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... * 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... * ERROR: Package dependencies must be on CRAN or Bioconductor. Remove 'Remotes:' from DESCRIPTION * Checking for 'LazyData: true' usage... * Checking version number... * Checking for version number mismatch... * Checking version number validity... * WARNING: y of x.y.z version should be even in release * 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... * WARNING: Import ggplot2, scales in NAMESPACE as well as DESCRIPTION. * Checking .Rbuildignore... * Checking vignette directory... * Checking library calls... * Checking for library/require of cosmosR... * Checking coding practice... * NOTE: Avoid sapply(); use vapply() Found in files: display_node_neighboorhood.R (line 60, column 21) display_node_neighboorhood.R (line 67, column 18) display_node_neighboorhood.R (line 75, column 18) filter_pkn_expressed_genes.R (line 68, column 24) filter_pkn_expressed_genes.R (line 71, column 24) format_COSMOS_results.R (line 166, column 19) format_COSMOS_results.R (line 259, column 21) format_COSMOS_results.R (line 339, column 29) format_COSMOS_results.R (line 346, column 29) format_COSMOS_results.R (line 376, column 29) * WARNING: Use TRUE/FALSE instead of T/F Found in R/ directory functions: preprocess_COSMOS_metabolism_to_signaling() preprocess_COSMOS_signaling_to_metabolism() * Checking parsed R code in R directory, examples, vignettes... * Checking function lengths....................................................... * NOTE: Recommended function length <= 50 lines. There are 10 functions > 50 lines. The longest 5 functions are: format_COSMOS_results_deprecated() (R/format_COSMOS_results.R, line 228): 202 lines preprocess_COSMOS_core() (R/preprocess_COSMOS.R, line 66): 180 lines display_node_neighboorhood() (R/display_node_neighboorhood.R, line 44): 77 lines format_COSMOS_res() (R/format_COSMOS_results.R, line 140): 75 lines filter_pkn_expressed_genes() (R/filter_pkn_expressed_genes.R, line 8): 69 lines * Checking man page documentation... * 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; 291 lines (7%) are > 80 characters long. First 6 lines: R/binarize_with_sign.R:3 #' binarizes the data based on the threshold u... R/check_COSMOS_inputs.R:22 stop("gene names in signaling_data s... R/check_COSMOS_inputs.R:25 stop("gene names in expression_data ... R/check_COSMOS_inputs.R:43 stopifnot(all(c("source","interactio... R/check_gene_names.R:10 stop("gene names in inputs should b... R/check_gene_names.R:18 stop("Duplicated gene names detecte... * NOTE: Consider multiples of 4 spaces for line indents, 515 lines(13%) are not. First 6 lines: R/check_inputs_CARNIVAL.R:22 inpu... R/check_inputs_CARNIVAL.R:23 meas... R/check_network_data_coverage.R:21 R/check_network_data_coverage.R:37 ... R/check_network_data_coverage.R:42 ... R/check_network_data_coverage.R:54 ... 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: 1 WARNING count: 3 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 BiocCheck FAILED. $error [1] "Package dependencies must be on CRAN or Bioconductor. Remove 'Remotes:' from DESCRIPTION" $warning [1] "y of x.y.z version should be even in release" [2] "Import ggplot2, scales in NAMESPACE as well as DESCRIPTION." [3] " Use TRUE/FALSE instead of T/F" $note [1] " Avoid sapply(); use vapply()" [2] "Recommended function length <= 50 lines." [3] "Consider shorter lines; 291 lines (7%) are > 80 characters long." [4] "Consider multiples of 4 spaces for line indents, 515 lines(13%) 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"