############################################################################## ############################################################################## ### ### Running command: ### ### E:\biocbuild\bbs-3.21-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:AlpsNMR.install-out.txt --library=E:\biocbuild\bbs-3.21-bioc\R\library --no-vignettes --timings AlpsNMR_4.9.0.tar.gz ### ############################################################################## ############################################################################## * using log directory 'E:/biocbuild/bbs-3.21-bioc/meat/AlpsNMR.Rcheck' * using R Under development (unstable) (2025-01-21 r87610 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 * using option '--no-vignettes' * checking for file 'AlpsNMR/DESCRIPTION' ... OK * checking extension type ... Package * this is package 'AlpsNMR' version '4.9.0' * 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 'AlpsNMR' can be installed ... OK * checking installed package size ... OK * 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 ... OK * checking whether the package can be loaded with stated dependencies ... OK * checking whether the package can be unloaded cleanly ... OK * checking whether the namespace can be loaded with stated dependencies ... OK * checking whether the namespace can be unloaded cleanly ... 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 ... OK * checking Rd files ... OK * checking Rd metadata ... OK * checking Rd cross-references ... NOTE Found the following Rd file(s) with Rd \link{} targets missing package anchors: filter.nmr_dataset_family.Rd: dplyr Please provide package anchors for all Rd \link{} targets not in the package itself and the base packages. * 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 data for ASCII and uncompressed saves ... OK * checking sizes of PDF files under 'inst/doc' ... OK * checking files in 'vignettes' ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed SummarizedExperiment_to_nmr_data_1r 6.81 0.34 11.80 nmr_pca_outliers_robust 6.03 0.20 10.69 Peak_detection 3.16 0.25 29.91 plsda_auroc_vip_compare 3.09 0.04 18.42 permutation_test_model 2.22 0.03 16.27 nmr_meta_add 2.19 0.05 10.84 bp_VIP_analysis 2.05 0.08 14.23 nmr_pca_build_model 2.00 0.10 10.67 validate_nmr_dataset 1.97 0.12 10.59 permutation_test_plot 2.02 0.01 17.11 nmr_interpolate_1D 1.81 0.03 10.41 nmr_read_samples 1.67 0.06 10.75 nmr_data_analysis 1.52 0.01 10.02 plot_plsda_samples 1.47 0.03 9.08 bp_kfold_VIP_analysis 1.36 0.08 9.99 models_stability_plot_plsda 1.42 0.02 10.31 SummarizedExperiment_to_nmr_dataset_peak_table 1.37 0.06 5.89 nmr_data_1r_to_SummarizedExperiment 1.34 0.06 5.81 plot_plsda_multimodel 1.33 0.06 9.86 to_ChemoSpec 1.30 0.07 5.50 nmr_pca_outliers 1.18 0.08 5.65 AlpsNMR-package 1.21 0.03 5.67 nmr_dataset_peak_table_to_SummarizedExperiment 1.18 0.05 5.64 tidy.nmr_dataset_1D 1.11 0.04 5.19 is.nmr_dataset_peak_table 1.06 0.06 5.61 new_nmr_dataset_peak_table 1.08 0.03 5.49 validate_nmr_dataset_family 1.03 0.06 5.78 format.nmr_dataset_peak_table 1.03 0.04 5.23 nmr_pca_outliers_filter 1.06 0.00 5.57 filter.nmr_dataset_family 1.02 0.03 5.42 format.nmr_dataset_1D 0.92 0.06 5.39 print.nmr_dataset_peak_table 0.91 0.06 5.29 nmr_meta_get 0.93 0.02 5.20 print.nmr_dataset_1D 0.89 0.05 5.25 nmr_export_data_1r 0.90 0.03 5.16 is.nmr_dataset_1D 0.92 0.00 5.67 plot_interactive 0.90 0.02 5.42 format.nmr_dataset 0.89 0.02 5.21 print.nmr_dataset 0.89 0.00 5.40 nmr_meta_groups 0.86 0.01 5.59 sub-.nmr_dataset_1D 0.80 0.02 5.12 load_and_save_functions 0.80 0.00 5.32 nmr_meta_export 0.77 0.03 5.14 nmr_meta_get_column 0.75 0.03 5.08 * checking for unstated dependencies in 'tests' ... OK * checking tests ... Running 'testthat.R' OK * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... OK * checking running R code from vignettes ... SKIPPED * checking re-building of vignette outputs ... SKIPPED * checking PDF version of manual ... OK * DONE Status: 1 NOTE See 'E:/biocbuild/bbs-3.21-bioc/meat/AlpsNMR.Rcheck/00check.log' for details.