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### Running command:
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###   /home/rapidbuild/bbs-3.24-bioc-rapid/R/bin/Rscript -e "BiocCheck::BiocCheck('gdsfmt_1.49.1.tar.gz','quit-with-status'=TRUE)"
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── Installing gdsfmt ───────────────────────────────────────────────────────────
✔ Package installed successfully
── gdsfmt session metadata ─────────────────────────────────────────────────────
→ sourceDir: /tmp/RtmplnCIFq/file1b005e7d5849d9/gdsfmt
→ BiocVersion: 3.24
→ Package: gdsfmt
→ PackageVersion: 1.49.1
→ BiocCheckDir: /media/volume/teran2_disk/rapidbuild/bbs-3.24-bioc-rapid/meat/gdsfmt.BiocCheck
→ BiocCheckVersion: 1.49.4
→ sourceDir: /tmp/RtmplnCIFq/file1b005e7d5849d9/gdsfmt
→ installDir: /tmp/RtmplnCIFq/file1b005e5ccf731e
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on gdsfmt ─────────────────────────────────────────────────
* 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 2.15.0 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...
✖ ERROR: Remove Maintainer field. Use Authors@R [cre] designation.
* Checking License: for restrictive use...
* Checking for recommended DESCRIPTION fields...
* Checking for Bioconductor software dependencies...
ℹ NOTE: 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:
    • gdsfmt.Rmd
! WARNING: Avoid T/F variables; If logical, use TRUE/FALSE
  Found in files:
    • vignettes/gdsfmt.Rmd (chunk no. 34, line 456, column 40)
* Checking package installation calls in R code...
* Checking for library/require of gdsfmt...
! WARNING: Avoid the use of 'library' or 'require' in R code
  Found in files:
    • library() in R/gdsfmt-main.r (line 889, column 17)
    • require() in R/internal.r (line 26, column 26)
* Checking coding practice...
ℹ NOTE: Avoid sapply(); use vapply()
  Found in files:
    • R/gdsfmt-main.r (line 1015, column 17)
ℹ NOTE: Avoid 1:...; use seq_len() or seq_along()
  Found in files:
    • internal.r (line 144, column 23)
ℹ NOTE: Avoid 'cat' and 'print' outside of 'show' methods
  Found in files:
    • cat() in R/methods.r (line 55, column 9)
    • cat() in R/methods.r (line 113, column 9)
    • cat() in R/methods.r (line 123, column 13)
ℹ NOTE: Avoid redundant 'stop' and 'warn*' in signal conditions
  Found in files:
    • R/internal.r (line 154, column 26)
    • R/internal.r (line 316, column 25)
* Checking parsed R code in R directory, examples, vignettes...
ℹ NOTE: Avoid '<<-' if possible (found 1 times)
  • <<- in R/gdsfmt-main.r (line 1395, column 12)
* Checking function lengths...
ℹ NOTE: The recommended function length is 50 lines or less. There are 11
functions greater than 50 lines.
  The longest 5 functions are:
    • print.gdsn.class() (R/gdsfmt-main.r): 191 lines
    • ...
    • .DynamicClusterCall() (R/internal.r): 92 lines
* Checking man page documentation...
ℹ NOTE: Usage of dontrun / donttest tags found in man page examples. 8% of man
pages use at least one of these tags.
  Found in files:
    • addfolder.gdsn.Rd
    • ...
    • unload.gdsn.Rd
ℹ NOTE: Use donttest instead of dontrun.
  Found in files:
    • addfolder.gdsn.Rd
    • ...
    • unload.gdsn.Rd
* Checking package NEWS...
ℹ NOTE: More than one NEWS file found.See ?news for recognition ordering.
  Please remove one of the following:
    • gdsfmt/NEWS
    • LZ4/NEWS
    • xz-5.2.9/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; 41 lines (1%) are > 80 characters long.
  First few lines:
    • R/internal.r#L256 parallel::mcparallel(.fun(i, ... ...
    • ...
    • vignettes/gdsfmt.Rmd#L500 File: 1KG_autosome_phase3_shapeit2_mvnca ...
ℹ NOTE: Consider 4 spaces instead of tabs; 8 lines (0%) contain tabs.
  First few lines:
    • man/objdesp.gdsn.Rd#L44 "maxlen", "offset", "scale"} ...
    • ...
    • vignettes/gdsfmt.Rmd#L435 stopifnot(identical(dat[[i]], dat[[1L]] ...
ℹ NOTE: Consider multiples of 4 spaces for line indents; 2 lines (0%) are not.
  First few lines:
    • vignettes/gdsfmt.Rmd#L510 |--+ qual { Float32 81271745 ZIP_ra ...
    • vignettes/gdsfmt.Rmd#L511 \--+ filter { VStr8 81271745 ZIP_ra ...
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 ───────────────────────────────────────────────────
✖ 1 ERRORS | ⚠ 2 WARNINGS | ℹ 17 NOTES
ℹ See the gdsfmt.BiocCheck folder and run
  browseVignettes(package = 'BiocCheck')
  for details.