R Observatory: Metrics for lilikoi version 2.1.1

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

lilikoi

2.1.1Package record

Metabolomics Personalized Pathway Analysis Tool

0packages depend

3.6Kdownloads / year

–test coverage

9/13flavors OK

Overview

About

Maintained by Lana GarmireCRAN page ↗

A comprehensive analysis tool for metabolomics data. It consists a variety of functional modules, including several new modules: a pre-processing module for normalization and imputation, an exploratory data analysis module for dimension reduction and source of variation analysis, a classification module with the new deep-learning method and other machine-learning methods, a prognosis module with cox-PH and neural-network based Cox-nnet methods, and pathway analysis module to visualize the pathway and interpret metabolite-pathway relationships. References: H. Paul Benton http://www.metabolomics-forum.com/index.php?topic=281.0 Jeff Xia https://github.com/cangfengzhe/Metabo/blob/master/MetaboAnalyst/website/name_match.R Travers Ching, Xun Zhu, Lana X. Garmire (2018) doi:10.1371/journal.pcbi.1006076.

Install

R (CRAN)Ubuntu (r2u)

install.packages("lilikoi", repos = "https://cloud.r-project.org/")

Installs the current CRAN release. Prebuilt binaries on Windows and macOS.

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-lilikoi

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

Health

CRAN checks

2ERROR2NOTE9OK

Check messages

ERRORpackage dependenciesr-oldrel-macos-arm64, r-oldrel-macos-x86_64

r-oldrel-macos-arm64

Packages required but not available: 'M3C', 'RCy3'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.

r-oldrel-macos-x86_64

Package required but not available: ‘pathview’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.

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

Maintainer: ‘Lana Garmire <lana.garmire.group@gmail.com>’

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: 32.1 min · r-devel-windows-x86_64

Status changes

ERROR9 OK, 2 NOTE, 2 ERRORNow
ERROR10 OK, 2 NOTE, 2 ERROR2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 2.1.1

READMEYes · 164 wordsVignettesYes · 1 · dynamicNEWSYes · 67% structured · does not mention 2.1.1Citation fileYes · cites a publicationWebsitenot declared in DESCRIPTION

Help pages: 11
Examples that run: 0%8 only when donttest examples are enabled (R CMD check --as-cran) · 2 hold no code
Exported functions with examples: 91%
Documented parameters: 100%
Return-value docs: 100%
Help pages citing references: 9%

Vignettes (1)

Lilikoi V2.0 HTML

How these are measured

Downloads

3.6K

CRAN downloads in the past year

Rank #8,661 · ~10/day · ~298/mo

Releases R versions

Daily download trend is not available in this view yet.

46830 days

1.1K90 days

3.6K1 year

Compare downloads with other packages →

Also on90 r2u

How downloads are counted

Dependencies

Declared dependencies

27 external dependencies (excludes base and recommended)

Installing lilikoi adds 136 packages (74 with compiled code, 113 MB of source tarballs). Heaviest: stringi 11 MB, RWekajars 9.6 MB, ggplot2 6.0 MB. 6 more not on CRAN are not measured.

Depends (1)

R >= 3.5.0

Imports (28)

car caret dplyr gbm ggplot2 glmnet h2o impute infotheo limma M3C Metrics MLmetricsparallelprincurve pathview plyr preprocessCore pROC RCy3 reticulate reshape RWeka scalesstatsstringr survminersurvival

LinkingTo (0)

none

Suggests (2)

knitr rmarkdown

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 (6)

Lana Garmire

Author, Maintainer since 2.0.0 (2020) · added in 2.0.0

Fadhl Alakwaa

Author

Xinying Fang

Author · added in 2.0.0

Sijia Huang

Author

Yu Liu

Author · added in 2.0.0

Zhijie Ren

Author · added in 2.0.0

Previously maintained by Fadhl Alakwaa (0.1.0).

Releases (8)

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
2.1.1Latest
record
2023-11-13 · current release · diff ↗
unarchivedReturned to CRAN
2023-11-12
'RCyr3@BioC' was updated to become installable
archivedRemoved from CRAN
2023-11-12
issues were not corrected in time
R
R 4.3.0 released · 2023-04-21
R
R 4.2.0 released · 2022-04-22
2.1.0
record
2022-02-22 · diff ↗
R
R 4.1.0 released · 2021-05-18
2.0.4
record
2021-01-15 · diff ↗
unarchivedReturned to CRAN
2020-11-10
2.0.3
record
2020-11-10 · diff ↗
archivedRemoved from CRAN
2020-10-22
check problems were not corrected in time '\donttest' examples
2.0.2
record
2020-10-03 · diff ↗
unarchivedReturned to CRAN
2020-08-24

Show 10 earlier eventsHide 10 earlier events

2.0.1
record
2020-08-24 · diff ↗
removedRemoved from CRAN
Version 2.0.0 has been removed
archivedRemoved from CRAN
2020-07-22
policy violation Alleged misrepresentation of authorship and copyright
unarchivedReturned to CRAN
2020-07-03
2.0.0
record
2020-07-03 · diff ↗ ·
removed 4 exports
lilikoi.adjust_model, lilikoi.get_pd_scores, lilikoi.metab_to_pathway, lilikoi.select_pathways

added 10 exports
lilikoi.KEGGplot, lilikoi.Loaddata, lilikoi.MetaTOpathway, lilikoi.PDSfun, lilikoi.explr, lilikoi.featuresSelection, lilikoi.meta_path, lilikoi.preproc_knn, lilikoi.preproc_norm, lilikoi.prognosis
R
R 4.0.0 released · 2020-04-24
archivedRemoved from CRAN
2020-04-09
check problems were not corrected despite reminders
R
R 3.6.0 released · 2019-04-26
0.1.0
record
2018-07-30
R
R 3.5.0 released · 2018-04-23

Package metadata

First published: 2018-07-30
Total releases: 8 / 8 yrs
License: GPL-2 OSI
Minimum R: ≥ 3.5.0
Download size: 1.8 MB

Appears in task views

Missing Data Genomics, Proteomics, Metabolomics, Transcriptomics, and Other Omics

Cite

Cite this package

Run in R for the authors' entry:

citation("lilikoi")

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

It points to 10.1101/2020.07.09.195677, 10.1093/gigascience/giy136.

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 lilikoi version 2.1.1 [Data set]. HJJB, LLC. Data release v2026-10-18. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-18, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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