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### Running command:
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###   /home/biocbuild/bbs-3.24-bioc/R/bin/Rscript -e "BiocCheck::BiocCheck('hierinf_1.31.0.tar.gz','quit-with-status'=TRUE)"
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── Installing hierinf ──────────────────────────────────────────────────────────
✔ Package installed successfully
── hierinf session metadata ────────────────────────────────────────────────────
→ sourceDir: /tmp/RtmpsQXDox/fileb05c760ca9931/hierinf
→ BiocVersion: 3.24
→ Package: hierinf
→ PackageVersion: 1.31.0
→ BiocCheckDir: /home/biocbuild/bbs-3.24-bioc/meat/hierinf.BiocCheck
→ BiocCheckVersion: 1.49.4
→ sourceDir: /tmp/RtmpsQXDox/fileb05c760ca9931/hierinf
→ installDir: /tmp/RtmpsQXDox/fileb05c71b47208
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on hierinf ────────────────────────────────────────────────
* 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 3.6.0 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...
ℹ NOTE: Consider adding these automatically suggested biocViews: ATACSeq
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...
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...
ℹ NOTE: Provide 'URL', '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...
! WARNING: Use RMarkdown instead of Sweave 'Rnw' vignettes.
  Rnw vignette(s) found:
    • vignette-hierinf.Rnw
ℹ NOTE: Vignette(s) found with missing chunk labels
  Found in files:
    • vignette-hierinf.Rnw
ℹ NOTE: 'sessionInfo' not found in vignette(s)
  Missing from file(s):
    • vignettes/vignette-hierinf.Rnw
* Checking package installation calls in R code...
* Checking for library/require of hierinf...
* Checking coding practice...
ℹ NOTE: Avoid sapply(); use vapply()
  Found in files:
    • R/MEL.R (line 75, column 9)
ℹ NOTE: Avoid the use of 'paste' in condition signals
  Found in files:
    • R/comp-cluster-pval.R (line 90, column 13)
    • ...
    • R/test-only-hierarchy.R (line 209, column 13)
ℹ NOTE: Avoid redundant 'stop' and 'warn*' in signal conditions
  Found in files:
    • R/cluster-position.R (line 184, column 13)
    • ...
    • R/test-only-hierarchy.R (line 637, column 13)
* Checking parsed R code in R directory, examples, vignettes...
ℹ NOTE: Avoid '<<-' if possible (found 2 times)
  • <<- in R/tryCatch-W-E.R (line 15, column 10)
  • <<- in R/tryCatch-W-E.R (line 21, column 9)
ℹ NOTE: Avoid 'suppressWarnings'/'*Messages' if possible (found 1 times)
  • suppressWarnings() in R/MEL.R (line 42, column 3)
* 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:
    • test_only_hierarchy() (R/test-only-hierarchy.R): 497 lines
    • ...
    • cluster_position() (R/cluster-position.R): 112 lines
* Checking man page documentation...
* Checking package NEWS...
! WARNING: news(package='hierinf') failed with news file:
hierinf/NEWS.md:news() failed to parse news file: hierinf/NEWS.md Refer to
https://contributions.bioconductor.org/news.html to be included in Bioconductor
release announcements.
* Checking unit tests...
* Checking skip_on_bioc() in tests...
ℹ NOTE: skip_on_bioc() found in testthat files: test-cluster_var.R
test-multisplit.R test-test_hierarchy.R test-test_only_hierarchy.R
* Checking formatting of DESCRIPTION, NAMESPACE, man pages, R source, and
vignette source...
ℹ NOTE: Consider shorter lines; 175 lines (5%) are > 80 characters long.
  First few lines:
    • R/check-input.R#L19 stop("The argument block can only ...
    • ...
    • vignettes/vignette-hierinf.Rnw#L430 \subsection{Software for aggregating
    p-v ...
ℹ NOTE: Consider multiples of 4 spaces for line indents; 1308 lines (34%) are
not.
  First few lines:
    • R/check-input.R#L3 ## check general assumptions ...
    • ...
    • vignettes/vignette-hierinf.Rnw#L575 }; ...
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 | ⚠ 3 WARNINGS | ℹ 18 NOTES
ℹ See the hierinf.BiocCheck folder and run
  browseVignettes(package = 'BiocCheck')
  for details.