R Observatory: Metrics for thisutils version 0.5.0

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

thisutils

0.5.0Package record

Reliable Utilities for Reusable Research Workflows

2packages depend

10.2Kdownloads / year

69.3%test coverage

13/13flavors OK

Overview

About

Maintained by Meng XuCRAN page ↗GitHub ↗Website ↗Issues ↗

Provides reusable building blocks for research packages across matrix representation, numerical computation, neighborhood evaluation, controlled execution, and runtime interoperability. Core tools preserve declared sparse semantics, expose dense-memory and output boundaries, standardize neighborhood and classification results, and align serial and parallel result and error behavior. Additional helpers support structured messages, optional dependency checks, and common statistical workflows.

Changes in 0.5.0

**compatibility**:
Preserve the historical matrix_to_table(keep_zero = TRUE) default. Compact table output remains an explicit choice.
Preserve the stored-entry semantics and zero-value padding of run_sparse_topk_by_column(). The new run_sparse_topk() includes implicit sparse zeros by default so it matches ordinary dense-matrix semantics.
**feat**:
Add run_dense_topk() with an explicit by = "col" or by = "row" direction and a decreasing top-k default.
Add run_sparse_topk() and run_sparse_topk_stored() with an explicit by = "col" or by = "row" direction. The earlier column-wise names remain available as compatibility wrappers.

Show all changes in 0.5.0Hide the rest of the changes in 0.5.0

Allow parallelize_fun(verbose = TRUE, progress = FALSE) to retain standardized log_message() lifecycle output without a dynamic terminal progress bar.
Make Pearson sparse_cor() blockwise and add correlation threshold, dense working-memory, and opt-in sparse output-size controls. The output limit defaults to Inf for compatibility. Spearman and Kendall paths now check their dense allocation boundary before conversion.
Expose exact LISI neighbor-search strategy, C++ thread count, and dense input-memory controls through compute_lisi().
**fix**:
Detect cancellation-prone row variance calculations and recompute only the affected dense or sparse rows with a stable two-pass calculation, preserving the existing fast path for ordinary inputs.
Pad stored-entry sparse top-k results with NA values instead of zeros.
Replace infinite correlations with zero when remove_inf = TRUE.
Summarize failed structured or matrix-valued tasks by their task name or shape, preventing verbose error reporting from masking the original worker error.
**docs**:
Document sparse expansion, implicit-zero, dense-intermediate, and CPU boundaries, and reorganize the package reference around sparse and resource-controlled research workflows.
Add a full-workflow vignette that connects semantic, numerical, resource, and execution contracts, plus an R Journal-oriented benchmark plan.
Demonstrate stable verbose lifecycle messages separately from dynamic progress output in report-oriented examples.
Add a package-wide workflow vignette spanning representation, neighborhood evaluation, execution, messages, and optional dependency diagnostics.
**tests**:
Exercise fork interruption from an external parent process and verify that workers are reaped before a subsequent fork call. Clarify that the in-process interrupt-sender test covers the default PSOCK backend.

From NEWS.md in the release

Install

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

install.packages("thisutils", 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("mengxu98/thisutils")

Development version from mengxu98/thisutils. 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-thisutils

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-thisutils

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-thisutils

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: 4.9 min · r-oldrel-macos-x86_64

Status changes

OK13 OK2026-08-26
ERROR12 OK, 1 ERROR2026-08-16
OK13 OK2026-08-10
ERROR12 OK, 1 ERROR2026-08-05
OK13 OK2026-08-04

Show 6 earlier changesHide 6 earlier changes

NOTE12 OK, 1 NOTE2026-08-01
OK14 OK2026-04-22
ERROR13 OK, 1 ERROR2026-04-18
OK14 OK2026-04-09
NOTE13 OK, 1 NOTE2026-03-28
OK14 OK2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 0.5.0

READMEYes · 88 wordsVignettesYes · 2 · dynamicNEWSYes · 100% structured · mentions 0.5.0Citation fileNoWebsiteYes · pkgdown

Help pages: 56includes a package overview page
Examples that run: 100%39 run in a plain check
Exported functions with examples: 72%
Documented parameters: 98%
Return-value docs: 77%
Help pages citing references: 9%

Vignettes (2)

How these are measured

Downloads

10.2K

CRAN downloads in the past year

Rank #4,121 · ~28/day · ~847/mo

Releases R versions

Daily download trend is not available in this view yet.

63630 days

2.2K90 days

10.2K1 year

Compare downloads with other packages →

Also on523 r2u10 autocran2.2K conda_forge

How downloads are counted

Repository

mengxu98/thisutils ↗Account: mengxu98

6Stars

1Forks

0Open issues

0Open PRs

0Releases

140Commits

2Commit identities

140 commits · Last activity 2026-10-16 · 0% stars, 30d · Default branch at 0.5.2, ahead of CRAN 0.5.0 (checked 2026-10-11)

Responsiveness

How these are sampled

PRs merged (all time): 92%
Median days to close, 50 most recently updated closed issues: 59
Median days to close, 50 most recently updated closed PRs: 0

Stars over time

2025-08-20 · 22026-09-09 · 6

How these are measured

PracticesBeta

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

Checks run against github.com/mengxu98/thisutils on 2026-10-11.

Continuous integration (2)

GitHub ActionsR CMD check workflow

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

Docs source (3)

pkgdown

GitHub Pages site last deployed 2026-10-08 · The repository has a site deploy workflow

pkgdown site last built 2026-10-08

Coverage (1)

Coverage reporting

Reproducibility and dev environment (1)

renv

Show all practicesHide 1 practice

CRAN release process (2)

cran-comments.mdCRAN-SUBMISSION

How this is detected·Detection ruleset v3 (2026-09-26)

AI coding toolsBeta

This repository shows signs of AI coding tools.

GitHub Copilotfirst seen 2025-10-31
Pull request: opened by its own account
Commits: some by its own account, count not recorded
Claude Codefirst seen 2026-03-25
Named in .Rbuildignore: .claude
Codexfirst seen 2026-04-24
Named in .Rbuildignore: .codex
Named in .gitignore: .codex

How this is detected·Detection ruleset v4 (updated 2026-09-27)

Dependencies

Declared dependencies

13 external dependencies (excludes base and recommended)

Installing thisutils adds 9 packages (6 with compiled code, 7.6 MB of source tarballs). Heaviest: pak 3.8 MB, Rcpp 1.8 MB, rlang 766 KB.

Depends (1)

R >= 4.1.0

Imports (11)

callr climethodsMatrixpakparallelps Rcpp rlangstatsutils

LinkingTo (2)

cli Rcpp

Suggests (5)

BiocNeighbors knitr remotes rmarkdown testthat

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

2direct

0indirect

Imports 2

Depends, Imports or LinkingTo, most downloaded first

thisplot inferCSN

How these are counted

Code & Tests

People & History

People (2)

Meng Xu

Author, Maintainer since 0.0.4 (2025)

Haoliang Zhu

Author · added in 0.4.7

Releases (15)

Pick two releases to compare their code metrics.

0.5.0Latest
record
2026-08-21 · current release · diff ↗ ·
removed 1 export
run_dense_topk_by_column

added 4 exports
run_dense_topk, run_sparse_stored_topk_by_column, run_sparse_topk, run_sparse_topk_stored
0.4.9
record
2026-08-04 · diff ↗ ·
added 6 exports
classification_metrics_compute, fast_row_vars, filter_nonzero_variance_features, run_biocneighbors_knn, run_dense_topk_by_column, run_sparse_topk_by_column
0.4.7
record
2026-05-24 · diff ↗ ·
removed 1 export
compute_simpson_index
0.4.5
record
2026-04-24 · diff ↗ ·
added 1 export
collapse_sparse_rows
R
R 4.6.0 released · 2026-04-24
0.4.4
record
2026-04-02 · diff ↗ ·
added 6 exports
compute_lisi, compute_simpson_index, is_apple_silicon, is_linux, is_osx, is_windows
0.4.3
record
2026-03-06 · diff ↗ ·
added 3 exports
check_ci_env, check_pkg_status, is_outlier
0.4.2
record
2026-02-23 · diff ↗ ·
added 2 exports
check_r, remove_r
0.3.6
record
2026-01-08 · diff ↗ ·
added 1 export
get_namespace_fun
0.3.1
record
2025-11-17 · diff ↗
0.2.0
record
2025-10-06 · diff ↗ ·
removed 2 exports
list_figlet_fonts, rescale

added 9 exports
get_verbose, max_depth, maximump, meanp, minimump, parse_inline_expressions, sump, votep, wilkinsonp
0.1.5
record
2025-09-11 · diff ↗ ·
removed 1 export
str_wrap
0.1.2
record
2025-08-19 · diff ↗ ·
added 3 exports
matrix_process, matrix_to_table, table_to_matrix
0.0.7
record
2025-07-20 · diff ↗
0.0.5
record
2025-07-03 · diff ↗ ·
added 8 exports
capitalize, download, invoke_fun, remove_space, rescale, str_wrap, try_get, unnest_fun
0.0.4
record
2025-06-17

Show 1 earlier eventHide 1 earlier event

R
R 4.5.0 released · 2025-04-11

Package metadata

First published: 2025-06-17
Total releases: 15 / 1 yrs
License: MIT + file LICENSE OSI
Minimum R: ≥ 4.1.0
Download size: 148 KB

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("thisutils")

Format

Xu, M., & Zhu, H. (2026). thisutils: Reliable Utilities for Reusable Research Workflows (Version 0.5.0) [Computer software]. https://doi.org/10.32614/CRAN.package.thisutils

This package has no citation file, so citation() returns this entry built from DESCRIPTION.

Cite the R Observatory

For a number measured here: a download total, a coverage figure, an archival date.

Format

APA

Balamuta, J. J. (2026). R Observatory: Metrics for thisutils version 0.5.0 [Data set]. HJJB, LLC. Data release v2026-10-18. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-18, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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