############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.19-bioc/R/bin/Rscript -e "BiocCheck::BiocCheck('ggbio_1.53.0.tar.gz')" ### ############################################################################## ############################################################################## * Installing package... ─ sourceDir: /tmp/RtmpruuVmr/fileeda5f3e66aa6c/ggbio ─ BiocVersion: 3.20 ─ Package: ggbio ─ PackageVersion: 1.53.0 ─ BiocCheckDir: /home/biocbuild/bbs-3.19-bioc-testing/meat/ggbio.BiocCheck ─ BiocCheckVersion: 1.41.5 ─ sourceDir: /tmp/RtmpruuVmr/fileeda5f3e66aa6c/ggbio ─ installDir: /tmp/RtmpruuVmr/fileeda5f58cd59f9 ─ isTarBall: TRUE ─ platform: unix * 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... * 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... * NOTE: Consider adding the maintainer's ORCID iD in 'Authors@R' with 'comment=c(ORCID="...")' * Checking License: for restrictive use... * Checking for recommended DESCRIPTION fields... * Checking for Bioconductor software dependencies... Bioconductor dependencies found in Imports & Depends (58%). * Checking for pinned package versions in DESCRIPTION... * Checking .Rbuildignore... * Checking for stray BiocCheck output folders... * Checking vignette directory... * ERROR: 'VignetteBuilder' listed in DESCRIPTION but not found as 'VignetteEngine' in any vignettes: * WARNING: Use RMarkdown instead of Sweave 'Rnw' vignettes. * NOTE: 'sessionInfo' not found in vignette(s) * Checking package installation calls in R code... * Checking for library/require of ggbio... * WARNING: Avoid the use of 'library' or 'require' in R code * Checking coding practice... * NOTE: Avoid sapply(); use vapply() * NOTE: Avoid 1:...; use seq_len() or seq_along() * NOTE: Avoid 'cat' and 'print' outside of 'show' methods * NOTE: Avoid using '=' for assignment and use '<-' instead * NOTE: Avoid the use of 'paste' in condition signals * WARNING: .Deprecated / .Defunct usage (found 1 times) * Checking parsed R code in R directory, examples, vignettes... * NOTE: Avoid 'suppressWarnings'/'*Messages' if possible (found 8 times) * Checking function lengths... * NOTE: The recommended function length is 50 lines or less. There are 49 functions greater than 50 lines. * Checking man page documentation... * WARNING: Empty or missing \value sections found in man page(s). Registered S3 method overwritten by 'GGally': method from +.gg ggplot2 * ERROR: At least 80% of man pages documenting exported objects must have runnable examples. * NOTE: Usage of dontrun{} / donttest{} tags found in man page examples. 17% of man pages use at least one of these tags. * NOTE: Use donttest{} instead of dontrun{}. * 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; 368 lines (3%) are > 80 characters long. * NOTE: Consider 4 spaces instead of tabs; 1 lines (0%) contain tabs. * NOTE: Consider multiples of 4 spaces for line indents; 4313 lines (30%) 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... * 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. * ERROR: Add package to Watched Tags in your Support Site profile; visit https://support.bioconductor.org/accounts/edit/profile ─ BiocCheck results ── 3 ERRORS | 4 WARNINGS | 15 NOTES See the ggbio.BiocCheck folder and run browseVignettes(package = 'BiocCheck') for details.