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Changelog

bincraft (development version)

  • The two remaining existence gates now tell a source fallback from a binary. Fixing check_s3_root_package() let a rebuild get as far as the build step, where a second gate in build_single_tag() skipped it again with “already exists in S3 and force = FALSE”, and a third in upload_single_binary() would then have refused to publish the binary because the source occupied its key. All three now share one helper, remote_object_state(), which answers "absent", "source" or "binary" rather than a bare yes/no, and a source fallback is overwritten rather than left in place. Unknown stays “binary” throughout, so an unreadable ETag or an unreachable CRAN still cannot schedule a rebuild of the repository.

  • The source-fallback detection now actually reads the object’s MD5. remote_object_md5() looked for an ETag column, but s3fs::s3_file_info() snake-cases the head_object response and renames e_tag to etag. Reading a missing column yields NULL rather than an error, so every object came back as “MD5 unknown”, every caller took the conservative “assume it is a binary” branch, and the checks added in 5.1.1 and 5.1.2 were inert. A 13,389-package rebuild of amd64/alpine324 running 5.1.2 still skipped every package with “All packages to be built already exist in the remote bucket”. Both spellings are now accepted, and the regression is covered by tests that feed remote_object_md5() a realistic s3fs return value instead of stubbing it out.

  • The pre-build skip now also tells a source fallback from a binary. check_s3_root_package() decides whether a build runs at all, and it tested only that something occupied the key. A package whose build failed has its CRAN source published under exactly that name, so a rebuild skipped every one of them with “All packages to be built already exist in the remote bucket” – precisely the set a rebuild exists to fix. Observed on arm64/alpine324, where a 13,647-package rebuild skipped every package it was given. The previous release fixed the same blind spot in check_for_binary(), which decides whether to publish a fallback, but not this one, which decides whether to build. An object whose MD5 matches CRAN’s published MD5sum is now reported as absent, and an MD5 that cannot be established still counts as a binary so an outage cannot trigger a full rebuild.

  • A package that failed to build is no longer mistaken for a binary. When a build fails, handle_post_build_actions() publishes the CRAN source tarball in its place so the package stays installable, but check_for_binary() only tested that an object existed at the path. The fallback therefore became permanent: the build was never retried, and the missing-binaries audit never reported it, because the object was there. On amd64/alpine324 that left 13,547 of 24,134 comparable objects (56%) as CRAN sources, all published during the June 2026 bootstrap; amd64/noble sits at 4.6% for comparison. check_for_binary() now compares the object’s MD5 against CRAN’s published MD5sum, which costs no downloads, and reports a source fallback as missing. When the MD5 cannot be established (a multipart ETag, or CRAN unreachable) the object still counts as a binary, so neither can trigger an endless rebuild.

  • check_for_binary() now honours is_r_minor_sensitive. It looked in the generic slot even for per-minor packages, while the source fallback wrote them to the per-minor slot, so it never found an existing per-minor build.

  • The Built stamp is no longer written onto packages served as their CRAN source. The stamp is applied to a whole slot at once, so it landed on the source fallbacks too and advertised them as binaries: uvr then installs one without the system -dev libraries a source build needs, and paquetier files it under a platform it was never built for. upload_package_index() now clears Built on records whose MD5 matches CRAN’s. Archived versions are left alone, since CRAN’s index carries only current releases.

  • A per-minor PACKAGES* index is now republished as a union with the generic slot. A per-minor slot carries only the ABI-sensitive packages, and contrib.url() can only ever address <repos>/src/contrib, so those packages were unreachable from install.packages(): on amd64/alpine324 2,886 packages, curl among them, existed only in the per-minor slot and were absent from the index base R reads. upload_package_index() now merges the generic slot’s records into the per-minor index before uploading it, tagging the per-minor records with Path: <r_minor> so their tarballs still resolve into …/src/contrib/<r_minor>/ while the generic ones resolve into …/src/contrib/. Nothing is copied or duplicated, and a package built for this minor shadows the generic one entirely. An unreadable or empty generic index is an error rather than a partial publish, because replacing a published union with a per-minor-only index would hide most of the repository from every client on that minor.

  • built_stamp() now refuses an unusable platform or R version instead of stamping it. The stamp is written verbatim into every entry of a slot’s PACKAGES index and uvr decides binary-vs-source by matching the triple it carries, so a missing value does not degrade gracefully: it stamped the literal NA, no client matched it, and the whole slot silently reverted to source-only. This is how arm64/alpine321 (22,930 entries, Built: R 4.4.0; NA) and arm64/alpine322 (24,696 entries, Built: R 4.5.0; NA) were written during the one-time re-index on 2026-07-31; both slots need another full re-index to recover. Failing the index write is the cheaper outcome, so an absent, NA, empty or non-scalar platform/r_version is now an error.

  • Dependency names are now written as quoted keys in the generated uvr.toml. R package names may contain dots, and a bare data.table = "*" is a dotted TOML key: it parses as package data with a sub-key table rather than as data.table. Where the parent name is itself a dependency, for example rpart alongside rpart.plot, the parse fails outright with “dotted key rpart attempted to extend non-table type (string)”. Either way uvr lock aborted and the build failed with “Error in installing dependencies for package …”, so every package depending on a dotted name was unbuildable.

  • uvr is now pinned to the R version that runs the build. run_uvr_install() writes a .r-version file into the package clone before uvr lock, so both lock and sync target the session’s R. Previously bincraft told uvr nothing about the R version, and uvr picked the newest R it could find (managed installs first, then system R). On an image carrying a second, newer R, for example a /opt/R/current symlink already moved to 4.6 while the build runs in 4.5, uvr resolved the lockfile for the wrong R minor and uvr sync then refused to install anything: “Refusing to install: uvr is running inside R 4.5 but the project pin/lockfile resolves to R 4.6”. That aborted every dependency install on the affected images.

  • The S3 package index now advertises its binaries via the Built field. upload_package_index() and add_to_package_index() pass a built stamp (build R version plus R.version$platform triple) to cranlike, which otherwise reads metadata from the CRAN source DESCRIPTION and leaves Built empty for every entry. Without it, binary-aware clients such as uvr treat cran.rpkgs.com as source-only and compile every package from source, which fails on Alpine when a system -dev library is missing (e.g. openssl). install.packages() was unaffected because it reads Built: from each tarball’s own DESCRIPTION. Existing indexes need a one-time full rebuild to backfill Built on entries already in the database.

  • Dependencies and their system requirements are now installed with uvr instead of pak during build_binary_package(). uvr reads /etc/os-release, resolves each dependency’s system requirements per distro, and installs them with the distro package manager (apk / dnf / apt-get) in the same pass as the R packages, so a build no longer fails when a dependency needs a system library the image does not ship (for example gert needing libgit2). Patched binaries are installed into the build library first so uvr sync keeps them, and pak is no longer a dependency (#83).

  • Patched binary caches are now validated before reuse and written atomically. prepare_patched_repo() verifies each cached/assembled tarball reads cleanly and carries the package DESCRIPTION plus a shared object (when it ships a libs/ dir) before serving it, and rebuilds instead of reusing a corrupt entry. Fresh binaries are staged to a temp file and renamed into place, so a build killed mid-copy can no longer leave a truncated cache entry that made every dependent build fail with tar: A lone zero block or a missing RcppParallel.so.

  • CRAN package versions are now resolved from CRAN’s own metadata (available.packages() plus Meta/archive.rds) instead of the GitHub REST tags API. The old gh::gh("GET /repos/cran/{pkg}/tags") call counted against the authenticated user’s 5,000 requests/hour REST limit, which the weekly rebuild exhausted (HTTP 403 “API rate limit exceeded for user ID …”). The GitHub API is still used for genuine non-CRAN forge sources.

  • classify_r_minor_sensitive() now downloads the CRAN source tarball (download_cran_source()) instead of cloning github.com/cran, and caches its verdict in the metadata database (table abi_classification, created on first use) keyed on (package, version) plus a signature of the curated ABI lists. Because the r-minor-sensitivity verdict is a property of the package source (independent of OS, arch and R minor), a full rebuild for a new OS release reuses cached verdicts and performs no downloads. The function is now exported and takes metadata_db_* arguments; pass them to enable caching.

bincraft 4.4.7

  • The local patched-binary repo served to pak is now assembled at a stable, content-addressed path under cache_dir instead of a fresh tempfile() per call. Every build_binary_package() resolution in a run passes the same patches/platform/arch/R, so they now resolve to the same file:// repo URL and pkgcache reuses a single _metadata snapshot. Previously each resolution minted a new repo path, so pkgcache wrote a fresh ~70 MB _metadata/patched-<hash> snapshot that never repeated and never evicted, growing unboundedly during full-platform builds (up to ~165 GB observed). A fully assembled repo is now also reused as-is on subsequent resolutions.

bincraft 4.4.3

  • Registry patches (and their env / configure_args / makevars overrides) are now applied to the target package’s own source before pkgbuild::build(), not only when building patched dependencies. Previously a package that was the build target had its patch applied to a throwaway dependency repo and ignored for the uploaded binary, so source-diff/override patches silently had no effect on the shipped binary. A target patch that fails to apply now aborts the build instead of uploading an unpatched binary.

bincraft 4.4.2

  • build_patched_binary() no longer fails with is.named(envs) is not TRUE for a patch entry that sets no environment variables (e.g. a pure source-diff patch). withr::with_envvar() errors on an empty list, so it is now skipped when the entry’s env is empty.

bincraft 4.4.1

  • Source patches are now applied with git apply instead of the patch CLI, which is not present in all build environments (e.g. minimal Alpine images). git is always available, so registry source diffs apply reliably across platforms.
  • prepare_patched_repo() no longer emits a spurious normalizePath: No such file warning when staging a freshly built patched binary.
  • build_patched_binary() no longer fails with is.named(envs) is not TRUE for a patch entry that sets no env vars (e.g. a pure source-diff patch); the withr::with_envvar() wrapper is now skipped when the env is empty.

bincraft 4.3.1

bincraft 4.3.0

  • build_binary_package() gains a patches argument: a registry of per-package env / configure / Makevars overrides and source diffs that are pre-built into patched binaries and served to pak, fixing compiler- and OS-specific failures (e.g. RcppParallel) including for transitive deps.

bincraft 4.2.1

  • write_archive_rds() (and thus upload_package_index()) no longer errors when a slot has no archived versions yet — it returns an empty index instead. Fixes the Meta/archive.rds failure the first time a package lands in a fresh per-minor slot.

bincraft 4.2.0

  • process_cran_updates() gains r_minor_detection ("none"/"issue"/"classifier") and r_minor_sensitive_only, classifying each candidate via the ABI classifier and routing only risky packages to per-minor slots.
  • upload_package_index() / add_to_package_index() gain an r_minor argument to write/serve a per-minor PACKAGES* index under …/contrib/<x.y>/.