R Observatory: Metrics for RDML version 1.1

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

RDML

1.1Package record

Importing Real-Time Thermo Cycler (qPCR) Data from RDML Format Files

0packages dependsuggested by 2

3.5Kdownloads / year

55.3%test coverage

11/13flavors OK

Overview

About

Maintained by Konstantin BlagodatskikhCRAN page ↗GitHub ↗

Imports real-time thermo cycler (qPCR) data from Real-time PCR Data Markup Language (RDML) and transforms to the appropriate formats of the 'qpcR' and 'chipPCR' packages, as described in Rodiger et al. (2017) doi:10.1093/bioinformatics/btx528. Contains a dendrogram visualization for the structure of RDML object and GUI for RDML editing.

Install

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

install.packages("RDML", repos = "https://cloud.r-project.org/")

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

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

Development version from PCRuniversum/RDML. Installs pak first if it is not already available.

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-rdml

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-RDML

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-RDML

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

NOTERd contentsr-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc

Rd files without \usage:
  ‘asdendrogram-method.Rd’ ‘astable-method.Rd’ ‘getfdata-method.Rd’
  ‘new-method.Rd’ ‘setfdata-method.Rd’
\arguments should not be documented without \usage.

CRAN check page ↗

Slowest check: 3.0 min · r-oldrel-windows-x86_64

Status changes

NOTE11 OK, 2 NOTE2026-09-08
ERROR10 OK, 2 NOTE, 1 ERROR2026-09-07
NOTE12 OK, 1 NOTE2026-07-11
OK14 OK2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 1.1

READMEYes · 236 wordsVignettes· In the repository, left out of the releaseNEWSNoCitation fileYes · cites a publication

Help pages: 58
Examples that run: 90%9 run in a plain check · 1 never run
Exported functions with examples: 11%
Documented parameters: 100%
Return-value docs: 0%
Help pages citing references: 2%

How these are measured

Downloads

3.5K

CRAN downloads in the past year

Rank #12,864 · ~9/day · ~289/mo

Releases R versions

Daily download trend is not available in this view yet.

32130 days

88590 days

3.5K1 year

Compare downloads with other packages →

Also on85 r2u7 autocran

How downloads are counted

Repository

pcruniversum/rdml ↗Organization: PCRuniversum

21Stars

8Forks

4Open issues

0Open PRs

0Releases

573Commits

5Commit identities

pcrbioinformaticscranqpcrrrdml

573 commits · Last activity 2024-08-30 · 0% stars, 30d · Default branch at 1.3, ahead of CRAN 1.1 (checked 2026-10-21)

Responsiveness

How these are sampled

PRs merged (all time): 50%
Median days to close, 50 most recently updated closed issues: 14
Median days to close, 50 most recently updated closed PRs: 678

Stars over time

2024-08-07 · 202026-07-17 · 21

How these are measured

PracticesBeta

3 development-tooling and community-health practices detected across 3 families in the upstream repository

Checks run against github.com/pcruniversum/rdml on 2026-10-21.

Continuous integration (1)

Travis CI (config file)

Docs source (1)

GitHub Pages site last deployed 2024-08-30

Lint, format, editor (1)

RStudio project

How this is detected·Detection ruleset v4 (2026-10-20)

Dependencies

Declared dependencies

23 external dependencies (excludes base and recommended)

Installing RDML adds 33 packages (18 with compiled code, 27 MB of source tarballs). Heaviest: stringi 11 MB, data.table 5.7 MB, readxl 2.1 MB.

Depends (1)

R >= 3.2.0

Imports (10)

checkmate data.table pipeR readxl rlist (>= 0.4)R6 stringrtoolsxml2 lubridate

LinkingTo (0)

none

Suggests (14)

chipPCR magrittr reshape2 qpcR dplyr ggplot2 knitr kfigr MBmca shiny shinyjs shinythemes V8 testthat

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Suggested by 2

Suggests, most downloaded first

chipPCR PCRedux

How these are counted

Code & Tests

Datasets

People & History

People (4)

Konstantin Blagodatskikh

Maintainer, Author · added in 1.1

Michal Burdukiewicz

Author

Stefan Roediger

Author

Andrej-Nikolai Spiess

Author · added in 0.9-7

Maintainer since 0.4-2 (2014)

Listed in earlier versions (1)

Konstantin A. Blagodatskikh

no longer listed · 0.4-2 to 1.0

Releases (12)

Pick two releases to compare their code metrics.

R
R 4.6.0 released · 2026-04-24
unarchivedReturned to CRAN
2025-07-23
1.1Latest
record
2025-07-23 · current release · diff ↗
archivedRemoved from CRAN
2025-06-12
issues were not corrected despite reminders
removedRemoved from CRAN
Version 0.8-2 was removed for policy violation
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
R
R 4.1.0 released · 2021-05-18
R
R 4.0.0 released · 2020-04-24
1.0
record
2019-06-25 · diff ↗
R
R 3.6.0 released · 2019-04-26
R
R 3.5.0 released · 2018-04-23
0.9-9
record
2017-09-25 · diff ↗
0.9-8
record
2017-09-05 · diff ↗

Show 12 earlier eventsHide 12 earlier events

0.9-7
record
2017-07-31 · diff ↗
0.9-6
record
2017-04-24 · diff ↗
R
R 3.4.0 released · 2017-04-21
0.9-5
record
2016-12-13 · diff ↗ ·
added 1 export
rdmlEdit
R
R 3.3.0 released · 2016-05-03
0.9-1
record
2015-07-22 · diff ↗ ·
added 45 exports
AsDendrogram, AsTable, GetFData, MergeRDMLs, SetFData, adpsType, annotationType, cdnaSynthesisMethodType, commercialAssayType, cqDetectionMethodType, dataCollectionSoftwareType, dataType, documentationType, dyeType, experimentType, experimenterType, gradientType, idReferencesType, idType, labelFormatType, lidOpenType, loopType, mdpsType, measureType, nucleotideType, oligoType, pauseType, pcrFormatType, primingMethodType, quantityType and 15 more
0.8-4
record
2015-04-21 · diff ↗
R
R 3.2.0 released · 2015-04-16
0.8-3
record
2015-04-08 · diff ↗
0.8-2
record
2015-04-07 · diff ↗
0.4-2
record
2015-04-06
R
R 3.1.0 released · 2014-04-10

Package metadata

First published: 2015-04-06
Total releases: 12 / 11 yrs
License: MIT + file LICENSE OSI · relicensed from GPL (>= 2) in 0.9-7
Minimum R: ≥ 3.2.0
Download size: 790 KB

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("RDML")

The package provides a citation file that builds its entry when R runs it. Run citation() to see it.

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 RDML version 1.1 [Data set]. HJJB, LLC. Data release v2026-10-24. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-24, which the citation names so these numbers can be found later. More on citing and the projects behind them.

Report a problem with this page →