* using log directory ‘/srv/hornik/tmp/CRAN_pretest/apLCMS.Rcheck’
* using R Under development (unstable) (2025-06-09 r88292)
* 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 13 (trixie)
* using session charset: UTF-8
* checking for file ‘apLCMS/DESCRIPTION’ ... OK
* this is package ‘apLCMS’ version ‘6.8.3’
* checking CRAN incoming feasibility ... [3s/3s] NOTE
Maintainer: ‘Tianwei Yu <yutianwei@cuhk.edu.cn>’

New submission

Possibly misspelled words in DESCRIPTION:
  Liu (9:394)
  Yu (9:340, 9:446, 9:500)
  al (9:346, 9:401, 9:452, 9:506)
  et (9:343, 9:398, 9:449, 9:503)
  metabolomics (9:73)

Uses the non-portable package: ‘mzR’

The Description field should not start with the package name,
  'This package' or similar.

Size of tarball: 5127941 bytes
* checking package namespace information ... OK
* checking package dependencies ... INFO
Depends: includes the non-default packages:
  'MASS', 'rgl', 'mzR', 'doParallel', 'foreach', 'splines',
  'iterators', 'gbm', 'e1071', 'randomForest', 'ROCR', 'ROCS', 'Rcpp'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
* 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 ‘apLCMS’ can be installed ... [14s/14s] OK
* used C++ compiler: ‘Debian clang version 19.1.7 (3)’
* 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 ... [2s/2s] OK
* checking whether the package can be loaded with stated dependencies ... [2s/2s] OK
* checking whether the package can be unloaded cleanly ... [2s/2s] OK
* checking whether the namespace can be loaded with stated dependencies ... [2s/2s] OK
* checking whether the namespace can be unloaded cleanly ... [2s/2s] OK
* checking loading without being on the library search path ... [2s/2s] 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 ... [17s/17s] 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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... [0s/0s] OK
* checking data for ASCII and uncompressed saves ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking pragmas in C/C++ headers and code ... OK
* checking compilation flags used ... OK
* checking compiled code ... OK
* checking examples ... [10s/10s] OK
* checking PDF version of manual ... [3s/3s] OK
* checking HTML version of manual ... [1s/1s] OK
* checking for non-standard things in the check directory ... OK
* checking for detritus in the temp directory ... OK
* DONE
Status: 1 NOTE