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### Running command:
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###   /home/rapidbuild/bbs-3.23-bioc-rapid/R/bin/Rscript -e "BiocCheck::BiocCheck('AnnotationHubData_1.42.0.tar.gz','quit-with-status'=TRUE)"
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── Installing AnnotationHubData ────────────────────────────────────────────────
✔ Package installed successfully
── AnnotationHubData session metadata ──────────────────────────────────────────
→ sourceDir: /tmp/RtmprQovk6/file7296ae3ff284/AnnotationHubData
→ BiocVersion: 3.23
→ Package: AnnotationHubData
→ PackageVersion: 1.42.0
→ BiocCheckDir: /media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/meat/AnnotationHubData.BiocCheck
→ BiocCheckVersion: 1.48.0
→ sourceDir: /tmp/RtmprQovk6/file7296ae3ff284/AnnotationHubData
→ installDir: /tmp/RtmprQovk6/file7296ada4e49c
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on AnnotationHubData ──────────────────────────────────────
* 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 3.2.2 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: Sequencing,
Coverage, ThirdPartyClient, GUI
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...
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', 'BugReports' field(s) in DESCRIPTION
* Checking for Bioconductor software dependencies...
ℹ Bioconductor dependencies found in Imports & Depends (67%).
* 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...
✖ ERROR: 'VignetteBuilder' listed in DESCRIPTION but not found as
'VignetteEngine' in any vignettes:
  • knitr
! WARNING: Vignette(s) missing Vignette metadata. See
https://r-pkgs.org/vignettes.html
  Update the following files:
    • IntroductionToAnnotationHubData.Rmd
✖ ERROR: 'VignetteEngine' specified but not in the DESCRIPTION.
  Add 'VignetteEngine' to DESCRIPTION from the following:
    • vignettes/IntroductionToAnnotationHubData.Rmd
! WARNING: Package listed as VignetteEngine or VignetteBuilder but not
currently Suggested.
  Add the following to Suggests in DESCRIPTION:
    • %knitr
! WARNING: Vignette(s) missing '\%VignetteIndexEntry{Vignette Title}'.
  Update the following files:
    • IntroductionToAnnotationHubData.Rmd
! WARNING: Evaluate more vignette chunks.
ℹ 1 out of 1 code chunks = 100% unevaluated
ℹ 
* Checking package installation calls in R code...
✖ ERROR: Avoid using install, biocLite, install.packages, or update.packages
  Found in files:
    • install() in R/makeStandardOrgDbsToSqlite.R (line 26, column 30)
    • install() in R/makeStandardTxDbsToSqlite.R (line 22, column 26)
* Checking for library/require of AnnotationHubData...
! WARNING: Avoid the use of 'library' or 'require' in R code
  Found in files:
    • require() in R/makeStandardTxDbsToSqlite.R (line 21, column 14)
* Checking coding practice...
ℹ NOTE: Avoid sapply(); use vapply()
  Found in files:
    • R/AnnotationHubMetadata-class.R (line 68, column 22)
    • ...
    • R/webAccessFunctions.R (line 78, column 22)
ℹ NOTE: Avoid 1:...; use seq_len() or seq_along()
  Found in files:
    • makeEncodeDCC.R (line 101, column 28)
    • ...
    • utils.R (line 98, column 15)
ℹ NOTE: Avoid 'cat' and 'print' outside of 'show' methods
  Found in files:
    • print() in R/validationFunctions.R (line 19, column 9)
    • print() in R/validationFunctions.R (line 77, column 9)
ℹ NOTE: Avoid using '=' for assignment and use '<-' instead
  Found in files:
    • R/AnnotationHubMetadata-class.R (line 91, column 67)
    • ...
    • R/webAccessFunctions.R (line 97, column 17)
ℹ NOTE: Avoid the use of 'paste' in condition signals
  Found in files:
    • R/AnnotationHubMetadata-class.R (line 202, column 19)
    • ...
    • R/webAccessFunctions.R (line 93, column 17)
ℹ NOTE: Avoid redundant 'stop' and 'warn*' in signal conditions
  Found in files:
    • R/makeGencodeGFF.R (line 89, column 14)
    • R/webAccessFunctions.R (line 108, column 18)
ℹ NOTE: Avoid system() ; use system2()
  Found in files:
    • system() in R/makeEnsemblTwoBit.R (line 91, column 9)
    • system() in R/makeEnsemblTwoBit.R (line 100, column 5)
* Checking parsed R code in R directory, examples, vignettes...
ℹ NOTE: Avoid '<<-' if possible (found 1 times)
  • <<- in R/makeUCSCTracks.R (line 30, column 21)
ℹ NOTE: Avoid 'suppressWarnings'/'*Messages' if possible (found 2 times)
  • suppressMessages() in R/utils.R (line 13, column 3)
  • suppressWarnings() in R/webAccessFunctions.R (line 63, column 17)
* Checking function lengths...
ℹ NOTE: The recommended function length is 50 lines or less. There are 31
functions greater than 50 lines.
  The longest 5 functions are:
    • .readMetadataFromCsv() (R/AnnotationHubMetadata-class.R): 133 lines
    • ...
    • AnnotationHubMetadata() (R/AnnotationHubMetadata-class.R): 83 lines
* Checking man page documentation...
No methods found in package ‘rtracklayer’ for request: ‘trackName<-’ when loading ‘AnnotationHubData’
✖ ERROR: At least 80% of man pages documenting exported objects must have
runnable examples.
  The following pages do not:
    • flog.Rd
    • ...
    • upload_to_S3.Rd
ℹ NOTE: Usage of dontrun / donttest tags found in man page examples. 58% of man
pages use at least one of these tags.
  Found in files:
    • makeAnnotationHubMetadata.Rd
    • ...
    • upload_to_S3.Rd
ℹ NOTE: Use donttest instead of dontrun.
  Found in files:
    • makeAnnotationHubMetadata.Rd
    • ...
    • upload_to_S3.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; 119 lines (2%) are > 80 characters long.
  First few lines:
    • R/ahmToJson.R#L47 lst[['SourceLastModifiedDate']] <- a ...
    • ...
    • man/upload_to_S3.Rd#L35 Should be one of \code{private}, \code{p ...
ℹ NOTE: Consider 4 spaces instead of tabs; 125 lines (2%) contain tabs.
  First few lines:
    • R/makeEncodeDCC.R#L75 } ...
    • ...
    • man/makeAnnotationHubMetadata.Rd#L214 "SummarizedExperiment"), ...
ℹ NOTE: Consider multiples of 4 spaces for line indents; 908 lines (13%) are
not.
  First few lines:
    • R/ahmToJson.R#L33 warning("no matching value fo ...
    • ...
    • man/validationFunctions.Rd#L106 } ...
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 ───────────────────────────────────────────────────
✖ 4 ERRORS | ⚠ 5 WARNINGS | ℹ 21 NOTES
ℹ See the AnnotationHubData.BiocCheck folder and run
  browseVignettes(package = 'BiocCheck')
  for details.