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### Running command:
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###   /home/biocbuild/bbs-3.24-bioc/R/bin/Rscript -e "BiocCheck::BiocCheck('funtooNorm_1.37.0.tar.gz','quit-with-status'=TRUE)"
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── Installing funtooNorm ───────────────────────────────────────────────────────
✔ Package installed successfully
── funtooNorm session metadata ─────────────────────────────────────────────────
→ sourceDir: /tmp/RtmpWgXaZl/file9ef316f2fe8d3/funtooNorm
→ BiocVersion: 3.24
→ Package: funtooNorm
→ PackageVersion: 1.37.0
→ BiocCheckDir: /home/biocbuild/bbs-3.24-bioc/meat/funtooNorm.BiocCheck
→ BiocCheckVersion: 1.49.4
→ sourceDir: /tmp/RtmpWgXaZl/file9ef316f2fe8d3/funtooNorm
→ installDir: /tmp/RtmpWgXaZl/file9ef3162934280
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on funtooNorm ─────────────────────────────────────────────
* 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 3.4 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 'URL', '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...
ℹ NOTE: Potential intermediate files found:
  • vignettes/funtoonorm.pdf
✖ ERROR: 'VignetteBuilder' listed in DESCRIPTION but not found as
'VignetteEngine' in any vignettes:
  • knitr
✖ ERROR: 'VignetteEngine' specified but not in the DESCRIPTION.
  Add 'VignetteEngine' to DESCRIPTION from the following:
    • vignettes/funtooNorm.Rmd
! WARNING: Package listed as VignetteEngine or VignetteBuilder but not
currently Suggested.
  Add the following to Suggests in DESCRIPTION:
    • %\VignetteIndexEntry{Normalizing Illumina Infinium Human Methylation 450k
    for multiple cell types with funtooNorm} knitr
ℹ NOTE: Vignette(s) found with missing chunk labels
  Found in files:
    • funtooNorm.Rmd
* Checking package installation calls in R code...
* Checking for library/require of funtooNorm...
* Checking coding practice...
ℹ NOTE: Avoid sapply(); use vapply()
  Found in files:
    • R/funtoonorm.R (line 132, column 16)
ℹ NOTE: Avoid 1:...; use seq_len() or seq_along()
  Found in files:
    • funtoonorm.R (line 72, column 16)
    • ...
    • SampleSet.R (line 714, column 19)
ℹ NOTE: Avoid using '=' for assignment and use '<-' instead
  Found in files:
    • R/funtoonorm.R (line 25, column 9)
    • ...
    • R/SampleSet.R (line 685, column 18)
ℹ NOTE: Avoid redundant 'stop' and 'warn*' in signal conditions
  Found in files:
    • R/SampleSet.R (line 495, column 24)
    • R/SampleSet.R (line 528, column 24)
    • R/SampleSet.R (line 562, column 24)
* 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 2
functions greater than 50 lines.
  The longest 5 functions are:
    • fromRGChannelSet() (R/SampleSet.R): 129 lines
    • fromGenStudFiles() (R/SampleSet.R): 97 lines
* Checking man page documentation...
Setting options('download.file.method.GEOquery'='auto')
Setting options('GEOquery.inmemory.gpl'=FALSE)
ℹ NOTE: Consider adding runnable examples to man pages that document exported
objects.
  • fromGenStudFiles.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; 35 lines (3%) are > 80 characters long.
  First few lines:
    • R/funtoonorm.R#L128 pred.mean.ctl <- unlist(lapply(p ...
    • ...
    • vignettes/funtooNorm.Rmd#L168 The default print method of a `GenomicRa
    ...
ℹ NOTE: Consider multiples of 4 spaces for line indents; 216 lines (19%) are
not.
  First few lines:
    • R/funtoonorm.R#L16 colMeans(controlgrn[cp.types== ...
    • ...
    • vignettes/funtooNorm.Rmd#L164 metadata=list(pDa ...
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 | ⚠ 1 WARNINGS | ℹ 15 NOTES
ℹ See the funtooNorm.BiocCheck folder and run
  browseVignettes(package = 'BiocCheck')
  for details.