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### Running command:
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###   /home/biocbuild/bbs-3.24-bioc/R/bin/Rscript -e "BiocCheck::BiocCheck('SynExtend_1.25.0.tar.gz','quit-with-status'=TRUE)"
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── Installing SynExtend ────────────────────────────────────────────────────────
✔ Package installed successfully
── SynExtend session metadata ──────────────────────────────────────────────────
→ sourceDir: /tmp/RtmpUflg8x/file149b0b22e38177/SynExtend
→ BiocVersion: 3.24
→ Package: SynExtend
→ PackageVersion: 1.25.0
→ BiocCheckDir: /home/biocbuild/bbs-3.24-bioc/meat/SynExtend.BiocCheck
→ BiocCheckVersion: 1.49.4
→ sourceDir: /tmp/RtmpUflg8x/file149b0b22e38177/SynExtend
→ installDir: /tmp/RtmpUflg8x/file149b0b30758c63
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on SynExtend ──────────────────────────────────────────────
* 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 4.5.0 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: Sequencing,
Microbiome, Microarray, Phylogenetics, FunctionalGenomics, Alignment, Network,
WholeGenome, ImmunoOncology, GenePrediction, QualityControl
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...
* Checking License: for restrictive use...
* Checking for recommended DESCRIPTION fields...
* Checking for Bioconductor software dependencies...
ℹ Bioconductor dependencies found in Imports & Depends (33%).
* 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:
    • UsingSynExtend.Rmd
* Checking package installation calls in R code...
* Checking for library/require of SynExtend...
* Checking coding practice...
ℹ NOTE: Avoid sapply(); use vapply()
  Found in files:
    • R/BlockExpansion.R (line 123, column 11)
    • ...
    • R/SummarizePairs.R (line 1329, column 16)
ℹ NOTE: Avoid 'cat' and 'print' outside of 'show' methods
  Found in files:
    • cat() in R/BlastSeqs.R (line 21, column 16)
    • ...
    • print() in R/WithinSetCompetition.R (line 285, column 5)
ℹ NOTE: Avoid system() ; use system2()
  Found in files:
    • system() in R/FastQFromSRR.R (line 42, column 3)
    • system() in R/FastQFromSRR.R (line 57, column 9)
    • system() in R/FastQFromSRR.R (line 64, column 7)
* Checking parsed R code in R directory, examples, vignettes...
ℹ NOTE: Avoid '<<-' if possible (found 6 times)
  • <<- in R/EvoWeaver-utils.R (line 1046, column 21)
  • ...
  • <<- in R/FastDend-class.R (line 218, column 21)
ℹ NOTE: Avoid 'suppressWarnings'/'*Messages' if possible (found 5 times)
  • suppressWarnings() in R/ClusterByK.R (line 120, column 18)
  • ...
  • suppressWarnings() in R/SelectByK.R (line 78, column 18)
* Checking function lengths...
ℹ NOTE: The recommended function length is 50 lines or less. There are 74
functions greater than 50 lines.
  The longest 5 functions are:
    • SummarizePairs() (R/SummarizePairs.R): 1370 lines
    • ...
    • BlockExpansion() (R/BlockExpansion.R): 1055 lines
* Checking man page documentation...
ℹ NOTE: Consider adding runnable examples to man pages that document exported
objects.
  • AAHitScoping.Rd
  • ...
  • RejectionBy.Rd
ℹ NOTE: Usage of dontrun / donttest tags found in man page examples. 5% of man
pages use at least one of these tags.
  Found in files:
    • BlockReconciliation.Rd
    • ExtractBy.Rd
    • FastQFromSRR.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; 1411 lines (6%) are > 80 characters long.
  First few lines:
    • R/ApproximateBackground.R#L39 res[m1] <- sum(aa1[register1[p1[m1 ...
    • ...
    • vignettes/UsingSynExtend.Rmd#L133 As of SynExtend v 1.3.13, the functions
    ...
ℹ NOTE: Consider 4 spaces instead of tabs; 47 lines (0%) contain tabs.
  First few lines:
    • R/LanczosEigen.R#L10 if (m <= 1L) ...
    • ...
    • R/LanczosEigen.R#L56 e ...
ℹ NOTE: Consider multiples of 4 spaces for line indents; 10882 lines (48%) are
not.
  First few lines:
    • R/AAHitScoping.R#L4 fstrand1, ...
    • ...
    • vignettes/UsingSynExtend.Rmd#L145 Verbose = TRUE) ...
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.
ℹ Package is in the Support Site Watched Tags.
── BiocCheck v1.49.4 results ───────────────────────────────────────────────────
✖ 0 ERRORS | ⚠ 0 WARNINGS | ℹ 16 NOTES
ℹ See the SynExtend.BiocCheck folder and run
  browseVignettes(package = 'BiocCheck')
  for details.