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### Running command:
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###   /home/biocbuild/bbs-3.24-bioc/R/bin/Rscript -e "BiocCheck::BiocCheck('ChromSCape_1.23.0.tar.gz','quit-with-status'=TRUE)"
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── Installing ChromSCape ───────────────────────────────────────────────────────
✔ Package installed successfully
── ChromSCape session metadata ─────────────────────────────────────────────────
→ sourceDir: /tmp/RtmpwDl81y/file693d965a6dc09/ChromSCape
→ BiocVersion: 3.24
→ Package: ChromSCape
→ PackageVersion: 1.23.0
→ BiocCheckDir: /home/biocbuild/bbs-3.24-bioc/meat/ChromSCape.BiocCheck
→ BiocCheckVersion: 1.49.4
→ sourceDir: /tmp/RtmpwDl81y/file693d965a6dc09/ChromSCape
→ installDir: /tmp/RtmpwDl81y/file693d933118d9e
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on ChromSCape ─────────────────────────────────────────────
* 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 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...
* 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 (24%).
* 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:
    • vignette.Rmd
* Checking package installation calls in R code...
* Checking for library/require of ChromSCape...
* Checking coding practice...
ℹ NOTE: Avoid sapply(); use vapply()
  Found in files:
    • R/copy_number.R (line 196, column 20)
    • ...
    • R/preprocessing_filtering_reduction.R (line 242, column 23)
ℹ NOTE: Avoid 1:...; use seq_len() or seq_along()
  Found in files:
    • coverage.R (line 153, column 49)
    • ...
    • preprocessing_filtering_reduction.R (line 2322, column 82)
ℹ NOTE: Avoid 'cat' and 'print' outside of 'show' methods
  Found in files:
    • print() in R/coverage.R (line 286, column 3)
    • ...
    • print() in R/support_functions.R (line 654, column 9)
ℹ NOTE: Avoid using '=' for assignment and use '<-' instead
  Found in files:
    • R/copy_number.R (line 32, column 25)
    • ...
    • R/support_functions.R (line 577, column 15)
ℹ NOTE: Avoid the use of 'paste' in condition signals
  Found in files:
    • R/correlation_filtering_clustering.R (line 574, column 14)
    • ...
    • R/support_functions.R (line 329, column 17)
ℹ NOTE: Avoid redundant 'stop' and 'warn*' in signal conditions
  Found in files:
    • R/generate_analysis.R (line 439, column 18)
    • R/preprocessing_filtering_reduction.R (line 986, column 13)
    • R/support_functions.R (line 355, column 14)
ℹ NOTE: Avoid system() ; use system2()
  Found in files:
    • system() in R/coverage.R (line 171, column 11)
    • system() in R/coverage.R (line 181, column 7)
    • system() in R/peak_calling.R (line 174, column 9)
* Checking parsed R code in R directory, examples, vignettes...
ℹ NOTE: Avoid 'suppressWarnings'/'*Messages' if possible (found 6 times)
  • suppressWarnings() in R/correlation_filtering_clustering.R (line 711,
  column 16)
  • ...
  • suppressWarnings() in R/preprocessing_filtering_reduction.R (line 1940,
  column 13)
* Checking function lengths...
ℹ NOTE: The recommended function length is 50 lines or less. There are 39
functions greater than 50 lines.
  The longest 5 functions are:
    • generate_analysis() (R/generate_analysis.R): 324 lines
    • ...
    • wrapper_Signac_FeatureMatrix() (R/preprocessing_filtering_reduction.R):
    99 lines
* Checking man page documentation...
ℹ NOTE: Consider adding runnable examples to man pages that document exported
objects.
  • annotation_from_merged_peaks.Rd
  • ...
  • wrapper_Signac_FeatureMatrix.Rd
ℹ NOTE: Usage of dontrun / donttest tags found in man page examples. 11% of man
pages use at least one of these tags.
  Found in files:
    • gene_set_enrichment_analysis_scExp.Rd
    • ...
    • wrapper_Signac_FeatureMatrix.Rd
ℹ NOTE: Use donttest instead of dontrun.
  Found in files:
    • gene_set_enrichment_analysis_scExp.Rd
    • ...
    • wrapper_Signac_FeatureMatrix.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; 315 lines (3%) are > 80 characters long.
  First few lines:
    • R/copy_number.R#L28 get_cyto_features <- function(scExp, ref ...
    • ...
    • vignettes/vignette.Rmd#L562 [Dropbox repository](https://www.dropbox ...
ℹ NOTE: Consider multiples of 4 spaces for line indents; 1055 lines (11%) are
not.
  First few lines:
    • R/copy_number.R#L43 as.character(S ...
    • ...
    • vignettes/vignette.Rmd#L509 ...
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...
✖ ERROR: Unable to find your email in the Support Site: HTTP 404 Not Found.
── BiocCheck v1.49.4 results ───────────────────────────────────────────────────
✖ 1 ERRORS | ⚠ 0 WARNINGS | ℹ 18 NOTES
ℹ See the ChromSCape.BiocCheck folder and run
  browseVignettes(package = 'BiocCheck')
  for details.