* using log directory 'd:/Rcompile/CRANpkg/local/4.4/csmpv.Rcheck'
* using R version 4.4.3 (2025-02-28 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 13.3.0
    GNU Fortran (GCC) 13.3.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* checking for file 'csmpv/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'csmpv' version '1.0.3'
* package encoding: UTF-8
* 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 hidden files and directories ... OK
* checking for portable file names ... OK
* checking whether package 'csmpv' can be installed ... OK
* checking installed package size ... NOTE
  installed size is  8.1Mb
  sub-directories of 1Mb or more:
    doc   7.9Mb
* checking package directory ... 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 ... [6s] OK
* checking whether the package can be loaded with stated dependencies ... [5s] OK
* checking whether the package can be unloaded cleanly ... [5s] OK
* checking whether the namespace can be loaded with stated dependencies ... [5s] OK
* checking whether the namespace can be unloaded cleanly ... [6s] OK
* checking loading without being on the library search path ... [5s] 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 ... [18s] OK
* checking Rd files ... [1s] OK
* checking Rd metadata ... 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 contents of 'data' directory ... OK
* checking data for non-ASCII characters ... [0s] OK
* checking LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ... [9s] ERROR
Running examples in 'csmpv-Ex.R' failed
The error most likely occurred in:

> ### Name: LASSO2_XGBtraining
> ### Title: Variable Selection with LASSO2 and Modeling with XGBoost
> ### Aliases: LASSO2_XGBtraining
> 
> ### ** Examples
> 
> # Load in data sets:
> data("datlist", package = "csmpv")
> tdat = datlist$training
> 
> # The function saves files locally. You can define your own temporary directory. 
> # If not, tempdir() can be used to get the system's temporary directory.
> temp_dir = tempdir()
> # As an example, let's define Xvars, which will be used later:
> Xvars = c("highIPI", "B.Symptoms", "MYC.IHC", "BCL2.IHC", "CD10.IHC", "BCL6.IHC")
> # The function can work with three different outcome types. 
> # Here, we use binary as an example:
> blxfit = LASSO2_XGBtraining(data = tdat, biomks = Xvars, Y = "DZsig",
+                            outfile = paste0(temp_dir, "/binary_LASSO2_XGBoost"))
Warning in throw_err_or_depr_msg("Passed unrecognized parameters: ", paste(head(names_unrecognized),  :
  Passed unrecognized parameters: verbose. This warning will become an error in a future version.
Warning in throw_err_or_depr_msg("Parameter '", match_old, "' has been renamed to '",  :
  Parameter 'data' has been renamed to 'x'. This warning will become an error in a future version.
Warning in throw_err_or_depr_msg("Parameter '", match_old, "' has been renamed to '",  :
  Parameter 'gamma' has been renamed to 'min_split_loss'. This warning will become an error in a future version.
Warning in throw_err_or_depr_msg("Parameter '", match_old, "' has been renamed to '",  :
  Parameter 'eta' has been renamed to 'learning_rate'. This warning will become an error in a future version.
Error in xgboost::xgboost(objective = "binary:logistic", data = Dtrain,  : 
  argument "y" is missing, with no default
Calls: LASSO2_XGBtraining ... <Anonymous> -> process.y.margin.and.objective -> NROW
Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... [165s] ERROR
Error(s) in re-building vignettes:
--- re-building 'csmpv_vignette.rmd' using rmarkdown

Quitting from csmpv_vignette.rmd:421-425 [unnamed-chunk-34]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `xgboost::xgboost()`:
! argument "y" is missing, with no default
---
Backtrace:
    ▆
 1. └─csmpv::XGBtraining(...)
 2.   └─xgboost::xgboost(...)
 3.     └─xgboost:::process.y.margin.and.objective(...)
 4.       └─base::NROW(y)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'csmpv_vignette.rmd' failed with diagnostics:
argument "y" is missing, with no default
--- failed re-building 'csmpv_vignette.rmd'

SUMMARY: processing the following file failed:
  'csmpv_vignette.rmd'

Error: Vignette re-building failed.
Execution halted

* checking PDF version of manual ... [24s] OK
* checking HTML version of manual ... [4s] OK
* DONE
Status: 2 ERRORs, 1 NOTE