* using log directory ‘/srv/hornik/tmp/CRAN_pretest/upset.hp.Rcheck’
* using R Under development (unstable) (2025-05-26 r88238)
* 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 ‘upset.hp/DESCRIPTION’ ... OK
* this is package ‘upset.hp’ version ‘0.0.1’
* package encoding: UTF-8
* checking CRAN incoming feasibility ... [3s/5s] NOTE
Maintainer: ‘Jiangshan Lai <lai@njfu.edu.cn>’

New submission

Possibly misspelled words in DESCRIPTION:
  Lai (8:315)
  Neto (8:347)
  Peres (8:341)
  UpSet (2:17)
  Zhang (8:331)
  Zou (8:323)
  rdacca (8:471)
* 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 ‘upset.hp’ can be installed ... [6s/6s] WARNING
Found the following significant warnings:
  Warning: replacing previous import ‘rdacca.hp::creatbin’ by ‘glmm.hp::creatbin’ when loading ‘upset.hp’
  Warning: replacing previous import ‘rdacca.hp::odd’ by ‘glmm.hp::odd’ when loading ‘upset.hp’
  Warning: replacing previous import ‘rdacca.hp::genList’ by ‘glmm.hp::genList’ when loading ‘upset.hp’
  Warning: replacing previous import ‘glmm.hp::creatbin’ by ‘gam.hp::creatbin’ when loading ‘upset.hp’
  Warning: replacing previous import ‘glmm.hp::odd’ by ‘gam.hp::odd’ when loading ‘upset.hp’
  Warning: replacing previous import ‘glmm.hp::genList’ by ‘gam.hp::genList’ when loading ‘upset.hp’
  Warning: replacing previous import ‘gam.hp::creatbin’ by ‘phylolm.hp::creatbin’ when loading ‘upset.hp’
  Warning: replacing previous import ‘gam.hp::odd’ by ‘phylolm.hp::odd’ when loading ‘upset.hp’
  Warning: replacing previous import ‘gam.hp::genList’ by ‘phylolm.hp::genList’ when loading ‘upset.hp’
See ‘/srv/hornik/tmp/CRAN_pretest/upset.hp.Rcheck/00install.out’ for details.
* 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 ... [8s/8s] OK
* checking Rd files ... [0s/0s] NOTE
checkRd: (-1) upset.hp.Rd:72: Lost braces
    72 | upset.hp diagram is an extension of UpSet technique to  and is used to visualize the object of \\code{rdacca.hp},\code{glmm.hp},\code{gam.hp},and \code{phylolm.hp}. (Lai et al. 2022a,2022b,2023,2024; Liu et al. 2023). The matrix layout enables the effective representation of relative importance of predictors, such as the unique effects and common effects in VP, as well as additional summary statistics or individual effects in HP. upset.hp diagram could, in principle, allow visualization of any number of predictor variables or groups of predictor variables. But considering the interpretability of data, we would like to recommend that the number of predictors (or groups of predictors) no more than 7.
       |                                                                                                      ^
* 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 examples ... [7s/7s] NOTE
Examples with CPU (user + system) or elapsed time > 5s
          user system elapsed
upset.hp 5.102    0.1   5.204
* 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, 3 NOTEs