NCutYX

Clustering of Omics Data of Multiple Types with a Multilayer Network Representation

v0.1.0 · Feb 9, 2018 · GPL-3

Description

Omics data come in different forms: gene expression, methylation, copy number, protein measurements and more. 'NCutYX' allows clustering of variables, of samples, and both variables and samples (biclustering), while incorporating the dependencies across multiple types of Omics data. (SJ Teran Hidalgo et al (2017), <doi:10.1186/s12864-017-3990-1>).

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CRAN Check Status

4 NOTE

9 OK

Show all 13 flavors

Flavor	Status	Time
r-devel-linux-x86_64-debian-clang	NOTE	92.4s
r-devel-linux-x86_64-debian-gcc	NOTE	67.4s
r-devel-linux-x86_64-fedora-clang	NOTE	136.8s
r-devel-linux-x86_64-fedora-gcc	NOTE	186.2s
r-devel-windows-x86_64	OK	127s
r-oldrel-macos-arm64	OK
r-oldrel-macos-x86_64	OK	89s
r-oldrel-windows-x86_64	OK	173s
r-patched-linux-x86_64	OK	85.6s
r-release-linux-x86_64	OK	85.5s
r-release-macos-arm64	OK	26s
r-release-macos-x86_64	OK	87s
r-release-windows-x86_64	OK	145s

Check details (4 non-OK)

NOTE r-devel-linux-x86_64-debian-clang

CRAN incoming feasibility

Maintainer: ‘Sebastian J. Teran Hidalgo <sebastianteranhidalgo@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = c("Sebastian", "J.", "Teran"),
                      family = "Hidalgo",
                      role = c("aut", "cre"),
                      email = "sebastianteranhidalgo@gmail.com"),
               person(given = "Shuangge",
                      family = "Ma",
                      role = "aut"),
               person(given = "Ruofan",
                      family = "Bie",
                      role = "aut"))
as necessary.

Found the following (possibly) invalid file URIs:
  URI: sebastianteranhidalgo@gmail.com
    From: man/ancut.Rd
  URI: sebastianteranhidalgo@gmail.com
    From: man/awncut.Rd
  URI: sebastianteranhidalgo@gmail.com
    From: man/ncut.Rd
  URI: commits/master
    From: README.md
  URI: /commits/master
    From: README.md

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

CRAN incoming feasibility

Maintainer: ‘Sebastian J. Teran Hidalgo <sebastianteranhidalgo@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = c("Sebastian", "J.", "Teran"),
                      family = "Hidalgo",
                      role = c("aut", "cre"),
                      email = "sebastianteranhidalgo@gmail.com"),
               person(given = "Shuangge",
                      family = "Ma",
                      role = "aut"),
               person(given = "Ruofan",
                      family = "Bie",
                      role = "aut"))
as necessary.

Found the following (possibly) invalid file URIs:
  URI: sebastianteranhidalgo@gmail.com
    From: man/ancut.Rd
  URI: sebastianteranhidalgo@gmail.com
    From: man/awncut.Rd
  URI: sebastianteranhidalgo@gmail.com
    From: man/ncut.Rd
  URI: commits/master
    From: README.md
  URI: /commits/master
    From: README.md

NOTE r-devel-linux-x86_64-fedora-clang

dependencies in R code

Namespaces in Imports field not imported from:
  ‘MASS’ ‘fields’ ‘mvtnorm’
  All declared Imports should be used.

NOTE r-devel-linux-x86_64-fedora-gcc

dependencies in R code

Namespaces in Imports field not imported from:
  ‘MASS’ ‘fields’ ‘mvtnorm’
  All declared Imports should be used.

Check History

NOTE 8 OK · 6 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE Apr 22, 2026

NOTE r-devel-linux-x86_64-debian-clang

CRAN incoming feasibility

Maintainer: ‘Sebastian J. Teran Hidalgo <sebastianteranhidalgo@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = c("Sebastian", "J.", "Teran"),
                      family = "Hidalgo",
          
...[truncated]...
nhidalgo@gmail.com
    From: man/ancut.Rd
  URI: sebastianteranhidalgo@gmail.com
    From: man/awncut.Rd
  URI: sebastianteranhidalgo@gmail.com
    From: man/ncut.Rd
  URI: commits/master
    From: README.md
  URI: /commits/master
    From: README.md

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

CRAN incoming feasibility

Maintainer: ‘Sebastian J. Teran Hidalgo <sebastianteranhidalgo@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = c("Sebastian", "J.", "Teran"),
                      family = "Hidalgo",
          
...[truncated]...
nhidalgo@gmail.com
    From: man/ancut.Rd
  URI: sebastianteranhidalgo@gmail.com
    From: man/awncut.Rd
  URI: sebastianteranhidalgo@gmail.com
    From: man/ncut.Rd
  URI: commits/master
    From: README.md
  URI: /commits/master
    From: README.md

NOTE r-devel-linux-x86_64-fedora-clang

dependencies in R code

Namespaces in Imports field not imported from:
  ‘MASS’ ‘fields’ ‘mvtnorm’
  All declared Imports should be used.

NOTE r-devel-linux-x86_64-fedora-gcc

dependencies in R code

Namespaces in Imports field not imported from:
  ‘MASS’ ‘fields’ ‘mvtnorm’
  All declared Imports should be used.

NOTE r-oldrel-macos-arm64

installed package size

installed size is  6.8Mb
  sub-directories of 1Mb or more:
    data   1.5Mb
    libs   4.4Mb

NOTE r-oldrel-macos-x86_64

installed package size

installed size is  6.7Mb
  sub-directories of 1Mb or more:
    data   1.5Mb
    libs   4.4Mb

ERROR 7 OK · 6 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE Apr 18, 2026

NOTE r-devel-linux-x86_64-debian-clang

CRAN incoming feasibility

Maintainer: ‘Sebastian J. Teran Hidalgo <sebastianteranhidalgo@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = c("Sebastian", "J.", "Teran"),
                      family = "Hidalgo",
          
...[truncated]...
nhidalgo@gmail.com
    From: man/ancut.Rd
  URI: sebastianteranhidalgo@gmail.com
    From: man/awncut.Rd
  URI: sebastianteranhidalgo@gmail.com
    From: man/ncut.Rd
  URI: commits/master
    From: README.md
  URI: /commits/master
    From: README.md

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

CRAN incoming feasibility

Maintainer: ‘Sebastian J. Teran Hidalgo <sebastianteranhidalgo@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = c("Sebastian", "J.", "Teran"),
                      family = "Hidalgo",
          
...[truncated]...
nhidalgo@gmail.com
    From: man/ancut.Rd
  URI: sebastianteranhidalgo@gmail.com
    From: man/awncut.Rd
  URI: sebastianteranhidalgo@gmail.com
    From: man/ncut.Rd
  URI: commits/master
    From: README.md
  URI: /commits/master
    From: README.md

NOTE r-devel-linux-x86_64-fedora-clang

dependencies in R code

Namespaces in Imports field not imported from:
  ‘MASS’ ‘fields’ ‘mvtnorm’
  All declared Imports should be used.

NOTE r-devel-linux-x86_64-fedora-gcc

dependencies in R code

Namespaces in Imports field not imported from:
  ‘MASS’ ‘fields’ ‘mvtnorm’
  All declared Imports should be used.

ERROR r-devel-windows-x86_64

whether package can be installed

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

NOTE r-oldrel-macos-arm64

installed package size

installed size is  6.8Mb
  sub-directories of 1Mb or more:
    data   1.5Mb
    libs   4.4Mb

NOTE r-oldrel-macos-x86_64

installed package size

installed size is  6.7Mb
  sub-directories of 1Mb or more:
    data   1.5Mb
    libs   4.4Mb

NOTE 8 OK · 6 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE Mar 10, 2026

NOTE r-devel-linux-x86_64-debian-clang

CRAN incoming feasibility

Maintainer: ‘Sebastian J. Teran Hidalgo <sebastianteranhidalgo@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = c("Sebastian", "J.", "Teran"),
                      family = "Hidalgo",
          
...[truncated]...
nhidalgo@gmail.com
    From: man/ancut.Rd
  URI: sebastianteranhidalgo@gmail.com
    From: man/awncut.Rd
  URI: sebastianteranhidalgo@gmail.com
    From: man/ncut.Rd
  URI: commits/master
    From: README.md
  URI: /commits/master
    From: README.md

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

CRAN incoming feasibility

Maintainer: ‘Sebastian J. Teran Hidalgo <sebastianteranhidalgo@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = c("Sebastian", "J.", "Teran"),
                      family = "Hidalgo",
          
...[truncated]...
nhidalgo@gmail.com
    From: man/ancut.Rd
  URI: sebastianteranhidalgo@gmail.com
    From: man/awncut.Rd
  URI: sebastianteranhidalgo@gmail.com
    From: man/ncut.Rd
  URI: commits/master
    From: README.md
  URI: /commits/master
    From: README.md

NOTE r-devel-linux-x86_64-fedora-clang

dependencies in R code

Namespaces in Imports field not imported from:
  ‘MASS’ ‘fields’ ‘mvtnorm’
  All declared Imports should be used.

NOTE r-devel-linux-x86_64-fedora-gcc

dependencies in R code

Namespaces in Imports field not imported from:
  ‘MASS’ ‘fields’ ‘mvtnorm’
  All declared Imports should be used.

NOTE r-oldrel-macos-arm64

installed package size

installed size is  6.8Mb
  sub-directories of 1Mb or more:
    data   1.5Mb
    libs   4.4Mb

NOTE r-oldrel-macos-x86_64

installed package size

installed size is  6.7Mb
  sub-directories of 1Mb or more:
    data   1.5Mb
    libs   4.4Mb

Code & tests

Open call graph →

Code intelligence has not been computed for this package yet.

Code

Structure

Lines of code

3,856

Files

Compiled share

12.4%

Has compiled src

Yes

Language breakdown

R 1,820 (47.2%)C/C++/src 477 (12.4%)Docs 951 (24.7%)Vignettes 608 (15.8%)

API

Exported functions

Internal functions

Recent export changes

v0.1.0+8 ancut, mlbncut, muncut +5 more

Testing & CI

Has tests

Test-to-code ratio

0.00

testthat edition

–

CI present

CI type

[]

PR gated

Docs

Return-value doc rate

62.5%

\dontrun example ratio

Roxygen coverage

100%

Has pkgdown

NEWS present

Health & Security signals

Informational signals; not verdicts.

on.exit coverage

–

Unsafe pattern score

Dep constraint coverage

100%

Secret pattern count

Bundled 3rd-party code

2 items

Portability & License

Min R version

3.4

System requirements

–

C++ standard

–

License

GPL-3

License flags

SPDX valid, OSI approved

History

Versions

First release

2018-02-09

Latest release

2018-02-09

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 0.1.0 Mar 10, 2026

R Observatory began tracking this package on Mar 10, 2026; it first appeared on CRAN Feb 9, 2018. Releases before tracking aren’t shown.

People

Sebastian J. Teran Hidalgo

Available on

CRAN r2u Bioconductor autoCRAN COPR

Dependencies

Depends

R (>= 3.4)

Imports

Rcpp (>= 0.12.2)glmnet (>= 2.0-5)MASS (>= 7.3-47)mvtnorm (>= 1.0-6)fields (>= 9.0)

Suggests

knitr rmarkdown

Compilation

Needs compilation

First Published

Feb 9, 2018

First appeared in R 3.4.3 · current R 4.6.1

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