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### Running command:
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###   /home/biocbuild/bbs-3.24-bioc/R/bin/Rscript -e "BiocCheck::BiocCheck('methylumi_2.59.0.tar.gz','quit-with-status'=TRUE)"
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── Installing methylumi ────────────────────────────────────────────────────────
✔ Package installed successfully
── methylumi session metadata ──────────────────────────────────────────────────
→ sourceDir: /tmp/RtmplIYjhE/filed6ee12c1f48cb/methylumi
→ BiocVersion: 3.24
→ Package: methylumi
→ PackageVersion: 2.59.0
→ BiocCheckDir: /home/biocbuild/bbs-3.24-bioc/meat/methylumi.BiocCheck
→ BiocCheckVersion: 1.49.4
→ sourceDir: /tmp/RtmplIYjhE/filed6ee12c1f48cb/methylumi
→ installDir: /tmp/RtmplIYjhE/filed6ee12aed1084
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on methylumi ──────────────────────────────────────────────
* 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 2.13 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/RtmplIYjhE/filed6ee12c1f48cb/methylumi/man/getAssayDataNameSubstitutions.Rd'
ℹ NOTE: Consider adding these automatically suggested biocViews: Microarray,
Epigenetics, Normalization, DataImport, MultiChannel, MethylationArray,
ImmunoOncology, DifferentialMethylation
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...
✖ ERROR: Remove Maintainer field. Use Authors@R [cre] designation.
* Checking License: for restrictive use...
* Checking for recommended DESCRIPTION fields...
ℹ NOTE: Provide 'URL' field(s) in DESCRIPTION
* Checking for Bioconductor software dependencies...
ℹ Bioconductor dependencies found in Imports & Depends (62%).
* 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...
! WARNING: Use RMarkdown instead of Sweave 'Rnw' vignettes.
  Rnw vignette(s) found:
    • methylumi.Rnw
    • methylumi450k.Rnw
ℹ NOTE: Vignette(s) found with missing chunk labels
  Found in files:
    • methylumi.Rnw
    • methylumi450k.Rnw
* Checking package installation calls in R code...
* Checking for library/require of methylumi...
! WARNING: Avoid the use of 'library' or 'require' in R code
  Found in files:
    • require() in R/bgcorr.R (line 193, column 5)
    • ...
    • require() in R/qc.probe.plot.R (line 8, column 3)
* Checking coding practice...
ℹ NOTE: Avoid sapply(); use vapply()
  Found in files:
    • R/bgcorr.R (line 71, column 32)
    • ...
    • R/utilities.R (line 12, column 15)
ℹ NOTE: Avoid 1:...; use seq_len() or seq_along()
  Found in files:
    • bgcorr.R (line 195, column 15)
    • ...
    • readIDAT2.R (line 101, column 32)
ℹ NOTE: Avoid 'cat' and 'print' outside of 'show' methods
  Found in files:
    • cat() in R/bgcorr.R (line 191, column 3)
    • ...
    • print() in R/utilities.R (line 14, column 5)
ℹ NOTE: Avoid using '=' for assignment and use '<-' instead
  Found in files:
    • R/bgcorr.R (line 8, column 11)
    • ...
    • R/varFilter.R (line 27, column 24)
ℹ NOTE: Avoid the use of 'paste' in condition signals
  Found in files:
    • R/bgcorr.R (line 188, column 13)
    • ...
    • R/normalization.R (line 16, column 11)
ℹ NOTE: Avoid redundant 'stop' and 'warn*' in signal conditions
  Found in files:
    • R/methylumiCSV.R (line 28, column 15)
    • ...
    • R/methylumIDAT.R (line 454, column 19)
! WARNING: Avoid T/F variables; If logical, use TRUE/FALSE
  Found 105 times:
    • T in R/bgcorr.R (line 6, column 80)
    • ...
    • T in R/utilities.R (line 91, column 46)
! WARNING: Avoid class membership checks with class() / is() and == / !=; Use
is(x, 'class') for S4 classes
  Found in files:
    • detectionpval.R (line 66, column 20)
    • ...
    • qc.probe.plot.R (line 17, column 24)
* Checking parsed R code in R directory, examples, vignettes...
! WARNING: Remove browser() statements (found 1 times)
  • browser() in R/MethyLumiSet-class.R (line 533, column 37)
* Checking function lengths...
ℹ NOTE: The recommended function length is 50 lines or less. There are 18
functions greater than 50 lines.
  The longest 5 functions are:
    • readIDAT2() (R/readIDAT2.R): 209 lines
    • ...
    • readBlock() (R/readIDAT2.R): 115 lines
* Checking man page documentation...
! WARNING: Empty or missing \format sections found in data man page(s).
  Found in files:
    • man/CpGs.Rd
    • man/mldat.Rd
! WARNING: Empty or missing \value sections found in man page(s).
  Found in files:
    • man/generics.Rd
    • ...
    • man/tcgaPipeline.Rd
Setting options('download.file.method.GEOquery'='auto')
Setting options('GEOquery.inmemory.gpl'=FALSE)
✖ ERROR: At least 80% of man pages documenting exported objects must have
runnable examples.
  The following pages do not:
    • estimateM.Rd
    • ...
    • tcgaPipeline.Rd
ℹ NOTE: Usage of dontrun / donttest tags found in man page examples. 4% of man
pages use at least one of these tags.
  Found in files:
    • methylumIDAT.Rd
ℹ NOTE: Use donttest instead of dontrun.
  Found in files:
    • methylumIDAT.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; 217 lines (5%) are > 80 characters long.
  First few lines:
    • R/AllGenerics.R#L3 if (is.null(getGeneric("getHistory"))) s ...
    • ...
    • vignettes/methylumi450k.Rnw#L164 suppressPackageStartupMessages(require(I
    ...
ℹ NOTE: Consider 4 spaces instead of tabs; 419 lines (9%) contain tabs.
  First few lines:
    • R/MethyLumiM-class.R#L4 representation(controlData='QCDataOrNUL ...
    • ...
    • R/readIDAT2.R#L13 stop("Older style IDAT files not supp ...
ℹ NOTE: Consider multiples of 4 spaces for line indents; 2078 lines (43%) are
not.
  First few lines:
    • R/AllGenerics.R#L39 function(eset, ...
    • ...
    • vignettes/methylumi450k.Rnw#L170 strand=c('*','*') ...
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.
✖ ERROR: Add package to Watched Tags in your Support Site profile; visit
https://support.bioconductor.org/accounts/edit/profile
── BiocCheck v1.49.4 results ───────────────────────────────────────────────────
✖ 3 ERRORS | ⚠ 7 WARNINGS | ℹ 20 NOTES
ℹ See the methylumi.BiocCheck folder and run
  browseVignettes(package = 'BiocCheck')
  for details.