R Observatory: Metrics for protHMM version 0.1.1

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

protHMM

0.1.1Package record

Protein Feature Extraction from Profile Hidden Markov Models

0packages depend

2Kdownloads / year

98.9%test coverage

13/13flavors OK

Overview

About

Maintained by Shayaan EmranCRAN page ↗GitHub ↗Website ↗Issues ↗

Calculates a comprehensive list of features from profile hidden Markov models (HMMs) of proteins. Adapts and ports features for use with HMMs instead of Position Specific Scoring Matrices, in order to take advantage of more accurate multiple sequence alignment by programs such as 'HHBlits' Remmert et al. (2012) DOI:10.1038/nmeth.1818 and 'HMMer' Eddy (2011) DOI:10.1371/journal.pcbi.1002195. Features calculated by this package can be used for protein fold classification, protein structural class prediction, sub-cellular localization and protein-protein interaction, among other tasks. Some examples of features extracted are found in Song et al. (2018) DOI:10.3390/app8010089, Jin & Zhu (2021) DOI:10.1155/2021/8629776, Lyons et al. (2015) DOI:10.1109/tnb.2015.2457906 and Saini et al. (2015) DOI:10.1016/j.jtbi.2015.05.030.

Install

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

install.packages("protHMM", 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("semran9/protHMM")

Development version from semran9/protHMM. 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-prothmm

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-protHMM

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-protHMM

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: 1.8 min · r-oldrel-windows-x86_64

Status changes

OK13 OK2026-08-05
NOTE12 OK, 1 NOTE2026-08-01
OK12 OK, 1 FAILURE2026-06-08
ERROR12 OK, 1 ERROR2026-06-07
OK14 OK2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 0.1.1

READMEYes · 235 wordsVignettesYes · 1 · dynamicNEWSYes · 67% structured · does not mention 0.1.1Citation fileNoWebsiteYes · pkgdown

Help pages: 21
Examples that run: 100%21 run in a plain check
Exported functions with examples: 100%
Documented parameters: 100%
Return-value docs: 100%
Help pages citing references: 95%

Vignettes (1)

protHMM HTML

How these are measured

Downloads

2K

CRAN downloads in the past year

Rank #23,437 · ~5/day · ~166/mo

Releases R versions

Daily download trend is not available in this view yet.

19530 days

55990 days

2K1 year

Compare downloads with other packages →

Also on68 r2u8 autocran

How downloads are counted

Repository

semran9/prothmm ↗Account: semran9

1Stars

1Forks

0Open issues

0Open PRs

0Releases

29Commits

1Commit identities

License file reads as GPL-3.0 · 29 commits · Last activity 2023-09-11

Responsiveness

not measured

Stars over time

2023-07-06 · 12026-07-07 · 1

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/semran9/prothmm on 2026-10-25.

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 (4)

README.Rmdpkgdown

GitHub Pages site last deployed 2023-09-11 · The repository has a site deploy workflow

pkgdown site last built 2023-09-11

Coverage (1)

Coverage reporting (Codecov)

CRAN release process (1)

cran-comments.md

Show all practicesHide 1 practice

Lint, format, editor (1)

RStudio project

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

Dependencies

Declared dependencies

6 external dependencies (excludes base and recommended)

Installing protHMM adds 2 packages (1 with compiled code, 414 KB of source tarballs). Heaviest: gtools 236 KB, phonTools 178 KB.

Depends (0)

none

Imports (4)

gtoolsutilsstatsphonTools

LinkingTo (0)

none

Suggests (4)

covr 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 (1)

Shayaan Emran

Releases (1)

R
R 4.6.0 released · 2026-04-24
R
R 4.5.0 released · 2025-04-11
R
R 4.4.0 released · 2024-04-24
0.1.1Latest
record
2023-07-05 · current release
R
R 4.3.0 released · 2023-04-21

Package metadata

First published: 2023-07-05
Total releases: 1 / 3 yrs
License: GPL (>= 3) OSI
Download size: 112 KB

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("protHMM")

Format

Emran, S. (2023). protHMM: Protein Feature Extraction from Profile Hidden Markov Models (Version 0.1.1) [Computer software]. https://doi.org/10.32614/CRAN.package.protHMM

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 protHMM version 0.1.1 [Data set]. HJJB, LLC. Data release v2026-10-26. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-26, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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