[ Started: 2023-11-21 11:57:41 CET ] [ cosmosR v1.5.2 for BioC-3.17 from https://github.com/saezlab/cosmosR@master ] Loading required package: BiocCheck ─ BiocCheckVersion: 1.36.1 ─ BiocVersion: 3.17 ─ Package: cosmosR ─ PackageVersion: 1.5.2 ─ sourceDir: /tmp/RtmpPTs4Jy/file3e821c50d07831/cosmosR ─ installDir: /tmp/RtmpPTs4Jy/file3e821c3f9e306a ─ BiocCheckDir: /mnt/disk0/build/bioc-check/cosmosr/bioc-3.17/2023-11-21_1157/cosmosR/cosmosR.BiocCheck ─ platform: unix ─ isTarBall: TRUE * Installing package... * 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... * WARNING: y of x.y.z version should be even in release * Checking R version dependency... * NOTE: Update R version dependency from 4.1 to 4.3.0. * 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... * NOTE: Consider adding these automatically suggested biocViews: GeneTarget Search 'biocViews' at https://contributions.bioconductor.org * Checking build system compatibility... * Checking for blank lines in DESCRIPTION... * Checking if DESCRIPTION is well formatted... * Checking for proper Description: field... * Checking for whitespace in DESCRIPTION field names... * Checking that Package field matches directory/tarball name... * Checking for Version field... * Checking for valid maintainer... * Checking License: for restrictive use... * Checking for pinned package versions... * Checking DESCRIPTION/NAMESPACE consistency... * Checking .Rbuildignore... * Checking for stray BiocCheck output folders... * Checking vignette directory... * Checking package installation calls in R code... * Checking for library/require of cosmosR... * Checking coding practice... * NOTE: Avoid sapply(); use vapply() * NOTE: Avoid 'cat' and 'print' outside of 'show' methods * NOTE: Avoid using '=' for assignment and use '<-' instead Warning in cond & parsedf$token[which(cond) - 1] != shQuote(lookback) : longer object length is not a multiple of shorter object length * WARNING: Avoid T/F variables; If logical, use TRUE/FALSE * Checking parsed R code in R directory, examples, vignettes... * Checking function lengths... * NOTE: The recommended function length is 50 lines or less. There are 10 functions greater than 50 lines. * Checking man page documentation... * WARNING: Empty or missing \value sections found in man pages. * NOTE: Consider adding runnable examples to man pages that document exported objects. * Checking package NEWS... * Checking unit tests... * Checking skip_on_bioc() in tests... * Checking formatting of DESCRIPTION, NAMESPACE, man pages, R source, and vignette source... * NOTE: Consider shorter lines; 461 lines (11%) are > 80 characters long. * NOTE: Consider multiples of 4 spaces for line indents; 756 lines (17%) are not. See https://contributions.bioconductor.org/r-code.html 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... * 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... Maintainer is registered at support site. Package name is in support site watched tags. ─ BiocCheck results ── 0 ERRORS | 3 WARNINGS | 10 NOTES See the cosmosR.BiocCheck folder and run browseVignettes(package = 'BiocCheck') for details. [ Finished: 2023-11-21 11:57:54 CET ]