############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.19-bioc/R/bin/Rscript -e "BiocCheck::BiocCheck('DESeq2_1.45.0.tar.gz')" ### ############################################################################## ############################################################################## * Installing package... ─ sourceDir: /tmp/Rtmp6Gl6Zx/file29c44220b9909b/DESeq2 ─ BiocVersion: 3.20 ─ Package: DESeq2 ─ PackageVersion: 1.45.0 ─ BiocCheckDir: /home/biocbuild/bbs-3.19-bioc-testing/meat/DESeq2.BiocCheck ─ BiocCheckVersion: 1.41.4 ─ sourceDir: /tmp/Rtmp6Gl6Zx/file29c44220b9909b/DESeq2 ─ installDir: /tmp/Rtmp6Gl6Zx/file29c44231e049ed ─ 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... * WARNING: Package files exceed the 5MB size limit. * 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: Coverage 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... * 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... * NOTE: Provide 'BugReports' field(s) in DESCRIPTION * Checking for Bioconductor software dependencies... Bioconductor dependencies found in Imports & Depends (57%). * 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: * Checking package installation calls in R code... * NOTE: Avoid using install, biocLite, install.packages, or update.packages * Checking for library/require of DESeq2... * 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 * NOTE: Avoid redundant 'stop' and 'warn*' in signal conditions * WARNING: Avoid T/F variables; If logical, use TRUE/FALSE * WARNING: Remove set.seed usage (found 1 times) * WARNING: .Deprecated / .Defunct usage (found 1 times) * Checking parsed R code in R directory, examples, vignettes... * ERROR: Remove install() calls (found 1 times) * NOTE: Avoid '<<-' if possible (found 1 times) * NOTE: Avoid 'suppressWarnings'/'*Messages' if possible (found 3 times) * Checking function lengths... * NOTE: The recommended function length is 50 lines or less. There are 32 functions greater than 50 lines. * Checking man page documentation... * WARNING: Empty or missing \value sections found in man page(s). * 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. 2% 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; 761 lines (7%) 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; 3360 lines (29%) 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. Package is in the Support Site Watched Tags. ─ BiocCheck results ── 3 ERRORS | 6 WARNINGS | 19 NOTES See the DESeq2.BiocCheck folder and run browseVignettes(package = 'BiocCheck') for details.