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### Running command:
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###   /home/biocbuild/bbs-3.24-bioc/R/bin/Rscript -e "BiocCheck::BiocCheck('HiCaptuRe_1.3.0.tar.gz','quit-with-status'=TRUE)"
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── Installing HiCaptuRe ────────────────────────────────────────────────────────
✔ Package installed successfully
── HiCaptuRe session metadata ──────────────────────────────────────────────────
→ sourceDir: /tmp/Rtmppt4EaR/fileb00732f8bec3d/HiCaptuRe
→ BiocVersion: 3.24
→ Package: HiCaptuRe
→ PackageVersion: 1.3.0
→ BiocCheckDir: /home/biocbuild/bbs-3.24-bioc/meat/HiCaptuRe.BiocCheck
→ BiocCheckVersion: 1.49.4
→ sourceDir: /tmp/Rtmppt4EaR/fileb00732f8bec3d/HiCaptuRe
→ installDir: /tmp/Rtmppt4EaR/fileb007330fab3e7
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on HiCaptuRe ──────────────────────────────────────────────
* 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...
* 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 (35%).
* 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_functions.Rmd
    • vignetteIntroduction.Rmd
* Checking package installation calls in R code...
* Checking for library/require of HiCaptuRe...
* Checking coding practice...
ℹ NOTE: Avoid 1:...; use seq_len() or seq_along()
  Found in files:
    • load_interactions.R (line 67, column 53)
    • ...
    • load_interactions.R (line 311, column 75)
* Checking parsed R code in R directory, examples, vignettes...
ℹ NOTE: Avoid '<<-' if possible (found 1 times)
  • <<- in R/zzz.R (line 9, column 19)
ℹ NOTE: Avoid 'suppressWarnings'/'*Messages' if possible (found 14 times)
  • suppressMessages() in R/annotate_interactions.R (line 48, column 9)
  • ...
  • suppressWarnings() in R/intersect_interactions.R (line 110, column 18)
* Checking function lengths...
ℹ NOTE: The recommended function length is 50 lines or less. There are 9
functions greater than 50 lines.
  The longest 5 functions are:
    • interactionsByRegions() (R/interactionsByRegions.R): 163 lines
    • ...
    • interactionsByBaits() (R/interactionsByBaits.R): 67 lines
* Checking man page documentation...
* 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; 401 lines (15%) are > 80 characters long.
  First few lines:
    • R/annotate_interactions.R#L3 #' This function annotate a HiCaptuRe ob ...
    • ...
    • vignettes/vignetteIntroduction.Rmd#L350 - Tomás-Daza, L., Rovirosa, L.
    *et al.* ...
ℹ NOTE: Consider multiples of 4 spaces for line indents; 61 lines (2%) are not.
  First few lines:
    • vignettes/vignette_functions.Rmd#L515 - A single peakmatrix file using
    `form ...
    • ...
    • vignettes/vignetteIntroduction.Rmd#L332 A tab-delimited file with bait
    annotat ...
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 10 NOTES
ℹ See the HiCaptuRe.BiocCheck folder and run
  browseVignettes(package = 'BiocCheck')
  for details.