[ Started: 2025-03-29 00:06:02 CET ] [ CARNIVAL v2.7.2 for BioC-3.21 from https://github.com/saezlab/CARNIVAL@master (2b8887a 2023-12-06 13:18:32) ] Loading required package: BiocCheck ── Installing CARNIVAL ───────────────────────────────────────────────────────── ✔ Package installed successfully ── CARNIVAL session metadata ─────────────────────────────────────────────────── → sourceDir: /tmp/RtmprbvfGy/filecd4687b5e257f/CARNIVAL → BiocVersion: 3.21 → Package: CARNIVAL → PackageVersion: 2.7.2 → BiocCheckDir: /mnt/disk0/build/bioc-check/carnival/bioc-3.21/2025-03-29_0005/CARNIVAL/CARNIVAL.BiocCheck → BiocCheckVersion: 1.43.12 → sourceDir: /tmp/RtmprbvfGy/filecd4687b5e257f/CARNIVAL → installDir: /tmp/RtmprbvfGy/filecd46864b0ad1b → isTarBall: TRUE → platform: unix ── Running BiocCheck on CARNIVAL ─────────────────────────────────────────────── * 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 4.0 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... * 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... ℹ NOTE: Consider adding the maintainer's ORCID iD in 'Authors@R' with 'comment=c(ORCID="...")' * Checking License: for restrictive use... * Checking for recommended DESCRIPTION fields... * Checking for Bioconductor software dependencies... ! WARNING: No Bioconductor dependencies detected. Note that some infrastructure packages may not have Bioconductor dependencies. For more information, reach out to the Bioconductor community and/or consider a CRAN submission. * 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... * Checking package installation calls in R code... * Checking for library/require of CARNIVAL... * Checking coding practice... ℹ NOTE: Avoid sapply(); use vapply() Found in files: • R/solvers_cplex__solve_cplex.R (line 41, column 10) • ... • R/solvers_cplex__solve_cplex.R (line 54, column 16) ℹ NOTE: Avoid 1:...; use seq_len() or seq_along() Found in files: • create_run_metainfo.R (line 14, column 18) • ... • solvers_gurobi__solve_gurobi.R (line 79, column 15) ℹ NOTE: Avoid 'cat' and 'print' outside of 'show' methods Found in files: • print() in R/control_node_identifiers.R (line 22, column 13) • print() in R/control_node_identifiers.R (line 29, column 13) ℹ NOTE: Avoid using '=' for assignment and use '<-' instead Found in files: • R/check_inputs.R (line 35, column 22) • ... • R/solvers_gurobi__solve_gurobi.R (line 14, column 23) ℹ NOTE: Avoid the use of 'paste' in condition signals Found in files: • R/check_perturbations.R (line 17, column 10) • ... • R/check_weights.R (line 14, column 10) ℹ NOTE: Avoid system() ; use system2() Found in files: • system() in R/set_solver_path.R (line 48, column 23) • ... • system() in R/solvers_gurobi__solve_gurobi.R (line 51, column 5) * Checking parsed R code in R directory, examples, vignettes... ℹ NOTE: Avoid '<<-' if possible (found 2 times) • <<- in R/constraints_create_constraints_6_7.R (line 29, column 19) • <<- in R/constraints_create_constraints_6_7.R (line 36, column 19) * Checking function lengths... ℹ NOTE: The recommended function length is 50 lines or less. There are 6 functions greater than 50 lines. The longest 5 functions are: • exportIlpSolutionFromSolutionMatrix() (R/solvers_export_results.R): 100 lines • ... • convergenceTextToTable() (R/solvers_cplex__parse_cplex_log.R): 57 lines * Checking man page documentation... ℹ NOTE: Consider adding runnable examples to man pages that document exported objects. • defaultCbcSolveCarnivalOptions.Rd • getOptionsList.Rd • getSupportedSolvers.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; 275 lines (7%) are > 80 characters long. First few lines: • R/add_perturbation_node.R#L1 #' Introduces a perturbation node connec ... • ... • vignettes/CARNIVAL.Rmd#L253 services](https://www.gurobi.com/documen ... ℹ NOTE: Consider multiples of 4 spaces for line indents; 1522 lines (39%) are not. First few lines: • R/add_perturbation_node.R#L11 ... • ... • vignettes/CARNIVAL.Rmd#L240 carni ... 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 15 NOTES ℹ See the CARNIVAL.BiocCheck folder and run browseVignettes(package = 'BiocCheck') for details. [ Finished: 2025-03-29 00:06:22 CET ]