R Observatory: Metrics for gdsfmt version 1.1.0.1

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

This package was removed from CRAN on 2014-12-20. Its history is shown below.

Reason: repeated policy violations by the maintainer. This package is now available from Bioconductor only, see <https://www.bioconductor.org/packages/release/bioc/html/gdsfmt.html>

Details below reflect version 1.1.0.1, its last release before removal.

gdsfmt

1.1.0.1Package record

R Interface to CoreArray Genomic Data Structure (GDS) files

5packages depend

–downloads / year

–test coverage

–flavors OK

Overview

About

Maintained by Xiuwen ZhengCRAN page ↗GitHub ↗Website ↗

This package provides a high-level R interface to CoreArray Genomic Data Structure (GDS) data files, which are portable across platforms and include hierarchical structure to store multiple scalable array-oriented data sets with metadata information. It is suited for large-scale datasets, especially for data which are much larger than the available random-access memory. The gdsfmt package offers the efficient operations specifically designed for integers with less than 8 bits, since a single genetic/genomic variant, such like single-nucleotide polymorphism, usually occupies fewer bits than a byte. Data compression and decompression are also supported. It is allowed to read a GDS file in parallel with multiple R processes supported by the parallel package.

Install

BioconductorR (source archive)pak (dev)

BiocManager::install("gdsfmt")

Installs the current Bioconductor release. Requires the BiocManager package.

url <- "https://cran.r-project.org/src/contrib/Archive/gdsfmt/gdsfmt_1.1.0.1.tar.gz"
pkgFile <- "gdsfmt_1.1.0.1.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 (1.1.0.1) 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("zhengxwen/gdsfmt")

Development version from zhengxwen/gdsfmt. Installs pak first if it is not already available.

Health

CRAN checks

CRAN check results are not tracked yet.

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 1.1.0.1

READMEYes · 196 wordsVignettesNoNEWSYes · 67% structuredCitation fileYes · cites a publicationWebsiteYes

Help pages: 40includes a package overview page
Examples that run: 100%28 run in a plain check
Exported functions with examples: 73%
Documented parameters: 99%
Return-value docs: 81%
Help pages citing references: 100%

How these are measured

Downloads

Releases R versions

Daily download trend is not available in this view yet.

Compare downloads with other packages →

Also on1.6K r2u10K bioconda

How downloads are counted

Dependencies

Declared dependencies

1 external dependency (excludes base and recommended)

Depends (1)

R >= 2.14.0

Imports (1)

methods

LinkingTo (0)

none

Suggests (2)

parallelRUnit

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

5direct

–indirect (not tracked)

Imports 5

Depends, Imports or LinkingTo, most downloaded first

simplePHENOTYPES EthSEQ snplinkage gwid CoxMK

How these are counted

Code & Tests

People & History

People (1)

Xiuwen Zheng

Contributor

Maintainer since 0.9 (2010)

Releases (23)

Pick two releases to compare their code metrics.

R
R 3.2.0 released · 2015-04-16
archivedRemoved from CRAN
2014-12-20
repeated policy violations by the maintainer. This package is now available from Bioconductor only, see <https://www.bioconductor.org/packages/release/bioc/html/gdsfmt.html>
removedRemoved from CRAN
Version 1.1.3 was removed for copyright violation
1.1.0.1
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2014-09-19 · diff ↗
1.1.0
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2014-09-10 · diff ↗ ·
removed 1 export
pattern:.

added 38 exports
add.gdsn, addfile.gdsn, addfolder.gdsn, append.gdsn, apply.gdsn, assign.gdsn, cache.gdsn, cleanup.gds, closefn.gds, clusterApply.gdsn, cnt.gdsn, compression.gdsn, createfn.gds, delete.attr.gdsn, delete.gdsn, diagnosis.gds, get.attr.gdsn, getfile.gdsn, index.gdsn, is.element.gdsn, lasterr.gds, ls.gdsn, moveto.gdsn, name.gdsn, objdesp.gdsn, openfn.gds, print.gds.class, print.gdsn.class, put.attr.gdsn, read.gdsn and 8 more
1.0.4
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2014-04-15 · diff ↗
R
R 3.1.0 released · 2014-04-10
1.0.3
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2014-03-18 · diff ↗
1.0.2
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2014-01-23 · diff ↗
1.0.1
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2014-01-06 · diff ↗
1.0.0
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2013-09-22 · diff ↗
0.9.15
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2013-08-22 · diff ↗
0.9.14
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2013-05-28 · diff ↗
R
R 3.0.0 released · 2013-04-03
0.9.13
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2013-03-28 · diff ↗
0.9.12
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2013-02-15 · diff ↗

Show 16 earlier eventsHide 16 earlier events

0.9.11
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2013-01-24 · diff ↗
0.9.10
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2012-08-27 · diff ↗
0.9.9
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2012-05-15 · diff ↗
0.9.8
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2012-04-14 · diff ↗
R
R 2.15.0 released · 2012-03-30
0.9.7
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2012-03-16 · diff ↗
0.9.6
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2012-02-18 · diff ↗ ·
added 1 export
pattern:.
R
R 2.14.0 released · 2011-10-31
0.9.5
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2011-08-09 · diff ↗
0.9.4
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2011-06-10 · diff ↗
0.9.3
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2011-05-01 · diff ↗
R
R 2.13.0 released · 2011-04-13
0.9.2
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2011-03-29 · diff ↗
0.9.1
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2011-01-07 · diff ↗
0.9
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2010-12-01
R
R 2.12.0 released · 2010-10-15

Package metadata

First published: 2010-12-01
Total releases: 23 / 16 yrs
License: LGPL-3 OSI
Minimum R: ≥ 2.14.0

Cite

Cite this package

Run in R for the authors' entry:

citation("gdsfmt")

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

It points to 10.1093/bioinformatics/bts606.

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 gdsfmt version 1.1.0.1 [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.

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