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### Running command:
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###   /home/biocbuild/bbs-3.24-bioc/R/bin/Rscript -e "BiocCheck::BiocCheck('celaref_1.31.0.tar.gz','quit-with-status'=TRUE)"
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── Installing celaref ──────────────────────────────────────────────────────────
✔ Package installed successfully
── celaref session metadata ────────────────────────────────────────────────────
→ sourceDir: /tmp/RtmpUjHHR7/file62f8e36e86373/celaref
→ BiocVersion: 3.24
→ Package: celaref
→ PackageVersion: 1.31.0
→ BiocCheckDir: /home/biocbuild/bbs-3.24-bioc/meat/celaref.BiocCheck
→ BiocCheckVersion: 1.49.4
→ sourceDir: /tmp/RtmpUjHHR7/file62f8e36e86373/celaref
→ installDir: /tmp/RtmpUjHHR7/file62f8e38c3d644
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on celaref ────────────────────────────────────────────────
* 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 3.5.0 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...
ℹ NOTE: Consider adding these automatically suggested biocViews:
GeneExpression, Sequencing, Microarray, Coverage, DifferentialExpression,
WorkflowStep, Clustering, RNASeq
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: Provide 'URL', 'BugReports' field(s) in DESCRIPTION
* Checking for Bioconductor software dependencies...
ℹ Bioconductor dependencies found in Imports & Depends (36%).
* 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:
    • celaref_doco.Rmd
* Checking package installation calls in R code...
* Checking for library/require of celaref...
* Checking coding practice...
ℹ NOTE: Avoid using '=' for assignment and use '<-' instead
  Found in files:
    • R/contrasting_functions.r (line 86, column 19)
    • ...
    • R/loading_helper_functions.r (line 424, column 11)
ℹ NOTE: Avoid the use of 'paste' in condition signals
  Found in files:
    • R/contrasting_functions.r (line 1078, column 9)
ℹ NOTE: Avoid redundant 'stop' and 'warn*' in signal conditions
  Found in files:
    • R/contrasting_functions.r (line 116, column 18)
    • R/contrasting_functions.r (line 122, column 18)
    • R/contrasting_functions.r (line 571, column 15)
* Checking parsed R code in R directory, examples, vignettes...
ℹ NOTE: Avoid 'suppressWarnings'/'*Messages' if possible (found 2 times)
  • suppressWarnings() in R/group_labelling_functions.r (line 761, column 21)
  • suppressMessages() in R/group_labelling_functions.r (line 761, column 4)
* 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:
    • contrast_the_group_to_the_rest() (R/contrasting_functions.r): 166 lines
    • ...
    • make_ref_similarity_names_using_marked() (R/group_labelling_functions.r):
    92 lines
* Checking man page documentation...
ℹ NOTE: Usage of dontrun / donttest tags found in man page examples. 6% of man
pages use at least one of these tags.
  Found in files:
    • contrast_each_group_to_the_rest_for_norm_ma_with_limma.Rd
    • load_dataset_10Xdata.Rd
ℹ NOTE: Use donttest instead of dontrun.
  Found in files:
    • contrast_each_group_to_the_rest_for_norm_ma_with_limma.Rd
    • load_dataset_10Xdata.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; 274 lines (6%) are > 80 characters long.
  First few lines:
    • R/contrasting_functions.r#L105 as.numeric(scale(DelayedArray:: ...
    • ...
    • vignettes/celaref_doco.Rmd#L1384 make_ref_similarity_names(de_table.ze
    ...
ℹ NOTE: Consider multiples of 4 spaces for line indents; 1369 lines (32%) are
not.
  First few lines:
    • R/contrasting_functions.r#L79 dataset_se, dataset_name, groups2test ...
    • ...
    • vignettes/celaref_doco.Rmd#L1384 make_ref_similarity_names(de_table.ze
    ...
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 17 NOTES
ℹ See the celaref.BiocCheck folder and run
  browseVignettes(package = 'BiocCheck')
  for details.