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### Running command:
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###   /home/biocbuild/bbs-3.24-bioc/R/bin/Rscript -e "BiocCheck::BiocCheck('sangeranalyseR_1.23.0.tar.gz','quit-with-status'=TRUE)"
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── Installing sangeranalyseR ───────────────────────────────────────────────────
✔ Package installed successfully
── sangeranalyseR session metadata ─────────────────────────────────────────────
→ sourceDir: /tmp/RtmpGHn9mq/file12847a756cf3d4/sangeranalyseR
→ BiocVersion: 3.24
→ Package: sangeranalyseR
→ PackageVersion: 1.23.0
→ BiocCheckDir: /home/biocbuild/bbs-3.24-bioc/meat/sangeranalyseR.BiocCheck
→ BiocCheckVersion: 1.49.4
→ sourceDir: /tmp/RtmpGHn9mq/file12847a756cf3d4/sangeranalyseR
→ installDir: /tmp/RtmpGHn9mq/file12847a206dd103
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on sangeranalyseR ─────────────────────────────────────────
* 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: Microbiome,
Microarray, Phylogenetics, Clustering, WholeGenome, ComparativeGenomics,
ImmunoOncology, GenePrediction, SequenceMatching, DataImport
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...
* Checking for Bioconductor software dependencies...
ℹ Bioconductor dependencies found in Imports & Depends (22%).
* 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...
! WARNING: Evaluate more vignette chunks.
ℹ 14 out of 18 code chunks = 77% unevaluated
ℹ 
* Checking package installation calls in R code...
* Checking for library/require of sangeranalyseR...
* Checking coding practice...
ℹ NOTE: Avoid sapply(); use vapply()
  Found in files:
    • R/ClassSangerAlignment.R (line 654, column 9)
    • ...
    • R/sangeranalyseR_show_method.R (line 189, column 9)
ℹ NOTE: Avoid 1:...; use seq_len() or seq_along()
  Found in files:
    • UtilitiesFunc.R (line 1296, column 30)
    • ...
    • UtilitiesFunc.R (line 1382, column 18)
ℹ NOTE: Avoid using '=' for assignment and use '<-' instead
  Found in files:
    • R/ClassSangerAlignment.R (line 230, column 38)
    • ...
    • R/UtilitiesFunc.R (line 1405, column 11)
* Checking parsed R code in R directory, examples, vignettes...
ℹ NOTE: Avoid '<<-' if possible (found 356 times)
  • <<- in R/ClassSangerAlignment.R (line 383, column 44)
  • ...
  • <<- in R/ShinySangerContigServer.R (line 1810, column 51)
ℹ NOTE: Avoid 'suppressWarnings'/'*Messages' if possible (found 27 times)
  • suppressWarnings() in R/MethodSangerAlignment.R (line 109, column 13)
  • ...
  • suppressMessages() in R/UtilitiesFunc.R (line 46, column 5)
* Checking function lengths...
ℹ NOTE: The recommended function length is 50 lines or less. There are 31
functions greater than 50 lines.
  The longest 5 functions are:
    • SangerAlignmentServer() (R/ShinySangerAlignmentServer.R): 2349 lines
    • ...
    • calculateContigSeq() (R/UtilitiesFunc.R): 353 lines
* Checking man page documentation...
! WARNING: Empty or missing \value sections found in man page(s).
  Found in files:
    • man/sangeranalyseR.Rd
ℹ NOTE: Consider adding runnable examples to man pages that document exported
objects.
  • globalTrimApp.Rd
ℹ NOTE: Usage of dontrun / donttest tags found in man page examples. 42% of man
pages use at least one of these tags.
  Found in files:
    • chromatogram_overwrite.Rd
    • ...
    • writeFasta.Rd
ℹ NOTE: Use donttest instead of dontrun.
  Found in files:
    • globalTrimApp.Rd
    • ...
    • launchAppSC-methods.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; 749 lines (6%) are > 80 characters long.
  First few lines:
    • R/AllGenerics.R#L79 #' @param object A QualityReport, Sanger ...
    • ...
    • vignettes/sangeranalyseR.Rmd#L339 | Reports render with empty AA tables
    ...
ℹ NOTE: Consider multiples of 4 spaces for line indents; 2584 lines (20%) are
not.
  First few lines:
    • R/AllGenerics.R#L116 ...
    • ...
    • vignettes/sangeranalyseR.Rmd#L238 secondary peak is dropped. ...
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 16 NOTES
ℹ See the sangeranalyseR.BiocCheck folder and run
  browseVignettes(package = 'BiocCheck')
  for details.