susieR 0.16.6 compat: drop defunct R_mismatch_method/check_prior forwarding - #557
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…arding These moved into susie_rss_control() in susieR 0.16.6; .fmFitSusieRss no longer forwards them (control defaults apply). R_mismatch still passes through, incl. the new eb_mix. Pin susieR (>= 0.16.6). Behavior-preserving for default/eb runs.
susie_rss() is no longer passed R_mismatch_method/check_prior (they moved into susie_rss_control() in 0.16.6), so the code runs on susieR 0.16.4+. The >= 0.16.6 pin couldn't be satisfied by the CI conda channel (max 0.16.4) and failed every CI job. Docs now note eb_mix needs 0.16.6 while the package itself works on 0.16.4+.
gaow
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Jul 30, 2026
| #' \code{check_prior} forwarded to \code{susieR::susie_rss()} when | ||
| #' non-\code{NULL}. | ||
| #' \code{"eb"} for empirical Bayes, \code{"eb_mix"} for residual-mixture EB; | ||
| #' \code{"eb_mix"} requires susieR >= 0.16.6). Default \code{"none"} (susieR's |
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You can clean up these documentations related to backwards compatibility --- this is not relevant to users in the long run
gaow
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Jul 30, 2026
| #' default). \code{R_mismatch_method} and \code{check_prior} are no longer set | ||
| #' here: they became \code{susie_rss_control()} settings in susieR >= 0.16.6 | ||
| #' and are left at their control defaults, so this package works with | ||
| #' susieR 0.16.4+. |
gaow
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Jul 30, 2026
| if (!is.null(rMismatchMethod)) baseArgs$R_mismatch_method <- rMismatchMethod | ||
| if (!is.null(checkPrior)) baseArgs$check_prior <- checkPrior | ||
| # R_mismatch_method / check_prior are susie_rss_control() settings in susieR | ||
| # >= 0.16.6 (not top-level susie_rss args); left at their control defaults. |
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Also you should provide input interface for RSS controller?
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RSS controller added for pecotmr. Will add to pipeline too
…review) Address review: drop the susieR 0.16.4/0.16.6 backwards-compat narrative from the rMismatch roxygen/.Rd and the fineMappingWrappers comment, and expose susie_rss_control() via a new rssControl named-list arg on fineMappingPipeline (forwarded as susie_rss(control=...)); NULL leaves the control defaults, a non-named-list errors. Threaded through .fmFitRssBlock and .fmFitSusieRss, with unit + real-data tests.
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The .fmFitSusieRss rssControl-forwarding test mocks susie_rss_control(), which only exists in susieR >= 0.16.6; on the CI r44 env (susieR 0.16.4) local_mocked_bindings() can't find the binding and errors. Skip it when susieR lacks susie_rss_control - rssControl is a 0.16.6-only feature anyway. (Test came in with StatFunGen#557; it also fails CI here on this branch.)
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These moved into susie_rss_control() in susieR 0.16.6; .fmFitSusieRss no longer
forwards them (control defaults apply). R_mismatch still passes through, incl. the
new eb_mix. Pin susieR (>= 0.16.6). Behavior-preserving for default/eb runs.