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### Running command:
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###   /home/biocbuild/bbs-3.24-bioc/R/bin/Rscript -e "BiocCheck::BiocCheck('simplifyEnrichment_2.7.0.tar.gz','quit-with-status'=TRUE)"
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── Installing simplifyEnrichment ───────────────────────────────────────────────
✔ Package installed successfully
── simplifyEnrichment session metadata ─────────────────────────────────────────
→ sourceDir: /tmp/RtmpJTYqkk/file1329c878a87fa3/simplifyEnrichment
→ BiocVersion: 3.24
→ Package: simplifyEnrichment
→ PackageVersion: 2.7.0
→ BiocCheckDir: /home/biocbuild/bbs-3.24-bioc/meat/simplifyEnrichment.BiocCheck
→ BiocCheckVersion: 1.49.4
→ sourceDir: /tmp/RtmpJTYqkk/file1329c878a87fa3/simplifyEnrichment
→ installDir: /tmp/RtmpJTYqkk/file1329c82cd04a5c
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on simplifyEnrichment ─────────────────────────────────────
* 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 4.1.0 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...
* Checking License: for restrictive use...
* Checking for recommended DESCRIPTION fields...
ℹ NOTE: Provide 'BugReports' field(s) in DESCRIPTION
* Checking for Bioconductor software dependencies...
ℹ Bioconductor dependencies found in Imports & Depends (17%).
* 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...
* Checking package installation calls in R code...
✖ ERROR: Avoid using install, biocLite, install.packages, or update.packages
  Found in files:
    • install.packages() in R/utils.R (line 70, column 21)
    • install.packages() in R/utils.R (line 78, column 17)
    • install() in R/utils.R (line 72, column 30)
* Checking for library/require of simplifyEnrichment...
* Checking coding practice...
ℹ NOTE: Avoid sapply(); use vapply()
  Found in files:
    • R/binary_cut.R (line 234, column 18)
    • ...
    • R/word_cloud.R (line 332, column 41)
ℹ NOTE: Avoid 1:...; use seq_len() or seq_along()
  Found in files:
    • binary_cut.R (line 20, column 13)
    • ...
    • simplify.R (line 260, column 18)
ℹ NOTE: Avoid 'cat' and 'print' outside of 'show' methods
  Found in files:
    • print() in R/binary_cut.R (line 679, column 26)
    • print() in R/compare_methods.R (line 136, column 34)
ℹ NOTE: Avoid using '=' for assignment and use '<-' instead
  Found in files:
    • R/binary_cut.R (line 2, column 16)
    • ...
    • R/zzz.R (line 27, column 21)
* Checking parsed R code in R directory, examples, vignettes...
ℹ NOTE: Avoid '<<-' if possible (found 2 times)
  • <<- in R/dend_utils.R (line 6, column 27)
  • <<- in R/dend_utils.R (line 8, column 27)
ℹ NOTE: Avoid 'suppressWarnings'/'*Messages' if possible (found 17 times)
  • suppressWarnings() in R/binary_cut.R (line 294, column 26)
  • ...
  • suppressMessages() in R/word_cloud.R (line 350, column 25)
* Checking function lengths...
ℹ NOTE: The recommended function length is 50 lines or less. There are 15
functions greater than 50 lines.
  The longest 5 functions are:
    • simplifyGOFromMultipleLists() (R/simplify.R): 208 lines
    • ...
    • ht_clusters() (R/ht_clusters.R): 139 lines
* Checking man page documentation...
! WARNING: Empty or missing \value sections found in man page(s).
  Found in files:
    • man/anno_word_cloud_from_GO.Rd
    • ...
    • man/summarizeGO.Rd

✖ ERROR: At least 80% of man pages documenting exported objects must have
runnable examples.
  The following pages do not:
    • anno_word_cloud_from_GO.Rd
    • ...
    • summarizeGO.Rd
ℹ NOTE: Usage of dontrun / donttest tags found in man page examples. 36% of man
pages use at least one of these tags.
  Found in files:
    • binary_cut.Rd
    • ...
    • simplifyGOFromMultipleLists.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; 366 lines (10%) are > 80 characters long.
  First few lines:
    • R/binary_cut.R#L13 #' Denote `F(x)` as the eCDF (empirical ...
    • ...
    • vignettes/simplifyEnrichment.Rmd#L12 Please go to the package's website:
    http ...
ℹ NOTE: Consider 4 spaces instead of tabs; 2049 lines (55%) contain tabs.
  First few lines:
    • R/binary_cut.R#L3 max(unlist(dend_node_apply(dend, functi ...
    • ...
    • R/zzz.R#L19 ") ...
ℹ NOTE: Consider multiples of 4 spaces for line indents; 5 lines (0%) are not.
  First few lines:
    • R/stats.R#L80 # sapply(clt,function(cl)modularity(g, ...
    • ...
    • R/zzz.R#L17 suppressPackageStartupMessages(library ...
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 v1.49.4 results ───────────────────────────────────────────────────
✖ 3 ERRORS | ⚠ 1 WARNINGS | ℹ 15 NOTES
ℹ See the simplifyEnrichment.BiocCheck folder and run
  browseVignettes(package = 'BiocCheck')
  for details.