* using log directory ‘/srv/hornik/tmp/CRAN_pretest/BayesAT.Rcheck’
* using R Under development (unstable) (2025-01-30 r87669)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    Debian clang version 19.1.6 (1+b1)
    Debian flang-new version 19.1.6 (1+b1)
* running under: Debian GNU/Linux trixie/sid
* using session charset: UTF-8
* checking for file ‘BayesAT/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘BayesAT’ version ‘0.1.0’
* package encoding: UTF-8
* checking CRAN incoming feasibility ... [3s/3s] NOTE
Maintainer: ‘Yuan Zhong <aqua.zhong@gmail.com>’

New submission

Unknown, possibly misspelled, fields in DESCRIPTION:
  ‘References’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Yuan",
                      family = "Zhong",
                      role = c("aut", "cre"),
                      email = "aqua.zhong@gmail.com"),
               person(given = "Zeynep",
                      family = "Baskurt",
                      role = "aut"),
               person(given = "Wei",
                      family = "Xu",
                      role = "aut"))
as necessary.

This build time stamp is over a month old.
* 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 serialization versions ... OK
* checking whether package ‘BayesAT’ can be installed ... [1s/1s] OK
* checking package directory ... OK
* checking for future file timestamps ... OK
* checking ‘build’ directory ... 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 ... [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 ... WARNING
summary:
  function(object, ...)
summary.BayesAT:
  function(object)

summary:
  function(object, ...)
summary.Bayes_test:
  function(object)

plot:
  function(x, ...)
plot.BayesAT:
  function(object)
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... [2s/2s] NOTE
.gamma_exponential: no visible global function definition for ‘rgamma’
.gamma_exponential: no visible global function definition for ‘sd’
.gamma_exponential: no visible global function definition for
  ‘quantile’
.simul: no visible global function definition for ‘rexp’
.simul: no visible global function definition for ‘runif’
BayesAT: no visible global function definition for ‘qnorm’
Bayes_test: no visible global function definition for ‘qnorm’
plot.BayesAT: no visible global function definition for ‘lines’
plot.BayesAT: no visible global function definition for ‘polygon’
plot.BayesAT: no visible global function definition for ‘text’
plot.BayesAT: no visible global function definition for ‘legend’
Undefined global functions or variables:
  legend lines polygon qnorm quantile rexp rgamma runif sd text
Consider adding
  importFrom("graphics", "legend", "lines", "polygon", "text")
  importFrom("stats", "qnorm", "quantile", "rexp", "rgamma", "runif",
             "sd")
to your NAMESPACE file.

Found if() conditions comparing class() to string:
File ‘BayesAT/R/Main.R’: if (class(data) == "data.frame") ...
File ‘BayesAT/R/Main.R’: if (class(data) == "list") ...
Use inherits() (or maybe is()) instead.
* checking Rd files ... [0s/0s] OK
* checking Rd metadata ... OK
* checking Rd line widths ... NOTE
Rd file 'BayesAT.Rd':
  \examples lines wider than 100 characters:
     data <- Simulate_Enroll(n = c(30,20,20,15,30), lambda = 0.03, event = 0.1, M = 3, group = 5, maxt = 5,
     IA <- BayesAT(data,D = 3,stage = 5,threshold = 0.9, start = 1.5, objective = 2, alpha = 3, beta = 82)

These lines will be truncated in the PDF manual.
* 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 ... [1s/1s] ERROR
Running examples in ‘BayesAT-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: Bayes_test
> ### Title: Bayesian inference for survival analysis
> ### Aliases: Bayes_test
> 
> ### ** Examples
> 
> data <- Simulate_Enroll(n = c(50,20,20), lambda = 0.03, event = 0.1, M = 1, group = 3, maxt = 5,
+                   accrual = 3, censor = 0.9, followup = 2,partition = "Uneven")
> test <- Bayes_test(data, alpha = 3, beta = 82, test = "greater", pred = 2, threshold = 0.9,
+                 type = "Predictive",diagnosis = T)
Error in Bayes_test(data, alpha = 3, beta = 82, test = "greater", pred = 2,  : 
  T used instead of TRUE
Execution halted
* checking for unstated dependencies in vignettes ... NOTE
'library' or 'require' call not declared from: ‘reportRmd’
* checking package vignettes ... OK
* checking re-building of vignette outputs ... [4s/4s] ERROR
Error(s) in re-building vignettes:
  ...
--- re-building ‘BayesianInferece.Rmd’ using rmarkdown
** Processing: /srv/hornik/tmp/CRAN_pretest/BayesAT.Rcheck/vign_test/BayesAT/vignettes/BayesianInferece_files/figure-html/unnamed-chunk-6-1.png
288x288 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 16592 bytes
Input file size = 16694 bytes

Trying:
  zc = 9  zm = 8  zs = 0  f = 0		IDAT size = 12341
  zc = 9  zm = 8  zs = 1  f = 0
  zc = 1  zm = 8  zs = 2  f = 0
  zc = 9  zm = 8  zs = 3  f = 0
  zc = 9  zm = 8  zs = 0  f = 5
  zc = 9  zm = 8  zs = 1  f = 5
  zc = 1  zm = 8  zs = 2  f = 5
  zc = 9  zm = 8  zs = 3  f = 5
                               
Selecting parameters:
  zc = 9  zm = 8  zs = 0  f = 0		IDAT size = 12341

Output IDAT size = 12341 bytes (4251 bytes decrease)
Output file size = 12419 bytes (4275 bytes = 25.61% decrease)

--- finished re-building ‘BayesianInferece.Rmd’

--- re-building ‘SimulationEnroll.Rmd’ using rmarkdown

Quitting from lines 69-72 [unnamed-chunk-2] (SimulationEnroll.Rmd)
Error: processing vignette 'SimulationEnroll.Rmd' failed with diagnostics:
there is no package called 'reportRmd'
--- failed re-building ‘SimulationEnroll.Rmd’

SUMMARY: processing the following file failed:
  ‘SimulationEnroll.Rmd’

Error: Vignette re-building failed.
Execution halted

* 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 ERRORs, 1 WARNING, 4 NOTEs