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### Running command:
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###   /home/biocbuild/bbs-3.24-bioc/R/bin/Rscript -e "BiocCheck::BiocCheck('arrayQuality_1.91.0.tar.gz','quit-with-status'=TRUE)"
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── Installing arrayQuality ─────────────────────────────────────────────────────
✔ Package installed successfully
── arrayQuality session metadata ───────────────────────────────────────────────
→ sourceDir: /tmp/RtmpXABPLJ/file56c62551542ac/arrayQuality
→ BiocVersion: 3.24
→ Package: arrayQuality
→ PackageVersion: 1.91.0
→ BiocCheckDir: /home/biocbuild/bbs-3.24-bioc/meat/arrayQuality.BiocCheck
→ BiocCheckVersion: 1.49.4
→ sourceDir: /tmp/RtmpXABPLJ/file56c62551542ac/arrayQuality
→ installDir: /tmp/RtmpXABPLJ/file56c62623b77f0
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on arrayQuality ───────────────────────────────────────────
* 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 2.2.0 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...
* Checking build system compatibility...
* Checking for proper Description: field...
* Checking if DESCRIPTION is well formatted...
* Checking for whitespace in DESCRIPTION field names...
* Checking if 'Package:' field matches directory / tarball...
* Checking for Version: field...
✖ ERROR: Remove Maintainer field. Use Authors@R [cre] designation.
* Checking License: for restrictive use...
* Checking for recommended DESCRIPTION fields...
ℹ NOTE: Provide 'BugReports' field(s) in DESCRIPTION
* Checking for Bioconductor software dependencies...
ℹ Bioconductor dependencies found in Imports & Depends (18%).
* 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: No vignette sources in vignettes/ directory.
* Checking package installation calls in R code...
* Checking for library/require of arrayQuality...
! WARNING: Avoid the use of 'library' or 'require' in R code
  Found in files:
    • require() in R/heeboQuality.R (line 35, column 5)
    • ...
    • library() in R/spikeIn.R (line 15, column 1)
* Checking coding practice...
ℹ NOTE: Avoid sapply(); use vapply()
  Found in files:
    • R/spikeIn.R (line 106, column 15)
    • R/spikeIn.R (line 313, column 15)
ℹ NOTE: Avoid 1:...; use seq_len() or seq_along()
  Found in files:
    • agQuality.R (line 237, column 19)
    • ...
    • spotQuality.R (line 337, column 18)
ℹ NOTE: Avoid 'cat' and 'print' outside of 'show' methods
  Found in files:
    • print() in R/agQuality.R (line 19, column 16)
    • ...
    • print() in R/spotQuality.R (line 411, column 11)
ℹ NOTE: Avoid using '=' for assignment and use '<-' instead
  Found in files:
    • R/agQuality.R (line 184, column 13)
    • ...
    • R/spotQuality.R (line 209, column 13)
ℹ NOTE: Avoid redundant 'stop' and 'warn*' in signal conditions
  Found in files:
    • R/qualFunc.R (line 362, column 10)
    • R/qualFunc.R (line 398, column 16)
! WARNING: Avoid T/F variables; If logical, use TRUE/FALSE
  Found 2 times:
    • T in R/qualFunc.R (line 673, column 66)
    • T in R/qualFunc.R (line 770, column 66)
* Checking parsed R code in R directory, examples, vignettes...
* Checking function lengths...
ℹ NOTE: The recommended function length is 50 lines or less. There are 26
functions greater than 50 lines.
  The longest 5 functions are:
    • meeboQuality() (R/meeboQuality.R): 375 lines
    • ...
    • gpQuality() (R/gpQuality.R): 247 lines
* Checking man page documentation...
! WARNING: Empty or missing \value sections found in man page(s).
  Found in files:
    • man/arrayQuality-internal.Rd
    • ...
    • man/prdata.Rd
✖ ERROR: At least 80% of man pages documenting exported objects must have
runnable examples.
  The following pages do not:
    • arrayQuality-internal.Rd
    • ...
    • spotQuality.Rd
* Checking package NEWS...
ℹ NOTE: Consider adding a NEWS file, so your package news will be included in
Bioconductor release announcements.
* Checking unit tests...
ℹ 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...
ℹ NOTE: Consider shorter lines; 466 lines (7%) are > 80 characters long.
  First few lines:
    • R/agQuality.R#L102 Flags <- cbind(Flags, as.numeric(as. ...
    • ...
    • man/spotQuality.Rd#L77 scores are gathered in a HTML report. Fo ...
ℹ NOTE: Consider multiples of 4 spaces for line indents; 2273 lines (33%) are
not.
  First few lines:
    • R/agQuality.R#L17 sep ="\t", quote= " ...
    • ...
    • man/spotQuality.Rd#L84 \item{quality}{A matrix containing Qua ...
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 is registered at support site.
ℹ Package is in the Support Site Watched Tags.
── BiocCheck v1.49.4 results ───────────────────────────────────────────────────
✖ 3 ERRORS | ⚠ 3 WARNINGS | ℹ 14 NOTES
ℹ See the arrayQuality.BiocCheck folder and run
  browseVignettes(package = 'BiocCheck')
  for details.