HiCociety

Inferring Chromatin Interaction Modules from 3C-Based Data

v0.1.39 · Feb 16, 2026 · GPL-3

Description

Identifies chromatin interaction modules by constructing a Hi-C contact network based on statistically significant interactions, followed by network clustering. The method enables comparison of module connectivity across two Hi-C datasets and is capable of detecting cell-type-specific regulatory modules. By integrating network analysis with chromatin conformation data, this approach provides insights into the spatial organization of the genome and its functional implications in gene regulation. Author: Sora Yoon (2025) <https://github.com/ysora/HiCociety>.

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CRAN Check Status

5 ERROR

1 NOTE

8 OK

Show all 14 flavors

Flavor	Status	Time
r-devel-linux-x86_64-debian-clang	ERROR	3.1s
r-devel-linux-x86_64-debian-gcc	OK	292.9s
r-devel-linux-x86_64-fedora-clang	OK	640.5s
r-devel-linux-x86_64-fedora-gcc	OK	697.9s
r-devel-macos-arm64	OK	118s
r-devel-windows-x86_64	OK	374s
r-oldrel-macos-arm64	ERROR	104s
r-oldrel-macos-x86_64	ERROR	360s
r-oldrel-windows-x86_64	NOTE	501s
r-patched-linux-x86_64	OK	392.9s
r-release-linux-x86_64	OK	392.8s
r-release-macos-arm64	ERROR	107s
r-release-macos-x86_64	ERROR	341s
r-release-windows-x86_64	OK	366s

Check details (18 non-OK)

ERROR r-devel-linux-x86_64-debian-clang

package dependencies

Packages required but not available: 'AnnotationDbi', 'GenomicFeatures'

Packages suggested but not available for checking:
  'biomaRt', 'TxDb.Hsapiens.UCSC.hg38.knownGene',
  'TxDb.Mmusculus.UCSC.mm10.knownGene', 'org.Mm.eg.db', 'org.Hs.eg.db'

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

OK r-devel-linux-x86_64-debian-gcc

OK r-devel-linux-x86_64-fedora-clang

OK r-devel-linux-x86_64-fedora-gcc

OK r-devel-macos-arm64

OK r-devel-windows-x86_64

ERROR r-oldrel-macos-arm64

examples

Running examples in ‘HiCociety-Ex.R’ failed
The error most likely occurred in:

> ### Name: add_Genes
> ### Title: Add gene information
> ### Aliases: add_Genes
> 
> ### ** Examples
> 
> modulefile = system.file('extdata','mouse_naiveCD4T_Vahedi_short.rds',
+ package = 'HiCocietyExample')
> mycom = readRDS(modulefile)
> mycom$ModuleSummary = add_Genes(mycom$ModuleSummary,
+ 'TxDb.Mmusculus.UCSC.mm10.knownGene')
Error in add_Genes(mycom$ModuleSummary, "TxDb.Mmusculus.UCSC.mm10.knownGene") : 
  Package TxDb.Mmusculus.UCSC.mm10.knownGene not found
Execution halted

NOTE r-oldrel-macos-arm64

installed package size

  installed size is  6.6Mb

NOTE r-oldrel-macos-arm64

package dependencies

Packages suggested but not available for checking:
  'TxDb.Hsapiens.UCSC.hg38.knownGene',
  'TxDb.Mmusculus.UCSC.mm10.knownGene', 'org.Mm.eg.db'

ERROR r-oldrel-macos-x86_64

examples

Running examples in ‘HiCociety-Ex.R’ failed
The error most likely occurred in:

> ### Name: add_Genes
> ### Title: Add gene information
> ### Aliases: add_Genes
> 
> ### ** Examples
> 
> modulefile = system.file('extdata','mouse_naiveCD4T_Vahedi_short.rds',
+ package = 'HiCocietyExample')
> mycom = readRDS(modulefile)
> mycom$ModuleSummary = add_Genes(mycom$ModuleSummary,
+ 'TxDb.Mmusculus.UCSC.mm10.knownGene')
Error in add_Genes(mycom$ModuleSummary, "TxDb.Mmusculus.UCSC.mm10.knownGene") : 
  Package TxDb.Mmusculus.UCSC.mm10.knownGene not found
Execution halted

NOTE r-oldrel-macos-x86_64

installed package size

  installed size is  6.6Mb

NOTE r-oldrel-macos-x86_64

package dependencies

Packages suggested but not available for checking:
  'TxDb.Hsapiens.UCSC.hg38.knownGene',
  'TxDb.Mmusculus.UCSC.mm10.knownGene'

NOTE r-oldrel-windows-x86_64

installed package size

  installed size is  6.8Mb

OK r-patched-linux-x86_64

OK r-release-linux-x86_64

ERROR r-release-macos-arm64

examples

Running examples in ‘HiCociety-Ex.R’ failed
The error most likely occurred in:

> ### Name: add_Genes
> ### Title: Add gene information
> ### Aliases: add_Genes
> 
> ### ** Examples
> 
> modulefile = system.file('extdata','mouse_naiveCD4T_Vahedi_short.rds',
+ package = 'HiCocietyExample')
> mycom = readRDS(modulefile)
> mycom$ModuleSummary = add_Genes(mycom$ModuleSummary,
+ 'TxDb.Mmusculus.UCSC.mm10.knownGene')
Error in add_Genes(mycom$ModuleSummary, "TxDb.Mmusculus.UCSC.mm10.knownGene") : 
  Package TxDb.Mmusculus.UCSC.mm10.knownGene not found
Execution halted

ERROR r-release-macos-x86_64

examples

Running examples in ‘HiCociety-Ex.R’ failed
The error most likely occurred in:

> ### Name: add_Genes
> ### Title: Add gene information
> ### Aliases: add_Genes
> 
> ### ** Examples
> 
> modulefile = system.file('extdata','mouse_naiveCD4T_Vahedi_short.rds',
+ package = 'HiCocietyExample')
> mycom = readRDS(modulefile)
> mycom$ModuleSummary = add_Genes(mycom$ModuleSummary,
+ 'TxDb.Mmusculus.UCSC.mm10.knownGene')
Error in add_Genes(mycom$ModuleSummary, "TxDb.Mmusculus.UCSC.mm10.knownGene") : 
  Package TxDb.Mmusculus.UCSC.mm10.knownGene not found
Execution halted

OK r-release-windows-x86_64

Additional Issues

noSuggests Details →

Check History

ERROR 8 OK · 1 NOTE · 0 WARNING · 5 ERROR · 0 FAILURE Mar 9, 2026

ERROR r-devel-linux-x86_64-debian-clang

package dependencies

Packages required but not available: 'AnnotationDbi', 'GenomicFeatures'

Packages suggested but not available for checking:
  'biomaRt', 'TxDb.Hsapiens.UCSC.hg38.knownGene',
  'TxDb.Mmusculus.UCSC.mm10.knownGene', 'org.Mm.eg.db', 'org.Hs.eg.db'

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

ERROR r-release-macos-arm64

examples

Running examples in ‘HiCociety-Ex.R’ failed
The error most likely occurred in:

> ### Name: add_Genes
> ### Title: Add gene information
> ### Aliases: add_Genes
> 
> ### ** Examples
> 
> modulefile = system.file('extdata','mouse_naiveCD4T_Vahedi_short.rds',
+ package = 'HiCocietyExample')
> mycom = readRDS(modulefile)
> mycom$ModuleSummary = add_Genes(mycom$ModuleSummary,
+ 'TxDb.Mmusculus.UCSC.mm10.knownGene')
Error in add_Genes(mycom$ModuleSummary, "TxDb.Mmusculus.UCSC.mm10.knownGene") : 
  Pa

ERROR r-release-macos-x86_64

examples

Running examples in ‘HiCociety-Ex.R’ failed
The error most likely occurred in:

> ### Name: add_Genes
> ### Title: Add gene information
> ### Aliases: add_Genes
> 
> ### ** Examples
> 
> modulefile = system.file('extdata','mouse_naiveCD4T_Vahedi_short.rds',
+ package = 'HiCocietyExample')
> mycom = readRDS(modulefile)
> mycom$ModuleSummary = add_Genes(mycom$ModuleSummary,
+ 'TxDb.Mmusculus.UCSC.mm10.knownGene')
Error in add_Genes(mycom$ModuleSummary, "TxDb.Mmusculus.UCSC.mm10.knownGene") : 
  Pa

ERROR r-oldrel-macos-arm64

package dependencies

Packages suggested but not available for checking:
  'TxDb.Hsapiens.UCSC.hg38.knownGene',
  'TxDb.Mmusculus.UCSC.mm10.knownGene', 'org.Mm.eg.db'

ERROR r-oldrel-macos-x86_64

package dependencies

Packages suggested but not available for checking:
  'TxDb.Hsapiens.UCSC.hg38.knownGene',
  'TxDb.Mmusculus.UCSC.mm10.knownGene'

NOTE r-oldrel-windows-x86_64

installed package size

  installed size is  6.8Mb

Dependency Network

Version History

new 0.1.39 Mar 9, 2026