R Observatory: Metrics for SoyNAM version 1.6.2

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

SoyNAM

1.6.2Package record

Soybean Nested Association Mapping Dataset

0packages depend

3.5Kdownloads / year

–test coverage

9/13flavors OK

Overview

About

Maintained by Alencar XavierCRAN page ↗

Genomic and multi-environmental soybean data. Soybean Nested Association Mapping (SoyNAM) project dataset funded by the United Soybean Board (USB). BLUP function formats data for genome-wide prediction and association analysis.

Install

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

install.packages("SoyNAM", 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-soynam

Fast Ubuntu binaries via r2u (no compilation). The cranapt setup runs once and is skipped when it is already enabled. We list this channel from recorded r2u download activity rather than from a live index of the repository, so treat it as last known rather than guaranteed.

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

# enable the iucar/cran COPR if it is not already present, then install
ls /etc/yum.repos.d/*iucar*cran*.repo >/dev/null 2>&1 \
  || sudo dnf copr enable -y iucar/cran
sudo dnf install -y R-CRAN-SoyNAM

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

For install.packages() integration in R, also: sudo dnf install R-CoprManager

# add the autoCRAN OBS repo (Tumbleweed) if it is missing, then install
zypper -q lr | grep -qi autoCRAN \
  || sudo zypper addrepo https://download.opensuse.org/repositories/devel:/languages:/R:/autoCRAN/openSUSE_Tumbleweed/devel:languages:R:autoCRAN.repo
sudo zypper install -y R-SoyNAM

RPMs auto-built from CRAN on openSUSE OBS (Tumbleweed). We list this channel from recorded autoCRAN download activity rather than from a live index of the repository, so treat it as last known rather than guaranteed.

Health

CRAN checks

4NOTE9OK

Check messages

NOTECRAN incoming feasibilityr-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc

Maintainer: ‘Alencar Xavier <alenxav@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Alencar",
                      family = "Xavier",
                      role = c("aut", "cre"),
                      email = "alenxav@gmail.com"),
               person(given = "William",
                      family = "Beavis",
                      role = "aut"),
               person(given = "James",
                      family = "Specht",
                      role = "aut"),
               person(given = "Brian",
                      family = "Diers",
                      role = "aut"),
               person(given = "Rouf",
                      family = "Mian",
                      role = "aut"),
               person(given = "Reka",
                      family = "Howard",
                      role = "aut"),
               person(given = "George",
                      family = "Graef",
                      role = "aut"),
          
...[truncated]...
= "Schapaugh",
                      role = "aut"),
               person(given = "Dechun",
                      family = "Wang",
                      role = "aut"),
               person(given = "Grover",
                      family = "Shannon",
                      role = "aut"),
               person(given = "Leah",
                      family = "McHale",
                      role = "aut"),
               person(given = "Perry",
                      family = "Cregan",
                      role = "aut"),
               person(given = "Qijian",
                      family = "Song",
                      role = "aut"),
               person(given = "Miguel",
                      family = "Lopez",
                      role = "aut"),
               person(given = "William",
                      family = "Muir",
                      role = "aut"),
               person(given = "Katy",
                      family = "Rainey.",
                      role = "aut"))
as necessary.

NOTEdependencies in R coder-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc

Namespace in Imports field not imported from:
  ‘RcppEigen’
All declared Imports should be used.

CRAN check page ↗

Slowest check: 3.7 min · r-devel-windows-x86_64

Status changes

NOTE9 OK, 4 NOTE2026-09-08
ERROR9 OK, 3 NOTE, 1 ERROR2026-09-07
NOTE7 OK, 7 NOTE2026-04-22
ERROR6 OK, 7 NOTE, 1 ERROR2026-04-18
NOTE7 OK, 7 NOTE2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 1.6.2

READMENoVignettesNoNEWSNoCitation fileNoWebsitenot declared in DESCRIPTION

Help pages: 3includes a package overview page
Examples that run: 100%2 run in a plain check
Exported functions with examples: 100%
Documented parameters: not tracked
Return-value docs: not tracked
Help pages citing references: 67%

How these are measured

Downloads

3.5K

CRAN downloads in the past year

Rank #13,353 · ~10/day · ~294/mo

Releases R versions

Daily download trend is not available in this view yet.

29730 days

86890 days

3.5K1 year

Compare downloads with other packages →

Also on425 r2u4 autocran138 c2d4u

How downloads are counted

Dependencies

Declared dependencies

7 external dependencies (excludes base and recommended)

Installing SoyNAM adds 19 packages (15 with compiled code, 27 MB of source tarballs). Heaviest: stringi 11 MB, lme4 4.3 MB, nloptr 2.1 MB.

Depends (1)

R >= 3.6.0

Imports (5)

NAM lme4 reshape2 Rcpp RcppEigen

LinkingTo (2)

Rcpp RcppEigen

Suggests (0)

none

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

How these are counted

Code & Tests

Datasets

People & History

People (from the free-text Author field) (17)

· added in 1.5

· added in 1.2

· added in 1.5

· added in 1.5

· added in 1.5

· added in 1.5

· added in 1.5

· added in 1.5

· added in 1.5

· added in 1.5

· added in 1.5

Maintainer since 1.0 (2015)

Releases (9)

Pick two releases to compare their code metrics.

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
R
R 4.2.0 released · 2022-04-22
1.6.2Latest
record
2022-01-04 · current release · diff ↗
R
R 4.1.0 released · 2021-05-18
1.6.1
record
2021-01-21 · diff ↗
R
R 4.0.0 released · 2020-04-24
R
R 3.6.0 released · 2019-04-26
1.6
record
2019-02-13 · diff ↗
1.5
record
2018-10-01 · diff ↗
R
R 3.5.0 released · 2018-04-23
1.4
record
2018-02-02 · diff ↗
R
R 3.4.0 released · 2017-04-21
1.3
record
2016-12-13 · diff ↗

Show 5 earlier eventsHide 5 earlier events

R
R 3.3.0 released · 2016-05-03
1.2
record
2015-11-18 · diff ↗
1.1
record
2015-10-16 · diff ↗
1.0
record
2015-07-29
R
R 3.2.0 released · 2015-04-16

Package metadata

First published: 2015-07-29
Total releases: 9 / 11 yrs
License: GPL-3 OSI
Minimum R: ≥ 3.6.0
Bundled data: 4.7 MB / 4 files
Download size: 4.7 MB

Appears in task views

Agricultural Science

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("SoyNAM")

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 SoyNAM version 1.6.2 [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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