* using log directory ‘/srv/hornik/tmp/CRAN/ApplyPolygenicScore.Rcheck’
* using R Under development (unstable) (2024-07-25 r86925)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    Debian clang version 18.1.8 (1+b1)
    Debian flang-new version 18.1.8 (1+b1)
* running under: Debian GNU/Linux trixie/sid
* using session charset: UTF-8
* checking for file ‘ApplyPolygenicScore/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘ApplyPolygenicScore’ version ‘1.0.0’
* package encoding: UTF-8
* checking CRAN incoming feasibility ... [3s/4s] NOTE
Maintainer: ‘Paul Boutros <PBoutros@mednet.ucla.edu>’

New submission

Possibly misspelled words in DESCRIPTION:
  Polygenic (3:43)
  VCF (3:64, 10:40)
  polygenic (11:42, 12:43)
* 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 ‘ApplyPolygenicScore’ can be installed ... [5s/5s] OK
* checking package directory ... OK
* checking for future file timestamps ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Authors@R field gives persons with invalid ORCID identifiers:
  Nicole Zeltser [aut] (000-0001-7246-2771)
* 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 ... [1s/1s] OK
* checking whether the package can be loaded with stated dependencies ... [1s/1s] OK
* checking whether the package can be unloaded cleanly ... [1s/1s] OK
* checking whether the namespace can be loaded with stated dependencies ... [1s/1s] OK
* checking whether the namespace can be unloaded cleanly ... [1s/1s] OK
* checking loading without being on the library search path ... [1s/1s] 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:
merge:
  function(x, y, ...)
merge.pgs.bed:
  function(pgs.bed.list, add.annotation.data, annotation.column.index,
           slop)

merge:
  function(x, y, ...)
merge.vcf.with.pgs:
  function(vcf.data, pgs.weight.data)
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 ... [7s/7s] 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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [36s/37s] NOTE
Examples with CPU (user + system) or elapsed time > 5s
                                            user system elapsed
create.pgs.density.plot                   16.605  0.582  17.777
create.pgs.with.continuous.phenotype.plot 11.307  0.361  11.663
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ... [58s/58s] OK
  Running ‘testthat.R’ [58s/58s]
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... [21s/21s] 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: 4 NOTEs