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### Running command:
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###   /home/biocbuild/bbs-3.24-bioc/R/bin/Rscript -e "BiocCheck::BiocCheck('HIBAG_1.49.0.tar.gz','quit-with-status'=TRUE)"
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── Installing HIBAG ────────────────────────────────────────────────────────────
✔ Package installed successfully
── HIBAG session metadata ──────────────────────────────────────────────────────
→ sourceDir: /tmp/RtmpxmjEmc/fileb00252111fd54/HIBAG
→ BiocVersion: 3.24
→ Package: HIBAG
→ PackageVersion: 1.49.0
→ BiocCheckDir: /home/biocbuild/bbs-3.24-bioc/meat/HIBAG.BiocCheck
→ BiocCheckVersion: 1.49.4
→ sourceDir: /tmp/RtmpxmjEmc/fileb00252111fd54/HIBAG
→ installDir: /tmp/RtmpxmjEmc/fileb00252d5b8568
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on HIBAG ──────────────────────────────────────────────────
* 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 3.2.0 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...
* Checking License: for restrictive use...
* Checking for recommended DESCRIPTION fields...
ℹ NOTE: Provide 'BugReports' field(s) in DESCRIPTION
* Checking for Bioconductor software dependencies...
! WARNING: No Bioconductor dependencies detected. Note that some infrastructure
packages may not have Bioconductor dependencies. For more information, reach
out to the Bioconductor community and/or consider a CRAN submission.
* 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:
    • HIBAG.Rmd
    • HLA_Association.Rmd
    • Implementation.Rmd
* Checking package installation calls in R code...
* Checking for library/require of HIBAG...
! WARNING: Avoid the use of 'library' or 'require' in R code
  Found in files:
    • library() in R/HIBAG.R (line 773, column 21)
* Checking coding practice...
ℹ NOTE: Avoid sapply(); use vapply()
  Found in files:
    • R/Association.R (line 174, column 30)
    • ...
    • R/SeqFormat.R (line 421, column 9)
ℹ NOTE: Avoid 1:...; use seq_len() or seq_along()
  Found in files:
    • HIBAG.R (line 515, column 38)
    • HIBAG.R (line 1517, column 36)
    • SeqFormat.R (line 152, column 48)
ℹ NOTE: Avoid 'cat' and 'print' outside of 'show' methods
  Found in files:
    • cat() in R/Association.R (line 117, column 13)
    • ...
    • cat() in R/SeqFormat.R (line 446, column 13)
ℹ NOTE: Avoid redundant 'stop' and 'warn*' in signal conditions
  Found in files:
    • R/DataUtilities.R (line 193, column 26)
! WARNING: Avoid class membership checks with class() / is() and == / !=; Use
is(x, 'class') for S4 classes
  Found in files:
    • DataUtilities.R (line 2585, column 64)
    • DataUtilities.R (line 2586, column 24)
* Checking parsed R code in R directory, examples, vignettes...
ℹ NOTE: Avoid '<<-' if possible (found 2 times)
  • <<- in R/Association.R (line 578, column 17)
  • <<- in R/HIBAG.R (line 370, column 27)
ℹ NOTE: Avoid 'suppressWarnings'/'*Messages' if possible (found 11 times)
  • suppressWarnings() in R/Association.R (line 169, column 9)
  • ...
  • suppressWarnings() in R/HIBAG.R (line 1502, column 11)
* Checking function lengths...
ℹ NOTE: The recommended function length is 50 lines or less. There are 29
functions greater than 50 lines.
  The longest 5 functions are:
    • hlaAssocTest.hlaAlleleClass() (R/Association.R): 371 lines
    • ...
    • hlaReport() (R/DataUtilities.R): 239 lines
* Checking man page documentation...
! WARNING: Empty or missing \format sections found in data man page(s).
  Found in files:
    • man/HapMap_CEU_Geno.Rd
    • man/HLA_Type_Table.Rd
ℹ NOTE: Consider adding runnable examples to man pages that document exported
objects.
  • hlaClose.Rd
  • summary.hlaAlleleClass.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; 118 lines (1%) are > 80 characters long.
  First few lines:
    • R/Association.R#L109 stop("No posterior probabili ...
    • ...
    • vignettes/Implementation.Rmd#L178 * National Center for Supercomputing
    App ...
ℹ NOTE: Consider 4 spaces instead of tabs; 36 lines (0%) contain tabs.
  First few lines:
    • R/HIBAG.R#L1694 data.frame = "data.frame", ...
    • ...
    • vignettes/Implementation.Rmd#L140 HLA-DQB1 1.0 7.2 12.9 1.7 11.4 19.0"
    ...
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.
✖ ERROR: Add package to Watched Tags in your Support Site profile; visit
https://support.bioconductor.org/accounts/edit/profile
── BiocCheck v1.49.4 results ───────────────────────────────────────────────────
✖ 1 ERRORS | ⚠ 4 WARNINGS | ℹ 16 NOTES
ℹ See the HIBAG.BiocCheck folder and run
  browseVignettes(package = 'BiocCheck')
  for details.