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### Running command:
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###   /home/biocbuild/bbs-3.24-bioc/R/bin/Rscript -e "BiocCheck::BiocCheck('beadarray_2.63.0.tar.gz','quit-with-status'=TRUE)"
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── Installing beadarray ────────────────────────────────────────────────────────
✔ Package installed successfully
── beadarray session metadata ──────────────────────────────────────────────────
→ sourceDir: /tmp/RtmpmfeDY1/file5a08a3809aeb1/beadarray
→ BiocVersion: 3.24
→ Package: beadarray
→ PackageVersion: 2.63.0
→ BiocCheckDir: /home/biocbuild/bbs-3.24-bioc/meat/beadarray.BiocCheck
→ BiocCheckVersion: 1.49.4
→ sourceDir: /tmp/RtmpmfeDY1/file5a08a3809aeb1/beadarray
→ installDir: /tmp/RtmpmfeDY1/file5a08a155a6057
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on beadarray ──────────────────────────────────────────────
* Checking for deprecated package usage...
* Checking for remote package usage...
* Checking for 'LazyData: true' usage...
ℹ 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...
ℹ NOTE: Update R version dependency from 2.13.0 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...
Warning in FUN(X[[i]], ...) :
  incomplete final line found on '/tmp/RtmpmfeDY1/file5a08a3809aeb1/beadarray/man/addFeatureData.Rd'
Warning in FUN(X[[i]], ...) :
  incomplete final line found on '/tmp/RtmpmfeDY1/file5a08a3809aeb1/beadarray/man/class-limmaResults.Rd'
Warning in FUN(X[[i]], ...) :
  incomplete final line found on '/tmp/RtmpmfeDY1/file5a08a3809aeb1/beadarray/man/GEO.Rd'
Warning in FUN(X[[i]], ...) :
  incomplete final line found on '/tmp/RtmpmfeDY1/file5a08a3809aeb1/beadarray/man/medianNormalise.Rd'
Warning in FUN(X[[i]], ...) :
  incomplete final line found on '/tmp/RtmpmfeDY1/file5a08a3809aeb1/beadarray/man/numBeads.Rd'
* 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 'URL', 'BugReports' field(s) in DESCRIPTION
* Checking for Bioconductor software dependencies...
ℹ Bioconductor dependencies found in Imports & Depends (58%).
* 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:
    • beadarray.Rmd
    • beadlevel.Rmd
    • beadsummary.Rmd
! WARNING: Avoid T/F variables; If logical, use TRUE/FALSE
  Found in files:
    • vignettes/beadlevel.Rmd (chunk no. 14, line 238, column 32)
    • vignettes/beadsummary.Rmd (chunk no. 26, line 355, column 34)
ℹ NOTE: 'sessionInfo' not found in vignette(s)
  Missing from file(s):
    • vignettes/beadlevel.Rmd
    • vignettes/beadsummary.Rmd
    • vignettes/ImageProcessing.Rmd
* Checking package installation calls in R code...
* Checking for library/require of beadarray...
! WARNING: Avoid the use of 'library' or 'require' in R code
  Found in files:
    • require() in R/annotation.R (line 155, column 19)
    • ...
    • require() in R/readIdatFiles.R (line 82, column 23)
* Checking coding practice...
ℹ NOTE: Avoid sapply(); use vapply()
  Found in files:
    • R/annotation.R (line 29, column 15)
    • ...
    • R/swathData_genSwaths.R (line 280, column 16)
ℹ NOTE: Avoid 1:...; use seq_len() or seq_along()
  Found in files:
    • analyseDirectory.R (line 127, column 137)
    • ...
    • swathData_writeFiles.R (line 64, column 49)
ℹ NOTE: Avoid 'cat' and 'print' outside of 'show' methods
  Found in files:
    • cat() in R/analyseDirectory.R (line 7, column 21)
    • ...
    • cat() in R/swathData_processData.R (line 61, column 17)
ℹ NOTE: Avoid using '=' for assignment and use '<-' instead
  Found in files:
    • R/analyseDirectory.R (line 88, column 25)
    • ...
    • R/swathData_processData.R (line 30, column 23)
ℹ NOTE: Avoid the use of 'paste' in condition signals
  Found in files:
    • R/analyseDirectory.R (line 92, column 30)
    • ...
    • R/readIllumina.R (line 158, column 17)
ℹ NOTE: Avoid redundant 'stop' and 'warn*' in signal conditions
  Found in files:
    • R/BASH.R (line 106, column 30)
    • ...
    • R/beadLevelData_spatialPlot.R (line 24, column 36)
! WARNING: Avoid T/F variables; If logical, use TRUE/FALSE
  Found 73 times:
    • T in R/analyseDirectory.R (line 33, column 107)
    • ...
    • F in R/plotChipLayout.R (line 100, column 88)
! WARNING: Avoid class membership checks with class() / is() and == / !=; Use
is(x, 'class') for S4 classes
  Found in files:
    • annotation.R (line 13, column 24)
    • ...
    • readIllumina.R (line 12, column 26)
ℹ NOTE: Avoid system() ; use system2()
  Found in files:
    • system() in R/miscFunctions.R (line 30, column 25)
! WARNING: .Deprecated / .Defunct usage (found 5 times)
  • .Deprecated() in R/annotation.R (line 4, column 5)
  • ...
  • .Deprecated() in R/ExpressionSetIlluminaPlotting.R (line 111, column 3)
* Checking parsed R code in R directory, examples, vignettes...
ℹ Found @ in man/insertSectionData.Rd
ℹ NOTE: Use accessors; don't access S4 class slots via '@' in
examples/vignettes.
* Checking function lengths...
ℹ NOTE: The recommended function length is 50 lines or less. There are 44
functions greater than 50 lines.
  The longest 5 functions are:
    • summarize() (R/beadLevelData_summarize.R): 470 lines
    • ...
    • readBeadSummaryData() (R/readBeadSummaryData.R): 230 lines
* Checking man page documentation...
ℹ NOTE: Auto-generated '%% ~' comments found in Rd man pages.
  • man/backgroundCorrectSingleSection.Rd
  • ...
  • man/poscontPlot.Rd
! WARNING: Empty or missing \format sections found in data man page(s).
  Found in files:
    • man/GEOtemplate.Rd
    • man/platformSigs.Rd
! WARNING: Empty or missing \value sections found in man page(s).
  Found in files:
    • man/annotationInterface.Rd
    • ...
    • man/show.Rd
✖ ERROR: At least 80% of man pages documenting exported objects must have
runnable examples.
  The following pages do not:
    • backgroundCorrectSingleSection.Rd
    • ...
    • weightsOutlierMethod.Rd
ℹ NOTE: Usage of dontrun / donttest tags found in man page examples. 19% of man
pages use at least one of these tags.
  Found in files:
    • backgroundCorrectSingleSection.Rd
    • ...
    • weightsOutlierMethod.Rd
ℹ NOTE: Use donttest instead of dontrun.
  Found in files:
    • backgroundCorrectSingleSection.Rd
    • ...
    • weightsOutlierMethod.Rd
* Checking package NEWS...
* 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; 1393 lines (11%) are > 80 characters long.
  First few lines:
    • R/AllClasses.R#L17 representation(transFun ="list" ...
    • ...
    • vignettes/ImageProcessing.Rmd#L122 [2] Smith ML, Dunning MJ, Tavare S and
    L ...
ℹ NOTE: Consider 4 spaces instead of tabs; 1592 lines (12%) contain tabs.
  First few lines:
    • R/analyseDirectory.R#L35 if(length(fmet)) ## patch from Juerg St ...
    • ...
    • vignettes/beadlevel.Rmd#L196 BLData <- setWeights(exampleBLData, wts ...
ℹ NOTE: Consider multiples of 4 spaces for line indents; 1746 lines (13%) are
not.
  First few lines:
    • R/AllClasses.R#L3 representation(beadData = "lis ...
    • ...
    • vignettes/ImageProcessing.Rmd#L118 ...
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...
✖ ERROR: Unable to find your email in the Support Site: HTTP 404 Not Found.
── BiocCheck v1.49.4 results ───────────────────────────────────────────────────
✖ 3 ERRORS | ⚠ 7 WARNINGS | ℹ 23 NOTES
ℹ See the beadarray.BiocCheck folder and run
  browseVignettes(package = 'BiocCheck')
  for details.