Loading required package: BiocCheck This is BiocCheck version 1.28.0. BiocCheck is a work in progress. Output and severity of issues may change. Installing package... [2022-03-24 06:03:44] [INFO] [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`. [2022-03-24 06:03:44] [INFO] [OmnipathR] Welcome to OmnipathR! [2022-03-24 06:03:44] [TRACE] [OmnipathR] Cache locked: FALSE * Checking Package Dependencies... * Checking if other packages can import this one... * Checking to see if we understand object initialization... * NOTE: Consider clarifying how 2 object(s) are initialized. Maybe they are part of a data set loaded with data(), or perhaps part of an object referenced in with() or within(). function (object) get_connections (description) get_connections (con_id) * Checking for deprecated package usage... * Checking for remote package usage... * Checking for 'LazyData: true' usage... * Checking version number... * Checking for version number mismatch... * Checking version number validity... * Checking R Version dependency... * NOTE: Update R version dependency from 4.0 to 4.1. * Checking package size... * Checking individual file sizes... * Checking biocViews... * Checking that biocViews are present... * Checking package type based on biocViews... Software * Checking for non-trivial biocViews... * Checking that biocViews come from the same category... * Checking biocViews validity... * Checking for recommended biocViews... * NOTE: Consider adding these automatically suggested biocViews: GenePrediction See http://bioconductor.org/developers/how-to/biocViews/ * Checking build system compatibility... * Checking for blank lines in DESCRIPTION... * Checking if DESCRIPTION is well formatted... * Checking for proper Description: field... * Checking for whitespace in DESCRIPTION field names... * Checking that Package field matches directory/tarball name... * Checking for Version field... * Checking for valid maintainer... * Checking License: for restrictive use... * Checking DESCRIPTION/NAMESPACE consistency... * Checking .Rbuildignore... * Checking vignette directory... * Checking library calls... * Checking for library/require of OmnipathR... * Checking coding practice... 'getOption("repos")' replaces Bioconductor standard repositories, see '?repositories' for details replacement repositories: CRAN: https://cloud.r-project.org * Checking parsed R code in R directory, examples, vignettes... * Checking function lengths..................................................................................................................................................................................................................... * NOTE: Recommended function length <= 50 lines. There are 41 functions > 50 lines. The longest 5 functions are: download_base() (R/internals.R, line 129): 168 lines filter_intercell_network() (R/omnipath.R, line 3028): 166 lines import_intercell_network() (R/omnipath.R, line 2743): 161 lines obo_parser() (R/obo.R, line 82): 149 lines nichenet_optimization() (R/nichenet.R, line 311): 125 lines * Checking man page documentation... * NOTE: Consider adding runnable examples to the following man pages which document exported objects: consensuspathdb_download.Rd, go_annot_slim.Rd, inbiomap_download.Rd, inbiomap_raw.Rd, kegg_pathway_annotations.Rd, kegg_pathways_download.Rd, nichenet_gr_network_remap.Rd, nichenet_ligand_activities.Rd, nichenet_ligand_target_links.Rd, nichenet_ligand_target_matrix.Rd, nichenet_main.Rd, nichenet_optimization.Rd, nichenet_signaling_network_cpdb.Rd, nichenet_signaling_network_inbiomap.Rd, nichenet_test.Rd, nichenet_workarounds.Rd, omnipath_cache_autoclean.Rd, omnipath_cache_latest_version.Rd, omnipath_cache_wipe.Rd, omnipath_load_config.Rd, omnipath_log.Rd, omnipath_reset_config.Rd, omnipath_save_config.Rd, remap_filtered.Rd, remap_tf_target_download.Rd, zenodo_download.Rd * NOTE: Usage of dontrun{} / donttest{} found in man page examples. 18% of man pages use one of these cases. Found in the following files: consensuspathdb_download.Rd go_annot_slim.Rd inbiomap_download.Rd inbiomap_raw.Rd kegg_pathway_annotations.Rd kegg_pathways_download.Rd nichenet_build_model.Rd nichenet_gr_network_remap.Rd nichenet_gr_network.Rd nichenet_ligand_activities.Rd nichenet_ligand_target_links.Rd nichenet_ligand_target_matrix.Rd nichenet_main.Rd nichenet_networks.Rd nichenet_optimization.Rd nichenet_signaling_network_cpdb.Rd nichenet_signaling_network_inbiomap.Rd nichenet_test.Rd nichenet_workarounds.Rd omnipath_cache_autoclean.Rd omnipath_cache_latest_or_new.Rd omnipath_cache_remove.Rd omnipath_cache_wipe.Rd omnipath_load_config.Rd omnipath_log.Rd omnipath_reset_config.Rd omnipath_save_config.Rd OmnipathR.Rd remap_filtered.Rd remap_tf_target_download.Rd zenodo_download.Rd * NOTE: Use donttest{} instead of dontrun{}. Found in the following files: consensuspathdb_download.Rd nichenet_signaling_network_cpdb.Rd * Checking package NEWS... * Checking unit tests... * Checking skip_on_bioc() in tests... * Checking formatting of DESCRIPTION, NAMESPACE, man pages, R source, and vignette source... * NOTE: Consider shorter lines; 21 lines (0%) are > 80 characters long. First 6 lines: R/omnipath.R:1981 #' \url{https://archive.omnipathdb.org/omnipath_webse... R/remap.R:36 #' \url{https://github.com/saezlab/dorothea/blob/master/in... man/ancestors.Rd:11 relations = c("is_a", "part_of", "occurs_in", "re... man/descendants.Rd:11 relations = c("is_a", "part_of", "occurs_in", "... man/go_ontology_download.Rd:11 relations = c("is_a", "part_of", "occu... man/obo_parser.Rd:9 relations = c("is_a", "part_of", "occurs_in", "re... * NOTE: Consider multiples of 4 spaces for line indents, 503 lines(2%) are not. First 6 lines: man/ancestors.Rd:8 terms, man/ancestors.Rd:9 db_key = "go_basic", man/ancestors.Rd:10 ids = TRUE, man/ancestors.Rd:11 relations = c("is_a", "part_of", "occurs_in", "re... man/descendants.Rd:8 terms, man/descendants.Rd:9 db_key = "go_basic", See http://bioconductor.org/developers/how-to/coding-style/ See styler package: https://cran.r-project.org/package=styler as described in the BiocCheck vignette. * Checking if package already exists in CRAN... 'getOption("repos")' replaces Bioconductor standard repositories, see '?repositories' for details replacement repositories: CRAN: https://cloud.r-project.org * Checking for bioc-devel mailing list subscription... * NOTE: Cannot determine whether maintainer is subscribed to the bioc-devel mailing list (requires admin credentials). Subscribe here: https://stat.ethz.ch/mailman/listinfo/bioc-devel * Checking for support site registration... Maintainer is registered at support site. Package name is in support site watched tags. Summary: ERROR count: 0 WARNING count: 0 NOTE count: 10 For detailed information about these checks, see the BiocCheck vignette, available at https://bioconductor.org/packages/3.13/bioc/vignettes/BiocCheck/inst/doc/BiocCheck.html#interpreting-bioccheck-output $error character(0) $warning character(0) $note [1] "Consider clarifying how 2 object(s) are initialized. Maybe they are part of a data set loaded with data(), or perhaps part of an object referenced in with() or within()." [2] "Update R version dependency from 4.0 to 4.1." [3] "Consider adding these automatically suggested biocViews: GenePrediction" [4] "Recommended function length <= 50 lines." [5] "Consider adding runnable examples to the following man pages which document exported objects:" [6] "Usage of dontrun{} / donttest{} found in man page examples." [7] "Use donttest{} instead of dontrun{}." [8] "Consider shorter lines; 21 lines (0%) are > 80 characters long." [9] "Consider multiples of 4 spaces for line indents, 503 lines(2%) are not." [10] "Cannot determine whether maintainer is subscribed to the bioc-devel\nmailing list (requires admin credentials). Subscribe here:\nhttps://stat.ethz.ch/mailman/listinfo/bioc-devel"