Older releaseCurrent release Bioconductor 3.23
DMRcaller
‹Bioconductor 3.21
- Bioconductor 3.2329 Apr 2026, current
- Bioconductor 3.2230 Oct 2025
- Bioconductor 3.2116 Apr 2025
- Bioconductor 3.2030 Oct 2024
- Bioconductor 3.191 May 2024
- Bioconductor 3.1825 Oct 2023
- Bioconductor 3.1726 Apr 2023
- Bioconductor 3.162 Nov 2022
- Bioconductor 3.1527 Apr 2022
- Bioconductor 3.1427 Oct 2021
- Bioconductor 3.1320 May 2021
- Bioconductor 3.1228 Oct 2020
- Bioconductor 3.1128 Apr 2020
- Bioconductor 3.1030 Oct 2019
- Bioconductor 3.93 May 2019
- Bioconductor 3.831 Oct 2018
- Bioconductor 3.71 May 2018
- Bioconductor 3.631 Oct 2017
- Bioconductor 3.525 Apr 2017
- Bioconductor 3.418 Oct 2016
- Bioconductor 3.34 May 2016
- Bioconductor 3.214 Oct 2015
- Bioconductor 3.117 Apr 2015
- Released
- 16 Apr 2025with R 4.5
- Advisories, method
Method
Security advisories
Advisories come from the R Consortium advisory database, a community record of security problems in R packages, as OSV publishes it.
- The copy
- The record is read once a day. The data is published under the Apache License 2.0 and is credited on the advisories list.
- Box under the name
- Under the package's name, a box names any advisory that affects the current release, with its fix or that there is none.
- Ranges
- Advisories state ranges, such as from 0.9.12 up to but not including 1.8.8. Each range is checked against every version CRAN has published, using the version rules R itself uses, so a release that came out after the advisory was written is still caught by its range.
- Not the package
- The rating is for the library flaw itself, not for how exposed the R package is, and it is never added up into a figure for the package.
- None publishedfor Bioconductor
- Test coverage, method
Method
Test coverage
Test coverage is measured by downloading each CRAN package's current source file, installing its dependencies, building it and running its tests under covr.
- Almost half of CRAN has no tests to run
- Only CRAN packages are measured. Many have no percentage, most often because the package has no tests, and that blank is a recorded outcome, not missing data.
- NOT_CRAN
- Tests run with NOT_CRAN=true, so tests that skip themselves on CRAN run here, and the figure can differ from what CRAN's own checks see.
- Current version only
- Only the current version is measured, and a new version on CRAN is measured again. Older rows are kept but never filled in later. This is one package's run.
- Never 0%
- On a package page three states stay apart: measured, no tests, and not measured. Neither of the last two is ever shown as 0%.
- –not measured for Bioconductor
- Public exports, method
Method
Code metrics
Code metrics come from reading the released source of each package version. The package is never installed, loaded or run.
- One row a version
- Each analysed version gives one row of figures. The Code, Tests and Documentation sections, the pages of older releases and Release changes all read from those rows.
- CRAN
- CRAN versions are read from the github.com/cran mirror, which holds one commit for each released source file, and every version tag is analysed. Nothing is built, installed or run.
- Release, not repository
- Documentation describes what the analysed release holds: a
README, vignettes, aNEWSfile and the shares read from its help pages. Files kept only in the repository, such as a pkgdown configuration or CI files, are read by the repository scan instead. - Zero
- Zero means the analysis looked and found none.
- 22none added or removed
Record made 28 Oct 2026, 23:24 UTC from data release v2026-10-28, merged 18:49 UTC. Project DOI 10.5281/zenodo.21843040.
https:/
This page reports what R Observatory measured for this release. It is not a validation, and it does not say whether the package is fit for your intended use.
Compare
Compared with Bioconductor 3.23, released 29 Apr 2026.
- Time between
- 378 days1 release in between
- Advisories
- None publishedfor Bioconductor
- Exports
- 11 addednone removed
- Files changed
- 86+11,171 −1,432 lines
Values that differ (12)
| Measure | Section | Bioconductor 3.21 | Bioconductor 3.23 |
|---|---|---|---|
| Package version | Release | 1.40.0 | 1.44.0 |
| R version | Release | 4.5 | 4.6 |
| Authors | Release | Nicolae Radu Zabet, Jonathan Tsang, Alessandro Greco, Ryan Merritt | Nicolae Radu Zabet, Jonathan Tsang, Alessandro Greco, Ryan Merritt, Young Jun Kim |
| Public exports | Code | 22 | 33 |
| Internal functions | Code | 67 | 102 |
| Lines of R code | Code | 5,921 | 11,205 |
| Complexity | Code | mean 4.1, highest 26 | mean 5.4, highest 110 |
| Tests | Tests | Yes, RUnit, 8 test functions | Yes, RUnit, 9 test functions |
| Help pages with running examples | Tests | 19 of 24 | 27 of 35 |
| Help pages | Documentation | 28 | 46 |
| Arguments documented | Documentation | 98% | 98.9% |
| Direct dependencies | Dependencies | 12 | 23 |
Exports added (11)
analyseReadsInsideRegionsForConditionPMDcomputeCoMethylatedPositionscomputeCoMethylatedRegionscomputePMDscomputeVMDsfilterPMDsfilterVMDsfilterVMRsONTmergePMDsIterativelyreadONTbamselectCytosine
Most changed files (12 of 86)
| File | Lines added | Lines deleted |
|---|---|---|
vignettes/apa.csl | 2,133 | 0 |
R/computePMDs.R | 1,139 | 0 |
vignettes/DMRcaller.Rmd | 943 | 0 |
R/ONTdata.R | 914 | 0 |
R/computeVMDs.R | 761 | 0 |
R/filterVMRsONT.R | 618 | 12 |
vignettes/DMRcaller.Rnw | 0 | 533 |
inst/unitTests/test_DMRcaller.R | 273 | 232 |
R/DMRcaller.R | 386 | 18 |
R/computeCoMethylatedPostions.R | 397 | 0 |
R/regions.R | 311 | 38 |
R/computeCoMethylatedRegions.R | 322 | 0 |
Release
- Package version
- 1.40.0
- Bioconductor release
- 16 Apr 2025
- R version
- 4.5
- Status
- Replaced by 3.22 on 30 Oct 2025
- Previous
- 3.20, 30 Oct 2024
- First Bioconductor release
- 3.1, 17 Apr 2015
- Last Bioconductor release
- 3.23, 29 Apr 2026
- License
- GPL-3, OSI approved
- Maintainer
- Nicolae Radu Zabet
- Authors
- Nicolae Radu Zabet, Jonathan Tsang, Alessandro Greco, Ryan Merritt
- Source code
- Not kept for this release
Advisories
- This release
- None published for Bioconductor
Checks
Method, Checks Method CRAN runs every current package through Checks and health
R CMD check on a set of machines and publishes a result for each one. The health shown on a package page comes from these results alone.
- Results
- Not collected for Bioconductor
Code
- Lines of R code
- 5,921
- Public exports
- 22
- Internal functions
- 67
- Mean complexity
- 4.1the most is 26
Lines by kind (8,492)
| Kind | Lines | Share |
|---|---|---|
| R code | 5,921 | 70% |
| Tests | 1 | 0.0% |
| Documentation | 1,979 | 23% |
| Guides | 591 | 7% |
Tests
- Test cases
- 8
- Lines of tests
- 1
- Exports named in tests
- 0%
- Tests
- Yes, RUnit, 8 test functions
- Test lines per line of code
- 0.00
- Coverage
- Not measured for Bioconductor packages
- Help pages with running examples
- 19 of 24
Documentation
- Exports documented
- 100%
- Arguments documented
- 98%
- Return value documented
- 100%
- Vignettes
- 1
- Help pages
- 28
- Exports with examples
- 100%
- NEWS
- Yes
- Citation file
- Yes, cites a publication
- Website
- Not kept for this release
Dependencies
Method, Dependencies Method Dependent packages are other packages that list this one under Reverse dependencies
Depends, Imports or LinkingTo in their DESCRIPTION file. Those fields list the packages a package needs to install, so dependents break if this one is archived or broken.Suggests install and run without it, and use it for tests, examples or an optional feature. They are counted as Suggested by, never among the dependents, and a package that also lists it under one of the three fields is a dependent and is not counted again.
- Direct dependencies
- 12
- Install tree
- Not collected for Bioconductor
Today
Checks, downloads, dependents, people and the repository describe the package as it is now, so they are on the current release.
Sources
| Part | From | As of |
|---|---|---|
| Release dates | Bioconductor release dates | 28 Oct 2026 |
| Advisories | osv-advisories 1.0.0, R version 4.6.1 (2026-06-24) | 28 Oct 2026 |
| Checks | Not collected for Bioconductor | |
| Tests, documentation, code | Bioconductor metrics, rpkg-analyzer 0.5.0 | 28 Sep 2026 |
| Coverage | Not measured for Bioconductor packages | |
| Use | Bioconductor downloads, reverse dependencies, repository | Not shown for this release |
Daily data releases are kept on GitHub, so the data behind this record can be fetched again from v2026-10-28 (merged 18:49 UTC). Values not kept for a release say so and are never filled in from another release.