############################################################################## ############################################################################## ### ### Running command: ### ### D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL OmnipathR ### ############################################################################## ############################################################################## * installing to library 'D:/biocbuild/bbs-3.15-bioc/R/library' * installing *source* package 'OmnipathR' ... ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices converting help for package 'OmnipathR' finding HTML links ... done OmnipathR html all_uniprots html ancestors html annotated_network html annotation_categories html bioplex1 html bioplex2 html bioplex3 html bioplex_all html bioplex_hct116_1 html bma_motif_es html bma_motif_vs html consensuspathdb_download html consensuspathdb_raw_table html curated_ligand_receptor_interactions html curated_ligrec_stats html descendants html dot-omnipath_options_defaults html enzsub_graph html evex_download html extra_attr_values html extra_attrs html extra_attrs_to_cols html filter_by_resource html filter_extra_attrs html filter_intercell html filter_intercell_network html find_all_paths html get_annotation_resources html get_complex_genes html get_complex_resources html get_db html get_enzsub_resources html get_interaction_resources html get_intercell_categories html get_intercell_generic_categories html get_intercell_resources html get_ontology_db html get_resources html get_signed_ptms html giant_component html go_annot_download html go_annot_slim html go_ontology_download html guide2pharma_download html harmonizome_download html has_extra_attrs html hpo_download html htridb_download html import_all_interactions html import_dorothea_interactions html REDIRECT:topic Previous alias or file overwritten by alias: D:/biocbuild/bbs-3.15-bioc/R/library/00LOCK-OmnipathR/00new/OmnipathR/help/import_tfregulons_interactions.html import_intercell_network html import_kinaseextra_interactions html REDIRECT:topic Previous alias or file overwritten by alias: D:/biocbuild/bbs-3.15-bioc/R/library/00LOCK-OmnipathR/00new/OmnipathR/help/import_KinaseExtra_Interactions.html import_ligrecextra_interactions html REDIRECT:topic Previous alias or file overwritten by alias: D:/biocbuild/bbs-3.15-bioc/R/library/00LOCK-OmnipathR/00new/OmnipathR/help/import_LigrecExtra_Interactions.html import_lncrna_mrna_interactions html import_mirnatarget_interactions html REDIRECT:topic Previous alias or file overwritten by alias: D:/biocbuild/bbs-3.15-bioc/R/library/00LOCK-OmnipathR/00new/OmnipathR/help/import_miRNAtarget_Interactions.html import_omnipath_annotations html REDIRECT:topic Previous alias or file overwritten by alias: D:/biocbuild/bbs-3.15-bioc/R/library/00LOCK-OmnipathR/00new/OmnipathR/help/import_Omnipath_annotations.html REDIRECT:topic Previous alias or file overwritten by alias: D:/biocbuild/bbs-3.15-bioc/R/library/00LOCK-OmnipathR/00new/OmnipathR/help/import_OmniPath_annotations.html import_omnipath_complexes html REDIRECT:topic Previous alias or file overwritten by alias: D:/biocbuild/bbs-3.15-bioc/R/library/00LOCK-OmnipathR/00new/OmnipathR/help/import_Omnipath_complexes.html REDIRECT:topic Previous alias or file overwritten by alias: D:/biocbuild/bbs-3.15-bioc/R/library/00LOCK-OmnipathR/00new/OmnipathR/help/import_OmniPath_complexes.html import_omnipath_enzsub html REDIRECT:topic Previous alias or file overwritten by alias: D:/biocbuild/bbs-3.15-bioc/R/library/00LOCK-OmnipathR/00new/OmnipathR/help/import_OmniPath_PTMS.html import_omnipath_interactions html REDIRECT:topic Previous alias or file overwritten by alias: D:/biocbuild/bbs-3.15-bioc/R/library/00LOCK-OmnipathR/00new/OmnipathR/help/import_Omnipath_Interactions.html REDIRECT:topic Previous alias or file overwritten by alias: D:/biocbuild/bbs-3.15-bioc/R/library/00LOCK-OmnipathR/00new/OmnipathR/help/import_OmniPath_Interactions.html import_omnipath_intercell html REDIRECT:topic Previous alias or file overwritten by alias: D:/biocbuild/bbs-3.15-bioc/R/library/00LOCK-OmnipathR/00new/OmnipathR/help/import_Omnipath_intercell.html REDIRECT:topic Previous alias or file overwritten by alias: D:/biocbuild/bbs-3.15-bioc/R/library/00LOCK-OmnipathR/00new/OmnipathR/help/import_OmniPath_intercell.html import_pathwayextra_interactions html REDIRECT:topic Previous alias or file overwritten by alias: D:/biocbuild/bbs-3.15-bioc/R/library/00LOCK-OmnipathR/00new/OmnipathR/help/import_PathwayExtra_Interactions.html import_post_translational_interactions html import_small_molecule_protein_interactions html import_tf_mirna_interactions html import_tf_target_interactions html import_transcriptional_interactions html inbiomap_download html inbiomap_raw html interaction_graph html intercell_categories html intercell_consensus_filter html is_ontology_id html kegg_info html kegg_open html kegg_pathway_annotations html kegg_pathway_download html kegg_pathway_list html kegg_pathways_download html kegg_picture html kegg_process html load_db html nichenet_build_model html nichenet_expression_data html nichenet_gr_network html nichenet_gr_network_evex html nichenet_gr_network_harmonizome html nichenet_gr_network_htridb html nichenet_gr_network_omnipath html nichenet_gr_network_pathwaycommons html nichenet_gr_network_regnetwork html nichenet_gr_network_remap html nichenet_gr_network_trrust html nichenet_ligand_activities html nichenet_ligand_target_links html nichenet_ligand_target_matrix html nichenet_lr_network html nichenet_lr_network_guide2pharma html nichenet_lr_network_omnipath html nichenet_lr_network_ramilowski html nichenet_main html nichenet_networks html nichenet_optimization html nichenet_remove_orphan_ligands html nichenet_results_dir html nichenet_signaling_network html nichenet_signaling_network_cpdb html nichenet_signaling_network_evex html nichenet_signaling_network_harmonizome html nichenet_signaling_network_inbiomap html nichenet_signaling_network_omnipath html nichenet_signaling_network_pathwaycommons html nichenet_signaling_network_vinayagam html nichenet_test html nichenet_workarounds html obo_parser html omnipath_cache_autoclean html omnipath_cache_clean html omnipath_cache_clean_db html omnipath_cache_download_ready html omnipath_cache_filter_versions html omnipath_cache_get html omnipath_cache_key html omnipath_cache_latest_or_new html omnipath_cache_latest_version html omnipath_cache_load html omnipath_cache_move_in html omnipath_cache_remove html omnipath_cache_save html omnipath_cache_search html omnipath_cache_set_ext html omnipath_cache_update_status html omnipath_cache_wipe html omnipath_get_config_path html omnipath_load_config html omnipath_log html omnipath_logfile html omnipath_msg html omnipath_reset_config html omnipath_save_config html omnipath_set_cachedir html omnipath_set_console_loglevel html omnipath_set_logfile_loglevel html omnipath_set_loglevel html omnipath_show_db html omnipath_unlock_cache_db html ontology_ensure_id html ontology_ensure_name html ontology_name_id html pathwaycommons_download html pivot_annotations html preppi_download html preppi_filter html print_bma_motif_es html print_bma_motif_vs html print_interactions html print_path_es html print_path_vs html ramilowski_download html regnetwork_directions html regnetwork_download html relations_list_to_table html relations_table_to_graph html relations_table_to_list html remap_dorothea_download html remap_filtered html remap_tf_target_download html resources_colname html simplify_intercell_network html swap_relations html tfcensus_download html translate_ids html trrust_download html uniprot_full_id_mapping_table html uniprot_id_mapping_table html unique_intercell_network html vinayagam_download html walk_ontology_tree html with_extra_attrs html with_references html zenodo_download html *** copying figures ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location [2022-03-17 15:56:02] [INFO] [OmnipathR] Initialized cache: `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR`. [2022-03-17 15:56:02] [INFO] [OmnipathR] Welcome to OmnipathR! [2022-03-17 15:56:02] [TRACE] [OmnipathR] Cache locked: FALSE ** testing if installed package can be loaded from final location [2022-03-17 15:56:03] [INFO] [OmnipathR] Initialized cache: `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR`. [2022-03-17 15:56:04] [INFO] [OmnipathR] Welcome to OmnipathR! [2022-03-17 15:56:04] [TRACE] [OmnipathR] Cache locked: FALSE ** testing if installed package keeps a record of temporary installation path * DONE (OmnipathR) Making 'packages.html' ...Warning in packageDescription(i, lib.loc = lib, fields = "Title", encoding = "UTF-8") : DESCRIPTION file of package 'PoDCall' is missing or broken done