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### Running command:
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###   /home/rapidbuild/bbs-3.23-bioc-rapid/R/bin/Rscript -e "BiocCheck::BiocCheck('rhdf5_2.56.0.tar.gz','quit-with-status'=TRUE)"
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── Installing rhdf5 ────────────────────────────────────────────────────────────
✔ Package installed successfully
── rhdf5 session metadata ──────────────────────────────────────────────────────
→ sourceDir: /tmp/Rtmp8hLcVv/file89dfc48f846f3/rhdf5
→ BiocVersion: 3.23
→ Package: rhdf5
→ PackageVersion: 2.56.0
→ BiocCheckDir: /media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/meat/rhdf5.BiocCheck
→ BiocCheckVersion: 1.48.0
→ sourceDir: /tmp/Rtmp8hLcVv/file89dfc48f846f3/rhdf5
→ installDir: /tmp/Rtmp8hLcVv/file89dfc4de97cd2
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on rhdf5 ──────────────────────────────────────────────────
* 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 4.0.0 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 that Package field matches directory/tarball name...
* 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 (67%).
* 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:
    • practical_tips.Rmd
    • rhdf5_cloud_reading.Rmd
! WARNING: Avoid T/F variables; If logical, use TRUE/FALSE
  Found in files:
    • vignettes/rhdf5.Rmd (chunk no. 5, line 93, column 1)
* Checking package installation calls in R code...
* Checking for library/require of rhdf5...
* Checking coding practice...
ℹ NOTE: Avoid sapply(); use vapply()
  Found in files:
    • R/H5S_extras.R (line 188, column 26)
ℹ NOTE: Avoid redundant 'stop' and 'warn*' in signal conditions
  Found in files:
    • R/H5.R (line 95, column 10)
    • ...
    • R/H5S.R (line 515, column 13)
! WARNING: .Deprecated / .Defunct usage (found 1 times)
  • .Deprecated() in R/Deprecated.R (line 13, column 3)
* Checking parsed R code in R directory, examples, vignettes...
ℹ NOTE: Avoid '<<-' if possible (found 1 times)
  • <<- in R/zzz.R (line 2, column 15)
! WARNING: Avoid 'Sys.setenv' (found 1 times)
  • Sys.setenv() in R/h5fileLocking.R (line 92, column 3)
* Checking function lengths...
ℹ NOTE: The recommended function length is 50 lines or less. There are 20
functions greater than 50 lines.
  The longest 5 functions are:
    • h5checktype() (R/h5checktype.R): 146 lines
    • ...
    • h5createAttribute() (R/h5create.R): 103 lines
* Checking man page documentation...
! WARNING: Empty or missing \value sections found in man page(s).
  Found in files:
    • man/h5_delete.Rd
    • ...
    • man/rhdf5.Rd
✖ ERROR: At least 80% of man pages documenting exported objects must have
runnable examples.
  The following pages do not:
    • h5_delete.Rd
    • ...
    • H5Zfilter_avail.Rd
ℹ NOTE: Usage of dontrun / donttest tags found in man page examples. 4% of man
pages use at least one of these tags.
  Found in files:
    • h5_dump.Rd
    • ...
    • H5Pset_fapl_ros3.Rd
ℹ NOTE: Use donttest instead of dontrun.
  Found in files:
    • H5functions.Rd
    • H5Pset_fapl_ros3.Rd
* Checking package NEWS...
* Checking unit tests...
* Checking skip_on_bioc() in tests...
ℹ NOTE: skip_on_bioc() found in testthat files: test_S3.R
* Checking formatting of DESCRIPTION, NAMESPACE, man pages, R source, and
vignette source...
ℹ NOTE: Consider shorter lines; 220 lines (2%) are > 80 characters long.
  First few lines:
    • R/AllMethods.R#L67 #' group or dataset `name` in the HDF5 ...
    • ...
    • vignettes/rhdf5.Rmd#L480 % Please note, that arrays appear as tra ...
ℹ NOTE: Consider multiples of 4 spaces for line indents; 2636 lines (29%) are
not.
  First few lines:
    • R/AllMethods.R#L5 res <- .Call("_handleInfo", object@ID, ...
    • ...
    • vignettes/rhdf5.Rmd#L493 } ...
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...
✖ ERROR: Unable to find your email in the Support Site: HTTP 404 Not Found.
── BiocCheck v1.48.0 results ───────────────────────────────────────────────────
✖ 2 ERRORS | ⚠ 4 WARNINGS | ℹ 12 NOTES
ℹ See the rhdf5.BiocCheck folder and run
  browseVignettes(package = 'BiocCheck')
  for details.