R Observatory: Metrics for mgi.report.reader version 0.1.3

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

mgi.report.reader

0.1.3Package record

Read Mouse Genome Informatics Reports

0packages depend

2.7Kdownloads / year

16.1%test coverage

0/13flavors OK

Overview

About

Maintained by Ramiro MagnoCRAN page ↗GitHub ↗Website ↗Issues ↗Declared funders: Nencki Institute of Experimental Biology, Pattern Institute and 2 more

Provides readers for easy and consistent importing of Mouse Genome Informatics (MGI) report files: https://www.informatics.jax.org/downloads/reports/index.html. These data are provided by Baldarelli RM, Smith CL, Ringwald M, Richardson JE, Bult CJ, Mouse Genome Informatics Group (2024) doi:10.1093/genetics/iyae031.

Changes in 0.1.3

Added marker_type_definitions data set.
Renamed update_marker_symbol() to symbol_to_symbol().
Renamed convert_to_marker_id() to symbol_to_identifier().
symbol_to_symbol() and symbol_to_identifier() use data table backend with

keyed column for improved look-up performance.

Mappings from symbols to symbols/identifiers is backed up by memoised functions

making interactive experience a bit nicer.

Added bundled tiny examples of MRK_List1.rpt, accessible with

report_example(), for examples and unit tests.

Renamed open_marker_in_mgi() to open_marker_id_in_mgi(), and added

open_marker_symbol_in_mgi().

From NEWS.md in the release

Install

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

install.packages("mgi.report.reader", 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("patterninstitute/mgi.report.reader")

Development version from patterninstitute/mgi.report.reader. 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-mgi.report.reader

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-mgi.report.reader

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-mgi.report.reader

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

NOTEDESCRIPTION meta-informationr-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

r-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-oldrel-macos-arm64, r-oldrel-macos-x86_64, r-patched-linux-x86_64, r-release-linux-x86_64, r-release-macos-arm64, r-release-macos-x86_64

Missing dependency on R >= 4.2.0 because package code uses the pipe
  placeholder syntax added in R 4.2.0.
  File(s) using such syntax:
    ‘read_mgi_biotype_conflict_rpt.R’

r-devel-windows-x86_64, r-oldrel-windows-x86_64, r-release-windows-x86_64

Missing dependency on R >= 4.2.0 because package code uses the pipe
  placeholder syntax added in R 4.2.0.
  File(s) using such syntax:
    'read_mgi_biotype_conflict_rpt.R'

CRAN check page ↗

Slowest check: 1.4 min · r-oldrel-windows-x86_64

Status changes

NOTE13 NOTENow
NOTE3 OK, 11 NOTE2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 0.1.3

READMEYes · 272 wordsVignettesNoNEWSYes · 100% structured · mentions 0.1.3Citation fileNoWebsiteYes · pkgdown

The repository also keeps web-only articles.

Help pages: 24 (9 internal)includes a package overview page
Examples that run: 100%14 run in a plain check
Exported functions with examples: 92%
Documented parameters: 100%
Return-value docs: 83%
Help pages citing references: 0%

How these are measured

Downloads

2.7K

CRAN downloads in the past year

Rank #19,337 · ~7/day · ~227/mo

Releases R versions

Daily download trend is not available in this view yet.

25430 days

68890 days

2.7K1 year

Compare downloads with other packages →

Also on65 r2u3 autocran

How downloads are counted

Repository

patterninstitute/mgi.report.reader ↗Organization: patterninstitute

1Stars

0Forks

0Open issues

0Open PRs

0Releases

62Commits

1Commit identities

62 commits · Last activity 2025-03-26 · 0% stars, 30d

Responsiveness

How these are sampled

PRs merged (all time): not measured
Median days to close, 50 most recently updated closed issues: 6
Median days to close, 50 most recently updated closed PRs: not measured

Stars over time

2025-12-01 · 12026-07-07 · 1

How these are measured

PracticesBeta

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

Checks run against github.com/patterninstitute/mgi.report.reader 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

Governance and community (3)

Code of conductContributing guideSupport guide

Docs source (4)

README.Rmdpkgdown

GitHub Pages site last deployed 2025-03-26 · The repository has a site deploy workflow

pkgdown site last built 2025-03-26

Reproducibility and dev environment (1)

data-raw/

Show all practicesHide 2 practices

CRAN release process (1)

cran-comments.md

Lint, format, editor (1)

RStudio project

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

Dependencies

Declared dependencies

10 external dependencies (excludes base and recommended)

Installing mgi.report.reader adds 35 packages (21 with compiled code, 26 MB of source tarballs). Heaviest: stringi 11 MB, data.table 5.7 MB, openssl 1.1 MB.

Depends (1)

R >= 2.10

Imports (8)

data.table dplyr httr2 memoise rlang stringr tibble vroom

LinkingTo (0)

none

Suggests (2)

testthat tidyr

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 (9)

Ramiro Magno

Author, Maintainer since 0.0.1 (2024)

Author

Author

Author

Author · added in 0.1.2

Pattern Institute

Copyright holder, Funder

Nencki Institute of Experimental Biology

Funder

The Jackson Laboratory

Funder · added in 0.1.2

University of Algarve

Funder

Releases (3)

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
0.1.3Latest
record
2024-07-07 · current release · diff ↗ ·
removed 3 exports
convert_to_marker_id, open_marker_in_mgi, update_marker_symbol

added 5 exports
open_marker_id_in_mgi, open_marker_symbol_in_mgi, report_example, symbol_to_identifier, symbol_to_symbol
0.1.2
record
2024-07-05 · diff ↗ ·
added 11 exports
convert_to_marker_id, feature_types, marker_types, open_marker_in_mgi, report_file, report_last_modified, report_name, report_source, report_type, report_url, update_marker_symbol
0.0.1
record
2024-06-28
R
R 4.4.0 released · 2024-04-24

Package metadata

First published: 2024-06-28
Total releases: 3 / 2 yrs
License: MIT + file LICENSE OSI
Minimum R: ≥ 2.10
Bundled data: 6.3 KB / 3 files
Download size: 45 KB

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("mgi.report.reader")

Format

Magno, R., Nencki Institute of Experimental Biology, Pattern Institute, The Jackson Laboratory, University of Algarve, Duarte, I., Gbadamosi, I., Jawaid, A., & Shaw, D. (2024). mgi.report.reader: Read Mouse Genome Informatics Reports (Version 0.1.3) [Computer software]. https://doi.org/10.32614/CRAN.package.mgi.report.reader

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 mgi.report.reader version 0.1.3 [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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