############################################################################## ############################################################################## ### ### 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_4.7.2.tar.gz ### ############################################################################## ############################################################################## * using log directory 'F:/biocbuild/bbs-3.20-bioc/meat/AlpsNMR.Rcheck' * using R version 4.4.1 (2024-06-14 ucrt) * using platform: x86_64-w64-mingw32 * R was compiled by gcc.exe (GCC) 13.2.0 GNU Fortran (GCC) 13.2.0 * 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 '4.7.2' * 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 6.92 0.29 12.04 nmr_pca_outliers_robust 5.92 0.12 10.58 Peak_detection 3.19 0.30 31.69 plsda_auroc_vip_compare 3.12 0.13 18.75 permutation_test_plot 2.30 0.11 16.69 nmr_meta_add 2.12 0.17 11.54 bp_VIP_analysis 2.16 0.03 15.89 nmr_interpolate_1D 2.06 0.06 11.00 nmr_pca_build_model 2.06 0.06 12.12 permutation_test_model 2.08 0.04 16.60 validate_nmr_dataset 1.98 0.07 10.97 nmr_read_samples 1.80 0.06 11.05 nmr_data_analysis 1.61 0.00 10.42 bp_kfold_VIP_analysis 1.50 0.03 10.42 AlpsNMR-package 1.43 0.05 6.24 models_stability_plot_plsda 1.44 0.02 9.98 plot_plsda_multimodel 1.41 0.03 10.04 plot_plsda_samples 1.43 0.00 9.69 to_ChemoSpec 1.36 0.06 6.14 nmr_data_1r_to_SummarizedExperiment 1.31 0.05 5.88 nmr_dataset_peak_table_to_SummarizedExperiment 1.30 0.05 5.87 SummarizedExperiment_to_nmr_dataset_peak_table 1.20 0.05 6.24 nmr_pca_outliers 1.13 0.08 7.97 tidy.nmr_dataset_1D 1.15 0.03 5.61 nmr_pca_outliers_filter 1.14 0.02 5.39 validate_nmr_dataset_family 1.03 0.08 5.53 format.nmr_dataset_1D 1.00 0.07 5.62 is.nmr_dataset_peak_table 1.03 0.04 5.89 format.nmr_dataset_peak_table 1.05 0.01 5.64 sub-.nmr_dataset_peak_table 1.02 0.03 5.55 is.nmr_dataset_1D 0.97 0.07 5.73 print.nmr_dataset_peak_table 1.03 0.00 8.80 plot_interactive 0.96 0.05 5.53 new_nmr_dataset_peak_table 0.94 0.06 5.62 print.nmr_dataset_1D 0.95 0.05 5.37 sub-.nmr_dataset_1D 0.96 0.04 5.50 nmr_autophase 0.89 0.08 5.33 nmr_export_data_1r 0.93 0.03 5.44 nmr_meta_get_column 0.92 0.04 5.40 filter.nmr_dataset_family 0.95 0.01 5.83 print.nmr_dataset 0.94 0.01 5.49 format.nmr_dataset 0.90 0.03 5.47 sub-.nmr_dataset 0.90 0.02 5.60 nmr_meta_export 0.86 0.05 5.67 nmr_meta_get 0.86 0.05 5.75 is.nmr_dataset 0.86 0.03 5.33 load_and_save_functions 0.81 0.08 5.49 nmr_meta_groups 0.86 0.02 5.33 * 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