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### Running command:
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###   /home/rapidbuild/bbs-3.23-bioc-rapid/R/bin/Rscript -e "BiocCheck::BiocCheck('SpatialExperiment_1.22.0.tar.gz','quit-with-status'=TRUE)"
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── Installing SpatialExperiment ────────────────────────────────────────────────
✔ Package installed successfully
── SpatialExperiment session metadata ──────────────────────────────────────────
→ sourceDir: /tmp/RtmpoRjVyu/file98e724e4ba73e/SpatialExperiment
→ BiocVersion: 3.23
→ Package: SpatialExperiment
→ PackageVersion: 1.22.0
→ BiocCheckDir: /media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/meat/SpatialExperiment.BiocCheck
→ BiocCheckVersion: 1.48.0
→ sourceDir: /tmp/RtmpoRjVyu/file98e724e4ba73e/SpatialExperiment
→ installDir: /tmp/RtmpoRjVyu/file98e722b9dc3fd
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on SpatialExperiment ──────────────────────────────────────
* 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 4.1.0 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...
* Checking for Bioconductor software dependencies...
ℹ Bioconductor dependencies found in Imports & Depends (50%).
* 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:
    • SpatialExperiment.Rmd
* Checking package installation calls in R code...
* Checking for library/require of SpatialExperiment...
* Checking coding practice...
ℹ NOTE: Avoid 'cat' and 'print' outside of 'show' methods
  Found in files:
    • cat() in R/show.R (line 53, column 5)
    • cat() in R/show.R (line 61, column 9)
ℹ NOTE: Avoid the use of 'paste' in condition signals
  Found in files:
    • R/SpatialExperiment-methods.R (line 273, column 13)
    • ...
    • R/SpatialExperiment-rotate-mirror.R (line 214, column 17)
ℹ NOTE: Avoid redundant 'stop' and 'warn*' in signal conditions
  Found in files:
    • R/SpatialExperiment.R (line 289, column 9)
! WARNING: .Deprecated / .Defunct usage (found 1 times)
  • .Deprecated() in R/read10xVisium.R (line 95, column 5)
* Checking parsed R code in R directory, examples, vignettes...
ℹ NOTE: Avoid 'suppressWarnings'/'*Messages' if possible (found 1 times)
  • suppressWarnings() in R/Validity.R (line 122, column 5)
* Checking function lengths...
ℹ NOTE: The recommended function length is 50 lines or less. There are 4
functions greater than 50 lines.
  The longest 5 functions are:
    • .sce_to_spe() (R/SpatialExperiment.R): 117 lines
    • ...
    • _anonymous_.183() (R/SpatialExperiment-rotate-mirror.R): 65 lines
* Checking man page documentation...
! WARNING: Empty or missing \value sections found in man page(s).
  Found in files:
    • man/SpatialExperiment-assays.Rd
    • man/SpatialExperiment-coercion.Rd
    • man/SpatialImage-class.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; 25 lines (1%) are > 80 characters long.
  First few lines:
    • R/AllGenerics.R#L48 setGeneric("spatialDataNames<-", functio ...
    • ...
    • vignettes/SpatialExperiment.Rmd#L521 * `rotateImg(x, degrees)` expects as
    `de ...
ℹ NOTE: Consider multiples of 4 spaces for line indents; 28 lines (1%) are not.
  First few lines:
    • R/SpatialExperiment.R#L274 .msg_spatialData() ...
    • ...
    • vignettes/SpatialExperiment.Rmd#L347 · · · | — tissue_positions.csv ...
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 v1.48.0 results ───────────────────────────────────────────────────
✖ 0 ERRORS | ⚠ 2 WARNINGS | ℹ 11 NOTES
ℹ See the SpatialExperiment.BiocCheck folder and run
  browseVignettes(package = 'BiocCheck')
  for details.