cmmr

1.0.3

CEU Mass Mediator RESTful API

0packages depend

2.3Kdownloads / year

28.5%test coverage

12/13checks pass

Overview

About

Maintained by Yaoxiang LiFirst published 2019-04-162 releasesCRAN page ↗GitHub ↗

CEU (CEU San Pablo University) Mass Mediator is an on-line tool for aiding researchers in performing metabolite annotation. 'cmmr' (CEU Mass Mediator RESTful API) allows for programmatic access in R: batch search, batch advanced search, MS/MS (tandem mass spectrometry) search, etc. For more information about the API Endpoint please go to https://github.com/YaoxiangLi/cmmr.

Install

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

install.packages("cmmr", 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("YaoxiangLi/cmmr")

Development version from YaoxiangLi/cmmr. 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-cmmr

Fast Ubuntu binaries via r2u (no compilation). The cranapt setup runs once and is skipped when it is already enabled.

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-cmmr

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-cmmr

RPMs auto-built from CRAN on openSUSE OBS (Tumbleweed).

Health

CRAN checks

1NOTE12OK

Failing flavors

NOTE r-devel-linux-x86_64-debian-gcc

Slowest check: 51 s · r-oldrel-windows-x86_64

Code health

Yes

Tests · ratio 0.16

28.5%

Coverage · measured lines

100%

Documentation · exports

Dependencies · direct

Check history

NOTE2026-08-01
12 OK · 1 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
OK2026-03-10
14 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Documentation

READMEYes · 309 wordsVignettesNopkgdown siteNoNEWSNoCode of conductNoContributing guideNo

Examples that run: 25%
Documented parameters: 99%
Return-value docs: 100%
References docs: 0%

Downloads

2.3K

CRAN downloads in the past year

Rank #18,901 · ~6/day · ~195/mo

Releases R versions

Daily download trend is not available in this view yet.

15830 days

58590 days

2.3K1 year

Compare downloads with other packages →

Also on154 r2u

Repository

GitHub ↗ yaoxiangli/cmmr

16Stars

4Forks

0Open issues

0Open PRs

0Releases

57Commits

1Contributors

ceu-mass-mediatorbatch-searchms-searchmetablomics

57 commits · Last activity 2024-10-11

Stars over time

2025-03-29 · 162026-07-07 · 16

Repository practices

Upstream repositoryBeta

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

Checks run against github.com/yaoxiangli/cmmr on 2026-07-31.

Continuous integration (1)

Travis CI

Lint, format, editor (1)

RStudio project

How this is detected·Detection ruleset v1 (2026-07-18)

Dependencies

Declared dependencies

5 external dependencies (excludes base and recommended)

Depends (1)

R >= 4.4.0

Imports (4)

httr progress RJSONIO cli

LinkingTo (0)

none

Suggests (1)

testthat

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

Code & Tests

People & History

People (4)

Maintainer (1)

Yaoxiang Li

Author, Maintainer

Authors (4)

Yaoxiang Li

Author, Maintainer

Amrita Cheema

Author · added in 1.0.3

Alberto Gil de la Fuente

Author · added in 1.0.3

Charles Hinzman

Author · added in 1.0.3

Listed in earlier versions (2)

Amrita K Cheema

no longer listed · 0.1.2

Charles P. Hinzman

no longer listed · 0.1.2

Package Timeline

2 releases. Pick two to compare their code metrics. R releases are shown for context.

R
R 4.6.0 released · 2026-04-24
R
R 4.5.0 released · 2025-04-11
1.0.3Latest
2024-10-04 · current release · diff ↗
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
R
R 3.6.0 released · 2019-04-26
0.1.2
2019-04-16
R
R 3.5.0 released · 2018-04-23

Package metadata

First published: 2019-04-16
Total releases: 2 / 7 yrs
License: GPL-3 OSI
Minimum R: ≥ 4.4.0
Download size: 13 KB
Installed size: not tracked yet
With dependencies: not tracked yet

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