R Observatory: Metrics for ppiPre version 1.9

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

This package was removed from CRAN on 2018-04-05. Its history is shown below.

Reason: check problems were not corrected despite reminders

Details below reflect version 1.9, its last release before removal.

ppiPre

1.9Package record

Predict Protein-Protein Interactions Based on Functional and Topological Similarities

0packages depend

–downloads / year

–test coverage

–flavors OK

Overview

About

Maintained by Yue DengCRAN page ↗

Computing similarities between proteins based on their GO annotation, KEGG annotation and PPI network topology. It integrates seven features (TCSS, IntelliGO, Wang, KEGG, Jaccard, RA and AA) to predict PPIs using an SVM classifier. Some internal functions to calculate GO semantic similarities are re-used from R package GOSemSim authored by Guangchuang Yu.

Changes in 1.9

Update the description of package and manual of several functions.

From NEWS in the release

Install

R (source archive)

url <- "https://cran.r-project.org/src/contrib/Archive/ppiPre/ppiPre_1.9.tar.gz"
pkgFile <- "ppiPre_1.9.tar.gz"
download.file(url, pkgFile)
install.packages(pkgFile, type = "source", repos = NULL)

This package is no longer on CRAN, so install.packages() cannot fetch it by name. This downloads the last archived source (1.9) and builds it locally. Install its dependencies first, and note that building from source needs the usual compiler toolchain.

Health

CRAN checks

CRAN check results are not tracked yet.

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 1.9

READMENoVignettesNoNEWSYes · 100% structured · mentions 1.9Citation fileNoWebsitenot declared in DESCRIPTION

Help pages: 15 (1 internal)includes a package overview page
Examples that run: 38%5 run in a plain check · 8 hold no code
Exported functions with examples: 100%
Documented parameters: 100%
Return-value docs: 54%
Help pages citing references: 73%

How these are measured

Downloads

ppiPre Releases R versions

Daily download trend is not available in this view yet.

Compare downloads with other packages →

How downloads are counted

Dependencies

Declared dependencies

5 external dependencies (excludes base and recommended)

Depends (1)

R >= 3.1.0

Imports (7)

AnnotationDbi igraph e1071 GOSemSim GO.dbstatsutils

LinkingTo (0)

none

Suggests (0)

none

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

–indirect (not tracked)

Nothing depends on this yet.

How these are counted

Code & Tests

People & History

People (4)

Yue Deng

Contributor

Rongjie Shao

Contributor · added in 1.5

Gang Wang

Contributor · added in 1.5

Yuanjun Sun

Contributor · added in 1.5

Maintainer since 1.2 (2011)

Listed in earlier versions (1)

with contributions from Guangchuang Yu.

no longer listed · 1.6

Releases (8)

Pick two releases to compare their code metrics.

R
R 3.5.0 released · 2018-04-23
archivedRemoved from CRAN
2018-04-05
check problems were not corrected despite reminders
R
R 3.4.0 released · 2017-04-21
R
R 3.3.0 released · 2016-05-03
1.9
record
2015-07-21 · diff ↗
1.8
record
2015-06-24 · diff ↗
R
R 3.2.0 released · 2015-04-16
1.7
record
2015-02-27 · diff ↗
1.6
record
2015-01-25 · diff ↗ ·
removed 1 export
pattern:.

added 13 exports
AASim, ComputeAllEvidences, FNPre, GOKEGGSims, GOKEGGSimsFromFile, IntelliGOGeneSim, JaccardSim, KEGGSim, RASim, SVMPredict, SVMTrain, TCSSGeneSim, TopologicSims
R
R 3.1.0 released · 2014-04-10
1.5
record
2013-07-27 · diff ↗
1.4
record
2013-06-29 · diff ↗
R
R 3.0.0 released · 2013-04-03
R
R 2.15.0 released · 2012-03-30
1.3
record
2012-03-19 · diff ↗ ·
added 1 export
pattern:.
R
R 2.14.0 released · 2011-10-31

Show 2 earlier eventsHide 2 earlier events

1.2
record
2011-10-16
R
R 2.13.0 released · 2011-04-13

Package metadata

First published: 2011-10-16
Total releases: 8 / 15 yrs
License: GPL-2 OSI · relicensed from Artistic-2.0 in 1.6
Minimum R: ≥ 3.1.0

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("ppiPre")

Format

Deng, Y., Shao, R., Wang, G., & Sun, Y. (n.d.). ppiPre: Predict Protein-Protein Interactions Based on Functional and Topological Similarities (Version 1.9) [Computer software]. Retrieved October 26, 2026, from https://CRAN.R-project.org/package=ppiPre

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 ppiPre version 1.9 [Data set]. HJJB, LLC. Data release v2026-10-25. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-25, which the citation names so these numbers can be found later. More on citing and the projects behind them.

Report a problem with this page →