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### Running command:
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###   /home/biocbuild/bbs-3.24-bioc/R/bin/Rscript -e "BiocCheck::BiocCheck('HiContacts_1.15.0.tar.gz','quit-with-status'=TRUE)"
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── Installing HiContacts ───────────────────────────────────────────────────────
✔ Package installed successfully
── HiContacts session metadata ─────────────────────────────────────────────────
→ sourceDir: /tmp/RtmpkjlXI7/fileb03a137a92ee2/HiContacts
→ BiocVersion: 3.24
→ Package: HiContacts
→ PackageVersion: 1.15.0
→ BiocCheckDir: /home/biocbuild/bbs-3.24-bioc/meat/HiContacts.BiocCheck
→ BiocCheckVersion: 1.49.4
→ sourceDir: /tmp/RtmpkjlXI7/fileb03a137a92ee2/HiContacts
→ installDir: /tmp/RtmpkjlXI7/fileb03a14cd80750
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on HiContacts ─────────────────────────────────────────────
* 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 4.2 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,
DataImport
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...
* Checking License: for restrictive use...
* Checking for recommended DESCRIPTION fields...
* Checking for Bioconductor software dependencies...
ℹ Bioconductor dependencies found in Imports & Depends (43%).
* 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...
ℹ NOTE: Vignette(s) found with missing chunk labels
  Found in files:
    • HiContacts.Rmd
* Checking package installation calls in R code...
* Checking for library/require of HiContacts...
* Checking coding practice...
ℹ NOTE: Avoid using '=' for assignment and use '<-' instead
  Found in files:
    • R/plotting.R (line 363, column 23)
ℹ NOTE: Avoid the use of 'paste' in condition signals
  Found in files:
    • R/compartments.R (line 305, column 13)
    • R/plotting.R (line 97, column 14)
! WARNING: Avoid T/F variables; If logical, use TRUE/FALSE
  Found 3 times:
    • F in R/boost.R (line 18, column 5)
    • F in R/boost.R (line 22, column 47)
    • F in R/boost.R (line 25, column 24)
! WARNING: .Deprecated / .Defunct usage (found 1 times)
  • .Deprecated() in R/contacts.R (line 51, column 5)
* 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 18
functions greater than 50 lines.
  The longest 5 functions are:
    • _anonymous_.168() (R/plotting.R): 353 lines
    • ...
    • _anonymous_.525() (R/plotting.R): 85 lines
* Checking man page documentation...
! WARNING: Empty or missing \value sections found in man page(s).
  Found in files:
    • man/getLoops.Rd
    • man/HiContacts-plots.Rd
Consider using the `HiContacts` package to perform advanced genomic operations 
on `HiCExperiment` objects.

Read "Orchestrating Hi-C analysis with Bioconductor" online book to learn more:
https://js2264.github.io/OHCA/
Registered S3 methods overwritten by 'readr':
  method                    from 
  as.data.frame.spec_tbl_df vroom
  as_tibble.spec_tbl_df     vroom
  format.col_spec           vroom
  print.col_spec            vroom
  print.collector           vroom
  print.date_names          vroom
  print.locale              vroom
  str.col_spec              vroom
ℹ NOTE: Consider adding runnable examples to man pages that document exported
objects.
  • getLoops.Rd
  • plotSaddle.Rd
  • reexports.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...
* Checking skip_on_bioc() in tests...
* Checking formatting of DESCRIPTION, NAMESPACE, man pages, R source, and
vignette source...
ℹ NOTE: Consider shorter lines; 176 lines (5%) are > 80 characters long.
  First few lines:
    • R/AllGenerics.R#L2 #' @param x Can be a `HiCExperiment`, a ...
    • ...
    • vignettes/HiContacts.Rmd#L272 plotPsSlope(ps, ggplot2::aes(x = binned_
    ...
ℹ NOTE: Consider multiples of 4 spaces for line indents; 2 lines (0%) are not.
  First few lines:
    • R/plotting.R#L628 ) { ...
    • R/plotting.R#L672 ) { ...
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 | ⚠ 3 WARNINGS | ℹ 12 NOTES
ℹ See the HiContacts.BiocCheck folder and run
  browseVignettes(package = 'BiocCheck')
  for details.