[ Started: 2026-10-02 15:02:45 CEST ] [ MetaProViz v4.1.1 for BioC-3.24 from https://github.com/saezlab/MetaProViz@devel (a3ac947 2026-10-02 14:43:51) | R version 4.6.1 (2026-06-24) -- "Happy Hop" | docker | OVERRIDES from GitHub: saezlab/OmnipathR@devel ] Loading required package: BiocCheck ── Installing MetaProViz ─────────────────────────────────────────────────────── ✔ Package installed successfully ── MetaProViz session metadata ───────────────────────────────────────────────── → sourceDir: /tmp/Rtmp14FAXB/file200d5cae7dd5/MetaProViz → BiocVersion: 3.24 → Package: MetaProViz → PackageVersion: 4.1.1 → BiocCheckDir: /work/MetaProViz/MetaProViz.BiocCheck → BiocCheckVersion: 1.49.31 → sourceDir: /tmp/Rtmp14FAXB/file200d5cae7dd5/MetaProViz → installDir: /tmp/Rtmp14FAXB/file200d6e0d76da/lib → isTarBall: TRUE → platform: unix ── Running BiocCheck on MetaProViz ───────────────────────────────────────────── * Checking for deprecated package usage... adding rname 'https://bioconductor.org/checkResults/3.23/bioc-LATEST/meat-index.dcf' adding rname 'https://bioconductor.org/checkResults/3.24/bioc-LATEST/meat-index.dcf' * 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 4.1.0 to 4.6.0 * 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: Reactome ℹ Search 'biocViews' at https://contributions.bioconductor.org * Checking build system compatibility... * Checking if 'Package:' field matches directory / tarball... * Checking for Version: field... * Checking DESCRIPTION readability... * Checking validity of DESCRIPTION fields... * Checking License: for restrictive use... * Checking for recommended DESCRIPTION fields... * Checking for whitespace in DESCRIPTION field names... * Checking for proper Description: field... * Checking for Bioconductor software dependencies... ℹ Bioconductor dependencies found in Imports & Depends (15%). * Checking for pinned package versions in DESCRIPTION... * Checking for 'fnd' role in Authors@R... ℹ 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 CITATION... * Checking that provided CITATION file is correctly formatted... * Checking NAMESPACE... * Checking .Rbuildignore... * Checking for stray BiocCheck output folders... * Checking vignette directory... * Checking package installation calls in R code... * Checking for library/require of MetaProViz... * Checking coding practice... ℹ NOTE: Avoid 'cat' and 'print' outside of 'show' methods Found in files: • cat() in R/RefactorPriorKnoweldge.R (line 2712, column 9) • ... • print() in R/VizMetaboliteProteinNetwork.R (line 316, column 13) ℹ NOTE: Avoid the use of 'paste' in condition signals Found in files: • R/RefactorPriorKnoweldge.R (line 2485, column 13) • R/RefactorPriorKnoweldge.R (line 2490, column 13) • R/RefactorPriorKnoweldge.R (line 2503, column 17) ! WARNING: Remove set.seed usage (found 2 times) • set.seed() in R/VizMetaboliteProteinNetwork.R (line 735, column 5) • set.seed() in R/VizMetaboliteProteinNetwork.R (line 812, column 5) * Checking parsed R code in R directory, examples, vignettes... ℹ NOTE: Avoid 'suppressWarnings'/'*Messages' if possible (found 1 times) • suppressWarnings() in R/VizMetaboliteProteinNetwork.R (line 673, column 9) * Checking function lengths... ℹ NOTE: The recommended function length is 50 lines or less. There are 85 functions greater than 50 lines. The longest 5 functions are: • mca_core() (R/MetaboliteClusteringAnalysis.R): 1686 lines • ... • mapping_ambiguity() (R/RefactorPriorKnoweldge.R): 574 lines * Checking man page documentation... ℹ NOTE: Consider adding runnable examples to man pages that document exported objects. • checkmatch_pk_to_data.Rd • ... • translate_id.Rd ℹ NOTE: Usage of dontrun / donttest tags found in man page examples. 9% of man pages use at least one of these tags. Found in files: • checkmatch_pk_to_data.Rd • ... • translate_id.Rd ℹ NOTE: Use donttest instead of dontrun. Found in files: • checkmatch_pk_to_data.Rd • ... • translate_id.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; 1660 lines (6%) are > 80 characters long. First few lines: • R/DifferentialMetaboliteAnalysis.R#L38 #' @param metadata_info Named character ... • ... • vignettes/quick-start.Rmd#L476 For a detailed example of the visualisat ... ℹ NOTE: Consider multiples of 4 spaces for line indents; 11 lines (0%) are not. First few lines: • vignettes/quick-start.Rmd#L61