[ms609-agent]

Two CI legs have failed on main and on every PR since 23 October.

R 4.1 leg: testthat runs past the 60-minute job limit

Root cause: a base-R copy, made quadratic by CompareAll(). ape's [[.multiPhylo starts with class(x) <- NULL. On R ≤ 4.3 that assignment copies the whole list on every element access; R 4.4 and later avoid the copy. Here are 2,000 calls of a plain function(x, i) { class(x) <- NULL; x[[i]] } on a 500k-element list, without ape:

R	4.1	4.2	4.3	4.4	4.5
seconds	10.0	6.3	7.0	0.015	0.015

CompareAll() built two multiPhylo objects with one element per pair, then indexed each of them once per pair. Its time therefore grew with the square of the number of pairs. #222's 7-leaf test calls NNIDist() on all 945 trees (446,040 pairs), which took over 50 minutes on 4.1.

Fix: CompareAll() now converts x to a plain list once and indexes it with integer pair vectors. The code is no more complex than before: it builds two integer vectors instead of two pair-length tree lists, so it also uses less memory and makes fewer S3 dispatches. On GHA, NNIDist() on the 945 trees now takes 49 s on R 4.1 and 46 s on R 4.6.

The 7-leaf test also calls cpp_nni_distance() directly, because what it checks is the bounds, not the R wrapper. It now takes about 7 s instead of about 80 s. The 6-leaf case still checks the C++ results against NNIDist().

benchmark: "Set up R" times out after 15 minutes

ubuntu-latest now resolves to Ubuntu 26.04, where setup-r apt-installs about 175 packages from a slow mirror. The job's RSPM serves noble (24.04) binaries anyway, so benchmark is now pinned to ubuntu-24.04. rev-dep-check uses the same setup, so it is pinned too.

Verification

• Local tests pass: NNI, path, tree_distance and utilities test files.
• test-parallel.R fails locally in the same way with and without this change: its worker processes load an older globally installed TreeDist.

🤖 Generated with Claude Code

[codecov]

Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 97.74%. Comparing base (2f6776d) to head (7ec6e8f).

Additional details and impacted files

@@           Coverage Diff           @@
##             main     #227   +/-   ##
=======================================
  Coverage   97.74%   97.74%           
=======================================
  Files          60       60           
  Lines        6575     6577    +2     
=======================================
+ Hits         6427     6429    +2     
  Misses        148      148           

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[github-actions]

Performance benchmark results

Call	Status	Change	Time (ms)
ClusteringInfoDistance(tr280)	⚪ NSD	0.61%	8.81, 8.81 → 8.77, 8.75
ClusteringInfoDistance(tr50)	⚪ NSD	1.7%	6.49, 6.57 → 6.43, 6.39
LAPJV(test2000)	⚪ NSD	3.89%	131, 134 → 127, 128
LAPJV(test40)	⚪ NSD	-0.53%	0.0189, 0.019 → 0.0191, 0.0191
LAPJV(test400)	⚪ NSD	0%	3.58, 3.58 → 3.59, 3.57
MutualClusteringInfo(tr280)	⚪ NSD	0.77%	18.1, 18.3 → 18.1, 18.1
MutualClusteringInfo(tr50)	⚪ NSD	2.5%	17.2, 17.4 → 17.8, 16.8
NNIMaxStep(2000, normalize = TRUE)	⚪ NSD	-0.08%	0.209, 0.21 → 0.21, 0.209
NNIMaxStep(300, normalize = TRUE)	⚪ NSD	-0.61%	0.0308, 0.0309 → 0.0311, 0.0309
NNIMaxStep(300)	⚪ NSD	-2.24%	0.00887, 0.009 → 0.00928, 0.00893
PathDist(postTrees)	⚪ NSD	-13.92%	1.64, 1.72 → 1.99, 1.65
PhylogeneticInfoDistance(tr180)	⚪ NSD	-0.01%	60.8, 60.8 → 60.9, 60.8
PhylogeneticInfoDistance(tr50)	⚪ NSD	0.48%	42.4, 41.5 → 41.9, 42.2
RobinsonFoulds(tr280)	⚪ NSD	1%	4.64, 4.66 → 4.6, 4.61
RobinsonFoulds(tr280)	⚪ NSD	0.3%	4.45, 4.48 → 4.46, 4.45
RobinsonFoulds(tr50)	⚪ NSD	0.04%	4.56, 4.62 → 4.6, 4.58