[ Started: 2024-10-12 16:42:57 CEST ] [ mistyR v1.10.0 for BioC-3.20 from https://github.com/saezlab/mistyR@master (8bb8ba9 2024-03-25 14:10:38) ] Loading required package: BiocCheck ── Installing mistyR ─────────────────────────────────────────────────────────── ✔ Package installed successfully ── mistyR session metadata ───────────────────────────────────────────────────── → sourceDir: /tmp/RtmpqwNCka/file3b20405b7d267f/mistyR → BiocVersion: 3.20 → Package: mistyR → PackageVersion: 1.10.0 → BiocCheckDir: /mnt/disk0/build/bioc-check/mistyr/bioc-3.20/2024-10-12_1640/mistyR/mistyR.BiocCheck → BiocCheckVersion: 1.41.17 → sourceDir: /tmp/RtmpqwNCka/file3b20405b7d267f/mistyR → installDir: /tmp/RtmpqwNCka/file3b204071f09580 → isTarBall: TRUE → platform: unix ── Running BiocCheck on mistyR ───────────────────────────────────────────────── * 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 odd in devel * Checking R version dependency... ℹ NOTE: Update R version dependency from 4.0 to 4.4.0. * 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... * 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 .Rbuildignore... * Checking for stray BiocCheck output folders... * Checking vignette directory... * Checking package installation calls in R code... * Checking for library/require of mistyR... * Checking coding practice... ℹ NOTE: Avoid 1:...; use seq_len() or seq_along() Found in files: • model-functions.R (line 196, column 27) ℹ NOTE: Avoid 'cat' and 'print' outside of 'show' methods Found in files: • print() in R/plots.R (line 73, column 3) • ... • print() in R/plots.R (line 619, column 5) * 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 16 functions greater than 50 lines. The longest 5 functions are: • run_misty() (R/misty.R): 239 lines • ... • collect_results() (R/utils.R): 110 lines * Checking man page documentation... ! WARNING: Empty or missing \value sections found in man page(s). Found in files: • man/reexports.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; 146 lines (4%) are > 80 characters long. First few lines: • R/data.R#L2 # Copyleft (ɔ) 2020 Jovan Tanevski, Atti ... • ... • vignettes/mistyR.Rmd#L277 Here is the output of `sessionInfo()` at ... ℹ NOTE: Consider multiples of 4 spaces for line indents; 845 lines (25%) are not. First few lines: • R/misty.R#L7 packageStartupMessage("mistyR is able ... • ... • vignettes/mistyR.Rmd#L207 arrange(mean.p) ... 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. ℹ Package is in the Support Site Watched Tags. ── BiocCheck v1.41.17 results ────────────────────────────────────────────────── ✖ 0 ERRORS | ⚠ 3 WARNINGS | • 7 NOTES ℹ See the mistyR.BiocCheck folder and run browseVignettes(package = 'BiocCheck') for details. [ Finished: 2024-10-12 16:43:10 CEST ]