* using log directory ‘/srv/hornik/tmp/CRAN/PH1XBAR.Rcheck’
* using R Under development (unstable) (2024-05-22 r86581)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    Debian clang version 18.1.4 (1)
    Debian flang-new version 18.1.4 (1)
* running under: Debian GNU/Linux trixie/sid
* using session charset: UTF-8
* checking for file ‘PH1XBAR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘PH1XBAR’ version ‘0.11.2’
* package encoding: UTF-8
* checking CRAN incoming feasibility ... [4s/5s] NOTE
Maintainer: ‘Yuhui Yao <yyao17@ua.edu>’

Possibly misspelled words in DESCRIPTION:
  al (13:348)
  et (13:345)
* 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:
  .github
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.

CRAN-pack does not know about
  .github
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘PH1XBAR’ can be installed ... [3s/3s] OK
* 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 ... [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 ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... [5s/5s] NOTE
PH1ARMA: no visible binding for global variable ‘phi’
PH1ARMA: no visible binding for global variable ‘theta’
Undefined global functions or variables:
  phi theta
* 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 ... WARNING
Codoc mismatches from Rd file 'PH1ARMA.Rd':
PH1ARMA
  Code: function(X, cc = NULL, fap0 = 0.05, order = c(1, 0, 0),
                 plot.option = TRUE, interval = c(1, 4), case = "U",
                 phi.vec = NULL, theta.vec = NULL, mu0 = NULL, sigma0 =
                 NULL, method = "MLE+MOM", nsim.coefs = 100,
                 nsim.process = 1000, burn.in = 50, sim.type =
                 "Matrix", standardize = TRUE, verbose = FALSE)
  Docs: function(X, cc = NULL, fap0 = 0.05, order = c(1, 0, 0),
                 plot.option = TRUE, interval = c(1, 4), case = "U",
                 phi.vec = NULL, theta.vec = NULL, mu0 = NULL, , sigma0
                 = NULL, method = "MLE+MOM", nsim.coefs = 100,
                 nsim.process = 1000, burn.in = 50, sim.type =
                 "Matrix", standardize = TRUE, verbose = FALSE)
  Argument names in docs not in code:

  Mismatches in argument names (first 3):
    Position: 11 Code: sigma0 Docs: 
    Position: 12 Code: method Docs: sigma0
    Position: 13 Code: nsim.coefs Docs: method

Codoc mismatches from Rd file 'getCC.ARMA.Rd':
getCC.ARMA
  Code: function(fap0 = 0.1, interval = c(1, 4), n = 50, order = c(1,
                 0, 0), phi.vec = 0.5, theta.vec = NULL, case = "U",
                 method = "MLE+MOM", nsim.coefs = 100, nsim.process =
                 1000, burn.in = 50, sim.type = "Matrix", verbose =
                 FALSE)
  Docs: function(fap0 = 0.05, interval = c(1, 4), n = 50, order = c(1,
                 0, 0), phi.vec = 0.5, theta.vec = NULL, case = "U",
                 method = "Method 3", nsim.coefs = 100, nsim.process =
                 1000, burn.in = 50, sim.type = "Matrix", verbose =
                 FALSE)
  Mismatches in argument default values:
    Name: 'fap0' Code: 0.1 Docs: 0.05
    Name: 'method' Code: "MLE+MOM" Docs: "Method 3"

* checking Rd \usage sections ... WARNING
Undocumented arguments in Rd file 'PH1ARMA.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 ... [5s/5s] 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: 2 WARNINGs, 3 NOTEs