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### Running command:
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###   /home/biocbuild/bbs-3.24-bioc/R/bin/Rscript -e "BiocCheck::BiocCheck('autonomics_1.21.0.tar.gz','quit-with-status'=TRUE)"
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── Installing autonomics ───────────────────────────────────────────────────────
✔ Package installed successfully
── autonomics session metadata ─────────────────────────────────────────────────
→ sourceDir: /tmp/RtmpjuR4O6/file57f3a13452974/autonomics
→ BiocVersion: 3.24
→ Package: autonomics
→ PackageVersion: 1.21.0
→ BiocCheckDir: /home/biocbuild/bbs-3.24-bioc/meat/autonomics.BiocCheck
→ BiocCheckVersion: 1.49.4
→ sourceDir: /tmp/RtmpjuR4O6/file57f3a13452974/autonomics
→ installDir: /tmp/RtmpjuR4O6/file57f3a27f18c76
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on autonomics ─────────────────────────────────────────────
* 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 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: Clustering,
Survival
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' field(s) in DESCRIPTION
* Checking for Bioconductor software dependencies...
ℹ Bioconductor dependencies found in Imports & Depends (20%).
* 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:
    • autonomics_platformaware_analysis.Rmd
* Checking package installation calls in R code...
* Checking for library/require of autonomics...
* Checking coding practice...
ℹ NOTE: Avoid sapply(); use vapply()
  Found in files:
    • R/02_assertions.R (line 569, column 25)
    • R/02_assertions.R (line 572, column 7)
    • R/17_read_compounddiscoverer.R (line 347, column 7)
ℹ NOTE: Avoid 1:...; use seq_len() or seq_along()
  Found in files:
    • 03_download.R (line 93, column 19)
    • ...
    • 33_survival.R (line 31, column 46)
ℹ NOTE: Avoid 'cat' and 'print' outside of 'show' methods
  Found in files:
    • print() in R/01_assertive.R (line 278, column 50)
    • ...
    • print() in R/31_plot_volcano.R (line 355, column 5)
ℹ NOTE: Avoid using '=' for assignment and use '<-' instead
  Found in files:
    • R/22_transform.R (line 691, column 36)
    • R/22_transform.R (line 692, column 32)
ℹ NOTE: Avoid the use of 'paste' in condition signals
  Found in files:
    • R/08_read_omics.R (line 112, column 39)
! WARNING: Remove set.seed usage (found 2 times)
  • set.seed() in R/20_plot.R (line 1832, column 5)
  • set.seed() in R/33_survival.R (line 48, column 5)
! WARNING: .Deprecated / .Defunct usage (found 15 times)
  • .Deprecated() in R/08_read_omics.R (line 416, column 5)
  • ...
  • .Deprecated() in R/27_linmod_wilcoxon.R (line 150, column 32)
* Checking parsed R code in R directory, examples, vignettes...
ℹ NOTE: Avoid 'suppressWarnings'/'*Messages' if possible (found 18 times)
  • suppressWarnings() in R/01_assertive.R (line 1096, column 34)
  • ...
  • suppressWarnings() in R/33_survival.R (line 220, column 16)
* Checking function lengths...
ℹ NOTE: The recommended function length is 50 lines or less. There are 45
functions greater than 50 lines.
  The longest 5 functions are:
    • plot_volcano() (R/31_plot_volcano.R): 125 lines
    • ...
    • plot_exprs() (R/20_plot.R): 103 lines
* Checking man page documentation...
! WARNING: Empty or missing \value sections found in man page(s).
  Found in files:
    • man/altenrich.Rd
    • ...
    • man/uncollapse.Rd
ℹ NOTE: Consider adding runnable examples to man pages that document exported
objects.
  • altenrich.Rd
  • ...
  • twofactor_sumexp.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:
    • guess_compounddiscoverer_quantity.Rd
    • read_rnaseq_counts.Rd
ℹ NOTE: Use donttest instead of dontrun.
  Found in files:
    • guess_compounddiscoverer_quantity.Rd
    • read_rnaseq_counts.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; 1835 lines (9%) are > 80 characters long.
  First few lines:
    • R/00_import.R#L40 #' @importFrom graphics abline a ...
    • ...
    • vignettes/autonomics_platformaware_analysis.Rmd#L191 A Halama, H Kahal, A
    M Bhagwat, J Zierer ...
ℹ NOTE: Consider multiples of 4 spaces for line indents; 1875 lines (9%) are
not.
  First few lines:
    • R/01_assertive.R#L24 x, ...
    • ...
    • vignettes/autonomics_platformaware_analysis.Rmd#L90
    colSums(summarize_fit(fdt(object), 'li ...
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.
✖ ERROR: Add package to Watched Tags in your Support Site profile; visit
https://support.bioconductor.org/accounts/edit/profile
── BiocCheck v1.49.4 results ───────────────────────────────────────────────────
✖ 1 ERRORS | ⚠ 3 WARNINGS | ℹ 19 NOTES
ℹ See the autonomics.BiocCheck folder and run
  browseVignettes(package = 'BiocCheck')
  for details.