R Observatory: Metrics for OpenSpecy version 2.0.3

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

OpenSpecy

2.0.3Package record

Analyze, Process, Identify, and Share Raman and (FT)IR Spectra

0packages depend

4.4Kdownloads / year

85.4%test coverage

12/13flavors OK

Overview

About

Maintained by Win CowgerCRAN page ↗GitHub ↗Website ↗Issues ↗Declared funders: National Renewable Energy Laboratory and Possibility Lab

Raman and (FT)IR spectral analysis tool for plastic particles and other environmental samples (Cowger et al. 2025, doi:10.1021/acs.analchem.5c00962). With read_any(), Open Specy provides a single function for reading individual, batch, or map spectral data files like .asp, .csv, .jdx, .spc, .spa, .0, and .zip. process_spec() simplifies processing spectra, including smoothing, baseline correction, range restriction and flattening, intensity conversions, wavenumber alignment, and min-max normalization. Spectra can be identified in batch using an onboard reference library using match_spec(). A bundled Shiny app is available via run_app() or online at https://www.openanalysis.org/OpenSpecyV2/.

Changes in 2.0.3

Fixed cross-platform checks for the 2.0 release: relative normalization now returns zeros for finite constant spectra instead of NaN, keeping default build_lib() outputs valid when alternate BLAS implementations produce an exact polynomial-baseline fit; ENVI companion-image paths are canonicalized before being stored; and OPUS fixture tests accept harmless parser warnings while retaining strict object, dimension, range, and metadata assertions. Hamming similarity retains its established equal-frequency-bin behavior.

From NEWS.md in the release

Install

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

install.packages("OpenSpecy", 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("wincowgerDEV/OpenSpecy-package")

Development version from wincowgerDEV/OpenSpecy-package. 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-openspecy

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-OpenSpecy

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-OpenSpecy

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

1ERROR12OK

Check messages

ERRORtestsr-oldrel-windows-x86_64

Running 'testthat.R' [206s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(OpenSpecy)
  > 
  > library(data.table)
  > setDTthreads(2)
  > 
  > test_check("OpenSpecy")
  Particle analysis [file-backed source]: read into memory (1 regions; 16 spectra; 4 bands)
  Particle analysis [Region1]: memory materialization (region 1/1; 16 spectra)
  Particle analysis [Region1]: memory materialization complete (elapsed 0.0 s)
  Particle analysis [Region1]: read (sample 1 of 1)
  Particle analysis [Region1]: signal/noise
  Particle analysis [Region1]: particle detection and collapse
  Particle analysis [Region1]: library matching
  Particle analysis [Region1]: outputs
  Particle analysis [Region1]: complete
  Particle analysis [file-backed source]: read into memory (1 regions; 16 spectra; 4 bands)
  Particle analysis [Region1]: memory materialization (region 1/1; 16 spectra)
  Particle analysis [Region1]: memory materialization complete (elapsed 0
...[truncated]...
l (1):
    'test-shinylive_wasm.R:730:5'
  • Repository-only workflow files are not in the package tarball (2):
    'test-shinylive_wasm.R:635:5', 'test-shinylive_wasm.R:864:5'
  • Repository-only workspace path contract is not in the package tarball (1):
    'test-shinylive_wasm.R:845:5'
  • repository-only reference workflow tables are not installed (4):
    'test-build_lib.R:1679:3', 'test-build_lib.R:1865:3',
    'test-build_lib.R:3151:3', 'test-build_lib.R:3188:3'
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test-run_app.R:1998:3'): bundled app applies spike correction through the registered API ──
  Error in `file(con, "r")`: cannot open the connection
  Backtrace:
      ▆
   1. ├─base::grepl(...) at test-run_app.R:1998:3
   2. │ └─base::is.factor(x)
   3. └─base::readLines(namespace_path, warn = FALSE)
   4.   └─base::file(con, "r")
  
  [ FAIL 1 | WARN 31 | SKIP 27 | PASS 3748 ]
  Error:
  ! Test failures.
  Execution halted

CRAN check page ↗

Slowest check: 10.1 min · r-oldrel-windows-x86_64

Status changes

ERROR12 OK, 1 ERRORNow
ERROR11 OK, 1 NOTE, 1 ERROR2026-09-13
NOTE11 OK, 2 NOTE2026-06-09
ERROR11 OK, 1 NOTE, 1 ERROR2026-06-08
NOTE12 OK, 2 NOTE2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 2.0.3

READMEYes · 278 wordsVignettesYes · 2 · dynamicNEWSYes · 100% structured · mentions 2.0.3Citation fileYes · cites a publicationWebsiteYes

Help pages: 51 (1 internal)includes a package overview page
Examples that run: 93%39 run in a plain check (1 of them under a condition) · 3 never run
Exported functions with examples: 85%
Documented parameters: 78%
Return-value docs: 100%
Help pages citing references: 18%

Vignettes (2)

Build a Mini Reference Library HTML
Open Specy Package Tutorial HTML

How these are measured

Downloads

4.4K

CRAN downloads in the past year

Rank #5,298 · ~12/day · ~370/mo

Releases R versions

Daily download trend is not available in this view yet.

73530 days

1.6K90 days

4.4K1 year

Compare downloads with other packages →

Also on73 r2u5 autocran

How downloads are counted

Repository

wincowgerdev/openspecy-package ↗Account: wincowgerDEV

44Stars

13Forks

23Open issues

3Open PRs

21Releases

1,079Commits

6Commit identities

License file reads as CC-BY-4.0 · 1,079 commits · Last activity 2026-10-21 · 0% stars, 30d · Discussions: 4 posts

Responsiveness

How these are sampled

PRs merged (all time): 91%
Median days to close, 50 most recently updated closed issues: 36
Median days to close, 50 most recently updated closed PRs: 1

Stars over time

2025-10-23 · 312026-09-10 · 44

How these are measured

PracticesBeta

12 development-tooling and community-health practices detected across 5 families in the upstream repository

Checks run against github.com/wincowgerdev/openspecy-package on 2026-10-22.

Continuous integration (2)

GitHub ActionsR CMD check workflow

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

Governance and community (5)

Code of conduct (inherited from wincowgerdev)Contributing guide (inherited from wincowgerdev)PR template (inherited from wincowgerdev)Funding

Funding links: GitHub Sponsors

The repository owner accepts GitHub Sponsors

Docs source (3)

pkgdown

GitHub Pages site last deployed 2026-10-21 · The repository has a site deploy workflow

Coverage (1)

Coverage reporting (Codecov)

Show all practicesHide 1 practice

CRAN release process (1)

cran-comments.md

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

AI coding toolsBeta

This repository shows signs of AI coding tools.

Codexfirst seen 2025-07-10
Pull request it wrote: opened by a project member
Gemini CLIfirst seen 2026-05-21
Config: a file or ignore line, not recorded which
Claude Codefirst seen 2026-08-12
Seen in the repository: .claude, .claude/skills, CLAUDE.md
Named in .Rbuildignore: .claude, CLAUDE.md
Named in .gitignore: .claude, .claude/skills

Shared conventions any agent may read, so they name no particular tool.

Seen in the repository: .agents, .agents/skills, AGENTS.md

How this is detected·Detection ruleset v4 (updated 2026-09-27)

Dependencies

Declared dependencies

34 external dependencies (excludes base and recommended)

Installing OpenSpecy adds 102 packages (58 with compiled code, 84 MB of source tarballs). Heaviest: stringi 11 MB, ggplot2 6.0 MB, data.table 5.7 MB.

Depends (1)

R >= 4.3.0

Imports (16)

methodsdata.table jsonlite caTools hyperSpec mmand plotly digest zip glmnetclusterjpeg png shiny hdf5r matrixStats

LinkingTo (0)

none

Suggests (20)

knitr rmarkdown testthat doFuture doRNG foreach future ranger sgolay curl shinyjs shinyWidgets shinyFiles bs4Dash dplyr DT reshape2 ggplot2 htmltools scales

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

How these are counted

Code & Tests

Datasets

People & History

People (32)

Win Cowger

Maintainer since 0.8.2 (2021), Author, Data contributor

Andrea Faltynkova

Author, Data contributor · added in 1.0.2

Nick Leong

Author · added in 1.0.2

Hannah Sherrod

Author · added in 1.0.7

Zacharias Steinmetz

Author

Hazel Vaquero

Author · added in 1.4.0

Philipp Baumann

Contributor · added in 1.0.4

Nicolas Coca Lopez

Contributor · added in 2.0.1

Garth Covernton

Contributor, Data contributor · added in 2.0.1

Hannah De Frond

Contributor, Data contributor

Andrew B Gray

Contributor · added in 1.0.2

Hannah Hapich

Contributor

Adam Hauser

Contributor · added in 2.0.1

Orestis Herodotou

Contributor

Show 16 more contributorsHide 16 contributors

Aleksandra Karapetrova

Contributor, Data contributor, Reviewer · added in 1.0.2

Christine M Knauss

Contributor · added in 1.0.2

Rachel Kozloski

Contributor, Data contributor · added in 1.0.3

Katherine Lasdin

Contributor · added in 1.0.2

Jennifer Lynch

Contributor, Data contributor

Laura A. T. Markley

Contributor · added in 1.0.2

Keenan Munno

Contributor, Data contributor

Clare Murphy-Hagan

Contributor · added in 1.0.4

Mary C Norris

Contributor · added in 1.0.2

Shreyas Patankar

Contributor, Data contributor · added in 1.0.2

Sebastian Primpke

Contributor, Data contributor

Chelsea Rochman

Contributor, Data contributor

Pierre Roudier

Contributor · added in 1.0.4

Samiksha Singh

Contributor · added in 1.0.3

Vesna Teofilovic

Contributor · added in 1.0.2

Cristiane Vidal

Contributor · added in 1.0.4

National Renewable Energy Laboratory

Funder · added in 1.0.2

Possibility Lab

Funder · added in 1.0.2

Listed in earlier versions (1)

Andrew Gray

no longer listed · 0.8.2 to 0.9.5

Releases (19)

Pick two releases to compare their code metrics.

2.0.3Latest
record
2026-10-07 · current release · diff ↗ ·
listed once in CRAN's queue
Seen in one reading of CRAN's incoming queue, at 2026-10-07 06:45 UTC, so it stayed less than the time between readings.
unarchivedReturned to CRAN
2026-10-06
2.0.1
record
2026-10-05 · diff ↗ ·
added 52 exports
Specs, add_visual_image, area_under_band, as_Specs, assess_lib, assess_spec, automate_particle_analysis, batch_detection_limit, build_lib, build_model_lib, calculate_emissivity, check_Specs, correct_spike, crowd_lookup, decode_specs_hilbert, decompress_spec, dedupe_spec, detect_image_origin, encode_specs_hilbert, estimate_temperature, fit_specs_pca, is_Specs, join_lib_metadata, join_material_hierarchy, lib_clean_metadata, lib_clean_name, lib_metadata_name_lookup, make_lib_lookup_template, material_percentage_uncertainty, minimum_detectable_amount and 22 more
archivedRemoved from CRAN
2026-10-04
issues were not corrected in time
R
R 4.6.0 released · 2026-04-24
1.5.3
record
2025-04-26 · diff ↗
R
R 4.5.0 released · 2025-04-11
1.4.0
record
2024-11-04 · diff ↗ ·
added 1 export
spatial_smooth
1.2.0
record
2024-09-14 · diff ↗ ·
removed 1 export
share_spec
1.1.0
record
2024-06-14 · diff ↗ ·
added 2 exports
adj_wave, merge_map
R
R 4.4.0 released · 2024-04-24
1.0.8
record
2024-03-15 · diff ↗ ·
added 1 export
read_many
1.0.7
record
2024-03-12 · diff ↗ ·
added 5 exports
calc_window_points, fill_spec, manage_na, os_similarity, split_spec
1.0.6
record
2023-11-26 · diff ↗
1.0.5
record
2023-10-31 · diff ↗
1.0.4
record
2023-10-02 · diff ↗

Show 12 earlier eventsHide 12 earlier events

1.0.3
record
2023-09-14 · diff ↗
1.0.2
record
2023-09-05 · diff ↗ ·
removed 3 exports
find_spec, read_0, subtr_bg

added 37 exports
OpenSpecy, adj_res, ai_classify, as_OpenSpecy, as_hyperSpec, c_spec, check_OpenSpecy, collapse_spec, conform_res, conform_spec, cor_spec, def_features, filter_spec, flatten_range, gen_grid, get_metadata, heatmap_spec, ident_spec, interactive_plot, is_OpenSpecy, is_empty_vector, max_cor_named, mean_replace, plotly_spec, process_spec, read_any, read_envi, read_opus, read_opus_raw, read_spec and 7 more
R
R 4.3.0 released · 2023-04-21
0.9.5
record
2022-07-06 · diff ↗
R
R 4.2.0 released · 2022-04-22
0.9.3
record
2021-10-13 · diff ↗
0.9.2
record
2021-05-20 · diff ↗
R
R 4.1.0 released · 2021-05-18
0.9.1
record
2021-04-11 · diff ↗
0.9.0
record
2021-04-09 · diff ↗
0.8.2
record
2021-03-31
R
R 4.0.0 released · 2020-04-24

Across CRAN, the median accepted release of the past year spent 26 hours in the queue, 90% under 11 days.How queue time is measured

Package metadata

First published: 2021-03-31
Total releases: 19 / 5 yrs
License: CC BY 4.0
Minimum R: ≥ 4.3.0
Bundled data: 249 KB / 2 files
Download size: 1.9 MB

Cite

Cite this package

Run in R for the authors' entry:

citation("OpenSpecy")

The package provides a citation file, so citation() returns the authors' own entry.

It points to 10.1021/acs.analchem.5c00962.

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 OpenSpecy version 2.0.3 [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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