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### Running command:
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###   /home/rapidbuild/bbs-3.23-bioc-rapid/R/bin/Rscript -e "BiocCheck::BiocCheck('EnrichedHeatmap_1.42.0.tar.gz','quit-with-status'=TRUE)"
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── Installing EnrichedHeatmap ──────────────────────────────────────────────────
✔ Package installed successfully
── EnrichedHeatmap session metadata ────────────────────────────────────────────
→ sourceDir: /tmp/RtmpoFk3Eu/file77b6f67bb9865/EnrichedHeatmap
→ BiocVersion: 3.23
→ Package: EnrichedHeatmap
→ PackageVersion: 1.42.0
→ BiocCheckDir: /media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/meat/EnrichedHeatmap.BiocCheck
→ BiocCheckVersion: 1.48.0
→ sourceDir: /tmp/RtmpoFk3Eu/file77b6f67bb9865/EnrichedHeatmap
→ installDir: /tmp/RtmpoFk3Eu/file77b6f4a5cd31c
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on EnrichedHeatmap ────────────────────────────────────────
* 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...
ℹ NOTE: Provide 'BugReports' field(s) in DESCRIPTION
* Checking for Bioconductor software dependencies...
ℹ Bioconductor dependencies found in Imports & Depends (25%).
* 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...
✖ ERROR: 'VignetteBuilder' listed in DESCRIPTION but not found as
'VignetteEngine' in any vignettes:
  • knitr
! WARNING: Vignette(s) missing Vignette metadata. See
https://r-pkgs.org/vignettes.html
  Update the following files:
    • row_ordering.Rmd
✖ ERROR: No 'VignetteEngine' specified in vignette.
  Add 'VignetteEngine' to the following files:
    • vignettes/row_ordering.Rmd
! WARNING: Vignette(s) missing '\%VignetteIndexEntry{Vignette Title}'.
  Update the following files:
    • row_ordering.Rmd
ℹ NOTE: Vignette(s) found with missing chunk labels
  Found in files:
    • row_ordering.Rmd
ℹ NOTE: 'sessionInfo' not found in vignette(s)
  Missing from file(s):
    • vignettes/row_ordering.Rmd
* Checking package installation calls in R code...
* Checking for library/require of EnrichedHeatmap...
* Checking coding practice...
ℹ NOTE: Avoid sapply(); use vapply()
  Found in files:
    • R/EnrichedHeatmap.R (line 561, column 45)
    • ...
    • R/normalize.R (line 1001, column 17)
ℹ NOTE: Avoid 1:...; use seq_len() or seq_along()
  Found in files:
    • EnrichedHeatmap.R (line 350, column 107)
    • ...
    • normalize.R (line 371, column 35)
ℹ NOTE: Avoid using '=' for assignment and use '<-' instead
  Found in files:
    • R/EnrichedHeatmap.R (line 30, column 16)
    • ...
    • R/zzz.R (line 4, column 13)
* Checking parsed R code in R directory, examples, vignettes...
ℹ NOTE: Avoid '<<-' if possible (found 4 times)
  • <<- in R/normalize.R (line 243, column 31)
  • ...
  • <<- in R/normalize.R (line 1077, column 45)
ℹ NOTE: Avoid 'suppressWarnings'/'*Messages' if possible (found 7 times)
  • suppressWarnings() in R/normalize.R (line 172, column 17)
  • ...
  • suppressWarnings() in R/normalize.R (line 1075, column 39)
* 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:
    • EnrichedHeatmap() (R/EnrichedHeatmap.R): 302 lines
    • ...
    • axis_fun() (R/EnrichedHeatmap.R): 123 lines
* Checking man page documentation...
! WARNING: Empty or missing \value sections found in man page(s).
  Found in files:
    • man/copyAttr.rd
    • ...
    • man/extract_anno_enriched.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; 324 lines (11%) are > 80 characters long.
  First few lines:
    • R/EnrichedHeatmap.R#L12 # For a numeric vector, assume the vecto ...
    • ...
    • vignettes/row_ordering.Rmd#L92 row_title = "by hierarchcal clusteri ...
ℹ NOTE: Consider 4 spaces instead of tabs; 1216 lines (41%) contain tabs.
  First few lines:
    • R/EnrichedHeatmap.R#L32 calc_score = function(x1, x2, x3) { ...
    • ...
    • man/copyAttr.rd#L32 end = 100)) ...
ℹ NOTE: Consider multiples of 4 spaces for line indents; 182 lines (6%) are
not.
  First few lines:
    • R/normalize.R#L134 ...
    • ...
    • vignettes/row_ordering.Rmd#L56 negCR windows in the two genes. ...
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 ───────────────────────────────────────────────────
✖ 3 ERRORS | ⚠ 3 WARNINGS | ℹ 15 NOTES
ℹ See the EnrichedHeatmap.BiocCheck folder and run
  browseVignettes(package = 'BiocCheck')
  for details.