* using log directory ‘/srv/hornik/tmp/CRAN_pretest/EZTCGA.Rcheck’
* using R Under development (unstable) (2024-11-15 r87338)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    Debian clang version 19.1.1 (1)
    Debian flang-new version 19.1.1 (1)
* running under: Debian GNU/Linux trixie/sid
* using session charset: UTF-8
* checking for file ‘EZTCGA/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘EZTCGA’ version ‘0.1.0’
* package encoding: UTF-8
* checking CRAN incoming feasibility ... [3s/3s] NOTE
Maintainer: ‘Ehsan Keramati <ehsan.keramati14@gmail.com>’

New submission

Possibly misspelled words in DESCRIPTION:
  TCGA (3:13, 11:36)
* 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 ‘EZTCGA’ can be installed ... [19s/19s] OK
* 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:    ‘Ehsan Keramati’
  Authors@R: ‘Ehsan Keramati [aut, cre]’

* 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 ... [6s/6s] OK
* checking whether the package can be loaded with stated dependencies ... [6s/6s] OK
* checking whether the package can be unloaded cleanly ... [6s/6s] OK
* checking whether the namespace can be loaded with stated dependencies ... [6s/6s] OK
* checking whether the namespace can be unloaded cleanly ... [6s/6s] OK
* checking loading without being on the library search path ... [6s/6s] 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 ... [25s/25s] OK
* 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 ... [356s/592s] NOTE
Examples with CPU (user + system) or elapsed time > 5s
                     user system elapsed
eztcga_just_do_it 339.678  8.322 583.787
* 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 ... NOTE
Found the following files/directories:
  ‘All Samples Informations.txt’ ‘Annotation File.txt’ ‘Clinical
  Informations.txt’ ‘DEG filtered and sorted by pajd 0.05 and abslog2fc
  2.txt’ ‘DEG without any filtration.txt’ ‘GDCdata’ ‘MANIFEST.txt’
  ‘MetaData.txt’ ‘Normal Samples.txt’ ‘PCA_plot.png’ ‘Protein Coding
  DEG filtered and sorted by pajd 0.05 and abslog2fc 2.txt’
  ‘Protein_Coding_volcano_plot.png’ ‘Raw Matrix without not expressed
  genes .txt’ ‘Raw Matrix.txt’ ‘Tumor Samples.txt’ ‘data.rda’ ‘genes of
  DEG Expression Matrix (SYMBOL).txt’ ‘genes of DEG Expression
  Matrix.txt’ ‘lncRNA DEG filtered and sorted by pajd 0.05 and
  abslog2fc 2.txt’ ‘lncRNA of DEG Expression Matrix (SYMBOL).txt’
  ‘lncRNA of DEG Expression Matrix.txt’ ‘lncRNA of DEG heatmap.png’
  ‘lncRNA_volcano_plot.png’ ‘miRNA DEG filtered and sorted by pajd 0.05
  and abslog2fc 2.txt’ ‘microRNA of DEG Expression Matrix (SYMBOL).txt’
  ‘microRNA of DEG Expression Matrix.txt’ ‘microRNA of DEG heatmap.png’
  ‘microRNA_volcano_plot.png’ ‘volcano_plot.png’
* checking for detritus in the temp directory ... OK
* DONE
Status: 4 NOTEs