R Observatory: Metrics for MLML2R version 0.3.3

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

MLML2R

0.3.3Package record

Maximum Likelihood Estimation of DNA Methylation and Hydroxymethylation Proportions

0packages depend

2.5Kdownloads / year

–test coverage

11/13flavors OK

Overview

About

Maintained by Samara KiihlCRAN page ↗GitHub ↗Issues ↗

Maximum likelihood estimates (MLE) of the proportions of 5-mC and 5-hmC in the DNA using information from BS-conversion, TAB-conversion, and oxBS-conversion methods. One can use information from all three methods or any combination of two of them. Estimates are based on Binomial model by Qu et al. (2013) doi:10.1093/bioinformatics/btt459 and Kiihl et al. (2019) doi:10.1515/sagmb-2018-0031.

Install

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

install.packages("MLML2R", 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("samarafk/MLML2R")

Development version from samarafk/MLML2R. 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-mlml2r

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-MLML2R

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-MLML2R

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

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

Maintainer: ‘Samara Kiihl <samara@ime.unicamp.br>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Samara",
                      family = "Kiihl",
                      role = c("aut", "cre"),
                      email = "samara@ime.unicamp.br"),
               person(given = c("Maria", "Jose"),
                      family = "Martinez-Garrido",
                      role = "aut"),
               person(given = "Arce",
                      family = "Domingo-Relloso",
                      role = "aut"),
               person(given = "Jose",
                      family = "Bermudez",
                      role = "aut"),
               person(given = "Maria",
                      family = "Tellez-Plaza",
                      role = "aut"))
as necessary.

Package CITATION file contains call(s) to old-style personList() or
as.personList().  Please use c() on person objects instead.
Package CITATION file contains call(s) to old-style citEntry().  Please
use bibentry() instead.

CRAN check page ↗

Slowest check: 1.0 min · r-devel-windows-x86_64

Status changes

NOTE11 OK, 2 NOTE2026-09-08
ERROR10 OK, 2 NOTE, 1 ERROR2026-09-07
NOTE10 OK, 4 NOTE2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 0.3.3

README· In the repository, left out of the releaseVignettesYes · 1 · dynamicNEWSNoCitation fileYes · cites a publicationWebsitenot declared in DESCRIPTION

Help pages: 7
Examples that run: 100%1 run in a plain check
Exported functions with examples: 100%
Documented parameters: not tracked
Return-value docs: not tracked
Help pages citing references: 14%

Vignettes (1)

Using MLML2R HTML

How these are measured

Downloads

2.5K

CRAN downloads in the past year

Rank #18,502 · ~7/day · ~205/mo

Releases R versions

Daily download trend is not available in this view yet.

27630 days

70090 days

2.5K1 year

Compare downloads with other packages →

Also on69 r2u3 autocran

How downloads are counted

Repository

samarafk/mlml2r ↗Account: samarafk

2Stars

2Forks

0Open issues

0Open PRs

0Releases

164Commits

1Commit identities

164 commits · Last activity 2019-10-17

Responsiveness

not measured

Stars over time

2020-04-24 · 22026-07-07 · 2

How these are measured

PracticesBeta

3 development-tooling and community-health practices detected across 3 families in the upstream repository

Checks run against github.com/samarafk/mlml2r on 2026-10-18.

Reproducibility and dev environment (1)

data-raw/

CRAN release process (1)

cran-comments.md

Lint, format, editor (1)

RStudio project

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

Dependencies

Declared dependencies

6 external dependencies (excludes base and recommended)

Installing MLML2R adds no packages beyond those that come with R.

Depends (0)

none

Imports (0)

none

LinkingTo (0)

none

Suggests (6)

minfi microbenchmark GEOquery knitr rmarkdown IlluminaHumanMethylation450kmanifest

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

How these are counted

Code & Tests

Datasets

People & History

People (from the free-text Author field) (5)

Samara Kiihl

Author, Maintainer since 0.1.0 (2018)

Maria Jose Martinez-Garrido

Author

Arce Domingo-Relloso

Author

Jose Bermudez

Author

Maria Tellez-Plaza

Author

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
0.3.3Latest
record
2019-10-17 · current release · diff ↗
R
R 3.6.0 released · 2019-04-26
0.3.2
record
2019-04-06 · diff ↗
0.3.1
record
2018-11-12 · diff ↗
0.3.0
record
2018-09-30 · diff ↗
0.2.1
record
2018-05-17 · diff ↗
R
R 3.5.0 released · 2018-04-23
0.2.0
record
2018-02-21 · diff ↗
0.1.0
record
2018-02-13

Show 1 earlier eventHide 1 earlier event

R
R 3.4.0 released · 2017-04-21

Package metadata

First published: 2018-02-13
Total releases: 7 / 8 yrs
License: MIT + file LICENSE OSI
Bundled data: 7.3 KB / 6 files
Download size: 1.2 MB

Cite

Cite this package

Run in R for the authors' entry:

citation("MLML2R")

The package provides a citation file, so citation() returns the authors' own entry.

It points to 10.1515/sagmb-2018-0031.

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 MLML2R version 0.3.3 [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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