* using log directory ‘/srv/hornik/tmp/CRAN/origamiPlot.Rcheck’
* using R Under development (unstable) (2024-06-11 r86723)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    Debian clang version 18.1.5 (2)
    Debian flang-new version 18.1.5 (2)
* running under: Debian GNU/Linux trixie/sid
* using session charset: UTF-8
* checking for file ‘origamiPlot/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘origamiPlot’ version ‘0.1.0’
* package encoding: UTF-8
* checking CRAN incoming feasibility ... [3s/3s] NOTE
Maintainer: ‘yiwenlu <yiwenlu@sas.upenn.edu>’

New submission

Possibly misspelled words in DESCRIPTION:
  OrigamiPlot (3:8)

The Title field starts with the package name.

The Description field should not start with the package name,
  'This package' or similar.
* 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 ... NOTE
Found the following hidden files and directories:
  .Rd2pdf90613
  .Rd2pdf90632
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.

CRAN-pack does not know about
  .Rd2pdf90613
  .Rd2pdf90632
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘origamiPlot’ can be installed ... [1s/1s] WARNING
Found the following significant warnings:
  Warning: object ‘data’ is created by more than one data call
See ‘/srv/hornik/tmp/CRAN/origamiPlot.Rcheck/00install.out’ for details.
* checking package directory ... OK
* checking for future file timestamps ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... NOTE
Non-standard file/directory found at top level:
  ‘Rd2.pdf’
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... WARNING
Found the following directories with names of Rd2pdf directories:
  ./.Rd2pdf90613
  ./.Rd2pdf90632
Most likely, these were included erroneously.
* 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 ... [3s/3s] OK
* checking Rd files ... [0s/0s] OK
* checking Rd metadata ... OK
* checking Rd line widths ... NOTE
Rd file 'origami_plot.Rd':
  \examples lines wider than 100 characters:
     origami_plot(df=df_list[[1]], pcol = rgb(0.2,0.5,0.5,1),pfcol = rgb(0.2,0.5,0.5,0.1),axistype=1, pty = 32)

Rd file 'origami_plot_pairwise.Rd':
  \examples lines wider than 100 characters:
     origami_plot_pairwise(df1=df_list[[3]], df2=df_list[[6]], pcol1 = rgb(0.2,0.5,0.5,1), pfcol1 = rgb(0.2,0.5,0.5,0.1),

Rd file 'origami_plot_weighted.Rd':
  \examples lines wider than 100 characters:
     origami_plot_weighted(df = df_list[[6]], weight = c(0.15,0.25,0.3,0.2,0.1),pcol = rgb(0.2,0.5,0.5,1),

These lines will be truncated in the PDF manual.
* checking Rd cross-references ... OK
* checking for missing documentation entries ... WARNING
Undocumented code objects:
  ‘data’
Undocumented data sets:
  ‘data’
All user-level objects in a package should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... WARNING
Undocumented arguments in Rd file 'data_preparation.Rd'
  ‘...’

Undocumented arguments in Rd file 'origami_plot.Rd'
  ‘full_point’ ‘point_col’ ‘point_pch’ ‘...’

Undocumented arguments in Rd file 'origami_plot_pairwise.Rd'
  ‘...’

Undocumented arguments in Rd file 'origami_plot_weighted.Rd'
  ‘...’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* 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 ... OK
* checking examples ... [0s/0s] 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 WARNINGs, 4 NOTEs