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### Running command:
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###   /home/rapidbuild/bbs-3.24-bioc-rapid/R/bin/Rscript -e "BiocCheck::BiocCheck('minfi_1.59.0.tar.gz','quit-with-status'=TRUE)"
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── Installing minfi ────────────────────────────────────────────────────────────
✔ Package installed successfully
── minfi session metadata ──────────────────────────────────────────────────────
→ sourceDir: /tmp/RtmpS0Eghf/file1b7d3f5ffc5c02/minfi
→ BiocVersion: 3.24
→ Package: minfi
→ PackageVersion: 1.59.0
→ BiocCheckDir: /media/volume/teran2_disk/rapidbuild/bbs-3.24-bioc-rapid/meat/minfi.BiocCheck
→ BiocCheckVersion: 1.49.4
→ sourceDir: /tmp/RtmpS0Eghf/file1b7d3f5ffc5c02/minfi
→ installDir: /tmp/RtmpS0Eghf/file1b7d3f7b53ec5d
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on minfi ──────────────────────────────────────────────────
* 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...
Warning in FUN(X[[i]], ...) :
  incomplete final line found on '/tmp/RtmpS0Eghf/file1b7d3f5ffc5c02/minfi/man/minfi-defunct.Rd'
Warning in FUN(X[[i]], ...) :
  incomplete final line found on '/tmp/RtmpS0Eghf/file1b7d3f5ffc5c02/minfi/man/minfi-deprecated.Rd'
ℹ NOTE: Consider adding these automatically suggested biocViews: Sequencing,
WholeGenome, Coverage, Alignment, Regression, SequenceMatching
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 if 'Package:' field matches directory / tarball...
* 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...
* Checking for Bioconductor software dependencies...
ℹ Bioconductor dependencies found in Imports & Depends (56%).
* 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...
* Checking package installation calls in R code...
* Checking for library/require of minfi...
! WARNING: Avoid the use of 'library' or 'require' in R code
  Found in files:
    • require() in R/estimateCellCounts.R (line 249, column 10)
    • ...
    • require() in R/RGChannelSet-class.R (line 226, column 10)
* Checking coding practice...
ℹ NOTE: Avoid sapply(); use vapply()
  Found in files:
    • R/blocks.R (line 90, column 20)
    • ...
    • R/utils.R (line 32, column 9)
ℹ NOTE: Avoid 1:...; use seq_len() or seq_along()
  Found in files:
    • estimateCellCounts.R (line 367, column 22)
    • ...
    • utils.R (line 19, column 36)
ℹ NOTE: Avoid 'cat' and 'print' outside of 'show' methods
  Found in files:
    • cat() in R/estimateCellCounts.R (line 154, column 18)
    • ...
    • cat() in R/utils.R (line 52, column 5)
ℹ NOTE: Avoid using '=' for assignment and use '<-' instead
  Found in files:
    • R/IlluminaMethylationAnnotation-class.R (line 95, column 23)
    • R/preprocessSwan.R (line 94, column 16)
    • R/read.manifest.R (line 471, column 23)
ℹ NOTE: Avoid redundant 'stop' and 'warn*' in signal conditions
  Found in files:
    • R/qc.R (line 72, column 21)
! WARNING: Avoid class membership checks with class() / is() and == / !=; Use
is(x, 'class') for S4 classes
  Found in files:
    • GenomicMethylSet-class.R (line 13, column 34)
ℹ NOTE: Avoid system() ; use system2()
  Found in files:
    • system() in R/read.manifest.R (line 5, column 21)
    • ...
    • system() in R/read.manifest.R (line 463, column 19)
! WARNING: .Deprecated / .Defunct usage (found 3 times)
  • .Defunct() in R/read.450k.R (line 4, column 5)
  • .Defunct() in R/read.450k.R (line 9, column 5)
  • .Defunct() in R/read.450k.R (line 15, column 5)
* Checking parsed R code in R directory, examples, vignettes...
ℹ Found @ in man/IlluminaMethylationManifest-class.Rd
ℹ NOTE: Use accessors; don't access S4 class slots via '@' in
examples/vignettes.
ℹ NOTE: Avoid '<<-' if possible (found 1 times)
  • <<- in R/read.meth2.R (line 84, column 19)
ℹ NOTE: Avoid 'suppressWarnings'/'*Messages' if possible (found 3 times)
  • suppressWarnings() in R/plotBetasByType.R (line 54, column 22)
  • suppressWarnings() in R/plotBetasByType.R (line 59, column 23)
  • suppressWarnings() in R/qc.R (line 21, column 19)
* Checking function lengths...
ℹ NOTE: The recommended function length is 50 lines or less. There are 42
functions greater than 50 lines.
  The longest 5 functions are:
    • estimateCellCounts() (R/estimateCellCounts.R): 157 lines
    • ...
    • gaphunter() (R/gaphunter.R): 136 lines
* Checking man page documentation...
! WARNING: Empty or missing \value sections found in man page(s).
  Found in files:
    • man/minfi-defunct.Rd
    • man/minfi-deprecated.Rd
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.
  • blockFinder.Rd
  • ...
  • readTCGA.Rd
ℹ NOTE: Usage of dontrun / donttest tags found in man page examples. 18% of man
pages use at least one of these tags.
  Found in files:
    • estimateCellCounts.Rd
    • ...
    • readTCGA.Rd
ℹ NOTE: Use donttest instead of dontrun.
  Found in files:
    • estimateCellCounts.Rd
    • ...
    • readTCGA.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; 280 lines (2%) are > 80 characters long.
  First few lines:
    • R/blocks.R#L335 res$coef <- bumphunter:::.getEstimat ...
    • ...
    • vignettes/minfi.Rmd#L221 - `preprocessQuantile` : Quantile normal ...
ℹ NOTE: Consider 4 spaces instead of tabs; 1 lines (0%) contain tabs.
  First few lines:
    • R/utils.R#L14 "IlluminaHumanMethylationEPICv2" ...
ℹ NOTE: Consider multiples of 4 spaces for line indents; 1693 lines (15%) are
not.
  First few lines:
    • R/blocks.R#L8 c("OpenSea", "Island", "She ...
    • ...
    • vignettes/minfi.Rmd#L174 ta ...
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 ───────────────────────────────────────────────────
✖ 0 ERRORS | ⚠ 4 WARNINGS | ℹ 20 NOTES
ℹ See the minfi.BiocCheck folder and run
  browseVignettes(package = 'BiocCheck')
  for details.