* using log directory ‘/srv/hornik/tmp/CRAN_pretest/csmpv.Rcheck’ * using R Under development (unstable) (2025-12-07 r89119) * 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/4s] NOTE Maintainer: ‘Aixiang Jiang ’ 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 , - Aoki et al. (2023) . Please refer to arXiv e-prints via their arXiv DOI . * 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 ... [6s/6s] ERROR Running examples in ‘csmpv-Ex.R’ failed The error most likely occurred in: > base::assign(".ptime", proc.time(), pos = "CheckExEnv") > ### Name: XGBtraining_predict > ### Title: Predicting XGBoost Model Scores and Performing Validation > ### Aliases: XGBtraining_predict > > ### ** 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 provide an example using the XGBoost model with a time-to-event outcome: > txfit = XGBtraining(data = tdat, biomks = Xvars, + outcomeType = "time-to-event", + time = "FFP..Years.",event = "Code.FFP", + outfile = paste0(temp_dir, "/survival_XGBoost")) > ptxfit = XGBtraining_predict(txfit, newdata = vdat, + outfile = paste0(temp_dir, "/pred_XGBoost_time_to_event")) Error in xgboost::xgb.DMatrix(as.matrix(testdat)) : [00:49:18] 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) [0x7f3577653ee4] [bt] (1) /home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/xgboost/libs/xgboost.so(+0x2363d2) [0x7f35778363d2] [bt] (2) /home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/xgboost/libs/xgboost.so(+0x2966d6) [0x7f35778966d6] [bt] (3) /home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/xgboost/libs/xgboost.so(XGDMatrixCreateFromDense+0x39) [0x7f3577a92409] [bt] (4) /home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/xgboost/libs/xgboost.so(XGDMatrixCreateFromMat_R+0x1e0) [0x7f3577649fb0] [bt] (5) /home/hornik/tmp/R-d-clang-21/lib/libR.so(+0xfa793) [0x7f35914fa793] [bt] (6) /home/hornik/tmp/R-d-clang-21/lib/libR.so(+0x1548b0) [0x7f35915548b0] [bt] (7) /home/hornik/tmp/R-d-clang-21/lib/libR.so(+0x13077c) [0x7f359153077c] Calls: XGBtraining_predict -> Execution halted * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... OK * checking re-building of vignette outputs ... [104s/104s] ERROR Error(s) in re-building vignettes: ... --- re-building ‘csmpv_vignette.rmd’ using rmarkdown Quitting from csmpv_vignette.rmd:718-721 [unnamed-chunk-59] ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error in `xgboost::xgb.DMatrix()`: ! [00:51:03] 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) [0x7f4977053ee4] [bt] (1) /home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/xgboost/libs/xgboost.so(+0x2363d2) [0x7f49772363d2] [bt] (2) /home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/xgboost/libs/xgboost.so(+0x2966d6) [0x7f49772966d6] [bt] (3) /home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/xgboost/libs/xgboost.so(XGDMatrixCreateFromDense+0x39) [0x7f4977492409] [bt] (4) /home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/xgboost/libs/xgboost.so(XGDMatrixCreateFromMat_R+0x1e0) [0x7f4977049fb0] [bt] (5) /home/hornik/tmp/R-d-clang-21/lib/libR.so(+0xfa793) [0x7f4991efa793] [bt] (6) /home/hornik/tmp/R-d-clang-21/lib/libR.so(+0x1548b0) [0x7f4991f548b0] [bt] (7) /home/hornik/tmp/R-d-clang-21/lib/libR.so(+0x13077c) [0x7f4991f3077c] [bt] (8 --- Backtrace: ▆ 1. └─csmpv::XGBtraining_predict(bxfit, newdata = vdat, outfile = "pred_XGBoost_binary") 2. └─xgboost::xgb.DMatrix(as.matrix(testdat)) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error: processing vignette 'csmpv_vignette.rmd' failed with diagnostics: [00:51:03] 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) [0x7f4977053ee4] [bt] (1) /home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/xgboost/libs/xgboost.so(+0x2363d2) [0x7f49772363d2] [bt] (2) /home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/xgboost/libs/xgboost.so(+0x2966d6) [0x7f49772966d6] [bt] (3) /home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/xgboost/libs/xgboost.so(XGDMatrixCreateFromDense+0x39) [0x7f4977492409] [bt] (4) /home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/xgboost/libs/xgboost.so(XGDMatrixCreateFromMat_R+0x1e0) [0x7f4977049fb0] [bt] (5) /home/hornik/tmp/R-d-clang-21/lib/libR.so(+0xfa793) [0x7f4991efa793] [bt] (6) /home/hornik/tmp/R-d-clang-21/lib/libR.so(+0x1548b0) [0x7f4991f548b0] [bt] (7) /home/hornik/tmp/R-d-clang-21/lib/libR.so(+0x13077c) [0x7f4991f3077c] [bt] (8 --- 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 ... [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: 2 ERRORs, 1 NOTE