R Observatory: Metrics for protr version 1.7-5

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

protr

1.7-5Package record

Generating Various Numerical Representation Schemes for Protein Sequences

0packages depend

8.3Kdownloads / year

–test coverage

13/13flavors OK

Overview

About

Maintained by Nan XiaoCRAN page ↗GitHub ↗Website ↗Issues ↗

Comprehensive toolkit for generating various numerical features of protein sequences described in Xiao et al. (2015) DOI:10.1093/bioinformatics/btv042. For full functionality, the software 'ncbi-blast+' is needed, see https://blast.ncbi.nlm.nih.gov/doc/blast-help/downloadblastdata.html for more information.

Changes in 1.7-5

Maintenance

Remove named comment for non-ORCID/ROR identifiers in DESCRIPTION to avoid R CMD check note reported only in Debian r-devel environments (#60).

From NEWS.md in the release

Install

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

install.packages("protr", 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("nanxstats/protr")

Development version from nanxstats/protr. 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-protr

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-protr

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-protr

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: 2.8 min · r-release-macos-x86_64

Status changes

OK13 OK2026-08-05
NOTE12 OK, 1 NOTE2026-08-01
OK14 OK2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 1.7-5

READMEYes · 472 wordsVignettesYes · 1 · dynamicNEWSYes · 100% structured · mentions 1.7-5Citation fileYes · cites a publicationWebsiteYes · pkgdown

Help pages: 80 (1 internal)includes a package overview page
Examples that run: 89%70 run in a plain check · 8 never run · 1 hold no code
Exported functions with examples: 100%
Documented parameters: 96%
Return-value docs: 100%
Help pages citing references: 34%

Vignettes (1)

protr: R package for generating various numerical representation schemes of protein sequences

How these are measured

Downloads

8.3K

CRAN downloads in the past year

Rank #5,251 · ~23/day · ~692/mo

Releases R versions

Daily download trend is not available in this view yet.

60530 days

1.6K90 days

8.3K1 year

Compare downloads with other packages →

Also on124 r2u8 autocran2K conda_forge65 c2d4u

How downloads are counted

Repository

nanxstats/protr ↗Account: nanxstats

53Stars

13Forks

5Open issues

0Open PRs

18Releases

343Commits

5Commit identities

protein-sequencesfeature-extractionmachine-learningbioinformaticsfeature-engineeringpeptidessequence-analysis

343 commits · Last activity 2025-08-21

Responsiveness

How these are sampled

PRs merged (all time): 96%
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

2025-08-04 · 522026-07-07 · 53

How these are measured

PracticesBeta

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

Checks run against github.com/nanxstats/protr on 2026-10-18.

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 (2)

Code of conductContributing guide

Docs source (3)

pkgdown

GitHub Pages site last deployed 2025-08-25 · The repository has a site deploy workflow

pkgdown site last built 2025-08-25

Lint, format, editor (1)

RStudio project

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

Dependencies

Declared dependencies

7 external dependencies (excludes base and recommended)

Installing protr adds no packages beyond those that come with R.

Depends (1)

R >= 3.0.2

Imports (0)

none

LinkingTo (0)

none

Suggests (7)

knitr rmarkdown Biostrings GOSemSim foreach doParallel org.Hs.eg.db

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 (4)

Nan Xiao

Author, Maintainer · added in 0.2-0

Dong-Sheng Cao

Author · added in 1.4-0

Qing-Song Xu

Author · added in 1.4-0

Sebastian Mueller

Contributor · added in 1.7-0

Alva Genomics

Maintainer since 0.1-0 (2012)

Listed in earlier versions (3)

Show 3 peopleHide 3 people

Dongsheng Cao

no longer listed · 0.1-0 to 1.3-0

Yizeng Liang

no longer listed · 0.1-0 to 2.15.3

Qingsong Xu

no longer listed · 0.1-0 to 1.3-0

Releases (29)

Pick two releases to compare their code metrics.

R
R 4.6.0 released · 2026-04-24
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
R
R 3.6.0 released · 2019-04-26
R
R 3.5.0 released · 2018-04-23
R
R 3.4.0 released · 2017-04-21
R
R 3.3.0 released · 2016-05-03
R
R 3.2.0 released · 2015-04-16
R
R 3.1.0 released · 2014-04-10
3.0.3Latest
record
2014-01-25 · current release · diff ↗
R
R 3.0.0 released · 2013-04-03
2.15.3
record
2012-11-18 · diff ↗

Show 28 earlier eventsHide 28 earlier events

1.7-5
record
2025-08-21 · diff ↗
1.7-4
record
2024-09-12 · diff ↗
1.7-3
record
2024-08-30 · diff ↗
1.7-2
record
2024-07-21 · diff ↗
1.7-1
record
2024-04-20 · diff ↗ ·
added 1 export
crossSetSimDisk
1.7-0
record
2023-10-30 · diff ↗ ·
added 1 export
crossSetSim
1.6-3
record
2023-03-05 · diff ↗
1.6-2
record
2019-05-18 · diff ↗
1.6-1
record
2019-02-24 · diff ↗ ·
added 1 export
parSeqSimDisk
1.6-0
record
2019-02-11 · diff ↗
1.5-2
record
2018-11-22 · diff ↗
1.5-1
record
2018-07-13 · diff ↗ ·
added 1 export
removeGaps
1.5-0
record
2017-11-18 · diff ↗
1.4-2
record
2017-09-29 · diff ↗
1.4-1
record
2017-07-09 · diff ↗
1.4-0
record
2017-06-06 · diff ↗
1.3-0
record
2017-05-08 · diff ↗
1.2-1
record
2016-12-30 · diff ↗
1.2-0
record
2016-11-12 · diff ↗
1.1-1
record
2015-12-29 · diff ↗
1.0-1
record
2015-11-27 · diff ↗
0.5-1
record
2014-12-24 · diff ↗ ·
removed 1 export
extractPropScales

added 7 exports
extractCTDCClass, extractCTDDClass, extractCTDTClass, extractCTriadClass, extractProtFP, extractProtFPGap, extractScalesGap
0.4-1
record
2014-10-10 · diff ↗ ·
removed 1 export
pattern:^[^\\.]

added 3 exports
extractPSSM, extractPSSMAcc, extractPSSMFeature
0.3-1
record
2014-08-24 · diff ↗
0.2-1
record
2014-01-25 · diff ↗
0.2-0
record
2013-12-19 · diff ↗ ·
added 12 exports
acc, extractBLOSUM, extractDescScales, extractFAScales, extractMDSScales, extractPropScales, extractScales, parGOSim, parSeqSim, readPDB, twoGOSim, twoSeqSim
0.1-0
record
2012-11-18
R
R 2.15.0 released · 2012-03-30

Package metadata

First published: 2012-11-18
Total releases: 29 / 14 yrs
License: BSD_3_clause + file LICENSE OSI
Minimum R: ≥ 3.0.2
Bundled data: 228 KB / 35 files
Download size: 1.8 MB

Cite

Cite this package

Run in R for the authors' entry:

citation("protr")

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

It points to 10.1093/bioinformatics/btv042.

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 protr version 1.7-5 [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.

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