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### Running command:
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###   /home/biocbuild/bbs-3.24-bioc/R/bin/Rscript -e "BiocCheck::BiocCheck('HiCExperiment_1.13.0.tar.gz','quit-with-status'=TRUE)"
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── Installing HiCExperiment ────────────────────────────────────────────────────
✔ Package installed successfully
── HiCExperiment session metadata ──────────────────────────────────────────────
→ sourceDir: /tmp/RtmprXL1mi/fileb02b02ebc5c77/HiCExperiment
→ BiocVersion: 3.24
→ Package: HiCExperiment
→ PackageVersion: 1.13.0
→ BiocCheckDir: /home/biocbuild/bbs-3.24-bioc/meat/HiCExperiment.BiocCheck
→ BiocCheckVersion: 1.49.4
→ sourceDir: /tmp/RtmprXL1mi/fileb02b02ebc5c77/HiCExperiment
→ installDir: /tmp/RtmprXL1mi/fileb02b03ffbabd9
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on HiCExperiment ──────────────────────────────────────────
* 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...
* 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 (60%).
* 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...
* Checking package installation calls in R code...
* Checking for library/require of HiCExperiment...
* Checking coding practice...
ℹ NOTE: Avoid sapply(); use vapply()
  Found in files:
    • R/parse-hic.R (line 146, column 22)
ℹ NOTE: Avoid using '=' for assignment and use '<-' instead
  Found in files:
    • R/CoolFile-methods.R (line 24, column 27)
    • R/HicFile-methods.R (line 23, column 27)
ℹ NOTE: Avoid the use of 'paste' in condition signals
  Found in files:
    • R/AggrHiCExperiment-methods.R (line 20, column 14)
    • ...
    • R/parse-cool.R (line 167, column 14)
* Checking parsed R code in R directory, examples, vignettes...
ℹ NOTE: Avoid 'suppressWarnings'/'*Messages' if possible (found 6 times)
  • suppressWarnings() in R/parse-hic.R (line 155, column 9)
  • ...
  • suppressWarnings() in R/utils.R (line 100, column 17)
* 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:
    • .hic2gi() (R/parse-hic.R): 270 lines
    • ...
    • AggrHiCExperiment() (R/AggrHiCExperiment-class.R): 109 lines
* Checking man page documentation...
! WARNING: Empty or missing \value sections found in man page(s).
  Found in files:
    • man/as.Rd
    • ...
    • man/PairsFile-class.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/
ℹ NOTE: Consider adding runnable examples to man pages that document exported
objects.
  • AllGenerics.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; 181 lines (3%) are > 80 characters long.
  First few lines:
    • R/AggrHiCExperiment-methods.R#L13 setMethod("slices", signature(x =
    "AggrH ...
    • ...
    • vignettes/HiCExperiment.Rmd#L289 - The `.(all)validPairs` file format, de
    ...
ℹ NOTE: Consider multiples of 4 spaces for line indents; 12 lines (0%) are not.
  First few lines:
    • R/parse-cool.R#L239 res$pixels, data.frame(an), by = ...
    • ...
    • vignettes/HiCExperiment.Rmd#L286 ...
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 | ⚠ 1 WARNINGS | ℹ 12 NOTES
ℹ See the HiCExperiment.BiocCheck folder and run
  browseVignettes(package = 'BiocCheck')
  for details.