R Observatory: Metrics for QTL.gCIMapping version 3.4

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

QTL.gCIMapping

3.4Package record

QTL Genome-Wide Composite Interval Mapping

1packages depend

4Kdownloads / year

–test coverage

11/13flavors OK

Overview

About

Maintained by Yuanming ZhangCRAN page ↗

Conduct multiple quantitative trait loci (QTL) and QTL-by-environment interaction (QEI) mapping via ordinary or compressed variance component mixed models with random- or fixed QTL/QEI effects. First, each position on the genome is detected in order to obtain a negative logarithm P-value curve against genome position. Then, all the peaks on each effect (additive or dominant) curve or on each locus curve are viewed as potential main-effect QTLs and QEIs, all their effects are included in a multi-locus model, their effects are estimated by both least angle regression and empirical Bayes (or adaptive lasso) in backcross and F2 populations, and true QTLs and QEIs are identified by likelihood radio test. See Zhou et al. (2022) doi:10.1093/bib/bbab596 and Wen et al. (2018) doi:10.1093/bib/bby058.

Install

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

install.packages("QTL.gCIMapping", 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-qtl.gcimapping

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-QTL.gCIMapping

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-QTL.gCIMapping

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

2NOTE11OK

Check messages

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

Maintainer: ‘Yuanming Zhang<soyzhang@mail.hzau.edu.cn>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Zhou",
                      family = "Ya-Hui",
                      role = "aut"),
               person(given = "Zhang",
                      family = "Ya-Wen",
                      role = "aut"),
               person(given = "Wen",
                      family = "Yang-Jun",
                      role = "aut"),
               person(given = "Wang",
                      family = "Shi-Bo",
                      role = "aut"),
               person(given = "Zhang",
                      family = "Yuan-Ming",
                      role = "aut"),
               person(given = "Yuanming",
                      family = "Zhang",
                      role = "cre",
                      email = "soyzhang@mail.hzau.edu.cn"))
as necessary.

CRAN check page ↗

Slowest check: 4.2 min · r-devel-windows-x86_64

Status changes

NOTE11 OK, 2 NOTE2026-09-25
ERROR10 OK, 2 NOTE, 1 ERROR2026-09-18
NOTE11 OK, 2 NOTE2026-09-08
ERROR10 OK, 2 NOTE, 1 ERROR2026-09-07
NOTE12 OK, 2 NOTE2026-04-22

Show 2 earlier changesHide 2 earlier changes

ERROR11 OK, 2 NOTE, 1 ERROR2026-04-18
NOTE12 OK, 2 NOTE2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 3.4

READMENoVignettesNoNEWSNoCitation fileNoWebsitenot declared in DESCRIPTION

Help pages: 13
Examples that run: 91%10 run in a plain check · 1 never run
Exported functions with examples: 100%
Documented parameters: 100%
Return-value docs: 90%
Help pages citing references: 0%

How these are measured

Downloads

4K

CRAN downloads in the past year

Rank #12,161 · ~11/day · ~330/mo

Releases R versions

Daily download trend is not available in this view yet.

33230 days

91390 days

4K1 year

Compare downloads with other packages →

Also on365 r2u4 autocran

How downloads are counted

Dependencies

Declared dependencies

11 external dependencies (excludes base and recommended)

Installing QTL.gCIMapping adds 33 packages (17 with compiled code, 37 MB of source tarballs). Heaviest: stringi 11 MB, data.table 5.7 MB, qtl 4.2 MB.

Depends (1)

R >= 3.5.0

Imports (12)

Rcpp (>= 0.12.17)methodsopenxlsx readxl lars stringr data.table glmnet doParallel foreachMASSqtl

LinkingTo (1)

Rcpp

Suggests (0)

none

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

1direct

0indirect

Imports 1

Depends, Imports or LinkingTo, most downloaded first

QTL.gCIMapping.GUI

How these are counted

Code & Tests

Datasets

People & History

People (from the free-text Author field) (5)

· added in 3.4

Maintainer since 1.0 (2018)

Releases (8)

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
3.4Latest
record
2022-02-24 · current release · diff ↗ ·
added 3 exports
ZhouF, ZhouMethod_single_env, ZhouMethod
R
R 4.1.0 released · 2021-05-18
3.3.1
record
2020-10-12 · diff ↗
3.3
record
2020-05-01 · diff ↗
R
R 4.0.0 released · 2020-04-24
3.2
record
2019-11-12 · diff ↗ ·
added 6 exports
WangF, WangS, WenF, WenS, Readdata, Dodata
R
R 3.6.0 released · 2019-04-26
3.1
record
2018-10-17 · diff ↗
3.0
record
2018-06-16 · diff ↗ ·
removed 2 exports
WangF, WenF

added 1 export
pattern:^[[:alpha:]]+
2.0
record
2018-04-30 · diff ↗ ·
added 2 exports
WangF, WenF
1.0
record
2018-04-24

Show 1 earlier eventHide 1 earlier event

R
R 3.5.0 released · 2018-04-23

Package metadata

First published: 2018-04-24
Total releases: 8 / 8 yrs
License: GPL (>= 2) OSI
Minimum R: ≥ 3.5.0
Bundled data: 3.2 KB / 2 files
Download size: 1.7 MB

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("QTL.gCIMapping")

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 QTL.gCIMapping version 3.4 [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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