* using log directory ‘/srv/hornik/tmp/CRAN_pretest/GencoDymo2.Rcheck’
* using R Under development (unstable) (2025-05-04 r88189)
* 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 trixie/sid
* using session charset: UTF-8
* checking for file ‘GencoDymo2/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘GencoDymo2’ version ‘1.0.1’
* package encoding: UTF-8
* checking CRAN incoming feasibility ... [4s/125s] NOTE
Maintainer: ‘Monah Abou Alezz <aboualezz.monah@hsr.it>’

New submission

Possibly misspelled words in DESCRIPTION:
  FASTA (15:43)
  GENCODE (3:34, 12:126, 13:134)
  GencoDymo (12:14, 15:19)
  MaxEntScan (15:136)
  acceptor (15:69)

Found the following (possibly) invalid URLs:
  URL: http://hollywood.mit.edu/burgelab/maxent/Xmaxentscan_scoreseq.html
    From: inst/doc/GencoDymo2_vignette.html
          README.md
    Status: Error
    Message: Timeout was reached [hollywood.mit.edu]: Connection timed out after 60002 milliseconds
  URL: http://hollywood.mit.edu/burgelab/maxent/Xmaxentscan_scoreseq_acc.html
    From: inst/doc/GencoDymo2_vignette.html
    Status: Error
    Message: Timeout was reached [hollywood.mit.edu]: Resolving timed out after 60004 milliseconds
  URL: https://doi:10.3389/fgene.2020.00488
    From: inst/doc/GencoDymo2_vignette.html
    Status: Error
    Message: URL using bad/illegal format or missing URL: URL rejected: Port number was not a decimal number between 0 and 65535

The Description field should not start with the package name,
  'This package' or similar.
The Description field contains
  (https://www.gencodegenes.org/).  Designed for human and mouse genome
Please enclose URLs in angle brackets (<...>).

Found the following \keyword or \concept entries
which likely give several index terms:
  File ‘get_gff3.Rd’:
    \keyword{GENCODE,}
    \keyword{GFF3,}
    \keyword{annotations,}
  File ‘get_gtf.Rd’:
    \keyword{GENCODE,}
    \keyword{GTF,}
    \keyword{annotations,}
  File ‘get_latest_release.Rd’:
    \keyword{GENCODE,}
    \keyword{release,}
  File ‘load_file.Rd’:
    \keyword{GENCODE,}
    \keyword{GTF,}
    \keyword{import,}
  File ‘tiny_example_gtf_files.Rd’:
    \keyword{GTF,}
    \keyword{datasets,}
* 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 ‘GencoDymo2’ can be installed ... [21s/21s] OK
* checking package directory ... OK
* checking for future file timestamps ... OK
* checking ‘build’ directory ... 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 ... [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 whether startup messages can be suppressed ... [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 ... 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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [21s/22s] OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ... [7s/7s] OK
  Running ‘testthat.R’ [7s/7s]
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... [2s/2s] OK
* checking PDF version of manual ... [3s/3s] 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 NOTE