* using log directory ‘/srv/hornik/tmp/CRAN_pretest/OmicFlow.Rcheck’
* using R Under development (unstable) (2025-08-17 r88631)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    Debian clang version 19.1.7 (3+b1)
    Debian flang-new version 19.1.7 (3+b1)
* running under: Debian GNU/Linux forky/sid
* using session charset: UTF-8
* checking for file ‘OmicFlow/DESCRIPTION’ ... OK
* this is package ‘OmicFlow’ version ‘1.3.0’
* package encoding: UTF-8
* checking CRAN incoming feasibility ... [3s/5s] NOTE
Maintainer: ‘Alem Gusinac <alem.gusinac@gmail.com>’

New submission

Possibly misspelled words in DESCRIPTION:
  OmicFlow (14:9, 16:141)
  Omics (15:5)
  autoFlow (17:147)
  omics (2:58, 14:124, 16:124)

The Title field should be in title case. Current version is:
  ‘Fast and Efficient (automated) analysis of sparse omics data’
In title case that is:
  ‘Fast and Efficient (Automated) Analysis of Sparse Omics Data’
* 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 ‘OmicFlow’ can be installed ... [7s/7s] 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 ... [2s/2s] OK
* checking whether the package can be loaded with stated dependencies ... [2s/2s] OK
* checking whether the package can be unloaded cleanly ... [2s/2s] OK
* checking whether the namespace can be loaded with stated dependencies ... [2s/2s] OK
* checking whether the namespace can be unloaded cleanly ... [2s/2s] OK
* checking loading without being on the library search path ... [2s/2s] 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 ... [9s/9s] NOTE
volcano_plot: no visible binding for global variable ‘diffexpressed’
Undefined global functions or variables:
  diffexpressed
* 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 examples ... [7s/7s] OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ... [10s/9s] OK
  Running ‘testthat.R’ [10s/9s]
* checking PDF version of manual ... [3s/3s] OK
* checking HTML version of manual ... [1s/1s] NOTE
Found the following HTML validation problems:
omics.html:248:18 (omics.Rd:284): Error: <name> is not recognized!
omics.html:248:18 (omics.Rd:284): Warning: discarding unexpected <name>
omics.html:251:18 (omics.Rd:285): Error: <name> is not recognized!
omics.html:251:18 (omics.Rd:285): Warning: discarding unexpected <name>
* checking for non-standard things in the check directory ... NOTE
Found the following files/directories:
  ‘output.biom’
* checking for detritus in the temp directory ... OK
* DONE
Status: 4 NOTEs