* using log directory 'd:/RCompile/CRANincoming/R-devel/immundata.Rcheck'
* using R version 4.5.0 RC (2025-04-04 r88113 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 'immundata/DESCRIPTION' ... OK
* this is package 'immundata' version '0.0.0.9001'
* package encoding: UTF-8
* checking CRAN incoming feasibility ... NOTE
Maintainer: 'Vadim Nazarov <support@immunomind.com>'

New submission

Version contains large components (0.0.0.9001)

Possibly misspelled words in DESCRIPTION:
  AIRR (10:23)
  Immunomics (3:9)
  clonotype (11:52)
* 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 serialization versions ... OK
* checking whether package 'immundata' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking for future file timestamps ... OK
* checking DESCRIPTION meta-information ... NOTE
  Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    'immundata.R' 'load_immundata.R' 'load_repertoires.R'
    'load_repertoires_utils.R' 'receptor_schema.R'
* 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 whether startup messages can be suppressed ... OK
* checking use of S3 registration ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... NOTE
Mismatches for apparent methods not registered:
collect:
  function(x, ...)
collect.ImmunData:
  function(immdata, ...)

compute:
  function(x, ...)
compute.ImmunData:
  function(immdata, ...)
See section 'Registering S3 methods' in the 'Writing R Extensions'
manual.
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd line widths ... OK
* checking Rd cross-references ... NOTE
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  load_immundata.Rd: read_parquet_duckdb
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
* 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 examples ... NONE
* checking for unstated dependencies in 'tests' ... OK
* checking tests ... OK
  Running 'testthat.R'
* checking PDF version of manual ... [13s] OK
* checking HTML version of manual ... NOTE
Found the following HTML validation problems:
ImmunData.html:99:9 (ImmunData.Rd:54): Warning: <a> illegal characters found in URI
* DONE
Status: 5 NOTEs