kmeRtone

Multi-Purpose and Flexible k-Meric Enrichment Analysis Software

v1.0 · Aug 30, 2024 · GPL-3

Description

A multi-purpose and flexible k-meric enrichment analysis software. 'kmeRtone' measures the enrichment of k-mers by comparing the population of k-mers in the case loci with a carefully devised internal negative control group, consisting of k-mers from regions close to, yet sufficiently distant from, the case loci to mitigate any potential sequencing bias. This method effectively captures both the local sequencing variations and broader sequence influences, while also correcting for potential biases, thereby ensuring more accurate analysis. The core functionality of 'kmeRtone' is the SCORE() function, which calculates the susceptibility scores for k-mers in case and control regions. Case regions are defined by the genomic coordinates provided in a file by the user and the control regions can be constructed relative to the case regions or provided directly. The k-meric susceptibility scores are calculated by using a one-proportion z-statistic. 'kmeRtone' is highly flexible by allowing users to also specify their target k-mer patterns and quantify the corresponding k-mer enrichment scores in the context of these patterns, allowing for a more comprehensive approach to understanding the functional implications of specific DNA sequences on a genomic scale (e.g., CT motifs upon UV radiation damage). Adib A. Abdullah, Patrick Pflughaupt, Claudia Feng, Aleksandr B. Sahakyan (2024) Bioinformatics (submitted).

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Flavor	Status	Time
r-devel-linux-x86_64-debian-clang	OK	289.6s
r-devel-linux-x86_64-debian-gcc	OK	204.7s
r-devel-linux-x86_64-fedora-clang	OK	479.3s
r-devel-linux-x86_64-fedora-gcc	OK	435.4s
r-devel-windows-x86_64	OK	399s
r-oldrel-macos-arm64	OK
r-oldrel-macos-x86_64	OK	226s
r-oldrel-windows-x86_64	OK	408s
r-patched-linux-x86_64	OK	263.7s
r-release-linux-x86_64	OK	262.7s
r-release-macos-arm64	OK	76s
r-release-macos-x86_64	OK	220s
r-release-windows-x86_64	OK	326s

Additional Issues

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Check History

OK 13 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE Jul 3, 2026

ERROR 10 OK · 0 NOTE · 0 WARNING · 3 ERROR · 0 FAILURE Jun 25, 2026

ERROR r-devel-linux-x86_64-debian-gcc

tests

Running ‘testthat.R’ [6s/67s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > # This file is part of the standard setup for testthat.
  > # It is recommended that you do not modify it.
  > #
  > # Where should you do additional t
...[truncated]...
    └─base (local) tryCatchOne(...)
    9.                 └─value[[3L]](cond)
   10.                   └─future.apply:::onError(e, futures = fs, debug = debug)
  
  [ FAIL 1 | WARN 2 | SKIP 0 | PASS 0 ]
  Error:
  ! Test failures.
  Execution halted

ERROR r-devel-windows-x86_64

tests

Running 'testthat.R' [260s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > # This file is part of the standard setup for testthat.
  > # It is recommended that you do not modify it.
  > #
  > # Where should you do additional tes
...[truncated]...
    └─base (local) tryCatchOne(...)
    9.                 └─value[[3L]](cond)
   10.                   └─future.apply:::onError(e, futures = fs, debug = debug)
  
  [ FAIL 1 | WARN 1 | SKIP 0 | PASS 0 ]
  Error:
  ! Test failures.
  Execution halted

ERROR r-patched-linux-x86_64

tests

Running ‘testthat.R’ [8s/70s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > # This file is part of the standard setup for testthat.
  > # It is recommended that you do not modify it.
  > #
  > # Where should you do additional t
...[truncated]...
    └─base (local) tryCatchOne(...)
    9.                 └─value[[3L]](cond)
   10.                   └─future.apply:::onError(e, futures = fs, debug = debug)
  
  [ FAIL 1 | WARN 2 | SKIP 0 | PASS 0 ]
  Error:
  ! Test failures.
  Execution halted

OK 13 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE Jun 24, 2026

ERROR 12 OK · 0 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE Jun 19, 2026

ERROR r-devel-linux-x86_64-debian-gcc

tests

Running ‘testthat.R’ [6s/10s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > # This file is part of the standard setup for testthat.
  > # It is recommended that you do not modify it.
  > #
  > # Where should you do additional t
...[truncated]...
    └─base (local) tryCatchOne(...)
    9.                 └─value[[3L]](cond)
   10.                   └─future.apply:::onError(e, futures = fs, debug = debug)
  
  [ FAIL 1 | WARN 2 | SKIP 0 | PASS 0 ]
  Error:
  ! Test failures.
  Execution halted

OK 13 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE Jun 9, 2026

NOTE 12 OK · 1 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE Jun 8, 2026

NOTE r-devel-linux-x86_64-debian-gcc

CRAN incoming feasibility

Maintainer: ‘Aleksandr Sahakyan <sahakyanlab@cantab.net>’

Reading Rd files failed with message:
  cannot open the connection

OK 12 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE Apr 25, 2026

NOTE 11 OK · 3 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE Apr 22, 2026

NOTE r-oldrel-macos-arm64

installed package size

installed size is  5.4Mb
  sub-directories of 1Mb or more:
    libs   3.8Mb

NOTE r-oldrel-macos-x86_64

installed package size

installed size is  5.4Mb
  sub-directories of 1Mb or more:
    libs   3.9Mb

NOTE r-oldrel-windows-x86_64

for GNU extensions in Makefiles

GNU make is a SystemRequirements.

ERROR 10 OK · 3 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE Apr 18, 2026

ERROR r-devel-windows-x86_64

whether package can be installed

Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.6/kmeRtone.Rcheck/00install.out' for details.

NOTE r-oldrel-macos-arm64

installed package size

installed size is  5.4Mb
  sub-directories of 1Mb or more:
    libs   3.8Mb

NOTE r-oldrel-macos-x86_64

installed package size

installed size is  5.4Mb
  sub-directories of 1Mb or more:
    libs   3.9Mb

NOTE r-oldrel-windows-x86_64

for GNU extensions in Makefiles

GNU make is a SystemRequirements.

NOTE 11 OK · 3 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE Apr 6, 2026

NOTE r-oldrel-macos-arm64

installed package size

installed size is  5.4Mb
  sub-directories of 1Mb or more:
    libs   3.8Mb

NOTE r-oldrel-macos-x86_64

installed package size

installed size is  5.4Mb
  sub-directories of 1Mb or more:
    libs   3.9Mb

NOTE r-oldrel-windows-x86_64

for GNU extensions in Makefiles

GNU make is a SystemRequirements.

ERROR 10 OK · 3 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE Apr 3, 2026

ERROR r-devel-linux-x86_64-debian-gcc

package dependencies

Package required but not available: ‘venneuler’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.

NOTE r-oldrel-macos-arm64

installed package size

installed size is  5.4Mb
  sub-directories of 1Mb or more:
    libs   3.8Mb

NOTE r-oldrel-macos-x86_64

installed package size

installed size is  5.4Mb
  sub-directories of 1Mb or more:
    libs   3.9Mb

NOTE r-oldrel-windows-x86_64

for GNU extensions in Makefiles

GNU make is a SystemRequirements.

NOTE 11 OK · 3 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE Mar 10, 2026

NOTE r-oldrel-macos-arm64

installed package size

installed size is  5.4Mb
  sub-directories of 1Mb or more:
    libs   3.8Mb

NOTE r-oldrel-macos-x86_64

installed package size

installed size is  5.4Mb
  sub-directories of 1Mb or more:
    libs   3.9Mb

NOTE r-oldrel-windows-x86_64

for GNU extensions in Makefiles

GNU make is a SystemRequirements.

Code & tests

Open call graph →

Code intelligence has not been computed for this package yet.

Code

Structure

Lines of code

12,169

Files

184

Compiled share

Has compiled src

Yes

Language breakdown

R 7,819 (64.3%)C/C++/src 1,095 (9%)Tests 68 (0.6%)Docs 3,187 (26.2%)

API

Exported functions

Internal functions

Recent export changes

v1.0+72 Coordinate, EXPLORE, Kmer_Table +69 more

Testing & CI

Has tests

Yes

Test-to-code ratio

0.01

testthat edition

CI present

CI type

[]

PR gated

Docs

Return-value doc rate

90.3%

\dontrun example ratio

100%

Roxygen coverage

100%

Has pkgdown

NEWS present

Health & Security signals

Informational signals; not verdicts.

on.exit coverage

60%

Unsafe pattern score

Dep constraint coverage

50%

Secret pattern count

Bundled 3rd-party code

2 items

Portability & License

Min R version

4.2

System requirements

C++ standard

–

License

GPL-3

License flags

SPDX valid, OSI approved

History

Versions

First release

2024-08-30

Latest release

2024-08-30

Avg cadence

–

Cold removal rate

–

Dep drift

Per-file churn detail lives in the source pipeline: https://github.com/r-observatory/cran-code-metrics.

Dependency Network

Version History

1 tracked

new 1.0 Mar 10, 2026

R Observatory began tracking this package on Mar 10, 2026; it first appeared on CRAN Aug 30, 2024. Releases before tracking aren’t shown.