[ Started: 2025-03-23 01:00:42 CET ] [ cosmosR v1.9.1 for BioC-3.21 from https://github.com/saezlab/cosmosR@master (ef9d5aa 2025-03-09 13:20:11) ] Loading required package: BiocCheck ── Installing cosmosR ────────────────────────────────────────────────────────── ✔ Package installed successfully ── cosmosR session metadata ──────────────────────────────────────────────────── → sourceDir: /tmp/Rtmpv6Sa1Q/file27039e59b4e1e1/cosmosR → BiocVersion: 3.21 → Package: cosmosR → PackageVersion: 1.9.1 → BiocCheckDir: /mnt/disk0/build/bioc-check/cosmosr/bioc-3.21/2025-03-23_0100/cosmosR/cosmosR.BiocCheck → BiocCheckVersion: 1.43.12 → sourceDir: /tmp/Rtmpv6Sa1Q/file27039e59b4e1e1/cosmosR → installDir: /tmp/Rtmpv6Sa1Q/file27039e446de329 → isTarBall: TRUE → platform: unix ── Running BiocCheck on cosmosR ──────────────────────────────────────────────── * 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... ℹ NOTE: Update R version dependency from 4.1 to 4.5.0. * 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... ℹ NOTE: Consider adding these automatically suggested biocViews: GeneTarget ℹ Search 'biocViews' at https://contributions.bioconductor.org * Checking build system compatibility... * Checking for proper Description: field... * Checking if DESCRIPTION is well formatted... * Checking for whitespace in DESCRIPTION field names... * Checking that Package field matches directory/tarball name... * Checking for Version: field... * Checking License: for restrictive use... * Checking for recommended DESCRIPTION fields... * Checking for Bioconductor software dependencies... ℹ Bioconductor dependencies found in Imports & Depends (25%). * Checking for pinned package versions in DESCRIPTION... * Checking for 'fnd' role in Authors@R... ℹ NOTE: No 'fnd' role found in Authors@R. If the work is supported by a grant, consider adding the 'fnd' role to the list of authors. * Checking .Rbuildignore... * Checking for stray BiocCheck output folders... * Checking vignette directory... ℹ NOTE: 'sessionInfo' not found in vignette(s) Missing from file(s): • vignettes/MOFA_to_COSMOS.Rmd • vignettes/NCI60_tutorial.Rmd * Checking package installation calls in R code... * Checking for library/require of cosmosR... * Checking coding practice... ℹ NOTE: Avoid sapply(); use vapply() Found in files: • R/compress_same_children.R (line 40, column 22) • ... • R/support_decoupleR.R (line 88, column 10) ℹ NOTE: Avoid 'cat' and 'print' outside of 'show' methods Found in files: • print() in R/check_network_data_coverage.R (line 47, column 21) • ... • print() in R/prepare_metab_inputs.R (line 29, column 5) ℹ NOTE: Avoid using '=' for assignment and use '<-' instead Found in files: • R/binarize_with_sign.R (line 10, column 9) • ... • R/support_ORA.R (line 38, column 12) ! WARNING: Avoid T/F variables; If logical, use TRUE/FALSE Found 17 times: • T in R/compress_same_children.R (line 43, column 46) • ... • F in R/support_pheatmap.R (line 21, column 54) * Checking parsed R code in R directory, examples, vignettes... * Checking function lengths... ℹ NOTE: The recommended function length is 50 lines or less. There are 12 functions greater than 50 lines. The longest 5 functions are: • preprocess_COSMOS_core() (R/preprocess_COSMOS.R): 198 lines • ... • filter_pkn_expressed_genes_fast() (R/filter_pkn_expressed_genes.R): 74 lines * Checking man page documentation... ℹ NOTE: Consider adding runnable examples to man pages that document exported objects. • decompress_moon_result.Rd • ... • prepare_metab_inputs.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... ℹ NOTE: Consider shorter lines; 439 lines (12%) are > 80 characters long. First few lines: • R/binarize_with_sign.R#L3 #' binarizes the data based on the thres ... • ... • vignettes/tutorial.Rmd#L221 confirmed experimentally. Those interact ... ℹ NOTE: Consider multiples of 4 spaces for line indents; 760 lines (21%) are not. First few lines: • R/check_inputs_CARNIVAL.R#L22 in ... • ... • vignettes/tutorial.Rmd#L245 ... ℹ See https://contributions.bioconductor.org/r-code.html ℹ See styler package: https://cran.r-project.org/package=styler as described in the BiocCheck vignette. * Checking if package already exists in CRAN... * Checking for bioc-devel mailing list subscription... ℹ 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... ℹ Maintainer is registered at support site. ℹ Package is in the Support Site Watched Tags. ── BiocCheck v1.43.12 results ────────────────────────────────────────────────── ✖ 0 ERRORS | ⚠ 1 WARNINGS | ℹ 12 NOTES ℹ See the cosmosR.BiocCheck folder and run browseVignettes(package = 'BiocCheck') for details. [ Finished: 2025-03-23 01:01:02 CET ]