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### Running command:
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###   /home/biocbuild/bbs-3.24-bioc/R/bin/Rscript -e "BiocCheck::BiocCheck('spiky_1.19.0.tar.gz','quit-with-status'=TRUE)"
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── Installing spiky ────────────────────────────────────────────────────────────
✔ Package installed successfully
── spiky session metadata ──────────────────────────────────────────────────────
→ sourceDir: /tmp/RtmpyK5cRe/file1456dc587a05e2/spiky
→ BiocVersion: 3.24
→ Package: spiky
→ PackageVersion: 1.19.0
→ BiocCheckDir: /home/biocbuild/bbs-3.24-bioc/meat/spiky.BiocCheck
→ BiocCheckVersion: 1.49.4
→ sourceDir: /tmp/RtmpyK5cRe/file1456dc587a05e2/spiky
→ installDir: /tmp/RtmpyK5cRe/file1456dc3a6e5756
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on spiky ──────────────────────────────────────────────────
* 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...
ℹ NOTE: Consider adding these automatically suggested biocViews: Coverage,
Alignment, 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 (47%).
* 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:
    • spiky_vignette.Rmd
Warning in checkVigEvalAllFalse(.BiocPackage) :
  More than one `opts_chunk$set()` in /tmp/RtmpyK5cRe/file1456dc587a05e2/spiky/vignettes/spiky_vignette.Rmd
* Checking package installation calls in R code...
* Checking for library/require of spiky...
* Checking coding practice...
ℹ NOTE: Avoid sapply(); use vapply()
  Found in files:
    • R/get_spike_depth.R (line 36, column 23)
    • ...
    • R/scan_spike_counts.R (line 45, column 29)
ℹ NOTE: Avoid using '=' for assignment and use '<-' instead
  Found in files:
    • R/model_glm_pmol.R (line 51, column 14)
    • R/predict_pmol.R (line 42, column 11)
* Checking parsed R code in R directory, examples, vignettes...
ℹ NOTE: Avoid 'suppressWarnings'/'*Messages' if possible (found 1 times)
  • suppressMessages() in R/predict_pmol.R (line 89, column 14)
* Checking function lengths...
ℹ NOTE: The recommended function length is 50 lines or less. There are 2
functions greater than 50 lines.
  The longest 5 functions are:
    • scan_genomic_contigs() (R/scan_genomic_contigs.R): 60 lines
    • scan_spiked_bam() (R/scan_spiked_bam.R): 52 lines
* Checking man page documentation...
ℹ NOTE: Consider adding runnable examples to man pages that document exported
objects.
  • convertPairedGRtoGR.Rd
  • ...
  • rename_spikes.Rd
ℹ NOTE: Usage of dontrun / donttest tags found in man page examples. 2% of man
pages use at least one of these tags.
  Found in files:
    • read_bedpe.Rd
ℹ NOTE: Use donttest instead of dontrun.
  Found in files:
    • read_bedpe.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; 64 lines (3%) are > 80 characters long.
  First few lines:
    • R/covg_to_df.R#L2 #' @param spike_gr GRanges of spike ...
    • ...
    • vignettes/spiky_vignette.Rmd#L195 For our analyses, we binned the genome
    i ...
ℹ NOTE: Consider multiples of 4 spaces for line indents; 536 lines (23%) are
not.
  First few lines:
    • R/add_frag_info.R#L25 fg <- gsub("[a-z]+", "", x[, frag_grp] ...
    • ...
    • vignettes/spiky_vignette.Rmd#L212 ...
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 17 NOTES
ℹ See the spiky.BiocCheck folder and run
  browseVignettes(package = 'BiocCheck')
  for details.