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### Running command:
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###   /home/biocbuild/bbs-3.24-bioc/R/bin/Rscript -e "BiocCheck::BiocCheck('CellBarcode_1.19.0.tar.gz','quit-with-status'=TRUE)"
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── Installing CellBarcode ──────────────────────────────────────────────────────
✔ Package installed successfully
── CellBarcode session metadata ────────────────────────────────────────────────
→ sourceDir: /tmp/RtmpoeiHlL/file6308212b876e8/CellBarcode
→ BiocVersion: 3.24
→ Package: CellBarcode
→ PackageVersion: 1.19.0
→ BiocCheckDir: /home/biocbuild/bbs-3.24-bioc/meat/CellBarcode.BiocCheck
→ BiocCheckVersion: 1.49.4
→ sourceDir: /tmp/RtmpoeiHlL/file6308212b876e8/CellBarcode
→ installDir: /tmp/RtmpoeiHlL/file6308257c2dd32
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on CellBarcode ────────────────────────────────────────────
* 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 4.1.0 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: LongRead
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 (25%).
* 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:
    • Barcode_in_10X_scRNASeq.Rmd
    • UMI_VDJ_Barcode.Rmd
* Checking package installation calls in R code...
* Checking for library/require of CellBarcode...
* Checking coding practice...
ℹ NOTE: Avoid sapply(); use vapply()
  Found in files:
    • R/function-verify_seq.R (line 85, column 16)
    • R/method-extract_barcode.R (line 298, column 13)
    • R/method-extract_barcode.R (line 344, column 13)
ℹ NOTE: Avoid 1:...; use seq_len() or seq_along()
  Found in files:
    • function-verify_seq.R (line 107, column 19)
    • ...
    • method-seqQc.R (line 133, column 16)
ℹ NOTE: Avoid 'cat' and 'print' outside of 'show' methods
  Found in files:
    • cat() in R/function-single_cell_seq.R (line 159, column 5)
    • cat() in R/function-single_cell_seq.R (line 160, column 5)
ℹ NOTE: Avoid using '=' for assignment and use '<-' instead
  Found in files:
    • R/function-single_cell_seq.R (line 163, column 9)
    • ...
    • R/method-plot_barcode.R (line 297, column 19)
ℹ NOTE: Avoid the use of 'paste' in condition signals
  Found in files:
    • R/method-extract_barcode.R (line 263, column 14)
* 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 11
functions greater than 50 lines.
  The longest 5 functions are:
    • splitVDJ1seq() (R/function-verify_seq.R): 396 lines
    • ...
    • _anonymous_.21() (R/method-BarcodeObj.R): 84 lines
* Checking man page documentation...
ℹ NOTE: Consider adding runnable examples to man pages that document exported
objects.
  • bc_extract_sc_fastq.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; 196 lines (4%) are > 80 characters long.
  First few lines:
    • R/AllGenerics.R#L166 #' @param isList A logical value, if TRU ...
    • ...
    • vignettes/UMI_VDJ_Barcode.Rmd#L601 # you can use the count_marks argument
    t ...
ℹ NOTE: Consider 4 spaces instead of tabs; 13 lines (0%) contain tabs.
  First few lines:
    • R/function-verify_seq.R#L11 # (a specific part of the sequence) ...
    • ...
    • R/function-verify_seq.R#L372 output$D.fwdorinv <- "short" ...
ℹ NOTE: Consider multiples of 4 spaces for line indents; 91 lines (2%) are not.
  First few lines:
    • R/AllGenerics.R#L296 ...
    • ...
    • vignettes/UMI_VDJ_Barcode.Rmd#L721 ## 2. Select the barcode got in s ...
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 15 NOTES
ℹ See the CellBarcode.BiocCheck folder and run
  browseVignettes(package = 'BiocCheck')
  for details.