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### Running command:
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###   /home/rapidbuild/bbs-3.23-bioc-rapid/R/bin/Rscript -e "BiocCheck::BiocCheck('AnnotationDbi_1.74.0.tar.gz','quit-with-status'=TRUE)"
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── Installing AnnotationDbi ────────────────────────────────────────────────────
✔ Package installed successfully
── AnnotationDbi session metadata ──────────────────────────────────────────────
→ sourceDir: /tmp/RtmpYVbFOC/file71b45656d31be/AnnotationDbi
→ BiocVersion: 3.23
→ Package: AnnotationDbi
→ PackageVersion: 1.74.0
→ BiocCheckDir: /media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/meat/AnnotationDbi.BiocCheck
→ BiocCheckVersion: 1.48.0
→ sourceDir: /tmp/RtmpYVbFOC/file71b45656d31be/AnnotationDbi
→ installDir: /tmp/RtmpYVbFOC/file71b451269d1d6
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on AnnotationDbi ──────────────────────────────────────────
* 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...
ℹ NOTE: Update R version dependency from 2.7.0 to 4.6.0
* 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...
ℹ NOTE: Consider adding these automatically suggested biocViews: GO
ℹ 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: Remove Maintainer field. Use Authors@R [cre] designation.
* Checking License: for restrictive use...
* Checking for recommended DESCRIPTION fields...
* Checking for Bioconductor software dependencies...
ℹ Bioconductor dependencies found in Imports & Depends (50%).
* Checking for pinned package versions in DESCRIPTION...
* Checking for 'fnd' role in Authors@R...
ℹ NOTE: No 'fnd' role found in Authors@R. If the work is supported by a grant,
consider adding the 'fnd' role to the list of authors.
* Checking NAMESPACE...
* Checking .Rbuildignore...
* Checking for stray BiocCheck output folders...
* Checking vignette directory...
! WARNING: Use RMarkdown instead of Sweave 'Rnw' vignettes.
  Rnw vignette(s) found:
    • IntroToAnnotationPackages.Rnw
ℹ NOTE: Vignette(s) found with missing chunk labels
  Found in files:
    • IntroToAnnotationPackages.Rnw
* Checking package installation calls in R code...
* Checking for library/require of AnnotationDbi...
! WARNING: Avoid the use of 'library' or 'require' in R code
  Found in files:
    • require() in R/AnnDbPkg-checker.R (line 66, column 5)
    • ...
    • require() in R/loadDb.R (line 93, column 31)
* Checking coding practice...
ℹ NOTE: Avoid sapply(); use vapply()
  Found in files:
    • R/AnnDbPkg-checker.R (line 32, column 18)
    • ...
    • R/SQL.R (line 171, column 16)
ℹ NOTE: Avoid 1:...; use seq_len() or seq_along()
  Found in files:
    • AnnDbObj-lowAPI.R (line 71, column 15)
    • Bimap.R (line 1005, column 22)
    • GOTerms.R (line 341, column 26)
ℹ NOTE: Avoid 'cat' and 'print' outside of 'show' methods
  Found in files:
    • cat() in R/AnnDbObj-lowAPI.R (line 40, column 6)
    • ...
    • cat() in R/SQL.R (line 612, column 17)
ℹ NOTE: Avoid using '=' for assignment and use '<-' instead
  Found in files:
    • R/AnnDbObj-lowAPI.R (line 58, column 11)
    • ...
    • R/SQL.R (line 303, column 23)
ℹ NOTE: Avoid the use of 'paste' in condition signals
  Found in files:
    • R/methods-geneCentricDbs-keys.R (line 20, column 18)
    • R/methods-geneCentricDbs.R (line 1025, column 17)
! WARNING: Avoid class membership checks with class() / is() and == / !=; Use
is(x, 'class') for S4 classes
  Found in files:
    • BimapFormatting.R (line 372, column 28)
    • ...
    • methods-geneCentricDbs.R (line 1083, column 14)
! WARNING: .Deprecated / .Defunct usage (found 3 times)
  • .Deprecated() in R/Bimap-envirAPI.R (line 216, column 9)
  • .Deprecated() in R/GOTerms.R (line 334, column 5)
  • .Deprecated() in R/methods-AnnotationDb.R (line 94, column 5)
* Checking parsed R code in R directory, examples, vignettes...
ℹ NOTE: Avoid 'suppressWarnings'/'*Messages' if possible (found 4 times)
  • suppressWarnings() in R/Bimap.R (line 1388, column 3)
  • ...
  • suppressWarnings() in R/methods-geneCentricDbs-keys.R (line 208, column 18)
* Checking function lengths...
ℹ NOTE: The recommended function length is 50 lines or less. There are 15
functions greater than 50 lines.
  The longest 5 functions are:
    • NCBICHIP_DB_SeedGenerator() (R/createAnnObjs.NCBICHIP_DBs.R): 371 lines
    • ...
    • compareAnnDataIn2Pkgs() (R/AnnDbPkg-checker.R): 91 lines
* Checking man page documentation...
! WARNING: Empty or missing \value sections found in man page(s).
  Found in files:
    • man/AnnDbPkg-checker.Rd
    • ...
    • man/unlist2.Rd
ℹ NOTE: Consider adding runnable examples to man pages that document exported
objects.
  • AnnotationDbi-internals.Rd
  • ...
  • orgPackageName.Rd
ℹ NOTE: Usage of dontrun / donttest tags found in man page examples. 12% of man
pages use at least one of these tags.
  Found in files:
    • GOTerms-class.Rd
    • inpIDMapper.Rd
    • makeGOGraph.Rd
ℹ NOTE: Use donttest instead of dontrun.
  Found in files:
    • GOTerms-class.Rd
    • inpIDMapper.Rd
    • makeGOGraph.Rd
* Checking package NEWS...
* Checking unit tests...
* Checking skip_on_bioc() in tests...
* Checking formatting of DESCRIPTION, NAMESPACE, man pages, R source, and
vignette source...
ℹ NOTE: Consider shorter lines; 275 lines (2%) are > 80 characters long.
  First few lines:
    • R/AllClasses.R#L13 ifnotfound=list() # em ...
    • ...
    • vignettes/IntroToAnnotationPackages.Rnw#L2
    %\VignetteDepends{org.Hs.eg.db, TxDb.Hsa ...
ℹ NOTE: Consider 4 spaces instead of tabs; 54 lines (0%) contain tabs.
  First few lines:
    • R/createAnnObjs-utils.R#L173 "HuExExonProbesetLocation" = "hg19", ...
    • ...
    • man/AnnotationDb-class.Rd#L179 used with pattern by the keys method)} ...
ℹ NOTE: Consider multiples of 4 spaces for line indents; 2461 lines (17%) are
not.
  First few lines:
    • R/AllClasses.R#L218 representation(data="data.frame ...
    • ...
    • vignettes/IntroToAnnotationPackages.Rnw#L402 columns=c("TXID", "TXSEQST
    ...
ℹ See https://contributions.bioconductor.org/r-code.html
ℹ 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...
ℹ 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...
ℹ Maintainer email is ok.
── BiocCheck v1.48.0 results ───────────────────────────────────────────────────
✖ 1 ERRORS | ⚠ 5 WARNINGS | ℹ 18 NOTES
ℹ See the AnnotationDbi.BiocCheck folder and run
  browseVignettes(package = 'BiocCheck')
  for details.