spgs

1.0-4

Statistical Patterns in Genomic Sequences

1packages depend

4.8Kdownloads / year

–test coverage

0/13checks pass

Overview

About

Maintained by Andrew HartFirst published 2015-03-285 releasesCRAN page ↗

A collection of statistical hypothesis tests and other techniques for identifying certain spatial relationships/phenomena in DNA sequences. In particular, it provides tests and graphical methods for determining whether or not DNA sequences comply with Chargaff's second parity rule or exhibit purine-pyrimidine parity. In addition, there are functions for efficiently simulating discrete state space Markov chains and testing arbitrary symbolic sequences of symbols for the presence of first-order Markovianness. Also, it has functions for counting words/k-mers (and cylinder patterns) in arbitrary symbolic sequences. Functions which take a DNA sequence as input can handle sequences stored as SeqFastadna objects from the 'seqinr' package.

Install

R (CRAN)Ubuntu (r2u)Fedora (COPR)openSUSE (OBS)

install.packages("spgs")

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

Release

# one-time r2u setup for Ubuntu (noble)

curl -fsSL https://raw.githubusercontent.com/eddelbuettel/r2u/master/inst/scripts/add_cranapt_noble.sh | sudo bash

# then install

sudo apt install r-cran-spgs

Fast Ubuntu binaries via r2u (no compilation). Run the setup once per machine.

bspm (used by r2u) also needs make: sudo apt install make

sudo dnf copr enable iucar/cran

sudo dnf install R-CRAN-spgs

RPMs from the iucar/cran COPR, rebuilt from CRAN.

sudo zypper install R-spgs

RPMs auto-built from CRAN on openSUSE OBS.

Health

CRAN checks

13NOTE

Failing flavors

NOTE r-devel-linux-x86_64-debian-clang
NOTE r-devel-linux-x86_64-debian-gcc
NOTE r-devel-linux-x86_64-fedora-clang
NOTE r-devel-linux-x86_64-fedora-gcc
NOTE r-devel-windows-x86_64
NOTE r-oldrel-macos-arm64
NOTE r-oldrel-macos-x86_64
NOTE r-oldrel-windows-x86_64
NOTE r-patched-linux-x86_64
NOTE r-release-linux-x86_64
NOTE r-release-macos-arm64
NOTE r-release-macos-x86_64
NOTE r-release-windows-x86_64

Code health

Yes

Tests · ratio 0.11

not tracked

Coverage

100%

Documentation · exports

None

Vignettes

README

Dependencies · direct

Check history

NOTE2026-03-10
0 OK · 14 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Downloads

4.8K

CRAN downloads in the past year

Rank #11,120 · ~13/day · ~403/mo

36530 days

95990 days

4.8K1 year

Also on402 r2u18 autocran

Source & community

Repository stars, issues, and contributor activity are not tracked yet.

Dependencies

Declared dependencies

0 external dependencies (excludes base and recommended)

Depends (1)

R >= 3.0

Imports (2)

graphics basestats base

LinkingTo (0)

none

Suggests (0)

none

Enhances (0)

none

Reverse dependencies

1direct

–indirect (not tracked)

prmisc

Code

6,217Lines of code

29Exported functions

Code & tests

Open call graph →

Code intelligence has not been computed for this package yet.

People & History

People (4)

Maintainer (1)

Andrew Hart

Author, Maintainer

Authors (1)

Servet Martínez

Author

INRIA-Chile

Universidad de Chile

Release timeline

5 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
1.0-4Latest
2023-10-03 · current release
R
R 4.3.0 released · 2023-04-21
R
R 4.2.0 released · 2022-04-22
R
R 4.1.0 released · 2021-05-18
R
R 4.0.0 released · 2020-04-24
1.0-3
2019-12-06 · diff ↗
R
R 3.6.0 released · 2019-04-26
1.0-2
2018-05-16 · diff ↗
R
R 3.5.0 released · 2018-04-23
1.0-1
2017-07-21 · diff ↗
R
R 3.4.0 released · 2017-04-21
R
R 3.3.0 released · 2016-05-03
R
R 3.2.0 released · 2015-04-16

Show 1 earlier events

1.0
2015-03-28

Package metadata

First published: 2015-03-28
Total releases: 5 / 11 yrs
License: GPL (>= 2) OSI
Download size: not tracked yet
Installed size: not tracked yet
With dependencies: not tracked yet