############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.19-bioc/R/bin/Rscript -e "BiocCheck::BiocCheck('affy_1.83.0.tar.gz')" ### ############################################################################## ############################################################################## ─ BiocCheckVersion: 1.41.3 ─ BiocVersion: 3.20 ─ Package: affy ─ PackageVersion: 1.83.0 ─ sourceDir: /tmp/RtmpHYBaXY/file3ac5c610b6a2da/affy ─ installDir: /tmp/RtmpHYBaXY/file3ac5c615867a45 ─ BiocCheckDir: /home/biocbuild/bbs-3.19-bioc-testing/meat/affy.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 2.8.0 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... * 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... * Checking for Bioconductor software dependencies... Bioconductor dependencies found in Imports & Depends (45%). * 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... * NOTE: Avoid using install, biocLite, install.packages, or update.packages * Checking for library/require of affy... * 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 class membership checks with class() / is() and == / !=; Use is(x, 'class') for S4 classes * WARNING: .Deprecated / .Defunct usage (found 1 times) * Checking parsed R code in R directory, examples, vignettes... Found @ in vignettes/affy.Rnw * NOTE: Use accessors; don't access S4 class slots via '@' in examples/vignettes. * ERROR: Remove install() calls (found 1 times) * NOTE: Avoid '<<-' if possible (found 11 times) * Checking function lengths... * NOTE: The recommended function length is 50 lines or less. There are 24 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... * 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; 312 lines (3%) are > 80 characters long. * NOTE: Consider 4 spaces instead of tabs; 141 lines (2%) contain tabs. * NOTE: Consider multiples of 4 spaces for line indents; 3041 lines (34%) 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. * ERROR: Add package to Watched Tags in your Support Site profile; visit https://support.bioconductor.org/accounts/edit/profile ─ BiocCheck results ── 5 ERRORS | 5 WARNINGS | 19 NOTES See the affy.BiocCheck folder and run browseVignettes(package = 'BiocCheck') for details.