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### Running command:
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###   /home/biocbuild/bbs-3.24-bioc/R/bin/Rscript -e "BiocCheck::BiocCheck('seqsetvis_1.33.0.tar.gz','quit-with-status'=TRUE)"
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── Installing seqsetvis ────────────────────────────────────────────────────────
✔ Package installed successfully
── seqsetvis session metadata ──────────────────────────────────────────────────
→ sourceDir: /tmp/Rtmp4FE9Ro/file12fb647545cc73/seqsetvis
→ BiocVersion: 3.24
→ Package: seqsetvis
→ PackageVersion: 1.33.0
→ BiocCheckDir: /home/biocbuild/bbs-3.24-bioc/meat/seqsetvis.BiocCheck
→ BiocCheckVersion: 1.49.4
→ sourceDir: /tmp/Rtmp4FE9Ro/file12fb647545cc73/seqsetvis
→ installDir: /tmp/Rtmp4FE9Ro/file12fb646822ebd2
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on seqsetvis ──────────────────────────────────────────────
* 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 4.3 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...
ℹ NOTE: Provide 'URL', 'BugReports' field(s) in DESCRIPTION
* Checking for Bioconductor software dependencies...
ℹ Bioconductor dependencies found in Imports & Depends (35%).
* 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:
    • seqsetvis_overview.Rmd
ℹ NOTE: 'sessionInfo' not found in vignette(s)
  Missing from file(s):
    • vignettes/seqsetvis_overview.Rmd
* Checking package installation calls in R code...
* Checking for library/require of seqsetvis...
* Checking coding practice...
ℹ NOTE: Avoid using '=' for assignment and use '<-' instead
  Found in files:
    • R/annotate_subject_GR.R (line 2, column 29)
    • ...
    • R/ssvMakeMembTable.R (line 173, column 18)
ℹ NOTE: Avoid redundant 'stop' and 'warn*' in signal conditions
  Found in files:
    • R/functions_signal_operations.R (line 245, column 21)
! WARNING: .Deprecated / .Defunct usage (found 1 times)
  • .Deprecated() in R/functions_fetch_signal.R (line 647, column 5)
* Checking parsed R code in R directory, examples, vignettes...
ℹ NOTE: Avoid 'suppressWarnings'/'*Messages' if possible (found 9 times)
  • suppressWarnings() in R/functions_easyLoad.R (line 77, column 18)
  • ...
  • suppressWarnings() in R/overlapIntervalSets.R (line 48, column 3)
* Checking function lengths...
ℹ NOTE: The recommended function length is 50 lines or less. There are 35
functions greater than 50 lines.
  The longest 5 functions are:
    • viewGRangesWinSummary_dt() (R/functions_fetch_signal.R): 170 lines
    • ...
    • fetchBam() (R/functions_fetch_bam.R): 152 lines
* Checking man page documentation...
! WARNING: Empty or missing \format sections found in data man page(s).
  Found in files:
    • man/chromHMM_demo_data.Rd
    • man/CTCF_in_10a_data.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; 257 lines (3%) are > 80 characters long.
  First few lines:
    • R/annotate_subject_GR.R#L44 " with default funct ...
    • ...
    • vignettes/seqsetvis_overview.Rmd#L664 B) Likewise for the comparison of
    MCF10A ...
ℹ NOTE: Consider 4 spaces instead of tabs; 1 lines (0%) contain tabs.
  First few lines:
    • R/functions_fetch_bamPE_RNA.R#L22 #' @param win_method character. one of
    ...
ℹ NOTE: Consider multiples of 4 spaces for line indents; 1129 lines (13%) are
not.
  First few lines:
    • R/annotate_subject_GR.R#L16 su ...
    • ...
    • vignettes/seqsetvis_overview.Rmd#L1016 height = 1 - bar_height - ...
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 | ⚠ 2 WARNINGS | ℹ 13 NOTES
ℹ See the seqsetvis.BiocCheck folder and run
  browseVignettes(package = 'BiocCheck')
  for details.