############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.19-bioc/R/bin/Rscript -e "BiocCheck::BiocCheck('Rsamtools_2.21.0.tar.gz')" ### ############################################################################## ############################################################################## ─ BiocCheckVersion: 1.41.3 ─ BiocVersion: 3.20 ─ Package: Rsamtools ─ PackageVersion: 2.21.0 ─ sourceDir: /tmp/Rtmp7fkPsw/file3b496d6e3a4ffd/Rsamtools ─ installDir: /tmp/Rtmp7fkPsw/file3b496da3c001c ─ BiocCheckDir: /home/biocbuild/bbs-3.19-bioc-testing/meat/Rsamtools.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... * NOTE: Update R version dependency from 3.5.0 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/Rtmp7fkPsw/file3b496d6e3a4ffd/Rsamtools/man/pileup.Rd' * NOTE: Consider adding these automatically suggested biocViews: ATACSeq, SequenceMatching, VariantAnnotation, MultipleSequenceAlignment 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... * NOTE: The Description field in the DESCRIPTION is made up of less than 3 sentences. Provide a more detailed description of the package. * 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 (69%). * 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 Rsamtools... * Checking coding practice... * NOTE: Avoid sapply(); use vapply() * NOTE: Avoid the use of 'paste' in condition signals * WARNING: .Deprecated / .Defunct usage (found 11 times) * Checking parsed R code in R directory, examples, vignettes... * NOTE: Avoid '<<-' if possible (found 2 times) * Checking function lengths... * NOTE: The recommended function length is 50 lines or less. There are 6 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. 11% 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; 21 lines (0%) are > 80 characters long. * NOTE: Consider 4 spaces instead of tabs; 70 lines (1%) contain tabs. * NOTE: Consider multiples of 4 spaces for line indents; 1635 lines (18%) 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 | 2 WARNINGS | 14 NOTES See the Rsamtools.BiocCheck folder and run browseVignettes(package = 'BiocCheck') for details.