R Observatory: Metrics for NGCHM version 1.0.4

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

NGCHM

1.0.4Package record

Next Generation Clustered Heat Maps

0packages depend

6.7Kdownloads / year

13.4%test coverage

11/13flavors OK

Overview

About

Maintained by Mary A RohrdanzCRAN page ↗GitHub ↗Website ↗

Next-Generation Clustered Heat Maps (NG-CHMs) allow for dynamic exploration of heat map data in a web browser. 'NGCHM' allows users to create both stand-alone HTML files containing a Next-Generation Clustered Heat Map, and .ngchm files to view in the NG-CHM viewer. See Ryan MC, Stucky M, et al (2020) doi:10.12688/f1000research.20590.2 for more details.

Install

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

install.packages("NGCHM", 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("MD-Anderson-Bioinformatics/NGCHM-R")

Development version from MD-Anderson-Bioinformatics/NGCHM-R. 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-ngchm

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-NGCHM

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-NGCHM

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

2NOTE11OK

Check messages

NOTERd contentsr-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc

Rd files without \usage:
  ‘chmLayer-set.Rd’
\arguments should not be documented without \usage.

CRAN check page ↗

Slowest check: 3.3 min · r-oldrel-windows-x86_64

Status changes

NOTE11 OK, 2 NOTE2026-09-08
ERROR10 OK, 2 NOTE, 1 ERROR2026-09-07
NOTE12 OK, 1 NOTE2026-07-11
OK12 OK2026-04-25
NOTE11 OK, 3 NOTE2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 1.0.4

READMEYes · 35 wordsVignettes· In the repository, left out of the releaseNEWSNoCitation fileNoWebsiteYes · pkgdown

Help pages: 199includes a package overview page
Examples that run: 74%23 run in a plain check (6 of them under a condition) · 8 never run
Exported functions with examples: 28%
Documented parameters: 100%
Return-value docs: 100%
Help pages citing references: 0%

How these are measured

Downloads

6.7K

CRAN downloads in the past year

Rank #8,938 · ~18/day · ~561/mo

Releases R versions

Daily download trend is not available in this view yet.

35930 days

1.1K90 days

6.7K1 year

Compare downloads with other packages →

Also on65 r2u4 autocran

How downloads are counted

Repository

md-anderson-bioinformatics/ngchm-r ↗Organization: MD-Anderson-Bioinformatics

9Stars

2Forks

18Open issues

0Open PRs

4Releases

479Commits

5Commit identities

ng-chmheatmapnci-itcr

479 commits · Last activity 2026-04-13 · Default branch at 1.1.0, ahead of CRAN 1.0.4 (checked 2026-10-18)

Responsiveness

How these are sampled

PRs merged (all time): 97%
Median days to close, 50 most recently updated closed issues: 92
Median days to close, 50 most recently updated closed PRs: 8

How these are measured

PracticesBeta

5 development-tooling and community-health practices detected across 2 families in the upstream repository

Checks run against github.com/md-anderson-bioinformatics/ngchm-r on 2026-10-18.

Continuous integration (2)

GitHub ActionsR CMD check workflow

The R CMD check workflow runs on Linux

Docs source (3)

pkgdown

GitHub Pages site last deployed 2026-05-04 · The repository has a site deploy workflow

pkgdown site last built 2026-05-04

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

AI coding toolsBeta

This repository has an AI review tool set up.

Review tools

Copilot code review
Commits: some accepting its review suggestions, count not recorded

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

Dependencies

Declared dependencies

12 external dependencies (excludes base and recommended)

Installing NGCHM adds 15 packages (12 with compiled code, 5.3 MB of source tarballs). Heaviest: logger 1.1 MB, openssl 1.1 MB, jsonlite 1.0 MB.

Depends (1)

R >= 3.5.0

Imports (10)

digestgrDeviceshtmltools httr jsonlite logger (>= 0.2.0)methodsstatstsvioutils

LinkingTo (0)

none

Suggests (6)

knitr rmarkdown Rtsne testthat umap uwot

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

How these are counted

Code & Tests

People & History

People (5)

Mary A Rohrdanz

Contributor, Maintainer since 1.0.1 (2024)

Bradley M Broom

Author

James M Melott

Contributor

Chris Wakefield

Contributor

MD Anderson Cancer Center

Copyright holder

Listed in earlier versions (4)

Show 4 peopleHide 4 people

Mary A

no longer listed · 1.0.1 to 1.0.4

Bradley M

no longer listed · 1.0.1 to 1.0.4

James Melott

no longer listed · 1.0.1 to 1.0.3

James M

no longer listed · 1.0.4

Releases (4)

Pick two releases to compare their code metrics.

R
R 4.6.0 released · 2026-04-24
R
R 4.5.0 released · 2025-04-11
1.0.4Latest
record
2024-12-17 · current release · diff ↗
1.0.3
record
2024-05-08 · diff ↗
R
R 4.4.0 released · 2024-04-24
1.0.2
record
2024-03-28 · diff ↗
1.0.1
record
2024-01-16
R
R 4.3.0 released · 2023-04-21

Package metadata

First published: 2024-01-16
Total releases: 4 / 2 yrs
License: GPL-3 OSI
Additional repositories: md-anderson-bioinformatics.r-universe.dev
Minimum R: ≥ 3.5.0
Download size: 142 KB

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("NGCHM")

Format

Rohrdanz, M. A., MD Anderson Cancer Center, Broom, B. M., Melott, J. M., & Wakefield, C. (2024). NGCHM: Next Generation Clustered Heat Maps (Version 1.0.4) [Computer software]. https://doi.org/10.32614/CRAN.package.NGCHM

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 NGCHM version 1.0.4 [Data set]. HJJB, LLC. Data release v2026-10-21. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-21, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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