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### Running command:
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###   /home/biocbuild/bbs-3.24-bioc/R/bin/Rscript -e "BiocCheck::BiocCheck('hypeR_2.11.0.tar.gz','quit-with-status'=TRUE)"
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── Installing hypeR ────────────────────────────────────────────────────────────
✔ Package installed successfully
── hypeR session metadata ──────────────────────────────────────────────────────
→ sourceDir: /tmp/RtmpJpE9aC/fileb25752f53f165/hypeR
→ BiocVersion: 3.24
→ Package: hypeR
→ PackageVersion: 2.11.0
→ BiocCheckDir: /home/biocbuild/bbs-3.24-bioc/meat/hypeR.BiocCheck
→ BiocCheckVersion: 1.49.4
→ sourceDir: /tmp/RtmpJpE9aC/fileb25752f53f165/hypeR
→ installDir: /tmp/RtmpJpE9aC/fileb25753dd26e4f
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on hypeR ──────────────────────────────────────────────────
* 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 3.6.0 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...
ℹ NOTE: Consider adding the maintainer's ORCID iD in 'Authors@R' with
'comment=c(ORCID="...")'
* Checking License: for restrictive use...
* Checking for recommended DESCRIPTION fields...
* Checking for Bioconductor software dependencies...
ℹ Bioconductor dependencies found in Imports & Depends (5%).
* 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:
    • hypeR.Rmd
ℹ NOTE: 'sessionInfo' not found in vignette(s)
  Missing from file(s):
    • vignettes/hypeR.Rmd
* Checking package installation calls in R code...
* Checking for library/require of hypeR...
* Checking coding practice...
ℹ NOTE: Avoid sapply(); use vapply()
  Found in files:
    • R/db_enrichr.R (line 74, column 17)
    • ...
    • R/utils.R (line 79, column 17)
ℹ NOTE: Avoid 1:...; use seq_len() or seq_along()
  Found in files:
    • ks_enrichment.R (line 41, column 15)
    • ...
    • utils.R (line 58, column 15)
ℹ NOTE: Avoid 'cat' and 'print' outside of 'show' methods
  Found in files:
    • cat() in R/db_msig.R (line 78, column 5)
    • ...
    • print() in R/rgsets.R (line 76, column 15)
ℹ NOTE: Avoid using '=' for assignment and use '<-' instead
  Found in files:
    • R/db_msig.R (line 144, column 18)
    • ...
    • R/hyp_to_table.R (line 39, column 16)
ℹ NOTE: Avoid the use of 'paste' in condition signals
  Found in files:
    • R/db_msig.R (line 39, column 58)
ℹ NOTE: Avoid redundant 'stop' and 'warn*' in signal conditions
  Found in files:
    • R/ks_enrichment.R (line 116, column 35)
! WARNING: Avoid T/F variables; If logical, use TRUE/FALSE
  Found 3 times:
    • F in R/db_hyper.R (line 44, column 75)
    • F in R/rgsets.R (line 126, column 39)
    • F in R/rgsets.R (line 127, column 85)
* Checking parsed R code in R directory, examples, vignettes...
ℹ NOTE: Avoid 'suppressWarnings'/'*Messages' if possible (found 5 times)
  • suppressWarnings() in R/hyp_dots.R (line 54, column 11)
  • ...
  • suppressWarnings() in R/ks_enrichment.R (line 79, column 14)
* 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:
    • hypeR() (R/hype.R): 154 lines
    • ...
    • .kstest() (R/ks_enrichment.R): 82 lines
* Checking man page documentation...
! WARNING: Empty or missing \value sections found in man page(s).
  Found in files:
    • man/clean_genesets.Rd
    • ...
    • man/rgsets.Rd
✖ ERROR: At least 80% of man pages documenting exported objects must have
runnable examples.
  The following pages do not:
    • genesets_Server.Rd
    • ...
    • rgsets.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; 190 lines (6%) are > 80 characters long.
  First few lines:
    • R/db_enrichr.R#L7 enrichr_urls <- function(db=c("Enrichr", ...
    • ...
    • vignettes/hypeR.Rmd#L114 All data related to enrichment arguments ...
ℹ NOTE: Consider multiples of 4 spaces for line indents; 313 lines (10%) are
not.
  First few lines:
    • R/db_msig.R#L144 db_species = "HS" ...
    • ...
    • vignettes/hypeR.Rmd#L147 author="Anthony Federico, Ste ...
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 ───────────────────────────────────────────────────
✖ 2 ERRORS | ⚠ 2 WARNINGS | ℹ 16 NOTES
ℹ See the hypeR.BiocCheck folder and run
  browseVignettes(package = 'BiocCheck')
  for details.