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### Running command:
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###   /home/biocbuild/bbs-3.24-bioc/R/bin/Rscript -e "BiocCheck::BiocCheck('VISTA_1.1.0.tar.gz','quit-with-status'=TRUE)"
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── Installing VISTA ────────────────────────────────────────────────────────────
✔ Package installed successfully
── VISTA session metadata ──────────────────────────────────────────────────────
→ sourceDir: /tmp/RtmpZLYpFk/file152dbc73ac00c4/VISTA
→ BiocVersion: 3.24
→ Package: VISTA
→ PackageVersion: 1.1.0
→ BiocCheckDir: /home/biocbuild/bbs-3.24-bioc/meat/VISTA.BiocCheck
→ BiocCheckVersion: 1.49.4
→ sourceDir: /tmp/RtmpZLYpFk/file152dbc73ac00c4/VISTA
→ installDir: /tmp/RtmpZLYpFk/file152dbc44671ba7
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on VISTA ──────────────────────────────────────────────────
* 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 4.3 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...
* Checking for Bioconductor software dependencies...
ℹ Bioconductor dependencies found in Imports & Depends (26%).
* 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...
* Checking package installation calls in R code...
* Checking for library/require of VISTA...
* Checking coding practice...
ℹ NOTE: Avoid using '=' for assignment and use '<-' instead
  Found in files:
    • R/input_preparation.R (line 562, column 42)
    • R/input_preparation.R (line 563, column 40)
ℹ NOTE: Avoid the use of 'paste' in condition signals
  Found in files:
    • R/utils-internal.R (line 1341, column 10)
* Checking parsed R code in R directory, examples, vignettes...
ℹ Found @ in vignettes/VISTA-airway.Rmd
ℹ NOTE: Use accessors; don't access S4 class slots via '@' in
examples/vignettes.
ℹ NOTE: Avoid 'suppressWarnings'/'*Messages' if possible (found 29 times)
  • suppressWarnings() in R/benchmarking.R (line 979, column 19)
  • ...
  • suppressWarnings() in R/viz_related.R (line 5788, column 57)
* Checking function lengths...
ℹ NOTE: The recommended function length is 50 lines or less. There are 82
functions greater than 50 lines.
  The longest 5 functions are:
    • run_vista_report() (R/reporting.R): 816 lines
    • ...
    • get_enrichment_chord() (R/functional_analysis.R): 333 lines
* Checking man page documentation...

ℹ NOTE: Consider adding runnable examples to man pages that document exported
objects.
  • get_enrichment_plot.Rd
  • ...
  • run_vista_report.Rd
ℹ NOTE: Usage of dontrun / donttest tags found in man page examples. 17% of man
pages use at least one of these tags.
  Found in files:
    • benchmark_vista_equivalence.Rd
    • ...
    • VISTA-accessors.Rd
ℹ NOTE: Use donttest instead of dontrun.
  Found in files:
    • get_enrichment_plot.Rd
    • ...
    • run_vista_report.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; 1427 lines (8%) are > 80 characters long.
  First few lines:
    • R/accessors.R#L2 #' @description These accessor functions ...
    • ...
    • vignettes/VISTA-airway.Rmd#L1538 - Yu G et al. (2012). clusterProfiler:
    ...
ℹ NOTE: Consider multiples of 4 spaces for line indents; 7104 lines (37%) are
not.
  First few lines:
    • R/accessors.R#L97 source <- match.arg(source) ...
    • ...
    • vignettes/VISTA-airway.Rmd#L1435 row.names = FALSE ...
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 14 NOTES
ℹ See the VISTA.BiocCheck folder and run
  browseVignettes(package = 'BiocCheck')
  for details.