxlkmbh4j3kp2"))
|
||||
(patches
|
||||
(search-patches "gajim-honour-GAJIM_PLUGIN_PATH.patch"))))
|
||||
(build-system pyproject-build-system)
|
||||
@@ -1278,6 +1278,7 @@ of xmpppy.")
|
||||
glib
|
||||
glib-networking
|
||||
gsettings-desktop-schemas
|
||||
gsound
|
||||
libspelling
|
||||
libadwaita
|
||||
gstreamer
|
||||
@@ -1292,7 +1293,6 @@ of xmpppy.")
|
||||
libsoup
|
||||
libxscrnsaver
|
||||
network-manager
|
||||
python-cryptography
|
||||
python-css-parser
|
||||
python-dbus-1.2
|
||||
python-emoji
|
||||
@@ -2839,7 +2839,7 @@ implementation of an MQTT version client class.")
|
||||
(define-public psi-plus
|
||||
(package
|
||||
(name "psi-plus")
|
||||
(version "1.5.2115")
|
||||
(version "1.5.1484")
|
||||
(source
|
||||
(origin
|
||||
(method git-fetch)
|
||||
@@ -2853,7 +2853,7 @@ implementation of an MQTT version client class.")
|
||||
`(begin
|
||||
(delete-file-recursively "3rdparty")))
|
||||
(sha256
|
||||
(base32 "14za9rh7nszv5px5a2w43ysi9977zws8a5mxsh7wc8ksr693faz2"))))
|
||||
(base32 "1jsm39nzzbqkp3zc0xqx7jid6p4q1ra28xad38wjr2l1jb8qjn24"))))
|
||||
(build-system qt-build-system)
|
||||
(arguments
|
||||
`(#:tests? #f ; No target
|
||||
@@ -2910,13 +2910,19 @@ implementation of an MQTT version client class.")
|
||||
"qite/qiteaudio.h")
|
||||
(("qiteaudiorecorder.h")
|
||||
"qite/qiteaudiorecorder.h"))))
|
||||
(add-after 'install 'wrap-executable
|
||||
(add-after 'install 'wrap-env
|
||||
(lambda* (#:key outputs #:allow-other-keys)
|
||||
(let ((out (assoc-ref outputs "out")))
|
||||
(wrap-program (string-append out "/bin/psi-plus")
|
||||
`("GST_PLUGIN_SYSTEM_PATH" ":" prefix (,(getenv "GST_PLUGIN_SYSTEM_PATH")))
|
||||
`("GI_TYPELIB_PATH" ":" prefix (,(getenv "GI_TYPELIB_PATH")))))))
|
||||
(add-after 'wrap-executable 'glib-or-gtk-compile-schemas
|
||||
(for-each
|
||||
(lambda (name)
|
||||
(let ((file (string-append out "/bin/" name))
|
||||
(gst-plugin-path (getenv "GST_PLUGIN_SYSTEM_PATH"))
|
||||
(gi-typelib-path (getenv "GI_TYPELIB_PATH")))
|
||||
(wrap-program file
|
||||
`("GST_PLUGIN_SYSTEM_PATH" ":" prefix (,gst-plugin-path))
|
||||
`("GI_TYPELIB_PATH" ":" prefix (,gi-typelib-path)))))
|
||||
'("psi-plus")))))
|
||||
(add-after 'wrap-env 'glib-or-gtk-compile-schemas
|
||||
(assoc-ref glib-or-gtk:%standard-phases 'glib-or-gtk-compile-schemas))
|
||||
(add-after 'glib-or-gtk-compile-schemas 'glib-or-gtk-wrap
|
||||
(assoc-ref glib-or-gtk:%standard-phases 'glib-or-gtk-wrap)))))
|
||||
@@ -2939,7 +2945,6 @@ implementation of an MQTT version client class.")
|
||||
libgcrypt
|
||||
libgpg-error
|
||||
libidn
|
||||
libomemo-c
|
||||
libotr
|
||||
libsignal-protocol-c
|
||||
tidy-html
|
||||
@@ -2959,11 +2964,11 @@ implementation of an MQTT version client class.")
|
||||
libxcb
|
||||
libxscrnsaver
|
||||
zlib))
|
||||
(home-page "https://psi-im.com/")
|
||||
(home-page "https://psi-plus.com/")
|
||||
(synopsis "Qt-based XMPP Client")
|
||||
(description
|
||||
"Psi+ is a powerful XMPP client designed for experienced users.
|
||||
It's a spin-off of the Psi XMPP client.")
|
||||
"Psi+ is a spin-off of Psi XMPP client. It is a powerful XMPP client
|
||||
designed for experienced users.")
|
||||
(license license:gpl2+)))
|
||||
|
||||
(define-deprecated-package psi
|
||||
|
||||
@@ -1,16 +1,11 @@
|
||||
;;; GNU Guix --- Functional package management for GNU
|
||||
;;; Copyright © 2013 Andreas Enge <andreas@enge.fr>
|
||||
;;; Copyright © 2015 Siniša Biđin <sinisa@bidin.eu>
|
||||
;;; Copyright © 2016 Efraim Flashner <efraim@flashner.co.il>
|
||||
;;; Copyright © 2016, 2021, 2021 Ludovic Courtès <ludo@gnu.org>
|
||||
;;; Copyright © 2016, 2021 Stefan Reichör <stefan@xsteve.at>
|
||||
;;; Copyright © 2017, 2018, 2019, 2020 Ricardo Wurmus <rekado@elephly.net>
|
||||
;;; Copyright © 2018 Sou Bunnbu <iyzsong@member.fsf.org>
|
||||
;;; Copyright © 2017, 2018, 2019, 2020 Ricardo Wurmus <rekado@elephly.net>
|
||||
;;; Copyright © 2018-2021 Tobias Geerinckx-Rice <me@tobias.gr>
|
||||
;;; Copyright © 2018 Gábor Boskovits <boskovits@gmail.com>
|
||||
;;; Copyright © 2018, 2019, 2020 Oleg Pykhalov <go.wigust@gmail.com>
|
||||
;;; Copyright © 2019 Pierre Neidhardt <mail@ambrevar.xyz>
|
||||
;;; Copyright © 2019, 2023 Vasile Dumitrascu <va511e@yahoo.com>
|
||||
;;; Copyright © 2020 Alex ter Weele <alex.ter.weele@gmail.com>
|
||||
;;; Copyright © 2020 Lars-Dominik Braun <ldb@leibniz-psychology.org>
|
||||
;;; Copyright © 2021, 2022 Marius Bakke <marius@gnu.org>
|
||||
@@ -24,6 +19,9 @@
|
||||
;;; Copyright © 2025 Nicolas Graves <ngraves@ngraves.fr>
|
||||
;;; Copyright © 2025 Giacomo Leidi <therewasa@fishinthecalculator.me>
|
||||
;;; Copyright © 2025 Christian Birk Sørensen <chrbirks@gmail.com>
|
||||
;;; Copyright © 2015 Siniša Biđin <sinisa@bidin.eu>
|
||||
;;; Copyright © 2019 Pierre Neidhardt <mail@ambrevar.xyz>
|
||||
;;; Copyright © 2019, 2023 Vasile Dumitrascu <va511e@yahoo.com>
|
||||
;;;
|
||||
;;; This file is part of GNU Guix.
|
||||
;;;
|
||||
@@ -72,7 +70,6 @@
|
||||
#:use-module (gnu packages golang-check)
|
||||
#:use-module (gnu packages golang-web)
|
||||
#:use-module (gnu packages golang-xyz)
|
||||
#:use-module (gnu packages gtk)
|
||||
#:use-module (gnu packages image)
|
||||
#:use-module (gnu packages lua)
|
||||
#:use-module (gnu packages mail)
|
||||
@@ -414,37 +411,6 @@ system statistics (CPU, disk, and memory usage, etc.) and more on the
|
||||
desktop.")
|
||||
(license license:gpl3+)))
|
||||
|
||||
(define-public gkrellm
|
||||
(package
|
||||
(name "gkrellm")
|
||||
(version "2.5.1")
|
||||
(source
|
||||
(origin
|
||||
(method url-fetch)
|
||||
(uri (string-append "https://gkrellm.srcbox.net/releases/gkrellm-"
|
||||
version ".tar.bz2"))
|
||||
(sha256
|
||||
(base32 "0qvy2xmwmfy5f0g09yn9lr262shnx82ba04r5il2wj4qscg3r7h8"))))
|
||||
(build-system gnu-build-system)
|
||||
(inputs (list gtk+-2 libsm))
|
||||
(native-inputs (list gettext-minimal pkg-config))
|
||||
(arguments
|
||||
(list
|
||||
#:tests? #f ;there is no check target
|
||||
#:phases
|
||||
#~(modify-phases %standard-phases
|
||||
(delete 'configure)) ;no configure script
|
||||
#:make-flags
|
||||
#~(list (string-append "INSTALLROOT=" #$output)
|
||||
(string-append "CC=" #$(cc-for-target)))))
|
||||
(home-page "https://gkrellm.srcbox.net/")
|
||||
(synopsis "System monitors")
|
||||
(description
|
||||
"GKrellM is a single process stack of system monitors which supports
|
||||
applying themes to match its appearance to your window manager, Gtk, or any
|
||||
other theme.")
|
||||
(license license:gpl3+)))
|
||||
|
||||
(define-public glances
|
||||
(package
|
||||
(name "glances")
|
||||
|
||||
@@ -76,7 +76,95 @@
|
||||
#:use-module (srfi srfi-1)
|
||||
#:use-module (ice-9 match))
|
||||
|
||||
(define-public hwloc
|
||||
(define-public hwloc-1
|
||||
(package
|
||||
(name "hwloc")
|
||||
(version "1.11.13")
|
||||
(source (origin
|
||||
(method url-fetch)
|
||||
(uri (string-append "https://www.open-mpi.org/software/hwloc/v"
|
||||
(version-major+minor version)
|
||||
"/downloads/hwloc-" version ".tar.bz2"))
|
||||
(sha256
|
||||
(base32
|
||||
"1j69p8a1pjpbpwn4w7l4dfxmaxxqikchjzqw1ncw05zmcmvlnjd4"))
|
||||
(patches (search-patches "hwloc-1-test-btrfs.patch"))))
|
||||
|
||||
(properties
|
||||
;; Tell the 'generic-html' updater to monitor this URL for updates.
|
||||
`((release-monitoring-url
|
||||
. "https://www-lb.open-mpi.org/software/hwloc/current")))
|
||||
|
||||
(build-system gnu-build-system)
|
||||
(outputs '("out" ;'lstopo' & co., depends on Cairo, libx11, etc.
|
||||
"lib" ;small closure
|
||||
"doc" ;400+ section 3 man pages
|
||||
"debug"))
|
||||
(inputs
|
||||
(append (if (%current-target-system)
|
||||
'() ;fewer dependencies when cross-compiling
|
||||
(list libx11 cairo ncurses expat))
|
||||
(if (target-arm32?) '() (list numactl))))
|
||||
(propagated-inputs
|
||||
;; hwloc.pc lists it in 'Requires.private'.
|
||||
(list libpciaccess))
|
||||
(native-inputs
|
||||
(list pkg-config))
|
||||
(arguments
|
||||
(list #:configure-flags
|
||||
#~(list "--localstatedir=/var")
|
||||
#:phases
|
||||
#~(modify-phases %standard-phases
|
||||
(add-before 'check 'skip-linux-libnuma-test
|
||||
(lambda _
|
||||
;; Arrange to skip 'tests/linux-libnuma', which fails on some
|
||||
;; machines: <https://github.com/open-mpi/hwloc/issues/213>.
|
||||
(substitute* "tests/linux-libnuma.c"
|
||||
(("numa_available\\(\\)")
|
||||
"-1"))))
|
||||
(add-after 'install 'refine-libnuma
|
||||
;; Give -L arguments for libraries to avoid propagation
|
||||
(lambda* (#:key inputs outputs #:allow-other-keys)
|
||||
(let ((out (assoc-ref outputs "lib"))
|
||||
(numa (assoc-ref inputs "numactl")))
|
||||
(substitute* (map (lambda (f) (string-append out "/" f))
|
||||
'("lib/pkgconfig/hwloc.pc" "lib/libhwloc.la"))
|
||||
(("-lnuma" lib)
|
||||
(string-append "-L" numa "/lib " lib))))))
|
||||
(add-after 'install 'avoid-circular-references
|
||||
(lambda* (#:key outputs #:allow-other-keys)
|
||||
(let ((lib (assoc-ref outputs "lib")))
|
||||
;; Suppress the 'prefix=' and 'exec_prefix=' lines so that the
|
||||
;; "lib" output doesn't refer to "out".
|
||||
(substitute* (string-append lib "/lib/pkgconfig/hwloc.pc")
|
||||
(("^.*prefix=.*$")
|
||||
"")))))
|
||||
(add-after 'install 'move-man3-pages
|
||||
(lambda* (#:key outputs #:allow-other-keys)
|
||||
;; Move section 3 man pages to the "doc" output.
|
||||
(let ((out (assoc-ref outputs "out"))
|
||||
(doc (assoc-ref outputs "doc")))
|
||||
(copy-recursively (string-append out "/share/man/man3")
|
||||
(string-append doc "/share/man/man3"))
|
||||
(delete-file-recursively
|
||||
(string-append out "/share/man/man3"))))))))
|
||||
(home-page "https://www.open-mpi.org/projects/hwloc/")
|
||||
(synopsis "Abstraction of hardware architectures")
|
||||
(description
|
||||
"hwloc provides a portable abstraction (across OS,
|
||||
versions, architectures, ...) of the hierarchical topology of modern
|
||||
architectures, including NUMA memory nodes, sockets, shared caches, cores and
|
||||
simultaneous multithreading. It also gathers various attributes such as cache
|
||||
and memory information. It primarily aims at helping high-performance
|
||||
computing applications with gathering information about the hardware so as to
|
||||
exploit it accordingly and efficiently.
|
||||
|
||||
hwloc may display the topology in multiple convenient formats. It also offers
|
||||
a powerful programming interface to gather information about the hardware,
|
||||
bind processes, and much more.")
|
||||
(license license:bsd-3)))
|
||||
|
||||
(define-public hwloc-2
|
||||
(package
|
||||
(name "hwloc")
|
||||
(version "2.13.0")
|
||||
@@ -186,6 +274,10 @@ a powerful programming interface to gather information about the hardware,
|
||||
bind processes, and much more.")
|
||||
(license license:bsd-3)))
|
||||
|
||||
(define-public hwloc
|
||||
;; The latest stable series of hwloc.
|
||||
hwloc-2)
|
||||
|
||||
(define-public openmpi-4
|
||||
(package
|
||||
(name "openmpi")
|
||||
@@ -214,7 +306,7 @@ bind processes, and much more.")
|
||||
(package-supported-systems package)))
|
||||
(list package)
|
||||
'()))))
|
||||
(append (list `(,hwloc "lib")
|
||||
(append (list `(,hwloc-2 "lib")
|
||||
gfortran
|
||||
libfabric-1 ;fails to build with 2.3
|
||||
libevent
|
||||
@@ -607,7 +699,7 @@ arrays) that expose a buffer interface.")
|
||||
(build-system gnu-build-system)
|
||||
(inputs
|
||||
`(,zlib
|
||||
(,hwloc "lib")
|
||||
(,hwloc-2 "lib")
|
||||
,slurm
|
||||
,@(if (and (not (%current-target-system))
|
||||
(member (%current-system) (package-supported-systems ucx)))
|
||||
|
||||
@@ -7465,6 +7465,31 @@ standalone JACK application.")
|
||||
;; Expat or CC0
|
||||
(license (list license:expat license:cc0))))
|
||||
|
||||
(define-public regrader
|
||||
(package
|
||||
(inherit vl1-emulator)
|
||||
(name "regrader")
|
||||
(version "1.0.0")
|
||||
(source
|
||||
(origin
|
||||
(method git-fetch)
|
||||
(uri (git-reference
|
||||
(url "https://github.com/linuxmao-org/regrader")
|
||||
(commit (string-append "v" version))
|
||||
;; bundles a specific commit of the DISTRHO plugin framework
|
||||
(recursive? #t)))
|
||||
(file-name (git-file-name name version))
|
||||
(sha256
|
||||
(base32
|
||||
"0gl4d5lf2afqknz22jz7hh7029sc9v1xrz6nbz9dlv42bwc0cvl0"))))
|
||||
(home-page "https://github.com/linuxmao-org/regrader")
|
||||
(synopsis "Delay effect plugin")
|
||||
(description
|
||||
"Regrader is a delay effect where the repeats degrade in resolution.
|
||||
This is an unofficial port of the Regrader plugin created by Igorski. It
|
||||
is available as an LV2 plugin and a standalone JACK application.")
|
||||
(license license:expat)))
|
||||
|
||||
(define-public fogpad
|
||||
(package
|
||||
(inherit vl1-emulator)
|
||||
|
||||
@@ -2139,6 +2139,62 @@ replies, fping will send out a ping packet and move on to the next target in a
|
||||
round-robin fashion.")
|
||||
(license license:expat)))
|
||||
|
||||
(define-public gandi-cli
|
||||
(package
|
||||
(name "gandi-cli")
|
||||
(version "1.6")
|
||||
(source
|
||||
(origin
|
||||
(method url-fetch)
|
||||
(uri (pypi-uri name version))
|
||||
(sha256
|
||||
(base32 "1h36jahbp7273wn3yd747kbiwjc0bm3sja67bcxdsd54ln0vyndg"))))
|
||||
(build-system pyproject-build-system)
|
||||
(arguments
|
||||
(list
|
||||
#:test-flags
|
||||
#~(list "--pyargs" "gandi.cli")
|
||||
#:phases
|
||||
#~(modify-phases %standard-phases
|
||||
(add-after 'unpack 'embed-store-file-names
|
||||
(lambda _
|
||||
(substitute* (list "gandi/cli/modules/cert.py"
|
||||
"gandi/cli/tests/commands/test_certificate.py")
|
||||
(("openssl") (which "openssl")))))
|
||||
(add-after 'install 'install-documentation
|
||||
;; The included man page may be outdated but we install it anyway,
|
||||
;; since it's mentioned in 'gandi --help' and better than nothing.
|
||||
(lambda _
|
||||
(let* ((man1 (string-append #$output "/share/man/man1")))
|
||||
(mkdir-p man1)
|
||||
(with-output-to-file (string-append man1 "/gandi.1")
|
||||
(lambda _
|
||||
(invoke "rst2man.py" "gandicli.man.rst")))))))))
|
||||
(native-inputs
|
||||
(list python-docutils-0.19
|
||||
python-pytest
|
||||
python-pytest-cov
|
||||
python-setuptools
|
||||
python-wheel))
|
||||
(inputs
|
||||
(list openssl
|
||||
python-click-7
|
||||
python-ipy
|
||||
python-pyyaml
|
||||
python-requests))
|
||||
(propagated-inputs
|
||||
(list openssh))
|
||||
(home-page "https://cli.gandi.net")
|
||||
(synopsis "Command-line interface to the Gandi.net Web API")
|
||||
(description
|
||||
"This package provides a command-line client (@command{gandi}) to buy,
|
||||
manage, and delete Internet resources from Gandi.net such as domain names,
|
||||
virtual machines, and certificates.")
|
||||
(license license:gpl3+)))
|
||||
|
||||
(define-deprecated-package gandi.cli
|
||||
gandi-cli)
|
||||
|
||||
(define-public go-sctp
|
||||
;; docker-libnetwork-cmd-proxy requires this exact commit.
|
||||
;; This commit is mentioned in docker-libnetwork-cmd-proxy's vendor.conf.
|
||||
|
||||
@@ -966,7 +966,7 @@ fi"
|
||||
icu4c-76
|
||||
libuv-for-node-lts
|
||||
`(,nghttp2 "lib")
|
||||
openssl-3.0
|
||||
openssl
|
||||
zlib
|
||||
; ngtcp2? nghttp3?
|
||||
;; Regular build-time dependencies.
|
||||
@@ -986,7 +986,7 @@ fi"
|
||||
ngtcp2
|
||||
nghttp3
|
||||
`(,nghttp2 "lib")
|
||||
openssl-3.0
|
||||
openssl
|
||||
zlib))
|
||||
(supported-systems
|
||||
(cons "riscv64-linux" (package-supported-systems node-bootstrap)))
|
||||
|
||||
@@ -286,7 +286,7 @@ This package tracks the Extended Support Release (ESR) channel.")
|
||||
(package
|
||||
(inherit nss)
|
||||
(name "nss-rapid")
|
||||
(version "3.123")
|
||||
(version "3.121")
|
||||
(source
|
||||
(origin
|
||||
(inherit (package-source nss))
|
||||
@@ -297,7 +297,7 @@ This package tracks the Extended Support Release (ESR) channel.")
|
||||
"releases/NSS_" version-with-underscores "_RTM/src/"
|
||||
"nss-" version ".tar.gz")))
|
||||
(sha256
|
||||
(base32 "0jafdl18q9j36bwk73i462qkc24070b5llchffd7fsd2k0ri2i91"))
|
||||
(base32 "0bk3lxmj364vlf4x2q01pf0li3mm5ixgnfnxirxqp9xyh63qyfnb"))
|
||||
(patches
|
||||
(search-patches "nss-3.56-pkgconfig.patch"
|
||||
"nss-getcwd-nonnull.patch"
|
||||
|
||||
@@ -173,7 +173,7 @@ time-stamping or reference clock, sub-microsecond accuracy is possible.")
|
||||
(native-inputs (list which pkg-config))
|
||||
(inputs (cons* guile-3.0 ; for wrap-script
|
||||
libevent
|
||||
openssl-3.0
|
||||
openssl
|
||||
perl
|
||||
perl-http-tiny
|
||||
perl-io-socket-ssl
|
||||
|
||||
@@ -81,3 +81,72 @@
|
||||
(description "This tool extracts cooking recipe from HTML structured data
|
||||
in the @url{https://schema.org/Recipe} format.")
|
||||
(license asl2.0)))
|
||||
|
||||
(define-public gourmet
|
||||
;; Use the latest commit to gain Python 3 support.
|
||||
(let ((revision "0")
|
||||
(commit "8af29c8ded24528030e5ae2ea3461f61c1e5a575"))
|
||||
(package
|
||||
(name "gourmet")
|
||||
(version (git-version "0.17.4" revision commit))
|
||||
(source
|
||||
(origin
|
||||
(method git-fetch)
|
||||
(uri (git-reference
|
||||
(url "https://github.com/thinkle/gourmet")
|
||||
(commit commit)))
|
||||
(file-name (git-file-name name version))
|
||||
(sha256
|
||||
(base32
|
||||
"08fbw6zp32ws6w9czwy2sqc9c9izlkglsskshj2114d0l79z4gj8"))
|
||||
(patches (search-patches "gourmet-sqlalchemy-compat.patch"))))
|
||||
(build-system pyproject-build-system)
|
||||
(arguments
|
||||
(list
|
||||
#:test-flags
|
||||
;; XXX: Some tests in deeper directories or otherwise discovered by
|
||||
;; Pytest are broken.
|
||||
#~(list "--ignore-glob=gourmet/tests/**/*.py")
|
||||
#:phases
|
||||
#~(modify-phases %standard-phases
|
||||
(add-before 'build 'set-environemnt
|
||||
(lambda _
|
||||
(setenv "HOME" "/tmp")
|
||||
(system "Xvfb &")
|
||||
(setenv "DISPLAY" ":0")))
|
||||
(add-after 'install 'install-dekstop-file-and-icons
|
||||
(lambda _
|
||||
(define share (string-append #$output "/share"))
|
||||
(install-file ".flatpak/io.github.thinkle.Gourmet.desktop"
|
||||
(string-append share "/applications"))
|
||||
(install-file ".flatpak/io.github.thinkle.Gourmet.svg"
|
||||
(string-append share "/icons/Gourmet")))))))
|
||||
(native-inputs
|
||||
(list python-dogtail
|
||||
python-pytest
|
||||
python-selenium
|
||||
python-setuptools
|
||||
xorg-server-for-tests))
|
||||
(inputs
|
||||
(list gtk+
|
||||
python-argcomplete
|
||||
python-beautifulsoup4
|
||||
python-gst
|
||||
python-keyring
|
||||
python-lxml
|
||||
python-pillow
|
||||
python-pycairo
|
||||
python-pyenchant
|
||||
python-pygobject
|
||||
python-requests
|
||||
python-scrape-schema-recipe
|
||||
python-sqlalchemy
|
||||
python-toml))
|
||||
(home-page "https://thinkle.github.io/gourmet/")
|
||||
(synopsis "Recipe organizer")
|
||||
(description
|
||||
"Gourmet Recipe Manager is a recipe organizer that allows you to collect,
|
||||
search, organize, and browse your recipes. Gourmet can also generate shopping
|
||||
lists and calculate nutritional information. It imports Mealmaster,
|
||||
MasterCook and KRecipe files and exports PDFs, webpages, and other formats.")
|
||||
(license gpl2+))))
|
||||
|
||||
@@ -91,7 +91,6 @@
|
||||
#:use-module (gnu packages tls)
|
||||
#:use-module (gnu packages unicode)
|
||||
#:use-module (gnu packages version-control)
|
||||
#:use-module (gnu packages vim)
|
||||
#:use-module (gnu packages virtualization)
|
||||
#:use-module (gnu packages web)
|
||||
#:use-module (gnu packages web-browsers)
|
||||
@@ -798,29 +797,30 @@ describing upgrade scenarios in package-based software distributions.")
|
||||
(define-public ocaml-mccs
|
||||
(package
|
||||
(name "ocaml-mccs")
|
||||
(version "1.1+19")
|
||||
(source
|
||||
(origin
|
||||
(method git-fetch)
|
||||
(uri (git-reference
|
||||
(url "https://github.com/AltGr/ocaml-mccs")
|
||||
(commit version)))
|
||||
(file-name (git-file-name name version))
|
||||
(sha256
|
||||
(base32 "1x1y5rhj4f0xakbgfn9f90a9xy09v99p8mc42pbnam5kghyjmxy6"))))
|
||||
(version "1.1+14")
|
||||
(source (origin
|
||||
(method git-fetch)
|
||||
(uri (git-reference
|
||||
(url "https://github.com/AltGr/ocaml-mccs")
|
||||
(commit version)))
|
||||
(file-name (git-file-name name version))
|
||||
(sha256
|
||||
(base32
|
||||
"17bvm0jhhs8h3p5sbb65asj53a8sxl634cc0kvcivpams74837zq"))))
|
||||
(build-system dune-build-system)
|
||||
(propagated-inputs (list ocaml-cudf))
|
||||
(home-page "https://www.i3s.unice.fr/~cpjm/misc/")
|
||||
(synopsis "Upgrade path problem solver")
|
||||
(description
|
||||
"Mccs (Multi Criteria CUDF Solver) is a CUDF problem solver.
|
||||
(description "Mccs (Multi Criteria CUDF Solver) is a CUDF problem solver.
|
||||
Mccs take as input a CUDF problem and computes the best solution according to
|
||||
a set of criteria. It relies on a Integer Programming solver or a
|
||||
Pseudo Boolean solver to achieve its task. Mccs can use a wide set of
|
||||
underlying solvers like Cplex, Gurobi, Lpsolver, Glpk, CbC, SCIP or WBO.")
|
||||
(license (list license:bsd-3 license:gpl3+
|
||||
;; With static-linking exception
|
||||
license:lgpl2.1+))))
|
||||
(license (list
|
||||
license:bsd-3
|
||||
license:gpl3+
|
||||
;; With static-linking exception
|
||||
license:lgpl2.1+))))
|
||||
|
||||
(define-public ocaml-dose3
|
||||
(package
|
||||
@@ -945,156 +945,47 @@ the opam file format.")
|
||||
;; With static-linking exception
|
||||
(license license:lgpl2.1+)))
|
||||
|
||||
(define-public ocaml-swhid-core
|
||||
(package
|
||||
(name "ocaml-swhid-core")
|
||||
(version "0.1")
|
||||
(source
|
||||
(origin
|
||||
(method git-fetch)
|
||||
(uri (git-reference
|
||||
(url "https://github.com/OCamlPro/swhid_core")
|
||||
(commit version)))
|
||||
(file-name (git-file-name name version))
|
||||
(sha256
|
||||
(base32 "0h3zndyk94lf2lakc3cb8b7a00jqh0y1m8xk6mg61gj2kdpdbfdq"))))
|
||||
(build-system dune-build-system)
|
||||
(properties `((upstream-name . "swhid_core")))
|
||||
(home-page "https://github.com/ocamlpro/swhid_core")
|
||||
(synopsis "OCaml library to work with swhids")
|
||||
(description
|
||||
"swhid_core is an OCaml library to work with Software Heritage persistent
|
||||
identifiers (swhids). This is the core library, for most use cases you should
|
||||
use the swhid library instead.")
|
||||
(license license:isc)))
|
||||
|
||||
(define-public ocaml-spdx-licenses
|
||||
(package
|
||||
(name "ocaml-spdx-licenses")
|
||||
(version "1.3.0")
|
||||
(source
|
||||
(origin
|
||||
(method git-fetch)
|
||||
(uri (git-reference
|
||||
(url "https://github.com/kit-ty-kate/spdx_licenses")
|
||||
(commit (string-append "v" version))))
|
||||
(file-name (git-file-name name version))
|
||||
(sha256
|
||||
(base32 "08vh9mfkq34f0l5ka94hhklc43kvz09wd04x1gkxkawn4786rf9z"))))
|
||||
(build-system dune-build-system)
|
||||
(native-inputs (list ocaml-alcotest))
|
||||
(properties `((upstream-name . "spdx_licenses")))
|
||||
(home-page "https://github.com/kit-ty-kate/spdx_licenses")
|
||||
(synopsis "Strict SPDX License Expression parser")
|
||||
(description
|
||||
"This package provides an up-to-date and strict SPDX License Expression
|
||||
parser. It implements the format described in:
|
||||
https://spdx.github.io/spdx-spec/v2.3/SPDX-license-expressions/
|
||||
See https://spdx.org/licenses/ for more details.")
|
||||
(license license:expat)))
|
||||
|
||||
(define-public ocaml-0install-solver
|
||||
(package
|
||||
(name "ocaml-0install-solver")
|
||||
(version "2.18")
|
||||
(source
|
||||
(origin
|
||||
(method git-fetch)
|
||||
(uri (git-reference
|
||||
(url "https://github.com/0install/0install")
|
||||
(commit (string-append "v" version))))
|
||||
(file-name (git-file-name name version))
|
||||
(sha256
|
||||
(base32 "1hm72k355qwgh16hngmnd77bgawf20ipnqxfncdzl10rqrc0640b"))))
|
||||
(build-system dune-build-system)
|
||||
(arguments
|
||||
`(#:package "0install-solver"))
|
||||
(native-inputs (list ocaml-ounit2))
|
||||
(home-page "https://docs.0install.net/developers/solver/")
|
||||
(synopsis "Package dependency solver")
|
||||
(description
|
||||
"This package provides a package dependency resolver based on a SAT solver.
|
||||
This was originally written for the 0install package manager, but is now
|
||||
generic and is also used as a solver backend for opam. The SAT solver is
|
||||
based on @code{MiniSat} (http://minisat.se/Papers.html) and the application to
|
||||
package management is based on OPIUM (Optimal Package Install/Uninstall
|
||||
Manager). 0install-solver uses a (novel?) strategy to find the optimal
|
||||
solution extremely quickly (even for a SAT-based solver).")
|
||||
(license license:lgpl2.1+)))
|
||||
|
||||
(define-public ocaml-opam-0install-cudf
|
||||
(package
|
||||
(name "ocaml-opam-0install-cudf")
|
||||
(version "0.5.0")
|
||||
(source
|
||||
(origin
|
||||
(method git-fetch)
|
||||
(uri (git-reference
|
||||
(url "https://github.com/ocaml-opam/opam-0install-cudf")
|
||||
(commit (string-append "v" version))))
|
||||
(file-name (git-file-name name version))
|
||||
(sha256
|
||||
(base32 "12v1bgnxcxdylgxbsjlcr90rzwcp39rjlv191cy8g2s33nyxyi2c"))))
|
||||
(build-system dune-build-system)
|
||||
(propagated-inputs (list ocaml-cudf ocaml-0install-solver))
|
||||
(native-inputs (list ocaml-alcotest))
|
||||
(home-page "https://opam.ocaml.org")
|
||||
(synopsis "Opam solver using 0install backend using the CUDF interface")
|
||||
(description
|
||||
"Opam's default solver is designed to maintain a set of packages over time,
|
||||
minimising disruption when installing new programs and finding a compromise
|
||||
solution across all packages. In many situations (e.g. CI, local roots or
|
||||
duniverse builds) this is not necessary, and we can get a solution much faster
|
||||
by using a different algorithm. This package provides a generic solver library
|
||||
which uses 0install's solver library. The library uses the CUDF library in
|
||||
order to interface with opam as it is the format common used to talk to all the
|
||||
supported solvers.")
|
||||
(license license:isc)))
|
||||
|
||||
(define ocaml-opam-core
|
||||
(package
|
||||
(name "ocaml-opam-core")
|
||||
(version "2.5.1")
|
||||
(source
|
||||
(origin
|
||||
(method git-fetch)
|
||||
(uri (git-reference
|
||||
(url "https://github.com/ocaml/opam")
|
||||
(commit version)))
|
||||
(file-name (git-file-name name version))
|
||||
(sha256
|
||||
(base32 "10diw6wdl6v89kbvb8x22dbfacw1ikhl63hybyp2s7560450hygc"))))
|
||||
(version "2.1.5")
|
||||
(source (origin
|
||||
(method git-fetch)
|
||||
(uri (git-reference
|
||||
(url "https://github.com/ocaml/opam")
|
||||
(commit version)))
|
||||
(file-name (git-file-name name version))
|
||||
(sha256
|
||||
(base32
|
||||
"0ckd87rcmcz11iyhhm5qnmy27jbdffx6n1fr06hvrqqrzi00jljh"))))
|
||||
(build-system dune-build-system)
|
||||
(arguments
|
||||
`(#:package "opam-core"
|
||||
;; tests are run with the opam package
|
||||
#:tests? #f
|
||||
#:phases (modify-phases %standard-phases
|
||||
(add-before 'build 'pre-build
|
||||
(lambda* (#:key inputs make-flags #:allow-other-keys)
|
||||
(let ((bash (assoc-ref inputs "bash"))
|
||||
(bwrap (search-input-file inputs "/bin/bwrap")))
|
||||
(substitute* "src/core/opamSystem.ml"
|
||||
(("\"/bin/sh\"")
|
||||
(string-append "\"" bash "/bin/sh\""))
|
||||
(("getconf")
|
||||
(which "getconf")))))))))
|
||||
(propagated-inputs (list ocaml-graph
|
||||
ocaml-re
|
||||
ocaml-patch
|
||||
ocaml-uutf
|
||||
ocaml-swhid-core
|
||||
ocaml-jsonm
|
||||
ocaml-sha))
|
||||
(arguments `(#:package "opam-core"
|
||||
;; tests are run with the opam package
|
||||
#:tests? #f
|
||||
#:phases
|
||||
(modify-phases %standard-phases
|
||||
(add-before 'build 'pre-build
|
||||
(lambda* (#:key inputs make-flags #:allow-other-keys)
|
||||
(let ((bash (assoc-ref inputs "bash"))
|
||||
(bwrap (search-input-file inputs "/bin/bwrap")))
|
||||
(substitute* "src/core/opamSystem.ml"
|
||||
(("\"/bin/sh\"")
|
||||
(string-append "\"" bash "/bin/sh\""))
|
||||
(("getconf")
|
||||
(which "getconf")))))))))
|
||||
(propagated-inputs
|
||||
(list ocaml-graph
|
||||
ocaml-re
|
||||
ocaml-cppo))
|
||||
(inputs (list bubblewrap))
|
||||
(home-page "https://opam.ocaml.org")
|
||||
(home-page "https://opam.ocamlpro.com/")
|
||||
(synopsis "Package manager for OCaml")
|
||||
(description
|
||||
"OPAM is a tool to manage OCaml packages. It supports multiple
|
||||
simultaneous compiler installations, flexible package constraints, and a
|
||||
Git-friendly development workflow.")
|
||||
;; The 'LICENSE' file waives some requirements compared to LGPLv2.1.
|
||||
(license license:lgpl2.1)))
|
||||
;; The 'LICENSE' file waives some requirements compared to LGPLv3.
|
||||
(license license:lgpl3)))
|
||||
|
||||
(define ocaml-opam-format
|
||||
(package
|
||||
@@ -1111,56 +1002,24 @@ Git-friendly development workflow.")
|
||||
|
||||
(define-public opam-installer
|
||||
(package
|
||||
(inherit ocaml-opam-core)
|
||||
(name "opam-installer")
|
||||
(version "2.5.1")
|
||||
;; opam has some library dependencies that in turn depend on
|
||||
;; opam-installer (https://codeberg.org/guix/guix/issues/3588). To break
|
||||
;; the cycle, we build opam-installer from a version of the release that
|
||||
;; vendors all dependencies. Then the remaining opam packages can be built
|
||||
;; in the usual way from git sources.
|
||||
(source
|
||||
(origin
|
||||
(method url-fetch)
|
||||
(uri (string-append "https://github.com/ocaml/opam/releases/download/"
|
||||
version "/opam-full-" version ".tar.gz"))
|
||||
(sha256
|
||||
(base32 "1v9k00az5lkdrlb64xb9h8xasnsz73kms0j0bz64hh2wbypvzia8"))))
|
||||
(build-system gnu-build-system)
|
||||
(arguments
|
||||
(list
|
||||
;; Tests depend on the full opam package.
|
||||
#:tests? #f
|
||||
#:configure-flags
|
||||
#~'("--with-vendored-deps")
|
||||
#:phases
|
||||
#~(modify-phases %standard-phases
|
||||
(add-after 'unpack 'fix-shell-path
|
||||
(lambda _
|
||||
(let ((sh (which "sh")))
|
||||
(substitute* "configure"
|
||||
(("/bin/sh") sh)))))
|
||||
;; The Makefile builds both opam and opam-installer, but we
|
||||
;; only want the latter.
|
||||
(replace 'install
|
||||
(lambda _
|
||||
(define (install source dest-dir)
|
||||
(install-file source
|
||||
(string-append #$output "/" dest-dir)))
|
||||
(install "opam-installer" "bin")
|
||||
(install "_build/default/doc/man/opam-installer.1"
|
||||
"share/man/man1"))))))
|
||||
(native-inputs (list ocaml))
|
||||
(home-page "https://opam.ocaml.org")
|
||||
(native-inputs (list ocaml-opam-format
|
||||
ocaml-cmdliner))
|
||||
(inputs '())
|
||||
(propagated-inputs '())
|
||||
(arguments `(#:package "opam-installer"
|
||||
;; requires all of opam
|
||||
#:tests? #f))
|
||||
(synopsis "Tool for installing OCaml packages")
|
||||
(description
|
||||
"@var{opam-installer} is a tool for installing OCaml packages
|
||||
(description "@var{opam-installer} is a tool for installing OCaml packages
|
||||
based on @code{.install} files defined by the OPAM package manager. It is
|
||||
useful for installing OCaml packages without requiring the entirety of
|
||||
OPAM.")
|
||||
(properties `((ocaml5.0-variant unquote
|
||||
(delay opam-installer))))
|
||||
;; The 'LICENSE' file waives some requirements compared to LGPLv2.1.
|
||||
(license license:lgpl2.1)))
|
||||
(properties
|
||||
;; opam-installer is used as a tool and not as a library, we can use the
|
||||
;; OCaml 4.14 compiled opam until opam is compatible with OCaml 5.0.
|
||||
`((ocaml5.0-variant . ,(delay opam-installer))))))
|
||||
|
||||
(define ocaml-opam-repository
|
||||
(package
|
||||
@@ -1197,7 +1056,7 @@ OPAM.")
|
||||
(string-append "add_sys_mounts "
|
||||
(%store-directory)
|
||||
" /run/current-system /usr")))))))))
|
||||
(inputs (list bubblewrap ocaml-spdx-licenses))
|
||||
(inputs (list bubblewrap))
|
||||
(propagated-inputs (list ocaml-opam-repository))))
|
||||
|
||||
(define ocaml-opam-solver
|
||||
@@ -1207,8 +1066,7 @@ OPAM.")
|
||||
(inputs '())
|
||||
(propagated-inputs (list ocaml-opam-format
|
||||
ocaml-mccs
|
||||
ocaml-dose3
|
||||
ocaml-opam-0install-cudf))
|
||||
ocaml-dose3))
|
||||
(arguments `(#:package "opam-solver"
|
||||
;; tests are run with the opam package
|
||||
#:tests? #f
|
||||
@@ -1235,7 +1093,7 @@ OPAM.")
|
||||
ocaml-opam-repository
|
||||
ocaml-base64
|
||||
ocaml-re
|
||||
ocaml-spdx-licenses))))
|
||||
ocaml-cmdliner))))
|
||||
|
||||
(define-public opam
|
||||
(package
|
||||
@@ -1244,171 +1102,120 @@ OPAM.")
|
||||
(build-system dune-build-system)
|
||||
(arguments
|
||||
`(#:package "opam"
|
||||
#:phases (modify-phases %standard-phases
|
||||
(add-before 'check 'prepare-checks
|
||||
(lambda* (#:key inputs #:allow-other-keys)
|
||||
;; Opam tests need to run an isolated environment from a writable
|
||||
;; home directory.
|
||||
(mkdir-p "test-home")
|
||||
(setenv "HOME"
|
||||
(string-append (getcwd) "/test-home"))
|
||||
(with-output-to-file (string-append (getcwd)
|
||||
"/test-home/.gitconfig")
|
||||
(lambda _
|
||||
(display "[user]
|
||||
#:phases
|
||||
(modify-phases %standard-phases
|
||||
(add-before 'check 'prepare-checks
|
||||
(lambda* (#:key inputs #:allow-other-keys)
|
||||
;; Opam tests need to run an isolated environment from a writable
|
||||
;; home directory.
|
||||
(mkdir-p "test-home")
|
||||
(setenv "HOME" (string-append (getcwd) "/test-home"))
|
||||
(with-output-to-file (string-append (getcwd) "/test-home/.gitconfig")
|
||||
(lambda _
|
||||
(display "[user]
|
||||
email = guix@localhost.none
|
||||
name = Guix Builder
|
||||
name = Guix Builder")
|
||||
(newline)))
|
||||
|
||||
[protocol \"file\"]
|
||||
allow = always")
|
||||
(newline)))
|
||||
;; Opam tests require data from opam-repository. Instead of
|
||||
;; downloading them with wget from the guix environment, copy the
|
||||
;; content to the expected directory.
|
||||
(substitute* "tests/reftests/dune.inc"
|
||||
(("tar -C.*opam-archive-([0-9a-f]*)[^)]*" _ commit)
|
||||
(string-append "rmdir %{targets}) (run cp -r "
|
||||
(assoc-ref inputs (string-append "opam-repo-" commit))
|
||||
"/ %{targets}) (run chmod +w -R %{targets}"))
|
||||
(("wget[^)]*") "touch %{targets}")
|
||||
;; Disable a failing test because it tries to clone a git
|
||||
;; repository from inside bwrap
|
||||
(("diff upgrade-format.test upgrade-format.out") "run true")
|
||||
;; Disable a failing test because it tries to figure out which
|
||||
;; distro this is, and it doesn't know Guix
|
||||
(("diff pin.unix.test pin.unix.out") "run true")
|
||||
;; Disable a failing test because of a failed expansion
|
||||
(("diff opamroot-versions.test opamroot-versions.out") "run true")
|
||||
;; Disable a failing test, probably because the repository we
|
||||
;; replaced is not as expected
|
||||
(("diff opamrt-big-upgrade.test opamrt-big-upgrade.out") "run true")
|
||||
;; Disable a failing test because of missing sandboxing
|
||||
;; functionality
|
||||
(("diff init.test init.out") "run true"))
|
||||
(substitute* "tests/reftests/dune"
|
||||
;; Because of our changes to the previous file, we cannot check
|
||||
;; it can be regenerated
|
||||
(("diff dune.inc dune.inc.gen") "run true"))
|
||||
;; Ensure we can run the generated build.sh (no /bin/sh)
|
||||
(substitute* '("tests/reftests/legacy-local.test"
|
||||
"tests/reftests/legacy-git.test")
|
||||
(("#! ?/bin/sh")
|
||||
(string-append "#!"
|
||||
(search-input-file inputs "/bin/sh"))))
|
||||
(substitute* "tests/reftests/testing-env"
|
||||
(("OPAMSTRICT=1")
|
||||
(string-append "OPAMSTRICT=1\nLIBRARY_PATH="
|
||||
(assoc-ref inputs "libc") "/lib"))))))))
|
||||
(native-inputs
|
||||
(let ((opam-repo (lambda (commit hash)
|
||||
(origin
|
||||
(method git-fetch)
|
||||
(uri (git-reference
|
||||
(url "https://github.com/ocaml/opam-repository")
|
||||
(commit commit)))
|
||||
(file-name (git-file-name "opam-repo" commit))
|
||||
(sha256 (base32 hash))))))
|
||||
`(("dune" ,dune)
|
||||
("ocaml-cppo" ,ocaml-cppo)
|
||||
|
||||
;; Opam tests require data from opam-repository. Instead
|
||||
;; of downloading them with wget from the guix
|
||||
;; environment, copy the content to the expected
|
||||
;; directory.
|
||||
(substitute* "tests/reftests/dune.inc"
|
||||
(("tar -C.*opam-archive-([0-9a-f]*)[^)]*" _ commit)
|
||||
(string-append "rmdir %{targets}) (run cp -r "
|
||||
(begin
|
||||
;; When updating opam, uncomment the following
|
||||
;; call. It will list "opam-repo" commit-ish
|
||||
;; required to run tests (see native-inputs
|
||||
;; below). Remove versions that are no longer
|
||||
;; required, and add new ones if necessary.
|
||||
;;
|
||||
;; (pk commit)
|
||||
(assoc-ref inputs
|
||||
(string-append "opam-repo-" commit)))
|
||||
"/ %{targets}) (run chmod +w -R %{targets}"))
|
||||
(("wget[^)]*")
|
||||
"touch %{targets}")
|
||||
;; For tests.
|
||||
("git" ,git-minimal/pinned)
|
||||
("openssl" ,openssl)
|
||||
("python" ,python-wrapper)
|
||||
("rsync" ,rsync)
|
||||
("unzip" ,unzip)
|
||||
("which" ,which)
|
||||
|
||||
;; Selectively disable a fraction of opam's "reftests"
|
||||
;; (CRAM-style regression tests). Most of these tests
|
||||
;; make assumptions about the build environment that
|
||||
;; don't hold for Guix.
|
||||
|
||||
;; Test tries to clone a git repository from inside
|
||||
;; bwrap
|
||||
(("diff upgrade-format.test upgrade-format.out")
|
||||
"run true")
|
||||
;; Test tries to figure out which distro this is, and
|
||||
;; it doesn't know Guix
|
||||
(("diff pin.unix.test pin.unix.out")
|
||||
"run true")
|
||||
;; A variable expansion fails.
|
||||
(("diff opamroot-versions.test opamroot-versions.out")
|
||||
"run true")
|
||||
;; The repository we replaced is probably not as
|
||||
;; expected
|
||||
(("diff opamrt-big-upgrade.test opamrt-big-upgrade.out")
|
||||
"run true")
|
||||
;; Disable a failing test because of missing sandboxing
|
||||
;; functionality
|
||||
(("diff init.test init.out")
|
||||
"run true")
|
||||
;; These tests try to normalize output to exclude
|
||||
;; version strings, but this seems to break some
|
||||
;; output assertions if $BASEDIR happens to include
|
||||
;; the version.
|
||||
(("diff cli-versioning.test cli-versioning.out")
|
||||
"run true")
|
||||
(("diff hooks-variables.test hooks-variables.out")
|
||||
"run true")
|
||||
;; Fails on noisy git output.
|
||||
(("diff action-disk.test action-disk.out")
|
||||
"run true")
|
||||
;; Requires network access.
|
||||
(("diff download.test download.out")
|
||||
"run true")
|
||||
(("diff swhid.unix.test swhid.unix.out")
|
||||
"run true")
|
||||
;; Depends on 3rd-party git repos.
|
||||
(("diff lock.test lock.out")
|
||||
"run true"))
|
||||
|
||||
(substitute* "tests/reftests/dune"
|
||||
;; Because of our changes to the previous file, we
|
||||
;; cannot check it can be regenerated
|
||||
(("diff dune.inc dune.inc.gen")
|
||||
"run true"))
|
||||
;; Ensure we can run the generated build.sh (no /bin/sh)
|
||||
(substitute* '("tests/reftests/legacy-local.test"
|
||||
"tests/reftests/legacy-git.test")
|
||||
(("#! ?/bin/sh")
|
||||
(string-append "#!"
|
||||
(search-input-file inputs "/bin/sh"))))
|
||||
(substitute* "tests/reftests/testing-env"
|
||||
(("OPAMSTRICT=1")
|
||||
(string-append "OPAMSTRICT=1\nLIBRARY_PATH="
|
||||
(assoc-ref inputs "libc") "/lib"))))))))
|
||||
|
||||
(native-inputs (let ((opam-repo (lambda (commit hash)
|
||||
(origin
|
||||
(method git-fetch)
|
||||
(uri (git-reference
|
||||
(url
|
||||
"https://github.com/ocaml/opam-repository")
|
||||
(commit commit)))
|
||||
(file-name (git-file-name "opam-repo"
|
||||
commit))
|
||||
(sha256 (base32 hash))))))
|
||||
`(("dune" ,dune)
|
||||
|
||||
;; For tests.
|
||||
("git" ,git-minimal/pinned)
|
||||
("openssl" ,openssl)
|
||||
("python" ,python-wrapper)
|
||||
("rsync" ,rsync)
|
||||
("unzip" ,unzip)
|
||||
("which" ,which)
|
||||
("xxd" ,xxd)
|
||||
|
||||
;; Data for tests
|
||||
("opam-repo-0070613707" ,(opam-repo
|
||||
"00706137074d536d2019d2d222fbe1bea929deda"
|
||||
"1gv1vvmfscj7wirfv6qncp8pf81wygnpzjwd0lyqcxm7g8r8lb4w"))
|
||||
("opam-repo-009e00fa" ,(opam-repo
|
||||
"009e00fa86300d11c311309a2544e5c6c3eb8de2"
|
||||
"1wwy0rwrsjf4q10j1rh1dazk32fbzhzy6f7zl6qmndidx9b1bq7w"))
|
||||
("opam-repo-11ea1cb" ,(opam-repo
|
||||
"11ea1cb6f2418b1f8a6679e4422771a04c9c3655"
|
||||
"1s4p0wfn3bx97yvm8xvj3yhzv2pz0jwml68g2ybv37hj9mpbrsq0"))
|
||||
("opam-repo-143dd2a2f59f5befbf3cb90bb2667f911737fbf8" ,
|
||||
(opam-repo "143dd2a2f59f5befbf3cb90bb2667f911737fbf8"
|
||||
"1kliiy9n2j8myxhbz1brq6yingfy0si1bmv15j1hbnbpyi3bavr9"))
|
||||
("opam-repo-297366c" ,(opam-repo
|
||||
"297366cd01c3aaf29b967bf0b34ccc7989d4d5b3"
|
||||
"1ysg69gys37nc2cxivs2ikh6xp0gj85if4rcrr874mqb9z12dm0j"))
|
||||
("opam-repo-3235916" ,(opam-repo
|
||||
"3235916a162a59d7c82dac3fe24214975d48f1aa"
|
||||
"1yf73rv2n740a4s9g7a9k4j91b4k7al88nwnw9cdw0k2ncbmr486"))
|
||||
("opam-repo-7090735c" ,(opam-repo
|
||||
"7090735c9d1dd2dc481c4128c5ef4d3667238f15"
|
||||
"1bccsgjhlp64lmvfjfn6viywf3x73ji75myg9ssf1ij1fkmabn0z"))
|
||||
("opam-repo-7371c1d9" ,(opam-repo
|
||||
"7371c1d9c53000840fb9a6d8ec13d87ffaa98401"
|
||||
"0lmy3rmp5liyp2dsx4s90rjdwc012947ig2fz6y97s3pmwsbf9g8"))
|
||||
("opam-repo-a5d7cdc0" ,(opam-repo
|
||||
"a5d7cdc0c91452b0aef4fa71c331ee5237f6dddd"
|
||||
"0z7kawqisy07088p5xjxwpvmvzlbj1d9cgdipsj90yx7nc5qh369"))
|
||||
("opam-repo-ad4dd344" ,(opam-repo
|
||||
"ad4dd344fe5cd1cab49ced49d6758a9844549fb4"
|
||||
"1a1qj47kj8xjdnc4zc50ijrix1kym1n7k20n3viki80a7518baw8"))
|
||||
("opam-repo-c1842d168d" ,(opam-repo
|
||||
"c1842d168de956caf06d7ac8588e65020d7594d8"
|
||||
"142y1ac7sprygyh91shcp0zcyfxjjkshi9g44qgg4rx60rbsbhai"))
|
||||
("opam-repo-c1ba97dafe95c865d37ad4d88f6e57c9ffbe7f0a" ,
|
||||
(opam-repo "c1ba97dafe95c865d37ad4d88f6e57c9ffbe7f0a"
|
||||
"0sllm110dvs3w1k7qhias5y8v6ikkk2knw97v1fk9lnw4lq45gv6"))
|
||||
("opam-repo-de897adf36c4230dfea812f40c98223b31c4521a" ,
|
||||
(opam-repo "de897adf36c4230dfea812f40c98223b31c4521a"
|
||||
"1m18x9gcwnbar8yv9sbfz8a3qpw412fp9cf4d6fb7syn0p0h96jw"))
|
||||
("opam-repo-f372039d" ,(opam-repo
|
||||
"f372039db86a970ef3e662adbfe0d4f5cd980701"
|
||||
"0ld7fcry6ss6fmrpswvr6bikgx299w97h0gwrjjh7kd7rydsjdws")))))
|
||||
(inputs (list ocaml-opam-client))))
|
||||
;; Data for tests
|
||||
("opam-repo-0070613707"
|
||||
,(opam-repo "00706137074d536d2019d2d222fbe1bea929deda"
|
||||
"1gv1vvmfscj7wirfv6qncp8pf81wygnpzjwd0lyqcxm7g8r8lb4w"))
|
||||
("opam-repo-009e00fa"
|
||||
,(opam-repo "009e00fa86300d11c311309a2544e5c6c3eb8de2"
|
||||
"1wwy0rwrsjf4q10j1rh1dazk32fbzhzy6f7zl6qmndidx9b1bq7w"))
|
||||
("opam-repo-7090735c"
|
||||
,(opam-repo "7090735c9d1dd2dc481c4128c5ef4d3667238f15"
|
||||
"1bccsgjhlp64lmvfjfn6viywf3x73ji75myg9ssf1ij1fkmabn0z"))
|
||||
("opam-repo-a5d7cdc0"
|
||||
,(opam-repo "a5d7cdc0c91452b0aef4fa71c331ee5237f6dddd"
|
||||
"0z7kawqisy07088p5xjxwpvmvzlbj1d9cgdipsj90yx7nc5qh369"))
|
||||
("opam-repo-ad4dd344"
|
||||
,(opam-repo "ad4dd344fe5cd1cab49ced49d6758a9844549fb4"
|
||||
"1a1qj47kj8xjdnc4zc50ijrix1kym1n7k20n3viki80a7518baw8"))
|
||||
("opam-repo-c1842d168d"
|
||||
,(opam-repo "c1842d168de956caf06d7ac8588e65020d7594d8"
|
||||
"142y1ac7sprygyh91shcp0zcyfxjjkshi9g44qgg4rx60rbsbhai"))
|
||||
("opam-repo-c1d23f0e"
|
||||
,(opam-repo "c1d23f0e17ec83a036ebfbad1c78311b898a2ca0"
|
||||
"0j9abisx3ifzm66ci3p45mngmz4f0fx7yd9jjxrz3f8w5jffc9ii"))
|
||||
("opam-repo-f372039d"
|
||||
,(opam-repo "f372039db86a970ef3e662adbfe0d4f5cd980701"
|
||||
"0ld7fcry6ss6fmrpswvr6bikgx299w97h0gwrjjh7kd7rydsjdws"))
|
||||
("opam-repo-11ea1cb"
|
||||
,(opam-repo "11ea1cb6f2418b1f8a6679e4422771a04c9c3655"
|
||||
"1s4p0wfn3bx97yvm8xvj3yhzv2pz0jwml68g2ybv37hj9mpbrsq0"))
|
||||
("opam-repo-297366c"
|
||||
,(opam-repo "297366cd01c3aaf29b967bf0b34ccc7989d4d5b3"
|
||||
"1ysg69gys37nc2cxivs2ikh6xp0gj85if4rcrr874mqb9z12dm0j"))
|
||||
("opam-repo-3235916"
|
||||
,(opam-repo "3235916a162a59d7c82dac3fe24214975d48f1aa"
|
||||
"1yf73rv2n740a4s9g7a9k4j91b4k7al88nwnw9cdw0k2ncbmr486"))
|
||||
("opam-repo-de897adf36c4230dfea812f40c98223b31c4521a"
|
||||
,(opam-repo "de897adf36c4230dfea812f40c98223b31c4521a"
|
||||
"1m18x9gcwnbar8yv9sbfz8a3qpw412fp9cf4d6fb7syn0p0h96jw")))))
|
||||
(inputs (list ocaml-opam-client))
|
||||
(properties
|
||||
;; OPAM is used as a tool and not as a library, we can use the OCaml 4.14
|
||||
;; compiled opam until opam is compatible with OCaml 5.0.
|
||||
`((ocaml5.0-variant . ,(delay opam))))))
|
||||
|
||||
(define-public ocaml-opam-monorepo
|
||||
(package
|
||||
@@ -4317,32 +4124,6 @@ and command-line tool.")
|
||||
length of domain names are preserved throughout the module.")
|
||||
(license license:isc)))
|
||||
|
||||
(define-public ocaml-patch
|
||||
(package
|
||||
(name "ocaml-patch")
|
||||
(version "3.1.0")
|
||||
(build-system dune-build-system)
|
||||
(source
|
||||
(origin
|
||||
(method git-fetch)
|
||||
(uri (git-reference
|
||||
(url "https://github.com/hannesm/patch")
|
||||
(commit (string-append "v" version))))
|
||||
(file-name (git-file-name name version))
|
||||
(sha256
|
||||
(base32 "1zg35f427ixd3jhkiwk91sil45pmf6ns7yfcgyi6gf2r0y241xn3"))))
|
||||
(native-inputs (list ocaml-alcotest))
|
||||
(home-page "https://github.com/hannesm/patch")
|
||||
(synopsis "Applies unified diffs in pure OCaml")
|
||||
(description
|
||||
"This package applies unified diffs in pure OCaml.
|
||||
|
||||
The loosely specified diff file format is widely used for transmitting
|
||||
differences of line-based information. The motivating example is opam, which
|
||||
is able to validate updates being cryptographically signed (e.g. conex) by
|
||||
providing a unified diff.")
|
||||
(license license:isc)))
|
||||
|
||||
(define-public ocaml-macaddr
|
||||
(package
|
||||
(name "ocaml-macaddr")
|
||||
|
||||
@@ -817,33 +817,7 @@ high-performance computing} clusters.")
|
||||
(list
|
||||
#:phases
|
||||
#~(modify-phases %standard-phases
|
||||
(add-after 'unpack 'set-load-paths-in-entry-point
|
||||
(lambda _
|
||||
(define load-path
|
||||
(cons (string-append #$output
|
||||
"/share/guile/site/"
|
||||
(target-guile-effective-version))
|
||||
(parse-path (getenv "GUILE_LOAD_PATH"))))
|
||||
(define load-compiled-path
|
||||
(cons (string-append #$output
|
||||
"/lib/guile/"
|
||||
(target-guile-effective-version)
|
||||
"/site-ccache")
|
||||
(parse-path (getenv "GUILE_LOAD_COMPILED_PATH"))))
|
||||
(define search-paths-header
|
||||
`(begin
|
||||
(set! %load-path
|
||||
(append (list ,@load-path) %load-path))
|
||||
(set! %load-compiled-path
|
||||
(append (list ,@load-compiled-path)
|
||||
%load-compiled-path))))
|
||||
(substitute* "guix/extensions/toys.scm"
|
||||
(("^\\(define-module \\(guix extensions toys\\)")
|
||||
(string-append
|
||||
(with-output-to-string
|
||||
(lambda () (write search-paths-header)))
|
||||
"\n(define-module (guix extensions toys)")))))
|
||||
(add-after 'set-load-paths-in-entry-point 'register-guix-extension
|
||||
(add-after 'unpack 'register-guix-extension
|
||||
(lambda* (#:key outputs #:allow-other-keys)
|
||||
(let ((ext-path (string-append #$output "/share/guix/extensions")))
|
||||
(mkdir-p ext-path)
|
||||
@@ -1204,8 +1178,8 @@ transactions from C or Python.")
|
||||
(license license:gpl2+)))
|
||||
|
||||
(define-public bffe
|
||||
(let ((commit "d6c90f217595674c7910a858edcb735f88d3a14f")
|
||||
(revision "18"))
|
||||
(let ((commit "723fd5ea6af1b14c215baf80524c8ff4b21fcc82")
|
||||
(revision "17"))
|
||||
(package
|
||||
(name "bffe")
|
||||
(version (git-version "0" revision commit))
|
||||
@@ -1216,7 +1190,7 @@ transactions from C or Python.")
|
||||
(commit commit)))
|
||||
(sha256
|
||||
(base32
|
||||
"0f7i68k6l5ylg8nch54xw4bxn0hayx2ng9j5dvwvai1vi887vmbj"))
|
||||
"1sd62arq80kkfjnynivrp7jh8j359965ank8sglq1wgfdah9k8ii"))
|
||||
(file-name (string-append name "-" version "-checkout"))))
|
||||
(build-system gnu-build-system)
|
||||
(native-inputs
|
||||
@@ -1225,13 +1199,13 @@ transactions from C or Python.")
|
||||
automake
|
||||
|
||||
;; Guile libraries are needed here for cross-compilation.
|
||||
guile-3.0-latest
|
||||
guile-next
|
||||
guile-gnutls
|
||||
guile-json-4
|
||||
guix
|
||||
guix-data-service
|
||||
guix-build-coordinator
|
||||
guile-fibers
|
||||
guile-fibers-next
|
||||
guile-knots
|
||||
guile-pfds
|
||||
guile-prometheus
|
||||
@@ -1242,7 +1216,7 @@ transactions from C or Python.")
|
||||
guix
|
||||
guix-data-service
|
||||
guix-build-coordinator
|
||||
guile-fibers
|
||||
guile-fibers-next
|
||||
guile-knots
|
||||
guile-pfds
|
||||
guile-prometheus
|
||||
@@ -2211,7 +2185,7 @@ environments.")
|
||||
"guile-gnutls"
|
||||
#$@(if (target-hurd?)
|
||||
'()
|
||||
'("guile-fibers"
|
||||
'("guile-fibers-next"
|
||||
"guile-knots")))))
|
||||
(wrap-program file
|
||||
`("PATH" ":" prefix
|
||||
@@ -2255,12 +2229,12 @@ environments.")
|
||||
guile-gcrypt
|
||||
guix
|
||||
guile-prometheus
|
||||
guile-fibers
|
||||
guile-fibers-next
|
||||
guile-knots
|
||||
guile-lib
|
||||
guile-3.0-latest))
|
||||
guile-next))
|
||||
(inputs
|
||||
(list guile-3.0-latest
|
||||
(list guile-next
|
||||
sqlite-next
|
||||
bash-minimal
|
||||
(libc-utf8-locales-for-target)
|
||||
@@ -2275,7 +2249,7 @@ environments.")
|
||||
guile-sqlite3
|
||||
guix
|
||||
guile-gnutls
|
||||
guile-fibers
|
||||
guile-fibers-next
|
||||
guile-knots))
|
||||
(home-page "https://git.cbaines.net/guix/build-coordinator/")
|
||||
(synopsis "Tool to help build derivations")
|
||||
@@ -2311,9 +2285,9 @@ outputs of those builds.")
|
||||
guix
|
||||
guile-prometheus
|
||||
guile-lib
|
||||
guile-3.0-latest))
|
||||
guile-next))
|
||||
(inputs
|
||||
(list guile-3.0-latest
|
||||
(list guile-next
|
||||
guix
|
||||
guile-prometheus
|
||||
guile-gcrypt
|
||||
@@ -2464,7 +2438,7 @@ in an isolated environment, in separate namespaces.")
|
||||
"guile-prometheus"
|
||||
"guile-sqlite3"
|
||||
"guile-gnutls"
|
||||
"guile-fibers"
|
||||
"guile-fibers-next"
|
||||
"guile-knots")))
|
||||
(wrap-program file
|
||||
`("GUILE_LOAD_PATH" ":" prefix
|
||||
@@ -2494,12 +2468,11 @@ in an isolated environment, in separate namespaces.")
|
||||
|
||||
;; Guile libraries are needed here for cross-compilation.
|
||||
guile-next
|
||||
guile-3.0-latest
|
||||
guile-aws
|
||||
guile-json-4
|
||||
guile-gcrypt
|
||||
guix
|
||||
guile-fibers
|
||||
guile-fibers-next
|
||||
guile-knots
|
||||
guile-prometheus
|
||||
guile-lib
|
||||
@@ -2508,13 +2481,13 @@ in an isolated environment, in separate namespaces.")
|
||||
guile-sqlite3))
|
||||
(inputs
|
||||
(list bash-minimal
|
||||
guile-3.0-latest))
|
||||
guile-next))
|
||||
(propagated-inputs
|
||||
(list guile-aws
|
||||
guile-json-4
|
||||
guile-gcrypt
|
||||
guix
|
||||
guile-fibers
|
||||
guile-fibers-next
|
||||
guile-knots
|
||||
guile-prometheus
|
||||
guile-lib
|
||||
|
||||
@@ -82,7 +82,7 @@
|
||||
(define-public parallel
|
||||
(package
|
||||
(name "parallel")
|
||||
(version "20260422")
|
||||
(version "20260322")
|
||||
(outputs '("out" "doc"))
|
||||
(source
|
||||
(origin
|
||||
@@ -90,7 +90,7 @@
|
||||
(uri (string-append "mirror://gnu/parallel/parallel-"
|
||||
version ".tar.bz2"))
|
||||
(sha256
|
||||
(base32 "1fq7v60x9jm8mg19qn8n0sfhrygccmw6mncwyjr1g8kfsrjz2k36"))
|
||||
(base32 "1q7g5f13nlwichgh0dk8w5fqjnfnxvwxk6rjy0fd5l7l6blq0ikn"))
|
||||
(snippet
|
||||
'(begin
|
||||
(use-modules (guix build utils))
|
||||
@@ -254,7 +254,7 @@ when jobs finish.")
|
||||
(inputs
|
||||
(append
|
||||
(list freeipmi
|
||||
`(,hwloc "lib")
|
||||
`(,hwloc-2 "lib")
|
||||
json-c
|
||||
linux-pam)
|
||||
(if (supported-package? openpmix-4)
|
||||
@@ -734,7 +734,7 @@ single-instruction multiple-data (SIMD) intrinsics.")
|
||||
(substitute* "src/include/pmix_config.h"
|
||||
(("#define PMIX_CONFIGURE_CLI .*")
|
||||
"#define PMIX_CONFIGURE_CLI \"[scrubbed]\"\n")))))))
|
||||
(inputs (list libevent `(,hwloc "lib") munge zlib))
|
||||
(inputs (list libevent `(,hwloc "lib") zlib))
|
||||
(native-inputs
|
||||
(list autoconf
|
||||
automake
|
||||
|
||||
@@ -39,7 +39,6 @@
|
||||
#:use-module (gnu packages ncurses)
|
||||
#:use-module (gnu packages perl)
|
||||
#:use-module (gnu packages pkg-config)
|
||||
#:use-module (gnu packages qt)
|
||||
#:use-module (gnu packages xml)
|
||||
#:use-module (gnu packages xorg)
|
||||
#:use-module (ice-9 match))
|
||||
@@ -324,7 +323,7 @@ Pascal programs.")
|
||||
(define-public lazarus
|
||||
(package
|
||||
(name "lazarus")
|
||||
(version "4.6")
|
||||
(version "2.2.6")
|
||||
(source (origin
|
||||
(method git-fetch)
|
||||
(uri (git-reference
|
||||
@@ -337,95 +336,48 @@ Pascal programs.")
|
||||
(file-name (string-append name "-" version "-checkout"))
|
||||
(sha256
|
||||
(base32
|
||||
"1mkimvd5hiwlsxpjwqnhd7lwb0x2icnf9ks09wza7j5xaq7xjswy"))))
|
||||
"0hpk6fxmy1h1q0df41jg1vnp8g8vynrg5v5ad43lv229nizfs3wj"))))
|
||||
(build-system gnu-build-system)
|
||||
(arguments
|
||||
(list #:tests? #f ;No tests exist
|
||||
#:make-flags #~(list (string-append "INSTALL_PREFIX="
|
||||
#$output)
|
||||
"LCL_PLATFORM=qt6")
|
||||
#:phases
|
||||
#~(modify-phases %standard-phases
|
||||
(delete 'configure)
|
||||
;; lcl/interfaces/qt6/cbindings/ ships the C++ source of
|
||||
;; libQt6Pas -- the Qt6 C-ABI bridge that LCL's qt6
|
||||
;; widgetset calls into. Build it with qmake6 and stage
|
||||
;; the library so the IDE finds it at runtime.
|
||||
(add-before 'build 'build-qt6pas
|
||||
(lambda _
|
||||
(with-directory-excursion "lcl/interfaces/qt6/cbindings"
|
||||
(invoke "qmake6" "Qt6Pas.pro"
|
||||
(string-append "PREFIX=" #$output))
|
||||
(invoke "make" "-j"
|
||||
(number->string (parallel-job-count))))))
|
||||
(replace 'build
|
||||
(lambda* (#:key inputs make-flags #:allow-other-keys)
|
||||
(let* ((qt6pas-build
|
||||
(string-append (getcwd)
|
||||
"/lcl/interfaces/qt6/cbindings"))
|
||||
(qt6pas-runtime
|
||||
(string-append #$output "/lib"))
|
||||
(input-libs
|
||||
(map (lambda (x)
|
||||
(string-append (assoc-ref inputs x) "/lib"))
|
||||
'("qtbase" "libx11")))
|
||||
;; Link against the build tree so the linker
|
||||
;; resolves libQt6Pas now; bake the final
|
||||
;; $out/lib into RUNPATH so the installed
|
||||
;; binary finds it at runtime.
|
||||
(fpc-args
|
||||
(append (map (lambda (d)
|
||||
(string-append "-Fl" d))
|
||||
(cons qt6pas-build input-libs))
|
||||
(map (lambda (d)
|
||||
(string-append "-k-rpath=" d))
|
||||
(cons qt6pas-runtime input-libs)))))
|
||||
(setenv "LAZARUS_LIBPATHS"
|
||||
(string-join fpc-args " "))
|
||||
(setenv "MAKEFLAGS"
|
||||
(string-append "LHELP_OPT="
|
||||
(string-join fpc-args "\\ "))))
|
||||
(apply invoke "make" "bigide" make-flags)))
|
||||
(add-after 'install 'wrap-qt
|
||||
(lambda* (#:key inputs #:allow-other-keys)
|
||||
;; Qt6 apps load their platform plugins
|
||||
;; (libqxcb.so, libqwayland.so, ...) from
|
||||
;; QT_PLUGIN_PATH; each qt input has its plugins
|
||||
;; under lib/qt6/plugins/. Wrap lazarus-ide so the
|
||||
;; wayland/xcb platform plugins are found at runtime.
|
||||
(let ((plugin-path
|
||||
(string-join
|
||||
(map (lambda (i)
|
||||
(string-append (assoc-ref inputs i)
|
||||
"/lib/qt6/plugins"))
|
||||
'("qtbase" "qtsvg" "qtwayland"))
|
||||
":")))
|
||||
(for-each
|
||||
(lambda (prog)
|
||||
(wrap-program (string-append #$output "/bin/" prog)
|
||||
`("QT_PLUGIN_PATH" ":" prefix (,plugin-path))))
|
||||
'("lazarus-ide" "startlazarus")))))
|
||||
(add-after 'install 'install-qt6pas
|
||||
(lambda _
|
||||
;; qmake's `make install' tries to copy libQt6Pas.so
|
||||
;; into Qt's install prefix (read-only store path);
|
||||
;; place it under $out/lib/ instead.
|
||||
(let ((src "lcl/interfaces/qt6/cbindings")
|
||||
(dst (string-append #$output "/lib")))
|
||||
(mkdir-p dst)
|
||||
(for-each
|
||||
(lambda (f)
|
||||
(let ((sf (string-append src "/" f))
|
||||
(df (string-append dst "/" f)))
|
||||
(if (eq? 'symlink (stat:type (lstat sf)))
|
||||
(symlink (readlink sf) df)
|
||||
(copy-file sf df))))
|
||||
'("libQt6Pas.so"
|
||||
"libQt6Pas.so.6"
|
||||
"libQt6Pas.so.6.2"
|
||||
"libQt6Pas.so.6.2.10"))))))))
|
||||
(native-inputs (list fpc pkg-config qtbase qttools))
|
||||
(inputs (list qtbase qtsvg qtwayland libx11))
|
||||
#$output))
|
||||
#:phases #~(modify-phases %standard-phases
|
||||
(delete 'configure)
|
||||
(replace 'build
|
||||
(lambda* (#:key inputs outputs #:allow-other-keys)
|
||||
(let* ((libdirs (map (lambda (x)
|
||||
(assoc-ref inputs x))
|
||||
'("glib" "gdk-pixbuf"
|
||||
"gtk+"
|
||||
"libx11"
|
||||
"libx11"
|
||||
"pango"
|
||||
"cairo"
|
||||
"at-spi2-core")))
|
||||
(libs (append (map (lambda (name)
|
||||
(string-append "-Fl"
|
||||
name
|
||||
"/lib"))
|
||||
libdirs)
|
||||
(map (lambda (name)
|
||||
(string-append
|
||||
"-k-rpath=" name
|
||||
"/lib")) libdirs))))
|
||||
(setenv "LAZARUS_LIBPATHS"
|
||||
(string-join libs " "))
|
||||
(setenv "MAKEFLAGS"
|
||||
(string-append "LHELP_OPT="
|
||||
(string-join libs "\\ "))))
|
||||
(invoke "make" "bigide"))))))
|
||||
(native-inputs (list fpc pkg-config))
|
||||
(inputs (list glib
|
||||
gdk-pixbuf
|
||||
gtk+-2
|
||||
libx11
|
||||
pango
|
||||
cairo
|
||||
at-spi2-core))
|
||||
(synopsis "Integrated development environment for Pascal")
|
||||
(description "This package provides an integrated development environment
|
||||
for Pascal.")
|
||||
|
||||
@@ -1,128 +0,0 @@
|
||||
Author: Danny Milosavljevic <dannym@friendly-machines.com>
|
||||
Date: 2026-04-13
|
||||
License: ASL2.0
|
||||
|
||||
Make V8 an optional dependency in codex-code-mode.
|
||||
|
||||
The V8 engine is only needed for actually executing JavaScript in the
|
||||
code-mode sandbox. The description helpers, tool name constants, and
|
||||
data types do not require V8. Gate the runtime and service modules
|
||||
behind a "v8-runtime" feature so that consumers like codex-acp that
|
||||
never use code-mode can avoid the V8 build dependency.
|
||||
|
||||
--- a/codex-rs/code-mode/Cargo.toml 2026-04-13 16:14:49.459504037 +0000
|
||||
+++ codex-rs/code-mode/Cargo.toml 2026-04-13 16:14:49.466438318 +0000
|
||||
@@ -12,6 +12,10 @@
|
||||
[lints]
|
||||
workspace = true
|
||||
|
||||
+[features]
|
||||
+default = ["v8-runtime"]
|
||||
+v8-runtime = ["dep:v8"]
|
||||
+
|
||||
[dependencies]
|
||||
async-trait = { workspace = true }
|
||||
serde = { workspace = true, features = ["derive"] }
|
||||
@@ -19,7 +23,7 @@
|
||||
tokio = { workspace = true, features = ["macros", "rt", "sync", "time"] }
|
||||
tokio-util = { workspace = true, features = ["rt"] }
|
||||
tracing = { workspace = true }
|
||||
-v8 = { workspace = true }
|
||||
+v8 = { workspace = true, optional = true }
|
||||
|
||||
[dev-dependencies]
|
||||
pretty_assertions = { workspace = true }
|
||||
--- a/codex-rs/code-mode/src/lib.rs 2026-04-13 16:14:49.461337956 +0000
|
||||
+++ codex-rs/code-mode/src/lib.rs 2026-04-13 16:14:49.470869556 +0000
|
||||
@@ -1,6 +1,8 @@
|
||||
mod description;
|
||||
mod response;
|
||||
+#[cfg(feature = "v8-runtime")]
|
||||
mod runtime;
|
||||
+#[cfg(feature = "v8-runtime")]
|
||||
mod service;
|
||||
|
||||
pub use description::CODE_MODE_PRAGMA_PREFIX;
|
||||
@@ -16,15 +18,82 @@
|
||||
pub use description::render_json_schema_to_typescript;
|
||||
pub use response::FunctionCallOutputContentItem;
|
||||
pub use response::ImageDetail;
|
||||
+
|
||||
+#[cfg(feature = "v8-runtime")]
|
||||
pub use runtime::DEFAULT_EXEC_YIELD_TIME_MS;
|
||||
+#[cfg(feature = "v8-runtime")]
|
||||
pub use runtime::DEFAULT_MAX_OUTPUT_TOKENS_PER_EXEC_CALL;
|
||||
+#[cfg(feature = "v8-runtime")]
|
||||
pub use runtime::DEFAULT_WAIT_YIELD_TIME_MS;
|
||||
+#[cfg(feature = "v8-runtime")]
|
||||
pub use runtime::ExecuteRequest;
|
||||
+#[cfg(feature = "v8-runtime")]
|
||||
pub use runtime::RuntimeResponse;
|
||||
+#[cfg(feature = "v8-runtime")]
|
||||
pub use runtime::WaitRequest;
|
||||
+#[cfg(feature = "v8-runtime")]
|
||||
pub use service::CodeModeService;
|
||||
+#[cfg(feature = "v8-runtime")]
|
||||
pub use service::CodeModeTurnHost;
|
||||
+#[cfg(feature = "v8-runtime")]
|
||||
pub use service::CodeModeTurnWorker;
|
||||
|
||||
+// Stub types when V8 is not available.
|
||||
+#[cfg(not(feature = "v8-runtime"))]
|
||||
+pub const DEFAULT_EXEC_YIELD_TIME_MS: u64 = 10_000;
|
||||
+#[cfg(not(feature = "v8-runtime"))]
|
||||
+pub const DEFAULT_MAX_OUTPUT_TOKENS_PER_EXEC_CALL: usize = 10_000;
|
||||
+#[cfg(not(feature = "v8-runtime"))]
|
||||
+pub const DEFAULT_WAIT_YIELD_TIME_MS: u64 = 10_000;
|
||||
+
|
||||
+#[cfg(not(feature = "v8-runtime"))]
|
||||
+pub struct ExecuteRequest {
|
||||
+ pub tool_call_id: String,
|
||||
+ pub enabled_tools: Vec<ToolDefinition>,
|
||||
+ pub source: String,
|
||||
+ pub stored_values: std::collections::HashMap<String, serde_json::Value>,
|
||||
+ pub yield_time_ms: Option<u64>,
|
||||
+ pub max_output_tokens: Option<usize>,
|
||||
+}
|
||||
+
|
||||
+#[cfg(not(feature = "v8-runtime"))]
|
||||
+#[derive(Clone, Debug)]
|
||||
+pub struct WaitRequest {
|
||||
+ pub cell_id: String,
|
||||
+ pub yield_time_ms: u64,
|
||||
+ pub terminate: bool,
|
||||
+}
|
||||
+
|
||||
+#[cfg(not(feature = "v8-runtime"))]
|
||||
+#[derive(Debug, PartialEq)]
|
||||
+pub enum RuntimeResponse {
|
||||
+ Yielded { cell_id: String, content_items: Vec<FunctionCallOutputContentItem> },
|
||||
+ Terminated { cell_id: String, content_items: Vec<FunctionCallOutputContentItem> },
|
||||
+ Result { cell_id: String, content_items: Vec<FunctionCallOutputContentItem>, stored_values: std::collections::HashMap<String, serde_json::Value>, error_text: Option<String> },
|
||||
+}
|
||||
+
|
||||
+#[cfg(not(feature = "v8-runtime"))]
|
||||
+#[async_trait::async_trait]
|
||||
+pub trait CodeModeTurnHost: Send + Sync {
|
||||
+ async fn invoke_tool(&self, tool_name: String, input: Option<serde_json::Value>, cancellation_token: tokio_util::sync::CancellationToken) -> Result<serde_json::Value, String>;
|
||||
+ async fn notify(&self, call_id: String, cell_id: String, text: String) -> Result<(), String>;
|
||||
+}
|
||||
+
|
||||
+#[cfg(not(feature = "v8-runtime"))]
|
||||
+pub struct CodeModeService;
|
||||
+
|
||||
+#[cfg(not(feature = "v8-runtime"))]
|
||||
+impl CodeModeService {
|
||||
+ pub fn new() -> Self { Self }
|
||||
+ pub async fn stored_values(&self) -> std::collections::HashMap<String, serde_json::Value> { Default::default() }
|
||||
+ pub async fn replace_stored_values(&self, _values: std::collections::HashMap<String, serde_json::Value>) {}
|
||||
+ pub async fn execute(&self, _request: ExecuteRequest) -> Result<RuntimeResponse, String> { Err("code-mode requires v8-runtime feature".into()) }
|
||||
+ pub async fn wait(&self, _request: WaitRequest) -> Result<RuntimeResponse, String> { Err("code-mode requires v8-runtime feature".into()) }
|
||||
+ pub fn start_turn_worker(&self, _host: std::sync::Arc<dyn CodeModeTurnHost>) -> CodeModeTurnWorker { CodeModeTurnWorker }
|
||||
+}
|
||||
+
|
||||
+#[cfg(not(feature = "v8-runtime"))]
|
||||
+pub struct CodeModeTurnWorker;
|
||||
+
|
||||
pub const PUBLIC_TOOL_NAME: &str = "exec";
|
||||
pub const WAIT_TOOL_NAME: &str = "wait";
|
||||
@@ -1,20 +0,0 @@
|
||||
Author: Danny Milosavljevic <dannym@friendly-machines.com>
|
||||
Date: 2026-02-08
|
||||
License: ASL2.0
|
||||
|
||||
Remove [patch.crates-io] section.
|
||||
|
||||
This section points to git repositories which are unavailable in an
|
||||
offline build. The vendored tokio-tungstenite and tungstenite forks
|
||||
are provided as cargo-inputs instead.
|
||||
|
||||
--- a/Cargo.toml
|
||||
+++ b/Cargo.toml
|
||||
@@ -52,7 +52,3 @@
|
||||
let-underscore = "warn"
|
||||
rust-2018-idioms = "warn"
|
||||
unused = "warn"
|
||||
-
|
||||
-[patch.crates-io]
|
||||
-tokio-tungstenite = { git = "https://github.com/openai-oss-forks/tokio-tungstenite", rev = "132f5b39c862e3a970f731d709608b3e6276d5f6" }
|
||||
-tungstenite = { git = "https://github.com/openai-oss-forks/tungstenite-rs", rev = "9200079d3b54a1ff51072e24d81fd354f085156f" }
|
||||
@@ -0,0 +1,21 @@
|
||||
Author: Danny Milosavljevic <dannym@friendly-machines.com>
|
||||
Date: 2026-02-08
|
||||
License: ASL2.0
|
||||
|
||||
Remove [patch.crates-io] and [patch.'ssh://...'] sections.
|
||||
|
||||
These sections point to git repositories which are unavailable in an
|
||||
offline build. The vendored tokio-tungstenite and tungstenite forks
|
||||
are provided as cargo-inputs instead.
|
||||
|
||||
diff -u a/Cargo.toml b/Cargo.toml
|
||||
--- a/Cargo.toml
|
||||
+++ b/Cargo.toml
|
||||
@@ -47,8 +47,2 @@
|
||||
unused = "warn"
|
||||
-
|
||||
-[patch.crates-io]
|
||||
-tokio-tungstenite = { git = "https://github.com/JakkuSakura/tokio-tungstenite", branch = "proxy-support" }
|
||||
-
|
||||
-[patch.'ssh://git@github.com/JakkuSakura/tungstenite-rs.git']
|
||||
-tungstenite = { git = "https://github.com/JakkuSakura/tungstenite-rs", branch = "proxy-support" }
|
||||
@@ -0,0 +1,52 @@
|
||||
Author: Danny Milosavljevic <dannym@friendly-machines.com>
|
||||
Date: 2026-02-08
|
||||
License: ASL2.0
|
||||
|
||||
Replace Result::flatten() with and_then(|x| x).
|
||||
|
||||
Result::flatten() was stabilized in Rust 1.89.0 but the build
|
||||
toolchain only provides Rust 1.88.0. Use the equivalent
|
||||
.and_then(|x| x) form which works on all stable Rust versions.
|
||||
|
||||
diff -u a/src/local_spawner.rs b/src/local_spawner.rs
|
||||
--- a/src/local_spawner.rs
|
||||
+++ b/src/local_spawner.rs
|
||||
@@ -156,7 +156,7 @@
|
||||
});
|
||||
rx.recv()
|
||||
.map_err(|e| std::io::Error::other(e.to_string()))
|
||||
- .flatten()
|
||||
+ .and_then(|x| x)
|
||||
}
|
||||
|
||||
fn write(&self, path: &std::path::Path, contents: &[u8]) -> std::io::Result<()> {
|
||||
@@ -174,7 +174,7 @@
|
||||
});
|
||||
rx.recv()
|
||||
.map_err(|e| std::io::Error::other(e.to_string()))
|
||||
- .flatten()
|
||||
+ .and_then(|x| x)
|
||||
}
|
||||
}
|
||||
|
||||
@@ -207,7 +207,7 @@
|
||||
let file = rx
|
||||
.await
|
||||
.map_err(|e| std::io::Error::other(e.to_string()))
|
||||
- .flatten()?;
|
||||
+ .and_then(|x| x)?;
|
||||
|
||||
Ok(Box::new(tokio::io::BufReader::new(Cursor::new(file.into_bytes()))) as _)
|
||||
})
|
||||
diff -u a/src/thread.rs b/src/thread.rs
|
||||
--- a/src/thread.rs
|
||||
+++ b/src/thread.rs
|
||||
@@ -1817,7 +1817,7 @@
|
||||
let mut new_custom_prompts = load_custom_prompts
|
||||
.await
|
||||
.map_err(|_| Error::internal_error())
|
||||
- .flatten()
|
||||
+ .and_then(|x| x)
|
||||
.inspect_err(|e| error!("Failed to load custom prompts {e:?}"))
|
||||
.unwrap_or_default();
|
||||
|
||||
16
gnu/packages/patches/git-clar-path-max.patch
Normal file
16
gnu/packages/patches/git-clar-path-max.patch
Normal file
@@ -0,0 +1,16 @@
|
||||
On GNU/Hurd, 'PATH_MAX' is undefined. Provide a reasonable default value.
|
||||
Adapted from <https://github.com/libgit2/libgit2/pull/7100>.
|
||||
|
||||
diff --git a/tests/clar/clar.h b/tests/clar/clar.h
|
||||
index ca72292ae91..98e2b14e880 100644
|
||||
--- a/t/unit-tests/clar/clar.h
|
||||
+++ b/t/unit-tests/clar/clar.h
|
||||
@@ -14,6 +14,8 @@
|
||||
# define CLAR_MAX_PATH 4096
|
||||
#elif defined(_WIN32)
|
||||
# define CLAR_MAX_PATH MAX_PATH
|
||||
+#elif !defined(PATH_MAX) /* GNU/Hurd */
|
||||
+# define CLAR_MAX_PATH 4096
|
||||
#else
|
||||
# define CLAR_MAX_PATH PATH_MAX
|
||||
#endif
|
||||
54
gnu/packages/patches/hwloc-1-test-btrfs.patch
Normal file
54
gnu/packages/patches/hwloc-1-test-btrfs.patch
Normal file
@@ -0,0 +1,54 @@
|
||||
From 093316a897a2eb4972a7a3a5888f40975d03f6bf Mon Sep 17 00:00:00 2001
|
||||
From: Brice Goglin <Brice.Goglin@inria.fr>
|
||||
Date: Tue, 5 Apr 2022 17:39:50 +0200
|
||||
Subject: [PATCH] linux: (partial) fix the discovery of hugepages on btrfs
|
||||
fsroot
|
||||
|
||||
btrfs always returns 1 in directory stat.st_nlink.
|
||||
It breaks make check in tests/linux/ because the hugepages discovery
|
||||
uses st_nlink to allocate the memory page_types array.
|
||||
|
||||
Always allocate at least 3 page_types slots
|
||||
(enough for all known cases, 1 for normal, 2 for huge pages)
|
||||
|
||||
(partially cherry-picked from commit 7f351cec9bfe54a031f35ad16c9cfb99784d76dc)
|
||||
|
||||
We don't reallocate later if needed as in 2.x commit 7f351cec9bfe54a031f35ad16c9cfb99784d76dc
|
||||
because v1.11 doesn't deserve a complete fix. Just commit the minimal change
|
||||
so that tests/linux/2i386-2t-hugepagesizecount with HWLOC_PAGESIZE_DEBUG=4096
|
||||
doesn't crash in btrfs anymore (test-topology.sh fails during make check if /tmp is in btrfs).
|
||||
|
||||
Thanks to Philippe Swartvagher for the report.
|
||||
|
||||
Signed-off-by: Brice Goglin <Brice.Goglin@inria.fr>
|
||||
---
|
||||
src/topology-linux.c | 11 +++++++++--
|
||||
1 file changed, 9 insertions(+), 2 deletions(-)
|
||||
|
||||
diff --git a/src/topology-linux.c b/src/topology-linux.c
|
||||
index 58c275fea..269eca7f5 100644
|
||||
--- a/src/topology-linux.c
|
||||
+++ b/src/topology-linux.c
|
||||
@@ -1,6 +1,6 @@
|
||||
/*
|
||||
* Copyright © 2009 CNRS
|
||||
- * Copyright © 2009-2019 Inria. All rights reserved.
|
||||
+ * Copyright © 2009-2022 Inria. All rights reserved.
|
||||
* Copyright © 2009-2013, 2015 Université Bordeaux
|
||||
* Copyright © 2009-2014 Cisco Systems, Inc. All rights reserved.
|
||||
* Copyright © 2015 Intel, Inc. All rights reserved.
|
||||
@@ -2329,7 +2329,14 @@ hwloc_get_procfs_meminfo_info(struct hwloc_topology *topology,
|
||||
|
||||
err = hwloc_stat("/sys/kernel/mm/hugepages", &st, data->root_fd);
|
||||
if (!err) {
|
||||
- types = 1 + st.st_nlink-2;
|
||||
+ types = 1 /* normal non-huge size */ + st.st_nlink - 2 /* ignore . and .. */;
|
||||
+ if (types < 3)
|
||||
+ /* some buggy filesystems (e.g. btrfs when reading from fsroot)
|
||||
+ * return wrong st_nlink for directories (always 1 for btrfs).
|
||||
+ * use 3 as a sane default (default page + 2 huge sizes).
|
||||
+ * hwloc_parse_hugepages_info() will extend it if needed.
|
||||
+ */
|
||||
+ types = 3;
|
||||
has_sysfs_hugepages = 1;
|
||||
}
|
||||
@@ -1,26 +0,0 @@
|
||||
To be remove when updating inetutils.
|
||||
See
|
||||
https://cgit.git.savannah.gnu.org/cgit/inetutils.git/commit/?id=556621adc3dcb62dbb28c54905cef15837947115
|
||||
https://codeberg.org/guix/guix/issues/7995
|
||||
|
||||
diff --git a/tests/libls.sh b/tests/libls.sh
|
||||
index 827020f2..9fdef8be 100755
|
||||
--- a/tests/libls.sh
|
||||
+++ b/tests/libls.sh
|
||||
@@ -91,7 +91,6 @@ REPLY_a1=`$LS -a1 $LSDIR`
|
||||
REPLY_A1=`$LS -A1 $LSDIR`
|
||||
|
||||
REPLY_C=`$LS -C $LSDIR`
|
||||
-REPLY_Cf=`$LS -Cf $LSDIR`
|
||||
REPLY_Cr=`$LS -Cr $LSDIR`
|
||||
REPLY_Ct=`$LS -Ct $LSDIR`
|
||||
REPLY_x=`$LS -x $LSDIR`
|
||||
@@ -130,9 +129,6 @@ test `echo "$diff" | $GREP -c -v '^[.]\{1,2\}$'` -eq 0 ||
|
||||
fi
|
||||
}
|
||||
|
||||
-test x"$REPLY_C" != x"$REPLY_Cf" ||
|
||||
- { errno=1; echo >&2 'Failed to disable sorting with "-f".'; }
|
||||
-
|
||||
test x"$REPLY_C" != x"$REPLY_Cr" ||
|
||||
{ errno=1; echo >&2 'Failed to reverse sorting with "-r".'; }
|
||||
43
gnu/packages/patches/libfossil-skip-amalgamation.patch
Normal file
43
gnu/packages/patches/libfossil-skip-amalgamation.patch
Normal file
@@ -0,0 +1,43 @@
|
||||
--- a/Makefile.in
|
||||
+++ b/Makefile.in
|
||||
@@ -265,15 +265,11 @@
|
||||
amal.flags = -nc
|
||||
amal.run = TOPDIR="$(DIR.top)" $(SHELL.bash) $(bin.make-amal) --quiet
|
||||
|
||||
libfossil.c: $(amal.deps)
|
||||
$(amal.run) $(amal.flags)
|
||||
-libfossil.h: libfossil.c
|
||||
-all: libfossil.c
|
||||
@if ENABLE_CXX
|
||||
-libfossil.hpp: libfossil.c
|
||||
-libfossil.c++: libfossil.c
|
||||
amal.flags += -c++
|
||||
@endif
|
||||
|
||||
.PHONY: amal
|
||||
amal: libfossil.c
|
||||
@@ -287,19 +283,16 @@
|
||||
fossil uv sync
|
||||
@endif
|
||||
@endif
|
||||
|
||||
install: install-headers
|
||||
-install-headers: libfossil.h $(install-dir.include)
|
||||
- $(INSTALL.noexec) libfossil.h $(install-dir.include)
|
||||
+install-headers: include/libfossil.h $(install-dir.include)
|
||||
+ $(INSTALL.noexec) $< $(install-dir.include)
|
||||
@if ENABLE_CXX
|
||||
-libfossil++.hpp: libfossil.h
|
||||
-libfossil++.cpp: libfossil++.hpp
|
||||
-all: libfossil++.cpp
|
||||
install-headers: install-headers++
|
||||
-install-headers++: libfossil++.hpp $(install-dir.include)
|
||||
- $(INSTALL.noexec) libfossil++.hpp $(install-dir.include)
|
||||
+install-headers++: include/libfossil.hpp $(install-dir.include)
|
||||
+ $(INSTALL.noexec) $< $(install-dir.include)
|
||||
@endif # ENABLE_CXX
|
||||
clean: clean-amalgamation
|
||||
clean-amalgamation:
|
||||
rm -f libfossil.c libfossil.h libfossil++.cpp libfossil++.hpp
|
||||
rm -f libfossil-config.h libfossil-amalgamation.zip VERSION.h
|
||||
|
||||
@@ -1,260 +0,0 @@
|
||||
From d8702527f4f1f67f765330f5018bfcb182946c45 Mon Sep 17 00:00:00 2001
|
||||
From: Henri Sivonen <hsivonen@hsivonen.fi>
|
||||
Date: Tue, 21 Apr 2026 07:09:20 +0000
|
||||
Subject: [PATCH] Bug 2033279 - Make --enable-rust-simd work with Rust 1.95.
|
||||
r=firefox-build-system-reviewers,supply-chain-reviewers,ahochheiden
|
||||
|
||||
Differential Revision: https://phabricator.services.mozilla.com/D295287
|
||||
---
|
||||
.cargo/config.toml.in | 5 ++
|
||||
Cargo.lock | 4 +-
|
||||
Cargo.toml | 2 +
|
||||
supply-chain/audits.toml | 6 ++
|
||||
supply-chain/config.toml | 4 ++
|
||||
.../rust/encoding_rs/.cargo-checksum.json | 2 +-
|
||||
.../rust/encoding_rs/.cargo_vcs_info.json | 6 --
|
||||
third_party/rust/encoding_rs/Cargo.toml | 60 ++++++++++---------
|
||||
third_party/rust/encoding_rs/Cargo.toml.orig | 45 --------------
|
||||
.../rust/encoding_rs/src/x_user_defined.rs | 2 +
|
||||
10 files changed, 54 insertions(+), 82 deletions(-)
|
||||
delete mode 100644 third_party/rust/encoding_rs/.cargo_vcs_info.json
|
||||
delete mode 100644 third_party/rust/encoding_rs/Cargo.toml.orig
|
||||
|
||||
diff --git a/.cargo/config.toml.in b/.cargo/config.toml.in
|
||||
index 8013ae5435dab..cabdee463415f 100644
|
||||
--- a/.cargo/config.toml.in
|
||||
+++ b/.cargo/config.toml.in
|
||||
@@ -55,6 +55,11 @@ git = "https://github.com/hsivonen/any_all_workaround"
|
||||
rev = "7fb1b7034c9f172aade21ee1c8554e8d8a48af80"
|
||||
replace-with = "vendored-sources"
|
||||
|
||||
+[source."git+https://github.com/hsivonen/encoding_rs?rev=1236d1bc423e6ba35a06485f74a6304db2d703b5"]
|
||||
+git = "https://github.com/hsivonen/encoding_rs"
|
||||
+rev = "1236d1bc423e6ba35a06485f74a6304db2d703b5"
|
||||
+replace-with = "vendored-sources"
|
||||
+
|
||||
[source."git+https://github.com/hsivonen/rust-harfbuzz?rev=9d58a23a98772a197291d04af93f7041b7093d95"]
|
||||
git = "https://github.com/hsivonen/rust-harfbuzz"
|
||||
rev = "9d58a23a98772a197291d04af93f7041b7093d95"
|
||||
diff --git a/Cargo.lock b/Cargo.lock
|
||||
index fea2f95fbb438..63b1f818d7971 100644
|
||||
--- a/Cargo.lock
|
||||
+++ b/Cargo.lock
|
||||
@@ -1914,11 +1914,11 @@ dependencies = [
|
||||
[[package]]
|
||||
name = "encoding_rs"
|
||||
version = "0.8.35"
|
||||
-source = "registry+https://github.com/rust-lang/crates.io-index"
|
||||
-checksum = "75030f3c4f45dafd7586dd6780965a8c7e8e285a5ecb86713e63a79c5b2766f3"
|
||||
+source = "git+https://github.com/hsivonen/encoding_rs?rev=1236d1bc423e6ba35a06485f74a6304db2d703b5#1236d1bc423e6ba35a06485f74a6304db2d703b5"
|
||||
dependencies = [
|
||||
"any_all_workaround",
|
||||
"cfg-if",
|
||||
+ "rustversion",
|
||||
]
|
||||
|
||||
[[package]]
|
||||
diff --git a/Cargo.toml b/Cargo.toml
|
||||
index 49c695809f302..2648c32ae57e8 100644
|
||||
--- a/Cargo.toml
|
||||
+++ b/Cargo.toml
|
||||
@@ -287,6 +287,8 @@ harfbuzz-sys = { git = "https://github.com/hsivonen/rust-harfbuzz", rev = "9d58a
|
||||
harfbuzz = { git = "https://github.com/hsivonen/rust-harfbuzz", rev = "9d58a23a98772a197291d04af93f7041b7093d95" }
|
||||
# Also vendor `harfbuzz-traits` to keep cargo-vendor happy.
|
||||
harfbuzz-traits = { git = "https://github.com/hsivonen/rust-harfbuzz", rev = "9d58a23a98772a197291d04af93f7041b7093d95" }
|
||||
+# Make --enable-rust-simd compatible with Rust 1.95
|
||||
+encoding_rs = { git = "https://github.com/hsivonen/encoding_rs", rev = "1236d1bc423e6ba35a06485f74a6304db2d703b5" }
|
||||
|
||||
# objc 0.2.7 + fa7ca43b862861dd1cd000d7ad01e6e0266cda13
|
||||
objc = { git = "https://github.com/glandium/rust-objc", rev = "4de89f5aa9851ceca4d40e7ac1e2759410c04324" }
|
||||
diff --git a/supply-chain/audits.toml b/supply-chain/audits.toml
|
||||
index 85b4037e03bdb..f4567ea6b6f94 100644
|
||||
--- a/supply-chain/audits.toml
|
||||
+++ b/supply-chain/audits.toml
|
||||
@@ -2385,6 +2385,12 @@ who = "Mike Hommey <mh+mozilla@glandium.org>"
|
||||
criteria = "safe-to-deploy"
|
||||
delta = "0.8.31 -> 0.8.32"
|
||||
|
||||
+[[audits.encoding_rs]]
|
||||
+who = "Henri Sivonen <hsivonen@hsivonen.fi>"
|
||||
+criteria = "safe-to-deploy"
|
||||
+delta = "0.8.35 -> 0.8.35@git:1236d1bc423e6ba35a06485f74a6304db2d703b5"
|
||||
+importable = false
|
||||
+
|
||||
[[audits.enum-map]]
|
||||
who = "Kershaw Chang <kershaw@mozilla.com>"
|
||||
criteria = "safe-to-deploy"
|
||||
diff --git a/supply-chain/config.toml b/supply-chain/config.toml
|
||||
index 4cfd83dc2d608..15deefbec0574 100644
|
||||
--- a/supply-chain/config.toml
|
||||
+++ b/supply-chain/config.toml
|
||||
@@ -39,6 +39,10 @@ notes = "This is the upstream code not yet released"
|
||||
audit-as-crates-io = true
|
||||
notes = "This is upstream plus a warning fix from bug 1823866."
|
||||
|
||||
+[policy.encoding_rs]
|
||||
+audit-as-crates-io = true
|
||||
+notes = "This is upstream plus a build fix for bug 2033279."
|
||||
+
|
||||
[policy.firefox-on-glean]
|
||||
audit-as-crates-io = false
|
||||
notes = "The crates.io version of this is just a placeholder to allow public crates to depend on firefox-on-glean."
|
||||
diff --git a/third_party/rust/encoding_rs/.cargo_vcs_info.json b/third_party/rust/encoding_rs/.cargo_vcs_info.json
|
||||
deleted file mode 100644
|
||||
index 6e5d699759e43..0000000000000
|
||||
--- a/third_party/rust/encoding_rs/.cargo_vcs_info.json
|
||||
+++ /dev/null
|
||||
@@ -1,6 +0,0 @@
|
||||
-{
|
||||
- "git": {
|
||||
- "sha1": "2fa58aecf537cc76ff52c0eb3d5e9f8fda466844"
|
||||
- },
|
||||
- "path_in_vcs": ""
|
||||
-}
|
||||
\ No newline at end of file
|
||||
diff --git a/third_party/rust/encoding_rs/Cargo.toml b/third_party/rust/encoding_rs/Cargo.toml
|
||||
index 2adac351c2edf..0239315bab180 100644
|
||||
--- a/third_party/rust/encoding_rs/Cargo.toml
|
||||
+++ b/third_party/rust/encoding_rs/Cargo.toml
|
||||
@@ -16,6 +16,7 @@ name = "encoding_rs"
|
||||
version = "0.8.35"
|
||||
authors = ["Henri Sivonen <hsivonen@hsivonen.fi>"]
|
||||
build = false
|
||||
+autolib = false
|
||||
autobins = false
|
||||
autoexamples = false
|
||||
autotests = false
|
||||
@@ -39,33 +40,6 @@ categories = [
|
||||
license = "(Apache-2.0 OR MIT) AND BSD-3-Clause"
|
||||
repository = "https://github.com/hsivonen/encoding_rs"
|
||||
|
||||
-[profile.release]
|
||||
-lto = true
|
||||
-
|
||||
-[lib]
|
||||
-name = "encoding_rs"
|
||||
-path = "src/lib.rs"
|
||||
-
|
||||
-[dependencies.any_all_workaround]
|
||||
-version = "0.1.0"
|
||||
-optional = true
|
||||
-
|
||||
-[dependencies.cfg-if]
|
||||
-version = "1.0"
|
||||
-
|
||||
-[dependencies.serde]
|
||||
-version = "1.0"
|
||||
-optional = true
|
||||
-
|
||||
-[dev-dependencies.bincode]
|
||||
-version = "1.0"
|
||||
-
|
||||
-[dev-dependencies.serde_derive]
|
||||
-version = "1.0"
|
||||
-
|
||||
-[dev-dependencies.serde_json]
|
||||
-version = "1.0"
|
||||
-
|
||||
[features]
|
||||
alloc = []
|
||||
default = ["alloc"]
|
||||
@@ -84,4 +58,34 @@ fast-legacy-encode = [
|
||||
less-slow-big5-hanzi-encode = []
|
||||
less-slow-gb-hanzi-encode = []
|
||||
less-slow-kanji-encode = []
|
||||
-simd-accel = ["any_all_workaround"]
|
||||
+simd-accel = [
|
||||
+ "any_all_workaround",
|
||||
+ "rustversion",
|
||||
+]
|
||||
+
|
||||
+[lib]
|
||||
+name = "encoding_rs"
|
||||
+path = "src/lib.rs"
|
||||
+
|
||||
+[dependencies]
|
||||
+cfg-if = "1.0"
|
||||
+
|
||||
+[dependencies.any_all_workaround]
|
||||
+version = "0.1.0"
|
||||
+optional = true
|
||||
+
|
||||
+[dependencies.rustversion]
|
||||
+version = "1.0.19"
|
||||
+optional = true
|
||||
+
|
||||
+[dependencies.serde]
|
||||
+version = "1.0"
|
||||
+optional = true
|
||||
+
|
||||
+[dev-dependencies]
|
||||
+bincode = "1.0"
|
||||
+serde_derive = "1.0"
|
||||
+serde_json = "1.0"
|
||||
+
|
||||
+[profile.release]
|
||||
+lto = true
|
||||
diff --git a/third_party/rust/encoding_rs/Cargo.toml.orig b/third_party/rust/encoding_rs/Cargo.toml.orig
|
||||
deleted file mode 100644
|
||||
index 0f7639d5f879b..0000000000000
|
||||
--- a/third_party/rust/encoding_rs/Cargo.toml.orig
|
||||
+++ /dev/null
|
||||
@@ -1,45 +0,0 @@
|
||||
-[package]
|
||||
-name = "encoding_rs"
|
||||
-description = "A Gecko-oriented implementation of the Encoding Standard"
|
||||
-version = "0.8.35"
|
||||
-edition = '2018'
|
||||
-authors = ["Henri Sivonen <hsivonen@hsivonen.fi>"]
|
||||
-license = "(Apache-2.0 OR MIT) AND BSD-3-Clause"
|
||||
-readme = "README.md"
|
||||
-documentation = "https://docs.rs/encoding_rs/"
|
||||
-homepage = "https://docs.rs/encoding_rs/"
|
||||
-repository = "https://github.com/hsivonen/encoding_rs"
|
||||
-keywords = ["encoding", "web", "unicode", "charset"]
|
||||
-categories = ["text-processing", "encoding", "web-programming", "internationalization"]
|
||||
-rust-version = "1.36"
|
||||
-
|
||||
-[features]
|
||||
-default = ["alloc"]
|
||||
-alloc = []
|
||||
-simd-accel = ["any_all_workaround"]
|
||||
-less-slow-kanji-encode = []
|
||||
-less-slow-big5-hanzi-encode = []
|
||||
-less-slow-gb-hanzi-encode = []
|
||||
-fast-hangul-encode = []
|
||||
-fast-hanja-encode = []
|
||||
-fast-kanji-encode = []
|
||||
-fast-gb-hanzi-encode = []
|
||||
-fast-big5-hanzi-encode = []
|
||||
-fast-legacy-encode = ["fast-hangul-encode",
|
||||
- "fast-hanja-encode",
|
||||
- "fast-kanji-encode",
|
||||
- "fast-gb-hanzi-encode",
|
||||
- "fast-big5-hanzi-encode"]
|
||||
-
|
||||
-[dependencies]
|
||||
-cfg-if = "1.0"
|
||||
-serde = { version = "1.0", optional = true }
|
||||
-any_all_workaround = { version = "0.1.0" , optional = true }
|
||||
-
|
||||
-[dev-dependencies]
|
||||
-serde_derive = "1.0"
|
||||
-bincode = "1.0"
|
||||
-serde_json = "1.0"
|
||||
-
|
||||
-[profile.release]
|
||||
-lto = true
|
||||
diff --git a/third_party/rust/encoding_rs/src/x_user_defined.rs b/third_party/rust/encoding_rs/src/x_user_defined.rs
|
||||
index 7af7d5e3d69da..16f1a18d7f6ce 100644
|
||||
--- a/third_party/rust/encoding_rs/src/x_user_defined.rs
|
||||
+++ b/third_party/rust/encoding_rs/src/x_user_defined.rs
|
||||
@@ -16,7 +16,8 @@ cfg_if! {
|
||||
use simd_funcs::*;
|
||||
use core::simd::u16x8;
|
||||
use core::simd::cmp::SimdPartialOrd;
|
||||
+ #[rustversion::since(1.95)]
|
||||
use core::simd::Select;
|
||||
|
||||
#[inline(always)]
|
||||
fn shift_upper(unpacked: u16x8) -> u16x8 {
|
||||
@@ -1,513 +0,0 @@
|
||||
This patch shas been backported from the development version or Biostrings.
|
||||
|
||||
From 100602242840322b5f6c267faaf8198c1a5aa2af Mon Sep 17 00:00:00 2001
|
||||
From: =?UTF-8?q?Herv=C3=A9=20Pag=C3=A8s?= <hpages.on.github@gmail.com>
|
||||
Date: Thu, 5 Mar 2026 22:36:30 -0800
|
||||
Subject: [PATCH] Biostrings 2.79.5: Get rid of never-used SparseMIndex and
|
||||
SparseList classes
|
||||
|
||||
This also eliminates the non-API calls to R.
|
||||
---
|
||||
DESCRIPTION | 3 +-
|
||||
NAMESPACE | 2 -
|
||||
R/MIndex-class.R | 79 -------------------------
|
||||
R/SparseList-class.R | 80 -------------------------
|
||||
man/Biostrings-internals.Rd | 9 ---
|
||||
src/Biostrings.h | 41 -------------
|
||||
src/MIndex_class.c | 67 ---------------------
|
||||
src/R_init_Biostrings.c | 1 -
|
||||
src/SparseList_utils.c | 113 ------------------------------------
|
||||
9 files changed, 1 insertion(+), 394 deletions(-)
|
||||
delete mode 100644 R/SparseList-class.R
|
||||
delete mode 100644 src/SparseList_utils.c
|
||||
|
||||
diff --git a/DESCRIPTION b/DESCRIPTION
|
||||
index a5d027cc..dbc323ea 100644
|
||||
--- a/DESCRIPTION
|
||||
+++ b/DESCRIPTION
|
||||
@@ -76,3 +76,3 @@ Collate: utils.R IUPAC_CODE_MAP.R AMINO_ACID_CODE.R GENETIC_CODE.R
|
||||
injectHardMask.R padAndClip.R strsplit-methods.R misc.R
|
||||
- SparseList-class.R MIndex-class.R lowlevel-matching.R
|
||||
+ MIndex-class.R lowlevel-matching.R
|
||||
match-utils.R matchPattern.R maskMotif.R matchLRPatterns.R
|
||||
diff --git a/NAMESPACE b/NAMESPACE
|
||||
index ba1e3bfa..cf14db67 100644
|
||||
--- a/NAMESPACE
|
||||
+++ b/NAMESPACE
|
||||
@@ -206,7 +206,6 @@ exportMethods(
|
||||
### ==========================================================================
|
||||
### STRING MATCHING
|
||||
### --------------------------------------------------------------------------
|
||||
-### SparseList-class.R
|
||||
### MIndex-class.R
|
||||
### lowlevel-matching.R
|
||||
### match-utils.R
|
||||
@@ -220,7 +219,6 @@ exportMethods(
|
||||
### matchPDict.R
|
||||
|
||||
exportClasses(
|
||||
- #SparseList,
|
||||
MIndex, ByPos_MIndex,
|
||||
PreprocessedTB, Twobit, ACtree2,
|
||||
PDict3Parts,
|
||||
diff --git a/R/MIndex-class.R b/R/MIndex-class.R
|
||||
index 022f6746..f50f215e 100644
|
||||
--- a/R/MIndex-class.R
|
||||
+++ b/R/MIndex-class.R
|
||||
@@ -218,82 +218,3 @@ ByPos_MIndex.combine <- function(mi_list)
|
||||
new("ByPos_MIndex", width0=ans_width0, NAMES=ans_names, ends=ans_ends)
|
||||
}
|
||||
|
||||
-
|
||||
-### - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
|
||||
-### The "SparseMIndex" class (DISABLED FOR NOW).
|
||||
-###
|
||||
-### Slot description:
|
||||
-###
|
||||
-### ends_envir: a key-value list (environment) where the values are integer
|
||||
-### vectors containing the ending positions of the pattern whose
|
||||
-### position in the original dictionary is given by the key (the keys are
|
||||
-### strings representing positive integers).
|
||||
-###
|
||||
-
|
||||
-if (FALSE) {
|
||||
-
|
||||
- setClass("SparseMIndex",
|
||||
- contains="MIndex",
|
||||
- representation(
|
||||
- ends_envir="environment"
|
||||
- )
|
||||
- )
|
||||
-
|
||||
- setMethod("show", "SparseMIndex",
|
||||
- function(object)
|
||||
- {
|
||||
- cat("Sparse MIndex object of length ", length(object), "\n", sep="")
|
||||
- }
|
||||
- )
|
||||
-
|
||||
- setMethod("[[", "SparseMIndex",
|
||||
- function(x, i, j, ...)
|
||||
- {
|
||||
- i <- normalizeDoubleBracketSubscript(i, x)
|
||||
- ans_end <- x@ends_envir[[formatC(i, width=10, format="d", flag="0")]]
|
||||
- if (is.null(ans_end))
|
||||
- ans_end <- integer(0)
|
||||
- ans_width <- rep.int(x@width0[i], length(ans_end))
|
||||
- ans_start <- ans_end - x@width0[i] + 1L
|
||||
- new2("IRanges", start=ans_start, width=ans_width, check=FALSE)
|
||||
- }
|
||||
- )
|
||||
-
|
||||
- ### An example of a SparseMIndex object of length 5 where only the
|
||||
- ### 2nd pattern has matches:
|
||||
- ### > width0 <- c(9L, 10L, 8L, 4L, 10L)
|
||||
- ### > ends_envir <- new.env(hash=TRUE, parent=emptyenv())
|
||||
- ### > ends_envir[['0000000002']] <- c(199L, 402L)
|
||||
- ### > mindex <- new("SparseMIndex", width0=width0, NAMES=letters[1:5], ends_envir=ends_envir)
|
||||
- ### > mindex[[1]]
|
||||
- ### > mindex[[2]]
|
||||
- ### > mindex[[6]] # Error in mindex[[6]] : subscript out of bounds
|
||||
- ### > names(mindex)
|
||||
- ### > mindex[["a"]]
|
||||
- ### > mindex[["b"]]
|
||||
- ### > mindex[["aa"]] # Error in mindex[["aa"]] : pattern name ‘aa’ not found
|
||||
- ### > startIndex(mindex)
|
||||
- ### > endIndex(mindex)
|
||||
- ### > elementNROWS(mindex)
|
||||
- ###
|
||||
- setMethod("startIndex", "SparseMIndex",
|
||||
- function(x)
|
||||
- {
|
||||
- all.names <- TRUE
|
||||
- .Call2("SparseMIndex_endIndex",
|
||||
- x@ends_envir, x@width0, x@NAMES, all.names,
|
||||
- PACKAGE="Biostrings")
|
||||
- }
|
||||
- )
|
||||
- setMethod("endIndex", "SparseMIndex",
|
||||
- function(x)
|
||||
- {
|
||||
- all.names <- TRUE
|
||||
- .Call2("SparseMIndex_endIndex",
|
||||
- x@ends_envir, NULL, x@NAMES, all.names,
|
||||
- PACKAGE="Biostrings")
|
||||
- }
|
||||
- )
|
||||
-
|
||||
-}
|
||||
-
|
||||
diff --git a/R/SparseList-class.R b/R/SparseList-class.R
|
||||
deleted file mode 100644
|
||||
index 8295fd0f..00000000
|
||||
--- a/R/SparseList-class.R
|
||||
+++ /dev/null
|
||||
@@ -1,80 +0,0 @@
|
||||
-### =========================================================================
|
||||
-### SparseList objects
|
||||
-### -------------------------------------------------------------------------
|
||||
-###
|
||||
-
|
||||
-setClass("SparseList",
|
||||
- representation(
|
||||
- length="integer",
|
||||
- env="environment"
|
||||
- )
|
||||
-)
|
||||
-
|
||||
-### Typical use:
|
||||
-### env <- new.env(hash=TRUE, parent=emptyenv())
|
||||
-### key <- formatC(98L, width=10, format="d", flag="0")
|
||||
-### value <- 3:-2
|
||||
-### assign(key, value, envir=env)
|
||||
-### x <- new("SparseList", length=100L, env=env)
|
||||
-### length(x)
|
||||
-### ls(x)
|
||||
-### ls(x, all.names=TRUE)
|
||||
-### as.list(x)
|
||||
-### as.list(x, all.names=TRUE)
|
||||
-### x[[1]]
|
||||
-### x[[98]
|
||||
-### x[[101]]]
|
||||
-###
|
||||
-
|
||||
-setMethod("length", "SparseList", function(x) x@length)
|
||||
-
|
||||
-### 'pos', 'envir' and 'pattern' args are ignored
|
||||
-setMethod("ls", signature(name="SparseList"),
|
||||
- function(name, pos, envir, all.names=FALSE, pattern)
|
||||
- {
|
||||
- if (!all.names)
|
||||
- return(ls(name@env, all.names=TRUE))
|
||||
- seq_len(length(name))
|
||||
- }
|
||||
-)
|
||||
-
|
||||
-setMethod("as.list", "SparseList",
|
||||
- function(x, all.names=FALSE, ...)
|
||||
- {
|
||||
- if (!all.names)
|
||||
- return(as.list(x@env, all.names=TRUE))
|
||||
- ans <- vector(mode="list", length=length(x))
|
||||
- symbols <- ls(x)
|
||||
- for (symb in symbols)
|
||||
- ans[[as.integer(symb)]] <- get(symb, envir=x@env)
|
||||
- ans
|
||||
- }
|
||||
-)
|
||||
-
|
||||
-### Supported 'i' types: character or numeric vector of length 1.
|
||||
-setMethod("[[", "SparseList",
|
||||
- function(x, i, j, ...)
|
||||
- {
|
||||
- if (!missing(j) || length(list(...)) > 0)
|
||||
- stop("invalid subsetting")
|
||||
- if (missing(i))
|
||||
- stop("subscript is missing")
|
||||
- if (!is.character(i) && !is.numeric(i))
|
||||
- stop("invalid subscript type")
|
||||
- if (length(i) < 1L)
|
||||
- stop("attempt to select less than one element")
|
||||
- if (length(i) > 1L)
|
||||
- stop("attempt to select more than one element")
|
||||
- if (is.na(i))
|
||||
- stop("subscript cannot be NA")
|
||||
- if (is.character(i))
|
||||
- return(get(i, envir=x@env))
|
||||
- if (!is.integer(i))
|
||||
- i <- as.integer(i)
|
||||
- if (i < 1L || i > length(x))
|
||||
- stop("subscript out of bounds")
|
||||
- i <- formatC(i, width=10, format="d", flag="0")
|
||||
- get(i, envir=x@env)
|
||||
- }
|
||||
-)
|
||||
-
|
||||
diff --git a/man/Biostrings-internals.Rd b/man/Biostrings-internals.Rd
|
||||
index 791b0870..609b7694 100644
|
||||
--- a/man/Biostrings-internals.Rd
|
||||
+++ b/man/Biostrings-internals.Rd
|
||||
@@ -26,15 +26,6 @@
|
||||
\alias{make_XStringSet_from_strings}
|
||||
\alias{make_XStringSet_from_strings,XStringSet-method}
|
||||
|
||||
-% SparseList class and methods:
|
||||
-\alias{class:SparseList}
|
||||
-\alias{SparseList-class}
|
||||
-\alias{SparseList}
|
||||
-
|
||||
-\alias{length,SparseList-method}
|
||||
-%\alias{ls,SparseList-method}
|
||||
-\alias{as.list,SparseList-method}
|
||||
-\alias{[[,SparseList-method}
|
||||
|
||||
\title{Biostrings internals}
|
||||
|
||||
diff --git a/src/Biostrings.h b/src/Biostrings.h
|
||||
index 6e725bd5..e86d0ff2 100644
|
||||
--- a/src/Biostrings.h
|
||||
+++ b/src/Biostrings.h
|
||||
@@ -446,40 +446,6 @@ SEXP XStringSetList_unstrsplit(
|
||||
);
|
||||
|
||||
|
||||
-/* SparseList_utils.c */
|
||||
-
|
||||
-SEXP _SparseList_int2symb(int symb_as_int);
|
||||
-
|
||||
-int _SparseList_symb2int(SEXP symbol);
|
||||
-
|
||||
-SEXP _get_val_from_env(
|
||||
- SEXP symbol,
|
||||
- SEXP env,
|
||||
- int error_on_unbound_value
|
||||
-);
|
||||
-
|
||||
-SEXP _get_val_from_SparseList(
|
||||
- int symb_as_int,
|
||||
- SEXP env,
|
||||
- int error_on_unbound_value
|
||||
-);
|
||||
-
|
||||
-int _get_int_from_SparseList(
|
||||
- int symb_as_int,
|
||||
- SEXP env
|
||||
-);
|
||||
-
|
||||
-void _set_env_from_IntAE(
|
||||
- SEXP env,
|
||||
- const IntAE *int_ae
|
||||
-);
|
||||
-
|
||||
-void _set_env_from_IntAEAE(
|
||||
- SEXP env,
|
||||
- const IntAEAE *int_aeae
|
||||
-);
|
||||
-
|
||||
-
|
||||
/* match_reporting.c */
|
||||
|
||||
int _get_match_storing_code(const char *ms_mode);
|
||||
@@ -558,13 +524,6 @@ SEXP ByPos_MIndex_endIndex(
|
||||
SEXP x_width0
|
||||
);
|
||||
|
||||
-SEXP SparseMIndex_endIndex(
|
||||
- SEXP x_ends_envir,
|
||||
- SEXP x_width0,
|
||||
- SEXP x_names,
|
||||
- SEXP all_names
|
||||
-);
|
||||
-
|
||||
SEXP ByPos_MIndex_combine(SEXP ends_listlist);
|
||||
|
||||
|
||||
diff --git a/src/MIndex_class.c b/src/MIndex_class.c
|
||||
index 00212fe9..dd6ad546 100644
|
||||
--- a/src/MIndex_class.c
|
||||
+++ b/src/MIndex_class.c
|
||||
@@ -157,73 +157,6 @@ SEXP ByPos_MIndex_endIndex(SEXP x_high2low, SEXP x_ends, SEXP x_width0)
|
||||
return ans;
|
||||
}
|
||||
|
||||
-/*
|
||||
- * --- .Call ENTRY POINT ---
|
||||
- * All the keys in 'x_ends_envir' must be representing integers left-padded with 0s
|
||||
- * so they have the same length. This works properly:
|
||||
- library(Biostrings)
|
||||
- ends_envir <- new.env(parent=emptyenv())
|
||||
- ends_envir[['0000000010']] <- -2:1
|
||||
- ends_envir[['0000000004']] <- 9:6
|
||||
- .Call("SparseMIndex_endIndex",
|
||||
- ends_envir, NULL, letters[1:10], TRUE,
|
||||
- PACKAGE="Biostrings")
|
||||
- .Call("SparseMIndex_endIndex",
|
||||
- ends_envir, NULL, letters[1:10], FALSE,
|
||||
- PACKAGE="Biostrings")
|
||||
- * but this doesn't:
|
||||
- ends_envir[['3']] <- 33L
|
||||
- .Call("SparseMIndex_endIndex",
|
||||
- ends_envir, NULL, letters[1:10], FALSE,
|
||||
- PACKAGE="Biostrings")
|
||||
- */
|
||||
-SEXP SparseMIndex_endIndex(SEXP x_ends_envir, SEXP x_width0, SEXP x_names, SEXP all_names)
|
||||
-{
|
||||
- SEXP ans, ans_elt, ans_names, symbols, end;
|
||||
- int nelt, i, j;
|
||||
- IntAE *poffsets, *poffsets_order;
|
||||
-
|
||||
- PROTECT(symbols = R_lsInternal(x_ends_envir, 1));
|
||||
- poffsets = new_IntAE_from_CHARACTER(symbols, -1);
|
||||
- nelt = IntAE_get_nelt(poffsets);
|
||||
- if (LOGICAL(all_names)[0]) {
|
||||
- PROTECT(ans = NEW_LIST(LENGTH(x_names)));
|
||||
- for (i = 0; i < nelt; i++) {
|
||||
- j = poffsets->elts[i];
|
||||
- end = _get_val_from_env(STRING_ELT(symbols, i), x_ends_envir, 1);
|
||||
- PROTECT(ans_elt = duplicate(end));
|
||||
- if (x_width0 != R_NilValue)
|
||||
- add_val_to_INTEGER(ans_elt, 1 - INTEGER(x_width0)[j]);
|
||||
- SET_ELEMENT(ans, j, ans_elt);
|
||||
- UNPROTECT(1);
|
||||
- }
|
||||
- SET_NAMES(ans, duplicate(x_names));
|
||||
- UNPROTECT(1);
|
||||
- } else {
|
||||
- //poffsets_order = new_IntAE(nelt, 0, 0);
|
||||
- //get_order_of_int_array(poffsets->elts, nelt, 0, 0,
|
||||
- // poffsets_order->elts, 0);
|
||||
- //IntAE_set_nelt(poffsets_order) = nelt; /* = poffsets_order->_buflength */
|
||||
- PROTECT(ans = NEW_LIST(nelt));
|
||||
- PROTECT(ans_names = NEW_CHARACTER(nelt));
|
||||
- for (i = 0; i < nelt; i++) {
|
||||
- //j = poffsets_order->elts[i];
|
||||
- j = i;
|
||||
- end = _get_val_from_env(STRING_ELT(symbols, j), x_ends_envir, 1);
|
||||
- PROTECT(ans_elt = duplicate(end));
|
||||
- if (x_width0 != R_NilValue)
|
||||
- add_val_to_INTEGER(ans_elt, 1 - INTEGER(x_width0)[i]);
|
||||
- SET_ELEMENT(ans, i, ans_elt);
|
||||
- UNPROTECT(1);
|
||||
- SET_STRING_ELT(ans_names, i, duplicate(STRING_ELT(x_names, poffsets->elts[j])));
|
||||
- }
|
||||
- SET_NAMES(ans, ans_names);
|
||||
- UNPROTECT(2);
|
||||
- }
|
||||
- UNPROTECT(1);
|
||||
- return ans;
|
||||
-}
|
||||
-
|
||||
/*
|
||||
* --- .Call ENTRY POINT ---
|
||||
*/
|
||||
diff --git a/src/R_init_Biostrings.c b/src/R_init_Biostrings.c
|
||||
index 4d2943f8..c1410dbd 100644
|
||||
--- a/src/R_init_Biostrings.c
|
||||
+++ b/src/R_init_Biostrings.c
|
||||
@@ -88,7 +88,6 @@ static const R_CallMethodDef callMethods[] = {
|
||||
|
||||
/* MIndex_class.c */
|
||||
CALLMETHOD_DEF(ByPos_MIndex_endIndex, 3),
|
||||
- CALLMETHOD_DEF(SparseMIndex_endIndex, 4),
|
||||
CALLMETHOD_DEF(ByPos_MIndex_combine, 1),
|
||||
|
||||
/* lowlevel_matching.c */
|
||||
diff --git a/src/SparseList_utils.c b/src/SparseList_utils.c
|
||||
deleted file mode 100644
|
||||
index 18597b55..00000000
|
||||
--- a/src/SparseList_utils.c
|
||||
+++ /dev/null
|
||||
@@ -1,113 +0,0 @@
|
||||
-/****************************************************************************
|
||||
- * Fast SparseList utilities *
|
||||
- * Author: H. Pag\`es *
|
||||
- ****************************************************************************/
|
||||
-#include "Biostrings.h"
|
||||
-#include "S4Vectors_interface.h"
|
||||
-
|
||||
-
|
||||
-SEXP _SparseList_int2symb(int symb_as_int)
|
||||
-{
|
||||
- char symbbuf[11];
|
||||
-
|
||||
- snprintf(symbbuf, sizeof(symbbuf), "%010d", symb_as_int);
|
||||
- return mkChar(symbbuf); /* UNPROTECTED! */
|
||||
-}
|
||||
-
|
||||
-int _SparseList_symb2int(SEXP symbol)
|
||||
-{
|
||||
- int symb_as_int;
|
||||
-
|
||||
- sscanf(CHAR(symbol), "%d", &symb_as_int);
|
||||
- return symb_as_int;
|
||||
-}
|
||||
-
|
||||
-/* 'symbol' must be a CHARSXP */
|
||||
-SEXP _get_val_from_env(SEXP symbol, SEXP env, int error_on_unbound_value)
|
||||
-{
|
||||
- SEXP ans;
|
||||
-
|
||||
- /* The following code was inspired by R's do_get() code.
|
||||
- * Note that do_get() doesn't use PROTECT at all and so do we...
|
||||
- */
|
||||
- ans = findVar(install(translateChar(symbol)), env);
|
||||
- if (ans == R_UnboundValue) {
|
||||
- if (error_on_unbound_value)
|
||||
- error("Biostrings internal error in _get_val_from_env(): "
|
||||
- "unbound value");
|
||||
- return R_UnboundValue;
|
||||
- }
|
||||
- if (TYPEOF(ans) == PROMSXP)
|
||||
- ans = eval(ans, env);
|
||||
- if (ans != R_NilValue && NAMED(ans) == 0)
|
||||
- SET_NAMED(ans, 1);
|
||||
- return ans;
|
||||
-}
|
||||
-
|
||||
-SEXP _get_val_from_SparseList(int symb_as_int, SEXP env, int error_on_unbound_value)
|
||||
-{
|
||||
- SEXP symbol, ans;
|
||||
-
|
||||
- PROTECT(symbol = _SparseList_int2symb(symb_as_int));
|
||||
- ans = _get_val_from_env(symbol, env, error_on_unbound_value);
|
||||
- UNPROTECT(1);
|
||||
- return ans;
|
||||
-}
|
||||
-
|
||||
-int _get_int_from_SparseList(int symb_as_int, SEXP env)
|
||||
-{
|
||||
- SEXP value;
|
||||
- int val;
|
||||
-
|
||||
- value = _get_val_from_SparseList(symb_as_int, env, 0);
|
||||
- if (value == R_UnboundValue)
|
||||
- return NA_INTEGER;
|
||||
- if (LENGTH(value) != 1)
|
||||
- error("Biostrings internal error in _get_int_from_SparseList(): "
|
||||
- "value is not a single integer");
|
||||
- val = INTEGER(value)[0];
|
||||
- if (val == NA_INTEGER)
|
||||
- error("Biostrings internal error in _get_int_from_SparseList(): "
|
||||
- "value is NA");
|
||||
- return val;
|
||||
-}
|
||||
-
|
||||
-void _set_env_from_IntAE(SEXP env, const IntAE *int_ae)
|
||||
-{
|
||||
- int nelt, symb_as_int, elt;
|
||||
- SEXP symbol, value;
|
||||
-
|
||||
- nelt = IntAE_get_nelt(int_ae);
|
||||
- for (symb_as_int = 1; symb_as_int <= nelt; symb_as_int++)
|
||||
- {
|
||||
- elt = int_ae->elts[symb_as_int - 1];
|
||||
- if (elt == NA_INTEGER)
|
||||
- continue;
|
||||
- PROTECT(symbol = _SparseList_int2symb(symb_as_int));
|
||||
- PROTECT(value = ScalarInteger(elt));
|
||||
- defineVar(install(translateChar(symbol)), value, env);
|
||||
- UNPROTECT(2);
|
||||
- }
|
||||
- return;
|
||||
-}
|
||||
-
|
||||
-void _set_env_from_IntAEAE(SEXP env, const IntAEAE *int_aeae)
|
||||
-{
|
||||
- int nelt, symb_as_int;
|
||||
- IntAE *ae;
|
||||
- SEXP symbol, value;
|
||||
-
|
||||
- nelt = IntAEAE_get_nelt(int_aeae);
|
||||
- for (symb_as_int = 1; symb_as_int <= nelt; symb_as_int++)
|
||||
- {
|
||||
- ae = int_aeae->elts[symb_as_int - 1];
|
||||
- if (IntAE_get_nelt(ae) == 0)
|
||||
- continue;
|
||||
- PROTECT(symbol = _SparseList_int2symb(symb_as_int));
|
||||
- PROTECT(value = new_INTEGER_from_IntAE(ae));
|
||||
- defineVar(install(translateChar(symbol)), value, env);
|
||||
- UNPROTECT(2);
|
||||
- }
|
||||
- return;
|
||||
-}
|
||||
-
|
||||
@@ -1,142 +0,0 @@
|
||||
From 7fe34542bff0183c3a6a35a62df9035a71698eb2 Mon Sep 17 00:00:00 2001
|
||||
From: =?UTF-8?q?Herv=C3=A9=20Pag=C3=A8s?= <hpages.on.github@gmail.com>
|
||||
Date: Fri, 6 Mar 2026 15:54:23 -0800
|
||||
Subject: [PATCH] h5mread 1.3.2: Get rid of non-API calls to R
|
||||
|
||||
---
|
||||
DESCRIPTION | 2 +-
|
||||
R/H5File-class.R | 27 ++++++++++++++++-----------
|
||||
src/h5mread_index.c | 5 +++--
|
||||
src/h5mread_startscounts.c | 3 ++-
|
||||
4 files changed, 22 insertions(+), 15 deletions(-)
|
||||
|
||||
diff --git a/R/H5File-class.R b/R/H5File-class.R
|
||||
index 2735166..6aeb80f 100644
|
||||
--- a/R/H5File-class.R
|
||||
+++ b/R/H5File-class.R
|
||||
@@ -73,19 +73,23 @@
|
||||
}
|
||||
}
|
||||
|
||||
-.h5openfile <- function(filepath, s3=FALSE, s3credentials=NULL, use.rhdf5=FALSE)
|
||||
+.h5openfile <- function(filepath, readonly=TRUE,
|
||||
+ s3=FALSE, s3credentials=NULL, use.rhdf5=FALSE)
|
||||
{
|
||||
if (!isSingleString(filepath))
|
||||
stop(wmsg("'filepath' must be a single string specifying ",
|
||||
"the path or URL to an HDF5 file"))
|
||||
+ if (!isTRUEorFALSE(readonly))
|
||||
+ stop(wmsg("'readonly' must be TRUE or FALSE"))
|
||||
if (!isTRUEorFALSE(s3))
|
||||
stop(wmsg("'s3' must be TRUE or FALSE"))
|
||||
-
|
||||
+ if (s3 && !readonly)
|
||||
+ stop(wmsg("'readonly' must be set to TRUE when 's3' is TRUE"))
|
||||
if (s3) {
|
||||
ID <- .h5openS3file(filepath, s3credentials=s3credentials,
|
||||
use.rhdf5=use.rhdf5)
|
||||
} else {
|
||||
- ID <- .h5openlocalfile(filepath, readonly=TRUE, use.rhdf5=use.rhdf5)
|
||||
+ ID <- .h5openlocalfile(filepath, readonly=readonly, use.rhdf5=use.rhdf5)
|
||||
}
|
||||
ID
|
||||
}
|
||||
@@ -136,16 +140,16 @@
|
||||
|
||||
.ID_is_closed <- function(ID) { is.null(ID) || is.na(ID) }
|
||||
|
||||
-.open_H5FileID_xp <- function(xp, filepath, s3=FALSE, s3credentials=NULL,
|
||||
- use.rhdf5=FALSE)
|
||||
+.open_H5FileID_xp <- function(xp, filepath, readonly=TRUE,
|
||||
+ s3=FALSE, s3credentials=NULL, use.rhdf5=FALSE)
|
||||
{
|
||||
ID <- .get_H5FileID_xp_ID(xp)
|
||||
if (!.ID_is_closed(ID)) {
|
||||
## H5FileID object is already open.
|
||||
return(FALSE)
|
||||
}
|
||||
- ID <- .h5openfile(filepath, s3=s3, s3credentials=s3credentials,
|
||||
- use.rhdf5=use.rhdf5)
|
||||
+ ID <- .h5openfile(filepath, readonly=readonly,
|
||||
+ s3=s3, s3credentials=s3credentials, use.rhdf5=use.rhdf5)
|
||||
.set_H5FileID_xp_ID(xp, ID)
|
||||
TRUE
|
||||
}
|
||||
@@ -183,10 +187,11 @@ close.H5FileID <- function(con, ...)
|
||||
.close_H5FileID_xp(con@xp, ..., use.rhdf5=con@from_rhdf5)
|
||||
}
|
||||
|
||||
-H5FileID <- function(filepath, s3=FALSE, s3credentials=NULL, use.rhdf5=FALSE)
|
||||
+H5FileID <- function(filepath, readonly=TRUE,
|
||||
+ s3=FALSE, s3credentials=NULL, use.rhdf5=FALSE)
|
||||
{
|
||||
- ID <- .h5openfile(filepath, s3=s3, s3credentials=s3credentials,
|
||||
- use.rhdf5=use.rhdf5)
|
||||
+ ID <- .h5openfile(filepath, readonly=readonly,
|
||||
+ s3=s3, s3credentials=s3credentials, use.rhdf5=use.rhdf5)
|
||||
xp <- .new_H5FileID_xp(ID)
|
||||
reg.finalizer(xp,
|
||||
function(e) .close_H5FileID_xp(e, use.rhdf5=use.rhdf5),
|
||||
@@ -272,7 +277,7 @@ H5File <- function(filepath, s3=FALSE, s3credentials=NULL, .no_rhdf5_h5id=FALSE)
|
||||
rhdf5_h5id <- new("H5FileID")
|
||||
} else {
|
||||
rhdf5_h5id <- H5FileID(filepath, s3=s3, s3credentials=s3credentials,
|
||||
- use.rhdf5=TRUE)
|
||||
+ use.rhdf5=TRUE)
|
||||
}
|
||||
if (!s3)
|
||||
filepath <- file_path_as_absolute(filepath)
|
||||
diff --git a/src/h5mread_index.c b/src/h5mread_index.c
|
||||
index 7284815..ec93c25 100644
|
||||
--- a/src/h5mread_index.c
|
||||
+++ b/src/h5mread_index.c
|
||||
@@ -9,6 +9,7 @@
|
||||
#include "h5mread_helpers.h"
|
||||
#include "TouchedChunks.h"
|
||||
|
||||
+#include <R_ext/Altrep.h> /* only for DATAPTR_RW() */
|
||||
#include <stdlib.h> /* for malloc, free */
|
||||
#include <string.h> /* for memcmp */
|
||||
//#include <time.h>
|
||||
@@ -444,7 +445,7 @@ static int read_chunk_data_4_5(const H5DSetDescriptor *h5dset,
|
||||
const size_t *Rarray_dim, SEXP Rarray,
|
||||
int method, int use_H5Dread_chunk)
|
||||
{
|
||||
- void *out = DATAPTR(Rarray);
|
||||
+ void *out = DATAPTR_RW(Rarray);
|
||||
if (out == NULL)
|
||||
return -1;
|
||||
|
||||
@@ -874,7 +875,7 @@ static int read_data_6(const AllTChunks *all_tchunks,
|
||||
size_t *inner_nchip_buf = R_alloc0_size_t_array(ndim);
|
||||
LLongAEAE *inner_breakpoint_bufs = new_LLongAEAE(ndim, ndim);
|
||||
|
||||
- void *out = DATAPTR(Rarray);
|
||||
+ void *out = DATAPTR_RW(Rarray);
|
||||
if (out == NULL) {
|
||||
_destroy_TChunkIterator(&tchunk_iter);
|
||||
return -1;
|
||||
diff --git a/src/h5mread_startscounts.c b/src/h5mread_startscounts.c
|
||||
index de57fd5..959014f 100644
|
||||
--- a/src/h5mread_startscounts.c
|
||||
+++ b/src/h5mread_startscounts.c
|
||||
@@ -8,6 +8,7 @@
|
||||
#include "uaselection.h"
|
||||
#include "h5mread_helpers.h"
|
||||
|
||||
+#include <R_ext/Altrep.h> /* only for DATAPTR_RW() */
|
||||
#include <stdlib.h> /* for malloc, free */
|
||||
//#include <time.h>
|
||||
|
||||
@@ -402,7 +403,7 @@ SEXP _h5mread_startscounts(const H5DSetDescriptor *h5dset,
|
||||
SEXP ans = PROTECT(allocVector(h5dset->h5type->Rtype, ans_len));
|
||||
|
||||
if (ans_len != 0) {
|
||||
- void *mem = DATAPTR(ans);
|
||||
+ void *mem = DATAPTR_RW(ans);
|
||||
if (mem == NULL)
|
||||
goto on_error;
|
||||
|
||||
--
|
||||
2.52.0
|
||||
|
||||
@@ -1,67 +0,0 @@
|
||||
From a827c9fdeb77edefe6cca81bdb9e0344bc8d3742 Mon Sep 17 00:00:00 2001
|
||||
From: Sebastian Gibb <mail@sebastiangibb.de>
|
||||
Date: Sat, 13 Dec 2025 23:06:12 +0100
|
||||
Subject: [PATCH] fix: non-API call to R: SETLENGTH by using lengthgets
|
||||
|
||||
---
|
||||
DESCRIPTION | 2 +-
|
||||
NEWS.md | 6 ++++++
|
||||
src/join.c | 12 ++++--------
|
||||
src/reduce.c | 6 ++----
|
||||
4 files changed, 13 insertions(+), 13 deletions(-)
|
||||
|
||||
diff --git a/src/join.c b/src/join.c
|
||||
index f13a703..3849fdf 100644
|
||||
--- a/src/join.c
|
||||
+++ b/src/join.c
|
||||
@@ -111,12 +111,10 @@ SEXP C_join_inner(SEXP x, SEXP y, SEXP tolerance, SEXP nomatch) {
|
||||
++j;
|
||||
}
|
||||
}
|
||||
- SETLENGTH(rx, j);
|
||||
- SETLENGTH(ry, j);
|
||||
SEXP out = PROTECT(allocVector(VECSXP, 2));
|
||||
SEXP nms = PROTECT(allocVector(STRSXP, 2));
|
||||
- SET_VECTOR_ELT(out, 0, rx);
|
||||
- SET_VECTOR_ELT(out, 1, ry);
|
||||
+ SET_VECTOR_ELT(out, 0, lengthgets(rx, j));
|
||||
+ SET_VECTOR_ELT(out, 1, lengthgets(ry, j));
|
||||
SET_STRING_ELT(nms, 0, mkChar("x"));
|
||||
SET_STRING_ELT(nms, 1, mkChar("y"));
|
||||
setAttrib(out, R_NamesSymbol, nms);
|
||||
@@ -201,12 +199,10 @@ SEXP C_join_outer(SEXP x, SEXP y, SEXP tolerance, SEXP nomatch) {
|
||||
++i;
|
||||
}
|
||||
|
||||
- SETLENGTH(rx, i);
|
||||
- SETLENGTH(ry, i);
|
||||
SEXP out = PROTECT(allocVector(VECSXP, 2));
|
||||
SEXP nms = PROTECT(allocVector(STRSXP, 2));
|
||||
- SET_VECTOR_ELT(out, 0, rx);
|
||||
- SET_VECTOR_ELT(out, 1, ry);
|
||||
+ SET_VECTOR_ELT(out, 0, lengthgets(rx, i));
|
||||
+ SET_VECTOR_ELT(out, 1, lengthgets(ry, i));
|
||||
SET_STRING_ELT(nms, 0, mkChar("x"));
|
||||
SET_STRING_ELT(nms, 1, mkChar("y"));
|
||||
setAttrib(out, R_NamesSymbol, nms);
|
||||
diff --git a/src/reduce.c b/src/reduce.c
|
||||
index 5f87966..8e48058 100644
|
||||
--- a/src/reduce.c
|
||||
+++ b/src/reduce.c
|
||||
@@ -66,11 +66,9 @@ SEXP C_reduce(SEXP start, SEXP end, SEXP check) {
|
||||
}
|
||||
}
|
||||
|
||||
- SETLENGTH(rs, pos + 1);
|
||||
- SETLENGTH(re, pos + 1);
|
||||
SEXP out = PROTECT(allocVector(VECSXP, 2));
|
||||
- SET_VECTOR_ELT(out, 0, rs);
|
||||
- SET_VECTOR_ELT(out, 1, re);
|
||||
+ SET_VECTOR_ELT(out, 0, lengthgets(rs, pos + 1));
|
||||
+ SET_VECTOR_ELT(out, 1, lengthgets(re, pos + 1));
|
||||
|
||||
UNPROTECT(4);
|
||||
|
||||
--
|
||||
2.52.0
|
||||
|
||||
@@ -1,114 +0,0 @@
|
||||
From 57dc6579d8b53af9e633016705fa9a1cbe58c8c8 Mon Sep 17 00:00:00 2001
|
||||
From: =?UTF-8?q?Herv=C3=A9=20Pag=C3=A8s?= <hpages.on.github@gmail.com>
|
||||
Date: Fri, 6 Mar 2026 16:48:20 -0800
|
||||
Subject: [PATCH] Rsamtools 2.27.1: Get rid of non-API calls to R
|
||||
|
||||
---
|
||||
DESCRIPTION | 2 +-
|
||||
src/utilities.h | 3 +--
|
||||
2 files changed, 2 insertions(+), 3 deletions(-)
|
||||
|
||||
diff --git a/src/utilities.h b/src/utilities.h
|
||||
index bffb98f7..f9d5e09f 100644
|
||||
--- a/src/utilities.h
|
||||
+++ b/src/utilities.h
|
||||
@@ -51,8 +51,7 @@ SEXP find_mate_within_groups(SEXP group_sizes,
|
||||
/* call-building macros */
|
||||
|
||||
#define NEW_CALL(S, T, NAME, ENV, N) \
|
||||
- PROTECT(S = T = allocList(N)); \
|
||||
- SET_TYPEOF(T, LANGSXP); \
|
||||
+ PROTECT(S = T = LCONS(R_NilValue, allocList(N-1))); \
|
||||
SETCAR(T, findFun(install(NAME), ENV)); \
|
||||
T = CDR(T)
|
||||
#define CSET_CDR(T, NAME, VALUE) \
|
||||
|
||||
From 8cdec143023e8348a4f8bdc310acd609d14fe493 Mon Sep 17 00:00:00 2001
|
||||
From: =?UTF-8?q?Herv=C3=A9=20Pag=C3=A8s?= <hpages.on.github@gmail.com>
|
||||
Date: Fri, 6 Mar 2026 16:59:42 -0800
|
||||
Subject: [PATCH] oops, forgot to also get rid of non-API call to FORMALS()
|
||||
|
||||
---
|
||||
src/pileupbam.c | 2 +-
|
||||
1 file changed, 1 insertion(+), 1 deletion(-)
|
||||
|
||||
diff --git a/src/pileupbam.c b/src/pileupbam.c
|
||||
index f3256ba..7725628 100644
|
||||
--- a/src/pileupbam.c
|
||||
+++ b/src/pileupbam.c
|
||||
@@ -655,7 +655,7 @@ SEXP apply_pileups(SEXP files, SEXP names, SEXP regions, SEXP param,
|
||||
if (R_NilValue == regions)
|
||||
Rf_error("'NULL' regions not (yet) supported");
|
||||
_checkparams(regions, R_NilValue, R_NilValue);
|
||||
- if (!Rf_isFunction(callback) || 1L != Rf_length(FORMALS(callback)))
|
||||
+ if (!Rf_isFunction(callback) || 1L != Rf_length(R_ClosureFormals(callback)))
|
||||
Rf_error("'callback' must be a function of 1 argument");
|
||||
call = PROTECT(Rf_lang2(callback, R_NilValue));
|
||||
|
||||
|
||||
From ee01a1f13f3b012b0717247d1f21580225b6f3a0 Mon Sep 17 00:00:00 2001
|
||||
From: vjcitn <stvjc@channing.harvard.edu>
|
||||
Date: Wed, 8 Apr 2026 14:04:26 -0400
|
||||
Subject: [PATCH] API solutions
|
||||
|
||||
---
|
||||
DESCRIPTION | 2 +-
|
||||
src/tabixfile.c | 4 ++++
|
||||
src/utilities.c | 13 ++++++++++---
|
||||
3 files changed, 15 insertions(+), 4 deletions(-)
|
||||
|
||||
diff --git a/src/tabixfile.c b/src/tabixfile.c
|
||||
index 230a381..6f96568 100644
|
||||
--- a/src/tabixfile.c
|
||||
+++ b/src/tabixfile.c
|
||||
@@ -187,8 +187,12 @@ SEXP index_tabix(SEXP filename, SEXP format, SEXP seq, SEXP begin, SEXP end,
|
||||
LOGICAL(zeroBased)[0] == TRUE)
|
||||
conf.preset |= TBX_UCSC;
|
||||
|
||||
+/* following is deprecated in HTSLIB with no precise replacement proposed */
|
||||
+/* seems unimportant */
|
||||
+/*
|
||||
if (bgzf_is_bgzf(fn) != 1)
|
||||
Rf_error("file does not appear to be bgzip'd");
|
||||
+*/
|
||||
if (tbx_index_build(fn, 0, &conf) == -1)
|
||||
Rf_error("index build failed");
|
||||
|
||||
diff --git a/src/utilities.c b/src/utilities.c
|
||||
index e224f91..d15c1d1 100644
|
||||
--- a/src/utilities.c
|
||||
+++ b/src/utilities.c
|
||||
@@ -5,6 +5,13 @@
|
||||
#include "XVector_interface.h"
|
||||
#include <htslib/khash.h>
|
||||
|
||||
+#include <Rversion.h>
|
||||
+
|
||||
+#if R_VERSION < R_Version(4, 6, 0)
|
||||
+# define R_getVar(x,y,z) findVar(x,y)
|
||||
+#endif
|
||||
+
|
||||
+
|
||||
void *_Rs_Realloc_impl(void *p, size_t n, size_t t)
|
||||
{
|
||||
/* R_Realloc(p, 0, *) fails inappropriately */
|
||||
@@ -30,7 +37,7 @@ SEXP _get_namespace(const char *pkg)
|
||||
void _as_strand(SEXP vec)
|
||||
{
|
||||
SEXP nmspc = PROTECT(_get_namespace("Rsamtools"));
|
||||
- SEXP lvls = PROTECT(eval(findVar(install(".STRAND_LEVELS"), nmspc), nmspc));
|
||||
+ SEXP lvls = PROTECT(eval(R_getVar(install(".STRAND_LEVELS"), nmspc, TRUE), nmspc));
|
||||
_as_factor_SEXP(vec, lvls);
|
||||
UNPROTECT(2);
|
||||
}
|
||||
@@ -38,8 +45,8 @@ void _as_strand(SEXP vec)
|
||||
void _as_nucleotide(SEXP vec)
|
||||
{
|
||||
SEXP nmspc = PROTECT(_get_namespace("Rsamtools"));
|
||||
- SEXP lvls = PROTECT(eval(findVar(install(".PILEUP_NUCLEOTIDE_LEVELS"),
|
||||
- nmspc), nmspc));
|
||||
+ SEXP lvls = PROTECT(eval(R_getVar(install(".PILEUP_NUCLEOTIDE_LEVELS"),
|
||||
+ nmspc, TRUE), nmspc));
|
||||
_as_factor_SEXP(vec, lvls);
|
||||
UNPROTECT(2);
|
||||
}
|
||||
@@ -1,103 +0,0 @@
|
||||
From e39852a54312bbc6ba435848890cc2a7f612357c Mon Sep 17 00:00:00 2001
|
||||
From: =?UTF-8?q?Herv=C3=A9=20Pag=C3=A8s?= <hpages.on.github@gmail.com>
|
||||
Date: Fri, 6 Mar 2026 17:04:19 -0800
|
||||
Subject: [PATCH] ShortRead 1.69.3: Get rid of non-API calls to R
|
||||
|
||||
---
|
||||
DESCRIPTION | 2 +-
|
||||
src/call.h | 3 +--
|
||||
src/io.c | 10 +++++-----
|
||||
3 files changed, 7 insertions(+), 8 deletions(-)
|
||||
|
||||
diff --git a/src/call.h b/src/call.h
|
||||
index e15bb5e..e72bbd6 100644
|
||||
--- a/src/call.h
|
||||
+++ b/src/call.h
|
||||
@@ -6,8 +6,7 @@ extern "C" {
|
||||
#endif
|
||||
|
||||
#define NEW_CALL(S, T, NAME, ENV, N) \
|
||||
- PROTECT((S) = (T) = allocList((N))); \
|
||||
- SET_TYPEOF((T), LANGSXP); \
|
||||
+ PROTECT((S) = (T) = LCONS(R_NilValue, allocList((N)-1))); \
|
||||
SETCAR((T), findFun(install((NAME)), (ENV))); \
|
||||
(T) = CDR((T))
|
||||
#define CSET_CDR(T, NAME, VALUE) \
|
||||
diff --git a/src/io.c b/src/io.c
|
||||
index 25a0111..9cf4bf8 100644
|
||||
--- a/src/io.c
|
||||
+++ b/src/io.c
|
||||
@@ -46,9 +46,9 @@ SEXP write_fastq(SEXP id, SEXP sread, SEXP quality,
|
||||
SEXP fname, SEXP fmode, SEXP full, SEXP compress,
|
||||
SEXP max_width)
|
||||
{
|
||||
- if (!(IS_S4_OBJECT(id) && strcmp(get_classname(id), "BStringSet") == 0))
|
||||
+ if (!(Rf_isS4(id) && strcmp(get_classname(id), "BStringSet") == 0))
|
||||
Rf_error("'%s' must be '%s'", "id", "BStringSet");
|
||||
- if (!(IS_S4_OBJECT(sread) &&
|
||||
+ if (!(Rf_isS4(sread) &&
|
||||
strcmp(get_classname(sread), "DNAStringSet") == 0))
|
||||
Rf_error("'%s' must be '%s'", "sread", "DNAStringSet");
|
||||
/* check in R -- C-level R_check_super... is not adequate */
|
||||
@@ -693,14 +693,14 @@ int _solexa_export_make_id(SEXP result)
|
||||
*x = INTEGER(VECTOR_ELT(result, SLX_X)),
|
||||
*y = INTEGER(VECTOR_ELT(result, SLX_Y)), *pairedReadNumber = NULL;
|
||||
const SEXP
|
||||
- * run = STRING_PTR(VECTOR_ELT(result, SLX_RUN)),
|
||||
+ * run = STRING_PTR_RO(VECTOR_ELT(result, SLX_RUN)),
|
||||
*multiplexIndex = NULL,
|
||||
- *machine = STRING_PTR(VECTOR_ELT(result, SLX_MACHINE));
|
||||
+ *machine = STRING_PTR_RO(VECTOR_ELT(result, SLX_MACHINE));
|
||||
const Rboolean
|
||||
withMultiplexIndex = R_NilValue != VECTOR_ELT(result, SLX_MULTIPLEX),
|
||||
withPairedReadNumber = R_NilValue != VECTOR_ELT(result, SLX_PAIRID);
|
||||
if (withMultiplexIndex)
|
||||
- multiplexIndex = STRING_PTR(VECTOR_ELT(result, SLX_MULTIPLEX));
|
||||
+ multiplexIndex = STRING_PTR_RO(VECTOR_ELT(result, SLX_MULTIPLEX));
|
||||
if (withPairedReadNumber)
|
||||
pairedReadNumber = INTEGER(VECTOR_ELT(result, SLX_PAIRID));
|
||||
|
||||
--
|
||||
2.52.0
|
||||
|
||||
|
||||
From 2e3368a35e3955a0a92b7f3e2c8dface6709d135 Mon Sep 17 00:00:00 2001
|
||||
From: vjcitn <stvjc@channing.harvard.edu>
|
||||
Date: Thu, 16 Apr 2026 16:54:15 +0000
|
||||
Subject: [PATCH] fixapi
|
||||
|
||||
---
|
||||
src/util.c | 10 +++++++++-
|
||||
1 file changed, 9 insertions(+), 1 deletion(-)
|
||||
|
||||
diff --git a/src/util.c b/src/util.c
|
||||
index 4a10a90..59c089b 100644
|
||||
--- a/src/util.c
|
||||
+++ b/src/util.c
|
||||
@@ -6,6 +6,14 @@ unsigned char _bDecode(char);
|
||||
unsigned char _dnaDecode(char);
|
||||
unsigned char _rnaDecode(char);
|
||||
|
||||
+
|
||||
+#include <Rversion.h>
|
||||
+
|
||||
+#if R_VERSION < R_Version(4, 6, 0)
|
||||
+# define R_getVar(x,y,z) findVar(x,y)
|
||||
+#endif
|
||||
+
|
||||
+
|
||||
/*
|
||||
* Encode / decode XString wrappers
|
||||
*/
|
||||
@@ -80,7 +88,7 @@ SEXP _get_namespace(const char *pkg)
|
||||
SEXP _get_strand_levels()
|
||||
{
|
||||
SEXP nmspc = PROTECT(_get_namespace("ShortRead"));
|
||||
- SEXP ans = eval(findVar(install(".STRAND_LEVELS"), nmspc), nmspc);
|
||||
+ SEXP ans = eval(R_getVar(install(".STRAND_LEVELS"), nmspc, TRUE), nmspc);
|
||||
UNPROTECT(1);
|
||||
return ans;
|
||||
}
|
||||
--
|
||||
2.52.0
|
||||
|
||||
@@ -1,412 +0,0 @@
|
||||
From 803cda41994a22890e0a6e379e6588084d4bc91b Mon Sep 17 00:00:00 2001
|
||||
From: vjcitn <stvjc@channing.harvard.edu>
|
||||
Date: Fri, 13 Mar 2026 04:04:59 -0400
|
||||
Subject: [PATCH 1/2] fixed non-API except for IS_S4_OBJECT
|
||||
|
||||
---
|
||||
src/bind.c | 8 ++++----
|
||||
src/glm_test_R.c | 20 ++++++++++----------
|
||||
src/imputation.c | 8 ++++----
|
||||
src/input.c | 2 +-
|
||||
src/plink.c | 2 +-
|
||||
src/read_uncertain.c | 4 ++--
|
||||
src/readped.c | 2 +-
|
||||
src/single_snp_tests.c | 8 ++++----
|
||||
src/snp_summary.c | 8 ++++----
|
||||
src/snpmpy.c | 8 ++++----
|
||||
src/structure.c | 4 ++--
|
||||
src/subset.c | 2 +-
|
||||
src/switch.c | 2 +-
|
||||
src/tdt.c | 8 ++++----
|
||||
src/testBig.c | 2 +-
|
||||
15 files changed, 44 insertions(+), 44 deletions(-)
|
||||
|
||||
diff --git a/src/bind.c b/src/bind.c
|
||||
index 44b1536..fa87e7c 100644
|
||||
--- a/src/bind.c
|
||||
+++ b/src/bind.c
|
||||
@@ -19,7 +19,7 @@ SEXP snp_rbind(SEXP args) {
|
||||
const SEXP This = CAR(args);
|
||||
Class = getAttrib(This, R_ClassSymbol);
|
||||
if (TYPEOF(Class) != STRSXP) {
|
||||
- Class = R_data_class(This, FALSE);
|
||||
+ Class = R_class(This);
|
||||
}
|
||||
const char *cli = CHAR(STRING_ELT(Class, 0));
|
||||
if(!IS_S4_OBJECT(This)) {
|
||||
@@ -66,7 +66,7 @@ SEXP snp_rbind(SEXP args) {
|
||||
SEXP Result, Rnames, Dnames, Diploid = R_NilValue;
|
||||
PROTECT(Result = allocMatrix(RAWSXP, nr, nc));
|
||||
classgets(Result, duplicate(Class));
|
||||
- SET_S4_OBJECT(Result);
|
||||
+ Rf_asS4(Result, TRUE, 0);
|
||||
PROTECT(Rnames = allocVector(STRSXP, nr));
|
||||
PROTECT(Dnames = allocVector(VECSXP, 2));
|
||||
SET_VECTOR_ELT(Dnames, 0, Rnames);
|
||||
@@ -148,7 +148,7 @@ SEXP snp_cbind(SEXP args) {
|
||||
SEXP This = CAR(args);
|
||||
Class = getAttrib(This, R_ClassSymbol);
|
||||
if (TYPEOF(Class) != STRSXP) {
|
||||
- Class = R_data_class(This, FALSE);
|
||||
+ Class = R_class(This);
|
||||
}
|
||||
const char *cli = CHAR(STRING_ELT(Class, 0));
|
||||
if(!IS_S4_OBJECT(This)) {
|
||||
@@ -205,7 +205,7 @@ SEXP snp_cbind(SEXP args) {
|
||||
SEXP Result, Cnames, Dnames;
|
||||
PROTECT(Result = allocMatrix(RAWSXP, nr, nc));
|
||||
classgets(Result, duplicate(Class));
|
||||
- SET_S4_OBJECT(Result);
|
||||
+ Rf_asS4(Result, TRUE, 0);
|
||||
PROTECT(Dnames = allocVector(VECSXP, 2));
|
||||
setAttrib(Result, R_DimNamesSymbol, Dnames);
|
||||
PROTECT(Cnames = allocVector(STRSXP, nc));
|
||||
diff --git a/src/glm_test_R.c b/src/glm_test_R.c
|
||||
index d865182..dc8ebef 100644
|
||||
--- a/src/glm_test_R.c
|
||||
+++ b/src/glm_test_R.c
|
||||
@@ -19,8 +19,8 @@ SEXP snp_lhs_score(const SEXP Y, const SEXP X, const SEXP Stratum,
|
||||
|
||||
/* Y should be a SnpMatrix or an XSnpMatrix */
|
||||
const char *classY = NULL;
|
||||
- if (TYPEOF(R_data_class(Y, FALSE)) == STRSXP) {
|
||||
- classY = CHAR(STRING_ELT(R_data_class(Y, FALSE), 0));
|
||||
+ if (TYPEOF(R_class(Y)) == STRSXP) {
|
||||
+ classY = CHAR(STRING_ELT(R_class(Y), 0));
|
||||
} else {
|
||||
classY = CHAR(STRING_ELT(getAttrib(Y, R_ClassSymbol), 0));
|
||||
}
|
||||
@@ -431,8 +431,8 @@ SEXP snp_rhs_score(SEXP Y, SEXP family, SEXP link,
|
||||
/* Z should be a SnpMatrix or an XSnpMatrix */
|
||||
|
||||
const char *classZ = NULL;
|
||||
- if (TYPEOF(R_data_class(Z, FALSE)) == STRSXP) {
|
||||
- classZ = CHAR(STRING_ELT(R_data_class(Z, FALSE), 0));
|
||||
+ if (TYPEOF(R_class(Z)) == STRSXP) {
|
||||
+ classZ = CHAR(STRING_ELT(R_class(Z), 0));
|
||||
} else {
|
||||
classZ = CHAR(STRING_ELT(getAttrib(Z, R_ClassSymbol), 0));
|
||||
}
|
||||
@@ -1003,8 +1003,8 @@ SEXP snp_lhs_estimate(const SEXP Y, const SEXP X, const SEXP Stratum,
|
||||
|
||||
/* Y should be a SnpMatrix or an XSnpMatrix */
|
||||
const char *classY = NULL;
|
||||
- if (TYPEOF(R_data_class(Y, FALSE)) == STRSXP) {
|
||||
- classY = CHAR(STRING_ELT(R_data_class(Y, FALSE), 0));
|
||||
+ if (TYPEOF(R_class(Y)) == STRSXP) {
|
||||
+ classY = CHAR(STRING_ELT(R_class(Y), 0));
|
||||
} else {
|
||||
classY = CHAR(STRING_ELT(getAttrib(Y, R_ClassSymbol), 0));
|
||||
}
|
||||
@@ -1286,7 +1286,7 @@ SEXP snp_lhs_estimate(const SEXP Y, const SEXP X, const SEXP Stratum,
|
||||
LOGICAL(Lhs)[0] = 1;
|
||||
setAttrib(Estimates, install("snpLHS"), Lhs);
|
||||
UNPROTECT(6);
|
||||
- SET_S4_OBJECT(Estimates);
|
||||
+ Rf_asS4(Estimates, TRUE, 0);
|
||||
return(Estimates);
|
||||
}
|
||||
|
||||
@@ -1360,8 +1360,8 @@ SEXP snp_rhs_estimate(SEXP Y, SEXP family, SEXP link,
|
||||
/* Z should be a SnpMatrix or an XSnpMatrix */
|
||||
|
||||
const char *classZ = NULL;
|
||||
- if (TYPEOF(R_data_class(Z, FALSE)) == STRSXP) {
|
||||
- classZ = CHAR(STRING_ELT(R_data_class(Z, FALSE), 0));
|
||||
+ if (TYPEOF(R_class(Z)) == STRSXP) {
|
||||
+ classZ = CHAR(STRING_ELT(R_class(Z), 0));
|
||||
} else {
|
||||
classZ = CHAR(STRING_ELT(getAttrib(Z, R_ClassSymbol), 0));
|
||||
}
|
||||
@@ -1724,7 +1724,7 @@ SEXP snp_rhs_estimate(SEXP Y, SEXP family, SEXP link,
|
||||
|
||||
UNPROTECT(gen_names? 7: 6);
|
||||
|
||||
- SET_S4_OBJECT(Estimates);
|
||||
+ Rf_asS4(Estimates, TRUE, 0);
|
||||
return(Estimates);
|
||||
|
||||
}
|
||||
diff --git a/src/imputation.c b/src/imputation.c
|
||||
index ff9403b..d796c1b 100644
|
||||
--- a/src/imputation.c
|
||||
+++ b/src/imputation.c
|
||||
@@ -77,7 +77,7 @@ SEXP snp_impute(const SEXP X, const SEXP Y, const SEXP Xord, const SEXP Yord,
|
||||
int *diploid = NULL;
|
||||
SEXP cl = GET_CLASS(X);
|
||||
if (TYPEOF(cl) != STRSXP) {
|
||||
- cl = R_data_class(X, FALSE); /* S4 way of getting class attribute */
|
||||
+ cl = R_class(X); /* S4 way of getting class attribute */
|
||||
}
|
||||
if (!strcmp(CHAR(STRING_ELT(cl, 0)), "XSnpMatrix")) {
|
||||
SEXP Diploid = R_do_slot(X, mkString("diploid"));
|
||||
@@ -395,7 +395,7 @@ SEXP snp_impute(const SEXP X, const SEXP Y, const SEXP Xord, const SEXP Yord,
|
||||
PROTECT(Maxpred = allocVector(INTSXP, 1));
|
||||
INTEGER(Maxpred)[0] = maxpred;
|
||||
setAttrib(Result, install("Max.predictors"), Maxpred);
|
||||
- SET_S4_OBJECT(Result);
|
||||
+ Rf_asS4(Result, TRUE, 0);
|
||||
|
||||
/* Tidy up */
|
||||
|
||||
@@ -701,7 +701,7 @@ SEXP impute_snps(const SEXP Rules, const SEXP Snps, const SEXP Subset,
|
||||
int *diploid_in=NULL, *diploid=NULL;
|
||||
SEXP cl = GET_CLASS(Snps);
|
||||
if (TYPEOF(cl) != STRSXP) {
|
||||
- cl = R_data_class(Snps, FALSE); /* S4 way of getting class attribute */
|
||||
+ cl = R_class(Snps); /* S4 way of getting class attribute */
|
||||
}
|
||||
if (!strcmp(CHAR(STRING_ELT(cl, 0)), "XSnpMatrix")) {
|
||||
SEXP Diploid = R_do_slot(Snps, mkString("diploid"));
|
||||
@@ -753,7 +753,7 @@ SEXP impute_snps(const SEXP Rules, const SEXP Snps, const SEXP Subset,
|
||||
SET_STRING_ELT(Package, 0, mkChar("snpStats"));
|
||||
setAttrib(Class, install("package"), Package);
|
||||
classgets(Result, Class);
|
||||
- SET_S4_OBJECT(Result);
|
||||
+ Rf_asS4(Result, TRUE, 0);
|
||||
}
|
||||
PROTECT(Dimnames = allocVector(VECSXP, 2));
|
||||
SET_VECTOR_ELT(Dimnames, 0, VECTOR_ELT(names, 0));
|
||||
diff --git a/src/input.c b/src/input.c
|
||||
index 1d2a95b..60cdad8 100644
|
||||
--- a/src/input.c
|
||||
+++ b/src/input.c
|
||||
@@ -330,7 +330,7 @@ SEXP insnp_new(const SEXP Filenames, const SEXP Sample_id, const SEXP Snp_id,
|
||||
SET_STRING_ELT(Package, 0, mkChar("snpStats"));
|
||||
setAttrib(Class, install("package"), Package);
|
||||
classgets(Result, Class);
|
||||
- SET_S4_OBJECT(Result);
|
||||
+ Rf_asS4(Result, TRUE, 0);
|
||||
unsigned char *result = RAW(Result);
|
||||
memset(result, 0x00, Nsample*Nsnp);
|
||||
|
||||
diff --git a/src/plink.c b/src/plink.c
|
||||
index a413440..9095c2d 100644
|
||||
--- a/src/plink.c
|
||||
+++ b/src/plink.c
|
||||
@@ -59,7 +59,7 @@ SEXP readbed(SEXP Bed, SEXP Id, SEXP Snps, SEXP Rsel, SEXP Csel) {
|
||||
SET_STRING_ELT(Package, 0, mkChar("snpStats"));
|
||||
setAttrib(Class, install("package"), Package);
|
||||
classgets(Result, Class);
|
||||
- SET_S4_OBJECT(Result);
|
||||
+ Rf_asS4(Result, TRUE, 0);
|
||||
|
||||
unsigned char *result = RAW(Result);
|
||||
R_xlen_t ncell = (R_xlen_t)nrow*(R_xlen_t)ncol;
|
||||
diff --git a/src/read_uncertain.c b/src/read_uncertain.c
|
||||
index 2e3b901..fd82617 100644
|
||||
--- a/src/read_uncertain.c
|
||||
+++ b/src/read_uncertain.c
|
||||
@@ -137,7 +137,7 @@ SEXP read_mach(const SEXP Filename, const SEXP Colnames, const SEXP Nsubject) {
|
||||
SET_STRING_ELT(Package, 0, mkChar("snpStats"));
|
||||
setAttrib(Class, install("package"), Package);
|
||||
classgets(Result, Class);
|
||||
- SET_S4_OBJECT(Result);
|
||||
+ Rf_asS4(Result, TRUE, 0);
|
||||
UNPROTECT(2);
|
||||
|
||||
/* Read in data */
|
||||
@@ -278,7 +278,7 @@ SEXP read_impute(const SEXP Filename, const SEXP Rownames, const SEXP Nsnp,
|
||||
SET_STRING_ELT(Package, 0, mkChar("snpStats"));
|
||||
setAttrib(Class, install("package"), Package);
|
||||
classgets(Result, Class);
|
||||
- SET_S4_OBJECT(Result);
|
||||
+ Rf_asS4(Result, TRUE, 0);
|
||||
UNPROTECT(2);
|
||||
|
||||
char buffer[BUFFERSIZE];
|
||||
diff --git a/src/readped.c b/src/readped.c
|
||||
index 4e8563e..020d05f 100644
|
||||
--- a/src/readped.c
|
||||
+++ b/src/readped.c
|
||||
@@ -327,7 +327,7 @@ SEXP readped(SEXP filename, SEXP snp_names, SEXP missing, SEXP X, SEXP sep) {
|
||||
else
|
||||
SET_STRING_ELT(SMClass, 0, mkChar("SnpMatrix"));
|
||||
classgets(Smat, SMClass);
|
||||
- SET_S4_OBJECT(Smat);
|
||||
+ Rf_asS4(Smat, TRUE, 0);
|
||||
PROTECT(DimNames = allocVector(VECSXP, 2));
|
||||
SET_VECTOR_ELT(DimNames, 0, duplicate(Rnames));
|
||||
protected += 2;
|
||||
diff --git a/src/single_snp_tests.c b/src/single_snp_tests.c
|
||||
index a242e17..08bd098 100644
|
||||
--- a/src/single_snp_tests.c
|
||||
+++ b/src/single_snp_tests.c
|
||||
@@ -53,8 +53,8 @@ SEXP score_single(const SEXP Phenotype, const SEXP Stratum, const SEXP Snps,
|
||||
/* SNPs ---- should be a SnpMatrix or an XSnpMatrix */
|
||||
|
||||
const char *classS = NULL;
|
||||
- if (TYPEOF(R_data_class(Snps, FALSE)) == STRSXP) {
|
||||
- classS = CHAR(STRING_ELT(R_data_class(Snps, FALSE), 0));
|
||||
+ if (TYPEOF(R_class(Snps)) == STRSXP) {
|
||||
+ classS = CHAR(STRING_ELT(R_class(Snps), 0));
|
||||
} else {
|
||||
classS = CHAR(STRING_ELT(getAttrib(Snps, R_ClassSymbol), 0));
|
||||
}
|
||||
@@ -108,8 +108,8 @@ SEXP score_single(const SEXP Phenotype, const SEXP Stratum, const SEXP Snps,
|
||||
index_db name_index;
|
||||
if (!isNull(Rules)) {
|
||||
const char *classR = NULL;
|
||||
- if (TYPEOF(R_data_class(Rules, FALSE)) == STRSXP) {
|
||||
- classR = CHAR(STRING_ELT(R_data_class(Rules, FALSE), 0));
|
||||
+ if (TYPEOF(R_class(Rules)) == STRSXP) {
|
||||
+ classR = CHAR(STRING_ELT(R_class(Rules), 0));
|
||||
} else {
|
||||
classR = CHAR(STRING_ELT(getAttrib(Rules, R_ClassSymbol), 0));
|
||||
}
|
||||
diff --git a/src/snp_summary.c b/src/snp_summary.c
|
||||
index 9b53693..6f181c9 100644
|
||||
--- a/src/snp_summary.c
|
||||
+++ b/src/snp_summary.c
|
||||
@@ -47,8 +47,8 @@ SEXP X_snp_summary(const SEXP Snps, const SEXP Rules, const SEXP Uncertain) {
|
||||
SEXP ruleNames = R_NilValue;
|
||||
if (!isNull(Rules)) {
|
||||
const char *classR = NULL;
|
||||
- if (TYPEOF(R_data_class(Rules, FALSE)) == STRSXP) {
|
||||
- classR = CHAR(STRING_ELT(R_data_class(Rules, FALSE), 0));
|
||||
+ if (TYPEOF(R_class(Rules)) == STRSXP) {
|
||||
+ classR = CHAR(STRING_ELT(R_class(Rules), 0));
|
||||
} else {
|
||||
classR = CHAR(STRING_ELT(getAttrib(Rules, R_ClassSymbol), 0));
|
||||
}
|
||||
@@ -321,8 +321,8 @@ SEXP snp_summary(const SEXP Snps, const SEXP Rules, const SEXP Uncertain) {
|
||||
SEXP ruleNames = R_NilValue;
|
||||
if (!isNull(Rules)) {
|
||||
const char *classR = NULL;
|
||||
- if (TYPEOF(R_data_class(Rules, FALSE)) == STRSXP) {
|
||||
- classR = CHAR(STRING_ELT(R_data_class(Rules, FALSE), 0));
|
||||
+ if (TYPEOF(R_class(Rules)) == STRSXP) {
|
||||
+ classR = CHAR(STRING_ELT(R_class(Rules), 0));
|
||||
} else {
|
||||
classR = CHAR(STRING_ELT(getAttrib(Rules, R_ClassSymbol), 0));
|
||||
}
|
||||
diff --git a/src/snpmpy.c b/src/snpmpy.c
|
||||
index 2447048..56b84d9 100644
|
||||
--- a/src/snpmpy.c
|
||||
+++ b/src/snpmpy.c
|
||||
@@ -34,7 +34,7 @@ SEXP snp_pre(const SEXP Snps, const SEXP Mat, const SEXP Frequency,
|
||||
int *ifdiploid = NULL;
|
||||
SEXP cl = GET_CLASS(Snps);
|
||||
if (TYPEOF(cl) != STRSXP) {
|
||||
- cl = R_data_class(Snps, FALSE); /* S4 way of getting class attribute */
|
||||
+ cl = R_class(Snps); /* S4 way of getting class attribute */
|
||||
}
|
||||
if (!strcmp(CHAR(STRING_ELT(cl, 0)), "XSnpMatrix")) {
|
||||
SEXP diploid = R_do_slot(Snps, mkString("diploid"));
|
||||
@@ -55,7 +55,7 @@ SEXP snp_pre(const SEXP Snps, const SEXP Mat, const SEXP Frequency,
|
||||
|
||||
cl = GET_CLASS(Mat);
|
||||
if (TYPEOF(cl) != STRSXP) {
|
||||
- cl = R_data_class(Mat, FALSE); /* S4 way of getting class attribute */
|
||||
+ cl = R_class(Mat); /* S4 way of getting class attribute */
|
||||
}
|
||||
if (strcmp(CHAR(STRING_ELT(cl, 0)), "matrix"))
|
||||
error("Argument error - Mat wrong type");
|
||||
@@ -161,7 +161,7 @@ SEXP snp_post(const SEXP Snps, const SEXP Mat, const SEXP Frequency,
|
||||
int *ifdiploid = NULL;
|
||||
SEXP cl = GET_CLASS(Snps);
|
||||
if (TYPEOF(cl) != STRSXP) {
|
||||
- cl = R_data_class(Snps, FALSE); /* S4 way of getting class attribute */
|
||||
+ cl = R_class(Snps); /* S4 way of getting class attribute */
|
||||
}
|
||||
if (!strcmp(CHAR(STRING_ELT(cl, 0)), "XSnpMatrix")) {
|
||||
SEXP diploid = R_do_slot(Snps, mkString("diploid"));
|
||||
@@ -182,7 +182,7 @@ SEXP snp_post(const SEXP Snps, const SEXP Mat, const SEXP Frequency,
|
||||
|
||||
cl = GET_CLASS(Mat);
|
||||
if (TYPEOF(cl) != STRSXP) {
|
||||
- cl = R_data_class(Mat, FALSE); /* S4 way of getting class attribute */
|
||||
+ cl = R_class(Mat); /* S4 way of getting class attribute */
|
||||
}
|
||||
if (strcmp(CHAR(STRING_ELT(cl, 0)), "matrix"))
|
||||
error("Argument error - Mat wrong type");
|
||||
diff --git a/src/structure.c b/src/structure.c
|
||||
index 2a05635..1f9b62e 100644
|
||||
--- a/src/structure.c
|
||||
+++ b/src/structure.c
|
||||
@@ -66,7 +66,7 @@ SEXP xxt(const SEXP Snps, const SEXP Strata, const SEXP Correct_for_missing,
|
||||
int *ifDiploid = NULL;
|
||||
SEXP cl = GET_CLASS(Snps);
|
||||
if (TYPEOF(cl) != STRSXP) {
|
||||
- cl = R_data_class(Snps, FALSE); /* S4 way of getting class attribute */
|
||||
+ cl = R_class(Snps); /* S4 way of getting class attribute */
|
||||
}
|
||||
if (!strcmp(CHAR(STRING_ELT(cl, 0)), "XSnpMatrix")) {
|
||||
SEXP Diploid = R_do_slot(Snps, mkString("diploid"));
|
||||
@@ -409,7 +409,7 @@ SEXP ibs_count(const SEXP Snps, const SEXP Uncertain) {
|
||||
int *ifDiploid = NULL;
|
||||
SEXP cl = GET_CLASS(Snps);
|
||||
if (TYPEOF(cl) != STRSXP) {
|
||||
- cl = R_data_class(Snps, FALSE); /* S4 way of getting class attribute */
|
||||
+ cl = R_class(Snps); /* S4 way of getting class attribute */
|
||||
}
|
||||
if (!strcmp(CHAR(STRING_ELT(cl, 0)), "XSnpMatrix")) {
|
||||
SEXP Diploid = R_do_slot(Snps, mkString("diploid"));
|
||||
diff --git a/src/subset.c b/src/subset.c
|
||||
index cc7992d..4c2e2c4 100644
|
||||
--- a/src/subset.c
|
||||
+++ b/src/subset.c
|
||||
@@ -55,7 +55,7 @@ SEXP subset(SEXP X, SEXP Rows, SEXP Cols) {
|
||||
SET_STRING_ELT(Package, 0, mkChar("snpStats"));
|
||||
setAttrib(Rclass, install("package"), Package);
|
||||
setAttrib(Result, R_ClassSymbol, Rclass);
|
||||
- SET_S4_OBJECT(Result);
|
||||
+ Rf_asS4(Result, TRUE, 0);
|
||||
PROTECT(Rdim = allocVector(INTSXP, 2));
|
||||
int *rdim = INTEGER(Rdim);
|
||||
rdim[0] = nrows;
|
||||
diff --git a/src/switch.c b/src/switch.c
|
||||
index 60f7e6c..e2a3287 100644
|
||||
--- a/src/switch.c
|
||||
+++ b/src/switch.c
|
||||
@@ -16,7 +16,7 @@ SEXP test_switch(const SEXP Snps, const SEXP Snps2, const SEXP Split,
|
||||
int *female = NULL;
|
||||
SEXP cl = GET_CLASS(Snps);
|
||||
if (TYPEOF(cl) != STRSXP) {
|
||||
- cl = R_data_class(Snps, FALSE); /* S4 way of getting class attribute */
|
||||
+ cl = R_class(Snps); /* S4 way of getting class attribute */
|
||||
}
|
||||
SEXP diploid = NULL;
|
||||
if (!strcmp(CHAR(STRING_ELT(cl, 0)), "XSnpMatrix")) {
|
||||
diff --git a/src/tdt.c b/src/tdt.c
|
||||
index cece0d9..000d1c7 100644
|
||||
--- a/src/tdt.c
|
||||
+++ b/src/tdt.c
|
||||
@@ -43,8 +43,8 @@ SEXP score_tdt(const SEXP Proband, const SEXP Father, const SEXP Mother,
|
||||
/* SNPs ---- should be a SnpMatrix or an XSnpMatrix */
|
||||
|
||||
const char *classS = NULL;
|
||||
- if (TYPEOF(R_data_class(Snps, FALSE)) == STRSXP) {
|
||||
- classS = CHAR(STRING_ELT(R_data_class(Snps, FALSE), 0));
|
||||
+ if (TYPEOF(R_class(Snps)) == STRSXP) {
|
||||
+ classS = CHAR(STRING_ELT(R_class(Snps), 0));
|
||||
} else {
|
||||
classS = CHAR(STRING_ELT(getAttrib(Snps, R_ClassSymbol), 0));
|
||||
}
|
||||
@@ -84,8 +84,8 @@ SEXP score_tdt(const SEXP Proband, const SEXP Father, const SEXP Mother,
|
||||
GTYPE **gt2ht = NULL;
|
||||
if (!isNull(Rules)) {
|
||||
const char *classR = NULL;
|
||||
- if (TYPEOF(R_data_class(Rules, FALSE)) == STRSXP) {
|
||||
- classR = CHAR(STRING_ELT(R_data_class(Rules, FALSE), 0));
|
||||
+ if (TYPEOF(R_class(Rules)) == STRSXP) {
|
||||
+ classR = CHAR(STRING_ELT(R_class(Rules), 0));
|
||||
} else {
|
||||
classR = CHAR(STRING_ELT(getAttrib(Rules, R_ClassSymbol), 0));
|
||||
}
|
||||
diff --git a/src/testBig.c b/src/testBig.c
|
||||
index a6eb76f..3dca1da 100644
|
||||
--- a/src/testBig.c
|
||||
+++ b/src/testBig.c
|
||||
@@ -18,7 +18,7 @@ SEXP snp_big(SEXP nrow, SEXP ncol) {
|
||||
SET_STRING_ELT(Package, 0, mkChar("snpStats"));
|
||||
setAttrib(Class, install("package"), Package);
|
||||
classgets(Result, Class);
|
||||
- SET_S4_OBJECT(Result);
|
||||
+ Rf_asS4(Result, TRUE, 0);
|
||||
|
||||
PROTECT(Dnames = allocVector(VECSXP, 2));
|
||||
setAttrib(Result, R_DimNamesSymbol, Dnames);
|
||||
--
|
||||
2.52.0
|
||||
|
||||
@@ -1,149 +0,0 @@
|
||||
From a505297e347aa72510ecfc83e7009668693e1260 Mon Sep 17 00:00:00 2001
|
||||
From: vjcitn <stvjc@channing.harvard.edu>
|
||||
Date: Fri, 13 Mar 2026 04:06:37 -0400
|
||||
Subject: [PATCH 2/2] fixed IS_S4_OBJECT
|
||||
|
||||
---
|
||||
src/bind.c | 4 ++--
|
||||
src/fst.c | 2 +-
|
||||
src/glm_test_R.c | 8 ++++----
|
||||
src/single_snp_tests.c | 2 +-
|
||||
src/snp_summary.c | 6 +++---
|
||||
src/tdt.c | 2 +-
|
||||
6 files changed, 12 insertions(+), 12 deletions(-)
|
||||
|
||||
diff --git a/src/bind.c b/src/bind.c
|
||||
index fa87e7c..b3ef928 100644
|
||||
--- a/src/bind.c
|
||||
+++ b/src/bind.c
|
||||
@@ -22,7 +22,7 @@ SEXP snp_rbind(SEXP args) {
|
||||
Class = R_class(This);
|
||||
}
|
||||
const char *cli = CHAR(STRING_ELT(Class, 0));
|
||||
- if(!IS_S4_OBJECT(This)) {
|
||||
+ if(!Rf_isS4(This)) {
|
||||
warning("rbinding SnpMatrix object without S4 object bit");
|
||||
}
|
||||
int nci = ncols(This);
|
||||
@@ -151,7 +151,7 @@ SEXP snp_cbind(SEXP args) {
|
||||
Class = R_class(This);
|
||||
}
|
||||
const char *cli = CHAR(STRING_ELT(Class, 0));
|
||||
- if(!IS_S4_OBJECT(This)) {
|
||||
+ if(!Rf_isS4(This)) {
|
||||
warning("cbinding SnpMatrix object without S4 object bit");
|
||||
}
|
||||
SEXP Di = R_NilValue;
|
||||
diff --git a/src/fst.c b/src/fst.c
|
||||
index bbc39c0..5451a51 100644
|
||||
--- a/src/fst.c
|
||||
+++ b/src/fst.c
|
||||
@@ -23,7 +23,7 @@ SEXP Fst(SEXP Snps, SEXP Group, SEXP HapMap) {
|
||||
ifX = 0; /* to avoid warning message */
|
||||
error("Argument error - class(Snps)");
|
||||
}
|
||||
- if(!IS_S4_OBJECT(Snps)) {
|
||||
+ if(!Rf_isS4(Snps)) {
|
||||
error("Argument error - Snps is not S4 object");
|
||||
}
|
||||
|
||||
diff --git a/src/glm_test_R.c b/src/glm_test_R.c
|
||||
index dc8ebef..fe9d9c8 100644
|
||||
--- a/src/glm_test_R.c
|
||||
+++ b/src/glm_test_R.c
|
||||
@@ -24,7 +24,7 @@ SEXP snp_lhs_score(const SEXP Y, const SEXP X, const SEXP Stratum,
|
||||
} else {
|
||||
classY = CHAR(STRING_ELT(getAttrib(Y, R_ClassSymbol), 0));
|
||||
}
|
||||
- if(!IS_S4_OBJECT(Y)) {
|
||||
+ if(!Rf_isS4(Y)) {
|
||||
error("Y in snp_lhs_score is missing S4 Object bit");
|
||||
}
|
||||
int ifX = 0;
|
||||
@@ -443,7 +443,7 @@ SEXP snp_rhs_score(SEXP Y, SEXP family, SEXP link,
|
||||
ifX = 1;
|
||||
else
|
||||
error("Argument error - class(Z)");
|
||||
- if (!IS_S4_OBJECT(Z)) {
|
||||
+ if (!Rf_isS4(Z)) {
|
||||
error("Z in snp_rhs_score is missing S4 Object bit");
|
||||
}
|
||||
|
||||
@@ -1008,7 +1008,7 @@ SEXP snp_lhs_estimate(const SEXP Y, const SEXP X, const SEXP Stratum,
|
||||
} else {
|
||||
classY = CHAR(STRING_ELT(getAttrib(Y, R_ClassSymbol), 0));
|
||||
}
|
||||
- if(!IS_S4_OBJECT(Y)) {
|
||||
+ if(!Rf_isS4(Y)) {
|
||||
error("Y in snp_lhs_score is missing S4 Object bit");
|
||||
}
|
||||
int ifX = 0;
|
||||
@@ -1365,7 +1365,7 @@ SEXP snp_rhs_estimate(SEXP Y, SEXP family, SEXP link,
|
||||
} else {
|
||||
classZ = CHAR(STRING_ELT(getAttrib(Z, R_ClassSymbol), 0));
|
||||
}
|
||||
- if(!IS_S4_OBJECT(Z)) {
|
||||
+ if(!Rf_isS4(Z)) {
|
||||
error("Z in snp_rhs_score is missing S4 Object bit");
|
||||
}
|
||||
int ifX = 0;
|
||||
diff --git a/src/single_snp_tests.c b/src/single_snp_tests.c
|
||||
index 08bd098..b577300 100644
|
||||
--- a/src/single_snp_tests.c
|
||||
+++ b/src/single_snp_tests.c
|
||||
@@ -67,7 +67,7 @@ SEXP score_single(const SEXP Phenotype, const SEXP Stratum, const SEXP Snps,
|
||||
ifX = 0; /* to avoid warning message */
|
||||
error("Argument error - class(Snps)");
|
||||
}
|
||||
- if(!IS_S4_OBJECT(Snps)) {
|
||||
+ if(!Rf_isS4(Snps)) {
|
||||
error("Argument error - Snps is not S4 object");
|
||||
}
|
||||
|
||||
diff --git a/src/snp_summary.c b/src/snp_summary.c
|
||||
index 6f181c9..c2f1c73 100644
|
||||
--- a/src/snp_summary.c
|
||||
+++ b/src/snp_summary.c
|
||||
@@ -24,7 +24,7 @@ SEXP X_snp_summary(const SEXP Snps, const SEXP Rules, const SEXP Uncertain) {
|
||||
if (Snps == R_NilValue) {
|
||||
error("Argument error - Snps = NULL");
|
||||
}
|
||||
- if(!IS_S4_OBJECT(Snps)) {
|
||||
+ if(!Rf_isS4(Snps)) {
|
||||
error("Argument error - Snps is not S4 object");
|
||||
}
|
||||
const unsigned char *snps = RAW(Snps);
|
||||
@@ -298,7 +298,7 @@ SEXP snp_summary(const SEXP Snps, const SEXP Rules, const SEXP Uncertain) {
|
||||
if (Snps == R_NilValue) {
|
||||
error("Argument error - Snps = NULL");
|
||||
}
|
||||
- if(!IS_S4_OBJECT(Snps)) {
|
||||
+ if(!Rf_isS4(Snps)) {
|
||||
error("Argument error - Snps is not S4 object");
|
||||
}
|
||||
const unsigned char *snps = RAW(Snps);
|
||||
@@ -538,7 +538,7 @@ SEXP row_summary(const SEXP Snps) {
|
||||
if (Snps == R_NilValue) {
|
||||
error("Argument error - Snps = NULL");
|
||||
}
|
||||
- if(!IS_S4_OBJECT(Snps)) {
|
||||
+ if(!Rf_isS4(Snps)) {
|
||||
error("Argument error - Snps is not S4 object");
|
||||
}
|
||||
const unsigned char *snps = RAW(Snps);
|
||||
diff --git a/src/tdt.c b/src/tdt.c
|
||||
index 000d1c7..634e1b3 100644
|
||||
--- a/src/tdt.c
|
||||
+++ b/src/tdt.c
|
||||
@@ -57,7 +57,7 @@ SEXP score_tdt(const SEXP Proband, const SEXP Father, const SEXP Mother,
|
||||
ifX = 0; /* to avoid warning message */
|
||||
error("Argument error - class(Snps)");
|
||||
}
|
||||
- if(!IS_S4_OBJECT(Snps)) {
|
||||
+ if(!Rf_isS4(Snps)) {
|
||||
error("Argument error - Snps is not S4 object");
|
||||
}
|
||||
|
||||
--
|
||||
2.52.0
|
||||
|
||||
@@ -1,259 +0,0 @@
|
||||
From 633aa6e3f671e9b58b3508b3944ff0dd45f34f8a Mon Sep 17 00:00:00 2001
|
||||
From: =?UTF-8?q?Herv=C3=A9=20Pag=C3=A8s?= <hpages.on.github@gmail.com>
|
||||
Date: Thu, 5 Mar 2026 14:58:23 -0800
|
||||
Subject: [PATCH] SparseArray 1.11.11: Get rid of non-API calls to R
|
||||
|
||||
From 65383c02f986832b1416c6ad39da800d8ced05df Mon Sep 17 00:00:00 2001
|
||||
From: =?UTF-8?q?Herv=C3=A9=20Pag=C3=A8s?= <hpages.on.github@gmail.com>
|
||||
Date: Tue, 31 Mar 2026 11:38:20 -0700
|
||||
Subject: [PATCH] SparseArray 1.11.13: Use R_getVar() instead of findVar() when
|
||||
R >= 4.6.0
|
||||
|
||||
---
|
||||
DESCRIPTION | 2 +-
|
||||
src/Makevars | 1 +
|
||||
src/Rvector_utils.c | 15 ++++++++-------
|
||||
src/SparseArray_aperm.c | 2 +-
|
||||
src/SparseArray_matrixStats.c | 5 +++--
|
||||
src/SparseArray_subassignment.c | 6 +++---
|
||||
src/SparseVec.h | 3 ++-
|
||||
src/leaf_utils.c | 5 +++--
|
||||
src/test.c | 3 +++
|
||||
9 files changed, 25 insertions(+), 17 deletions(-)
|
||||
|
||||
diff --git a/src/Makevars b/src/Makevars
|
||||
index 0ee3615..1c5b86e 100644
|
||||
--- a/src/Makevars
|
||||
+++ b/src/Makevars
|
||||
@@ -1,2 +1,3 @@
|
||||
+## See https://cran.r-project.org/doc/manuals/r-release/R-exts.html#OpenMP-support
|
||||
PKG_CFLAGS = $(SHLIB_OPENMP_CFLAGS)
|
||||
PKG_LIBS = $(SHLIB_OPENMP_CFLAGS)
|
||||
diff --git a/src/Rvector_utils.c b/src/Rvector_utils.c
|
||||
index ad80168..7e61ac1 100644
|
||||
--- a/src/Rvector_utils.c
|
||||
+++ b/src/Rvector_utils.c
|
||||
@@ -4,6 +4,7 @@
|
||||
****************************************************************************/
|
||||
#include "Rvector_utils.h"
|
||||
|
||||
+#include <R_ext/Altrep.h> /* only for DATAPTR_RW() */
|
||||
#include <string.h> /* for memset() and memcpy() */
|
||||
|
||||
|
||||
@@ -242,7 +243,7 @@ void _fill_Rvector_block_with_val(SEXP Rvector,
|
||||
(const SEXP) val);
|
||||
return;
|
||||
}
|
||||
- _set_elts_to_val(TYPEOF(Rvector), DATAPTR(Rvector),
|
||||
+ _set_elts_to_val(TYPEOF(Rvector), DATAPTR_RW(Rvector),
|
||||
block_offset, block_len, val);
|
||||
}
|
||||
|
||||
@@ -260,7 +261,7 @@ void _fill_Rvector_block_with_zeros(SEXP Rvector,
|
||||
R_NilValue);
|
||||
return;
|
||||
}
|
||||
- _set_elts_to_zero(Rtype, DATAPTR(Rvector), block_offset, block_len);
|
||||
+ _set_elts_to_zero(Rtype, DATAPTR_RW(Rvector), block_offset, block_len);
|
||||
return;
|
||||
}
|
||||
|
||||
@@ -268,7 +269,7 @@ void _fill_Rvector_block_with_zeros(SEXP Rvector,
|
||||
void _fill_Rvector_block_with_ones(SEXP Rvector,
|
||||
R_xlen_t block_offset, R_xlen_t block_len)
|
||||
{
|
||||
- _set_elts_to_one(TYPEOF(Rvector), DATAPTR(Rvector),
|
||||
+ _set_elts_to_one(TYPEOF(Rvector), DATAPTR_RW(Rvector),
|
||||
block_offset, block_len);
|
||||
return;
|
||||
}
|
||||
@@ -277,7 +278,7 @@ void _fill_Rvector_block_with_ones(SEXP Rvector,
|
||||
void _fill_Rvector_block_with_minus_one(SEXP Rvector,
|
||||
R_xlen_t block_offset, R_xlen_t block_len)
|
||||
{
|
||||
- _set_elts_to_minus_one(TYPEOF(Rvector), DATAPTR(Rvector),
|
||||
+ _set_elts_to_minus_one(TYPEOF(Rvector), DATAPTR_RW(Rvector),
|
||||
block_offset, block_len);
|
||||
return;
|
||||
}
|
||||
@@ -293,7 +294,7 @@ void _fill_Rvector_block_with_NA(SEXP Rvector,
|
||||
NA_STRING);
|
||||
return;
|
||||
}
|
||||
- _set_elts_to_NA(Rtype, DATAPTR(Rvector), block_offset, block_len);
|
||||
+ _set_elts_to_NA(Rtype, DATAPTR_RW(Rvector), block_offset, block_len);
|
||||
return;
|
||||
}
|
||||
|
||||
@@ -460,7 +461,7 @@ void _fill_Rvector_subset_with_zeros(SEXP Rvector,
|
||||
R_NilValue);
|
||||
return;
|
||||
}
|
||||
- _set_selected_elts_to_zero(Rtype, DATAPTR(Rvector),
|
||||
+ _set_selected_elts_to_zero(Rtype, DATAPTR_RW(Rvector),
|
||||
selection, selection_len, selection_offset);
|
||||
return;
|
||||
}
|
||||
@@ -470,7 +471,7 @@ void _fill_Rvector_subset_with_ones(SEXP Rvector,
|
||||
const int *selection, int selection_len,
|
||||
R_xlen_t selection_offset)
|
||||
{
|
||||
- _set_selected_elts_to_one(TYPEOF(Rvector), DATAPTR(Rvector),
|
||||
+ _set_selected_elts_to_one(TYPEOF(Rvector), DATAPTR_RW(Rvector),
|
||||
selection, selection_len, selection_offset);
|
||||
return;
|
||||
}
|
||||
diff --git a/src/SparseArray_aperm.c b/src/SparseArray_aperm.c
|
||||
index 0bd092e..bbeaf2c 100644
|
||||
--- a/src/SparseArray_aperm.c
|
||||
+++ b/src/SparseArray_aperm.c
|
||||
@@ -721,7 +721,7 @@ static SEXP REC_grow_output_tree(const int *dim, int ndim,
|
||||
const type *nzvals_p = NULL; /* -Wmaybe-uninitialized */ \
|
||||
type v; \
|
||||
if (nzvals != R_NilValue) { /* standard leaf */ \
|
||||
- nzvals_p = (const type *) DATAPTR(nzvals); \
|
||||
+ nzvals_p = DATAPTR_RO(nzvals); \
|
||||
} else { /* lacunar leaf */ \
|
||||
v = type ## 1; \
|
||||
} \
|
||||
diff --git a/src/SparseArray_matrixStats.c b/src/SparseArray_matrixStats.c
|
||||
index b626553..debacf6 100644
|
||||
--- a/src/SparseArray_matrixStats.c
|
||||
+++ b/src/SparseArray_matrixStats.c
|
||||
@@ -16,6 +16,7 @@
|
||||
#include "leaf_utils.h"
|
||||
#include "SparseArray_summarization.h"
|
||||
|
||||
+#include <R_ext/Altrep.h> /* only for DATAPTR_RW() */
|
||||
#include <string.h> /* for memcpy() and memset() */
|
||||
|
||||
|
||||
@@ -272,7 +273,7 @@ SEXP C_colStats_SVT(SEXP x_dim, SEXP x_dimnames, SEXP x_type,
|
||||
int warn = 0;
|
||||
REC_colStats_SVT(x_SVT, x_bg_is_na, INTEGER(x_dim), LENGTH(x_dim),
|
||||
&summarize_op,
|
||||
- DATAPTR(ans), ans_Rtype,
|
||||
+ DATAPTR_RW(ans), ans_Rtype,
|
||||
out_incs, ans_ndim, pardim,
|
||||
&warn);
|
||||
if (warn)
|
||||
@@ -1175,7 +1176,7 @@ SEXP C_rowStats_SVT(SEXP x_dim, SEXP x_dimnames, SEXP x_type,
|
||||
SVT_rowMinsMaxs(x_SVT, x_Rtype, x_bg_is_na,
|
||||
INTEGER(x_dim), LENGTH(x_dim),
|
||||
opcode, narm,
|
||||
- DATAPTR(ans), LENGTH(ans), ans_Rtype,
|
||||
+ DATAPTR_RW(ans), LENGTH(ans), ans_Rtype,
|
||||
out_incs, ans_ndim, nstrata);
|
||||
break;
|
||||
case SUM_OPCODE:
|
||||
diff --git a/src/SparseArray_subassignment.c b/src/SparseArray_subassignment.c
|
||||
index 4cf1c3d..c3b2d5e 100644
|
||||
--- a/src/SparseArray_subassignment.c
|
||||
+++ b/src/SparseArray_subassignment.c
|
||||
@@ -966,13 +966,13 @@ static inline int next_coords0(NindexIterator *Nindex_iter)
|
||||
midx_p++;
|
||||
coords0_p++;
|
||||
}
|
||||
- printf("coords0: ");
|
||||
+ //printf("coords0: ");
|
||||
coords0_p = Nindex_iter->coords0_buf;
|
||||
for (along = Nindex_iter->margin; along < Nindex_iter->ndim; along++) {
|
||||
- printf(" %3d", *coords0_p);
|
||||
+ //printf(" %3d", *coords0_p);
|
||||
coords0_p++;
|
||||
}
|
||||
- printf("\n");
|
||||
+ //printf("\n");
|
||||
return 1;
|
||||
}
|
||||
|
||||
diff --git a/src/SparseVec.h b/src/SparseVec.h
|
||||
index 894709b..73cd841 100644
|
||||
--- a/src/SparseVec.h
|
||||
+++ b/src/SparseVec.h
|
||||
@@ -5,6 +5,7 @@
|
||||
|
||||
#include "Rvector_utils.h"
|
||||
|
||||
+#include <R_ext/Altrep.h> /* only for DATAPTR_RW() */
|
||||
#include <limits.h> /* for INT_MAX */
|
||||
|
||||
|
||||
@@ -122,7 +123,7 @@ static inline SparseVec toSparseVec(SEXP nzvals, SEXP nzoffs,
|
||||
if (IS_STRSXP_OR_VECSXP(Rtype)) {
|
||||
sv.nzvals = nzvals;
|
||||
} else {
|
||||
- sv.nzvals = DATAPTR(nzvals);
|
||||
+ sv.nzvals = DATAPTR_RW(nzvals);
|
||||
}
|
||||
}
|
||||
sv.nzoffs = INTEGER(nzoffs);
|
||||
diff --git a/src/leaf_utils.c b/src/leaf_utils.c
|
||||
index e8066c3..c5ff3aa 100644
|
||||
--- a/src/leaf_utils.c
|
||||
+++ b/src/leaf_utils.c
|
||||
@@ -10,6 +10,7 @@
|
||||
#include "SparseVec_subsetting.h"
|
||||
#include "SparseVec_subassignment.h"
|
||||
|
||||
+#include <R_ext/Altrep.h> /* only for DATAPTR_RW() */
|
||||
#include <string.h> /* for memcpy() */
|
||||
|
||||
|
||||
@@ -129,7 +130,7 @@ SEXP _make_leaf_from_two_arrays(SEXPTYPE Rtype,
|
||||
return ans;
|
||||
}
|
||||
ans_nzvals = PROTECT(allocVector(Rtype, nzcount));
|
||||
- memcpy(DATAPTR(ans_nzvals), nzvals_p, Rtype_size * nzcount);
|
||||
+ memcpy(DATAPTR_RW(ans_nzvals), nzvals_p, Rtype_size * nzcount);
|
||||
}
|
||||
SEXP ans = zip_leaf(ans_nzvals, ans_nzoffs, 0);
|
||||
UNPROTECT(2);
|
||||
@@ -156,7 +157,7 @@ static SEXP make_leaf_from_Rvector_subset(SEXP Rvector,
|
||||
|
||||
if (avoid_copy_if_all_selected &&
|
||||
selection_offset == 0 && selection_len == XLENGTH(Rvector) &&
|
||||
- ATTRIB(Rvector) == R_NilValue)
|
||||
+ !ANY_ATTRIB(Rvector))
|
||||
{
|
||||
/* The full 'Rvector' is selected so can be reused as-is
|
||||
with no need to copy the selected elements to a new SEXP. */
|
||||
diff --git a/src/test.c b/src/test.c
|
||||
index 493538f..2205fa2 100644
|
||||
--- a/src/test.c
|
||||
+++ b/src/test.c
|
||||
@@ -111,6 +111,9 @@ SEXP C_simple_omp_parallel_for_loop(SEXP nloop)
|
||||
for (int i = 0; i < INTEGER(nloop)[0]; i++) {
|
||||
#ifdef _OPENMP
|
||||
int thread_num = omp_get_thread_num();
|
||||
+ /* Can't use Rprintf() here because it's not thread-safe (it
|
||||
+ can trigger R's garbage collector which itself is not
|
||||
+ thread-safe). */
|
||||
printf("thread_num = %d\n", thread_num);
|
||||
#endif
|
||||
}
|
||||
diff --git a/src/readSparseCSV.c b/src/readSparseCSV.c
|
||||
index a3d8da0..de1cb95 100644
|
||||
--- a/src/readSparseCSV.c
|
||||
+++ b/src/readSparseCSV.c
|
||||
@@ -11,6 +11,7 @@
|
||||
#include "ExtendableJaggedArray.h"
|
||||
|
||||
#include <R_ext/Connections.h>
|
||||
+#include <Rversion.h>
|
||||
|
||||
#include <string.h> /* for memcpy() */
|
||||
|
||||
@@ -111,7 +112,11 @@ static SEXP dump_env_as_list_or_R_NilValue(SEXP env, int ans_len)
|
||||
is_empty = 1;
|
||||
for (i = 0; i < ans_len; i++) {
|
||||
key = PROTECT(idx0_to_key(i));
|
||||
+#if R_VERSION < R_Version(4, 6, 0)
|
||||
ans_elt = findVar(install(translateChar(key)), env);
|
||||
+#else
|
||||
+ ans_elt = R_getVar(install(translateChar(key)), env, FALSE);
|
||||
+#endif
|
||||
UNPROTECT(1);
|
||||
if (ans_elt == R_UnboundValue)
|
||||
continue;
|
||||
@@ -1,20 +0,0 @@
|
||||
Author: Danny Milosavljevic <dannym@friendly-machines.com>
|
||||
Date: 2026-02-08
|
||||
License: ASL2.0
|
||||
Subject: Remove codex-core circular dev-dependencies.
|
||||
|
||||
codex-core has a dev-dependency on codex-arg0 which in turn depends on
|
||||
codex-core. This causes cargo package to fail when resolving from the
|
||||
vendor directory because codex-arg0 is not yet available at the time
|
||||
codex-core is packaged.
|
||||
|
||||
--- a/codex-rs/core/Cargo.toml
|
||||
+++ b/codex-rs/core/Cargo.toml
|
||||
@@ -144,7 +144,6 @@
|
||||
[dev-dependencies]
|
||||
assert_cmd = { workspace = true }
|
||||
assert_matches = { workspace = true }
|
||||
-codex-arg0 = { workspace = true }
|
||||
codex-otel = { workspace = true, features = [
|
||||
"disable-default-metrics-exporter",
|
||||
] }
|
||||
@@ -1,30 +0,0 @@
|
||||
Author: Danny Milosavljevic <dannym@friendly-machines.com>
|
||||
Date: 2026-02-08
|
||||
License: ASL2.0
|
||||
Subject: Remove [patch.crates-io] and [patch.'ssh://...'] sections.
|
||||
|
||||
The [patch] sections point to git repositories which are unavailable
|
||||
in an offline build. The vendored crossterm, ratatui,
|
||||
tokio-tungstenite and tungstenite forks are provided as cargo-inputs
|
||||
instead.
|
||||
|
||||
--- a/codex-rs/Cargo.toml
|
||||
+++ b/codex-rs/Cargo.toml
|
||||
@@ -423,17 +423,3 @@
|
||||
debug = 1 # Reduce debug symbol size
|
||||
inherits = "test"
|
||||
opt-level = 0
|
||||
-
|
||||
-[patch.crates-io]
|
||||
-# Uncomment to debug local changes.
|
||||
-# ratatui = { path = "../../ratatui" }
|
||||
-crossterm = { git = "https://github.com/nornagon/crossterm", branch = "nornagon/color-query" }
|
||||
-ratatui = { git = "https://github.com/nornagon/ratatui", branch = "nornagon-v0.29.0-patch" }
|
||||
-tokio-tungstenite = { git = "https://github.com/openai-oss-forks/tokio-tungstenite", rev = "132f5b39c862e3a970f731d709608b3e6276d5f6" }
|
||||
-tungstenite = { git = "https://github.com/openai-oss-forks/tungstenite-rs", rev = "9200079d3b54a1ff51072e24d81fd354f085156f" }
|
||||
-
|
||||
-# Uncomment to debug local changes.
|
||||
-# rmcp = { path = "../../rust-sdk/crates/rmcp" }
|
||||
-
|
||||
-[patch."ssh://git@github.com/openai-oss-forks/tungstenite-rs.git"]
|
||||
-tungstenite = { git = "https://github.com/openai-oss-forks/tungstenite-rs", rev = "9200079d3b54a1ff51072e24d81fd354f085156f" }
|
||||
@@ -1,26 +0,0 @@
|
||||
Author: Danny Milosavljevic <dannym@friendly-machines.com>
|
||||
Date: 2026-04-14
|
||||
License: ASL2.0
|
||||
Subject: Fix race condition in codex-connectors cache test.
|
||||
|
||||
ALL_CONNECTORS_CACHE is a single global Option, not a map. When Rust's
|
||||
test runner executes tests in parallel, the
|
||||
list_all_connectors_merges_and_normalizes_directory_apps test can
|
||||
overwrite the cache entry between the two calls in
|
||||
list_all_connectors_uses_shared_cache, causing a key mismatch and a
|
||||
spurious "cache should have been used" failure.
|
||||
|
||||
Fix by clearing the cache at the start of the cache test so it does not
|
||||
depend on execution order relative to other tests.
|
||||
|
||||
--- a/codex-rs/connectors/src/lib.rs
|
||||
+++ b/codex-rs/connectors/src/lib.rs
|
||||
@@ -441,6 +441,9 @@
|
||||
#[tokio::test]
|
||||
async fn list_all_connectors_uses_shared_cache() -> anyhow::Result<()> {
|
||||
+ // Clear any stale cache entry left by a concurrently running test.
|
||||
+ *ALL_CONNECTORS_CACHE.lock().unwrap() = None;
|
||||
+
|
||||
let calls = Arc::new(AtomicUsize::new(0));
|
||||
let call_counter = Arc::clone(&calls);
|
||||
let key = cache_key("shared");
|
||||
@@ -1,20 +0,0 @@
|
||||
Author: Danny Milosavljevic <dannym@friendly-machines.com>
|
||||
Date: 2026-02-08
|
||||
License: ASL2.0
|
||||
Subject: Remove codex-core circular dev-dependencies.
|
||||
|
||||
codex-core has a dev-dependency on codex-arg0 which in turn depends on
|
||||
codex-core. This causes cargo package to fail when resolving from the
|
||||
vendor directory because codex-arg0 is not yet available at the time
|
||||
codex-core is packaged.
|
||||
|
||||
--- a/codex-rs/core/Cargo.toml
|
||||
+++ b/codex-rs/core/Cargo.toml
|
||||
@@ -134,7 +134,6 @@
|
||||
[dev-dependencies]
|
||||
assert_cmd = { workspace = true }
|
||||
assert_matches = { workspace = true }
|
||||
-codex-arg0 = { workspace = true }
|
||||
codex-otel = { workspace = true }
|
||||
codex-utils-cargo-bin = { workspace = true }
|
||||
core_test_support = { workspace = true }
|
||||
@@ -1,16 +0,0 @@
|
||||
Author: Danny Milosavljevic <dannym@friendly-machines.com>
|
||||
Date: 2026-04-14
|
||||
License: ASL2.0
|
||||
Subject: Remove macOS-only libwebrtc git dependency.
|
||||
|
||||
--- a/codex-rs/realtime-webrtc/Cargo.toml
|
||||
+++ b/codex-rs/realtime-webrtc/Cargo.toml
|
||||
@@ -12,8 +12,5 @@
|
||||
thiserror = { workspace = true }
|
||||
tokio = { workspace = true, features = ["rt-multi-thread"] }
|
||||
|
||||
-[target.'cfg(target_os = "macos")'.dependencies]
|
||||
-libwebrtc = { version = "0.3.26", git = "https://github.com/juberti-oai/rust-sdks.git", rev = "e2d1d1d230c6fc9df171ccb181423f957bb3c1f0" }
|
||||
-
|
||||
[lints]
|
||||
workspace = true
|
||||
@@ -1,20 +0,0 @@
|
||||
Author: Danny Milosavljevic <dannym@friendly-machines.com>
|
||||
Date: 2026-03-05
|
||||
License: ASL2.0
|
||||
Subject: Increase per-event test timeout from 10 to 30 seconds.
|
||||
|
||||
In resource-constrained build environments, image processing (resize,
|
||||
base64-encode, JSON serialization) can exceed 10 seconds under CPU
|
||||
contention, causing intermittent test failures.
|
||||
|
||||
--- a/codex-rs/core/tests/common/lib.rs
|
||||
+++ b/codex-rs/core/tests/common/lib.rs
|
||||
@@ -283,7 +283,7 @@
|
||||
use tokio::time::timeout;
|
||||
loop {
|
||||
// Allow a bit more time to accommodate async startup work (e.g. config IO, tool discovery)
|
||||
- let ev = timeout(wait_time.max(Duration::from_secs(10)), codex.next_event())
|
||||
+ let ev = timeout(wait_time.max(Duration::from_secs(30)), codex.next_event())
|
||||
.await
|
||||
.expect("timeout waiting for event")
|
||||
.expect("stream ended unexpectedly");
|
||||
Some files were not shown because too many files have changed in this diff Show More
Reference in New Issue
Block a user