* using log directory ‘/srv/hornik/tmp/CRAN/ExprNet.Rcheck’
* using R Under development (unstable) (2023-06-30 r84625)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    Debian clang version 16.0.6 (1)
    GNU Fortran (Debian 12.2.0-14) 12.2.0
* running under: Debian GNU/Linux trixie/sid
* using session charset: UTF-8
* checking for file ‘ExprNet/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘ExprNet’ version ‘1.0.0’
* package encoding: UTF-8
* checking CRAN incoming feasibility ... [3s/3s] NOTE
Maintainer: ‘Wenbin Wu <drkwu999@gmail.com>’

New submission

Possibly misspelled words in DESCRIPTION:
  ExprNet (8:14)
  phenotypes (8:187)

The Description field should not start with the package name,
  'This package' or similar.
* 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 ‘ExprNet’ can be installed ... [1s/1s] OK
* checking package directory ... OK
* checking for future file timestamps ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... [0s/0s] OK
* checking whether the package can be loaded with stated dependencies ... [0s/0s] OK
* checking whether the package can be unloaded cleanly ... [0s/0s] OK
* checking whether the namespace can be loaded with stated dependencies ... [0s/0s] OK
* checking whether the namespace can be unloaded cleanly ... [0s/0s] OK
* checking loading without being on the library search path ... [0s/0s] 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 ... [3s/3s] NOTE
compute_AT: no visible binding for global variable ‘perm_idx’
Undefined global functions or variables:
  perm_idx
* checking Rd files ... [0s/0s] OK
* checking Rd metadata ... OK
* checking Rd line widths ... NOTE
Rd file 'analysis_ExprNet.Rd':
  \examples lines wider than 100 characters:
     edge_pair_selected <- c("1-8", "1-15", "2-16", "3-16", "5-10", "5-16", "8-11", "8-13", "8-14", "8-15", "13-15")
                                edge_pair_selected = edge_pair_selected, type1_name = "LGG", type2_name = "GBM",

Rd file 'compute_AT.Rd':
  \examples lines wider than 100 characters:
     edge_pair_selected <- c("1-8", "1-15", "2-16", "3-16", "5-10", "5-16", "8-11", "8-13", "8-14", "8-15", "13-15")
     res <- compute_edge_t_stat(data_type1, data_type2, network, type1_name = "LGG", type2_name = "GBM", save_dir = save_dir)
     compute_AT(edge_t_stat = edge_t_stat, edge_dist_mat = edge_dist_mat, network = network, edge_pair_selected = edge_pair_selected, num_co ... [TRUNCATED]
               subnet_label = "Demo_GO0006306_DNA_methylation(LGG-GBM)", vertex.label.cex = 1, vertex.size = 10, edge.width = 7)

These lines will be truncated in the PDF manual.
* checking Rd cross-references ... NOTE
Unknown package ‘demo network’ in Rd xrefs
* 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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... [0s/0s] OK
* checking LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking examples ... [11s/6s] NOTE
Examples with CPU (user + system) or elapsed time > 5s
                  user system elapsed
analysis_ExprNet 5.421  0.065   2.833
compute_AT       5.345  0.056   2.770
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ... [1s/1s] OK
  Running ‘testthat.R’ [1s/1s]
* 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: 5 NOTEs