R Observatory: Metrics for biogram version 1.6.3

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

CRAN requires the check problems on this package to be fixed before Nov 2 or it will be archived. See the check details

biogram

1.6.3Package record

N-Gram Analysis of Biological Sequences

3packages depend

4Kdownloads / year

46.3%test coverage

0/13flavors OK

Overview

About

Maintained by Michal BurdukiewiczCRAN page ↗GitHub ↗Issues ↗

Tools for extraction and analysis of various n-grams (k-mers) derived from biological sequences (proteins or nucleic acids). Contains QuiPT (quick permutation test) for fast feature-filtering of the n-gram data.

Install

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

install.packages("biogram", 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("michbur/biogram")

Development version from michbur/biogram. 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-biogram

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-biogram

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-biogram

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

13NOTE

Check messages

NOTERd filesr-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc, r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-devel-windows-x86_64, r-oldrel-macos-arm64, r-oldrel-macos-x86_64, r-oldrel-windows-x86_64, r-patched-linux-x86_64, r-release-linux-x86_64, r-release-macos-arm64, r-release-macos-x86_64, r-release-windows-x86_64

checkRd: (-1) calc_ed.Rd:14: Lost braces; missing escapes or markup?
    14 | of groups or less than \code{a}. Both \code{a} and {b} must have the the same 
       |                                                    ^
checkRd: (-1) calc_pi.Rd:14: Lost braces; missing escapes or markup?
    14 | of groups or less than \code{a}. Both \code{a} and {b} must have the the same 
       |                                                    ^
checkRd: (-1) calc_si.Rd:14: Lost braces; missing escapes or markup?
    14 | of groups or less than \code{a}. Both \code{a} and {b} must have the the same 
       |                                                    ^
checkRd: (-1) cluster_reg_exp.Rd:15: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) cluster_reg_exp.Rd:16: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) cluster_reg_exp.Rd:17: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) cluster_reg_exp.Rd:18: Lost braces in \itemize; \value handles \item{}{} directly

NOTER code for possible problemsr-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc, r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-devel-windows-x86_64

Found calls to structure() using deprecated special names:
  biogram/tests/testthat/test_count_ngrams.R (.Dim: 2, .Dimnames: 2)
  biogram/tests/testthat/test_position_ngrams.R (.Label: 16, .Names: 3, .Dim: 1)
  biogram/tests/testthat/test_seq2grams.R (.Dim: 4)
  biogram/man/simple2full.Rd (.Names: 1)
'.Dim' should be changed to 'dim'.
'.Dimnames' should be changed to 'dimnames'.
'.Label' should be changed to 'levels'.
'.Names' should be changed to 'names'.

NOTECRAN incoming feasibilityr-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc

Maintainer: ‘Michal Burdukiewicz <michalburdukiewicz@gmail.com>’

Package CITATION file contains call(s) to old-style citEntry().  Please
use bibentry() instead.

CRAN check page ↗

Slowest check: 1.9 min · r-oldrel-windows-x86_64

Status changes

NOTE13 NOTENow
NOTE14 NOTE2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 1.6.3

READMEYes · 98 wordsVignettesYes · 1 · dynamicNEWSNoCitation fileYes · computed when R runs it

Help pages: 59includes a package overview page
Examples that run: 98%46 run in a plain check · 1 never run
Exported functions with examples: 91%
Documented parameters: 99%
Return-value docs: 85%
Help pages citing references: 8%

Vignettes (1)

biogram package - an overview

How these are measured

Downloads

4K

CRAN downloads in the past year

Rank #7,238 · ~11/day · ~334/mo

Releases R versions

Daily download trend is not available in this view yet.

49330 days

1.2K90 days

4K1 year

Compare downloads with other packages →

Also on175 r2u22 autocran

How downloads are counted

Repository

michbur/biogram ↗Account: michbur

10Stars

2Forks

7Open issues

0Open PRs

3Releases

443Commits

6Commit identities

biological-sequencesngram-analysisr

443 commits · Last activity 2026-07-07

Responsiveness

How these are sampled

PRs merged (all time): 100%
Median days to close, 50 most recently updated closed issues: 50
Median days to close, 50 most recently updated closed PRs: 0

Stars over time

2024-09-02 · 102026-07-07 · 10

How these are measured

PracticesBeta

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

Checks run against github.com/michbur/biogram on 2026-10-18.

Continuous integration (1)

Travis CI (config file)

Docs source (1)

GitHub Pages site last deployed 2026-07-07

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

Dependencies

Declared dependencies

7 external dependencies (excludes base and recommended)

Installing biogram adds 9 packages (5 with compiled code, 2.7 MB of source tarballs). Heaviest: rbibutils 1.1 MB, partitions 479 KB, Rdpack 370 KB.

Depends (2)

R >= 3.0.0slam

Imports (3)

combinat entropy partitions

LinkingTo (0)

none

Suggests (3)

ggplot2 knitr testthat

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

3direct

0indirect

Imports 3

Depends, Imports or LinkingTo, most downloaded first

AmyloGram AmpGram CancerGram

How these are counted

Code & Tests

Datasets

People & History

People (5)

Michal Burdukiewicz

Maintainer since 1.0 (2014), Author

Chris Lauber

Author

Dominik Rafacz

Author · added in 1.6.1

Piotr Sobczyk

Author

Katarzyna Sidorczuk

Contributor · added in 1.6.3

Releases (7)

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
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
R
R 4.1.0 released · 2021-05-18
R
R 4.0.0 released · 2020-04-24
1.6.3Latest
record
2020-03-31 · current release · diff ↗ ·
added 2 exports
check_criterion, degenerate_ngrams
1.6.1
record
2020-01-09 · diff ↗ ·
added 9 exports
full2simple, generate_single_region, generate_single_unigram, generate_unigrams, read_fasta, regenerate, simple2full, write_encoding, write_fasta
R
R 3.6.0 released · 2019-04-26
R
R 3.5.0 released · 2018-04-23
R
R 3.4.0 released · 2017-04-21
1.4
record
2017-01-06 · diff ↗ ·
added 2 exports
calc_pi, create_encoding
1.3
record
2016-09-21 · diff ↗ ·
added 8 exports
binarize, calc_cs, calc_ed, calc_si, cluster_reg_exp, encoding2df, list2matrix, validate_encoding
R
R 3.3.0 released · 2016-05-03
1.2
record
2015-06-22 · diff ↗ ·
removed 2 exports
calc_ig_single, criterion_distribution

added 11 exports
add_1grams, calc_criterion, calc_kl, code_ngrams, construct_ngrams, count_specified, count_total, distr_crit, gap_ngrams, ngrams2df, table_ngrams

Show 4 earlier eventsHide 4 earlier events

R
R 3.2.0 released · 2015-04-16
1.1
record
2015-02-03 · diff ↗ ·
removed 2 exports
data_sample, prepare_data

added 3 exports
decode_ngrams, is_ngram, position_ngrams
1.0
record
2014-12-19
R
R 3.1.0 released · 2014-04-10

Package metadata

First published: 2014-12-19
Total releases: 7 / 12 yrs
License: GPL-3 OSI
Minimum R: ≥ 3.0.0
Bundled data: 67 KB / 2 files
Download size: 235 KB

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("biogram")

The package provides a citation file that builds its entry when R runs it. Run citation() to see it.

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 biogram version 1.6.3 [Data set]. HJJB, LLC. Data release v2026-10-22. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-22, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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