CRAN Package Check Results for Package csmpv

Last updated on 2025-12-04 15:50:15 CET.

Flavor	Version	Tinstall	Tcheck	Ttotal	Status	Flags
r-devel-linux-x86_64-debian-clang	1.0.3	16.42	520.68	537.10	NOTE
r-devel-linux-x86_64-debian-gcc	1.0.3	12.42	345.33	357.75	NOTE
r-devel-linux-x86_64-fedora-clang	1.0.3	86.00	433.88	519.88	ERROR
r-devel-linux-x86_64-fedora-gcc	1.0.3	98.00	421.43	519.43	ERROR
r-devel-windows-x86_64	1.0.3	19.00	407.00	426.00	OK
r-patched-linux-x86_64	1.0.3	17.20	493.83	511.03	OK
r-release-linux-x86_64	1.0.3	15.94	491.31	507.25	OK
r-release-macos-arm64	1.0.3				OK
r-release-macos-x86_64	1.0.3	13.00	353.00	366.00	OK
r-release-windows-x86_64	1.0.3	18.00	404.00	422.00	OK
r-oldrel-macos-arm64	1.0.3				NOTE
r-oldrel-macos-x86_64	1.0.3	10.00	234.00	244.00	NOTE
r-oldrel-windows-x86_64	1.0.3	26.00	554.00	580.00	NOTE

Check Details

Version: 1.0.3
Check: CRAN incoming feasibility
Result: 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>. Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc

Version: 1.0.3
Check: examples
Result: 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 Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc

Version: 1.0.3
Check: re-building of vignette outputs
Result: 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 Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc

Version: 1.0.3
Check: installed package size
Result: NOTE installed size is 8.1Mb sub-directories of 1Mb or more: doc 7.9Mb Flavors: r-oldrel-macos-arm64, r-oldrel-macos-x86_64, r-oldrel-windows-x86_64