* using log directory 'd:/RCompile/CRANincoming/R-devel/MSclassifR.Rcheck'
* using R Under development (unstable) (2025-06-30 r88369 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 14.2.0
    GNU Fortran (GCC) 14.2.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* checking for file 'MSclassifR/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'MSclassifR' version '0.4.0'
* package encoding: UTF-8
* checking CRAN incoming feasibility ... WARNING
Maintainer: 'Alexandre Godmer <alexandre.godmer@aphp.fr>'

New submission

Package was archived on CRAN

Possibly misspelled words in DESCRIPTION:
  pre (11:161)

CRAN repository db overrides:
  X-CRAN-Comment: Archived on 2025-06-30 as requires archived package
    'UBL'.

Strong dependencies not in mainstream repositories:
  UBL

Found the following (possibly) invalid URLs:
  URL: https://www.sciencedirect.com/science/article/pii/S0957417425024145
    From: DESCRIPTION
    Status: 403
    Message: Forbidden
Please use DOIs for the following publisher URLs:
  https://www.sciencedirect.com/science/article/pii/S0957417425024145

The Description field contains
  (https://doi.org/10.1016/j.eswa.2025.128796). For a comprehensive
  (https://github.com/agodmer/MSclassifR_examples).
Please enclose URLs in angle brackets (<...>).
The Description field contains
  (https://doi.org/10.1016/j.eswa.2025.128796). For a comprehensive
Please write DOIs as <doi:prefix/suffix>.

The BugReports field in DESCRIPTION has
  https://github.com/agodmer/MSclassifR_examples/discussions
which should likely be
  https://github.com/agodmer/MSclassifR_examples/discussions/issues
instead.

Found the following URLs which should use \doi (with the DOI name only):
  File 'MSclassifR.Rd':
    https://doi.org/10.1016/j.eswa.2025.128796
* 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 whether package 'MSclassifR' 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 ... [36s] OK
* checking Rd files ... NOTE
checkRd: (-1) SignalProcessing.Rd:42: Lost braces; missing escapes or markup?
    42 |   \item{calibrateIntensity_method}{a \code{character} indicating the intensities calibration method used (\code{"TIC"} method by default).  This calibration method can be remplaced by \code{"PQN"} or {"median"}.See \code{calibrateIntensity-methods} of the \code{MALDIquant} R package for details.}
       |                                                                                                                                                                                                         ^
* 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 contents of 'data' directory ... OK
* checking data for non-ASCII characters ... OK
* checking LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking examples ... [20s] OK
* checking PDF version of manual ... [22s] OK
* checking HTML version of manual ... OK
* DONE
Status: 1 WARNING, 1 NOTE