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### Running command:
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###   /home/biocbuild/bbs-3.24-bioc/R/bin/Rscript -e "BiocCheck::BiocCheck('MinimumDistance_1.57.0.tar.gz','quit-with-status'=TRUE)"
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── Installing MinimumDistance ──────────────────────────────────────────────────
✔ Package installed successfully
── MinimumDistance session metadata ────────────────────────────────────────────
→ sourceDir: /tmp/Rtmpuc3SY5/filed9abf15bc4dc5/MinimumDistance
→ BiocVersion: 3.24
→ Package: MinimumDistance
→ PackageVersion: 1.57.0
→ BiocCheckDir: /home/biocbuild/bbs-3.24-bioc/meat/MinimumDistance.BiocCheck
→ BiocCheckVersion: 1.49.4
→ sourceDir: /tmp/Rtmpuc3SY5/filed9abf15bc4dc5/MinimumDistance
→ installDir: /tmp/Rtmpuc3SY5/filed9abf38c07981
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on MinimumDistance ────────────────────────────────────────
* 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 3.5.0 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...
* 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...
ℹ NOTE: Provide 'URL', 'BugReports' field(s) in DESCRIPTION
* Checking for Bioconductor software dependencies...
ℹ Bioconductor dependencies found in Imports & Depends (55%).
* 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:
    • MinimumDistance.Rnw
* Checking package installation calls in R code...
* Checking for library/require of MinimumDistance...
! WARNING: Avoid the use of 'library' or 'require' in R code
  Found in files:
    • require() in R/coercion-methods.R (line 144, column 28)
* Checking coding practice...
ℹ NOTE: Avoid sapply(); use vapply()
  Found in files:
    • R/coercion-methods.R (line 170, column 25)
    • ...
    • R/segment2-methods.R (line 208, column 11)
ℹ NOTE: Avoid 1:...; use seq_len() or seq_along()
  Found in files:
    • functions.R (line 333, column 40)
    • ...
    • segment2-methods.R (line 178, column 29)
ℹ NOTE: Avoid using '=' for assignment and use '<-' instead
  Found in files:
    • R/functions.R (line 1303, column 7)
    • R/methods-MinDistExperiment.R (line 372, column 6)
ℹ NOTE: Avoid the use of 'paste' in condition signals
  Found in files:
    • R/methods-matrix.R (line 30, column 37)
! WARNING: Avoid T/F variables; If logical, use TRUE/FALSE
  Found 2 times:
    • F in R/methods-MinDistExperiment.R (line 13, column 3)
    • F in R/methods-MinDistExperiment.R (line 17, column 42)
! WARNING: .Deprecated / .Defunct usage (found 7 times)
  • .Defunct() in R/defunct.R (line 11, column 3)
  • ...
  • .Defunct() in R/methods-TrioSetList.R (line 581, column 19)
* 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 17
functions greater than 50 lines.
  The longest 5 functions are:
    • TrioSetList() (R/methods-TrioSetList.R): 151 lines
    • ...
    • madList() (R/mad-methods.R): 91 lines
* Checking man page documentation...
! WARNING: Empty or missing \value sections found in man page(s).
  Found in files:
    • man/acf2.Rd
    • ...
    • man/TrioSetList.Rd
No methods found in package ‘oligoClasses’ for request: ‘mean’ when loading ‘crlmm’
Warning: replacing previous import ‘ff::pattern’ by ‘grid::pattern’ when loading ‘MinimumDistance’
✖ ERROR: At least 80% of man pages documenting exported objects must have
runnable examples.
  The following pages do not:
    • calculateMindist.Rd
    • ...
    • TrioSetListLD.Rd
ℹ NOTE: Usage of dontrun / donttest tags found in man page examples. 5% of man
pages use at least one of these tags.
  Found in files:
    • MAP2.Rd
    • md_exp.Rd
ℹ NOTE: Use donttest instead of dontrun.
  Found in files:
    • MAP2.Rd
    • md_exp.Rd
* Checking package NEWS...
ℹ NOTE: More than one NEWS file found.See ?news for recognition ordering.
  Please remove one of the following:
    • inst/NEWS.Rd
    • MinimumDistance/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; 397 lines (5%) are > 80 characters long.
  First few lines:
    • R/AllClasses.R#L34 #' @slot fatherPhenoData \code{Annotated ...
    • ...
    • vignettes/MinimumDistance.Rnw#L346 sample_info <-
    read.csv(file.path(extdir ...
ℹ NOTE: Consider 4 spaces instead of tabs; 2300 lines (29%) contain tabs.
  First few lines:
    • R/AllClasses.R#L23 trioIndex="data.frame")) ...
    • ...
    • R/utils.R#L15 environ[[dataset]] ...
ℹ NOTE: Consider multiples of 4 spaces for line indents; 1469 lines (19%) are
not.
  First few lines:
    • R/AllClasses.R#L74 tra ...
    • ...
    • vignettes/MinimumDistance.Rnw#L429 \I_{[\left|\blrr_\Of - \blrr_\F\right|
    ...
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 | ⚠ 5 WARNINGS | ℹ 16 NOTES
ℹ See the MinimumDistance.BiocCheck folder and run
  browseVignettes(package = 'BiocCheck')
  for details.