############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.19-bioc/R/bin/Rscript -e "BiocCheck::BiocCheck('edgeR_4.3.4.tar.gz')" ### ############################################################################## ############################################################################## ─ BiocCheckVersion: 1.41.3 ─ BiocVersion: 3.20 ─ Package: edgeR ─ PackageVersion: 4.3.4 ─ sourceDir: /tmp/Rtmpwi0q1p/file3aef561ac9b4d/edgeR ─ installDir: /tmp/Rtmpwi0q1p/file3aef5614618999 ─ BiocCheckDir: /home/biocbuild/bbs-3.19-bioc-testing/meat/edgeR.BiocCheck ─ platform: unix ─ isTarBall: TRUE * Installing package... * 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 3.6.0 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... Warning in FUN(X[[i]], ...) : incomplete final line found on '/tmp/Rtmpwi0q1p/file3aef561ac9b4d/edgeR/man/dimnames.Rd' Warning in FUN(X[[i]], ...) : incomplete final line found on '/tmp/Rtmpwi0q1p/file3aef561ac9b4d/edgeR/man/nbinomUnitDeviance.Rd' * NOTE: Consider adding these automatically suggested biocViews: Microarray, ChipOnChip, Metabolomics, Proteomics, Cheminformatics, Preprocessing, ExonArray, OneChannel, TwoChannel, MicroRNAArray, mRNAMicroarray, ProprietaryPlatforms, DataImport 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... * ERROR: Remove Maintainer field. Use Authors@R [cre] designation. * 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 (14%). * Checking for pinned package versions in DESCRIPTION... * Checking .Rbuildignore... * Checking for stray BiocCheck output folders... * Checking vignette directory... * WARNING: Use RMarkdown instead of Sweave 'Rnw' vignettes. * WARNING: Evaluate more vignette chunks. 1 out of 2 code chunks = 50% unevaluated 0 non-exec code chunk(s) (e.g., '```r') * NOTE: 'sessionInfo' not found in vignette(s) * Checking package installation calls in R code... * Checking for library/require of edgeR... * 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: .Deprecated / .Defunct usage (found 1 times) * Checking parsed R code in R directory, examples, vignettes... * NOTE: Avoid 'suppressWarnings'/'*Messages' if possible (found 19 times) * Checking function lengths... * NOTE: The recommended function length is 50 lines or less. There are 48 functions greater than 50 lines. * Checking man page documentation... * 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. 8% 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; 2234 lines (14%) are > 80 characters long. * NOTE: Consider 4 spaces instead of tabs; 6351 lines (40%) contain tabs. * NOTE: Consider multiples of 4 spaces for line indents; 596 lines (4%) 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 ── 2 ERRORS | 4 WARNINGS | 18 NOTES See the edgeR.BiocCheck folder and run browseVignettes(package = 'BiocCheck') for details.