Fixed an issue with standardization. Variables with zero variance get turned into Inf. What we do instead is change the variance to Inf, and those variables become all 0 and are given zero coefficients. This problem can exhibit during CV.
Fixed the dense-matrix sp_tmul so that its serial
path honors n_threads. Its n_threads = 1
branch ran a raw Eigen product that ignored the requested thread count
and fell back to Eigen’s global default (all cores), inflating example
CPU time to user/elapsed ~10x with no wall-clock gain on a
many-core machine (the source of CRAN’s gcc-16 R-devel “CPU time >
2.5 times elapsed” NOTE). The inst/adelie submodule points
at the one-line fix on a forked branch
(bnaras/adelie@zero-variance). Investigation notes and a
Docker reprex live in debug/ (excluded from the package
tarball).
grpnet() and
cv.grpnet() triggered by inputs where the BASIL
kkt and screen checks disagreed by a 1-ULP gap
due to inconsistent multiplication ordering in the bundled
adelie_core solver. As a temporary workaround, the
inst/adelie submodule points at the fix on a forked branch
(bnaras/adelie@fix-kkt-ulp) until upstream pull request https://github.com/JamesYang007/adelie/pull/159 is
merged. A reprex and root-cause analysis live in
bug_reports/kkt_ulp/ (excluded from the package
tarball).IOSNPUnphased and
IOSNPPhasedAncestry classes.RStateMultiGlm64.NEWS.md file to track changes to the
package.