* using log directory 'd:/RCompile/CRANincoming/R-devel/HMMpa.Rcheck'
* using R Under development (unstable) (2025-01-27 r87654 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 13.3.0
    GNU Fortran (GCC) 13.3.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* checking for file 'HMMpa/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'HMMpa' version '1.0.2'
* package encoding: UTF-8
* checking CRAN incoming feasibility ... [10s] NOTE
Maintainer: 'Foraita Ronja <foraita@leibniz-bips.de>'

New maintainer:
  Foraita Ronja <foraita@leibniz-bips.de>
Old maintainer(s):
  Ronja Foraita <foraita@leibniz-bips.de>

The Description field contains
  \url{doi:10.1371/journal.pone.0114089}.
Please write DOIs as <doi:prefix/suffix>.

Found the following \keyword or \concept entries
which likely give several index terms:
  File 'Baum_Welch_algorithm.Rd':
    \keyword{ts,}
  File 'HMMpa-package.Rd':
    \keyword{ts,}

Found the following URLs which should use \doi (with the DOI name only):
  File 'HMM_based_method.Rd':
    http://dx.doi.org/10.1371/journal.pone.0114089
  File 'HMMpa-package.Rd':
    http://dx.doi.org/10.1371/journal.pone.0114089
* 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 hidden files and directories ... OK
* checking for portable file names ... OK
* checking serialization versions ... OK
* checking whether package 'HMMpa' can be installed ... OK
* checking installed package size ... 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 ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... 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 ... OK
* checking Rd files ... 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 ... OK
* checking PDF version of manual ... ERROR
Rd conversion errors:
Converting parsed Rd's to LaTeX Error in order(sectionOrder[sections], toupper(nm), nm) : 
  unimplemented type 'list' in 'listgreater'

* checking HTML version of manual ... OK
* DONE
Status: 1 ERROR, 1 NOTE