R Observatory: Metrics for Sysrecon version 0.1.3

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

Sysrecon

0.1.3

Systematical Metabolic Reconstruction

0packages depend

2.6Kdownloads / year

–test coverage

13/13checks pass

Overview

About

Maintained by Shilin OuyangFirst published 2022-10-184 releasesCRAN page ↗

In the past decade, genome-scale metabolic reconstructions have widely been used to comprehend the systems biology of metabolic pathways within an organism. Different GSMs are constructed using various techniques that require distinct steps, but the input data, information conversion and software tools are neither concisely defined nor mathematically or programmatically formulated in a context-specific manner.The tool that quantitatively and qualitatively specifies each reconstruction steps and can generate a template list of reconstruction steps dynamically selected from a reconstruction step reservoir, constructed based on all available published papers.

Install

R (CRAN)Ubuntu (r2u)

install.packages("Sysrecon", 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-sysrecon

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

Health

CRAN checks

13OK

Slowest check: 2.4 min · r-oldrel-windows-x86_64

Code health

None

Tests · ratio 0.00

not tracked

Coverage

100%

Documentation · exports

15

Dependencies · direct

Check history

OK2026-08-05
13 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
NOTE2026-08-01
12 OK · 1 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
OK2026-06-22
13 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-06-18
12 OK · 0 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
OK2026-06-09
13 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Show 6 earlier snapshots

ERROR2026-06-08
12 OK · 0 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
OK2026-05-10
13 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-05-03
12 OK · 0 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
OK2026-04-23
14 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-04-21
13 OK · 0 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
OK2026-03-10
14 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Documentation

READMEYes · 420 wordsVignettesNopkgdown siteNoNEWSNoCode of conductNoContributing guideNo

Examples that run: 13%
Documented parameters: 100%
Return-value docs: 100%
References docs: 0%

Downloads

2.6K

CRAN downloads in the past year

Rank #16,022 · ~7/day · ~216/mo

Releases R versions

Daily download trend is not available in this view yet.

16130 days

66090 days

2.6K1 year

Compare downloads with other packages →

Also on104 r2u

Repository

GitHub ↗ oyshilin/sysrecon

0Stars

0Forks

0Open issues

0Open PRs

0Releases

rr-packagevisualization

Last activity 2024-01-05

Repository practices

Upstream repositoryBeta

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

Checks run against github.com/oyshilin/sysrecon on 2026-08-16.

Continuous integration (1)

GitHub Actions

Reproducibility and dev environment (1)

data-raw/

Lint, format, editor (1)

RStudio project

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

Dependencies

Declared dependencies

12 external dependencies (excludes base and recommended)

Depends (1)

R >= 3.5.0

Imports (15)

ape dplyr ggplot2 ggtree magrittrmethodspatchwork plyr RColorBrewer rlang SnowballCstatsstringr tmutils

LinkingTo (0)

none

Suggests (0)

none

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

Code & Tests

Datasets

People & History

People (7)

Maintainer (1)

Shilin Ouyang

Author, Maintainer

Authors (6)

Author, Maintainer

Author

Author

Author

Author

Author

Copyright holders (1)

RStudio

Copyright holder, Funder

Funders (1)

RStudio

Copyright holder, Funder

Package Timeline

4 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
R
R 4.4.0 released · 2024-04-24
R
R 4.3.0 released · 2023-04-21
0.1.3Latest
2023-02-20 · current release · diff ↗
0.1.2
2022-11-13 · diff ↗
0.1.1
2022-10-31 · diff ↗
0.1.0
2022-10-18
R
R 4.2.0 released · 2022-04-22

Package metadata

First published: 2022-10-18
Total releases: 4 / 4 yrs
License: GPL-3 OSI
Minimum R: ≥ 3.5.0
Bundled data: 35 KB / 13 files
Download size: 198 KB
Installed size: not tracked yet
With dependencies: not tracked yet

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("Sysrecon")

Format

Ouyang, S., RStudio, Cao, M., Hu, J., Li, Z., Mao, L., & Yu, F. (2023). Sysrecon: Systematical Metabolic Reconstruction (Version 0.1.3) [Computer software]. https://doi.org/10.32614/CRAN.package.Sysrecon

This is what citation() produces when a package has no citation file of its own. If it prints something else, use that.

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 Sysrecon version 0.1.3 [Data set]. HJJB, LLC. Data release v2026-08-17. https://doi.org/10.5281/zenodo.21843040

From data release v2026-08-17, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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