* using log directory 'd:/RCompile/CRANincoming/R-devel/SpectroPipeR.Rcheck'
* using R Under development (unstable) (2024-09-23 r87189 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 13.2.0
    GNU Fortran (GCC) 13.2.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* checking for file 'SpectroPipeR/DESCRIPTION' ... OK
* this is package 'SpectroPipeR' version '0.3.0'
* package encoding: UTF-8
* checking CRAN incoming feasibility ... [12s] NOTE
Maintainer: 'Stephan Michalik <stephan.michalik@uni-greifswald.de>'

New submission

Found the following (possibly) invalid URLs:
  URL: https://academic.oup.com/bioinformatics/article/36/8/2611/5697917
    From: inst/doc/a02_SpectroPipeR_norm_quant.html
    Status: 403
    Message: Forbidden
  URL: https://academic.oup.com/biostatistics/article/8/1/118/252073
    From: inst/doc/a02_SpectroPipeR_norm_quant.html
    Status: 403
    Message: Forbidden
  URL: https://cran.r-project.org/web/packages/gprofiler2/vignettes/gprofiler2.html
    From: inst/doc/a07_Gprofiler2_code_suggestion.html
    Status: 200
    Message: OK
    CRAN URL not in canonical form
  URL: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1316121/
    From: inst/doc/a04_SpectroPipeR_statistics.html
    Status: 403
    Message: Forbidden
  URL: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2728531/
    From: inst/doc/a04_SpectroPipeR_statistics.html
    Status: 403
    Message: Forbidden
The canonical URL of the CRAN page for a package is 
  https://CRAN.R-project.org/package=pkgname

The Description field should start with a capital letter.

Size of tarball: 34571830 bytes
* 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 'SpectroPipeR' can be installed ... OK
* checking installed package size ... 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 ... [10s] OK
* checking whether the package can be loaded with stated dependencies ... [10s] OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... [10s] OK
* checking whether the namespace can be unloaded cleanly ... [10s] OK
* checking loading without being on the library search path ... [11s] OK
* checking whether startup messages can be suppressed ... [10s] 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 ... [60s] 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 installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ... [16m] NOTE
Examples with CPU (user + system) or elapsed time > 10s
                             user system elapsed
SpectroPipeR               135.17   9.75  253.57
SpectroPipeR_report_module 129.32  10.91  211.72
statistics_module          127.87   9.23  185.34
MVA_module                 113.39   9.89  164.92
norm_quant_module           51.64   7.28   54.04
read_spectronaut_module     19.77   2.75   20.59
XIC_plot_module              4.01   1.56   51.44
* checking for unstated dependencies in 'tests' ... OK
* checking tests ... [186s] OK
  Running 'testthat.R' [185s]
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... [22s] OK
* checking PDF version of manual ... [21s] OK
* checking HTML version of manual ... OK
* DONE
Status: 2 NOTEs