############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:AlpsNMR.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings AlpsNMR_4.8.0.tar.gz ### ############################################################################## ############################################################################## * using log directory 'F:/biocbuild/bbs-3.20-bioc/meat/AlpsNMR.Rcheck' * using R version 4.4.2 (2024-10-31 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 '4.8.0' * 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 ... 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 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 7.28 0.39 12.28 nmr_pca_outliers_robust 5.64 0.14 10.27 Peak_detection 3.20 0.33 30.50 plsda_auroc_vip_compare 3.20 0.03 18.50 nmr_pca_build_model 2.30 0.09 11.22 permutation_test_model 2.34 0.05 16.86 permutation_test_plot 2.33 0.03 17.51 bp_VIP_analysis 2.28 0.04 14.82 nmr_meta_add 2.13 0.07 11.06 validate_nmr_dataset 2.11 0.09 11.17 nmr_interpolate_1D 1.89 0.04 10.70 nmr_read_samples 1.78 0.06 10.69 nmr_data_analysis 1.67 0.03 10.34 plot_plsda_samples 1.68 0.00 9.21 plot_plsda_multimodel 1.61 0.02 9.67 bp_kfold_VIP_analysis 1.52 0.03 9.92 models_stability_plot_plsda 1.54 0.01 10.18 nmr_dataset_peak_table_to_SummarizedExperiment 1.42 0.08 6.06 AlpsNMR-package 1.36 0.11 6.11 SummarizedExperiment_to_nmr_dataset_peak_table 1.22 0.11 5.98 nmr_data_1r_to_SummarizedExperiment 1.20 0.05 6.02 to_ChemoSpec 1.19 0.05 6.02 tidy.nmr_dataset_1D 1.19 0.03 5.50 print.nmr_dataset_peak_table 1.06 0.08 5.45 sub-.nmr_dataset_peak_table 1.11 0.02 5.45 nmr_pca_outliers_filter 1.06 0.06 5.48 plot_interactive 1.09 0.03 8.47 new_nmr_dataset_peak_table 1.03 0.08 6.51 is.nmr_dataset_peak_table 1.03 0.07 5.44 format.nmr_dataset_peak_table 1.04 0.04 5.43 validate_nmr_dataset_family 1.00 0.06 5.36 print.nmr_dataset_1D 0.99 0.05 5.61 nmr_pca_outliers 0.95 0.08 5.55 filter.nmr_dataset_family 0.94 0.08 5.09 nmr_export_data_1r 0.96 0.03 5.28 nmr_autophase 0.92 0.05 6.16 format.nmr_dataset 0.90 0.06 5.42 is.nmr_dataset_1D 0.91 0.04 5.10 format.nmr_dataset_1D 0.89 0.05 5.36 nmr_meta_get 0.92 0.00 5.18 sub-.nmr_dataset_1D 0.89 0.03 5.19 nmr_meta_export 0.89 0.01 5.24 sub-.nmr_dataset 0.87 0.03 5.14 is.nmr_dataset 0.87 0.02 5.42 nmr_meta_groups 0.83 0.06 5.20 nmr_meta_get_column 0.86 0.02 5.16 load_and_save_functions 0.80 0.06 5.25 print.nmr_dataset 0.81 0.03 5.17 * 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: OK