* using log directory ‘/srv/hornik/tmp/CRAN_pretest/AntibodyForests.Rcheck’
* using R Under development (unstable) (2025-01-14 r87574)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    Debian clang version 19.1.6 (1+b1)
    Debian flang-new version 19.1.6 (1+b1)
* running under: Debian GNU/Linux trixie/sid
* using session charset: UTF-8
* checking for file ‘AntibodyForests/DESCRIPTION’ ... OK
* this is package ‘AntibodyForests’ version ‘1.0.0’
* package encoding: UTF-8
* checking CRAN incoming feasibility ... [3s/4s] NOTE
Maintainer: ‘Daphne van Ginneken <daphne.v.ginneken@gmail.com>’

New submission

Possibly misspelled words in DESCRIPTION:
  AntibodyForests (3:9, 15:47)
  Intra (2:31)
  intra (14:5, 16:44)

Found the following (possibly) invalid URLs:
  URL: https://www.sciencedirect.com/science/article/pii/S2405471222000382?via%3Dihub
    From: inst/doc/AntibodyForests_vignette.html
    Status: 403
    Message: Forbidden
  URL: https://www.sciencedirect.com/science/article/pii/S2666389922001052?via%3Dihub
    From: inst/doc/AntibodyForests_vignette.html
    Status: 403
    Message: Forbidden
Please use DOIs for the following publisher URLs:
  https://www.sciencedirect.com/science/article/pii/S2405471222000382?via%3Dihub
  https://www.sciencedirect.com/science/article/pii/S2666389922001052?via%3Dihub

Found the following (possibly) invalid file URI:
  URI: %7B
    From: inst/doc/AntibodyForests_vignette.html

Size of tarball: 6019512 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 executable files ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘AntibodyForests’ can be installed ... [5s/5s] 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 ... [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 ... [11s/11s] 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 LazyData ... OK
* checking data for ASCII and uncompressed saves ... WARNING
  
  Note: significantly better compression could be obtained
        by using R CMD build --resave-data
                 old_size new_size compress
  af_default.rda     19Kb     13Kb       xz
  af_mst.rda         19Kb     13Kb       xz
  af_nj.rda          25Kb     17Kb       xz
  small_af.rda       64Kb     39Kb    bzip2
  small_vdj.rda     452Kb    145Kb       xz
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [57s/11s] NOTE
Examples with CPU (user + system) or elapsed time > 5s
           user system elapsed
Af_build 47.319  1.687    4.75
Examples with CPU time > 2.5 times elapsed time
                                user system elapsed  ratio
Af_build                      47.319  1.687   4.750 10.317
Af_compare_across_repertoires  1.137  0.015   0.418  2.756
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... [10s/10s] OK
* checking PDF version of manual ... [3s/3s] OK
* checking HTML version of manual ... [0s/0s] OK
* checking for non-standard things in the check directory ... OK
* checking for detritus in the temp directory ... OK
* DONE
Status: 1 WARNING, 2 NOTEs