R Observatory: Metrics for sundialr version 0.2.1

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

sundialr

0.2.1Package record

An Interface to 'SUNDIALS' Ordinary Differential Equation (ODE) Solvers

0packages depend

5.9Kdownloads / year

95.9%test coverage

13/13flavors OK

Overview

About

Maintained by Satyaprakash NayakCRAN page ↗GitHub ↗Website ↗Issues ↗

Provides a way to call the functions in 'SUNDIALS' C ODE solving library (https://computing.llnl.gov/projects/sundials). Currently the serial version of ODE solver, 'CVODE', sensitivity calculator 'CVODES' and differential algebraic solver 'IDA' from the 'SUNDIALS' library are implemented. The package requires ODE to be written as an 'R' or 'Rcpp' function and does not require the 'SUNDIALS' library to be installed on the local machine.

Changes in 0.2.1

**New feature**: the C API gains a second integrator, ARKODE run as a fully implicit ESDIRK method (singly diagonally implicit Runge-Kutta with an explicit first stage) with Newton iteration and a dense linear solver. Its sundialr_arkode_* entry points mirror the sundialr_cvode_* ones one for one — the same callback types, handle lifecycle, tolerance and step-size setters, set_udata, step counting, and the same no-throw, no-allocation-on-reuse and one-handle-per-thread contracts — so a host loop written against the CVODE API can switch integrator by changing which entry points it looks up. The method defaults to ARKODE_ESDIRK436L2SA_6_3_4 (order 4); sundialr_arkode_set_order() picks ARKODE's default ESDIRK of order 2 to 5 and sundialr_arkode_set_table_name() any ARKODE DIRK table by name. Status codes are ARKODE's, mirrored as SUNDIALR_ARK_*; they coincide with the CVODE codes for the common failures but not everywhere. sundialr_arkode_reinit() is warm: it uses ARKodeReset, which keeps the step size and the error controller's history from the previous segment, the natural restart after a dose within one trajectory. sundialr_arkode_reinit_cold() is the full re-initialisation (ARKStepReInit), with CVodeReInit's semantics: it leaves a used handle exactly as a new one would be (pinned bit for bit by a test), so a handle reused across unrelated problems, such as the subjects of a population, gives results that do not depend on what it solved before; the step count keeps running across it. The addition is binary-compatible, so SUNDIALR_ABI_VERSION stays 1. To support it the bundled build now compiles ARKODE, with CRAN-compliance patches for the stdout references in its parameter-printing paths
Updated the underlying SUNDIALS library to v7.9.0 (Sep 2026). The changes relevant to the bundled solvers are bug fixes: the SUNNonlinearSolver_Auto stiffness switch no longer moves to Newton iteration prematurely, and IDA no longer writes duplicate keys in its logging output (logging is disabled in this build). The sundialr interface and the C API are unchanged, and the existing CRAN-compliance patches apply to the new sources without modification. The installed headers change accordingly: the N_Vector operations table gains an nvsetdevicearraypointer entry, so code compiled against these headers must also be built against 7.9.0 sources
The cmake call now uses the current option names SUNDIALS_ENABLE_C_EXAMPLES and SUNDIALS_ENABLE_CXX_EXAMPLES, silencing two deprecation warnings during installation
The build no longer needs Perl's open module. The step that normalises the line endings of the two cmake-generated headers used perl -Mopen=IO,:raw, and open is not part of the minimal perl-base, so installing from source on a minimal Debian/Ubuntu image (for example rocker/r-ver) failed with "Can't locate open.pm in @INC". The step now uses POSIX tr, which behaves the same on Linux, macOS and Windows (Rtools)
**New feature**: two additions to the C API for host loops that drive many small solves. sundialr_cvode_set_udata() replaces the callback-data pointer on an existing handle, so one handle can serve many parameter sets — a population of subjects — instead of paying a create/free cycle (SUNContext, cvode_mem, matrix and linear solver allocations) per set. sundialr_cvode_reset_stats() zeroes the accumulated step count so sundialr_cvode_get_num_steps() can report per-subject counts from a shared handle. Both are additive and binary-compatible, so SUNDIALR_ABI_VERSION stays 1
Fixed sundialr_cvode_get_num_steps() under the reinit-per-segment pattern: CVodeReInit zeroes CVODE's internal step counter, so the count previously restarted at every sundialr_cvode_reinit() and never reflected more than the current segment, despite being documented as a running total. The handle now accumulates the count across reinits, counting from create() or the last reset_stats()
The C API's handle-reuse and thread-safety contracts are now documented in sundialr_capi.h and pinned by tests: after the first reinit+solve cycle, further reinit/solve calls on a handle perform no heap allocation (a tight-loop test drives 10^4 segments and checks the state buffer is never reallocated), and distinct handles — each owning its own SUNContext and error record, with no global mutable state and no R API on any entry point — may be driven from concurrent threads, one handle per thread (pinned by a two-thread test)
The vignette has a new section, "Using ARKODE and CVODE from compiled code", showing how another package uses the C API: it looks up the sundialr_arkode_* entry points with R_GetCCallable, simulates repeated doses of a one-compartment model with ARKODE, restarting the integrator at each dose, and checks the result against the closed-form solution. It also covers method selection, warm and cold reinitialisation and switching to CVODE. The Introduction and Summary no longer describe ARKODE as a future addition; it is available through the C API, though not yet as an R function

From NEWS.md in the release

Install

R (CRAN)pak (dev)Ubuntu (r2u)Fedora (COPR)openSUSE (OBS)

install.packages("sundialr", repos = "https://cloud.r-project.org/")

Installs the current CRAN release. Prebuilt binaries on Windows and macOS.

if (!requireNamespace("pak", quietly = TRUE))
  install.packages("pak", repos = "https://cloud.r-project.org/")
pak::pak("sn248/sundialr")

Development version from sn248/sundialr. Installs pak first if it is not already available.

Release

# enable cranapt (r2u) if it is not already set up, then install
grep -rqs r2u.stat.illinois.edu /etc/apt/sources.list /etc/apt/sources.list.d/ \
  || curl -fsSL https://raw.githubusercontent.com/eddelbuettel/r2u/master/inst/scripts/add_cranapt_noble.sh | sudo bash
sudo apt install -y r-cran-sundialr

Fast Ubuntu binaries via r2u (no compilation). The cranapt setup runs once and is skipped when it is already enabled. We list this channel from recorded r2u download activity rather than from a live index of the repository, so treat it as last known rather than guaranteed.

bspm (used by r2u) also needs make: sudo apt install make

# enable the iucar/cran COPR if it is not already present, then install
ls /etc/yum.repos.d/*iucar*cran*.repo >/dev/null 2>&1 \
  || sudo dnf copr enable -y iucar/cran
sudo dnf install -y R-CRAN-sundialr

RPMs from the iucar/cran COPR, rebuilt from CRAN.

For install.packages() integration in R, also: sudo dnf install R-CoprManager

# add the autoCRAN OBS repo (Tumbleweed) if it is missing, then install
zypper -q lr | grep -qi autoCRAN \
  || sudo zypper addrepo https://download.opensuse.org/repositories/devel:/languages:/R:/autoCRAN/openSUSE_Tumbleweed/devel:languages:R:autoCRAN.repo
sudo zypper install -y R-sundialr

RPMs auto-built from CRAN on openSUSE OBS (Tumbleweed). We list this channel from recorded autoCRAN download activity rather than from a live index of the repository, so treat it as last known rather than guaranteed.

Health

CRAN checks

13OK

CRAN check page ↗

Slowest check: 10.4 min · r-devel-windows-x86_64

Status changes

OK13 OK2026-08-04
NOTE12 OK, 1 NOTE2026-08-01
OK10 OK2026-04-25
ERROR5 OK, 2 NOTE, 1 WARNING, 1 ERROR2026-04-22

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 0.2.1

READMEYes · 868 wordsVignettesYes · 1 · dynamicNEWSYes · 33% structured · mentions 0.2.1Citation fileYes · software entry onlyWebsiteYes · pkgdown

Help pages: 4
Examples that run: 100%4 run in a plain check
Exported functions with examples: 100%
Documented parameters: not tracked
Return-value docs: not tracked
Help pages citing references: 0%

Vignettes (1)

sundialr - An Interface to 'SUNDIALS' Ordinary Differential Equation (ODE) Solvers HTML

How these are measured

Downloads

5.9K

CRAN downloads in the past year

Rank #5,836 · ~16/day · ~489/mo

Releases R versions

Daily download trend is not available in this view yet.

53330 days

1.4K90 days

5.9K1 year

Compare downloads with other packages →

Also on419 r2u3 autocran120 c2d4u

How downloads are counted

Repository

sn248/sundialr ↗Account: sn248

11Stars

6Forks

3Open issues

0Open PRs

7Releases

375Commits

6Commit identities

sundialsode-solver

375 commits · Last activity 2026-10-18

Responsiveness

How these are sampled

PRs merged (all time): 88%
Median days to close, 50 most recently updated closed issues: not measured
Median days to close, 50 most recently updated closed PRs: 0

Stars over time

2025-03-20 · 112026-07-07 · 11

How these are measured

PracticesBeta

11 development-tooling and community-health practices detected across 5 families in the upstream repository

Checks run against github.com/sn248/sundialr on 2026-10-25.

Continuous integration (4)

GitHub ActionsR CMD check workflowTravis CI (config file)AppVeyor

The R CMD check workflow runs on Linux, macOS and Windows, and on R-devel

Docs source (3)

pkgdown

GitHub Pages site last deployed 2026-10-18 · The repository has a site deploy workflow

pkgdown site last built 2026-10-18

CRAN release process (2)

cran-comments.mdCRAN-SUBMISSION

Lint, format, editor (1)

RStudio project

Show all practicesHide 1 practice

Git structural (1)

.gitattributes

How this is detected·Detection ruleset v4 (2026-10-20)

AI coding toolsBeta

This repository shows signs of AI coding tools.

Claude Codefirst seen 2026-03-28
Named in .Rbuildignore: .claude, CLAUDE.md
Named in .gitignore: CLAUDE.md
Pull request it wrote: opened by a project member
Commits: at least 16 crediting it in the message

Models named in its commits

Claude Opus 5.58 commits · Oct 2026
Claude Opus 54 commits · Aug 2026
Claude Sonnet 4.63 commits · Mar 2026

Counts are commits, not lines of code. Commits by a tool's accounts count once across all of its accounts. Commits crediting it are the largest count among its credit lines, a minimum.How this is detected·Detection ruleset v4 (updated 2026-09-27)

Dependencies

Declared dependencies

6 external dependencies (excludes base and recommended)

Installing sundialr adds 2 packages (2 with compiled code, 2.8 MB of source tarballs). Heaviest: Rcpp 1.8 MB, RcppArmadillo 1.0 MB.

Depends (0)

none

Imports (1)

Rcpp

LinkingTo (2)

Rcpp RcppArmadillo

Suggests (3)

knitr rmarkdown testthat

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

How these are counted

Code & Tests

People & History

People (4)

Satyaprakash Nayak

Lawrence Livermore National Security

Copyright holder

Southern Methodist University

Copyright holder

University of Maryland Baltimore County

Copyright holder · added in 0.2.0

Listed in earlier versions (12)

Show 8 of 12 peopleHide 8 people

Peter Brown