| Back to Multiple platform build/check report for BioC 3.16: simplified long |
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This page was generated on 2023-04-12 11:06:18 -0400 (Wed, 12 Apr 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 20.04.5 LTS) | x86_64 | 4.2.3 (2023-03-15) -- "Shortstop Beagle" | 4502 |
| palomino4 | Windows Server 2022 Datacenter | x64 | 4.2.3 (2023-03-15 ucrt) -- "Shortstop Beagle" | 4282 |
| lconway | macOS 12.5.1 Monterey | x86_64 | 4.2.3 (2023-03-15) -- "Shortstop Beagle" | 4310 |
| 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 | ||||
|
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. |
| Package 1393/2183 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| OmnipathR 3.6.6 (landing page) Denes Turei
| nebbiolo2 | Linux (Ubuntu 20.04.5 LTS) / x86_64 | OK | OK | TIMEOUT | |||||||||
| palomino4 | Windows Server 2022 Datacenter / x64 | OK | OK | TIMEOUT | OK | |||||||||
| lconway | macOS 12.5.1 Monterey / x86_64 | OK | OK | TIMEOUT | OK | |||||||||
| Package: OmnipathR |
| Version: 3.6.6 |
| Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:OmnipathR.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings OmnipathR_3.6.6.tar.gz |
| StartedAt: 2023-04-10 21:37:14 -0400 (Mon, 10 Apr 2023) |
| EndedAt: 2023-04-10 22:17:15 -0400 (Mon, 10 Apr 2023) |
| EllapsedTime: 2400.8 seconds |
| RetCode: None |
| Status: TIMEOUT |
| CheckDir: OmnipathR.Rcheck |
| Warnings: NA |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:OmnipathR.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings OmnipathR_3.6.6.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.16-bioc/meat/OmnipathR.Rcheck’ * using R version 4.2.3 (2023-03-15) * using platform: x86_64-apple-darwin17.0 (64-bit) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘OmnipathR/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘OmnipathR’ version ‘3.6.6’ * 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 for sufficient/correct file permissions ... OK * checking whether package ‘OmnipathR’ can be installed ... OK * checking installed package size ... OK * checking package 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 R 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 ... NOTE [2023-04-10 21:37:42] [INFO] [OmnipathR] Initialized cache: `/Users/biocbuild/Library/Caches/OmnipathR`. [2023-04-10 21:37:42] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2023-04-10 21:37:42] [TRACE] [OmnipathR] Cache is at `/Users/biocbuild/Library/Caches/OmnipathR`. [2023-04-10 21:37:42] [TRACE] [OmnipathR] Contains 1 files. [2023-04-10 21:37:42] [TRACE] [OmnipathR] Cache is locked: FALSE. [2023-04-10 21:37:42] [SUCCESS] [OmnipathR] Removing all cache contents from `/Users/biocbuild/Library/Caches/OmnipathR`. [2023-04-10 21:37:42] [TRACE] [OmnipathR] Pandoc version: `2.7.3`. [2023-04-10 21:37:42] [TRACE] [OmnipathR] Cache locked: FALSE * 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 R/sysdata.rda ... OK * checking files in ‘vignettes’ ... OK * checking examples ...
OmnipathR.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL OmnipathR ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.2/Resources/library’ * installing *source* package ‘OmnipathR’ ... ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices *** copying figures ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location [2023-04-10 15:18:54] [INFO] [OmnipathR] Initialized cache: `/Users/biocbuild/Library/Caches/OmnipathR`. [2023-04-10 15:18:54] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2023-04-10 15:18:54] [TRACE] [OmnipathR] Cache is at `/Users/biocbuild/Library/Caches/OmnipathR`. [2023-04-10 15:18:54] [TRACE] [OmnipathR] Contains 1 files. [2023-04-10 15:18:54] [TRACE] [OmnipathR] Cache is locked: FALSE. [2023-04-10 15:18:54] [SUCCESS] [OmnipathR] Removing all cache contents from `/Users/biocbuild/Library/Caches/OmnipathR`. [2023-04-10 15:18:54] [TRACE] [OmnipathR] Pandoc version: `2.7.3`. [2023-04-10 15:18:54] [TRACE] [OmnipathR] Cache locked: FALSE ** testing if installed package can be loaded from final location [2023-04-10 15:18:56] [INFO] [OmnipathR] Initialized cache: `/Users/biocbuild/Library/Caches/OmnipathR`. [2023-04-10 15:18:56] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2023-04-10 15:18:56] [TRACE] [OmnipathR] Cache is at `/Users/biocbuild/Library/Caches/OmnipathR`. [2023-04-10 15:18:56] [TRACE] [OmnipathR] Contains 1 files. [2023-04-10 15:18:56] [TRACE] [OmnipathR] Cache is locked: FALSE. [2023-04-10 15:18:56] [SUCCESS] [OmnipathR] Removing all cache contents from `/Users/biocbuild/Library/Caches/OmnipathR`. [2023-04-10 15:18:56] [TRACE] [OmnipathR] Pandoc version: `2.7.3`. [2023-04-10 15:18:56] [TRACE] [OmnipathR] Cache locked: FALSE ** testing if installed package keeps a record of temporary installation path * DONE (OmnipathR)
OmnipathR.Rcheck/OmnipathR-Ex.timings
| name | user | system | elapsed | |
| OmnipathR | 0.000 | 0.001 | 0.001 | |
| all_uniprot_acs | 0.753 | 0.068 | 16.613 | |
| all_uniprots | 0.192 | 0.017 | 6.762 | |
| ancestors | 7.918 | 0.538 | 8.987 | |
| annotated_network | 0.511 | 0.056 | 3.907 | |
| annotation_categories | 69.846 | 0.169 | 71.575 | |
| biomart_query | 0.718 | 0.067 | 4.550 | |
| bioplex1 | 0.371 | 0.053 | 0.880 | |
| bioplex2 | 0.610 | 0.098 | 1.133 | |
| bioplex3 | 1.171 | 0.267 | 2.815 | |
| bioplex_all | 45.981 | 1.263 | 47.826 | |
| bioplex_hct116_1 | 0.121 | 0.004 | 0.125 | |
| bma_motif_es | 0.288 | 0.035 | 1.641 | |
| bma_motif_vs | 0.099 | 0.006 | 0.803 | |
| common_name | 0.026 | 0.000 | 0.027 | |
| consensuspathdb_download | 0.001 | 0.000 | 0.000 | |
| consensuspathdb_raw_table | 14.048 | 1.275 | 50.838 | |
| curated_ligand_receptor_interactions | 5.441 | 3.835 | 25.875 | |
| curated_ligrec_stats | 23.566 | 6.926 | 110.709 | |
| descendants | 0.955 | 0.024 | 1.479 | |
| ensembl_dataset | 0.014 | 0.000 | 0.015 | |
| ensembl_id_mapping_table | 0.960 | 0.112 | 40.103 | |
| ensembl_id_type | 0.006 | 0.001 | 0.007 | |
| ensembl_name | 0.082 | 0.003 | 0.131 | |
| ensembl_organisms | 0.232 | 0.023 | 0.440 | |
| ensembl_organisms_raw | 0.389 | 0.033 | 0.682 | |
| ensembl_orthology | 0.000 | 0.000 | 0.001 | |
| enzsub_graph | 1.755 | 0.147 | 4.951 | |
| evex_download | 156.983 | 2.963 | 198.777 | |
| extra_attr_values | 14.371 | 0.278 | 17.259 | |
| extra_attrs | 8.165 | 0.107 | 8.286 | |
| extra_attrs_to_cols | 11.128 | 0.032 | 11.173 | |
| filter_by_resource | 5.343 | 0.121 | 7.997 | |
| filter_extra_attrs | 19.263 | 0.075 | 19.930 | |
| filter_intercell | 4.189 | 0.318 | 8.547 | |
| filter_intercell_network | 175.590 | 1.613 | 194.050 | |
| find_all_paths | 5.356 | 0.180 | 5.548 | |
| get_annotation_resources | 0.123 | 0.006 | 0.821 | |
| get_complex_genes | 1.047 | 0.056 | 3.040 | |
| get_complex_resources | 0.043 | 0.003 | 0.660 | |
| get_db | 0.347 | 0.023 | 0.425 | |
| get_enzsub_resources | 0.047 | 0.003 | 0.589 | |
| get_interaction_resources | 0.041 | 0.005 | 0.587 | |
| get_intercell_categories | 0.331 | 0.033 | 0.603 | |
| get_intercell_generic_categories | 0.022 | 0.002 | 0.025 | |
| get_intercell_resources | 0.046 | 0.002 | 0.590 | |
| get_ontology_db | 0.195 | 0.002 | 0.198 | |
| get_resources | 0.049 | 0.003 | 0.596 | |
| get_signed_ptms | 6.361 | 0.138 | 7.049 | |
| giant_component | 8.131 | 0.467 | 11.177 | |
| go_annot_download | 6.899 | 1.122 | 6.962 | |
| go_annot_slim | 0.000 | 0.001 | 0.000 | |
| go_ontology_download | 0.088 | 0.003 | 0.092 | |
| guide2pharma_download | 1.448 | 0.115 | 4.482 | |
| harmonizome_download | 0.296 | 0.024 | 0.553 | |
| has_extra_attrs | 10.453 | 0.086 | 10.557 | |
| homologene_download | 2.654 | 0.202 | 5.216 | |
| homologene_raw | 0.965 | 0.012 | 0.982 | |
| homologene_uniprot_orthology | 3.421 | 0.173 | 14.888 | |
| homology_translate | 0 | 0 | 0 | |
| hpo_download | 1.428 | 0.163 | 2.642 | |
| htridb_download | 0.635 | 0.054 | 8.211 | |
| import_all_interactions | 2.379 | 0.099 | 4.958 | |
| import_dorothea_interactions | 2.231 | 0.071 | 4.529 | |
| import_intercell_network | 21.080 | 0.250 | 26.028 | |
| import_kinaseextra_interactions | 1.483 | 0.061 | 3.715 | |
| import_ligrecextra_interactions | 1.272 | 0.175 | 3.131 | |
| import_lncrna_mrna_interactions | 0.360 | 0.037 | 1.163 | |
| import_mirnatarget_interactions | 0.714 | 0.057 | 2.277 | |
| import_omnipath_annotations | 0.385 | 0.032 | 1.195 | |
| import_omnipath_complexes | 0.414 | 0.037 | 2.208 | |
| import_omnipath_enzsub | 0.834 | 0.008 | 1.382 | |
| import_omnipath_interactions | 0.156 | 0.008 | 0.706 | |
| import_omnipath_intercell | 0.404 | 0.035 | 0.968 | |
| import_pathwayextra_interactions | 0.519 | 0.047 | 2.233 | |
| import_post_translational_interactions | 0.639 | 0.052 | 2.432 | |
| import_small_molecule_protein_interactions | 0.361 | 0.020 | 0.616 | |
| import_tf_mirna_interactions | 0.556 | 0.040 | 1.672 | |
| import_tf_target_interactions | 0.998 | 0.054 | 2.773 | |
| import_transcriptional_interactions | 1.446 | 0.060 | 3.497 | |
| inbiomap_download | 0.000 | 0.001 | 0.000 | |
| inbiomap_raw | 0.000 | 0.001 | 0.000 | |
| interaction_graph | 0.359 | 0.006 | 0.906 | |
| intercell_categories | 0.040 | 0.003 | 0.043 | |
| intercell_consensus_filter | 0.952 | 0.083 | 2.491 | |
| is_ontology_id | 0.000 | 0.000 | 0.001 | |
| is_swissprot | 0.071 | 0.004 | 0.076 | |
| is_trembl | 0.732 | 0.074 | 20.554 | |
| is_uniprot | 0.257 | 0.007 | 0.264 | |
| kegg_info | 0.344 | 0.022 | 3.933 | |
| kegg_open | 0.003 | 0.005 | 0.020 | |
| kegg_pathway_annotations | 0.001 | 0.000 | 0.001 | |
| kegg_pathway_download | 1.415 | 0.083 | 10.430 | |
| kegg_pathway_list | 0.465 | 0.044 | 3.229 | |
| kegg_pathways_download | 0 | 0 | 0 | |
| kegg_picture | 0.065 | 0.008 | 1.104 | |
| kegg_process | 0.106 | 0.002 | 0.109 | |
| latin_name | 0.056 | 0.001 | 0.058 | |
| load_db | 0.409 | 0.016 | 0.427 | |
| ncbi_taxid | 0.054 | 0.001 | 0.055 | |
| nichenet_build_model | 0 | 0 | 0 | |
| nichenet_expression_data | 0 | 0 | 0 | |
| nichenet_gr_network | 6.294 | 0.281 | 8.106 | |
| nichenet_gr_network_evex | 141.032 | 1.493 | 142.002 | |
| nichenet_gr_network_harmonizome | 3.922 | 0.554 | 5.324 | |
| nichenet_gr_network_htridb | 0.055 | 0.002 | 0.059 | |
| nichenet_gr_network_omnipath | 6.054 | 0.369 | 8.294 | |
| nichenet_gr_network_pathwaycommons | 4.557 | 0.375 | 8.459 | |
| nichenet_gr_network_regnetwork | 1.612 | 0.181 | 8.916 | |
| nichenet_gr_network_remap | 0 | 0 | 0 | |
| nichenet_gr_network_trrust | 0.453 | 0.029 | 5.801 | |
| nichenet_ligand_activities | 0.000 | 0.000 | 0.001 | |
| nichenet_ligand_target_links | 0 | 0 | 0 | |
| nichenet_ligand_target_matrix | 0.000 | 0.001 | 0.001 | |
| nichenet_lr_network | 522.383 | 4.899 | 531.816 | |
| nichenet_lr_network_guide2pharma | 0.450 | 0.014 | 0.465 | |
| nichenet_lr_network_omnipath | 103.748 | 1.477 | 118.218 | |
| nichenet_lr_network_ramilowski | 0.110 | 0.027 | 0.136 | |
| nichenet_main | 0 | 0 | 0 | |
| nichenet_networks | 192.768 | 1.998 | 197.646 | |
| nichenet_optimization | 0 | 0 | 0 | |
| nichenet_remove_orphan_ligands | 0.000 | 0.000 | 0.001 | |
| nichenet_results_dir | 0.001 | 0.001 | 0.000 | |
| nichenet_signaling_network | 54.157 | 3.244 | 70.928 | |
| nichenet_signaling_network_cpdb | 0 | 0 | 0 | |
| nichenet_signaling_network_evex | 15.957 | 0.820 | 16.066 | |
| nichenet_signaling_network_harmonizome | 0.146 | 0.014 | 0.158 | |
| nichenet_signaling_network_inbiomap | 0 | 0 | 0 | |
| nichenet_signaling_network_omnipath | 6.891 | 0.332 | 7.260 | |
| nichenet_signaling_network_pathwaycommons | 2.073 | 0.013 | 2.097 | |
| nichenet_signaling_network_vinayagam | 0.316 | 0.066 | 0.383 | |
| nichenet_test | 0 | 0 | 0 | |
| nichenet_workarounds | 0 | 0 | 0 | |
| obo_parser | 0.088 | 0.008 | 0.247 | |
| omnipath_cache_autoclean | 0 | 0 | 0 | |
| omnipath_cache_clean | 0.025 | 0.001 | 0.027 | |
| omnipath_cache_clean_db | 0.081 | 0.005 | 0.086 | |
| omnipath_cache_download_ready | 0.466 | 0.077 | 0.780 | |
| omnipath_cache_filter_versions | 0.041 | 0.009 | 0.067 | |
| omnipath_cache_get | 0.027 | 0.007 | 0.045 | |
| omnipath_cache_key | 0.002 | 0.000 | 0.002 | |
| omnipath_cache_latest_or_new | 0.027 | 0.006 | 0.132 | |
| omnipath_cache_load | 0.386 | 0.022 | 2.764 | |
| omnipath_cache_move_in | 0.083 | 0.017 | 0.119 | |
| omnipath_cache_remove | 0.043 | 0.010 | 0.071 | |
| omnipath_cache_save | 0.100 | 0.016 | 0.182 | |
| omnipath_cache_search | 0.000 | 0.000 | 0.001 | |
| omnipath_cache_set_ext | 0.041 | 0.012 | 0.069 | |
| omnipath_cache_update_status | 0.097 | 0.013 | 0.112 | |
| omnipath_cache_wipe | 0 | 0 | 0 | |
| omnipath_get_config_path | 0 | 0 | 0 | |
| omnipath_load_config | 0.000 | 0.000 | 0.001 | |
| omnipath_log | 0 | 0 | 0 | |
| omnipath_logfile | 0 | 0 | 0 | |
| omnipath_msg | 0.005 | 0.001 | 0.006 | |
| omnipath_reset_config | 0 | 0 | 0 | |
| omnipath_save_config | 0 | 0 | 0 | |
| omnipath_set_cachedir | 0.007 | 0.002 | 0.009 | |
| omnipath_set_console_loglevel | 0.002 | 0.001 | 0.002 | |
| omnipath_set_logfile_loglevel | 0.002 | 0.001 | 0.002 | |
| omnipath_set_loglevel | 0.001 | 0.000 | 0.001 | |
| omnipath_show_db | 0.095 | 0.001 | 0.096 | |
| omnipath_unlock_cache_db | 0 | 0 | 0 | |
| ontology_ensure_id | 0.010 | 0.001 | 0.010 | |
| ontology_ensure_name | 0.013 | 0.000 | 0.012 | |
| ontology_name_id | 0.028 | 0.000 | 0.028 | |
| pathwaycommons_download | 4.133 | 0.327 | 7.323 | |
| pivot_annotations | 7.518 | 0.722 | 17.002 | |
| preppi_download | 6.982 | 1.787 | 28.860 | |
| preppi_filter | 7.453 | 1.560 | 5.268 | |
| print_bma_motif_es | 0.165 | 0.032 | 1.303 | |
| print_bma_motif_vs | 0.115 | 0.008 | 0.663 | |
| print_interactions | 4.436 | 0.185 | 17.150 | |
| print_path_es | 0.413 | 0.034 | 2.479 | |
| print_path_vs | 1.909 | 0.093 | 5.706 | |
| pubmed_open | 4.422 | 0.180 | 6.916 | |
| ramilowski_download | 0.187 | 0.078 | 1.806 | |
| regnetwork_directions | 0.100 | 0.011 | 0.465 | |
| regnetwork_download | 0.793 | 0.121 | 1.288 | |
| relations_list_to_table | 0.080 | 0.005 | 0.129 | |
| relations_table_to_graph | 0.079 | 0.003 | 0.081 | |
| relations_table_to_list | 0.059 | 0.002 | 0.093 | |
| remap_dorothea_download | 0.248 | 0.056 | 0.755 | |
| remap_filtered | 0.001 | 0.000 | 0.000 | |
| remap_tf_target_download | 0.000 | 0.000 | 0.001 | |
| resources_colname | 0.453 | 0.049 | 14.096 | |