############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.18-bioc/R/bin/Rscript -e "BiocCheck::BiocCheck('affy_1.81.0.tar.gz')" ### ############################################################################## ############################################################################## ─ BiocCheckVersion: 1.39.0 ─ BiocVersion: 3.18 ─ Package: affy ─ PackageVersion: 1.81.0 ─ sourceDir: /tmp/Rtmp7z7aNo/file38967c2201d902/affy ─ installDir: /tmp/Rtmp7z7aNo/file38967c28a8eb80 ─ BiocCheckDir: /home/biocbuild/bbs-3.18-bioc-testing/meat/affy.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 2.8.0 to 4.3.0. * 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... * NOTE: License 'LGPL (>= 2.0)' unknown; licenses cannot restrict use * Checking for recommeded fields in DESCRIPTION... * Checking for pinned package versions... * Checking DESCRIPTION/NAMESPACE consistency... * Checking .Rbuildignore... * Checking for stray BiocCheck output folders... * Checking vignette directory... * 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 * 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 pages. * 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: Maintainer must add package name to Watched Tags on the support site; Edit your Support Site User Profile to add Watched Tags. ─ BiocCheck results ── 4 ERRORS | 3 WARNINGS | 20 NOTES See the affy.BiocCheck folder and run browseVignettes(package = 'BiocCheck') for details.