* using log directory ‘/srv/hornik/tmp/CRAN_pretest/HiCociety.Rcheck’
* using R Under development (unstable) (2024-09-18 r87177)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    Debian clang version 18.1.8 (9)
    Debian flang-new version 18.1.8 (9)
* running under: Debian GNU/Linux trixie/sid
* using session charset: UTF-8
* checking for file ‘HiCociety/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘HiCociety’ version ‘0.1.1’
* package encoding: UTF-8
* checking CRAN incoming feasibility ... [3s/3s] NOTE
Maintainer: ‘Sora Yoon <sora.yoon@pennmedicine.upenn.edu>’

New submission

Possibly misspelled words in DESCRIPTION:
  HiC (8:25, 9:60)
  HiCociety (3:8)

The Title field starts with the package name.
The Title field should be in title case. Current version is:
  ‘HiCociety Creates Chromatin Interaction Modules From Chromatin Conformation Capture-Based Data’
In title case that is:
  ‘HiCociety Creates Chromatin Interaction Modules from Chromatin Conformation Capture-Based Data’

This build time stamp is over a month old.
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for executable files ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking serialization versions ... OK
* checking whether package ‘HiCociety’ can be installed ... [15s/15s] OK
* used C compiler: ‘Debian clang version 18.1.8 (11)’
* used C++ compiler: ‘Debian clang version 18.1.8 (11)’
* checking package directory ... OK
* checking for future file timestamps ... OK
* checking DESCRIPTION meta-information ... NOTE
Author field differs from that derived from Authors@R
  Author:    ‘Sora Yoon, PhD’
  Authors@R: ‘Sora Yoon [aut, cre], PhD [aut]’

* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... [3s/3s] OK
* checking whether the package can be loaded with stated dependencies ... [3s/3s] OK
* checking whether the package can be unloaded cleanly ... [3s/3s] OK
* checking whether the namespace can be loaded with stated dependencies ... [3s/3s] OK
* checking whether the namespace can be unloaded cleanly ... [3s/3s] OK
* checking loading without being on the library search path ... [3s/3s] OK
* checking use of S3 registration ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... [16s/16s] NOTE
getContactProbability: no visible binding for global variable ‘mylen’
visualizeModule: no visible global function definition for
  ‘colorRampPalette’
visualizeModule: no visible binding for global variable
  ‘TxDb.Mmusculus.UCSC.mm10.knownGene’
visualizeModule: no visible global function definition for ‘polygon’
visualizeModule: no visible global function definition for ‘par’
visualizeModule: no visible global function definition for ‘lines’
visualizeModule: no visible global function definition for ‘points’
visualizeModule: no visible global function definition for ‘exit’
visualizeModule: no visible global function definition for ‘abline’
visualizeModule: no visible global function definition for ‘segments’
visualizeModule: no visible global function definition for ‘text’
visualizeModule: no visible global function definition for ‘start’
visualizeModule: no visible global function definition for ‘end’
visualizeModule: no visible global function definition for ‘Arrows’
Undefined global functions or variables:
  Arrows TxDb.Mmusculus.UCSC.mm10.knownGene abline colorRampPalette end
  exit lines mylen par points polygon segments start text
Consider adding
  importFrom("grDevices", "colorRampPalette")
  importFrom("graphics", "abline", "lines", "par", "points", "polygon",
             "segments", "text")
  importFrom("stats", "end", "start")
to your NAMESPACE file.
* checking Rd files ... [0s/0s] OK
* checking Rd metadata ... OK
* checking Rd line widths ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking pragmas in C/C++ headers and code ... OK
* checking compilation flags used ... OK
* checking compiled code ... OK
* checking examples ... [8s/11s] OK
* checking PDF version of manual ... [3s/3s] OK
* checking HTML version of manual ... [0s/0s] OK
* checking for non-standard things in the check directory ... OK
* checking for detritus in the temp directory ... OK
* DONE
Status: 3 NOTEs