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### Running command:
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###   /home/rapidbuild/bbs-3.23-bioc-rapid/R/bin/Rscript -e "BiocCheck::BiocCheck('ComplexHeatmap_2.28.0.tar.gz','quit-with-status'=TRUE)"
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── Installing ComplexHeatmap ───────────────────────────────────────────────────
✔ Package installed successfully
── ComplexHeatmap session metadata ─────────────────────────────────────────────
→ sourceDir: /tmp/RtmpFjtYuX/file75a51123064e9/ComplexHeatmap
→ BiocVersion: 3.23
→ Package: ComplexHeatmap
→ PackageVersion: 2.28.0
→ BiocCheckDir: /media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/meat/ComplexHeatmap.BiocCheck
→ BiocCheckVersion: 1.48.0
→ sourceDir: /tmp/RtmpFjtYuX/file75a51123064e9/ComplexHeatmap
→ installDir: /tmp/RtmpFjtYuX/file75a5131d16fc
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on ComplexHeatmap ─────────────────────────────────────────
* 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 (6%).
* 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: Vignette(s) missing Vignette metadata. See
https://r-pkgs.org/vignettes.html
  Update the following files:
    • complex_heatmap.rmd
    • most_probably_asked_questions.Rmd
! WARNING: Vignette(s) missing '\%VignetteIndexEntry{Vignette Title}'.
  Update the following files:
    • complex_heatmap.rmd
    • most_probably_asked_questions.Rmd
ℹ NOTE: Vignette(s) found with missing chunk labels
  Found in files:
    • most_probably_asked_questions.Rmd
ℹ NOTE: 'sessionInfo' not found in vignette(s)
  Missing from file(s):
    • vignettes/most_probably_asked_questions.Rmd
* Checking package installation calls in R code...
* Checking for library/require of ComplexHeatmap...
* Checking coding practice...
ℹ NOTE: Avoid sapply(); use vapply()
  Found in files:
    • R/anno_textbox.R (line 82, column 22)
    • ...
    • R/utils.R (line 1108, column 5)
ℹ NOTE: Avoid 1:...; use seq_len() or seq_along()
  Found in files:
    • 3d.R (line 65, column 18)
    • ...
    • utils.R (line 1084, column 21)
ℹ NOTE: Avoid 'cat' and 'print' outside of 'show' methods
  Found in files:
    • cat() in R/oncoPrint.R (line 925, column 17)
    • ...
    • cat() in R/utils.R (line 87, column 21)
ℹ NOTE: Avoid using '=' for assignment and use '<-' instead
  Found in files:
    • R/00_size.R (line 2, column 7)
    • ...
    • R/zzz.R (line 50, column 17)
ℹ NOTE: Avoid the use of 'paste' in condition signals
  Found in files:
    • R/AnnotationFunction-class.R (line 295, column 41)
ℹ NOTE: Avoid redundant 'stop' and 'warn*' in signal conditions
  Found in files:
    • R/AnnotationFunction-class.R (line 295, column 48)
    • R/AnnotationFunction-function.R (line 4349, column 36)
! WARNING: Avoid class membership checks with class() / is() and == / !=; Use
is(x, 'class') for S4 classes
  Found in files:
    • pheatmap_translate.R (line 95, column 49)
    • pheatmap_translate.R (line 96, column 49)
* Checking parsed R code in R directory, examples, vignettes...
ℹ Found @ in man/Legends-class.Rd
ℹ NOTE: Use accessors; don't access S4 class slots via '@' in
examples/vignettes.
ℹ NOTE: Avoid '<<-' if possible (found 30 times)
  • <<- in R/box_align.R (line 113, column 11)
  • ...
  • <<- in R/HeatmapList-class.R (line 1023, column 20)
ℹ NOTE: Avoid 'suppressWarnings'/'*Messages' if possible (found 2 times)
  • suppressWarnings() in R/densityHeatmap.R (line 309, column 17)
  • suppressWarnings() in R/densityHeatmap.R (line 348, column 13)
* Checking function lengths...
ℹ NOTE: The recommended function length is 50 lines or less. There are 77
functions greater than 50 lines.
  The longest 5 functions are:
    • Heatmap() (R/Heatmap-class.R): 844 lines
    • ...
    • anno_zoom() (R/AnnotationFunction-function.R): 443 lines
* Checking man page documentation...
! WARNING: Empty or missing \value sections found in man page(s).
  Found in files:
    • man/add_heatmap-dispatch.Rd
    • ...
    • man/widthDetails.packed_legends.Rd
ℹ NOTE: Consider adding runnable examples to man pages that document exported
objects.
  • anno_image.Rd
  • normalize_genomic_signals_to_bins.Rd
ℹ NOTE: Usage of dontrun / donttest tags found in man page examples. 1% of man
pages use at least one of these tags.
  Found in files:
    • anno_image.Rd
    • make_comb_mat.Rd
    • normalize_genomic_signals_to_bins.Rd
ℹ NOTE: Use donttest instead of dontrun.
  Found in files:
    • anno_image.Rd
    • make_comb_mat.Rd
    • normalize_genomic_signals_to_bins.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; 2638 lines (9%) are > 80 characters long.
  First few lines:
    • R/00_S4_generic_methods.R#L1 setGeneric('draw_annotation_legend', fun ...
    • ...
    • vignettes/most_probably_asked_questions.Rmd#L199 Yes, please refer to
    [the **InteractiveC ...
ℹ NOTE: Consider 4 spaces instead of tabs; 9298 lines (32%) contain tabs.
  First few lines:
    • R/00_size.R#L3 UseMethod("width", x) ...
    • ...
    • vignettes/most_probably_asked_questions.Rmd#L181 row_split = 2) ...
ℹ NOTE: Consider multiples of 4 spaces for line indents; 114 lines (0%) are
not.
  First few lines:
    • R/AnnotationFunction-class.R#L193 var_import[[v]] = get(v, envi ...
    • ...
    • vignettes/most_probably_asked_questions.Rmd#L168 results, but the chance
    is much small ...
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 ───────────────────────────────────────────────────
✖ 1 ERRORS | ⚠ 4 WARNINGS | ℹ 22 NOTES
ℹ See the ComplexHeatmap.BiocCheck folder and run
  browseVignettes(package = 'BiocCheck')
  for details.