##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.24-bioc/R/bin/Rscript -e "BiocCheck::BiocCheck('Cardinal_3.15.0.tar.gz','quit-with-status'=TRUE)"
###
##############################################################################
##############################################################################


── Installing Cardinal ─────────────────────────────────────────────────────────
✔ Package installed successfully
── Cardinal session metadata ───────────────────────────────────────────────────
→ sourceDir: /tmp/Rtmp3UpQ9W/file61412c894618/Cardinal
→ BiocVersion: 3.24
→ Package: Cardinal
→ PackageVersion: 3.15.0
→ BiocCheckDir: /home/biocbuild/bbs-3.24-bioc/meat/Cardinal.BiocCheck
→ BiocCheckVersion: 1.49.4
→ sourceDir: /tmp/Rtmp3UpQ9W/file61412c894618/Cardinal
→ installDir: /tmp/Rtmp3UpQ9W/file61412322d78f7
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on Cardinal ───────────────────────────────────────────────
* 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 4.4 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...
ℹ NOTE: Consider adding these automatically suggested biocViews: Spatial
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: 'Date:' field format is not 'YYYY-MM-DD': 2015-1-12
* 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...
ℹ NOTE: Vignette(s) found with missing chunk labels
  Found in files:
    • Cardinal3-guide.Rmd
* Checking package installation calls in R code...
* Checking for library/require of Cardinal...
* Checking coding practice...
ℹ NOTE: Avoid sapply(); use vapply()
  Found in files:
    • R/stats-meansTest.R (line 89, column 29)
    • ...
    • R/stats-meansTest.R (line 470, column 44)
ℹ NOTE: Avoid 1:...; use seq_len() or seq_along()
  Found in files:
    • methods-SpatialResults.R (line 284, column 42)
    • ...
    • methods-SpectraArrays.R (line 179, column 40)
ℹ NOTE: Avoid 'cat' and 'print' outside of 'show' methods
  Found in files:
    • cat() in R/methods-SpectralImagingExperiment.R (line 553, column 17)
    • ...
    • cat() in R/methods-SpectralImagingExperiment.R (line 557, column 17)
! WARNING: Avoid class membership checks with class() / is() and == / !=; Use
is(x, 'class') for S4 classes
  Found in files:
    • methods-XDFrame.R (line 52, column 34)
! WARNING: .Deprecated / .Defunct usage (found 47 times)
  • .Defunct() in R/AllGenerics.R (line 80, column 17)
  • ...
  • .Deprecated() in R/summarize.R (line 50, column 17)
* Checking parsed R code in R directory, examples, vignettes...
* Checking function lengths...
ℹ NOTE: The recommended function length is 50 lines or less. There are 35
functions greater than 50 lines.
  The longest 5 functions are:
    • presetImageDef() (R/simulateSpectra.R): 393 lines
    • ...
    • _anonymous_.6() (R/process-peaks.R): 113 lines
* Checking man page documentation...
! WARNING: Empty or missing \value sections found in man page(s).
  Found in files:
    • man/deprecated.Rd
    • ...
    • man/XDataFrame-class.Rd
✖ ERROR: At least 80% of man pages documenting exported objects must have
runnable examples.
  The following pages do not:
    • Cardinal-package.Rd
    • ...
    • writeMSIData.Rd
ℹ NOTE: Usage of dontrun / donttest tags found in man page examples. 2% of man
pages use at least one of these tags.
  Found in files:
    • MeansTest.Rd
ℹ NOTE: Use donttest instead of dontrun.
  Found in files:
    • MeansTest.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; 795 lines (5%) are > 80 characters long.
  First few lines:
    • R/AllGenerics.R#L15 setGeneric("pixelData<-", function(objec ...
    • ...
    • vignettes/Cardinal3-stats.Rmd#L423 As with `meansTest()`, the models are
    su ...
ℹ NOTE: Consider 4 spaces instead of tabs; 7674 lines (49%) contain tabs.
  First few lines:
    • R/AllClasses.R#L5 contains = c("VIRTUAL", "DataFrame"), ...
    • ...
    • vignettes/Cardinal3-stats.Rmd#L355 nrun=4, peakdiff=2, centroided=TRUE)
    ...
ℹ NOTE: Consider multiples of 4 spaces for line indents; 50 lines (0%) are not.
  First few lines:
    • man/MeansTest.Rd#L156 method="pairwise", ...
    • ...
    • vignettes/Cardinal3-guide.Rmd#L86 + New `SpatialResults` output with sim
    ...
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 ───────────────────────────────────────────────────
✖ 1 ERRORS | ⚠ 3 WARNINGS | ℹ 16 NOTES
ℹ See the Cardinal.BiocCheck folder and run
  browseVignettes(package = 'BiocCheck')
  for details.