CVS commit: pkgsrc/math/R-nimble

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

Module Name:    pkgsrc
Committed By:   mef
Date:           Sat Feb 15 05:46:28 UTC 2025

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

Log Message:
(math/R-nimble) Updated 1.2.1 to 1.3.0

#                            CHANGES IN VERSION 1.3.0 (December 2024)

## USER LEVEL CHANGES

- Provide the Barker proposal sampler as an alternative to the `RW_block`
  (block Metropolis) sampler. The Barker sampler uses
  gradient information and may improve adaptation behavior, including
  better mixing when parameter are on different scales or the initial
  proposal scale is too large (PR #1492).

- Improve Laplace/AGHQ implementation in various ways, including use
  of nlminb for both inner and outer optimization (for better
  optimization performance), improved messaging and output naming,
  returning the log-likelihood and degrees of freedom for model
  selection calculations, and unified control of optimization method and
  other controls at either the build stage or through the `updateSettings`
  method (PR #1496).

- Add BOBYQA as an optimization method available through `nimOptim`,
  registered via `nimOptimMethod` (PR #1496).

- Prevent use of nimbleFunction method names and nimbleFunction
  names that conflict with names in the nimble language (DSL) (PRs #1517
  and #1519).

- More carefully check for and warn of cases of NaN and non-finite
  log probability values in various samplers that in some cases may indicate invalid
  MCMC sampling (PR #1512).

- More carefully handle NaN and non-finite log probability values in
  the CRP sampler, in particular error out if all values are minus
  infinity and warning if multiple values are infinity (PR #1509).

- Error trap cases of dynamic indices producing a non-scalar result in
  AD-enabled models, and provide a suggested work-around (PR #1515).

- Error trap use of non-existent nimbleList (PR #1518).

- Prevent use of a single seed when running multiple chains via
  `runMCMC` (PR #1494).

- Improve messaging related to lack of derivative support for
  functions (PR #1502).

- Add information about model macros to the manual (PR #1499).

- Add an argument to `deregisterDistributions` to turn off warning
  that a distribution being deregistered does not exist.

## BUG FIXES

- Fix bug in caching values in `sampler_CRP` when maximum number of
  clusters is exceeded, which would have caused incorrect sampling (albeit
  with the user having been warned that they should increase the maximum number
  of clusters) (PR #1513).

- Fix issue preventing use of nimbleList elements in `nimCat` (PR
  #1518).

- Prevent adaptation interval of one for various block samplers for
  which an interval of one leads to an error.

- Allow `runLaplace` to use an uncompiled Laplace object (PR #1496).

## DEVELOPER LEVEL CHANGES

- Improve and provide additional infrastructure for model macros (PR #1502).

- Add new model method, `MixedDataNodeNames` to retrieve node names
  which are partially observed (whose elements are partially but not
  entirely data) (PR #1489).

- Turn off the use of `--preclean` during C++ compilation when
  `nimbleExternalCall` is invoked to avoid removing .o files that
  might have been created by `Rcpp` (PR #1520).


To generate a diff of this commit:
cvs rdiff -u -r1.9 -r1.10 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:1.9 pkgsrc/math/R-nimble/Makefile:1.10
--- pkgsrc/math/R-nimble/Makefile:1.9   Wed Nov  6 13:43:48 2024
+++ pkgsrc/math/R-nimble/Makefile       Sat Feb 15 05:46:28 2025
@@ -1,7 +1,7 @@
-# $NetBSD: Makefile,v 1.9 2024/11/06 13:43:48 mef Exp $
+# $NetBSD: Makefile,v 1.10 2025/02/15 05:46:28 mef Exp $
 
 R_PKGNAME=     nimble
-R_PKGVER=      1.2.1
+R_PKGVER=      1.3.0
 
 MAINTAINER=    pkgsrc-users%NetBSD.org@localhost
 COMMENT=       MCMC, Particle Filtering, and Programmable Hierarchical Modeling
@@ -15,6 +15,7 @@ DEPENDS+=     R-pracma-[0-9]*:../../math/R-p
 
 # Package suggested but not available: 'mcmcse'
 
+TEST_DEPENDS+= R-nloptr-[0-9]*:../../math/R-nloptr
 TEST_DEPENDS+= R-testthat-[0-9]*:../../devel/R-testthat
 
 USE_LANGUAGES= c++ fortran
Index: pkgsrc/math/R-nimble/distinfo
diff -u pkgsrc/math/R-nimble/distinfo:1.9 pkgsrc/math/R-nimble/distinfo:1.10
--- pkgsrc/math/R-nimble/distinfo:1.9   Wed Nov  6 13:43:48 2024
+++ pkgsrc/math/R-nimble/distinfo       Sat Feb 15 05:46:28 2025
@@ -1,5 +1,5 @@
-$NetBSD: distinfo,v 1.9 2024/11/06 13:43:48 mef Exp $
+$NetBSD: distinfo,v 1.10 2025/02/15 05:46:28 mef Exp $
 
-BLAKE2s (R/nimble_1.2.1.tar.gz) = ebfadae5e6b899e128ffee5099090114fc1f71218692133152015a073886c52b
-SHA512 (R/nimble_1.2.1.tar.gz) = 7443b397ea8ed3982dbdf105ff9539210c84daf833ac05cdbeebab26d71f3978f0e86178968809b2de0e84852041d9eb94c589429835221420b0b444bd569a31
-Size (R/nimble_1.2.1.tar.gz) = 3392131 bytes
+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