opalr

3.6.1

'Opal' Data Repository Client and 'DataSHIELD' Utils

3packages depend

13.7Kdownloads / year

7.0%test coverage

13/13checks pass

Overview

About

Maintained by Yannick MarconFirst published 2019-02-1831 releasesCRAN page ↗GitHub ↗

Data integration Web application for biobanks by 'OBiBa'. 'Opal' is the core database application for biobanks. Participant data, once collected from any data source, must be integrated and stored in a central data repository under a uniform model. 'Opal' is such a central repository. It can import, process, validate, query, analyze, report, and export data. 'Opal' is typically used in a research center to analyze the data acquired at assessment centres. Its ultimate purpose is to achieve seamless data-sharing among biobanks. This 'Opal' client allows to interact with 'Opal' web services and to perform operations on the R server side. 'DataSHIELD' administration tools are also provided.

Install

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

install.packages("opalr", 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("obiba/opalr")

Development version from obiba/opalr. 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-opalr

Fast Ubuntu binaries via r2u (no compilation). The cranapt setup runs once and is skipped when it is already enabled.

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-opalr

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-opalr

RPMs auto-built from CRAN on openSUSE OBS (Tumbleweed).

Health

CRAN checks

13OK

Slowest check: 3.6 min · r-oldrel-windows-x86_64

Code health

Yes

Tests · ratio 0.09

7.0%

Coverage · measured lines

100%

Documentation · exports

Dependencies · direct

Check history

OK2026-06-09
13 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-06-08
12 OK · 0 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
OK2026-03-10
14 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Documentation

READMEYes · 211 wordsVignettesYes · staticpkgdown siteNoNEWSNoCode of conductNoContributing guideNo

Examples that run: 0%
Documented parameters: 100%
Return-value docs: 24%
References docs: 0%

Downloads

13.7K

CRAN downloads in the past year

Rank #3,541 · ~38/day · ~1.1K/mo

Releases R versions

Daily download trend is not available in this view yet.

70830 days

3.1K90 days

13.7K1 year

Compare downloads with other packages →

Also on149 r2u2 autocran

Repository

GitHub ↗ obiba/opalr

3Stars

3Forks

4Open issues

0Open PRs

31Releases

470Commits

7Contributors

470 commits · Last activity 2026-05-27

Stars over time

2021-07-07 · 32026-07-07 · 3

Repository practices

Upstream repositoryBeta

2 development-tooling and community-health practices detected across 2 families in the upstream repository

Checks run against github.com/obiba/opalr on 2026-07-30.

Continuous integration (1)

GitHub Actions

CRAN release process (1)

CRAN-SUBMISSION

How this is detected·Detection ruleset v1 (2026-07-18)

Dependencies

Declared dependencies

12 external dependencies (excludes base and recommended)

Depends (2)

R >= 3.1httr

Imports (6)

jsonlite readr mime progress labelled tibble

LinkingTo (0)

none

Suggests (5)

e1071 knitr knitrBootstrap rmarkdown testthat

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

3direct

0indirect

DSOpal dsROCrate mlstrOpalr

Code & Tests

People & History

People (3)

Maintainer (1)

Yannick Marcon

Author, Maintainer

Authors (1)

Yannick Marcon

Author, Maintainer

Contributors (1)

Amadou Gaye

Contributor

OBiBa group

Package Timeline

31 releases. Pick two to compare their code metrics. R releases are shown for context.

3.6.1Latest
2026-05-27 · current release · diff ↗
R
R 4.6.0 released · 2026-04-24
3.6.0
2026-04-17 · diff ↗
3.5.2
2025-12-09 · diff ↗
3.5.1
2025-11-16 · diff ↗
3.5.0
2025-11-05 · diff ↗
R
R 4.5.0 released · 2025-04-11
3.4.2
2024-09-18 · diff ↗
R
R 4.4.0 released · 2024-04-24
3.4.1
2024-01-10 · diff ↗
3.4.0
2023-10-06 · diff ↗
R
R 4.3.0 released · 2023-04-21
3.3.1
2023-02-28 · diff ↗
3.3.0
2023-02-03 · diff ↗
3.2.0
2022-10-13 · diff ↗
3.1.1
2022-06-09 · diff ↗

Show 24 earlier events

3.1.0
2022-05-02 · diff ↗
R
R 4.2.0 released · 2022-04-22
3.0.2
2021-10-26 · diff ↗
3.0.1
2021-08-23 · diff ↗
3.0.0
2021-07-05 · diff ↗
2.1.1
2021-05-31 · diff ↗
R
R 4.1.0 released · 2021-05-18
2.1.0
2021-04-29 · diff ↗
2.0.0
2021-03-09 · diff ↗
1.5.2
2021-01-21 · diff ↗
1.5.1
2020-12-16 · diff ↗
1.5.0
2020-11-03 · diff ↗
1.4.1
2020-06-08 · diff ↗
1.4.0
2020-05-18 · diff ↗
R
R 4.0.0 released · 2020-04-24
1.3.0
2019-12-10 · diff ↗
1.2.0
2019-08-19 · diff ↗
1.1.0
2019-06-26 · diff ↗
R
R 3.6.0 released · 2019-04-26
1.0.3
2019-03-21 · diff ↗
1.0.2
2019-03-19 · diff ↗
1.0.1
2019-02-26 · diff ↗
1.0.0
2019-02-18
R
R 3.5.0 released · 2018-04-23

Package metadata

First published: 2019-02-18
Total releases: 31 / 7 yrs
License: GPL-3 OSI
Minimum R: ≥ 3.1
Download size: 153 KB
Installed size: not tracked yet
With dependencies: not tracked yet

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