[ Started: 2025-03-20 01:33:32 CET ] [ progeny v1.17.3 for BioC-3.21 from https://github.com/saezlab/progeny@master (cad6be0 2023-01-30 11:01:10) ] Loading required package: BiocCheck ── Installing progeny ────────────────────────────────────────────────────────── ✔ Package installed successfully ── progeny session metadata ──────────────────────────────────────────────────── → sourceDir: /tmp/RtmpvrvbLi/file153ade1ed96981/progeny → BiocVersion: 3.21 → Package: progeny → PackageVersion: 1.17.3 → BiocCheckDir: /mnt/disk0/build/bioc-check/progeny/bioc-3.21/2025-03-20_0133/progeny/progeny.BiocCheck → BiocCheckVersion: 1.43.12 → sourceDir: /tmp/RtmpvrvbLi/file153ade1ed96981/progeny → installDir: /tmp/RtmpvrvbLi/file153ade58d4534e → isTarBall: TRUE → platform: unix ── Running BiocCheck on progeny ──────────────────────────────────────────────── * Checking for deprecated package usage... * Checking for remote package usage... * Checking for 'LazyData: true' usage... ℹ NOTE: 'LazyData:' in the 'DESCRIPTION' should be set to false or removed * Checking version number... * Checking for version number mismatch... * Checking version number validity... * Checking R version dependency... ℹ NOTE: Update R version dependency from 3.6.0 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... ℹ NOTE: Consider adding these automatically suggested biocViews: SingleCell, Transcriptomics 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... 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... ℹ Bioconductor dependencies found in Imports & Depends (22%). * 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/progeny.Rmd * Checking package installation calls in R code... * Checking for library/require of progeny... * Checking coding practice... ℹ NOTE: Avoid using '=' for assignment and use '<-' instead Found in files: • R/progeny.r (line 79, column 9) • ... • R/progeny.r (line 204, column 17) ℹ NOTE: Avoid the use of 'paste' in condition signals Found in files: • R/progeny.r (line 179, column 17) • R/progenySuppFunc.r (line 92, column 25) ! WARNING: Avoid T/F variables; If logical, use TRUE/FALSE Found 1 times: • F in R/progenySuppFunc.r (line 188, column 64) * 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 3 functions greater than 50 lines. The longest 5 functions are: • progenyScatter() (R/progenySuppFunc.r): 62 lines • progeny.matrix() (R/progeny.r): 61 lines • progenyPerm() (R/progenyPermutations.r): 61 lines * Checking man page documentation... ! WARNING: Empty or missing \value sections found in man page(s). Found in files: • man/model_human_full.Rd • man/model_mouse_full.Rd • man/vignette_data.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; 15 lines (2%) are > 80 characters long. First few lines: • R/data.r#L44 #' @format List with three elements: the ... • ... • vignettes/progeny.Rmd#L106 Each pathway show a different distributi ... ℹ NOTE: Consider multiples of 4 spaces for line indents; 30 lines (4%) are not. First few lines: • R/progeny.r#L143 ... • ... • vignettes/progeny.Rmd#L102 theme(legend.position = "none") ... 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 | ⚠ 2 WARNINGS | ℹ 12 NOTES ℹ See the progeny.BiocCheck folder and run browseVignettes(package = 'BiocCheck') for details. [ Finished: 2025-03-20 01:33:46 CET ]