R Observatory: Metrics for reproducible version 3.2.1

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

reproducible

3.2.1Package record

Enhance Reproducibility of R Code

2packages depend

15.4Kdownloads / year

50.6%test coverage

13/13flavors OK

Overview

About

Maintained by Eliot J B McIntireCRAN page ↗GitHub ↗Website ↗Issues ↗

A collection of high-level, machine- and OS-independent tools for making reproducible and reusable content in R. The two workhorse functions are 'Cache()' and 'prepInputs()'. 'Cache()' allows for nested caching, is robust to environments and objects with environments (like functions), and deals with some classes of file-backed R objects e.g., from 'terra' and 'raster' packages. Both functions have been developed to be foundational components of data retrieval and processing in continuous workflow situations. In both functions, efforts are made to make the first and subsequent calls of functions have the same result, but faster at subsequent times by way of checksums and digesting. Several features are still under development, including cloud storage of cached objects allowing for sharing between users. Several advanced options are available, see '?reproducibleOptions()'.

Changes in 3.2.1

bug fixes

**prepInputs() no longer errors on Linux distributions without apt.** The check for RAR support shelled out to apt, which exists only on Debian/Ubuntu; system(..., intern = TRUE) *errors* rather than returning non-zero when a command is absent, so this failed on Fedora, RHEL, Arch and SUSE. CRAN's r-devel-linux-x86_64-fedora-{clang,gcc} reported it as a check ERROR. It now asks 7z itself (7z i), which answers the real question ("does this 7z support RAR?") on every platform and needs no package manager.
detectActiveCores() no longer errors where ps is unavailable, and a missing unrar no longer fails silently: both now check for the binary with Sys.which() before calling it.
Guidance for installing an extraction binary now covers macOS (brew install p7zip) alongside Debian/Ubuntu and RHEL/Fedora.

From NEWS.md in the release

Install

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

install.packages("reproducible", 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("PredictiveEcology/reproducible")

Development version from PredictiveEcology/reproducible. 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-reproducible

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-reproducible

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-reproducible

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: 7.8 min · r-oldrel-windows-x86_64

Status changes

OK13 OK2026-10-17
WARNING12 OK, 1 WARNING2026-10-01
OK11 OK2026-08-28
ERROR6 OK, 1 ERROR2026-08-26
OK13 OK2026-07-04

Show 14 earlier changesHide 14 earlier changes

WARNING12 OK, 1 WARNING2026-07-03
OK13 OK2026-07-01
ERROR12 OK, 1 ERROR2026-06-20
OK13 OK2026-06-19
WARNING12 OK, 1 WARNING2026-06-17
OK13 OK2026-06-10
ERROR12 OK, 1 ERROR2026-06-03
OK13 OK2026-05-23
ERROR12 OK, 1 ERROR2026-05-20
OK13 OK2026-05-17
ERROR12 OK, 1 ERROR2026-05-07
OK13 OK2026-05-02
ERROR11 OK, 1 ERROR2026-04-25
OK14 OK2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 3.2.1

READMEYes · 524 wordsVignettesYes · 1 · dynamicNEWSYes · 100% structured · mentions 3.2.1Citation fileYes · computed when R runs itWebsiteYes · pkgdown

Help pages: 114 (36 internal)includes a package overview page
Examples that run: 100%52 run in a plain check (14 of them under a condition)
Exported functions with examples: 76%
Documented parameters: 91%
Return-value docs: 94%
Help pages citing references: 0%

Vignettes (1)

Introduction to Cache

How these are measured

Downloads

15.4K

CRAN downloads in the past year

Rank #3,744 · ~42/day · ~1.3K/mo

Releases R versions

Daily download trend is not available in this view yet.

85930 days

2.6K90 days

15.4K1 year

Compare downloads with other packages →

Also on195 r2u4 autocran103 c2d4u

How downloads are counted

Repository

predictiveecology/reproducible ↗Organization: PredictiveEcology

39Stars

17Forks

13Open issues

0Open PRs

36Releases

6,821Commits

16Commit identities

reproducibilityreproducible-researchr-package

6,821 commits · Last activity 2026-08-31 · 0% stars, 30d · Discussions: 2 posts

Responsiveness

How these are sampled

PRs merged (all time): 89%
Median days to close, 50 most recently updated closed issues: 74
Median days to close, 50 most recently updated closed PRs: 0

Releases over time

2026-05-16 · 342026-08-26 · 36

How these are measured

PracticesBeta

13 development-tooling and community-health practices detected across 8 families in the upstream repository

Checks run against github.com/predictiveecology/reproducible on 2026-10-11.

Continuous integration (2)

GitHub ActionsR CMD check workflow

The R CMD check workflow runs on Linux

Governance and community (1)

Contributing guide

Docs source (2)

pkgdown

GitHub Pages site last deployed 2026-08-25

pkgdown site last built 2026-08-25

Coverage (1)

Coverage reporting (Codecov)

Show all practicesHide 4 practices

CRAN release process (3)

cran-comments.mdrevdep/CRAN-SUBMISSION

Research and citation (1)

CITATION.cff

Lint, format, editor (2)

lintrRStudio project

Git structural (1)

.gitattributes

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

AI coding toolsBeta

This repository shows signs of AI coding tools.

Claude Codefirst seen 2026-03-03
Named in .Rbuildignore: .claude
Named in .gitignore: .claude
Pull request it wrote: opened by a project member
Commits: at least 303 crediting it in the message
Aiderfirst seen 2026-06-09
Named in .gitignore: .aider*

From outside contributors

Claude Code
Pull requests: 152 from outside contributors, first on 2026-03-03

Models named in its commits

Claude Opus 562 commits · Aug 2026
Claude Sonnet 4.661 commits · Mar to Apr 2026
Claude Opus 4.739 commits · Apr to May 2026
Claude Opus 4.84 commits · Aug 2026

Some of these counts are a minimum, because the search stopped before the oldest commits.

Counts are commits, not lines of code. Commits by a tool's accounts count once across all of its accounts. Commits crediting it are the largest count among its credit lines, a minimum.How this is detected·Detection ruleset v4 (updated 2026-09-27)

Dependencies

Declared dependencies

33 external dependencies (excludes base and recommended)

Installing reproducible adds 12 packages (7 with compiled code, 9.4 MB of source tarballs). Heaviest: data.table 5.7 MB, fs 1.4 MB, rlang 766 KB.

Depends (1)

R >= 4.3

Imports (12)

cli data.table digest filelock fpCompare fs lifecycle lobstrmethodsstatstoolsutils

LinkingTo (0)

none

Suggests (26)

archive covr curl DBI future geodata glue googledrive httr httr2 knitrparallelparallelly qs2 raster RCurl rlang rmarkdown RSQLite R.utils rvest sf sp terra testthat withr

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

2direct

0indirect

Depends 1 · Imports 1

Depends, Imports or LinkingTo, most downloaded first

SpaDES.core SpaDES.tools

How these are counted

Code & Tests

People & History

People (6)

Eliot J B McIntire

Author, Maintainer since 0.1.1 (2017)

Alex M Chubaty

Author

Ceres Barros

Contributor · added in 0.2.5

Ian Eddy

Contributor · added in 0.2.5

Tati Micheletti

Contributor · added in 0.2.5

His Majesty the King in Right of Canada, as represented by the Minister of Natural Resources Canada

Copyright holder · added in 1.2.16

Listed in earlier versions (1)

Her Majesty the Queen in Right of Canada, as represented by the Minister of Natural Resources Canada

no longer listed · 0.1.1 to 1.2.11

Releases (43)

Pick two releases to compare their code metrics.

unarchivedReturned to CRAN
2026-08-25
3.2.1Latest
record
2026-08-25 · current release · diff ↗
3.2.0
record
first seen 2026-08-25 · diff ↗ ·
removed 5 exports
checkAndMakeCloudFolderID, downloadFile, internetExists, loadFile, prepInputsCOG

added 4 exports
clearUrlLog, listGoogleDriveFolder, makeUrlRemap, prepInputsLog
archivedRemoved from CRAN
2026-07-13
repeated policy violation On Internet access
3.1.1
record
2026-05-18 · diff ↗
3.1.0
record
2026-05-16 · diff ↗ ·
added 2 exports
prepInputsCOG, prepopulateCacheAsync
R
R 4.6.0 released · 2026-04-24
3.0.0
record
2026-01-08 · diff ↗ ·
removed 1 export
fastMask

added 17 exports
.addTagsRepo, .isCRSany, .isGridded, .isSF, .isSpat, .isSpatialAny, .isVector, .objSizeWithTry, .updateTagsRepo, .whereInStack, CacheV2, cacheId, detectActiveCores, numCoresToUse, prepInputsWithTiles, purgeChecksums, usesPointer
R
R 4.5.0 released · 2025-04-11
2.1.2
record
2024-12-12 · diff ↗
2.1.0
record
2024-05-30 · diff ↗ ·
added 14 exports
.cacheMessageObjectToRetrieve, .isMemoised, extractFromCache, gdalMask, gdalProject, gdalResample, listNamed, loadFile, messageCache, messageColoured, messagePreProcess, messagePrepInputs, messageQuestion, remapFilenames
R
R 4.4.0 released · 2024-04-24
unarchivedReturned to CRAN
2024-04-15
2.0.12
record
2024-04-15 · diff ↗
archivedRemoved from CRAN
2024-04-12
issues were not corrected in time
2.0.11
record
2024-03-30 · diff ↗

Show 45 earlier eventsHide 45 earlier events

2.0.10
record
2023-11-22 · diff ↗
2.0.9
record
2023-11-09 · diff ↗ ·
added 4 exports
getRelative, isUpdated, makeRelative, normPathRel
2.0.8
record
2023-08-23 · diff ↗
2.0.7
record
2023-08-07 · diff ↗ ·
added 2 exports
internetExists, urlExists
2.0.5
record
2023-07-03 · diff ↗ ·
removed 2 exports
.dealWithClass, .dealWithClassOnRecovery

added 2 exports
.unwrap, .wrap
2.0.4
record
2023-05-31 · diff ↗
2.0.2
record
2023-05-07 · diff ↗ ·
removed 3 exports
assessDataTypeGDAL, clearStubArtifacts, fixErrorsTerra

added 12 exports
.dealWithClass, .dealWithClassOnRecovery, CacheGeo, dataType2, fixErrorsIn, maxFn, minFn, nlayers2, postProcessTo, rasterRead, set.randomseed, values2
R
R 4.3.0 released · 2023-04-21
unarchivedReturned to CRAN
2022-12-22
1.2.16
record
2022-12-22 · diff ↗ ·
removed 15 exports
%<%, %C%, .prepareFileBackedRaster, Require, checkoutVersion, cloudCache, cloudCheckOld, cloudSyncCacheOld, cloudWriteOld, file.move, getArtifact, getCacheId, getUserTags, pkgDep, trimVersionNumber

added 4 exports
.file.move, maskTo, projectTo, writeTo
archivedRemoved from CRAN
2022-11-09
requires archived package 'Require'
1.2.11
record
2022-11-09 · diff ↗
1.2.10
record
2022-08-17 · diff ↗ ·
removed 3 exports
checkGDALVersion, getGDALVersion, isTopLevelEnv

added 3 exports
cropTo, fixErrorsTerra, postProcessTerra
R
R 4.2.0 released · 2022-04-22
1.2.8
record
2021-09-26 · diff ↗
unarchivedReturned to CRAN
2021-05-28
1.2.7
record
2021-05-28 · diff ↗ ·
added 2 exports
isTopLevelEnv, updateFilenameSlots
archivedRemoved from CRAN
2021-05-22
policy violation on filespace access ('~/tmp')
R
R 4.1.0 released · 2021-05-18
1.2.6
record
2021-02-17 · diff ↗
1.2.4
record
2020-12-07 · diff ↗ ·
added 1 export
paddedFloatToChar
1.2.1
record
2020-08-18 · diff ↗
1.2.0
record
2020-08-03 · diff ↗ ·
removed 6 exports
installVersions, installedVersions, newLibPaths, pkgDep2, pkgDepTopoSort, pkgSnapshot

added 3 exports
file.move, messageDF, preProcessParams
1.1.1
record
2020-05-20 · diff ↗
1.1.0
record
2020-05-15 · diff ↗ ·
added 6 exports
.requireNamespace, movedCache, pkgDepTopoSort, studyAreaName, tempfile2, trimVersionNumber
R
R 4.0.0 released · 2020-04-24
1.0.0
record
2020-02-20 · diff ↗ ·
removed 1 export
.objSizeInclEnviros

added 8 exports
CacheDBFile, CacheDBTableName, CacheIsACache, CacheStorageDir, CacheStoredFile, createCache, loadFromCache, rmFromCache
0.2.11
record
2019-11-19 · diff ↗ ·
removed 2 exports
cloudDownloadChecksumsOld, cloudUpdateChecksumsOld

added 1 export
tempdir2
0.2.10
record
2019-09-12 · diff ↗ ·
added 2 exports
objSizeSession, pkgDep2
0.2.9
record
2019-07-09 · diff ↗ ·
removed 6 exports
cloudCheck, cloudDownloadChecksums, cloudSyncCache, cloudUpdateChecksums, cloudWrite, readLinesRcpp

added 8 exports
Filenames, checkAndMakeCloudFolderID, cloudCheckOld, cloudDownloadChecksumsOld, cloudSyncCacheOld, cloudUpdateChecksumsOld, cloudWriteOld, retry
R
R 3.6.0 released · 2019-04-26
0.2.8
record
2019-03-18 · diff ↗ ·
added 3 exports
getArtifact, getCacheId, getUserTags
0.2.7
record
2019-03-07 · diff ↗
0.2.6
record
2019-02-01 · diff ↗ ·
removed 8 exports
%>%, UTM_to_longlat, cache, find_UTM_hemisphere, find_UTM_zone, longlat_to_UTM, makeMemoiseable, unmakeMemoiseable

added 13 exports
.setSubAttrInList, CacheDigest, basename2, cc, cloudCache, cloudCheck, cloudDownloadChecksums, cloudSyncCache, cloudUpdateChecksums, cloudWrite, makeMemoisable, reproducibleOptions, unmakeMemoisable
0.2.5
record
2018-11-16 · diff ↗ ·
added 8 exports
.formalsNotInCurrentDots, .grepSysCalls, UTM_to_longlat, assessDataTypeGDAL, find_UTM_hemisphere, find_UTM_zone, linkOrCopy, longlat_to_UTM
0.2.3
record
2018-08-07 · diff ↗
0.2.2
record
2018-08-01 · diff ↗ ·
added 3 exports
.addChangedAttr, assessDataType, writeFuture
0.2.1
record
2018-07-07 · diff ↗ ·
added 4 exports
convertPaths, convertRasterPaths, makeMemoiseable, unmakeMemoiseable
0.2.0
record
2018-06-17 · diff ↗ ·
added 17 exports
%<%, .prefix, .suffix, Checksums, checkGDALVersion, cropInputs, downloadFile, fastMask, fixErrors, getGDALVersion, maskInputs, objSize, postProcess, preProcess, prepInputs, projectInputs, writeOutputs
R
R 3.5.0 released · 2018-04-23
0.1.4
record
2018-01-25 · diff ↗ ·
added 13 exports
%>%, %C%, .orderDotsUnderscoreFirst, Require, compareNA, installVersions, installedVersions, newLibPaths, pkgDep, pkgSnapshot, readLinesRcpp, searchFull, searchFullEx
0.1.3
record
2017-08-11 · diff ↗
0.1.2
record
2017-08-09 · diff ↗
0.1.1
record
2017-08-05
R
R 3.4.0 released · 2017-04-21

Package metadata

First published: 2017-08-05
Total releases: 43 / 9 yrs
License: GPL-3 OSI
Minimum R: ≥ 4.3
Download size: 669 KB

Appears in task views

Reproducible Research

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("reproducible")

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

The repository also keeps a CITATION.cff.

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 reproducible version 3.2.1 [Data set]. HJJB, LLC. Data release v2026-10-18. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-18, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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