##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.24-bioc/R/bin/Rscript -e "BiocCheck::BiocCheck('SpaNorm_1.7.0.tar.gz','quit-with-status'=TRUE)"
###
##############################################################################
##############################################################################


── Installing SpaNorm ──────────────────────────────────────────────────────────
✔ Package installed successfully
── SpaNorm session metadata ────────────────────────────────────────────────────
→ sourceDir: /tmp/RtmpNbu30a/file13c1766b6054d/SpaNorm
→ BiocVersion: 3.24
→ Package: SpaNorm
→ PackageVersion: 1.7.0
→ BiocCheckDir: /home/biocbuild/bbs-3.24-bioc/meat/SpaNorm.BiocCheck
→ BiocCheckVersion: 1.49.4
→ sourceDir: /tmp/RtmpNbu30a/file13c1766b6054d/SpaNorm
→ installDir: /tmp/RtmpNbu30a/file13c17625285d2c
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on SpaNorm ────────────────────────────────────────────────
* 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...
* 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...
* 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:
    • SpaNorm.Rmd
* Checking package installation calls in R code...
* Checking for library/require of SpaNorm...
* Checking coding practice...
ℹ NOTE: Avoid sapply(); use vapply()
  Found in files:
    • R/plotCovariates.R (line 36, column 26)
    • R/plotSpatial.R (line 68, column 16)
    • R/plotSpatial.R (line 71, column 30)
ℹ NOTE: Avoid 1:...; use seq_len() or seq_along()
  Found in files:
    • checkers.R (line 77, column 30)
    • ...
    • mainSpaNorm.R (line 284, column 30)
ℹ NOTE: Avoid using '=' for assignment and use '<-' instead
  Found in files:
    • R/AllClasses.R (line 64, column 14)
    • ...
    • R/plotSpatial.R (line 224, column 8)
* Checking parsed R code in R directory, examples, vignettes...
ℹ Found @ in vignettes/SpaNorm.Rmd
ℹ NOTE: Use accessors; don't access S4 class slots via '@' in
examples/vignettes.
ℹ NOTE: Avoid '<<-' if possible (found 1 times)
  • <<- in R/mainSpaNormSVG.R (line 52, column 22)
* Checking function lengths...
ℹ NOTE: The recommended function length is 50 lines or less. There are 7
functions greater than 50 lines.
  The longest 5 functions are:
    • fitNBGivenPsi() (R/fitSpaNormNB.R): 200 lines
    • ...
    • validSpaNormFit() (R/AllClasses.R): 76 lines
* Checking man page documentation...
ℹ NOTE: Usage of dontrun / donttest tags found in man page examples. 18% of man
pages use at least one of these tags.
  Found in files:
    • plotCovariate.Rd
    • SpaNorm.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; 213 lines (8%) are > 80 characters long.
  First few lines:
    • R/AllClasses.R#L6 #' @slot gene.model a character, specify ...
    • ...
    • vignettes/SpaNorm.Rmd#L345 scale_colour_brewer(palette = "Paired" ...
ℹ NOTE: Consider multiples of 4 spaces for line indents; 959 lines (36%) are
not.
  First few lines:
    • R/AllClasses.R#L30 Class = "SpaNormFit", ...
    • ...
    • vignettes/SpaNorm.Rmd#L346 labs(title = "UMAP derived from SpaNor ...
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 13 NOTES
ℹ See the SpaNorm.BiocCheck folder and run
  browseVignettes(package = 'BiocCheck')
  for details.