• using R Under development (unstable) (2025-12-02 r89085)
• using platform: x86_64-pc-linux-gnu
• R was compiled by     gcc (GCC) 15.1.1 20250521 (Red Hat 15.1.1-2)     GNU Fortran (GCC) 15.1.1 20250521 (Red Hat 15.1.1-2)
• running under: Fedora Linux 42 (Workstation Edition)
• using session charset: UTF-8
• using option ‘--no-stop-on-test-error’
• 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 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 ‘csmpv’ can be installed ... [29s/98s] OK See the install log for details.
• 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 ... [8s/29s] OK
• checking whether the package can be loaded with stated dependencies ... [7s/22s] OK
• checking whether the package can be unloaded cleanly ... [7s/28s] OK
• checking whether the namespace can be loaded with stated dependencies ... [7s/30s] OK
• checking whether the namespace can be unloaded cleanly ... [8s/31s] OK
• checking loading without being on the library search path ... [8s/35s] 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 ... [43s/155s] OK
• checking Rd files ... 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 ... 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 ... 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 ... [11s/40s] 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 ... [5m/21m] 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 ... [10s/37s] OK
• checking HTML version of manual ... [3s/18s] OK
• checking for non-standard things in the check directory ... OK
• checking for detritus in the temp directory ... OK
• DONE

Status: 2 ERRORs