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### Running command:
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###   /home/rapidbuild/bbs-3.23-bioc-rapid/R/bin/Rscript -e "BiocCheck::BiocCheck('pwalign_1.8.0.tar.gz','quit-with-status'=TRUE)"
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── Installing pwalign ──────────────────────────────────────────────────────────
✔ Package installed successfully
── pwalign session metadata ────────────────────────────────────────────────────
→ sourceDir: /tmp/RtmpxRCF2h/file87a9a3061513d/pwalign
→ BiocVersion: 3.23
→ Package: pwalign
→ PackageVersion: 1.8.0
→ BiocCheckDir: /media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/meat/pwalign.BiocCheck
→ BiocCheckVersion: 1.48.0
→ sourceDir: /tmp/RtmpxRCF2h/file87a9a3061513d/pwalign
→ installDir: /tmp/RtmpxRCF2h/file87a9a54fd0f36
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on pwalign ────────────────────────────────────────────────
* 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...
* 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: Coverage, GUI,
GPU, 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 that Package field matches directory/tarball name...
* 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 (67%).
* 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: Use RMarkdown instead of Sweave 'Rnw' vignettes.
  Rnw vignette(s) found:
    • PairwiseAlignments.Rnw
* Checking package installation calls in R code...
* Checking for library/require of pwalign...
* Checking coding practice...
ℹ NOTE: Avoid 'cat' and 'print' outside of 'show' methods
  Found in files:
    • cat() in R/PairwiseAlignments-class.R (line 400, column 9)
    • ...
    • cat() in R/PairwiseAlignments-io.R (line 332, column 5)
ℹ NOTE: Avoid redundant 'stop' and 'warn*' in signal conditions
  Found in files:
    • R/PairwiseAlignments-io.R (line 85, column 14)
    • R/substitution_matrices.R (line 47, column 10)
* 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 10
functions greater than 50 lines.
  The longest 5 functions are:
    • newPairwiseAlignments() (R/PairwiseAlignments-class.R): 142 lines
    • ...
    • QualityScaledXStringSet.stringDist() (R/stringDist.R): 95 lines
* Checking man page documentation...
! WARNING: Empty or missing \value sections found in man page(s).
  Found in files:
    • man/PairwiseAlignments-class.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; 250 lines (4%) are > 80 characters long.
  First few lines:
    • R/align-utils.R#L13 nindel(subject(pattern))[, ...
    • ...
    • vignettes/PairwiseAlignments.Rnw#L1250 \newblock {\em Proceedings of the
    Nation ...
ℹ NOTE: Consider multiples of 4 spaces for line indents; 1360 lines (24%) are
not.
  First few lines:
    • R/align-utils.R#L13 nindel(subject(pattern))[, ...
    • ...
    • vignettes/PairwiseAlignments.Rnw#L1244 amino acid sequence of two
    proteins. ...
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 v1.48.0 results ───────────────────────────────────────────────────
✖ 0 ERRORS | ⚠ 2 WARNINGS | ℹ 8 NOTES
ℹ See the pwalign.BiocCheck folder and run
  browseVignettes(package = 'BiocCheck')
  for details.