############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.19-bioc/R/bin/Rscript -e "BiocCheck::BiocCheck('MSnbase_2.31.1.tar.gz')" ### ############################################################################## ############################################################################## * Installing package... ─ sourceDir: /tmp/RtmpdanJuj/fileef3a75e5f74c2/MSnbase ─ BiocVersion: 3.20 ─ Package: MSnbase ─ PackageVersion: 2.31.1 ─ BiocCheckDir: /home/biocbuild/bbs-3.19-bioc-testing/meat/MSnbase.BiocCheck ─ BiocCheckVersion: 1.41.5 ─ sourceDir: /tmp/RtmpdanJuj/fileef3a75e5f74c2/MSnbase ─ installDir: /tmp/RtmpdanJuj/fileef3a7736be106 ─ isTarBall: TRUE ─ platform: unix * Checking for deprecated package usage... * Checking for remote package usage... * Checking for 'LazyData: true' usage... * NOTE: 'LazyData:' in the 'DESCRIPTION' should be set to false or removed * Checking version number... * Checking for version number mismatch... * Checking version number validity... * Checking R version dependency... * NOTE: Update R version dependency from 3.5 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/RtmpdanJuj/fileef3a75e5f74c2/MSnbase/man/missing-data.Rd' Warning in FUN(X[[i]], ...) : incomplete final line found on '/tmp/RtmpdanJuj/fileef3a75e5f74c2/MSnbase/man/readMSnSet.Rd' * NOTE: Consider adding these automatically suggested biocViews: Metabolomics, SequenceMatching Search 'biocViews' at https://contributions.bioconductor.org * Checking build system compatibility... * Checking for proper Description: field... * Checking if DESCRIPTION is well formatted... * Checking for whitespace in DESCRIPTION field names... * Checking that Package field matches directory/tarball name... * Checking for Version: field... * ERROR: Designate only one maintainer with Authors@R [cre]. * Checking License: for restrictive use... * Checking for recommended DESCRIPTION fields... * Checking for Bioconductor software dependencies... Bioconductor dependencies found in Imports & Depends (56%). * Checking for pinned package versions in DESCRIPTION... * 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... * Checking for library/require of MSnbase... * 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 14 times) * Checking parsed R code in R directory, examples, vignettes... Found @ in man/Chromatogram-class.Rd Found @ in vignettes/v01-MSnbase-demo.Rmd * NOTE: Use accessors; don't access S4 class slots via '@' in examples/vignettes. * NOTE: Avoid '<<-' if possible (found 5 times) * NOTE: Avoid 'suppressWarnings'/'*Messages' if possible (found 11 times) * Checking function lengths... * NOTE: The recommended function length is 50 lines or less. There are 46 functions greater than 50 lines. * Checking man page documentation... * WARNING: Empty or missing \format sections found in data man page(s). * 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. 4% of man pages use at least one of these tags. * NOTE: Use donttest{} instead of dontrun{}. * Checking package NEWS... * NOTE: Consider adding a NEWS file, so your package news will be included in Bioconductor release announcements. * 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; 374 lines (2%) are > 80 characters long. * NOTE: Consider 4 spaces instead of tabs; 32 lines (0%) contain tabs. * NOTE: Consider multiples of 4 spaces for line indents; 5680 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 is registered at support site. Package is in the Support Site Watched Tags. ─ BiocCheck results ── 1 ERRORS | 5 WARNINGS | 22 NOTES See the MSnbase.BiocCheck folder and run browseVignettes(package = 'BiocCheck') for details.