CVS commit: pkgsrc/math/R-nimble

["Makoto Fujiwara" <mef%netbsd.org@localhost>]

Module Name:    pkgsrc
Committed By:   mef
Date:           Wed Jun 17 13:44:01 UTC 2026

Modified Files:
        pkgsrc/math/R-nimble: Makefile distinfo

Log Message:
(math/R-nimble) Updated 1.3.0 to 1.4.2, Fix build against R-4.6.0

#              CHANGES IN VERSION 1.4.2 (March 2026)

## USER LEVEL CHANGES

- Improve efficiency of `findSamplersOnNodes`, which is used in finding
samplers assigned to node(s) (PR #1614; thanks to 'hoxo-m').

## DEVELOPER LEVEL CHANGES

- Switch to using `R_getVar` and `R_getVarEx` in place of `Rf_findVar` and
`Rf_findVarInFrame` in C++ code at request of CRAN (PR #1616).

#              CHANGES IN VERSION 1.4.1 (February 2026)

## USER LEVEL CHANGES

- Add a new sampler to sample portions of a multivariate normal node when some
  elements are observed (i.e., data) and some elements are unknown. This
  sampler uses the exact conditional normal to sample from the posterior
  predictive distribution when the unknown elements have no dependent data nodes
  (PR #1612).

- Add ability to change the MCMC thinning interval when continuing an MCMC
  (PR #1609).

## BUG FIXES

- Fix a bug in the conjugacy size processing system when dependent nodes
  (of the target conjugate node) themselves have multivariate parameters
  with a different size from the dependent node itself (PR #1605).

## DEVELOPER LEVEL CHANGES

- Turn off an old work-around that prevented RStudio from hanging but
  which modified the global environment and no longer appears to be
  necessary (PR #1606).

#              CHANGES IN VERSION 1.4.0 (December 2025)

## USER LEVEL CHANGES

- Move Laplace/AGHQ approximation to new `nimbleQuad` package, which also has
  new INLA-like deterministic nested posterior approximation.

- Add system for computing and storing "derived quantities" during MCMC execution,
  for recording additional quantities of interest at every saved MCMC iteration
  (i.e., following thinning interval, or some other user-chosen
  interval). Derived quantities available provided by NIMBLE include means,
  variances, model log-densities, and predictive nodes. Users can also define
  their own derived quantities.

- Provide matrix exponential functionality via `expm` and `expAv`.

- Allow users to provide multiple code chunks to `nimbleCode` for greater
  flexibility in composing models.

- Greatly improve efficiency and memory use of AD system (PR #1574).

- Remove some references to "BUGS" when referring to models.

- Allow users to turn off `model$checkBasics` via a new option.

- Improve MCEM non-convergence error message (Issue #1535).

- Better handle inconsistencies between `inits` and `dimensions` (PR #1571).

- Make minor improvements to Pólya-gamma sampler to check for infinities
  in design matrix, fix where `inflationNodes` defined, and avoid design
  matrix initialization when passed by user (PR #1569).

- Add message when `addSampler` avoids assigning sampler for data nodes
  (PR #1580).

- Add additional checks for correct usage of derivative calls (PR #1566).

- Improve messaging when `checkLogProb` warning invoked (PR #1559).

- Error trap use of negation in indexing in nimbleFunction code (PR #1561).

- Error trap disallowed use of parentheses in indexing in model code
  (PR #1556).

- Avoid parameter transformation system causing an error with user-defined
  multivariate distributions (PR #1532).

- Error trap use of `x <- c()` (empty concatenate to initialize a variable)
  in nimbleFunction code (PR #1560).

- Added support for conjugate MCMC sampling of `tau` parameter of the
  intrinsic CAR (`dcar_normal`) distribution (PR #1596).

- Error trap if `inits` provided to `nimbleModel()` as a function (Issue #1598).

## BUG FIXES

- Fix bug in `makeModelDerivsInfo` for multiply-split LHSinferred nodes
  (PR #1594).

- Fix bug in `getConditionallyIndependentSets` arising with corner case
  involving particular order of `nodes` (PR #1576).

- Fix bug in initial types in `nimOptimDefaultControl` (PR #1581).

- Fix `rCRP` to return zero length if `size` is zero.

- Fix dimension issue in `sampleDPmeasure` (PR #1572).

- Fix compilation issue with min/max under some circumstances (PR #1557).

- Fix inconsistency in recycling rule for `rmnorm` (PR #1586).

- In `buildMCEM`, fix use of `pStart`, when provided by user, make thinning
  conform to other MCMC uses, add new error trapping, and clean up other
  details (PR #1601).

## DEVELOPER LEVEL CHANGES

- Provide AD-optimized `dmnormAD`.

- Greatly improve efficiency of `makeModelDerivsInfo_impl` by working with
  nodes rather than scalarComponents as much as possible (PR #1590).

- Greatly improve efficiency in `setData` by omitting RHS-only elements
  (Issue #1589).

- Omit unneeded marginalization nodes in `setupMargNodes` and rework
  messaging for setupMargNodes warnings (Issue #1582).

- Synthesize some Laplace-related tools useful more generally in
  `normTooling.R` and `setupMargNodes.R`.

- Document `reset` arg to `nimDerivs` (Issue #1555).

- Add derivative building for `transform` method of parameterTransform
  (PR #1565).

- Fix scoping for `nimbleMCMC` (PR #1554).

- Trap error in `buildMacro` when `use3pieces=TRUE` but the provided code
  is not an assignment (PR #1529).

- Improve efficiency of checking for nimbleFunction name conflicts (PR #1553).

- Set `replaceSamplers` to do lookup in parent frame (PR #1539).

- Check for dollar sign in `cc_expandDetermNodesInExpr` (PR #1534).

- Generalize system of dynamically generating conjugate MCMC samplers,
  to allow for multivariate parameters of dependent distributions to have
  distinct sizes from the dependent node itself (PR #1596).

- Make MCEM append new samples when increasing sample size using the
  ascent-based method, rather than starting a new sample (PR #1601).


To generate a diff of this commit:
cvs rdiff -u -r1.10 -r1.11 pkgsrc/math/R-nimble/Makefile \
    pkgsrc/math/R-nimble/distinfo

Please note that diffs are not public domain; they are subject to the
copyright notices on the relevant files.

Modified files:

Index: pkgsrc/math/R-nimble/Makefile
diff -u pkgsrc/math/R-nimble/Makefile:1.10 pkgsrc/math/R-nimble/Makefile:1.11
--- pkgsrc/math/R-nimble/Makefile:1.10  Sat Feb 15 05:46:28 2025
+++ pkgsrc/math/R-nimble/Makefile       Wed Jun 17 13:44:01 2026
@@ -1,7 +1,7 @@
-# $NetBSD: Makefile,v 1.10 2025/02/15 05:46:28 mef Exp $
+# $NetBSD: Makefile,v 1.11 2026/06/17 13:44:01 mef Exp $
 
 R_PKGNAME=     nimble
-R_PKGVER=      1.3.0
+R_PKGVER=      1.4.2
 
 MAINTAINER=    pkgsrc-users%NetBSD.org@localhost
 COMMENT=       MCMC, Particle Filtering, and Programmable Hierarchical Modeling
Index: pkgsrc/math/R-nimble/distinfo
diff -u pkgsrc/math/R-nimble/distinfo:1.10 pkgsrc/math/R-nimble/distinfo:1.11
--- pkgsrc/math/R-nimble/distinfo:1.10  Sat Feb 15 05:46:28 2025
+++ pkgsrc/math/R-nimble/distinfo       Wed Jun 17 13:44:01 2026
@@ -1,5 +1,5 @@
-$NetBSD: distinfo,v 1.10 2025/02/15 05:46:28 mef Exp $
+$NetBSD: distinfo,v 1.11 2026/06/17 13:44:01 mef Exp $
 
-BLAKE2s (R/nimble_1.3.0.tar.gz) = 1d4aa38b045afdf37b5603885fd1c7a4a86f67cfc3f0a2af19792629bf852e95
-SHA512 (R/nimble_1.3.0.tar.gz) = 6d5b5cd77f13782469fc7bf4bca1e82d1514b82f07162c16f2a8335ab8e6473323d6fd8525cd1e0f735ceda4f9e3b43fe282a183ea437a883d92af35b3f48096
-Size (R/nimble_1.3.0.tar.gz) = 3414374 bytes
+BLAKE2s (R/nimble_1.4.2.tar.gz) = 6d555785164f4dd13f92ffe3e594067c48652e847484128e08e907752ce1090c
+SHA512 (R/nimble_1.4.2.tar.gz) = 12134ca00dd08c1ec4f8cc5032f7057b5a2e19a51c27ca233d1145d9f30d637825a04fa533a3e893bc03752e00a4f875d89b444c20f9ccc45c1e951b7c9142d5
+Size (R/nimble_1.4.2.tar.gz) = 3407476 bytes