* installing to library ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages’ * installing *source* package ‘specmine’ ... ** this is package ‘specmine’ version ‘4.0.0’ ** package ‘specmine’ successfully unpacked and MD5 sums checked ** using staged installation ** R ** data *** moving datasets to lazyload DB ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices converting help for package ‘specmine’ finding HTML links ... done aggregate_samples html airPLS_fast_dataset html aov_all_vars html aov_one_var html apply_by_group html apply_by_groups html baseline_correction html convert_chebi_to_kegg html convert_from_chemospec html convert_hmdb_to_kegg html convert_keggpathway_2_reactiongraph html convert_multiple_spcmnm_to_kegg html count_missing_values html count_missing_values_per_sample html count_missing_values_per_variable html create_dataset html create_pathway_with_reactions html dataset_from_peaks html feature_selection html filter_feature_selection html flat_pattern_filter html get_MetabolitePath html get_OrganismsCodes html get_cpd_names html get_files_list_per_assay html get_metabPaths_org html get_metabolights_study html get_metabolights_study_files_assay html get_metabolights_study_metadata_assay html get_metabolights_study_samples_files html get_paths_with_cpds_org html get_peak_values html get_samples_names_dx html get_x_label html get_x_values_as_text html ica_analysis_dataset html ica_kmeans_plot2D html ica_kmeans_plot3D html ica_loadingsplot html ica_pairs_kmeans_plot html ica_pairs_plot html ica_scoresplot2D html ica_scoresplot3D html impute_nas_knn html impute_nas_mean html impute_nas_median html impute_nas_value html merge_data_metadata html metabolights_studies_list html missingvalues_imputation html multiClassSummary html pathway_analysis html pca_analysis_dataset html pca_biplot html pca_biplot3D html pca_importance html pca_kmeans_plot2D html pca_kmeans_plot3D html pca_pairs_kmeans_plot html pca_pairs_plot html pca_plot_3d html pca_robust html pca_scoresplot2D html pca_scoresplot3D html pca_scoresplot3D_rgl html pca_screeplot html peak_detection2d html raman_align_peaks html raman_crop_spectra html raman_despike html raman_find_peaks html raman_normalize html raman_normalize_peak_features html raman_sgolay_derivative html raman_transform_fourier html raman_transform_wavelet html read-spc html read_csvs_folder html read_data_csv html read_data_dx html read_dataset_csv html read_dataset_dx html read_metadata html read_ms_spectra html read_multiple_csvs html recursive_feature_elimination html remove_data html remove_data_variables html remove_metadata_variables html remove_samples html remove_samples_by_na_metadata html remove_samples_by_nas html remove_variables_by_nas html remove_x_values_by_interval html specmine-package html spectra_options html subset_by_samples_and_xvalues html subset_metadata html subset_random_samples html subset_samples html subset_samples_by_metadata_values html subset_x_values html subset_x_values_by_interval html summary_var_importance html train_and_predict html train_classifier html train_models_performance html tsne_analysis_dataset html tsne_kmeans_plot2D html tsne_kmeans_plot3D html tsne_pairs_kmeans_plot html tsne_pairs_plot html tsne_scoresplot2D html tsne_scoresplot3D html umap_analysis_dataset html umap_kmeans_plot2D html umap_kmeans_plot3D html umap_pairs_kmeans_plot html umap_pairs_plot html umap_scoresplot2D html umap_scoresplot3D html ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (specmine)