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... [2022-02-04 12:50:54] [INFO] [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`. [2022-02-04 12:50:54] [INFO] [OmnipathR] Welcome to OmnipathR! * Checking Package Dependencies... * Checking if other packages can import this one... * Checking to see if we understand object initialization... * 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... * 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... * 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 wppi... * Checking coding practice... * Checking parsed R code in R directory, examples, vignettes... * Checking function lengths........................ * NOTE: Recommended function length <= 50 lines. There are 2 functions > 50 lines. The longest 5 functions are: score_candidate_genes_from_PPI() (R/WPPI_app.R, line 108): 111 lines weighted_adj() (R/WPPI_functions.R, line 245): 92 lines random_walk() (R/WPPI_functions.R, line 385): 49 lines prioritization_genes() (R/WPPI_functions.R, line 492): 44 lines process_annot() (R/Annot_functions.R, line 33): 34 lines * Checking man page documentation... * Checking package NEWS... * Checking unit tests... * NOTE: Consider adding unit tests. We strongly encourage them. See http://bioconductor.org/developers/how-to/unitTesting-guidelines/. * Checking skip_on_bioc() in tests... * Checking formatting of DESCRIPTION, NAMESPACE, man pages, R source, and vignette source... * NOTE: Consider shorter lines; 2 lines (0%) are > 80 characters long. First 2 lines: vignettes/wppi_workflow.Rmd:41 it's possible to use custom databases.... vignettes/wppi_workflow.Rmd:222 plot(graph_op_1,vertex.label = ifelse(s... * NOTE: Consider multiples of 4 spaces for line indents, 50 lines(2%) are not. First 6 lines: man/prioritization_genes.Rd:8 graph_op, man/prioritization_genes.Rd:9 prob_matrix, man/prioritization_genes.Rd:10 genes_interest, man/prioritization_genes.Rd:11 percentage_genes_ranked = 100 man/score_candidate_genes_from_PPI.Rd:8 genes_interest, man/score_candidate_genes_from_PPI.Rd:9 HPO_interest = NULL, 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: 5 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] "Recommended function length <= 50 lines." [2] "Consider adding unit tests. We strongly encourage them. See\n http://bioconductor.org/developers/how-to/unitTesting-guidelines/." [3] "Consider shorter lines; 2 lines (0%) are > 80 characters long." [4] "Consider multiples of 4 spaces for line indents, 50 lines(2%) are not." [5] "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"