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feat: mention a missing or outdated GiottoKernels once per session - #136

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jiajic merged 1 commit into
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feat/giottokernels-hint
Oct 22, 2026
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jiajic merged 1 commit into
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feat/giottokernels-hint

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@jiajic jiajic commented Oct 22, 2026

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GiottoKernels was silent when missing: .gd_kernel() fell back to the R path, so a user never found out the compiled kernels exist. The first step that would use a kernel (gram-eigen PCA passes, edge pairs and products) now says so, once per session:

GiottoKernels is not installed, so this step runs in R: same results, slower. To use the compiled kernels:
install.packages("GiottoKernels",
    repos = c("https://giotto-suite.r-universe.dev", "https://cloud.r-project.org"))
This message is displayed once per session.

An installed GiottoKernels below the 0.3.0 Suggests floor gets one notice too. Before, kernels it lacked (such as edge_products_stream) were skipped without a word.

  • Uses package_check(on_missing = "message", once = TRUE) from GiottoUtils 0.2.9 (feat: package_check() on_missing levels and once GiottoUtils#193), so Imports: GiottoUtils (>= 0.2.9). Remotes: already takes GiottoUtils from @dev.
  • The fallback is unchanged. options(giottodisk.use_kernels = FALSE) skips the check entirely.
  • The check runs once per pass, not per tile.

Tests: a fake package is mentioned once and then silent, and use_kernels = FALSE never reaches the check. devtools::test(filter = "utils-edge|stream-pca") gives 0 failures and 163 passing. The 1 skip is the edge_products_stream kernel test, because the local GiottoKernels is 0.2.0.

🤖 Generated with Claude Code

The R fallback is unchanged; the message gives the r-universe install.

Co-Authored-By: Claude Opus 5.5 (1M context) <noreply@anthropic.com>
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jiajic merged commit 9a53d3c into dev Oct 22, 2026
@jiajic
jiajic deleted the feat/giottokernels-hint branch October 22, 2026 15:43
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