* using log directory ‘/srv/hornik/tmp/CRAN_pretest/HiCociety.Rcheck’
* using R Under development (unstable) (2025-04-08 r88126)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    Debian clang version 19.1.7 (1+b1)
    Debian flang-new version 19.1.7 (1+b1)
* 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 ‘0.1.30’
* 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:
  Sora (7:514)
  Yoon (7:519)

The Title field should be in title case. Current version is:
  ‘Inferring Chromatin Interaction Modules from 3C-Based Data’
In title case that is:
  ‘Inferring Chromatin Interaction Modules from 3c-Based Data’

Size of tarball: 36077382 bytes
* 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 whether package ‘HiCociety’ can be installed ... [26s/26s] OK
* used C compiler: ‘Debian clang version 19.1.7 (3)’
* used C++ compiler: ‘Debian clang version 19.1.7 (3)’
* checking package directory ... OK
* checking for future file timestamps ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Description field: should contain one or more complete sentences.
* 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 ... [7s/7s] OK
* checking whether the package can be loaded with stated dependencies ... [7s/7s] OK
* checking whether the package can be unloaded cleanly ... [7s/7s] OK
* checking whether the namespace can be loaded with stated dependencies ... [7s/7s] OK
* checking whether the namespace can be unloaded cleanly ... [7s/7s] OK
* checking loading without being on the library search path ... [7s/7s] 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 ... [29s/29s] OK
* checking Rd files ... [0s/0s] OK
* checking Rd metadata ... OK
* checking Rd line widths ... NOTE
Rd file 'visualizeModule.Rd':
  \examples lines wider than 100 characters:
     HC.object = hic2community(fname = myhic, chr = '19', resol = 5000, nbprob = 0.975, par.noise = 1, network.cluster.method = 'louvain')
     visualizeModule(hicpath = myhic, HC.object = HC.object, moduleNum = mNum, hic.norm = 'NONE', heatmap.color.range=c(0,10), heatmap.color ... [TRUNCATED]

These lines will be truncated in the PDF manual.
* 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 ... [25s/25s] ERROR
Running examples in ‘HiCociety-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: getElbowPoint
> ### Title: Estimation of elbow point from J-shaped-curve
> ### Aliases: getElbowPoint
> 
> ### ** Examples
> 
> modulefile = system.file('extdata','mouse_naiveCD4T_Vahedi.rds', package = 'HiCociety')
> connec = mycom$ModuleSummary$connectivity
Error: object 'mycom' not found
Execution halted
Examples with CPU (user + system) or elapsed time > 5s
                  user system elapsed
ConnectivityDiff 11.45  0.472  11.925
* checking PDF version of manual ... [2s/2s] 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: 1 ERROR, 3 NOTEs