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### Running command:
###
###   /home/biocbuild/bbs-3.24-bioc/R/bin/Rscript -e "BiocCheck::BiocCheck('igblastr_1.3.0.tar.gz','quit-with-status'=TRUE)"
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── Installing igblastr ─────────────────────────────────────────────────────────
✔ Package installed successfully
── igblastr session metadata ───────────────────────────────────────────────────
→ sourceDir: /tmp/RtmpTE4hBT/fileb38f75dd8cdf5/igblastr
→ BiocVersion: 3.24
→ Package: igblastr
→ PackageVersion: 1.3.0
→ BiocCheckDir: /home/biocbuild/bbs-3.24-bioc/meat/igblastr.BiocCheck
→ BiocCheckVersion: 1.49.4
→ sourceDir: /tmp/RtmpTE4hBT/fileb38f75dd8cdf5/igblastr
→ installDir: /tmp/RtmpTE4hBT/fileb38f72c715b78
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on igblastr ───────────────────────────────────────────────
* 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 4.2.0 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...
ℹ NOTE: Consider adding these automatically suggested biocViews: Sequencing,
Alignment, SequenceMatching, GO, 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 (25%).
* Checking for pinned package versions in DESCRIPTION...
* Checking for 'fnd' role in Authors@R...
* 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:
    • igblastr_overview.Rmd
! WARNING: Potential package installation calls found in vignette(s)
  Found in files:
    • vignettes/igblastr_overview.Rmd (chunk no. 4, line 127, column 5)
    • vignettes/igblastr_overview.Rmd (chunk no. 9, line 204, column 1)
    • vignettes/igblastr_overview.Rmd (chunk no. 32, line 499, column 12)
* Checking package installation calls in R code...
* Checking for library/require of igblastr...
* Checking coding practice...
ℹ NOTE: Avoid 1:...; use seq_len() or seq_along()
  Found in files:
    • clean_allele_set.R (line 144, column 15)
    • ...
    • read_igblastn_fmt7_output.R (line 324, column 63)
ℹ NOTE: Avoid 'cat' and 'print' outside of 'show' methods
  Found in files:
    • cat() in R/auxdata-IO.R (line 58, column 5)
    • ...
    • cat() in R/ndm_data-IO.R (line 125, column 5)
ℹ NOTE: Avoid the use of 'paste' in condition signals
  Found in files:
    • R/igblastn.R (line 172, column 24)
ℹ NOTE: Avoid redundant 'stop' and 'warn*' in signal conditions
  Found in files:
    • R/compute_auxdata.R (line 206, column 19)
    • ...
    • R/read_broken_table.R (line 86, column 19)
! WARNING: .Deprecated / .Defunct usage (found 7 times)
  • .Deprecated() in R/augment_germline_db.R (line 126, column 5)
  • ...
  • .Deprecated() in R/long_to_wide_airr.R (line 69, column 5)
* Checking parsed R code in R directory, examples, vignettes...
! WARNING: Avoid 'Sys.setenv' (found 3 times)
  • Sys.setenv() in R/utils.R (line 334, column 13)
  • Sys.setenv() in R/utils.R (line 336, column 9)
  • Sys.setenv() in R/utils.R (line 338, column 9)
ℹ NOTE: Avoid 'suppressWarnings'/'*Messages' if possible (found 16 times)
  • suppressWarnings() in R/file-utils.R (line 137, column 19)
  • ...
  • suppressWarnings() in R/utils.R (line 354, column 16)
* Checking function lengths...
ℹ NOTE: The recommended function length is 50 lines or less. There are 14
functions greater than 50 lines.
  The longest 5 functions are:
    • .make_dna_line() (R/igbrowser.R): 98 lines
    • ...
    • prepare_igblastn_cmdline_args() (R/prepare_igblastn_cmdline_args.R): 63
    lines
* Checking man page documentation...
! WARNING: Empty or missing \value sections found in man page(s).
  Found in files:
    • man/IGBLAST_ROOT.Rd
    • man/igblastr_usage_report.Rd
    • man/summarizeMismatches.Rd
ℹ NOTE: Consider adding runnable examples to man pages that document exported
objects.
  • augment_germline_db.Rd
  • ...
  • summarizeMismatches.Rd
ℹ NOTE: Usage of dontrun / donttest tags found in man page examples. 9% of man
pages use at least one of these tags.
  Found in files:
    • augment_germline_db.Rd
    • reset_c_region_dbs.Rd
    • reset_germline_dbs.Rd
ℹ NOTE: Use donttest instead of dontrun.
  Found in files:
    • augment_germline_db.Rd
    • reset_c_region_dbs.Rd
    • reset_germline_dbs.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; 7 lines (0%) are > 80 characters long.
  First few lines:
    • R/OGRDB-API.R#L10 ### https://wordpress.vdjbase.org/inde ...
    • ...
    • man/list_germline_dbs.Rd#L123 See \url{https://github.com/HyrienLa ...
ℹ NOTE: Consider 4 spaces instead of tabs; 2 lines (0%) contain tabs.
  First few lines:
    • R/translate_codons.R#L64 if (any(offset > widths)) ...
    • man/download_IMGT_germline_sequences.Rd#L71 with the "IG" prefix or one
    of the ...
ℹ NOTE: Consider multiples of 4 spaces for line indents; 2352 lines (13%) are
not.
  First few lines:
    • R/augment_germline_db.R#L23 "must have nam ...
    • ...
    • vignettes/igblastr_overview.Rmd#L529 Community’s Open Germline Receptor
    Dat ...
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 | ⚠ 4 WARNINGS | ℹ 16 NOTES
ℹ See the igblastr.BiocCheck folder and run
  browseVignettes(package = 'BiocCheck')
  for details.