[ Started: 2024-10-06 16:24:46 CEST ] [ dorothea v1.7.4 for BioC-3.20 from https://github.com/saezlab/dorothea@master (1461fb7 2024-02-24 12:55:48) ] Loading required package: BiocCheck ── Installing dorothea ───────────────────────────────────────────────────────── ✔ Package installed successfully ── dorothea session metadata ─────────────────────────────────────────────────── → sourceDir: /tmp/RtmpYuKfuA/file15ac405f2e7306/dorothea → BiocVersion: 3.20 → Package: dorothea → PackageVersion: 1.7.4 → BiocCheckDir: /mnt/disk0/build/bioc-check/dorothea/bioc-3.20/2024-10-06_1622/dorothea/dorothea.BiocCheck → BiocCheckVersion: 1.41.17 → sourceDir: /tmp/RtmpYuKfuA/file15ac405f2e7306/dorothea → installDir: /tmp/RtmpYuKfuA/file15ac4013ef3eb4 → isTarBall: TRUE → platform: unix ── Running BiocCheck on dorothea ─────────────────────────────────────────────── * 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 4.0 to 4.4.0. * Checking package size... * Checking individual file sizes... ! WARNING: Package files exceed the 5MB size limit. Files over the limit: • /tmp/RtmpYuKfuA/file15ac405f2e7306/dorothea//inst/extdata/for_vignette/seurat_object.RDS • /tmp/RtmpYuKfuA/file15ac405f2e7306/dorothea/inst/extdata/for_vignette/seurat_object.RDS • /tmp/RtmpYuKfuA/file15ac405f2e7306/dorothea/inst/extdata/for_vignette/seurat_object.RDS ! WARNING: Data files exceed the 5MB size limit. Use 'ExperimentHub' or 'AnnotationHub' for the files: • /tmp/RtmpYuKfuA/file15ac405f2e7306/dorothea/inst/extdata/for_vignette/seurat_object.RDS * Checking biocViews... * Checking that biocViews are present... * Checking package type based on biocViews... → ExperimentData * 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... * 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 .Rbuildignore... * Checking for stray BiocCheck output folders... * Checking vignette directory... ℹ NOTE: 'sessionInfo' not found in vignette(s) Missing from file(s): • vignettes/dorothea.Rmd * Checking package installation calls in R code... * Checking for library/require of dorothea... * Checking coding practice... ℹ NOTE: Avoid using '=' for assignment and use '<-' instead Found in files: • R/helpers.R (line 18, column 16) • R/helpers.R (line 20, column 18) • R/helpers.R (line 21, column 12) ! WARNING: .Deprecated / .Defunct usage (found 1 times) • .Deprecated() in R/viper_wrapper.R (line 128, column 3) * Checking parsed R code in R directory, examples, vignettes... * Checking function lengths... * Checking man page documentation... ! WARNING: Empty or missing \value sections found in man page(s). Found in files: • man/dorothea_hs_pancancer.Rd • ... • man/entire_database.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; 12 lines (2%) are > 80 characters long. First few lines: • R/data.R#L27 #' A table reporting signed human TF-tar ... • ... • vignettes/dorothea.Rmd#L171 Similarly to DoRothEA, the majority of T ... ℹ NOTE: Consider multiples of 4 spaces for line indents; 104 lines (19%) are not. First few lines: • R/helpers.R#L18 regulon_list = split(df, df$tf) ... • ... • vignettes/dorothea.Rmd#L192 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... 'getOption("repos")' replaces Bioconductor standard repositories, see 'help("repositories", package = "BiocManager")' for details. Replacement repositories: CRAN: https://cloud.r-project.org * 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. ✖ ERROR: Add package to Watched Tags in your Support Site profile; visit https://support.bioconductor.org/accounts/edit/profile ── BiocCheck v1.41.17 results ────────────────────────────────────────────────── ✖ 1 ERRORS | ⚠ 4 WARNINGS | • 7 NOTES ℹ See the dorothea.BiocCheck folder and run browseVignettes(package = 'BiocCheck') for details. [ Finished: 2024-10-06 16:25:27 CEST ]