build-cran-binaries/local/patches

Patch Registry

This directory contains the curated registry of per-package build-time patches consumed by bincraft's patches argument.

Schema

The registry is defined in registry.json as an array of patch entries. Each entry specifies lightweight build-time overrides (environment variables, configure arguments, Makevars) and optionally a source diff to apply before building.

Field semantics

Field	Type	Required	Description
package	string	yes	CRAN package name.
versions	string	yes	"*" for any, a constraint such as ">=5.1.0", or an exact version "5.1.11-2". Env-tier fixes are typically "*"; source diffs are normally exact or lower-bounded because a diff is pinned to the source it was generated against.
platforms	array of strings	yes	Matched against the running build's platform tokens — distro family (alpine, ubuntu, redhat), codename (ubuntu-2604, alpine-324), and arch (amd64, arm64). An entry matches if any listed token matches any build token. ["*"] matches all platforms.
env	object	no	Environment variables exported only for this package's isolated build.
configure_args	array	no	Arguments passed as --configure-args to the isolated build.
makevars	object	no	Key/value pairs written into a package-local Makevars for the isolated build.
patch	string or null	no	Path (relative to local/patches/) to a unified diff applied to the unpacked CRAN source before building.
reason	string	yes	Human explanation, surfaced in logs and metadata.

Adding an entry

To add a new patch entry:

1. Add an object to the array in registry.json with the fields documented above. Start with lightweight overrides (environment variables, configure arguments, Makevars) before resorting to source diffs.

2. If a source diff is needed, place it in local/patches/<package>/<file>.patch and reference its path in the patch field. For example, a diff for RcppParallel would go in local/patches/RcppParallel/fix.patch and be referenced as "patch": "RcppParallel/fix.patch".

3. The reason field should clearly explain why the patch is needed and what problem it solves.

Validation

The registry is validated and applied by bincraft during the build process. For manual validation, run the validator from the repo root:

Rscript local/validate-patches.R

This validates the schema, referenced patch-file existence, and checks for duplicate entries across platforms and versions.

Triaging failures into entries

local/failing-builds-report.R turns recorded build failures into triaged patch suggestions instead of hand-scraping Crow logs (issue #115, steps 1 + 2). It is read-only: it queries single_builds WHERE error_occurred, groups failures by a normalised error fingerprint, classifies each group against the known signature set in local/failing-builds-classify.R, and prints a report.

# All platforms/arches; needs the DB password.
PGPASS=... Rscript local/failing-builds-report.R
# Restrict scope and also emit a machine-readable report.
PGPASS=... Rscript local/failing-builds-report.R --platform alpine-321 --arch amd64 --json report.json

Each group is tagged AUTO-PROPOSABLE (a known env/makevars lever, or an already-curated package patch, safe to pre-fill as a registry.json entry) or HUMAN TRIAGE (unknown signature, or a fix that needs a novel source diff). For auto-proposable groups it prints a ready-to-review registry entry; still run validate-patches.R and an isolated trial build before merging. Novel source diffs and unknown signatures stay human-reviewed by design.

Add a new signature by appending a rule to build_signatures() in local/failing-builds-classify.R; the pure helpers are covered by local/tests/test-failing-builds-classify.R.

Proposing entries (step 3: propose, do not apply)

local/propose-patches.R takes the auto-proposable candidates one step further: for each classified, safe fix affecting a package with no current entry, it emits a pre-filled registry.json entry and validates the candidate set against a temporary merged registry (the real registry is never touched unless you ask). The human gate stays: it never merges.

# Default: print candidates + validation, take no action.
PGPASS=... Rscript local/propose-patches.R
# Append the candidates to registry.json + the proposals ledger (you commit + open the PR).
PGPASS=... Rscript local/propose-patches.R --write
# Or post/update a Forgejo tracking issue instead (needs FORGEJO_TOKEN).
PGPASS=... FORGEJO_TOKEN=... Rscript local/propose-patches.R --open-issue

The acceptance criteria before merging a proposal are: validate-patches.R passes (checked automatically), and an isolated trial build succeeds. Run the trial build inside the failing platform's build-env image; it uploads/archives nothing and writes no metadata:

Rscript local/trial-build-patch.R <package>

Autonomous PR + trial-build gate

--open-pr closes the loop: it writes the top-N candidates (by failure volume) onto the reused auto/registry-patch-proposals branch and opens/updates a single PR. .crow/auto-apply-patches.yaml runs this on a cron. FORGEJO_TOKEN is used for both the branch push and the PR (no separate write-scoped secret).

# Bounded batch; opens/updates one PR.
PGPASS=... FORGEJO_TOKEN=... Rscript local/propose-patches.R --open-pr --limit 10

The merge gate is .crow/trial-build-registry.yaml: matrixed over the build-env images, each platform trial-builds only the entries the branch adds (local/trial-build-registry.R, which diffs the registry against main) and is green only if every new entry builds. The repo uses no pull_request triggers, so this gate runs manually or on a cron against the auto-patch branch (--var patch_branch=...); wiring it to fire on the PR needs event: pull_request enabled on the forge.

--write and --open-issue also append to local/patches/proposals-log.json, a ledger of what was proposed.

Feedback loop (step 4)

local/proposal-tracking.R reports the signature hit rate, proposed-vs-merged status (a proposal counts as merged once its package appears in the registry), and retirement candidates (registry entries whose package no longer appears in any current failure, so the upstream cause was likely fixed). It also surfaces the classifier's blind spots: the unclassified failures (candidates for a new signature) and the groups blocked on a dependency build, so the unknown buckets get the same visibility as the proposals. It is read-only on the DB, with an optional Forgejo issue as the only write.

# Print the metrics + blind spots.
PGPASS=... Rscript local/proposal-tracking.R --json metrics.json
# Post/update a "needs signatures" tracking issue with the unclassified failures.
PGPASS=... FORGEJO_TOKEN=... Rscript local/proposal-tracking.R --open-issue

The unclassified groups are the natural place to discover which new signatures are worth adding to build_signatures(). The pure metric/ledger helpers live in local/proposal-tracking-lib.R and are covered by local/tests/test-proposal-tracking-lib.R.

Scheduled run

.crow/weekly-patch-proposals.yaml runs both steps weekly (register the weekly-patch-proposals cron in the crow UI). It posts/updates two Forgejo issues -- one with the auto-proposable entries, one with the unclassified/blocked failures -- and logs the feedback-loop metrics. It clones read-only; the only writes are the two tracking issues.