* using log directory ‘/srv/hornik/tmp/CRAN_pretest/csmpv.Rcheck’
* using R Under development (unstable) (2025-12-08 r89124)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    Debian clang version 21.1.6 (2)
    Debian flang version 21.1.6 (2)
* running under: Debian GNU/Linux forky/sid
* using session charset: UTF-8
* checking for file ‘csmpv/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘csmpv’ version ‘1.0.5’
* package encoding: UTF-8
* checking CRAN incoming feasibility ... [4s/31s] NOTE
Maintainer: ‘Aixiang Jiang <aijiang@bccrc.ca>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Aixiang",
                    family = "Jiang",
                    role = c("aut", "cre", "cph"),
                    email = "aijiang@bccrc.ca",
                    comment = c(ORCID = "0000-0002-6153-7595"))
as necessary.

The Description field contains
  <arXiv:1603.02754>, - Aoki et al. (2023) <doi:10.1200/JCO.23.01115>.
Please refer to arXiv e-prints via their arXiv DOI <doi:10.48550/arXiv.YYMM.NNNNN>.
* 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 ... [8s/8s] 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 ... [2s/2s] OK
* checking whether the package can be loaded with stated dependencies ... [2s/2s] OK
* checking whether the package can be unloaded cleanly ... [2s/2s] OK
* checking whether the namespace can be loaded with stated dependencies ... [2s/2s] OK
* checking whether the namespace can be unloaded cleanly ... [2s/2s] OK
* checking loading without being on the library search path ... [2s/2s] 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 ... [12s/12s] OK
* 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 ... 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/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 ... [15s/15s] ERROR
Running examples in ‘csmpv-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: validation
> ### Title: Validate Model Predictions
> ### Aliases: validation
> 
> ### ** Examples
> 
> # Load in data sets:
> data("datlist", package = "csmpv")
> tdat = datlist$training
> vdat = datlist$validation
> 
> # 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 multiple models and multiple outcome types. 
> # Here, we use XGBoost model with binary outcome as an example:
> bxfit = XGBtraining(data = tdat, biomks = Xvars, Y = "DZsig",
+                     outfile = paste0(temp_dir, "/binary_XGBoost"))
> testdat = vdat[,bxfit$XGBoost_model$feature_names]
> test = xgboost::xgb.DMatrix(data.matrix(testdat))
Error in xgboost::xgb.DMatrix(data.matrix(testdat)) : 
  [00:53:53] src/data/../collective/../data/array_interface.h:422: Check failed: ptr % alignment == 0 (1 vs. 0) : Input pointer misalignment.
Stack trace:
  [bt] (0) /home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/xgboost/libs/xgboost.so(+0x53ee4) [0x7fb340053ee4]
  [bt] (1) /home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/xgboost/libs/xgboost.so(+0x2363d2) [0x7fb3402363d2]
  [bt] (2) /home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/xgboost/libs/xgboost.so(+0x2966d6) [0x7fb3402966d6]
  [bt] (3) /home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/xgboost/libs/xgboost.so(XGDMatrixCreateFromDense+0x39) [0x7fb340492409]
  [bt] (4) /home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/xgboost/libs/xgboost.so(XGDMatrixCreateFromMat_R+0x1e0) [0x7fb340049fb0]
  [bt] (5) /home/hornik/tmp/R-d-clang-21/lib/libR.so(+0xfa793) [0x7fb359efa793]
  [bt] (6) /home/hornik/tmp/R-d-clang-21/lib/libR.so(+0x154900) [0x7fb359f54900]
  [bt] (7) /home/hornik/tmp/R-d-clang-21/lib/libR.so(+0x1307cc) [0x7fb359f307cc]
 
Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... [176s/177s] OK
* checking PDF version of manual ... [3s/3s] OK
* checking HTML version of manual ... [1s/1s] OK
* checking for non-standard things in the check directory ... OK
* checking for detritus in the temp directory ... OK
* DONE
Status: 1 ERROR, 1 NOTE