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### Running command:
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###   /home/biocbuild/bbs-3.24-bioc/R/bin/Rscript -e "BiocCheck::BiocCheck('scone_1.37.0.tar.gz','quit-with-status'=TRUE)"
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── Installing scone ────────────────────────────────────────────────────────────
✔ Package installed successfully
── scone session metadata ──────────────────────────────────────────────────────
→ sourceDir: /tmp/RtmpWG12lq/file12c8651ff44246/scone
→ BiocVersion: 3.24
→ Package: scone
→ PackageVersion: 1.37.0
→ BiocCheckDir: /home/biocbuild/bbs-3.24-bioc/meat/scone.BiocCheck
→ BiocCheckVersion: 1.49.4
→ sourceDir: /tmp/RtmpWG12lq/file12c8651ff44246/scone
→ installDir: /tmp/RtmpWG12lq/file12c86515b2cbb3
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on scone ──────────────────────────────────────────────────
* 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 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...
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 (41%).
* 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 '\%VignetteIndexEntry{Vignette Title}'.
  Update the following files:
    • PsiNorm.Rmd
    • sconeTutorial.Rmd
ℹ NOTE: Vignette(s) found with missing chunk labels
  Found in files:
    • PsiNorm.Rmd
* Checking package installation calls in R code...
* Checking for library/require of scone...
* Checking coding practice...
ℹ NOTE: Avoid sapply(); use vapply()
  Found in files:
    • R/scone_main.R (line 229, column 17)
    • R/scone_main.R (line 252, column 17)
    • R/sconeReport.R (line 157, column 25)
ℹ NOTE: Avoid 1:...; use seq_len() or seq_along()
  Found in files:
    • biplot.R (line 36, column 36)
    • ...
    • ziber.R (line 343, column 13)
ℹ NOTE: Avoid 'cat' and 'print' outside of 'show' methods
  Found in files:
    • cat() in R/scone_wrap.R (line 138, column 27)
    • ...
    • print() in R/ziber.R (line 184, column 17)
ℹ NOTE: Avoid using '=' for assignment and use '<-' instead
  Found in files:
    • R/biplot.R (line 41, column 7)
    • ...
    • R/ziber.R (line 414, column 7)
ℹ NOTE: Avoid the use of 'paste' in condition signals
  Found in files:
    • R/sample_filtering.R (line 60, column 7)
    • ...
    • R/ziber.R (line 356, column 17)
! WARNING: Avoid class membership checks with class() / is() and == / !=; Use
is(x, 'class') for S4 classes
  Found in files:
    • helper.R (line 244, column 18)
    • helper.R (line 250, column 20)
! WARNING: Remove set.seed usage (found 1 times)
  • set.seed() in R/scone_wrap.R (line 139, column 3)
* Checking parsed R code in R directory, examples, vignettes...
ℹ NOTE: Avoid 'suppressWarnings'/'*Messages' if possible (found 3 times)
  • suppressWarnings() in R/sample_filtering.R (line 70, column 11)
  • suppressWarnings() in R/ziber.R (line 123, column 11)
  • suppressWarnings() in R/ziber.R (line 345, column 11)
* Checking function lengths...
ℹ NOTE: The recommended function length is 50 lines or less. There are 12
functions greater than 50 lines.
  The longest 5 functions are:
    • sconeReport() (R/sconeReport.R): 908 lines
    • ...
    • metric_sample_filter() (R/sample_filtering.R): 413 lines
* Checking man page documentation...
! WARNING: Empty or missing \format sections found in data man page(s).
  Found in files:
    • man/control_genes.Rd
ℹ NOTE: Usage of dontrun / donttest tags found in man page examples. 8% of man
pages use at least one of these tags.
  Found in files:
    • biplot_interactive.Rd
    • scone_easybake.Rd
    • sconeReport.Rd
ℹ NOTE: Use donttest instead of dontrun.
  Found in files:
    • biplot_interactive.Rd
    • scone_easybake.Rd
    • sconeReport.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; 28 lines (0%) are > 80 characters long.
  First few lines:
    • vignettes/PsiNorm.Rmd#L5 affiliation: Department of Biology a ...
    • ...
    • vignettes/PsiNorm.Rmd#L204 Note that `logNormCounts` is a delayed o ...
ℹ NOTE: Consider multiples of 4 spaces for line indents; 2282 lines (34%) are
not.
  First few lines:
    • R/AllClasses.R#L81 Class = "SconeExperiment", ...
    • ...
    • vignettes/sconeTutorial.Rmd#L752 "none,none,no_uv,no_bi ...
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 | ⚠ 4 WARNINGS | ℹ 17 NOTES
ℹ See the scone.BiocCheck folder and run
  browseVignettes(package = 'BiocCheck')
  for details.