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### Running command:
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###   /home/biocbuild/bbs-3.24-bioc/R/bin/Rscript -e "BiocCheck::BiocCheck('MethylMix_2.43.0.tar.gz','quit-with-status'=TRUE)"
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── Installing MethylMix ────────────────────────────────────────────────────────
✔ Package installed successfully
── MethylMix session metadata ──────────────────────────────────────────────────
→ sourceDir: /tmp/RtmpU0UD9u/filed654f2e0a343a/MethylMix
→ BiocVersion: 3.24
→ Package: MethylMix
→ PackageVersion: 2.43.0
→ BiocCheckDir: /home/biocbuild/bbs-3.24-bioc/meat/MethylMix.BiocCheck
→ BiocCheckVersion: 1.49.4
→ sourceDir: /tmp/RtmpU0UD9u/filed654f2e0a343a/MethylMix
→ installDir: /tmp/RtmpU0UD9u/filed654f62029b9
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on MethylMix ──────────────────────────────────────────────
* 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 3.2.0 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 'URL', 'BugReports' field(s) in DESCRIPTION
* Checking for Bioconductor software dependencies...
ℹ Bioconductor dependencies found in Imports & Depends (20%).
* 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: Evaluate more vignette chunks.
ℹ 11 out of 15 code chunks = 73% unevaluated
ℹ 
ℹ NOTE: Vignette(s) found with missing chunk labels
  Found in files:
    • vignettes.Rmd
* Checking package installation calls in R code...
* Checking for library/require of MethylMix...
* Checking coding practice...
ℹ NOTE: Avoid sapply(); use vapply()
  Found in files:
    • R/ComBat_NoFiles.R (line 84, column 19)
    • ...
    • R/MethylMix.R (line 846, column 18)
ℹ NOTE: Avoid 1:...; use seq_len() or seq_along()
  Found in files:
    • ComBat_NoFiles.R (line 56, column 38)
    • ...
    • MethylMix.R (line 720, column 24)
ℹ NOTE: Avoid 'cat' and 'print' outside of 'show' methods
  Found in files:
    • cat() in R/ComBat_NoFiles.R (line 36, column 5)
    • ...
    • print() in R/MethylMix.R (line 627, column 13)
ℹ NOTE: Avoid using '=' for assignment and use '<-' instead
  Found in files:
    • R/ComBat_NoFiles.R (line 59, column 19)
    • ...
    • R/MethylMix.R (line 650, column 13)
! WARNING: Avoid T/F variables; If logical, use TRUE/FALSE
  Found 22 times:
    • T in R/ComBat_NoFiles.R (line 30, column 124)
    • ...
    • F in R/MethylMix.R (line 714, column 77)
ℹ NOTE: Avoid system() ; use system2()
  Found in files:
    • system() in R/Download_Preprocess.R (line 285, column 13)
    • ...
    • system() in R/Download_Preprocess.R (line 1141, column 50)
* 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 14
functions greater than 50 lines.
  The longest 5 functions are:
    • ComBat_NoFiles() (R/ComBat_NoFiles.R): 156 lines
    • ...
    • MethylMix_ModelSingleGene() (R/MethylMix.R): 107 lines
* Checking man page documentation...
! WARNING: Empty or missing \format sections found in data man page(s).
  Found in files:
    • man/BatchData.Rd
    • man/ProbeAnnotation.Rd
    • man/SNPprobes.Rd
✖ ERROR: At least 80% of man pages documenting exported objects must have
runnable examples.
  The following pages do not:
    • ClusterProbes.Rd
    • ...
    • Preprocess_GeneExpression.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:
    • ClusterProbes.Rd
    • ...
    • Preprocess_GeneExpression.Rd
ℹ NOTE: Use donttest instead of dontrun.
  Found in files:
    • ClusterProbes.Rd
    • ...
    • Preprocess_GeneExpression.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; 571 lines (19%) are > 80 characters long.
  First few lines:
    • R/ComBat_NoFiles.R#L7 #' @importFrom stats anova aov as.dist c ...
    • ...
    • vignettes/vignettes.Rmd#L271 Pierre-Louis Cedoz, Marcos Prunello, Kev ...
ℹ NOTE: Consider 4 spaces instead of tabs; 17 lines (1%) contain tabs.
  First few lines:
    • R/ComBat_NoFiles.R#L44 # # dat <- dat[,trim.dat(dat)] ...
    • ...
    • R/MethylMix.R#L120 (is(listOfGenes, "character") | is(list ...
ℹ NOTE: Consider multiples of 4 spaces for line indents; 259 lines (8%) are
not.
  First few lines:
    • R/ComBat_NoFiles.R#L31 #debug: expression_xls='exp.txt'; s ...
    • ...
    • R/MethylMix.R#L779 plot. ...
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 ───────────────────────────────────────────────────
✖ 2 ERRORS | ⚠ 3 WARNINGS | ℹ 17 NOTES
ℹ See the MethylMix.BiocCheck folder and run
  browseVignettes(package = 'BiocCheck')
  for details.