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### Running command:
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###   /home/biocbuild/bbs-3.24-bioc/R/bin/Rscript -e "BiocCheck::BiocCheck('SpatialDecon_1.23.0.tar.gz','quit-with-status'=TRUE)"
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── Installing SpatialDecon ─────────────────────────────────────────────────────
✔ Package installed successfully
── SpatialDecon session metadata ───────────────────────────────────────────────
→ sourceDir: /tmp/RtmpsHaeAK/file1440af2aa7220d/SpatialDecon
→ BiocVersion: 3.24
→ Package: SpatialDecon
→ PackageVersion: 1.23.0
→ BiocCheckDir: /home/biocbuild/bbs-3.24-bioc/meat/SpatialDecon.BiocCheck
→ BiocCheckVersion: 1.49.4
→ sourceDir: /tmp/RtmpsHaeAK/file1440af2aa7220d/SpatialDecon
→ installDir: /tmp/RtmpsHaeAK/file1440af301820c3
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on SpatialDecon ───────────────────────────────────────────
* Checking for deprecated package usage...
* Checking for remote package usage...
* Checking for 'LazyData: true' usage...
ℹ NOTE: 'LazyData:' in the 'DESCRIPTION' should be set to false or removed
* Checking version number...
* Checking for version number mismatch...
* Checking version number validity...
* Checking R version dependency...
ℹ NOTE: Update R version dependency from 4.0.0 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...
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 (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:
    • SpatialDecon_vignette_NSCLC.Rmd
    • SpatialDecon_vignette.Rmd
* Checking package installation calls in R code...
* Checking for library/require of SpatialDecon...
* Checking coding practice...
ℹ NOTE: Avoid 'cat' and 'print' outside of 'show' methods
  Found in files:
    • print() in R/create_profile_matrix.R (line 141, column 9)
    • ...
    • print() in R/create_profile_matrix.R (line 187, column 9)
ℹ NOTE: Avoid using '=' for assignment and use '<-' instead
  Found in files:
    • R/reverseDecon.R (line 61, column 8)
    • R/reverseDecon.R (line 63, column 7)
    • R/reverseDecon.R (line 64, column 8)
ℹ NOTE: Avoid the use of 'paste' in condition signals
  Found in files:
    • R/create_profile_matrix.R (line 146, column 14)
    • ...
    • R/spatialdecon.R (line 176, column 14)
* Checking parsed R code in R directory, examples, vignettes...
ℹ Found @ in man/runspatialdecon.Rd
ℹ Found @ in vignettes/SpatialDecon_vignette_NSCLC.Rmd
ℹ Found @ in vignettes/SpatialDecon_vignette.Rmd
ℹ NOTE: Use accessors; don't access S4 class slots via '@' in
examples/vignettes.
ℹ NOTE: Avoid 'suppressWarnings'/'*Messages' if possible (found 6 times)
  • suppressWarnings() in R/algorithm2.R (line 133, column 24)
  • ...
  • suppressWarnings() in R/spatialdecon.R (line 246, column 24)
* Checking function lengths...
ℹ NOTE: The recommended function length is 50 lines or less. There are 11
functions greater than 50 lines.
  The longest 5 functions are:
    • _anonymous_.131() (R/runspatialdecon.R): 255 lines
    • ...
    • runErrorModel() (R/runErrorModel.R): 85 lines
* Checking man page documentation...
* 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; 307 lines (8%) are > 80 characters long.
  First few lines:
    • R/collapseCellTypes.R#L72 out[[name]] <- A[, startingc ...
    • ...
    • vignettes/SpatialDecon_vignette.Rmd#L498 ```{r reverse2, fig.height=6,
    fig.width= ...
ℹ NOTE: Consider multiples of 4 spaces for line indents; 452 lines (11%) are
not.
  First few lines:
    • R/algorithm2.R#L68 resid_thresh = 3, ...
    • ...
    • vignettes/SpatialDecon_vignette.Rmd#L506 showgenes, cex = 0.75, col = 2)
    ...
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 15 NOTES
ℹ See the SpatialDecon.BiocCheck folder and run
  browseVignettes(package = 'BiocCheck')
  for details.