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### Running command:
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###   /home/biocbuild/bbs-3.24-bioc/R/bin/Rscript -e "BiocCheck::BiocCheck('SPLINTER_1.39.0.tar.gz','quit-with-status'=TRUE)"
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── Installing SPLINTER ─────────────────────────────────────────────────────────
✔ Package installed successfully
── SPLINTER session metadata ───────────────────────────────────────────────────
→ sourceDir: /tmp/Rtmp6waNr6/file145ddb4d8ddd5/SPLINTER
→ BiocVersion: 3.24
→ Package: SPLINTER
→ PackageVersion: 1.39.0
→ BiocCheckDir: /home/biocbuild/bbs-3.24-bioc/meat/SPLINTER.BiocCheck
→ BiocCheckVersion: 1.49.4
→ sourceDir: /tmp/Rtmp6waNr6/file145ddb4d8ddd5/SPLINTER
→ installDir: /tmp/Rtmp6waNr6/file145ddb143b63c2
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on SPLINTER ───────────────────────────────────────────────
* 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 3.6.0 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...
* 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...
* Checking for Bioconductor software dependencies...
ℹ Bioconductor dependencies found in Imports & Depends (52%).
* 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:
    • vignette.Rmd
* Checking package installation calls in R code...
* Checking for library/require of SPLINTER...
* Checking coding practice...
ℹ NOTE: Avoid 1:...; use seq_len() or seq_along()
  Found in files:
    • main_splinter.R (line 37, column 64)
    • ...
    • main_splinter.R (line 1461, column 14)
ℹ NOTE: Avoid 'cat' and 'print' outside of 'show' methods
  Found in files:
    • print() in R/main_splinter.R (line 178, column 5)
    • print() in R/main_splinter.R (line 1303, column 19)
ℹ NOTE: Avoid using '=' for assignment and use '<-' instead
  Found in files:
    • R/main_splinter.R (line 36, column 8)
    • ...
    • R/primerpcr.R (line 278, column 23)
ℹ NOTE: Avoid the use of 'paste' in condition signals
  Found in files:
    • R/main_splinter.R (line 57, column 13)
    • ...
    • R/primerpcr.R (line 50, column 23)
! WARNING: Avoid class membership checks with class() / is() and == / !=; Use
is(x, 'class') for S4 classes
  Found in files:
    • main_splinter.R (line 361, column 22)
    • ...
    • main_splinter.R (line 449, column 28)
ℹ NOTE: Avoid system() ; use system2()
  Found in files:
    • system() in R/primerpcr.R (line 228, column 7)
* Checking parsed R code in R directory, examples, vignettes...
ℹ NOTE: Avoid 'suppressWarnings'/'*Messages' if possible (found 4 times)
  • suppressWarnings() in R/main_splinter.R (line 362, column 16)
  • ...
  • suppressMessages() in R/main_splinter.R (line 575, column 11)
* 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:
    • eventOutcomeCompare() (R/main_splinter.R): 181 lines
    • ...
    • extractSpliceSites() (R/main_splinter.R): 71 lines
* Checking man page documentation...
! WARNING: Empty or missing \format sections found in data man page(s).
  Found in files:
    • man/compatible_cds.Rd
    • ...
    • man/valid_tx.Rd
ℹ NOTE: Consider adding runnable examples to man pages that document exported
objects.
  • annotateEvents.Rd
  • ...
  • shapiroDensity.Rd
* Checking package NEWS...
* Checking unit tests...
ℹ NOTE: Consider adding unit tests. We strongly encourage them. See
https://contributions.bioconductor.org/tests.html
* Checking skip_on_bioc() in tests...
* Checking formatting of DESCRIPTION, NAMESPACE, man pages, R source, and
vignette source...
ℹ NOTE: Consider shorter lines; 182 lines (8%) are > 80 characters long.
  First few lines:
    • R/main_splinter.R#L4 #' post translation. Currently supports ...
    • ...
    • vignettes/vignette.Rmd#L234 `splitPCRhit` will return PCR product si ...
ℹ NOTE: Consider multiples of 4 spaces for line indents; 640 lines (29%) are
not.
  First few lines:
    • R/main_splinter.R#L23 df<-thedata$data ...
    • ...
    • vignettes/vignette.Rmd#L249 annoLabel=single_id,rspan=2000 ...
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 | ⚠ 2 WARNINGS | ℹ 17 NOTES
ℹ See the SPLINTER.BiocCheck folder and run
  browseVignettes(package = 'BiocCheck')
  for details.