* using log directory ‘/srv/hornik/tmp/CRAN_pretest/CrossExpression.Rcheck’
* using R Under development (unstable) (2025-07-18 r88431)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    Debian clang version 19.1.7 (3)
    Debian flang-new version 19.1.7 (3)
* running under: Debian GNU/Linux 13 (trixie)
* using session charset: UTF-8
* checking for file ‘CrossExpression/DESCRIPTION’ ... OK
* this is package ‘CrossExpression’ version ‘1.0.0’
* package encoding: UTF-8
* checking CRAN incoming feasibility ... [3s/4s] NOTE
Maintainer: ‘Ameer Sarwar <dogar.ameer@gmail.com>’

New submission

Possibly misspelled words in DESCRIPTION:
  Sarwar (11:283)
  Transcriptomic (2:45)
  al (11:293)
  et (11:290)
  transcriptomic (11:31)
* 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 ‘CrossExpression’ 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 code 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 ... [2s/2s] OK
* checking Rd files ... [0s/0s] OK
* checking Rd metadata ... OK
* checking Rd line widths ... NOTE
Rd file 'rotate_coordinates.Rd':
  \examples lines wider than 100 characters:
     ggplot2::ggplot(data = locations) + ggplot2::aes(x = pos_x, y = pos_y) + ggplot2::geom_point(size = 0) + ggplot2::theme_classic()
     ggplot2::ggplot(data = locations) + ggplot2::aes(x = pos_x, y = pos_y) + ggplot2::geom_point(size = 0) + ggplot2::theme_classic()

Rd file 'spatial_enrichment.Rd':
  \examples lines wider than 100 characters:
     results    = spatial_enrichment(data = expression, locations = locations, gene1 = "Calb1", gene2 = "Rasgrf2", max_pairs = 1000)

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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... [1s/1s] OK
* checking data for ASCII and uncompressed saves ... OK
* checking examples ... [53s/53s] NOTE
Examples with CPU (user + system) or elapsed time > 5s
                   user system elapsed
bullseye_plot    12.170  0.457  12.636
bullseye_scores  10.649  0.376  11.033
cross_expression  7.085  0.307   7.399
* 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: 3 NOTEs