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### Running command:
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###   /home/biocbuild/bbs-3.24-bioc/R/bin/Rscript -e "BiocCheck::BiocCheck('destiny_3.27.0.tar.gz','quit-with-status'=TRUE)"
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── Installing destiny ──────────────────────────────────────────────────────────
✔ Package installed successfully
── destiny session metadata ────────────────────────────────────────────────────
→ sourceDir: /tmp/RtmpLhVA0v/file81cf262237284/destiny
→ BiocVersion: 3.24
→ Package: destiny
→ PackageVersion: 3.27.0
→ BiocCheckDir: /home/biocbuild/bbs-3.24-bioc/meat/destiny.BiocCheck
→ BiocCheckVersion: 1.49.4
→ sourceDir: /tmp/RtmpLhVA0v/file81cf262237284/destiny
→ installDir: /tmp/RtmpLhVA0v/file81cf21b3ed37a
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on destiny ────────────────────────────────────────────────
* 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 3.4.0 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...
* Checking for Bioconductor software dependencies...
ℹ Bioconductor dependencies found in Imports & Depends (18%).
* 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:
    • Diffusion-Map-recap.Rmd
    • ...
    • tidyverse.Rmd
ℹ NOTE: 'sessionInfo' not found in vignette(s)
  Missing from file(s):
    • vignettes/Diffusion-Map-recap.Rmd
    • ...
    • vignettes/tidyverse.Rmd
* Checking package installation calls in R code...
* Checking for library/require of destiny...
* Checking coding practice...
ℹ NOTE: Avoid sapply(); use vapply()
  Found in files:
    • R/dataset-helpers.r (line 7, column 40)
    • ...
    • R/smth-gaussian.r (line 40, column 15)
ℹ NOTE: Avoid 1:...; use seq_len() or seq_along()
  Found in files:
    • diffusionmap-plotting.r (line 62, column 19)
    • ...
    • smth-gaussian.r (line 49, column 23)
ℹ NOTE: Avoid 'cat' and 'print' outside of 'show' methods
  Found in files:
    • cat() in R/diffusionmap.r (line 344, column 38)
    • ...
    • cat() in R/predict.r (line 70, column 22)
ℹ NOTE: Avoid using '=' for assignment and use '<-' instead
  Found in files:
    • R/smth-gaussian.r (line 22, column 22)
    • ...
    • R/smth-gaussian.r (line 78, column 15)
ℹ NOTE: Avoid the use of 'paste' in condition signals
  Found in files:
    • R/smth-gaussian.r (line 65, column 22)
ℹ NOTE: Avoid redundant 'stop' and 'warn*' in signal conditions
  Found in files:
    • R/diffusionmap.r (line 372, column 45)
* Checking parsed R code in R directory, examples, vignettes...
ℹ NOTE: Avoid '<<-' if possible (found 1 times)
  • <<- in R/dpt-methods-matrix.r (line 46, column 35)
* Checking function lengths...
ℹ NOTE: The recommended function length is 50 lines or less. There are 9
functions greater than 50 lines.
  The longest 5 functions are:
    • plot.DiffusionMap() (R/diffusionmap-plotting.r): 155 lines
    • ...
    • _anonymous_.108() (R/gene-relevance.r): 102 lines
* Checking man page documentation...
ℹ NOTE: Consider adding runnable examples to man pages that document exported
objects.
  • knn.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; 571 lines (11%) are > 80 characters long.
  First few lines:
    • R/aaa.r#L1 bad_default_palette <- c('black', 'red', ...
    • ...
    • vignettes/tidyverse.Rmd#L108 Adding a constant `alpha` improves this ...
ℹ NOTE: Consider 4 spaces instead of tabs; 1881 lines (37%) contain tabs.
  First few lines:
    • R/aaa.r#L8 cp <- getFromNamespace('C_palette', 'gr ...
    • ...
    • vignettes/Diffusion-Maps.Rmd#L213 ncol = 2) ...
ℹ NOTE: Consider multiples of 4 spaces for line indents; 20 lines (0%) are not.
  First few lines:
    • R/smth-gaussian.r#L14 window = getOption('smoother.window', ...
    • ...
    • vignettes/tidyverse.Rmd#L20 else repr::repr_text(df) ...
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 | ⚠ 0 WARNINGS | ℹ 17 NOTES
ℹ See the destiny.BiocCheck folder and run
  browseVignettes(package = 'BiocCheck')
  for details.