[ Started: 2025-07-27 19:41:32 CEST ] [ decoupleR v2.9.7 for BioC-3.22 from https://github.com/saezlab/decoupleR@devel (930b765 2025-02-15 00:00:59) ] Loading required package: BiocCheck ── Installing decoupleR ──────────────────────────────────────────────────────── ✔ Package installed successfully ── decoupleR session metadata ────────────────────────────────────────────────── → sourceDir: /tmp/RtmpCWauCt/file20c83751037d79/decoupleR → BiocVersion: 3.22 → Package: decoupleR → PackageVersion: 2.9.7 → BiocCheckDir: /mnt/disk0/build/bioc-check/decoupler/bioc-3.22/2025-07-27_1939/decoupleR/decoupleR.BiocCheck → BiocCheckVersion: 1.45.11 → sourceDir: /tmp/RtmpCWauCt/file20c83751037d79/decoupleR → installDir: /tmp/RtmpCWauCt/file20c83718a481b5 → isTarBall: TRUE → platform: unix ── Running BiocCheck on decoupleR ────────────────────────────────────────────── * 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... ℹ NOTE: Consider adding these automatically suggested biocViews: Proteomics, Transcriptomics, GeneTarget 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... * Checking License: for restrictive use... * Checking for recommended DESCRIPTION fields... * Checking for Bioconductor software dependencies... ℹ Bioconductor dependencies found in Imports & Depends (7%). * 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... ! WARNING: Avoid T/F variables; If logical, use TRUE/FALSE Found in files: • vignettes/decoupleR.Rmd (chunk no. 7, line 111, column 30) • ... • vignettes/decoupleR.Rmd (chunk no. 14, line 254, column 58) * Checking package installation calls in R code... * Checking for library/require of decoupleR... * Checking coding practice... ℹ NOTE: Avoid 1:...; use seq_len() or seq_along() Found in files: • decoupleR-pre.R (line 130, column 13) • ... • statistic-fgsea.R (line 70, column 22) ℹ NOTE: Avoid using '=' for assignment and use '<-' instead Found in files: • R/decoupleR-decouple.R (line 91, column 22) • R/decoupleR-pre.R (line 216, column 7) • R/statistic-mlm.R (line 98, column 17) * Checking parsed R code in R directory, examples, vignettes... ℹ Found @ in vignettes/pw_sc.Rmd ℹ Found @ in vignettes/tf_sc.Rmd ℹ NOTE: Use accessors; don't access S4 class slots via '@' in examples/vignettes. ℹ NOTE: Avoid 'suppressWarnings'/'*Messages' if possible (found 1 times) • suppressWarnings() in R/statistic-fgsea.R (line 85, column 17) * Checking function lengths... ℹ NOTE: The recommended function length is 50 lines or less. There are 10 functions greater than 50 lines. The longest 5 functions are: • decouple() (R/decoupleR-decouple.R): 88 lines • ... • run_wmean() (R/statistic-wmean.R): 63 lines * Checking man page documentation... ! WARNING: Empty or missing \value sections found in man page(s). Found in files: • man/extract_sets.Rd • ... • man/show_resources.Rd ℹ NOTE: Consider adding runnable examples to man pages that document exported objects. • get_ksn_omnipath.Rd • pivot_wider_profile.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; 101 lines (2%) are > 80 characters long. First few lines: • R/decoupleR-consensus.R#L46 warning("Infs detected in score, wil ... • ... • vignettes/tf_sc.Rmd#L138 ```{r "projected_acts", message = FALSE, ... ℹ NOTE: Consider multiples of 4 spaces for line indents; 541 lines (12%) are not. First few lines: • R/decoupleR-consensus.R#L34 include_time=F ... • ... • vignettes/tf_sc.Rmd#L184 seq(0.05, 3, length.out=f ... 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 v1.45.11 results ────────────────────────────────────────────────── ✖ 0 ERRORS | ⚠ 2 WARNINGS | ℹ 12 NOTES ℹ See the decoupleR.BiocCheck folder and run browseVignettes(package = 'BiocCheck') for details. [ Finished: 2025-07-27 19:41:56 CEST ]