############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.19-bioc/R/bin/Rscript -e "BiocCheck::BiocCheck('qvalue_2.37.0.tar.gz')" ### ############################################################################## ############################################################################## ─ BiocCheckVersion: 1.41.3 ─ BiocVersion: 3.20 ─ Package: qvalue ─ PackageVersion: 2.37.0 ─ sourceDir: /tmp/RtmpTpoGfk/file3b283041c2b7b0/qvalue ─ installDir: /tmp/RtmpTpoGfk/file3b2830331afaca ─ BiocCheckDir: /home/biocbuild/bbs-3.19-bioc-testing/meat/qvalue.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 2.10 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... * WARNING: Invalid BiocViews term(s): * Checking for recommended biocViews... 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: Authors@R field must be valid R code. * Checking License: for restrictive use... * Checking for recommended DESCRIPTION fields... * NOTE: Provide 'BugReports' field(s) in DESCRIPTION * Checking for Bioconductor software dependencies... * WARNING: No Bioconductor dependencies detected. Note that some infrastructure packages may not have Bioconductor dependencies. For more information, reach out to the Bioconductor community and/or consider a CRAN submission. * 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. * NOTE: 'sessionInfo' not found in vignette(s) * Checking package installation calls in R code... * Checking for library/require of qvalue... * 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 class membership checks with class() / is() and == / !=; Use is(x, 'class') for S4 classes * Checking parsed R code in R directory, examples, vignettes... * Checking function lengths... * NOTE: The recommended function length is 50 lines or less. There are 3 functions greater than 50 lines. * Checking man page documentation... * Checking package NEWS... * Checking unit tests... * NOTE: Consider adding unit tests. We strongly encourage them. See https://contributions.bioconductor.org/tests.html * Checking skip_on_bioc() in tests... * Checking formatting of DESCRIPTION, NAMESPACE, man pages, R source, and vignette source... * NOTE: Consider shorter lines; 136 lines (11%) are > 80 characters long. * NOTE: Consider 4 spaces instead of tabs; 2 lines (0%) contain tabs. * NOTE: Consider multiples of 4 spaces for line indents; 228 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 is registered at support site. Package is in the Support Site Watched Tags. ─ BiocCheck results ── 1 ERRORS | 4 WARNINGS | 15 NOTES See the qvalue.BiocCheck folder and run browseVignettes(package = 'BiocCheck') for details.