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### Running command:
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###   /home/biocbuild/bbs-3.24-bioc/R/bin/Rscript -e "BiocCheck::BiocCheck('bambu_3.15.0.tar.gz','quit-with-status'=TRUE)"
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── Installing bambu ────────────────────────────────────────────────────────────
✔ Package installed successfully
── bambu session metadata ──────────────────────────────────────────────────────
→ sourceDir: /tmp/RtmpYKBy4D/file582b039833e78/bambu
→ BiocVersion: 3.24
→ Package: bambu
→ PackageVersion: 3.15.0
→ BiocCheckDir: /home/biocbuild/bbs-3.24-bioc/meat/bambu.BiocCheck
→ BiocCheckVersion: 1.49.4
→ sourceDir: /tmp/RtmpYKBy4D/file582b039833e78/bambu
→ installDir: /tmp/RtmpYKBy4D/file582b04d1251cf
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on bambu ──────────────────────────────────────────────────
* 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 4.1 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:
SequenceMatching
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 'BugReports' field(s) in DESCRIPTION
* Checking for Bioconductor software dependencies...
ℹ Bioconductor dependencies found in Imports & Depends (47%).
* 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:
    • bambu.Rmd
* Checking package installation calls in R code...
* Checking for library/require of bambu...
* Checking coding practice...
ℹ NOTE: Avoid sapply(); use vapply()
  Found in files:
    • R/bambu_utilityFunctions.R (line 118, column 22)
    • ...
    • R/bambu.R (line 155, column 18)
ℹ NOTE: Avoid using '=' for assignment and use '<-' instead
  Found in files:
    • R/bambu_utilityFunctions.R (line 118, column 16)
    • ...
    • R/readWrite.R (line 175, column 14)
ℹ NOTE: Avoid the use of 'paste' in condition signals
  Found in files:
    • R/bambu-extendAnnotations-utilityExtend.R (line 164, column 21)
ℹ NOTE: Avoid redundant 'stop' and 'warn*' in signal conditions
  Found in files:
    • R/bambu_utilityFunctions.R (line 194, column 17)
    • ...
    • R/bambu-extendAnnotations-utilityExtend.R (line 182, column 35)
* Checking parsed R code in R directory, examples, vignettes...
ℹ NOTE: Avoid 'suppressWarnings'/'*Messages' if possible (found 1 times)
  • suppressMessages() in R/prepareAnnotations.R (line 62, column 29)
* Checking function lengths...
ℹ NOTE: The recommended function length is 50 lines or less. There are 12
functions greater than 50 lines.
  The longest 5 functions are:
    • bambu.processReadsByFile() (R/bambu-processReads.R): 98 lines
    • ...
    • prepareAnnotationsFromGTF() (R/prepareAnnotations_utilityFunctions.R): 64
    lines
* Checking man page documentation...
! WARNING: Empty or missing \value sections found in man page(s).
  Found in files:
    • man/writeBambuOutput.Rd
ℹ NOTE: Consider adding runnable examples to man pages that document exported
objects.
  • trainBambu.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; 387 lines (6%) are > 80 characters long.
  First few lines:
    • R/bambu_utilityFunctions.R#L10 bpParameters$progressbar <- ifelse(l ...
    • ...
    • vignettes/bambu.Rmd#L423 [*DESeq2* tutorial](http://bioconductor. ...
ℹ NOTE: Consider 4 spaces instead of tabs; 6 lines (0%) contain tabs.
  First few lines:
    • R/bambu-extendAnnotations-utilityExtend.R#L133
    if(is.null(defaultModels$lmNDR[["terms" ...
    • ...
    • R/bambu-processReads_scoreReadClasses.R#L295 labels = as.logical(labels),
    ...
ℹ NOTE: Consider multiples of 4 spaces for line indents; 716 lines (12%) are
not.
  First few lines:
    • R/bambu_utilityFunctions.R#L80 colnames(mcols(anno ...
    • ...
    • vignettes/bambu.Rmd#L373 #alternatively train the model using a ...
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 v1.49.4 results ───────────────────────────────────────────────────
✖ 1 ERRORS | ⚠ 1 WARNINGS | ℹ 17 NOTES
ℹ See the bambu.BiocCheck folder and run
  browseVignettes(package = 'BiocCheck')
  for details.