Back to Multiple platform build/check report for BioC 3.14
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This page was generated on 2022-04-11 12:06:41 -0400 (Mon, 11 Apr 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_644.1.3 (2022-03-10) -- "One Push-Up" 4323
tokay2Windows Server 2012 R2 Standardx644.1.3 (2022-03-10) -- "One Push-Up" 4077
machv2macOS 10.14.6 Mojavex86_644.1.3 (2022-03-10) -- "One Push-Up" 4136
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

BUILD BIN results for OmnipathR on tokay2


To the developers/maintainers of the OmnipathR package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/OmnipathR.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 1330/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
OmnipathR 3.2.9  (landing page)
Denes Turei
Snapshot Date: 2022-04-10 01:55:06 -0400 (Sun, 10 Apr 2022)
git_url: https://git.bioconductor.org/packages/OmnipathR
git_branch: RELEASE_3_14
git_last_commit: 127afee
git_last_commit_date: 2022-04-05 19:00:39 -0400 (Tue, 05 Apr 2022)
nebbiolo2Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    ERROR  
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    ERROR    OK  
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    ERROR    OK  

Summary

Package: OmnipathR
Version: 3.2.9
Command: rm -rf OmnipathR.buildbin-libdir && mkdir OmnipathR.buildbin-libdir && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=OmnipathR.buildbin-libdir OmnipathR_3.2.9.tar.gz
StartedAt: 2022-04-11 06:50:58 -0400 (Mon, 11 Apr 2022)
EndedAt: 2022-04-11 06:51:26 -0400 (Mon, 11 Apr 2022)
EllapsedTime: 28.1 seconds
RetCode: 0
Status:   OK  
PackageFile: OmnipathR_3.2.9.zip
PackageFileSize: 2.146 MiB

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf OmnipathR.buildbin-libdir && mkdir OmnipathR.buildbin-libdir && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=OmnipathR.buildbin-libdir OmnipathR_3.2.9.tar.gz
###
##############################################################################
##############################################################################



install for i386

* 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  
    descendants                             html  
    dot-omnipath_options_defaults           html  
    enzsub_graph                            html  
    evex_download                           html  
    filter_by_resource                      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  
    hpo_download                            html  
    htridb_download                         html  
    import_all_interactions                 html  
    import_dorothea_interactions            html  
REDIRECT:topic	 Previous alias or file overwritten by alias: C:/Users/biocbuild/bbs-3.14-bioc/meat/OmnipathR.buildbin-libdir/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: C:/Users/biocbuild/bbs-3.14-bioc/meat/OmnipathR.buildbin-libdir/00LOCK-OmnipathR/00new/OmnipathR/help/import_KinaseExtra_Interactions.html
    import_ligrecextra_interactions         html  
REDIRECT:topic	 Previous alias or file overwritten by alias: C:/Users/biocbuild/bbs-3.14-bioc/meat/OmnipathR.buildbin-libdir/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: C:/Users/biocbuild/bbs-3.14-bioc/meat/OmnipathR.buildbin-libdir/00LOCK-OmnipathR/00new/OmnipathR/help/import_miRNAtarget_Interactions.html
    import_omnipath_annotations             html  
REDIRECT:topic	 Previous alias or file overwritten by alias: C:/Users/biocbuild/bbs-3.14-bioc/meat/OmnipathR.buildbin-libdir/00LOCK-OmnipathR/00new/OmnipathR/help/import_Omnipath_annotations.html
REDIRECT:topic	 Previous alias or file overwritten by alias: C:/Users/biocbuild/bbs-3.14-bioc/meat/OmnipathR.buildbin-libdir/00LOCK-OmnipathR/00new/OmnipathR/help/import_OmniPath_annotations.html
    import_omnipath_complexes               html  
REDIRECT:topic	 Previous alias or file overwritten by alias: C:/Users/biocbuild/bbs-3.14-bioc/meat/OmnipathR.buildbin-libdir/00LOCK-OmnipathR/00new/OmnipathR/help/import_Omnipath_complexes.html
REDIRECT:topic	 Previous alias or file overwritten by alias: C:/Users/biocbuild/bbs-3.14-bioc/meat/OmnipathR.buildbin-libdir/00LOCK-OmnipathR/00new/OmnipathR/help/import_OmniPath_complexes.html
    import_omnipath_enzsub                  html  
REDIRECT:topic	 Previous alias or file overwritten by alias: C:/Users/biocbuild/bbs-3.14-bioc/meat/OmnipathR.buildbin-libdir/00LOCK-OmnipathR/00new/OmnipathR/help/import_OmniPath_PTMS.html
    import_omnipath_interactions            html  
REDIRECT:topic	 Previous alias or file overwritten by alias: C:/Users/biocbuild/bbs-3.14-bioc/meat/OmnipathR.buildbin-libdir/00LOCK-OmnipathR/00new/OmnipathR/help/import_Omnipath_Interactions.html
REDIRECT:topic	 Previous alias or file overwritten by alias: C:/Users/biocbuild/bbs-3.14-bioc/meat/OmnipathR.buildbin-libdir/00LOCK-OmnipathR/00new/OmnipathR/help/import_OmniPath_Interactions.html
    import_omnipath_intercell               html  
REDIRECT:topic	 Previous alias or file overwritten by alias: C:/Users/biocbuild/bbs-3.14-bioc/meat/OmnipathR.buildbin-libdir/00LOCK-OmnipathR/00new/OmnipathR/help/import_Omnipath_intercell.html
REDIRECT:topic	 Previous alias or file overwritten by alias: C:/Users/biocbuild/bbs-3.14-bioc/meat/OmnipathR.buildbin-libdir/00LOCK-OmnipathR/00new/OmnipathR/help/import_OmniPath_intercell.html
    import_pathwayextra_interactions        html  
REDIRECT:topic	 Previous alias or file overwritten by alias: C:/Users/biocbuild/bbs-3.14-bioc/meat/OmnipathR.buildbin-libdir/00LOCK-OmnipathR/00new/OmnipathR/help/import_PathwayExtra_Interactions.html
    import_post_translational_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  
    zenodo_download                         html  
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
[2022-04-11 06:51:17] [INFO]    [OmnipathR] Initialized cache: `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR`.
[2022-04-11 06:51:17] [INFO]    [OmnipathR] Welcome to OmnipathR!
[2022-04-11 06:51:17] [TRACE]   [OmnipathR] Cache locked: FALSE
** testing if installed package can be loaded from final location
[2022-04-11 06:51:19] [INFO]    [OmnipathR] Initialized cache: `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR`.
[2022-04-11 06:51:19] [INFO]    [OmnipathR] Welcome to OmnipathR!
[2022-04-11 06:51:19] [TRACE]   [OmnipathR] Cache locked: FALSE
** testing if installed package keeps a record of temporary installation path

install for x64

* installing *source* package 'OmnipathR' ...
** testing if installed package can be loaded
[2022-04-11 06:51:24] [INFO]    [OmnipathR] Initialized cache: `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR`.
[2022-04-11 06:51:24] [INFO]    [OmnipathR] Welcome to OmnipathR!
[2022-04-11 06:51:24] [TRACE]   [OmnipathR] Cache locked: FALSE
* MD5 sums
packaged installation of 'OmnipathR' as OmnipathR_3.2.9.zip
* DONE (OmnipathR)