R Observatory: Metrics for opalr version 3.7.0

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

opalr

3.7.0Package record

'Opal' Data Repository Client and 'DataSHIELD' Utils

3packages depend

12.1Kdownloads / year

6.7%test coverage

13/13flavors OK

Overview

About

Maintained by Yannick MarconCRAN page ↗GitHub ↗Website ↗Issues ↗

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. 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-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). 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

13OK

CRAN check page ↗

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

Status changes

OK13 OK2026-08-05
NOTE12 OK, 1 NOTE2026-08-01
OK13 OK2026-06-09
ERROR12 OK, 1 ERROR2026-06-08
OK14 OK2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 3.7.0

READMEYes · 211 wordsVignettesYes · 4 · staticNEWSNoCitation fileNoWebsiteYes · pkgdown

Help pages: 247 (30 internal)includes a package overview page
Examples that run: 0%217 never run
Exported functions with examples: 100%
Documented parameters: 100%
Return-value docs: 25%
Help pages citing references: 0%

Vignettes (4)

How these are measured

Downloads

12.1K

CRAN downloads in the past year

Rank #3,722 · ~33/day · ~1K/mo

Releases R versions

Daily download trend is not available in this view yet.

92430 days

2.6K90 days

12.1K1 year

Compare downloads with other packages →

Also on172 r2u6 autocran

How downloads are counted

Repository

obiba/opalr ↗Organization: obiba

3Stars

3Forks

3Open issues

0Open PRs

32Releases

474Commits

7Commit identities

474 commits · Last activity 2026-09-18

Responsiveness

How these are sampled

PRs merged (all time): 100%
Median days to close, 50 most recently updated closed issues: 2
Median days to close, 50 most recently updated closed PRs: 0

Stars over time

2021-07-07 · 32026-07-07 · 3

How these are measured

PracticesBeta

6 development-tooling and community-health practices detected across 4 families in the upstream repository

Checks run against github.com/obiba/opalr on 2026-10-18.

Continuous integration (2)

GitHub ActionsR CMD check workflow

The R CMD check workflow runs on Linux, macOS and Windows

Governance and community (1)

The repository owner accepts GitHub Sponsors

Docs source (2)

pkgdown

GitHub Pages site last deployed 2026-09-18

pkgdown site last built 2026-05-27, before release 3.7.0 (2026-09-18)

CRAN release process (1)

CRAN-SUBMISSION

How this is detected·Detection ruleset v3 (2026-09-26)

Dependencies

Declared dependencies

12 external dependencies (excludes base and recommended)

Installing opalr adds 40 packages (24 with compiled code, 24 MB of source tarballs). Heaviest: stringi 11 MB, openssl 1.1 MB, jsonlite 1.0 MB.

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

Depends 1 · Imports 2

Depends, Imports or LinkingTo, most downloaded first

dsROCrate DSOpal mlstrOpalr

How these are counted

Code & Tests

People & History

People (3)

Yannick Marcon

Author, Maintainer since 1.0.0 (2019)

Amadou Gaye

Contributor

OBiBa group

Copyright holder

Releases (32)

Pick two releases to compare their code metrics.

3.7.0Latest
record
2026-09-18 · current release · diff ↗ ·
added 8 exports
dsadmin.quota, dsadmin.quota_delete, dsadmin.quota_enable, dsadmin.quota_exists, dsadmin.quota_save, dsadmin.quota_usage, dsadmin.quotas, opal.quotas
3.6.1
record
2026-05-27 · diff ↗
R
R 4.6.0 released · 2026-04-24
3.6.0
record
2026-04-17 · diff ↗ ·
added 2 exports
opal.file_info, opal.task_delete
3.5.2
record
2025-12-09 · diff ↗
3.5.1
record
2025-11-16 · diff ↗
3.5.0
record
2025-11-05 · diff ↗ ·
added 6 exports
opal.session, opal.session_delete, opal.session_events, opal.session_exists, opal.session_get, opal.session_running
R
R 4.5.0 released · 2025-04-11
3.4.2
record
2024-09-18 · diff ↗
R
R 4.4.0 released · 2024-04-24
3.4.1
record
2024-01-10 · diff ↗
3.4.0
record
2023-10-06 · diff ↗ ·
added 9 exports
dsadmin.activity, dsadmin.activity_summary, dsadmin.log, oadmin.activity, oadmin.activity_summary, oadmin.log, oadmin.log_rest, oadmin.log_sql, opal.perms
R
R 4.3.0 released · 2023-04-21
3.3.1
record
2023-02-28 · diff ↗
3.3.0
record
2023-02-03 · diff ↗ ·
added 1 export
opal.table_view_update
3.2.0
record
2022-10-13 · diff ↗ ·
added 1 export
opal.workspace_restore

Show 25 earlier eventsHide 25 earlier events

3.1.1
record
2022-06-09 · diff ↗
3.1.0
record
2022-05-02 · diff ↗ ·
added 5 exports
opal.resource_view_create, opal.resource_view_reconnect, opal.table_view_create, opal.token_renew, opal.variable_summary
R
R 4.2.0 released · 2022-04-22
3.0.2
record
2021-10-26 · diff ↗
3.0.1
record
2021-08-23 · diff ↗
3.0.0
record
2021-07-05 · diff ↗ ·
added 37 exports
dsadmin.profile, dsadmin.profile_access, dsadmin.profile_create, dsadmin.profile_delete, dsadmin.profile_enable, dsadmin.profile_exists, dsadmin.profile_init, dsadmin.profile_perm, dsadmin.profile_perm_add, dsadmin.profile_perm_delete, dsadmin.profile_rparser, dsadmin.profiles, dsadmin.publish_package, dsadmin.rm_options, dsadmin.unpublish_package, oadmin.install_cran_package, oadmin.r_perm, oadmin.r_perm_add, oadmin.r_perm_delete, oadmin.system_metrics, oadmin.system_perm, oadmin.system_perm_add, oadmin.system_perm_delete, oadmin.user_add, oadmin.user_delete, oadmin.user_enable, oadmin.user_exists, oadmin.user_profile_delete, oadmin.user_profiles, oadmin.user_reset_password and 7 more
2.1.1
record
2021-05-31 · diff ↗
R
R 4.1.0 released · 2021-05-18
2.1.0
record
2021-04-29 · diff ↗ ·
added 9 exports
opal.resource_extension_create, opal.sql, opal.sql_history, opal.token, opal.token_datashield_create, opal.token_delete, opal.token_r_create, opal.token_sql_create, opal.tokens
2.0.0
record
2021-03-09 · diff ↗ ·
removed 8 exports
harmo.annotate, harmo.annotate.status, harmo.annotations, harmo.dictionary_apply, harmo.dictionary_update, harmo.table_get, harmo.table_save, oadmin.install_github

added 3 exports
dictionary.inspect, opal.table_export, opal.table_import
1.5.2
record
2021-01-21 · diff ↗
1.5.1
record
2020-12-16 · diff ↗
1.5.0
record
2020-11-03 · diff ↗ ·
added 49 exports
dictionary.annotate, dictionary.annotate.harmo_status, dictionary.annotations, dictionary.apply, dsadmin.install_github_package, dsadmin.install_local_package, dsadmin.perm, dsadmin.perm_add, dsadmin.perm_delete, oadmin.install_bioconductor_package, oadmin.install_github_package, oadmin.install_local_package, oadmin.perm, oadmin.perm_add, oadmin.perm_delete, opal.file_mkdir_tmp, opal.project_create, opal.project_delete, opal.project_exists, opal.project_perm, opal.project_perm_add, opal.project_perm_delete, opal.resource_create, opal.resource_delete, opal.resource_exists, opal.resource_get, opal.resource_perm, opal.resource_perm_add, opal.resource_perm_delete, opal.resources_perm and 19 more
1.4.1
record
2020-06-08 · diff ↗ ·
added 1 export
opal.execute.source
1.4.0
record
2020-05-18 · diff ↗ ·
added 3 exports
opal.assign.resource, opal.resource, opal.resources
R
R 4.0.0 released · 2020-04-24
1.3.0
record
2019-12-10 · diff ↗ ·
added 7 exports
harmo.annotate, harmo.annotate.status, harmo.annotations, harmo.dictionary_apply, harmo.dictionary_update, harmo.table_get, harmo.table_save
1.2.0
record
2019-08-19 · diff ↗
1.1.0
record
2019-06-26 · diff ↗ ·
added 2 exports
opal.annotate, opal.annotations
R
R 3.6.0 released · 2019-04-26
1.0.3
record
2019-03-21 · diff ↗
1.0.2
record
2019-03-19 · diff ↗
1.0.1
record
2019-02-26 · diff ↗
1.0.0
record
2019-02-18
R
R 3.5.0 released · 2018-04-23

Package metadata

First published: 2019-02-18
Total releases: 32 / 7 yrs
License: GPL-3 OSI
Minimum R: ≥ 3.1
Download size: 166 KB

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("opalr")

Format

Marcon, Y., OBiBa group, & Gaye, A. (2026). opalr: 'Opal' Data Repository Client and 'DataSHIELD' Utils (Version 3.7.0) [Computer software]. https://doi.org/10.32614/CRAN.package.opalr

This package has no citation file, so citation() returns this entry built from DESCRIPTION.

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 opalr version 3.7.0 [Data set]. HJJB, LLC. Data release v2026-10-21. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-21, 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 →