runenv-r-lineage-trees

R run environment for the Lineage Trees block: Dowser, TIgGER, Alakazam and SHazaM, plus the tree builders raxml-ng 2.0.3, FastTree 2.1.11 and IgPhyML 2.0.0. R 4.4.2, Bioconductor 3.20, on linux x64/aarch64, macOS x64/aarch64 and windows x64.

Using It from a Block

Add the package as a devDependency of the block's software package and reference it from an R artifact:

"artifact": {
  "type": "R",
  "registry": "platforma-open",
  "environment": "@platforma-open/milaboratories.runenv-r-lineage-trees:main",
  "root": "./src"
}

The tree builders are on PATH (.exe on Windows), and IgPhyML's hotspot tables are in share/igphyml/motifs.

Releasing

Bump version in package.json and push to main. CI builds all five platforms in about 40 minutes; publishing waits for approval of the release environment. Clone with git lfs installed.

Building

npm run build runs tools/build.sh, which runs three steps:

1. pl-r-builder compiles R and restores dependencies/renv.lock into it. On Linux it needs Rocky Linux 8 with sudo dnf, whose glibc 2.28 is the oldest the environment runs on. On any other Linux, such as the Ubuntu CI runners, tools/build.sh runs the whole build in a Rocky 8 container, so it needs Docker.
2. tools/binaries/install-binaries.sh copies the tree builders from binaries/ into rdist/, and unpacks the hotspot tables from the pinned IgPhyML source.
3. pl-pkg build packages the result.

Two known failures:

• Posit binaries. They link libR.so, which pl-r-builder's R does not build, so dependencies/.Renviron turns them off and all 137 packages build from source.
• pkgdepends 0.9.1 fails in collect-dependencies.R with "missing value where TRUE/FALSE needed". Until @platforma-sdk/r-builder pins 0.9.0 itself, tools/patch-r-builder.mjs (run on npm install) patches the pin in.

Tree Builders

binaries/<platform>/ holds them prebuilt, in Git LFS, so CI needs no Docker. To rebuild after changing a pin in tools/binaries/pins.sh or a build file, run npm run build:binaries (needs Docker) and commit binaries/. The install step refuses binaries built from other pins, and LFS pointer files.

None of the three programs is released for Windows. tools/binaries/win-compat/ holds what mingw-w64 lacks: strsep and getline for IgPhyML, and a header and patch porting raxml-ng's memory, timing and CPU queries. The Windows raxml-ng is single-threaded; dowser always passes --threads 1, and a higher value hangs it. On the same input, each Windows program gives the Linux likelihoods, trees and ancestral states.

Regenerating the Lockfile

docker build -t rlock-base -f tools/lock.Dockerfile tools
docker run --rm -v "$PWD/tools:/w" rlock-base \
  bash -lc 'cp /w/generate-lock.R /app/ && R --no-echo -f /app/generate-lock.R && cat /app/renv.lock' \
  > dependencies/renv.lock

This takes about 25 minutes, since everything builds from source. Keep the result identical to the block's software/immcantation/context/renv.lock. Three traps, each hit producing the current lock:

• renv::init(bioconductor = "3.20") sets only CRAN. Alakazam then misses Biostrings, GenomicAlignments and IRanges, and Dowser, TIgGER and SHazaM fail after it. generate-lock.R sets all six repositories, copied from runenv-r-tcr-disco.
• ggplot2 4.x breaks ggtree 3.14.0, which calls the removed check_linewidth. Only ggplot2 is pinned, to 3.5.2; the rest comes from a 2026-09-10 Posit snapshot.
• renv will not snapshot without BiocManager and BiocVersion, although neither is needed to install. Install both first.

| Package | Version | Source | |---|---|---| | dowser | 2.5.1 | CRAN | | tigger | 1.1.3 | CRAN | | alakazam | 1.4.3 | CRAN | | shazam | 1.3.2 | CRAN | | airr | 2.0.0 | CRAN | | ggtree | 3.14.0 | Bioconductor | | treeio | 1.30.0 | Bioconductor | | pwalign | 1.2.0 | Bioconductor | | ggplot2 | 3.5.2 | CRAN, pinned |

The lock holds 137 packages, 24 of them from Bioconductor.