############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.19-bioc/R/bin/Rscript -e "BiocCheck::BiocCheck('ShortRead_1.63.0.tar.gz')" ### ############################################################################## ############################################################################## ─ BiocCheckVersion: 1.41.3 ─ BiocVersion: 3.20 ─ Package: ShortRead ─ PackageVersion: 1.63.0 ─ sourceDir: /tmp/RtmpGEq1uW/file3ba7883a1ecba4/ShortRead ─ installDir: /tmp/RtmpGEq1uW/file3ba788779a460d ─ BiocCheckDir: /home/biocbuild/bbs-3.19-bioc-testing/meat/ShortRead.BiocCheck ─ platform: unix ─ isTarBall: TRUE * Installing package... * Checking for deprecated package usage... * ERROR: Package dependency in the DESCRIPTION is 'Deprecated'. Update your package to not rely on the following: * 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... * ERROR: Package tarball exceeds the Bioconductor size requirement. * 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/RtmpGEq1uW/file3ba7883a1ecba4/ShortRead/man/ShortRead-deprecated.Rd' * NOTE: Consider adding these automatically suggested biocViews: Coverage, Alignment, RNASeq, ImmunoOncology 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... * 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 (75%). * Checking for pinned package versions in DESCRIPTION... * Checking .Rbuildignore... * Checking for stray BiocCheck output folders... * Checking vignette directory... * Checking package installation calls in R code... * Checking for library/require of ShortRead... * 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 redundant 'stop' and 'warn*' in signal conditions * WARNING: Avoid class membership checks with class() / is() and == / !=; Use is(x, 'class') for S4 classes * WARNING: .Deprecated / .Defunct usage (found 3 times) * Checking parsed R code in R directory, examples, vignettes... * NOTE: Avoid '<<-' if possible (found 7 times) * Checking function lengths... * NOTE: The recommended function length is 50 lines or less. There are 15 functions greater than 50 lines. * Checking man page documentation... * WARNING: Empty or missing \value sections found in man page(s). * NOTE: Consider adding runnable examples to man pages that document exported objects. * NOTE: Usage of dontrun{} / donttest{} tags found in man page examples. 3% 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; 72 lines (0%) are > 80 characters long. * NOTE: Consider 4 spaces instead of tabs; 122 lines (1%) contain tabs. * NOTE: Consider multiples of 4 spaces for line indents; 4206 lines (26%) 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 email is ok. ─ BiocCheck results ── 2 ERRORS | 3 WARNINGS | 16 NOTES See the ShortRead.BiocCheck folder and run browseVignettes(package = 'BiocCheck') for details.