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### Running command:
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###   /home/rapidbuild/bbs-3.23-bioc-rapid/R/bin/Rscript -e "BiocCheck::BiocCheck('AnnotationHub_4.2.0.tar.gz','quit-with-status'=TRUE)"
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── Installing AnnotationHub ────────────────────────────────────────────────────
✔ Package installed successfully
── AnnotationHub session metadata ──────────────────────────────────────────────
→ sourceDir: /tmp/Rtmppq1SMM/file729282353250e/AnnotationHub
→ BiocVersion: 3.23
→ Package: AnnotationHub
→ PackageVersion: 4.2.0
→ BiocCheckDir: /media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/meat/AnnotationHub.BiocCheck
→ BiocCheckVersion: 1.48.0
→ sourceDir: /tmp/Rtmppq1SMM/file729282353250e/AnnotationHub
→ installDir: /tmp/Rtmppq1SMM/file7292837594897
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on AnnotationHub ──────────────────────────────────────────
* 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...
* 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 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...
ℹ NOTE: Consider adding the maintainer's ORCID iD in 'Authors@R' with
'comment=c(ORCID="...")'
* Checking License: for restrictive use...
* Checking for recommended DESCRIPTION fields...
ℹ NOTE: Provide 'URL' field(s) in DESCRIPTION
* Checking for Bioconductor software dependencies...
ℹ Bioconductor dependencies found in Imports & Depends (38%).
* 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...
ℹ NOTE: Vignette(s) found with missing chunk labels
  Found in files:
    • AnnotationHub-HOWTO.Rmd
    • AnnotationHub.Rmd
    • TroubleshootingTheHubs.Rmd
ℹ NOTE: 'sessionInfo' not found in vignette(s)
  Missing from file(s):
    • vignettes/TroubleshootingTheHubs.Rmd
! WARNING: Vignette set global option 'eval=FALSE'
  Found in files:
    • vignettes/TroubleshootingTheHubs.Rmd
* Checking package installation calls in R code...
* Checking for library/require of AnnotationHub...
! WARNING: Avoid the use of 'library' or 'require' in R code
  Found in files:
    • require() in R/utilities.R (line 16, column 9)
* Checking coding practice...
ℹ NOTE: Avoid 1:...; use seq_len() or seq_along()
  Found in files:
    • EpigenomeResource-class.R (line 28, column 38)
    • EpigenomeResource-class.R (line 54, column 23)
ℹ NOTE: Avoid 'cat' and 'print' outside of 'show' methods
  Found in files:
    • cat() in R/Hub-class.R (line 611, column 5)
    • ...
    • print() in R/Hub-class.R (line 632, column 9)
ℹ NOTE: Avoid using '=' for assignment and use '<-' instead
  Found in files:
    • R/AnnotationHub-class.R (line 23, column 20)
    • ...
    • R/sql-utils.R (line 301, column 29)
ℹ NOTE: Avoid the use of 'paste' in condition signals
  Found in files:
    • R/AnnotationHub-class.R (line 25, column 22)
    • ...
    • R/Hub-utils.R (line 142, column 14)
ℹ NOTE: Avoid redundant 'stop' and 'warn*' in signal conditions
  Found in files:
    • R/Hub-utils.R (line 329, column 25)
* Checking parsed R code in R directory, examples, vignettes...
ℹ NOTE: Avoid 'suppressWarnings'/'*Messages' if possible (found 3 times)
  • suppressWarnings() in R/AnnotationHub-class.R (line 38, column 20)
  • suppressWarnings() in R/cache-utils.R (line 111, column 23)
  • suppressMessages() in R/Hub-class.R (line 381, column 5)
* Checking function lengths...
ℹ NOTE: The recommended function length is 50 lines or less. There are 10
functions greater than 50 lines.
  The longest 5 functions are:
    • .uid0() (R/sql-utils.R): 96 lines
    • ...
    • _anonymous_.385() (R/Hub-class.R): 70 lines
* Checking man page documentation...
! WARNING: Empty or missing \value sections found in man page(s).
  Found in files:
    • man/listResources.Rd
    • man/utils.Rd
ℹ NOTE: Consider adding runnable examples to man pages that document exported
objects.
  • AnnotationHubResource-class.Rd
ℹ NOTE: Usage of dontrun / donttest tags found in man page examples. 50% of man
pages use at least one of these tags.
  Found in files:
    • AnnotationHub-package.Rd
    • ...
    • Hub-utils.Rd
ℹ NOTE: Use donttest instead of dontrun.
  Found in files:
    • AnnotationHub-package.Rd
    • ...
    • Hub-utils.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; 96 lines (2%) are > 80 characters long.
  First few lines:
    • R/AnnotationHub-class.R#L12 ## Add code to check : https://annotatio ...
    • ...
    • vignettes/TroubleshootingTheHubs.Rmd#L473 AnnotationHub location, to
    continue usin ...
ℹ NOTE: Consider 4 spaces instead of tabs; 16 lines (0%) contain tabs.
  First few lines:
    • vignettes/TroubleshootingTheHubs.Rmd#L497 moveFiles<-function(package){
    ...
    • ...
    • vignettes/TroubleshootingTheHubs.Rmd#L514 moveFiles(package) ...
ℹ NOTE: Consider multiples of 4 spaces for line indents; 376 lines (9%) are
not.
  First few lines:
    • R/AnnotationHub-class.R#L16 cache=getAnnotationHubOptio ...
    • ...
    • vignettes/TroubleshootingTheHubs.Rmd#L550 resources will have to be
    re-downloade ...
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 ───────────────────────────────────────────────────
✖ 0 ERRORS | ⚠ 3 WARNINGS | ℹ 19 NOTES
ℹ See the AnnotationHub.BiocCheck folder and run
  browseVignettes(package = 'BiocCheck')
  for details.