* using log directory ‘/srv/hornik/tmp/CRAN/proteomicsr.Rcheck’
* using R Under development (unstable) (2023-12-04 r85659)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    Debian clang version 17.0.5 (1)
    Debian flang-new version 17.0.5 (1)
* running under: Debian GNU/Linux trixie/sid
* using session charset: UTF-8
* checking for file ‘proteomicsr/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘proteomicsr’ version ‘1.4.3’
* package encoding: UTF-8
* checking CRAN incoming feasibility ... [3s/4s] NOTE
Maintainer: ‘Isabel Karkossa <isabel.karkossa@ufz.de>’

New submission

Possibly misspelled words in DESCRIPTION:
  Isoform (7:1557)
  LFQ (7:449)
  MSigDB (7:1125)
  PCAs (7:513)
  PTM (7:1477)
  PTMs (7:209)
  Proteome (7:1527)
  Proteomics (3:57)
  Qiagen (7:1261)
  SILAC (7:403)
  TMT (7:396)
  metabolomics (7:303)
  omics (7:291)
  phosphoproteomics (7:1607)
  proteomics (7:90)
  reproducibility (7:496)
  spectrometry (7:71)
  transcriptomics (7:320)
  translational (7:180)
* 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 ‘proteomicsr’ can be installed ... [7s/7s] 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 R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... [0s/0s] OK
* checking whether the package can be loaded with stated dependencies ... [0s/0s] OK
* checking whether the package can be unloaded cleanly ... [0s/0s] OK
* checking whether the namespace can be loaded with stated dependencies ... [0s/0s] OK
* checking whether the namespace can be unloaded cleanly ... [0s/0s] OK
* checking loading without being on the library search path ... [0s/0s] 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 ... [9s/9s] 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 ... [1s/1s] OK
* checking LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [91s/91s] NOTE
Examples with CPU (user + system) or elapsed time > 5s
                      user system elapsed
run_msigdb_workflow 23.754  0.296  24.052
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking re-building of vignette outputs ... [238s/322s] OK
* checking PDF version of manual ... [4s/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: 2 NOTEs