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### Running command:
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###   /home/biocbuild/bbs-3.24-bioc/R/bin/Rscript -e "BiocCheck::BiocCheck('DominoEffect_1.33.0.tar.gz','quit-with-status'=TRUE)"
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── Installing DominoEffect ─────────────────────────────────────────────────────
✔ Package installed successfully
── DominoEffect session metadata ───────────────────────────────────────────────
→ sourceDir: /tmp/RtmpXB534I/file84962219d4766/DominoEffect
→ BiocVersion: 3.24
→ Package: DominoEffect
→ PackageVersion: 1.33.0
→ BiocCheckDir: /home/biocbuild/bbs-3.24-bioc/meat/DominoEffect.BiocCheck
→ BiocCheckVersion: 1.49.4
→ sourceDir: /tmp/RtmpXB534I/file84962219d4766/DominoEffect
→ installDir: /tmp/RtmpXB534I/file849624d29c926
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on DominoEffect ───────────────────────────────────────────
* 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 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...
✖ ERROR: Remove Maintainer field. Use Authors@R [cre] designation.
* 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 (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:
    • Vignette.Rmd
* Checking package installation calls in R code...
* Checking for library/require of DominoEffect...
* Checking coding practice...
ℹ NOTE: Avoid 'cat' and 'print' outside of 'show' methods
  Found in files:
    • print() in R/align_to_unip.R (line 4, column 9)
ℹ NOTE: Avoid using '=' for assignment and use '<-' instead
  Found in files:
    • R/align_to_unip.R (line 51, column 20)
    • ...
    • R/map_to_func_elem.R (line 205, column 21)
ℹ NOTE: Avoid redundant 'stop' and 'warn*' in signal conditions
  Found in files:
    • R/map_to_func_elem.R (line 30, column 14)
    • R/map_to_func_elem.R (line 73, column 26)
    • R/map_to_func_elem.R (line 96, column 26)
* Checking parsed R code in R directory, examples, vignettes...
* Checking function lengths...
ℹ NOTE: The recommended function length is 50 lines or less. There are 4
functions greater than 50 lines.
  The longest 5 functions are:
    • identify_hotspots() (R/identify_hotspots.R): 297 lines
    • ...
    • calculate_boundary() (R/calculate_boundary.R): 51 lines
* Checking man page documentation...
! WARNING: Empty or missing \format sections found in data man page(s).
  Found in files:
    • man/data.Rd
ℹ NOTE: Consider adding runnable examples to man pages that document exported
objects.
  • import_txdb.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; 81 lines (9%) are > 80 characters long.
  First few lines:
    • R/DominoEffect.R#L5 ratio.thr = 45, ...
    • ...
    • vignettes/Vignette.Rmd#L189 If the user is starting from genomic mut ...
ℹ NOTE: Consider multiples of 4 spaces for line indents; 89 lines (9%) are not.
  First few lines:
    • R/align_to_unip.R#L20 ensembl_mut_position < nchar(ens. ...
    • ...
    • vignettes/Vignette.Rmd#L158 ...
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...
✖ ERROR: Unable to find your email in the Support Site: HTTP 404 Not Found.
── BiocCheck v1.49.4 results ───────────────────────────────────────────────────
✖ 2 ERRORS | ⚠ 1 WARNINGS | ℹ 13 NOTES
ℹ See the DominoEffect.BiocCheck folder and run
  browseVignettes(package = 'BiocCheck')
  for details.