R Observatory: Metrics for huge version 2.0.1

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

huge

2.0.1Package record

High-Dimensional Undirected Graph Estimation

5packages dependsuggested by 9

80.9Kdownloads / year

91.3%test coverage

13/13flavors OK

Overview

About

Maintained by Tuo ZhaoCRAN page ↗GitHub ↗Issues ↗

Provides a general framework for high-dimensional undirected graph estimation. It integrates data preprocessing, neighborhood screening, graph estimation, and model selection techniques into a pipeline. In preprocessing stage, the nonparanormal(npn) transformation is applied to help relax the normality assumption. In the graph estimation stage, the graph structure is estimated by Meinshausen-Buhlmann graph estimation, the graphical lasso, or the TIGER (tuning-insensitive graph estimation and regression) method, and the first two can be further accelerated by the lossy screening rule preselecting the neighborhood of each variable by correlation thresholding. We target on high-dimensional data analysis usually d >> n, and the computation is memory-optimized using the sparse matrix output. We also provide a computationally efficient approach, correlation thresholding graph estimation. Three regularization/thresholding parameter selection methods are included in this package: (1)stability approach for regularization selection (2) rotation information criterion (3) extended Bayesian information criterion which is only available for the graphical lasso.

Changes in 2.0.1

Fixed a BLAS-dependent rounding issue in RIC selection. The rotated inner products are computed with matrix products, and a conforming BLAS may return any value inside a dot product's roundoff interval, so a mathematically zero regularization parameter could come back as a tiny positive value. RIC now certifies such values to exact zero using a pair-specific forward-error bound, which is scale-aware and keeps correlations the working precision can represent. Selected lambda values are therefore reproducible across BLAS implementations. Reported by CRAN's ATLAS additional check.
huge.select() (R) and huge_select() (Python) no longer gate the zero-lambda refit on a bitwise-zero lambda. A residual too small for a solver to certify but not exactly zero previously bypassed the safety fallback, which made graphical lasso fit rank-deficient data almost unregularized and raise a non-finite estimate error. Routing now uses the same roundoff scale in both packages.

From NEWS.md in the release

Install

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

install.packages("huge", 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("Gatech-Flash/huge")

Development version from Gatech-Flash/huge. 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-huge

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-huge

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-huge

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: 4.5 min · r-devel-windows-x86_64

Status changes

OK13 OK2026-08-05
NOTE12 OK, 1 NOTE2026-08-01
OK14 OK2026-04-22
ERROR13 OK, 1 ERROR2026-04-18
OK14 OK2026-03-12

Show 1 earlier changeHide 1 earlier change

NOTE12 OK, 2 NOTE2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 2.0.1

README· In the repository, left out of the releaseVignettesYes · 1 · staticNEWSYes · 100% structured · mentions 2.0.1Citation fileNo

Help pages: 21includes a package overview page
Examples that run: 100%8 run in a plain check
Exported functions with examples: 64%
Documented parameters: 100%
Return-value docs: 55%
Help pages citing references: 10%

Vignettes (1)

huge PDF

How these are measured

Downloads

80.9K

CRAN downloads in the past year

Rank #1,489 · ~222/day · ~6.7K/mo

Releases R versions

Daily download trend is not available in this view yet.

4.7K30 days

16.9K90 days

80.9K1 year

Compare downloads with other packages →

Also on1.2K r2u182 autocran9.1K conda_forge208 c2d4u

How downloads are counted

Repository

gatech-flash/huge ↗Organization: Gatech-FlashFork of HMJiangGatech/huge

0Stars

2Forks

1Open PRs

2Releases

167Commits

9Commit identities

167 commits · Last activity 2026-07-29

Responsiveness

How these are sampled

PRs merged (all time): 100%
Median days to close, 50 most recently updated closed issues: not measured
Median days to close, 50 most recently updated closed PRs: 0

Forks over time

2026-03-11 · 12026-09-30 · 2

How these are measured

PracticesBeta

6 development-tooling and community-health practices detected across 4 families in the upstream repository

Checks run against github.com/gatech-flash/huge on 2026-10-22.

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 (2)

GitHub Pages site last deployed 2026-07-29 · The repository has a site deploy workflow

CRAN release process (1)

cran-comments.md

Lint, format, editor (1)

RStudio project

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

AI coding toolsBeta

This repository shows signs of AI coding tools.

Claude Codefirst seen on or before 2026-03-10
Named in .Rbuildignore: CLAUDE.md
Named in .gitignore: .claude, CLAUDE.md
Commits: some crediting it in the message, count not recorded

From outside contributors

Claude Code
Pull requests: 6 from outside contributors, first on 2026-03-11, 6 from forks
Cursor
Pull requests: 1 from outside contributors, first on 2026-09-29, 1 from forks

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

Dependencies

Declared dependencies

4 external dependencies (excludes base and recommended)

Installing huge adds 10 packages (7 with compiled code, 9.8 MB of source tarballs). Heaviest: igraph 4.8 MB, Rcpp 1.8 MB, vctrs 1.0 MB.

Depends (1)

R >= 3.4.0

Imports (10)

MatrixigraphMASSgrDevicesgraphicsmethodsparallelstatsutilsRcpp

LinkingTo (1)

Rcpp

Suggests (1)

testthat

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

5direct

0indirect

Imports 5

Suggested by 9

Show all 14 packagesHide all 14 packages

Depends, Imports or LinkingTo, most downloaded first

netgwas heterocop SparseTSCGM nutriNetwork NetGreg

Suggests, most downloaded first

qgraph pcalg stm BDgraph stminsights sand edgebundleR CTD sdafilter

How these are counted

Code & Tests

Datasets

People & History

People (8)

Tuo Zhao

Author, Maintainer since 1.4 (2026)

Xinyu Fei

Author · added in 1.3.0

Haoming Jiang

Author · added in 1.3.0

John Lafferty

Author

Xingguo Li

Author · added in 1.2.7

Han Liu

Author

Kathryn Roeder

Author

Larry Wasserman

Author

Previously maintained by Haoming Jiang (1.3.0 to 1.3.5) and Tuo Zhao (0.7 to 1.2.7).

Listed in earlier versions (1)

Yukun Ma

no longer listed · 1.3.0 to 1.3.1

Releases (33)

Pick two releases to compare their code metrics.

2.0.1Latest
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2026-08-04 · current release · diff ↗
2.0.0
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2026-07-26 · diff ↗
R
R 4.6.0 released · 2026-04-24
1.6
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2026-04-13 · diff ↗
1.5.1
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2026-03-31 · diff ↗
1.5
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2026-03-11 · diff ↗
unarchivedReturned to CRAN
2026-02-19
1.4
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2026-02-19 · diff ↗
archivedRemoved from CRAN
2026-02-01
issues were not corrected in time
R
R 4.5.0 released · 2025-04-11
R
R 4.4.0 released · 2024-04-24
R
R 4.3.0 released · 2023-04-21
R
R 4.2.0 released · 2022-04-22
1.3.5
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2021-06-30 · diff ↗
R
R 4.1.0 released · 2021-05-18
R
R 4.0.0 released · 2020-04-24

Show 37 earlier eventsHide 37 earlier events

1.3.4.1
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2020-04-01 · diff ↗
1.3.4
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2019-10-28 · diff ↗
1.3.3
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2019-09-09 · diff ↗
R
R 3.6.0 released · 2019-04-26
1.3.2
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2019-04-08 · diff ↗ ·
added 4 exports
huge.ct, huge.glasso, huge.mb, huge.tiger
1.3.1
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2019-03-12 · diff ↗
1.3.0
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2019-02-22 · diff ↗ ·
removed 11 exports
huge.mb, huge.glasso, huge.ct, print.huge, plot.huge, print.sim, plot.sim, print.roc, plot.roc, print.select, plot.select

added 1 export
huge.inference
R
R 3.5.0 released · 2018-04-23
R
R 3.4.0 released · 2017-04-21
R
R 3.3.0 released · 2016-05-03
1.2.7
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2015-09-16 · diff ↗
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R 3.2.0 released · 2015-04-16
R
R 3.1.0 released · 2014-04-10
1.2.6
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2014-02-28 · diff ↗
1.2.5
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2013-12-07 · diff ↗
R
R 3.0.0 released · 2013-04-03
1.2.4
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2012-08-16 · diff ↗
R
R 2.15.0 released · 2012-03-30
1.2.3
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2012-03-22 · diff ↗
1.2.2
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2012-03-21 · diff ↗
1.2.1
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2012-01-27 · diff ↗
1.2
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2012-01-22 · diff ↗
R
R 2.14.0 released · 2011-10-31
1.1.2
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2011-08-22 · diff ↗
1.1.1
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2011-08-10 · diff ↗
1.1.0
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2011-07-23 · diff ↗ ·
removed 2 exports
huge.mbgel, huge.gect

added 2 exports
huge.mb, huge.ct
1.0.3
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2011-06-17 · diff ↗ ·
removed 12 exports
huge.NPN, huge.MBGEL, huge.glassoM, huge.GECT, print.GECT, plot.GECT, print.glassoM, plot.glassoM, print.NPN, plot.NPN, print.MBGEL, plot.MBGEL

added 4 exports
huge.npn, huge.mbgel, huge.glasso, huge.gect
1.0.2
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2011-06-15 · diff ↗ ·
removed 12 exports
lasso.stars, summary.huge, summary.sim, summary.GECT, summary.glassoM, summary.roc, summary.select, print.stars, plot.stars, summary.stars, summary.NPN, summary.MBGEL
R
R 2.13.0 released · 2011-04-13
1.0.1
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2011-04-11 · diff ↗
1.0
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2011-03-02 · diff ↗ ·
added 37 exports
huge, huge.select, huge.roc, huge.generator, huge.NPN, huge.plot, lasso.stars, huge.MBGEL, huge.glassoM, huge.GECT, print.huge, plot.huge, summary.huge, print.sim, plot.sim, summary.sim, print.GECT, plot.GECT, summary.GECT, print.glassoM, plot.glassoM, summary.glassoM, print.roc, plot.roc, summary.roc, print.select, plot.select, summary.select, print.stars, plot.stars and 7 more
0.9.1
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2011-02-13 · diff ↗
0.9
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2010-11-22 · diff ↗
0.8.1
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2010-11-17 · diff ↗
0.8
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2010-11-14 · diff ↗
0.7
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2010-11-11
R
R 2.12.0 released · 2010-10-15

Package metadata

First published: 2010-11-11
Total releases: 33 / 16 yrs
License: GPL-2 OSI
Minimum R: ≥ 3.4.0
Bundled data: 703 KB / 2 files
Download size: 1.9 MB

Appears in task views

Graphical Models

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("huge")

Format

Zhao, T., Fei, X., Jiang, H., Lafferty, J., Li, X., Liu, H., Roeder, K., & Wasserman, L. (2026). huge: High-Dimensional Undirected Graph Estimation (Version 2.0.1) [Computer software]. https://doi.org/10.32614/CRAN.package.huge

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 huge version 2.0.1 [Data set]. HJJB, LLC. Data release v2026-10-25. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-25, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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