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### Running command:
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###   /home/rapidbuild/bbs-3.23-bioc-rapid/R/bin/Rscript -e "BiocCheck::BiocCheck('SummarizedExperiment_1.42.0.tar.gz','quit-with-status'=TRUE)"
###
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── Installing SummarizedExperiment ─────────────────────────────────────────────
✔ Package installed successfully
── SummarizedExperiment session metadata ───────────────────────────────────────
→ sourceDir: /tmp/Rtmp0yGNFQ/file994f05796f8fe/SummarizedExperiment
→ BiocVersion: 3.23
→ Package: SummarizedExperiment
→ PackageVersion: 1.42.0
→ BiocCheckDir: /media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/meat/SummarizedExperiment.BiocCheck
→ BiocCheckVersion: 1.48.0
→ sourceDir: /tmp/Rtmp0yGNFQ/file994f05796f8fe/SummarizedExperiment
→ installDir: /tmp/Rtmp0yGNFQ/file994f062fbdf6
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on SummarizedExperiment ───────────────────────────────────
* 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 4.0.0 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...
ℹ NOTE: Consider adding these automatically suggested biocViews: KEGG
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 that Package field matches directory/tarball name...
* 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...
* Checking for Bioconductor software dependencies...
ℹ Bioconductor dependencies found in Imports & Depends (64%).
* 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:
    • Extensions.Rmd
    • SummarizedExperiment.Rmd
* Checking package installation calls in R code...
* Checking for library/require of SummarizedExperiment...
! WARNING: Avoid the use of 'library' or 'require' in R code
  Found in files:
    • require() in R/makeSummarizedExperimentFromExpressionSet.R (line 100,
    column 17)
    • require() in R/makeSummarizedExperimentFromExpressionSet.R (line 144,
    column 21)
* Checking coding practice...
ℹ NOTE: Avoid sapply(); use vapply()
  Found in files:
    • R/Assays-class.R (line 71, column 17)
    • ...
    • R/SummarizedExperiment-class.R (line 932, column 13)
ℹ NOTE: Avoid 1:...; use seq_len() or seq_along()
  Found in files:
    • Assays-class.R (line 71, column 59)
    • Assays-class.R (line 227, column 36)
    • SummarizedExperiment-class.R (line 176, column 28)
ℹ NOTE: Avoid the use of 'paste' in condition signals
  Found in files:
    • R/combine-methods.R (line 12, column 14)
    • ...
    • R/combine-methods.R (line 227, column 14)
* Checking parsed R code in R directory, examples, vignettes...
ℹ Found @ in vignettes/Extensions.Rmd
ℹ NOTE: Use accessors; don't access S4 class slots via '@' in
examples/vignettes.
* 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:
    • _anonymous_.631() (R/SummarizedExperiment-class.R): 111 lines
    • ...
    • combine_assays_by() (R/combine-methods.R): 62 lines
* Checking man page documentation...
! WARNING: Empty or missing \value sections found in man page(s).
  Found in files:
    • man/intra-range-methods.Rd
    • man/RangedSummarizedExperiment-class.Rd
    • man/SummarizedExperiment-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; 79 lines (1%) are > 80 characters long.
  First few lines:
    • R/Assays-class.R#L381 ### https://github.com/Bioconductor/ ...
    • ...
    • vignettes/SummarizedExperiment.Rmd#L306 - `r
    BiocStyle::Biocpkg("iSEEhub")` prov ...
ℹ NOTE: Consider multiples of 4 spaces for line indents; 799 lines (12%) are
not.
  First few lines:
    • R/Assays-class.R#L101 "matrix-like elements ...
    • ...
    • vignettes/SummarizedExperiment.Rmd#L257 rowData=Da ...
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.
✖ ERROR: Add package to Watched Tags in your Support Site profile; visit
https://support.bioconductor.org/accounts/edit/profile
── BiocCheck v1.48.0 results ───────────────────────────────────────────────────
✖ 1 ERRORS | ⚠ 2 WARNINGS | ℹ 13 NOTES
ℹ See the SummarizedExperiment.BiocCheck folder and run
  browseVignettes(package = 'BiocCheck')
  for details.