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### Running command:
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###   /home/biocbuild/bbs-3.24-bioc/R/bin/Rscript -e "BiocCheck::BiocCheck('DaMiRseq_2.25.0.tar.gz','quit-with-status'=TRUE)"
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── Installing DaMiRseq ─────────────────────────────────────────────────────────
✔ Package installed successfully
── DaMiRseq session metadata ───────────────────────────────────────────────────
→ sourceDir: /tmp/RtmpnV01xe/file7dc26597d5028/DaMiRseq
→ BiocVersion: 3.24
→ Package: DaMiRseq
→ PackageVersion: 2.25.0
→ BiocCheckDir: /home/biocbuild/bbs-3.24-bioc/meat/DaMiRseq.BiocCheck
→ BiocCheckVersion: 1.49.4
→ sourceDir: /tmp/RtmpnV01xe/file7dc26597d5028/DaMiRseq
→ installDir: /tmp/RtmpnV01xe/file7dc2624deb738
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on DaMiRseq ───────────────────────────────────────────────
* 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 3.5.0 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...
ℹ NOTE: Consider adding these automatically suggested biocViews: Coverage,
Normalization, Clustering, MultidimensionalScaling
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', 'BugReports' field(s) in DESCRIPTION
* Checking for Bioconductor software dependencies...
ℹ Bioconductor dependencies found in Imports & Depends (22%).
* 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:
    • DaMiRseq.Rnw
* Checking package installation calls in R code...
* Checking for library/require of DaMiRseq...
* Checking coding practice...
ℹ NOTE: Avoid 1:...; use seq_len() or seq_along()
  Found in files:
    • Classif_2_Classes_ModelSelection.R (line 112, column 18)
    • ...
    • plot.R (line 336, column 21)
ℹ NOTE: Avoid 'cat' and 'print' outside of 'show' methods
  Found in files:
    • cat() in R/Adjust.R (line 42, column 5)
    • ...
    • print() in R/sv_identification.R (line 151, column 5)
ℹ NOTE: Avoid using '=' for assignment and use '<-' instead
  Found in files:
    • R/Adjust.R (line 41, column 9)
! WARNING: Avoid T/F variables; If logical, use TRUE/FALSE
  Found 2 times:
    • T in R/plot.R (line 334, column 44)
    • T in R/plot.R (line 334, column 55)
* Checking parsed R code in R directory, examples, vignettes...
ℹ NOTE: Avoid 'suppressWarnings'/'*Messages' if possible (found 1 times)
  • suppressMessages() in R/Normalization_TestSet.R (line 364, column 1)
* Checking function lengths...
ℹ NOTE: The recommended function length is 50 lines or less. There are 21
functions greater than 50 lines.
  The longest 5 functions are:
    • DaMiR.EnsembleLearning2cl() (R/Classif_2_Classes.R): 618 lines
    • ...
    • DaMiR.Allplot() (R/plot.R): 241 lines
* Checking man page documentation...
Registered S3 method overwritten by 'plsVarSel':
  method       from
  print.mvrVal pls 
* 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; 192 lines (3%) are > 80 characters long.
  First few lines:
    • R/Classif_2_Classes_Predict.R#L98 tPred[ii,which(colnames(tPred) %in ...
    • ...
    • vignettes/DaMiRseq.Rnw#L860 \item{The new parameter \Rcode{second. ...
ℹ NOTE: Consider 4 spaces instead of tabs; 6 lines (0%) contain tabs.
  First few lines:
    • R/Feature_Selection.R#L178 class object (N. of factors > 2). ...
    • ...
    • R/Normalization.R#L177 rownames(data_norm) <- rownames(exprs_c ...
ℹ NOTE: Consider multiples of 4 spaces for line indents; 2126 lines (35%) are
not.
  First few lines:
    • R/Adjust.R#L35 # check missing arguments ...
    • ...
    • vignettes/DaMiRseq.Rnw#L861 \end{itemize} ...
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 ───────────────────────────────────────────────────
✖ 1 ERRORS | ⚠ 2 WARNINGS | ℹ 14 NOTES
ℹ See the DaMiRseq.BiocCheck folder and run
  browseVignettes(package = 'BiocCheck')
  for details.