This package was removed from CRAN on 2017-02-15. Its history is shown below.

Reason: check problems were not corrected despite reminders

Details below reflect version 0.3.12, its last release before removal.

biom

0.3.12

An interface package (beta) for the BIOM file format.

0packages depend

–downloads / year

–test coverage

–checks pass

Overview

About

Maintained by Paul J. McMurdie5 releasesCRAN page ↗GitHub ↗

This is an R package for interfacing with the BIOM format. This package includes basic tools for reading biom-format files, accessing and subsetting data tables from a biom object (which is more complex than a single table), as well as limited support for writing a biom-object back to a biom-format file. The design of this API is intended to match the python API and other tools included with the biom-format project, but with a decidedly "R flavor" that should be familiar to R users. This includes S4 classes and methods, as well as extensions of common core functions/methods.

Install

R (source archive)pak (dev)

url <- "https://cran.r-project.org/src/contrib/Archive/biom/biom_0.3.12.tar.gz"
pkgFile <- "biom_0.3.12.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 (0.3.12) and builds it locally. Install its dependencies first, and note that building from source needs the usual compiler toolchain.

if (!requireNamespace("pak", quietly = TRUE))
  install.packages("pak", repos = "https://cloud.r-project.org/")
pak::pak("joey711/biom")

Development version from joey711/biom. Installs pak first if it is not already available.

Health

CRAN checks

CRAN check results are not tracked yet.

Code health

Yes

Tests · ratio 0.00

not tracked

Coverage

100%

Documentation · exports

Dependencies · direct

Documentation

READMEYes · 230 wordsVignettesYes · dynamicpkgdown siteNoNEWSNoCode of conductNoContributing guideNo

Examples that run: 100%
Documented parameters: 100%
Return-value docs: 100%
References docs: 19%

Downloads

Releases R versions

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Also on380 bioconda27 c2d4u

Dependencies

Declared dependencies

4 external dependencies (excludes base and recommended)

Depends (2)

R >= 3.0.0methods

Imports (3)

plyr RJSONIOMatrix

LinkingTo (0)

none

Suggests (2)

testthat knitr

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

–indirect (not tracked)

Nothing depends on this yet.

Code & Tests

Code Composition

R 955 (54%)Rd 685 (39%)Vignettes 117 (7%)

Code characteristics

Object systems

S4 class1S4 generic7S4 method21

Cyclomatic complexity: 2.0 median / 20 max

Test coverage

Line coverage

–

Expression

–

Tests / Examples

–

Functions

4 2 exported

Complexity

6.3 avg / 20 max

Call network

4 nodes / 0 edges

Test coverage has not been measured for this package yet; nodes fall back to a neutral fill.

Call graph

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Lowest coverage

Per-function coverage is not measured for this package yet.

People & History

People (2)

Other (2)

Paul J. McMurdie

Contributor

the biom-format team http://biom-format.org/

Contributor

Package Timeline

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

R
R 3.4.0 released · 2017-04-21
archivedRemoved from CRAN
2017-02-15
check problems were not corrected despite reminders
R
R 3.3.0 released · 2016-05-03
R
R 3.2.0 released · 2015-04-16
R
R 3.1.0 released · 2014-04-10
0.3.12
2014-02-23 · diff ↗
0.3.11
2013-12-13 · diff ↗
0.3.10
2013-09-15 · diff ↗
0.3.9
2013-05-17 · diff ↗
0.3.8
2013-04-26
R
R 3.0.0 released · 2013-04-03

Package metadata

Total releases: 5
License: GPL-2 OSI
Minimum R: ≥ 3.0.0
Download size: not tracked yet
Installed size: not tracked yet
With dependencies: not tracked yet

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