[ Started: 2022-04-21 23:50 ] Loading required package: BiocCheck ─ BiocCheckVersion: 1.31.37 ─ BiocVersion: 3.15 ─ Package: decoupleR ─ PackageVersion: 2.1.11 ─ sourceDir: /tmp/RtmpJaq5k3/file2c8d5446555ef3/decoupleR ─ installDir: /tmp/RtmpJaq5k3/file2c8d5462bfd17 ─ BiocCheckDir: /home/omnipath/testing/decoupler/bioc-3.15/2022-04-21_2345/decoupleR/decoupleR.BiocCheck ─ platform: unix ─ isTarBall: TRUE * Installing package... * Checking package dependencies... * Checking if other packages can import this one... * Checking to see if we understand object initialization... * 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... * NOTE: Update R version dependency from 4.0 to 4.2.0. * 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: Proteomics, Transcriptomics, 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... * WARNING: Import utils in DESCRIPTION as well as NAMESPACE. * Checking .Rbuildignore... * Checking for stray BiocCheck output folders... * Checking vignette directory... Warning in png(..., res = dpi, units = "in") : unable to open connection to X11 display '' * WARNING: Avoid T/F variables; If logical, use TRUE/FALSE * Checking package installation calls in R code... * Checking for library/require of decoupleR... * Checking coding practice... * NOTE: Avoid 1:...; use seq_len() or seq_along() * NOTE: Avoid using '=' for assignment and use '<-' instead * WARNING: Avoid T/F variables; If logical, use TRUE/FALSE * Checking parsed R code in R directory, examples, vignettes... Found @ in vignettes/pw_sc.Rmd Found @ in vignettes/tf_sc.Rmd * NOTE: Use accessors; don't access S4 class slots via '@' in examples/vignettes. * NOTE: Avoid 'suppressWarnings'/'*Messages' if possible (found 1 times) * Checking function lengths... * NOTE: Recommended function length <= 50 lines.There are 4 functions > 50 lines. * Checking man page documentation... Warning in nzchar(fpath) && !is.na(fpath) : 'length(x) = 8 > 1' in coercion to 'logical(1)' Warning in nzchar(fpath) && !is.na(fpath) : 'length(x) = 8 > 1' in coercion to 'logical(1)' * WARNING: Add non-empty \value sections to the following man pages: man/extract_sets.Rd, man/get_dorothea.Rd, man/get_progeny.Rd, man/get_resource.Rd, man/rename_net.Rd, man/run_aucell.Rd, man/show_methods.Rd, man/show_resources.Rd * NOTE: Consider adding runnable examples to the following man pages which document exported objects: 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... * NOTE: Consider shorter lines; 127 lines (2%) are > 80 characters long. * NOTE: Consider multiples of 4 spaces for line indents; 697 lines (12%) are not. See http://bioconductor.org/developers/how-to/coding-style/ 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... * 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 | 4 WARNINGS | 11 NOTES See the decoupleR.BiocCheck folder and run browseVignettes(package = 'BiocCheck') for details. [ Finished: 2022-04-21 23:50 ]